 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 29, 2023 |
| Title |
A spatially resolved single cell genomic atlas of the adult human breast [scRNA_cells] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The adult human breast comprises an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue. While most previous studies have focused on the breast epithelial system, many of the non-epithelial cell types remain understudied. Here, we constructed a comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics data profiled 714,331 cells from 126 women, and 120,024 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states. These data revealed abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide an unprecedented reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer.
|
| |
|
| Overall design |
This data provides an unprecedented atlas of the normal cell types and cell states in the human breast, that will serve as an important reference for studying breast development and diseases such as breast cancer.
|
| |
|
| Contributor(s) |
Kumar T, Nee K, Wei R, Kessenbrock K, Navin N |
| Citation(s) |
37380767 |
| Submission date |
Jun 20, 2023 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Nicholas Navin |
| E-mail(s) |
nnavin@mdanderson.org
|
| Phone |
713-563-1287
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
System Biology
|
| Lab |
Navin Lab
|
| Street address |
6767 Bertner Ave
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (167)
|
| GSM7500359 |
hbca_c50,P44,replicate_1,left,overnight_digestion |
| GSM7500360 |
hbca_c51,P44,replicate_1,right,overnight_digestion |
| GSM7500361 |
hbca_c52,P45,replicate_1,right,3hr_digestion |
| GSM7500362 |
hbca_c53,P46,replicate_1,left,2hr_digstion |
| GSM7500363 |
hbca_c54,P46,replicate_1,right,2hr_digstion |
| GSM7500364 |
hbca_c55,P47,replicate_1,left,2hr_digstion |
| GSM7500365 |
hbca_c56,P47,replicate_1,right,2hr_digstion |
| GSM7500366 |
hbca_c57,P48,replicate_1,left,2hr_digstion |
| GSM7500367 |
hbca_c58,P48,replicate_1,right,2hr_digstion |
| GSM7500368 |
hbca_c60,P49,replicate_1,left,4hr_digestion |
| GSM7500369 |
hbca_c61,P49,replicate_1,right,4hr_digestion |
| GSM7500370 |
hbca_c59,P49,replicate_2,right,4hr_digestion |
| GSM7500371 |
hbca_c62,P50,replicate_1,left,3hr_digestion |
| GSM7500372 |
hbca_c63,P50,replicate_2,left,3hr_digestion |
| GSM7500373 |
hbca_c64,P50,replicate_1,right,3hr_digestion |
| GSM7500374 |
hbca_c65,P50,replicate_2,right,3hr_digestion |
| GSM7500375 |
hbca_c67,P51,replicate_1,left,3hr_digestion |
| GSM7500376 |
hbca_c66,P51,replicate_2,left,3hr_digestion |
| GSM7500377 |
hbca_c69,P51,replicate_1,right,3hr_digestion |
| GSM7500378 |
hbca_c68,P51,replicate_2,right,3hr_digestion |
| GSM7500379 |
hbca_c70,P52,replicate_1,left,3hr_digestion |
| GSM7500380 |
hbca_c71,P52,replicate_1,right,3hr_digestion |
| GSM7500381 |
hbca_c72,P53,replicate_1,left,3hr_digestion |
| GSM7500382 |
hbca_c73,P53,replicate_1,right,3hr_digestion |
| GSM7500383 |
hbca_c74,P54,replicate_1,left,3hr_digestion |
| GSM7500384 |
hbca_c75,P54,replicate_1,right,3hr_digestion |
| GSM7500385 |
