title: B16-Input_ChIP-Seq [FGC1367_s_3_CTGAAGCT-ATAGAGGC]


title: B16-Input_ChIP-Seq [FGC1367_s_4_CTGAAGCT-ATAGAGGC]

status: Public on Jun 13 2019

type: SRA

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

department: Genetics

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
ChIP-Seq: (1) Low quality base calls and sequencing adapters were trimmed using Trim Galore! (2) Trimmed reads were aligned to the reference human genome (hg19) using the BWA-MEM algorithm (3) Aligned reads were sorted and filtered based on a minimum mapping quality of 10 using SAMtools-1.3.1 (4) ChIP-Seq data from biological replicates (N=9 for H3K4me3 and N=18 for H3K27ac) as well as their corresponding input data (N=9 for Input of H3K4me3 and N=18 for Input of H3K27ac) were pooled into separate groups (5) MACS2 was used to call the peaks on the pooled ChIP-seq data of 9 and 18 individuals respectively while using the corresponding input data as control
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: Feature counts RNA-Seq:TPM values

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

extract_protocol:
NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina
QIAGEN’s AllPrep DNA/RNA/miRNA Universal Kit

tag: cohort

value: Penn Cohort 1

tag: tissue

value: liver

tag: individual

tag: chip antibody

value: none (input)


title: B15-Input_ChIP-Seq [FGC1261_s_5_TCCGGAGA-ATAGAGGC]


title: B14-Input_ChIP-Seq [FGC1376_s_2_TCTCGCGC-TAATCTTA]


title: B14-Input_ChIP-Seq [FGC1376_s_1_TCTCGCGC-TAATCTTA]


title: B15-Input_ChIP-Seq [FGC1367_s_3_TCCGGAGA-ATAGAGGC]


title: B14-Input_ChIP-Seq [FGC1367_s_1_TCTCGCGC-TAATCTTA]


title: B14-Input_ChIP-Seq [FGC1367_s_2_TCTCGCGC-TAATCTTA]


title: B19-Input_ChIP-Seq [FGC1367_s_2_ATTCAGAA-GGCTCTGA]


title: B12-Input_ChIP-Seq [FGC1376_s_2_TAATGCGC-AGGCGAAG]


title: B12-Input_ChIP-Seq [FGC1367_s_2_TAATGCGC-AGGCGAAG]


title: B12-Input_ChIP-Seq [FGC1376_s_1_TAATGCGC-AGGCGAAG]


title: B12-Input_ChIP-Seq [FGC1367_s_1_TAATGCGC-AGGCGAAG]


title: B14-Input_ChIP-Seq [FGC1261_s_4_TCTCGCGC-TAATCTTA]


title: B16-Input_ChIP-Seq [FGC1493_s_4_CTGAAGCT-ATAGAGGC]


title: B10-Input_ChIP-Seq [FGC1493_s_8_ATTCAGAA-TATAGCCT]


title: B10-Input_ChIP-Seq [FGC1493_s_7_ATTCAGAA-TATAGCCT]


title: B12-Input_ChIP-Seq [FGC1261_s_4_TAATGCGC-AGGCGAAG]


title: B16-Input_ChIP-Seq [FGC1376_s_4_CTGAAGCT-ATAGAGGC]


title: B10-Input_ChIP-Seq [FGC1493_s_4_ATTCAGAA-TATAGCCT]


title: B10-Input_ChIP-Seq [FGC1489_s_6_ATTCAGAA-TATAGCCT]


title: B10-Input_ChIP-Seq [FGC1493_s_6_ATTCAGAA-TATAGCCT]


title: B10-Input_ChIP-Seq [FGC1376_s_3_ATTCAGAA-TATAGCCT]


title: B10-Input_ChIP-Seq [FGC1493_s_5_ATTCAGAA-TATAGCCT]


title: B10-Input_ChIP-Seq [FGC1376_s_4_ATTCAGAA-TATAGCCT]


title: B10-Input_ChIP-Seq [FGC1367_s_4_ATTCAGAA-TATAGCCT]


title: B15-Input_ChIP-Seq [FGC1367_s_4_TCCGGAGA-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1572_s_4_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1543_s_8_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1572_s_5_CGCTCATT-ATAGAGGC]


title: B10-Input_ChIP-Seq [FGC1367_s_3_ATTCAGAA-TATAGCCT]


title: B9-Input_ChIP-Seq [FGC1493_s_3_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1489_s_5_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1493_s_1_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1493_s_2_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1376_s_2_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1376_s_1_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1367_s_2_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1367_s_1_CGCTCATT-ATAGAGGC]


title: B9-Input_ChIP-Seq [FGC1261_s_4_CGCTCATT-ATAGAGGC]


title: B8-Input_ChIP-Seq [FGC1376_s_4_CTGAAGCT-CCTATCCT]


title: B8-Input_ChIP-Seq [FGC1367_s_3_CTGAAGCT-CCTATCCT]


title: B8-Input_ChIP-Seq [FGC1261_s_5_CTGAAGCT-CCTATCCT]


title: B8-Input_ChIP-Seq [FGC1367_s_4_CTGAAGCT-CCTATCCT]


title: B10-Input_ChIP-Seq [FGC1261_s_5_ATTCAGAA-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1493_s_8_CTGAAGCT-TATAGCCT]


title: B8-Input_ChIP-Seq [FGC1376_s_3_CTGAAGCT-CCTATCCT]


title: B7-Input_ChIP-Seq [FGC1493_s_6_CTGAAGCT-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1489_s_6_CTGAAGCT-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1493_s_4_CTGAAGCT-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1493_s_7_CTGAAGCT-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1493_s_5_CTGAAGCT-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1367_s_3_CTGAAGCT-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1261_s_5_CTGAAGCT-TATAGCCT]


title: B4-Input_ChIP-Seq [FGC1376_s_2_GAGATTCC-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1367_s_4_CTGAAGCT-TATAGCCT]


title: B4-Input_ChIP-Seq [FGC1376_s_1_GAGATTCC-TATAGCCT]


title: B4-Input_ChIP-Seq [FGC1367_s_2_GAGATTCC-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1376_s_3_CTGAAGCT-TATAGCCT]


title: B4-Input_ChIP-Seq [FGC1367_s_1_GAGATTCC-TATAGCCT]


title: B1-Input_ChIP-Seq [FGC1572_s_1_TCCGCGAA-ATAGAGGC]


title: B1-Input_ChIP-Seq [FGC1543_s_6_TCCGCGAA-ATAGAGGC]


