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| Status |
Public on Jul 22, 2020 |
| Title |
CITEseq analysis of non-small-cell lung cancer lesions |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Immunotherapy is becoming a mainstay in the treatment of NSCLC. We profiled immune cells of 35 early stage NSCLC lesions using multiscale single cell sequencing, including scRNAseq, CITEseq, and TCRseq.
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| Overall design |
Samples of tumor and non-involved lung were obtained from surgical specimens of patients undergoing resection at Mount Sinai Hospital (New York, NY) after obtaining informed consent in accordance with a protocol reviewed and approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai (IRB Human Subjects Electronic Research Applications 10-00472 and 10-00135) and in collaboration with the Biorepository and Department of Pathology. Tissues were rinsed in PBS, minced and incubated for 40 minutes at 37C in Collagenase IV 0.25mg/ml, Collagenase D 200U/ml and DNAse I 0.1mg.ml (all Sigma). Cell suspensions were then aspirated through a 18G needle ten times and strained through a 70-micron mesh prior to RBC lysis. Cell suspensions were enriched for CD45+ cells by either bead positive selection (Miltenyi) per kit instructions or FACS sorting on a BD FACSAria flow sorter. Cells were directly loaded onto a 10X Chromium single-cell encapsulation chip according to manufacturer instructions for scRNAseq, or were stained with CITEseq and hashing antibody panels prior to loading, then subjected to downstream encapsulation and respective library prep. Alternatively, cells were subject to CD2+ bead enrichment prior to encapsulation and joint TCR/gene expression RNAseq. Raw data files are uploaded on NCBI with SRA Study SRP251372 BioProject ID PRJNA609924
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| Contributor(s) |
Leader AM, Grout JA, Chang C, Maier B, Tabachnikova A, Walker L, Lansky A, LeBerichel J, Malissen N, Davila M, Martin J, Magri G, Tuballes K, Zhao Z, Petralia F, Samstein R, Roy D'Amore N, Thurston G, Kamphorst A, Wolf A, Flores R, Wang P, Beasley MB, Salmon H, Rahman AH, Marron TU, Kenigsberg E, Merad M |
| Citation(s) |
34767762 |
| BioProject |
PRJNA609924 |
| Submission date |
Jul 21, 2020 |
| Last update date |
Nov 19, 2021 |
| Contact name |
Miriam Merad |
| E-mail(s) |
miriam.merad@mssm.edu
|
| Organization name |
ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
|
| Department |
Oncological Sciences
|
| Lab |
Merad Lab
|
| Street address |
1470 Madison Ave, Room 5-301
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| City |
NEW YORK |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (166)
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| Relations |
| SRA |
SRP251372 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE154826_amp_batch_ID_1.tar.gz |
17.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_10.tar.gz |
40.9 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_11.tar.gz |
26.9 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_14.tar.gz |
22.7 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_15.tar.gz |
29.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_16.tar.gz |
27.9 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_17.tar.gz |
34.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_18.tar.gz |
39.0 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_19.tar.gz |
38.8 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_2.tar.gz |
15.4 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_22.tar.gz |
8.0 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_23.tar.gz |
9.0 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_230.tar.gz |
14.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_231.tar.gz |
10.4 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_24.tar.gz |
10.5 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_244.tar.gz |
25.9 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_245.tar.gz |
38.7 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_25.tar.gz |
9.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_26.tar.gz |
6.0 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_27.tar.gz |
6.4 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_28.tar.gz |
22.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_29.tar.gz |
21.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_292.tar.gz |
19.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_293.tar.gz |
22.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_3.tar.gz |
22.0 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_30.tar.gz |
23.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_307.tar.gz |
32.1 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_308.tar.gz |
33.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_309.tar.gz |
72.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_31.tar.gz |
35.5 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_32.tar.gz |
14.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_33.tar.gz |
10.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_342.tar.gz |
108.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_343.tar.gz |
108.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_344.tar.gz |
107.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_345.tar.gz |
103.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_346.tar.gz |
110.0 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_347.tar.gz |
107.5 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_348.tar.gz |
111.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_350.tar.gz |
28.9 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_351.tar.gz |
31.7 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_36.tar.gz |
35.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_37.tar.gz |
39.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_38.tar.gz |
49.0 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_39.tar.gz |
17.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_4.tar.gz |
32.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_40.tar.gz |
21.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_41.tar.gz |
26.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_42.tar.gz |
20.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_43.tar.gz |
27.5 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_44.tar.gz |
27.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_45.tar.gz |
32.8 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_46.tar.gz |
22.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_47.tar.gz |
32.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_48.tar.gz |
34.5 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_49.tar.gz |
30.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_5.tar.gz |
24.7 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_50.tar.gz |
24.8 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_51.tar.gz |
30.7 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_52.tar.gz |
31.1 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_53.tar.gz |
70.6 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_54.tar.gz |
45.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_55.tar.gz |
44.5 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_56.tar.gz |
123.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_6.tar.gz |
12.7 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_668.tar.gz |
48.5 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_7.tar.gz |
60.1 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_8.tar.gz |
39.9 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_88.tar.gz |
146.2 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_89.tar.gz |
90.7 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_9.tar.gz |
36.4 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_90.tar.gz |
121.9 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_91.tar.gz |
123.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_92.tar.gz |
121.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_93.tar.gz |
123.4 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_94.tar.gz |
33.8 Mb |
(ftp)(http) |
TAR |
| GSE154826_amp_batch_ID_95.tar.gz |
21.3 Mb |
(ftp)(http) |
TAR |
| GSE154826_sample_annots.csv.gz |
1.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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