hbca_c76,P55,replicate_1,left,3hr_digestion |
| GSM7500386 |
hbca_c77,P55,replicate_1,right,3hr_digestion |
| GSM7500387 |
hbca_c78,P56,replicate_1,left,6hr_digestion |
| GSM7500388 |
hbca_c79,P56,replicate_1,right,6hr_digestion |
| GSM7500389 |
hbca_c80,P57,replicate_1,left,3hr_digestion |
| GSM7500390 |
hbca_c81,P57,replicate_1,right,3hr_digestion |
| GSM7500391 |
hbca_c82,P38,replicate_1,left,3hr_digestion |
| GSM7500392 |
hbca_c83,P38,replicate_1,right,3hr_digestion |
| GSM7500393 |
hbca_c84,P39,replicate_1,left,3hr_digestion |
| GSM7500394 |
hbca_c85,P39,replicate_1,right,3hr_digestion |
| GSM7500395 |
hbca_c86,P40,replicate_1,left,3hr_digestion |
| GSM7500396 |
hbca_c87,P40,replicate_1,right,3hr_digestion |
| GSM7500397 |
hbca_c88,P58,replicate_1,left,3hr_digestion |
| GSM7500398 |
hbca_c89,P58,replicate_1,right,3hr_digestion |
| GSM7500399 |
hbca_c90,P41,replicate_1,left,4hr_digestion |
| GSM7500400 |
hbca_c91,P41,replicate_1,right,4hr_digestion |
| GSM7500401 |
hbca_c92,P59,replicate_1,left,3hr_digestion |
| GSM7500402 |
hbca_c100,P59,replicate_2,left,3hr_digestion |
| GSM7500403 |
hbca_c93,P59,replicate_1,right,3hr_digestion |
| GSM7500404 |
hbca_c94,P60,replicate_1,left,3hr_digestion |
| GSM7500405 |
hbca_c95,P60,replicate_1,right,3hr_digestion |
| GSM7500406 |
hbca_c96,P61,replicate_1,left,4hr_digestion |
| GSM7500407 |
hbca_c97,P61,replicate_1,right,4hr_digestion |
| GSM7500408 |
hbca_c98,P62,replicate_1,left,2hr_digstion |
| GSM7500409 |
hbca_c99,P62,replicate_1,right,2hr_digstion |
| GSM7500410 |
hbca_c101,P63,replicate_1,left,3hr_digestion |
| GSM7500411 |
hbca_c102,P63,replicate_1,right,3hr_digestion |
| GSM7500412 |
hbca_c103,P64,replicate_1,left,2hr_digstion |
| GSM7500413 |
hbca_c104,P64,replicate_1,right,2hr_digstion |
| GSM7500414 |
hbca_c105,P65,replicate_1,left,2hr_digstion |
| GSM7500415 |
hbca_c106,P65,replicate_1,right,2hr_digstion |
| GSM7500416 |
hbca_c107,P66,replicate_1,right,3hr_digestion |
| GSM7500417 |
hbca_c108,P67,replicate_1,left,3hr_digestion |
| GSM7500418 |
hbca_c109,P68,replicate_1,left,2hr_digstion |
| GSM7500419 |
hbca_c110,P69,replicate_1,right,2hr_digstion |
| GSM7500420 |
hbca_c111,P70,replicate_1,right,3hr_digestion |
| GSM7500421 |
hbca_c112,P71,replicate_1,left,3hr_digestion |
| GSM7500422 |
hbca_c113,P72,replicate_1,right,2hr_digstion |
| GSM7500423 |
hbca_c114,P73,replicate_1,right,3hr_digestion |
| GSM7500424 |
hbca_c115,P74,replicate_1,right,2hr_digstion |
| GSM7500425 |
hbca_c116,P75,replicate_1,left,3hr_digestion |
| GSM7500426 |
hbca_c117,P76,replicate_1,left,3hr_digestion |
| GSM7500427 |
hbca_c118,P77,replicate_1,left,3hr_digestion |
| GSM7500428 |
hbca_c119,P78,replicate_1,right,2hr_digstion |
| GSM7500429 |
hbca_c120,P79,replicate_1,left,3hr_digestion |
| GSM7500430 |
hbca_c121,P80,replicate_1,right,2hr_digstion |
| GSM7500431 |
hbca_c122,P81,replicate_1,right,2hr_digstion |
| GSM7500432 |
hbca_c123,P82,replicate_1,right,3hr_digestion |
| GSM7500433 |
hbca_c124,P83,replicate_1,right,3hr_digestion |
| GSM7500434 |
hbca_c125,P84,replicate_1,right,2hr_digstion |
| GSM7500435 |