title: B1-Input_ChIP-Seq [FGC1376_s_4_TCCGCGAA-ATAGAGGC]


title: B1-Input_ChIP-Seq [FGC1376_s_3_TCCGCGAA-ATAGAGGC]


title: B1-Input_ChIP-Seq [FGC1367_s_4_TCCGCGAA-ATAGAGGC]


title: B1-Input_ChIP-Seq [FGC1261_s_5_TCCGCGAA-ATAGAGGC]


title: B1-Input_ChIP-Seq [FGC1367_s_3_TCCGCGAA-ATAGAGGC]


title: B47-H3K27ac_ChIP-Seq [FGC1572_s_4_TCTCGCGC-CCTATCCT]


title: B47-H3K27ac_ChIP-Seq [FGC1572_s_5_TCTCGCGC-CCTATCCT]


title: B4-Input_ChIP-Seq [FGC1261_s_4_GAGATTCC-TATAGCCT]


title: B7-Input_ChIP-Seq [FGC1376_s_4_CTGAAGCT-TATAGCCT]


title: B47-H3K27ac_ChIP-Seq [FGC1493_s_3_TCTCGCGC-CCTATCCT]


title: B47-H3K27ac_ChIP-Seq [FGC1543_s_8_TCTCGCGC-CCTATCCT]


title: B47-H3K27ac_ChIP-Seq [FGC1493_s_2_TCTCGCGC-CCTATCCT]


title: B47-H3K27ac_ChIP-Seq [FGC1493_s_1_TCTCGCGC-CCTATCCT]


title: B47-H3K27ac_ChIP-Seq [FGC1489_s_5_TCTCGCGC-CCTATCCT]


title: B47-H3K27ac_ChIP-Seq [FGC1376_s_4_TCTCGCGC-CCTATCCT]


title: B47-H3K27ac_ChIP-Seq [FGC1376_s_3_TCTCGCGC-CCTATCCT]


title: B46-H3K27ac_ChIP-Seq [FGC1572_s_1_TCTCGCGC-AGGCGAAG]


title: B47-H3K27ac_ChIP-Seq [FGC1367_s_3_TCTCGCGC-CCTATCCT]


title: B46-H3K27ac_ChIP-Seq [FGC1493_s_2_TCTCGCGC-AGGCGAAG]


title: B46-H3K27ac_ChIP-Seq [FGC1543_s_6_TCTCGCGC-AGGCGAAG]


title: B46-H3K27ac_ChIP-Seq [FGC1493_s_3_TCTCGCGC-AGGCGAAG]


title: B47-H3K27ac_ChIP-Seq [FGC1261_s_5_TCTCGCGC-CCTATCCT]


title: B46-H3K27ac_ChIP-Seq [FGC1493_s_1_TCTCGCGC-AGGCGAAG]


title: B46-H3K27ac_ChIP-Seq [FGC1376_s_1_TCTCGCGC-AGGCGAAG]


title: B46-H3K27ac_ChIP-Seq [FGC1367_s_1_TCTCGCGC-AGGCGAAG]


title: B47-H3K27ac_ChIP-Seq [FGC1367_s_4_TCTCGCGC-CCTATCCT]


title: B46-H3K27ac_ChIP-Seq [FGC1261_s_4_TCTCGCGC-AGGCGAAG]


title: B41-H3K27ac_ChIP-Seq [FGC1572_s_4_AGCGATAG-CAGGACGT]


title: B46-H3K27ac_ChIP-Seq [FGC1489_s_5_TCTCGCGC-AGGCGAAG]


title: B41-H3K27ac_ChIP-Seq [FGC1493_s_2_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1543_s_8_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1493_s_3_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1489_s_5_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1493_s_1_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1376_s_4_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1367_s_4_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1367_s_3_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1261_s_5_AGCGATAG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1376_s_3_AGCGATAG-CAGGACGT]


title: B38-H3K27ac_ChIP-Seq [FGC1572_s_3_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1572_s_2_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1573_s_2_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1543_s_7_GAATTCGT-AGGCGAAG]


title: B46-H3K27ac_ChIP-Seq [FGC1376_s_2_TCTCGCGC-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1493_s_4_GAATTCGT-AGGCGAAG]


title: B46-H3K27ac_ChIP-Seq [FGC1367_s_2_TCTCGCGC-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1493_s_8_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1493_s_5_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1489_s_6_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1376_s_1_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1367_s_2_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1493_s_7_GAATTCGT-AGGCGAAG]


title: B36-H3K27ac_ChIP-Seq [FGC1493_s_8_CGGCTATG-CAGGACGT]


title: B41-H3K27ac_ChIP-Seq [FGC1572_s_5_AGCGATAG-CAGGACGT]


title: B38-H3K27ac_ChIP-Seq [FGC1367_s_1_GAATTCGT-AGGCGAAG]


title: B36-H3K27ac_ChIP-Seq [FGC1493_s_7_CGGCTATG-CAGGACGT]


title: B38-H3K27ac_ChIP-Seq [FGC1261_s_4_GAATTCGT-AGGCGAAG]


title: B36-H3K27ac_ChIP-Seq [FGC1493_s_4_CGGCTATG-CAGGACGT]


title: B36-H3K27ac_ChIP-Seq [FGC1493_s_6_CGGCTATG-CAGGACGT]


title: B36-H3K27ac_ChIP-Seq [FGC1489_s_6_CGGCTATG-CAGGACGT]


title: B36-H3K27ac_ChIP-Seq [FGC1376_s_3_CGGCTATG-CAGGACGT]


title: B36-H3K27ac_ChIP-Seq [FGC1376_s_4_CGGCTATG-CAGGACGT]


title: B36-H3K27ac_ChIP-Seq [FGC1367_s_4_CGGCTATG-CAGGACGT]


title: B36-H3K27ac_ChIP-Seq [FGC1261_s_5_CGGCTATG-CAGGACGT]


title: B26-H3K27ac_ChIP-Seq [FGC1573_s_2_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1572_s_3_TCCGGAGA-ATAGAGGC]


title: B36-H3K27ac_ChIP-Seq [FGC1367_s_3_CGGCTATG-CAGGACGT]


title: B26-H3K27ac_ChIP-Seq [FGC1572_s_2_TCCGGAGA-ATAGAGGC]


title: B38-H3K27ac_ChIP-Seq [FGC1376_s_2_GAATTCGT-AGGCGAAG]


title: B38-H3K27ac_ChIP-Seq [FGC1493_s_6_GAATTCGT-AGGCGAAG]


title: B26-H3K27ac_ChIP-Seq [FGC1493_s_8_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1543_s_7_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1493_s_7_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1493_s_6_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1493_s_5_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1376_s_2_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1376_s_1_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1489_s_6_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1493_s_4_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1367_s_2_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1261_s_4_TCCGGAGA-ATAGAGGC]


title: B26-H3K27ac_ChIP-Seq [FGC1367_s_1_TCCGGAGA-ATAGAGGC]


title: B24-H3K27ac_ChIP-Seq [FGC1572_s_1_TCCGCGAA-TAATCTTA]


title: B24-H3K27ac_ChIP-Seq [FGC1543_s_6_TCCGCGAA-TAATCTTA]


title: B24-H3K27ac_ChIP-Seq [FGC1493_s_2_TCCGCGAA-TAATCTTA]


title: B24-H3K27ac_ChIP-Seq [FGC1493_s_1_TCCGCGAA-TAATCTTA]


title: B36-H3K27ac_ChIP-Seq [FGC1493_s_5_CGGCTATG-CAGGACGT]


title: B24-H3K27ac_ChIP-Seq [FGC1489_s_5_TCCGCGAA-TAATCTTA]


title: B24-H3K27ac_ChIP-Seq [FGC1376_s_2_TCCGCGAA-TAATCTTA]


title: B24-H3K27ac_ChIP-Seq [FGC1367_s_2_TCCGCGAA-TAATCTTA]


title: B24-H3K27ac_ChIP-Seq [FGC1367_s_1_TCCGCGAA-TAATCTTA]


title: B24-H3K27ac_ChIP-Seq [FGC1261_s_4_TCCGCGAA-TAATCTTA]


title: B22-H3K27ac_ChIP-Seq [FGC1572_s_4_CGCTCATT-CCTATCCT]


title: B22-H3K27ac_ChIP-Seq [FGC1572_s_5_CGCTCATT-CCTATCCT]


title: B22-H3K27ac_ChIP-Seq [FGC1493_s_3_CGCTCATT-CCTATCCT]


title: B22-H3K27ac_ChIP-Seq [FGC1543_s_8_CGCTCATT-CCTATCCT]


title: B22-H3K27ac_ChIP-Seq [FGC1489_s_5_CGCTCATT-CCTATCCT]


title: B22-H3K27ac_ChIP-Seq [FGC1376_s_3_CGCTCATT-CCTATCCT]


title: B22-H3K27ac_ChIP-Seq [FGC1493_s_1_CGCTCATT-CCTATCCT]


title: B22-H3K27ac_ChIP-Seq [FGC1493_s_2_CGCTCATT-CCTATCCT]


title: B22-H3K27ac_ChIP-Seq [FGC1367_s_4_CGCTCATT-CCTATCCT]


title: B24-H3K27ac_ChIP-Seq [FGC1493_s_3_TCCGCGAA-TAATCTTA]


title: B22-H3K27ac_ChIP-Seq [FGC1376_s_4_CGCTCATT-CCTATCCT]


title: B21-H3K27ac_ChIP-Seq [FGC1572_s_5_GAGATTCC-GGCTCTGA]


title: B21-H3K27ac_ChIP-Seq [FGC1572_s_4_GAGATTCC-GGCTCTGA]


title: B21-H3K27ac_ChIP-Seq [FGC1493_s_8_GAGATTCC-GGCTCTGA]


title: B22-H3K27ac_ChIP-Seq [FGC1261_s_5_CGCTCATT-CCTATCCT]


title: B21-H3K27ac_ChIP-Seq [FGC1493_s_5_GAGATTCC-GGCTCTGA]


title: B21-H3K27ac_ChIP-Seq [FGC1493_s_4_GAGATTCC-GGCTCTGA]


title: B21-H3K27ac_ChIP-Seq [FGC1493_s_7_GAGATTCC-GGCTCTGA]


title: B22-H3K27ac_ChIP-Seq [FGC1367_s_3_CGCTCATT-CCTATCCT]


title: B21-H3K27ac_ChIP-Seq [FGC1489_s_6_GAGATTCC-GGCTCTGA]


title: B21-H3K27ac_ChIP-Seq [FGC1376_s_1_GAGATTCC-GGCTCTGA]


title: B24-H3K27ac_ChIP-Seq [FGC1376_s_1_TCCGCGAA-TAATCTTA]


title: B21-H3K27ac_ChIP-Seq [FGC1367_s_2_GAGATTCC-GGCTCTGA]


title: B21-H3K27ac_ChIP-Seq [FGC1367_s_1_GAGATTCC-GGCTCTGA]


title: B21-H3K27ac_ChIP-Seq [FGC1261_s_4_GAGATTCC-GGCTCTGA]


title: B19-H3K27ac_ChIP-Seq [FGC1543_s_7_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1572_s_3_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1572_s_2_CGCTCATT-AGGCGAAG]


title: B21-H3K27ac_ChIP-Seq [FGC1543_s_8_GAGATTCC-GGCTCTGA]


title: B19-H3K27ac_ChIP-Seq [FGC1493_s_8_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1493_s_6_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1493_s_7_CGCTCATT-AGGCGAAG]


title: B21-H3K27ac_ChIP-Seq [FGC1493_s_6_GAGATTCC-GGCTCTGA]


title: B19-H3K27ac_ChIP-Seq [FGC1489_s_6_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1367_s_2_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1376_s_2_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1376_s_1_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1493_s_4_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1493_s_5_CGCTCATT-AGGCGAAG]


title: B19-H3K27ac_ChIP-Seq [FGC1261_s_4_CGCTCATT-AGGCGAAG]


title: B15-H3K27ac_ChIP-Seq [FGC1573_s_2_CGCTCATT-CAGGACGT]


title: B21-H3K27ac_ChIP-Seq [FGC1376_s_2_GAGATTCC-GGCTCTGA]


title: B15-H3K27ac_ChIP-Seq [FGC1572_s_3_CGCTCATT-CAGGACGT]


title: B19-H3K27ac_ChIP-Seq [FGC1367_s_1_CGCTCATT-AGGCGAAG]


title: B15-H3K27ac_ChIP-Seq [FGC1572_s_2_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1493_s_6_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1543_s_7_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1493_s_7_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1493_s_5_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1493_s_4_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1489_s_6_CGCTCATT-CAGGACGT]


title: B19-H3K27ac_ChIP-Seq [FGC1573_s_2_CGCTCATT-AGGCGAAG]