hbca_c126,P85,replicate_1,right,2hr_digstion |
| GSM7500436 |
hbca_c127,P86,replicate_1,right,2hr_digstion |
| GSM7500437 |
hbca_c128,P87,replicate_1,right,3hr_digestion |
| GSM7500438 |
hbca_c129,P88,replicate_1,right,3hr_digestion |
| GSM7500439 |
hbca_c130,P89,replicate_1,right,2hr_digstion |
| GSM7500440 |
hbca_c131,P90,replicate_1,right,3hr_digestion |
| GSM7500441 |
hbca_c132,P91,replicate_1,left,6hr_digestion |
| GSM7500442 |
hbca_c133,P92,replicate_1,right,2hr_digstion |
| GSM7500443 |
hbca_c134,P93,replicate_1,right,2hr_digstion |
| GSM7500444 |
hbca_c135,P94,replicate_1,right,3hr_digestion |
| GSM7500445 |
hbca_c136,P95,replicate_1,left,6hr_digestion |
| GSM7500446 |
hbca_c137,P96,replicate_1,left,2hr_digstion |
| GSM7500447 |
hbca_c138,P97,replicate_1,right,3hr_digestion |
| GSM7500448 |
hbca_c139,P98,replicate_1,left,3hr_digestion |
| GSM7500449 |
hbca_c140,P99,replicate_1,left,3hr_digestion |
| GSM7500450 |
hbca_c141,P100,replicate_1,right,2hr_digstion |
| GSM7500451 |
hbca_c142,P101,replicate_1,right,3hr_digestion |
| GSM7500452 |
hbca_c143,P102,replicate_1,left,2hr_digstion |
| GSM7500453 |
hbca_c144,P103,replicate_1,right,3hr_digestion |
| GSM7500454 |
hbca_c145,P104,replicate_1,right,2hr_digstion |
| GSM7500455 |
hbca_c146,P105,replicate_1,left,3hr_digestion |
| GSM7500456 |
hbca_c147,P106,replicate_1,right,3hr_digestion |
| GSM7500457 |
hbca_c148,P107,replicate_1,right,3hr_digestion |
| GSM7500458 |
hbca_c149,P108,replicate_1,right,3hr_digestion |
| GSM7500459 |
hbca_c150,P109,replicate_1,right,4hr_digestion |
| GSM7500460 |
hbca_c151,P110,replicate_1,left,3hr_digestion |
| GSM7500461 |
hbca_c152,P111,replicate_1,left,3hr_digestion |
| GSM7500462 |
hbca_c153,P112,replicate_1,left,3hr_digestion |
| GSM7500463 |
hbca_c01,P01,replicate_1,contra,short_digestion |
| GSM7500464 |
hbca_c02,P02,replicate_1,contra,short_digestion |
| GSM7500465 |
hbca_c03,P03,replicate_1,contra,short_digestion |
| GSM7500466 |
hbca_c04,P04,replicate_1,contra,short_digestion |
| GSM7500467 |
hbca_c05,P05,replicate_1,contra,short_digestion |
| GSM7500468 |
hbca_c06,P06,replicate_1,contra,short_digestion |
| GSM7500469 |
hbca_c07,P07,replicate_1,contra,short_digestion |
| GSM7500470 |
hbca_c08,P08,replicate_1,contra,short_digestion |
| GSM7500471 |
hbca_c09,P09,replicate_1,contra,short_digestion |
| GSM7500472 |
hbca_c10,P09,replicate_1,contra,overnight_digestion |
| GSM7500473 |
hbca_c11,P10,replicate_1,contra,short_digestion |
| GSM7500474 |
hbca_c12,P11,replicate_1,contra,short_digestion |
| GSM7500475 |
hbca_c13,P11,replicate_1,contra,overnight_digestion |
| GSM7500476 |
hbca_c34,P26,replicate_1,contra,overnight_digestion |
| GSM7500477 |
hbca_c35,P27,replicate_1,contra,short_digestion |
| GSM7500478 |
hbca_c36,P28,replicate_1,contra,overnight_digestion |
| GSM7500479 |
hbca_c37,P29,replicate_1,contra,overnight_digestion |
| GSM7500480 |
hbca_c38,P30,replicate_1,right,overnight_digestion |
| GSM7500481 |
hbca_c39,P31,replicate_1,left,overnight_digestion |
| GSM7500482 |
hbca_c33,P25,replicate_1,contra,overnight_digestion |
| GSM7500483 |
hbca_c40,P37,replicate_1,contra,short_digestion |