title: B15-H3K27ac_ChIP-Seq [FGC1376_s_4_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1376_s_3_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1367_s_3_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1367_s_4_CGCTCATT-CAGGACGT]


title: B15-H3K27ac_ChIP-Seq [FGC1261_s_5_CGCTCATT-CAGGACGT]


title: B14-H3K27ac_ChIP-Seq [FGC1493_s_2_TCTCGCGC-GGCTCTGA]


title: B14-H3K27ac_ChIP-Seq [FGC1489_s_5_TCTCGCGC-GGCTCTGA]


title: B14-H3K27ac_ChIP-Seq [FGC1376_s_4_TCTCGCGC-GGCTCTGA]


title: B14-H3K27ac_ChIP-Seq [FGC1493_s_3_TCTCGCGC-GGCTCTGA]


title: B14-H3K27ac_ChIP-Seq [FGC1493_s_1_TCTCGCGC-GGCTCTGA]


title: B14-H3K27ac_ChIP-Seq [FGC1367_s_4_TCTCGCGC-GGCTCTGA]


title: B14-H3K27ac_ChIP-Seq [FGC1367_s_3_TCTCGCGC-GGCTCTGA]


title: B14-H3K27ac_ChIP-Seq [FGC1376_s_3_TCTCGCGC-GGCTCTGA]


title: B14-H3K27ac_ChIP-Seq [FGC1261_s_5_TCTCGCGC-GGCTCTGA]


title: B15-H3K27ac_ChIP-Seq [FGC1493_s_8_CGCTCATT-CAGGACGT]


title: B12-H3K27ac_ChIP-Seq [FGC1493_s_7_GAATTCGT-CCTATCCT]


title: B12-H3K27ac_ChIP-Seq [FGC1489_s_6_GAATTCGT-CCTATCCT]


title: B12-H3K27ac_ChIP-Seq [FGC1493_s_6_GAATTCGT-CCTATCCT]


title: B12-H3K27ac_ChIP-Seq [FGC1367_s_3_GAATTCGT-CCTATCCT]


title: B12-H3K27ac_ChIP-Seq [FGC1493_s_8_GAATTCGT-CCTATCCT]


title: B12-H3K27ac_ChIP-Seq [FGC1261_s_5_GAATTCGT-CCTATCCT]


title: B12-H3K27ac_ChIP-Seq [FGC1493_s_4_GAATTCGT-CCTATCCT]


title: B10-H3K27ac_ChIP-Seq [FGC1493_s_2_TAATGCGC-CAGGACGT]


title: B10-H3K27ac_ChIP-Seq [FGC1493_s_1_TAATGCGC-CAGGACGT]


title: B10-H3K27ac_ChIP-Seq [FGC1489_s_5_TAATGCGC-CAGGACGT]


title: B10-H3K27ac_ChIP-Seq [FGC1376_s_4_TAATGCGC-CAGGACGT]


title: B10-H3K27ac_ChIP-Seq [FGC1493_s_3_TAATGCGC-CAGGACGT]


title: B10-H3K27ac_ChIP-Seq [FGC1367_s_4_TAATGCGC-CAGGACGT]


title: B9-H3K27ac_ChIP-Seq [FGC1493_s_3_TCCGGAGA-CAGGACGT]


title: B12-H3K27ac_ChIP-Seq [FGC1493_s_5_GAATTCGT-CCTATCCT]


title: B12-H3K27ac_ChIP-Seq [FGC1376_s_4_GAATTCGT-CCTATCCT]


title: B10-H3K27ac_ChIP-Seq [FGC1261_s_5_TAATGCGC-CAGGACGT]


title: B10-H3K27ac_ChIP-Seq [FGC1367_s_3_TAATGCGC-CAGGACGT]


title: B9-H3K27ac_ChIP-Seq [FGC1543_s_6_TCCGGAGA-CAGGACGT]


title: B12-H3K27ac_ChIP-Seq [FGC1367_s_4_GAATTCGT-CCTATCCT]


title: B9-H3K27ac_ChIP-Seq [FGC1493_s_1_TCCGGAGA-CAGGACGT]


title: B9-H3K27ac_ChIP-Seq [FGC1367_s_3_TCCGGAGA-CAGGACGT]


title: B9-H3K27ac_ChIP-Seq [FGC1376_s_3_TCCGGAGA-CAGGACGT]


title: B9-H3K27ac_ChIP-Seq [FGC1376_s_4_TCCGGAGA-CAGGACGT]


title: B8-H3K27ac_ChIP-Seq [FGC1376_s_4_TCCGGAGA-GTACTGAC]


title: B9-H3K27ac_ChIP-Seq [FGC1489_s_5_TCCGGAGA-CAGGACGT]


title: B9-H3K27ac_ChIP-Seq [FGC1261_s_5_TCCGGAGA-CAGGACGT]


title: B9-H3K27ac_ChIP-Seq [FGC1367_s_4_TCCGGAGA-CAGGACGT]


title: B9-H3K27ac_ChIP-Seq [FGC1493_s_2_TCCGGAGA-CAGGACGT]


title: B8-H3K27ac_ChIP-Seq [FGC1261_s_5_TCCGGAGA-GTACTGAC]


title: B8-H3K27ac_ChIP-Seq [FGC1367_s_4_TCCGGAGA-GTACTGAC]


title: B7-H3K27ac_ChIP-Seq [FGC1572_s_1_TAATGCGC-ATAGAGGC]


title: B10-H3K27ac_ChIP-Seq [FGC1376_s_3_TAATGCGC-CAGGACGT]


title: B7-H3K27ac_ChIP-Seq [FGC1543_s_6_TAATGCGC-ATAGAGGC]


title: B8-H3K27ac_ChIP-Seq [FGC1367_s_3_TCCGGAGA-GTACTGAC]


title: B7-H3K27ac_ChIP-Seq [FGC1493_s_2_TAATGCGC-ATAGAGGC]


title: B7-H3K27ac_ChIP-Seq [FGC1493_s_3_TAATGCGC-ATAGAGGC]


title: B9-H3K27ac_ChIP-Seq [FGC1572_s_1_TCCGGAGA-CAGGACGT]


title: B7-H3K27ac_ChIP-Seq [FGC1489_s_5_TAATGCGC-ATAGAGGC]


title: B7-H3K27ac_ChIP-Seq [FGC1376_s_1_TAATGCGC-ATAGAGGC]


title: B7-H3K27ac_ChIP-Seq [FGC1367_s_2_TAATGCGC-ATAGAGGC]


title: B1-H3K27ac_ChIP-Seq [FGC1572_s_5_ATTACTCG-AGGCGAAG]


title: B8-H3K27ac_ChIP-Seq [FGC1376_s_3_TCCGGAGA-GTACTGAC]


title: B1-H3K27ac_ChIP-Seq [FGC1572_s_4_ATTACTCG-AGGCGAAG]


title: B1-H3K27ac_ChIP-Seq [FGC1493_s_1_ATTACTCG-AGGCGAAG]


title: B7-H3K27ac_ChIP-Seq [FGC1261_s_4_TAATGCGC-ATAGAGGC]


title: B7-H3K27ac_ChIP-Seq [FGC1367_s_1_TAATGCGC-ATAGAGGC]


title: B1-H3K27ac_ChIP-Seq [FGC1493_s_3_ATTACTCG-AGGCGAAG]


title: B1-H3K27ac_ChIP-Seq [FGC1367_s_1_ATTACTCG-AGGCGAAG]


title: B1-H3K27ac_ChIP-Seq [FGC1376_s_1_ATTACTCG-AGGCGAAG]


title: B1-H3K27ac_ChIP-Seq [FGC1261_s_4_ATTACTCG-AGGCGAAG]


title: B1-H3K27ac_ChIP-Seq [FGC1489_s_5_ATTACTCG-AGGCGAAG]


title: B1-H3K27ac_ChIP-Seq [FGC1543_s_8_ATTACTCG-AGGCGAAG]


title: B1-H3K27ac_ChIP-Seq [FGC1367_s_2_ATTACTCG-AGGCGAAG]


title: B7-H3K27ac_ChIP-Seq [FGC1493_s_1_TAATGCGC-ATAGAGGC]


title: B48-H3K4me3_ChIP-Seq [FGC1572_s_2_ATTCAGAA-GGCTCTGA]


title: B1-H3K27ac_ChIP-Seq [FGC1493_s_2_ATTACTCG-AGGCGAAG]


title: B48-H3K4me3_ChIP-Seq [FGC1493_s_8_ATTCAGAA-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1493_s_5_ATTCAGAA-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1493_s_7_ATTCAGAA-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1543_s_7_ATTCAGAA-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1573_s_2_ATTCAGAA-GGCTCTGA]


title: B7-H3K27ac_ChIP-Seq [FGC1376_s_2_TAATGCGC-ATAGAGGC]


title: B48-H3K4me3_ChIP-Seq [FGC1493_s_4_ATTCAGAA-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1489_s_6_ATTCAGAA-GGCTCTGA]


title: B12-H3K27ac_ChIP-Seq [FGC1376_s_3_GAATTCGT-CCTATCCT]


title: B48-H3K4me3_ChIP-Seq [FGC1572_s_3_ATTCAGAA-GGCTCTGA]


title: B46-H3K4me3_ChIP-Seq [FGC1489_s_5_CGGCTATG-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1367_s_3_ATTCAGAA-GGCTCTGA]


title: B46-H3K4me3_ChIP-Seq [FGC1376_s_4_CGGCTATG-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1376_s_3_ATTCAGAA-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1261_s_5_ATTCAGAA-GGCTCTGA]


title: B46-H3K4me3_ChIP-Seq [FGC1376_s_3_CGGCTATG-GGCTCTGA]


title: B46-H3K4me3_ChIP-Seq [FGC1261_s_5_CGGCTATG-GGCTCTGA]


title: B45-H3K4me3_ChIP-Seq [FGC1493_s_7_CGCTCATT-CCTATCCT]


title: B46-H3K4me3_ChIP-Seq [FGC1367_s_4_CGGCTATG-GGCTCTGA]


title: B46-H3K4me3_ChIP-Seq [FGC1493_s_3_CGGCTATG-GGCTCTGA]


title: B45-H3K4me3_ChIP-Seq [FGC1493_s_6_CGCTCATT-CCTATCCT]


title: B45-H3K4me3_ChIP-Seq [FGC1493_s_5_CGCTCATT-CCTATCCT]


title: B1-H3K27ac_ChIP-Seq [FGC1376_s_2_ATTACTCG-AGGCGAAG]


title: B45-H3K4me3_ChIP-Seq [FGC1493_s_8_CGCTCATT-CCTATCCT]


title: B48-H3K4me3_ChIP-Seq [FGC1367_s_4_ATTCAGAA-GGCTCTGA]


title: B46-H3K4me3_ChIP-Seq [FGC1367_s_3_CGGCTATG-GGCTCTGA]


title: B48-H3K4me3_ChIP-Seq [FGC1376_s_4_ATTCAGAA-GGCTCTGA]


title: B45-H3K4me3_ChIP-Seq [FGC1376_s_1_CGCTCATT-CCTATCCT]


title: B45-H3K4me3_ChIP-Seq [FGC1367_s_2_CGCTCATT-CCTATCCT]


title: B45-H3K4me3_ChIP-Seq [FGC1261_s_4_CGCTCATT-CCTATCCT]


title: B46-H3K4me3_ChIP-Seq [FGC1493_s_1_CGGCTATG-GGCTCTGA]


title: B45-H3K4me3_ChIP-Seq [FGC1376_s_2_CGCTCATT-CCTATCCT]


title: B45-H3K4me3_ChIP-Seq [FGC1367_s_1_CGCTCATT-CCTATCCT]


title: B45-H3K4me3_ChIP-Seq [FGC1493_s_4_CGCTCATT-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1573_s_2_TCCGCGAA-CCTATCCT]


title: B46-H3K4me3_ChIP-Seq [FGC1493_s_2_CGGCTATG-GGCTCTGA]


title: B27-H3K4me3_ChIP-Seq [FGC1572_s_3_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1572_s_2_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1493_s_8_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1493_s_7_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1376_s_2_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1493_s_6_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1376_s_1_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1367_s_2_TCCGCGAA-CCTATCCT]


title: B45-H3K4me3_ChIP-Seq [FGC1489_s_6_CGCTCATT-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1367_s_1_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1261_s_4_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1489_s_6_TCCGCGAA-CCTATCCT]


title: B26-H3K4me3_ChIP-Seq [FGC1543_s_8_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1572_s_4_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1572_s_5_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1493_s_4_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1493_s_5_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1493_s_7_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1376_s_4_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1493_s_6_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1367_s_4_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1489_s_6_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1376_s_3_CTGAAGCT-GTACTGAC]


title: B27-H3K4me3_ChIP-Seq [FGC1493_s_4_TCCGCGAA-CCTATCCT]