| GSM7500484 |
hbca_c25,P20,replicate_1,NA,short_digestion |
| GSM7500485 |
hbca_c26,P20,replicate_1,NA,overnight_digestion |
| GSM7500486 |
hbca_c41,P32,replicate_1,contra,overnight_digestion |
| GSM7500487 |
hbca_c42,P33,replicate_1,contra,overnight_digestion |
| GSM7500488 |
hbca_c43,P34,replicate_1,contra,overnight_digestion |
| GSM7500489 |
hbca_c27,P21,replicate_1,contra,overnight_digestion |
| GSM7500490 |
hbca_c28,P22,replicate_1,contra,short_digestion |
| GSM7500491 |
hbca_c29,P23,replicate_1,contra,short_digestion |
| GSM7500492 |
hbca_c30,P23,replicate_2,contra,short_digestion |
| GSM7500493 |
hbca_c31,P24,replicate_1,NA,6hr_digestion |
| GSM7500494 |
hbca_c32,P24,replicate_1,NA,overnight_digestion |
| GSM7500495 |
hbca_c44,P35,replicate_1,contra,overnight_digestion |
| GSM7500496 |
hbca_c45,P36,replicate_1,contra,overnight_digestion |
| GSM7500497 |
hbca_c46,P42,replicate_1,contra,short_digestion |
| GSM7500498 |
hbca_c47,P43,replicate_1,contra,short_digestion |
| GSM7500499 |
hbca_c48,P43,replicate_1,contra,3hr_digestion |
| GSM7500500 |
hbca_c49,P43,replicate_1,contra,overnight_digestion |
| GSM7500501 |
hbca_c18,P14,replicate_1,both,overnight_digestion |
| GSM7500502 |
hbca_c16,P13,replicate_1,both,overnight_digestion |
| GSM7500503 |
hbca_c17,P13,replicate_2,both,overnight_digestion |
| GSM7500504 |
hbca_c21,P17,replicate_1,both,overnight_digestion |
| GSM7500505 |
hbca_c20,P16,replicate_1,both,overnight_digestion |
| GSM7500506 |
hbca_c14,P12,replicate_1,both,overnight_digestion |
| GSM7500507 |
hbca_c15,P12,replicate_2,both,overnight_digestion |
| GSM7500508 |
hbca_c22,P18,replicate_1,both,overnight_digestion |
| GSM7500509 |
hbca_c23,P18,replicate_2,both,overnight_digestion |
| GSM7500510 |
hbca_c24,P19,replicate_1,both,overnight_digestion |
| GSM7500511 |
hbca_c19,P15,replicate_1,both,overnight_digestion |
| GSM7500512 |
hbca_c165,P124,replicate_1,contra,3hr_digestion |
| GSM7500513 |
hbca_c154,P113,replicate_1,contra,3hr_digestion |
| GSM7500514 |
hbca_c166,P125,replicate_1,contra,3hr_digestion |
| GSM7500515 |
hbca_c158,P117,replicate_1,contra,3hr_digestion |
| GSM7500516 |
hbca_c163,P122,replicate_1,contra,3hr_digestion |
| GSM7500517 |
hbca_c159,P118,replicate_1,contra,3hr_digestion |
| GSM7500518 |
hbca_c155,P114,replicate_1,contra,3hr_digestion |
| GSM7500519 |
hbca_c161,P120,replicate_1,contra,3hr_digestion |
| GSM7500520 |
hbca_c164,P123,replicate_1,contra,3hr_digestion |
| GSM7500521 |
hbca_c167,P126,replicate_1,contra,3hr_digestion |
| GSM7500522 |
hbca_c157,P116,replicate_1,contra,3hr_digestion |
| GSM7500523 |
hbca_c160,P119,replicate_1,contra,3hr_digestion |
| GSM7500524 |
hbca_c156,P115,replicate_1,contra,3hr_digestion |
| GSM7500525 |
hbca_c162,P121,replicate_1,contra,3hr_digestion |
|
| This SubSeries is part of SuperSeries: |
| GSE195665 |
A spatially resolved single cell genomic atlas of the adult human breast |
|
| Relations |
| BioProject |
PRJNA985695 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE235326_RAW.tar |
29.3 Gb |
(http)(custom) |
TAR (of H5) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...