title: B26-H3K4me3_ChIP-Seq [FGC1367_s_3_CTGAAGCT-GTACTGAC]


title: B26-H3K4me3_ChIP-Seq [FGC1261_s_5_CTGAAGCT-GTACTGAC]


title: B27-H3K4me3_ChIP-Seq [FGC1543_s_7_TCCGCGAA-CCTATCCT]


title: B27-H3K4me3_ChIP-Seq [FGC1493_s_5_TCCGCGAA-CCTATCCT]


title: B16-H3K4me3_ChIP-Seq [FGC1572_s_1_GAATTCGT-CCTATCCT]


title: B16-H3K4me3_ChIP-Seq [FGC1543_s_6_GAATTCGT-CCTATCCT]


title: B16-H3K4me3_ChIP-Seq [FGC1493_s_3_GAATTCGT-CCTATCCT]


title: B26-H3K4me3_ChIP-Seq [FGC1493_s_8_CTGAAGCT-GTACTGAC]


title: B16-H3K4me3_ChIP-Seq [FGC1493_s_1_GAATTCGT-CCTATCCT]


title: B16-H3K4me3_ChIP-Seq [FGC1493_s_2_GAATTCGT-CCTATCCT]


title: B16-H3K4me3_ChIP-Seq [FGC1376_s_2_GAATTCGT-CCTATCCT]


title: B16-H3K4me3_ChIP-Seq [FGC1376_s_1_GAATTCGT-CCTATCCT]


title: B16-H3K4me3_ChIP-Seq [FGC1489_s_5_GAATTCGT-CCTATCCT]


title: B15-H3K4me3_ChIP-Seq [FGC1573_s_2_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1572_s_3_TCCGCGAA-AGGCGAAG]


title: B16-H3K4me3_ChIP-Seq [FGC1367_s_1_GAATTCGT-CCTATCCT]


title: B15-H3K4me3_ChIP-Seq [FGC1493_s_6_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1493_s_8_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1572_s_2_TCCGCGAA-AGGCGAAG]


title: B16-H3K4me3_ChIP-Seq [FGC1367_s_2_GAATTCGT-CCTATCCT]


title: B15-H3K4me3_ChIP-Seq [FGC1493_s_7_TCCGCGAA-AGGCGAAG]


title: B16-H3K4me3_ChIP-Seq [FGC1261_s_4_GAATTCGT-CCTATCCT]


title: B15-H3K4me3_ChIP-Seq [FGC1493_s_4_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1543_s_7_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1489_s_6_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1493_s_5_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1376_s_1_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1367_s_1_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1376_s_2_TCCGCGAA-AGGCGAAG]


title: B15-H3K4me3_ChIP-Seq [FGC1261_s_4_TCCGCGAA-AGGCGAAG]


title: B4-H3K4me3_ChIP-Seq [FGC1572_s_3_TCCGGAGA-GGCTCTGA]


title: B4-H3K4me3_ChIP-Seq [FGC1573_s_2_TCCGGAGA-GGCTCTGA]


title: B4-H3K4me3_ChIP-Seq [FGC1572_s_2_TCCGGAGA-GGCTCTGA]


title: B4-H3K4me3_ChIP-Seq [FGC1493_s_7_TCCGGAGA-GGCTCTGA]


title: B4-H3K4me3_ChIP-Seq [FGC1543_s_7_TCCGGAGA-GGCTCTGA]


title: B4-H3K4me3_ChIP-Seq [FGC1493_s_6_TCCGGAGA-GGCTCTGA]


title: B4-H3K4me3_ChIP-Seq [FGC1493_s_5_TCCGGAGA-GGCTCTGA]


title: B4-H3K4me3_ChIP-Seq [FGC1489_s_6_TCCGGAGA-GGCTCTGA]


title: B15-H3K4me3_ChIP-Seq [FGC1367_s_2_TCCGCGAA-AGGCGAAG]


title: B4-H3K4me3_ChIP-Seq [FGC1493_s_4_TCCGGAGA-GGCTCTGA]


title: B1-H3K4me3_ChIP-Seq [FGC1572_s_3_CGGCTATG-CCTATCCT]


title: B4-H3K4me3_ChIP-Seq [FGC1376_s_1_TCCGGAGA-GGCTCTGA]


title: B1-H3K4me3_ChIP-Seq [FGC1493_s_6_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1493_s_7_CGGCTATG-CCTATCCT]


title: B4-H3K4me3_ChIP-Seq [FGC1376_s_2_TCCGGAGA-GGCTCTGA]


title: B1-H3K4me3_ChIP-Seq [FGC1543_s_7_CGGCTATG-CCTATCCT]


title: B4-H3K4me3_ChIP-Seq [FGC1367_s_1_TCCGGAGA-GGCTCTGA]


title: B1-H3K4me3_ChIP-Seq [FGC1573_s_2_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1376_s_1_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1493_s_5_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1489_s_6_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1493_s_8_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1367_s_2_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1572_s_2_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1493_s_4_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1367_s_1_CGGCTATG-CCTATCCT]


title: B1-H3K4me3_ChIP-Seq [FGC1261_s_4_CGGCTATG-CCTATCCT]


title: B4-H3K4me3_ChIP-Seq [FGC1261_s_4_TCCGGAGA-GGCTCTGA]


title: B1-H3K4me3_ChIP-Seq [FGC1376_s_2_CGGCTATG-CCTATCCT]


title: Pool2B_Non_TRM

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description:
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
Non_TRM_NormCov.bw

data_processing:
OMNI-ATAC-seq data were mapped against the human hg19 reference genome
Technical replicates were randomly downsampled to up to 30,000,000 total reads and then merged
Reads were mapped with boetie2, using Samtools to select uniquely mappable reads with (MAPQ >=30)
Tag align files were shifted by 4 or 5 bases to account for the TN5
Genome_build: hg19
Supplementary_files_format_and_content: Non_TRM_NormCov.bw contains tag density files in bigWig format
Supplementary_files_format_and_content: TIM3Pos_IL7Rneg_TRM_NormCov.bw contains tag density files in bigWig format

source_name: Human cancer tissue

growth_protocol: CD8+ cell types were isolated from human tissue and directly sorted by Flow cytometry into 50% FBS 50% PBS. No particular cell growth procedure was required.

extract_protocol:
OMNI-ATAC-seq was performed as described in Corces, et al., 2017 (PMC5623106) with minor variations
OMNI-ATAC-seq was performed as described in Corces, et al., 2017 (PMC5623106) with minor variations

tag: cell type

tag: cell type surface markers

tag: treatment

value: Treatment naïve

tag: donor


title: B48-H3K4me3_ChIP-Seq [FGC1493_s_6_ATTCAGAA-GGCTCTGA]


title: Pool2A_Non_TRM


title: Pool1B_TIM3Pos_IL7Rneg_TRM

description:
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
TIM3Pos_IL7Rneg_TRM_NormCov.bw


title: human_Oo_R2

city: Shanghai

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

country: China

institute: Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
The raw reads in fastq files were trimmed to 50nt, then these reads were quality filtered and collapsed with FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Read sequences longer than 17 nt after adapter trimming were aligned to the reference genome (hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey) with Bowtie allowing no mismatch. The perfectly mapped reads were assigned to known miRNAs, rRNAs, sn/snoRNAs and tRNAs successively. The reads that couldn’t be mapped to these known small RNAs were used to predict piRNAs, endo-siRNAs and xiRNAs successively. For the reads that could be mapped to multiple genome loci, we used the program reallocate (http://www.smallrnagroup-mainz.de/software.html) to apportion the read counts of multiply mapped sequences according to their local transcription level calculated by uniquely mapped sequences within 5 kb flanking regions. The reads with low sequence complexity (>=75% of the sequence consists of one nucleotide) were removed from the datasets. The relative abundance of these small RNAs was normalized as reads assigned per million genome mapped reads (RPM).
Genome_build: hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey
Supplementary_files_format_and_content: sequence of miRNA, endo-siRNA, piRNA and their expression (RPM) in each sample were provided

molecule: total RNA

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 2, with synthetic spike-in

extract_protocol: cDNA library construction strategies of Illumina TruSeq, our CAS-seq and our previous 10ng-seq were utilized. Details were in the online method of our article.

tag: rna input

value: single oocyte

tag: library construction method

value: CAS-seq

tag: spike-in

value: no

value: human oocyte

tag: age

value: Adult

tag: molecule subtype

value: small RNA in length of 17-40 nt


title: human_Oo_R3

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 3


title: human_CumulusCell

source_name: small RNA-seq of human cumulus cells detected by CAS-seq with 1ng of total RNA

value: 1ng input of total RNA

value: human cumulus cell


title: human_Oo_R1

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 1


title: B4-H3K4me3_ChIP-Seq [FGC1367_s_2_TCCGGAGA-GGCTCTGA]


title: Pool1A_TIM3Pos_IL7Rneg_TRM


title: evCEnC_1

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

data_processing:
Raw reads in FASTQ files were aligned to the human hg38 genome build and transcript (Ensembl 92) quantities calculated using the kallisto (v0.44.0) per instructions.
Differential gene expression analysis was performed using the Sleuth (v0.30.0) R package. Differential expression was tested using a negative binomial test, and corrected for multiple testing using the Benjamini-Hochberg correction.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a tab delimited txt file with Ensembl 92 gene symbol ID in the first column. Sample names are given on the first row with TPM values for each gene running down the column.

source_name: corneal endothelium

extract_protocol:
TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit.
Enrichment for poly(A) RNAs was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module, followed by library preparation using the PrepX Complete ILM DNA Library Kit. Libraries were prepared as per the manufacturer's instructions.

tag: sample type

value: ex vivo

tag: age group

value: adult

value: corneal endothelium


title: evCEnC_2


title: evCEpC_3

source_name: corneal epithelium

value: corneal epithelium


title: evCEpC_2


title: evCEpC_1


title: evK_2

source_name: corneal keratocytes

value: corneal keratocytes


title: evK_3


title: BRH1000988

city: Gaithersburg

first: Shiliang

last: Wang

state: MD

address: 1 Medimmune Way

department: Translational science

institute: Medimmune, Inc.

data_processing:
Read QC using FastQC
Primer trimming using Trimmomatic
Sequence read mapping and transcript generation using STAR
Read counts mapped on individual genes using HTSeq-count
Differential expression gene analysis using DESeq2
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: mavri_baseline_hc_fpkm_data.Sept2018.xls, FPKM

source_name: whole blood

extract_protocol:
Total RNA
Illumina Truseq strandard total RNA

tag: disease state

value: healthy


title: BRH1000982


title: BRH1000984


title: BRH1000985


title: BRH1000987


title: BRH1000981


title: BRH1000980


title: BRH1000986


title: BRH1000977


title: BRH1000978


title: BRH1000983


title: BRH1000979


title: BRH1000975


title: BRH1000976


title: evCEnC_3


title: BRH1000974


title: BRH1000972


title: evK_1


title: BRH1000971


title: BRH1000970


title: BRH1000969


title: B4-H3K4me3_ChIP-Seq [FGC1493_s_8_TCCGGAGA-GGCTCTGA]

value: Penn Cohort 1

value: liver


title: EA295798-40

tag: timepoint

value: Day 1

value: rheumatoid arthritis


title: EB379042-41


title: EA295796-40


title: EB379041-40


title: EA292075-40


title: EB457713-40


title: EB457714-40


title: BRH1000973


title: EB357081-40


title: EA293505-40


title: EA293508-40


title: L1487958-42


title: L1396480-42


title: EB357082-40


title: EB357080-40


title: EA355375-40


title: AF780135-40


title: AF780134-40


title: EA006853-40


title: AF780132-40


title: AE726162-40


title: AE726226-40


title: AF366820-40


title: AE726227-40


title: EA359147-40


title: AE726224-40


title: AF174203-40


title: E9701873-40


title: EA365784-40


title: EA468985-40


title: E9701876-40


title: E9701874-40


title: AF780133-40


title: E9701875-40


title: AF780131-40


title: EB490049-40


title: AF174205-40


title: E9570461-41


title: EA362347-40


title: EA360114-40


title: EB126024-40


title: EA361506-40


title: EA355742-40


title: EB126023-40


title: AF682092-40


title: AE882453-40


title: L1525913-42


title: AE865149-40


title: AF565479-40


title: AE882454-40


title: AE865151-40


title: E9502592-41


title: AE882455-40


title: AE882457-38


title: EA359341-40


title: E9502590-41


title: EB410541-40


title: L1482289-42


title: L1485962-41


title: EB341669-40


title: L1456802-41


title: EA294834-17


title: L1396567-41


title: E9212635-41


title: EB126025-40


title: EA293861-40


title: EB126232-40


title: AE882456-40


title: E9545832-41


title: EB078609-40


title: EA293864-40


title: E9730864-40


title: EB078606-40


title: E9502589-41


title: EB551241-40


title: EB078610-40


title: EB078607-40


title: EA355494-40


title: E9730863-40


title: EA073508-40


title: EB324709-40


title: EB324712-40


title: E9730866-40


title: EB324713-40


title: EA355493-40


title: E9212519-42


title: E9212521-44


title: EB221884-40


title: EA171695-40


title: EB126234-40


title: E9701932-40


title: E9701931-40


title: EB091485-40


title: EA171696-40


title: EB415736-40


title: EB415731-40


title: E9701930-40


title: EB316882-42


title: EB340678-40


title: EB340676-40


title: EB609271-40


title: EB415733-40


title: EB415734-40


title: EB340677-40


title: EB415732-40


title: EA362665-40


title: EA171694-40


title: EA362667-40


title: EB157194-40


title: EB541041-40


title: EB541042-40


title: L1472041-42


title: L1472033-42


title: L1472036-42


title: L1472034-42


title: L1423344-42


title: EB541040-40


title: L1423347-42


title: L1397525-41


title: EA359415-40


title: L1524576-41


title: EB415735-40


title: L1397526-42


title: 187_Donor-53_TP01_CD3pos_C12

description:
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
Clarke_SC_raw_counts_upd.txt
Clarke_SC_TPM_upd.txt

data_processing:
Single-cell RNA–seq data were mapped against the human hg19 reference genome using TopHat
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Clarke_SC_raw_counts_upd.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Clarke_SC_TPM_upd.txt contains contains Transcript per Million normalized counts

molecule: polyA RNA

source_name: cancer tissue

growth_protocol: CD8+ cell types were isolated from human tissue and directly sorted by Flow cytometry into a 96-well plate wells with lysis buffer with RNAase inhibitor (Takara) - Described in Picelli et al. Nat Protoc. 2014, PMID:24385147. No particular cell growth procedure was required.

extract_protocol:
Single cell RNAseq was performed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. We performed 23 cycles of amplification.
Single cell RNAseq was perfromed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. Barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) were prepared as following manufacturer's protocol.
DNA sequencing - Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).

value: cancer tissue

value: CD14-CD19-CD20-CD45+ live cells CD3+


title: 189_Donor-53_TP01_CD3pos_E12


title: 190_Donor-53_TP01_CD3pos_F12


title: 192_Donor-53_TP01_CD3pos_H12


title: 186_Donor-53_TP01_CD3pos_B12


title: 188_Donor-53_TP01_CD3pos_D12


title: 185_Donor-53_TP01_CD3pos_A12


title: EB157192-40


title: L1524577-41


title: 191_Donor-53_TP01_CD3pos_G12


title: 183_Donor-53_TP01_CD3pos_G11


title: 184_Donor-53_TP01_CD3pos_H11


title: E9212848-41


title: 180_Donor-53_TP01_CD3pos_D11


title: L1472038-42


title: L1423348-42


title: 179_Donor-53_TP01_CD3pos_C11


title: 182_Donor-53_TP01_CD3pos_F11


title: 178_Donor-53_TP01_CD3pos_B11


title: 174_Donor-53_TP01_CD3pos_F10


title: 175_Donor-53_TP01_CD3pos_G10


title: 176_Donor-53_TP01_CD3pos_H10


title: 177_Donor-53_TP01_CD3pos_A11


title: 172_Donor-53_TP01_CD3pos_D10


title: 168_Donor-53_TP01_CD3pos_H9


title: 171_Donor-53_TP01_CD3pos_C10


title: 169_Donor-53_TP01_CD3pos_A10


title: 170_Donor-53_TP01_CD3pos_B10


title: 181_Donor-53_TP01_CD3pos_E11


title: 166_Donor-53_TP01_CD3pos_F9


title: 165_Donor-53_TP01_CD3pos_E9


title: 160_Donor-53_TP01_CD3pos_H8


title: 164_Donor-53_TP01_CD3pos_D9


title: 163_Donor-53_TP01_CD3pos_C9


title: 156_Donor-53_TP01_CD3pos_D8


title: 157_Donor-53_TP01_CD3pos_E8


title: 167_Donor-53_TP01_CD3pos_G9


title: 155_Donor-53_TP01_CD3pos_C8


title: 161_Donor-53_TP01_CD3pos_A9


title: 154_Donor-53_TP01_CD3pos_B8


title: 152_Donor-53_TP01_CD3pos_H7


title: 159_Donor-53_TP01_CD3pos_G8


title: 162_Donor-53_TP01_CD3pos_B9


title: 151_Donor-53_TP01_CD3pos_G7


title: 149_Donor-53_TP01_CD3pos_E7


title: 153_Donor-53_TP01_CD3pos_A8


title: 148_Donor-53_TP01_CD3pos_D7


title: 173_Donor-53_TP01_CD3pos_E10


title: 147_Donor-53_TP01_CD3pos_C7


title: 145_Donor-53_TP01_CD3pos_A7


title: 146_Donor-53_TP01_CD3pos_B7


title: 144_Donor-53_TP01_CD3pos_H6


title: 143_Donor-53_TP01_CD3pos_G6


title: 140_Donor-53_TP01_CD3pos_D6


title: 142_Donor-53_TP01_CD3pos_F6


title: 139_Donor-53_TP01_CD3pos_C6


title: 141_Donor-53_TP01_CD3pos_E6


title: 158_Donor-53_TP01_CD3pos_F8


title: 138_Donor-53_TP01_CD3pos_B6


title: 150_Donor-53_TP01_CD3pos_F7


title: 137_Donor-53_TP01_CD3pos_A6


title: 133_Donor-53_TP01_CD3pos_E5


title: 130_Donor-53_TP01_CD3pos_B5


title: 131_Donor-53_TP01_CD3pos_C5


title: 136_Donor-53_TP01_CD3pos_H5


title: 126_Donor-53_TP01_CD3pos_F4


title: 124_Donor-53_TP01_CD3pos_D4


title: 128_Donor-53_TP01_CD3pos_H4


title: 123_Donor-53_TP01_CD3pos_C4


title: 125_Donor-53_TP01_CD3pos_E4


title: 127_Donor-53_TP01_CD3pos_G4


title: 134_Donor-53_TP01_CD3pos_F5


title: 122_Donor-53_TP01_CD3pos_B4


title: 121_Donor-53_TP01_CD3pos_A4


title: 120_Donor-53_TP01_CD3pos_H3


title: 119_Donor-53_TP01_CD3pos_G3


title: 118_Donor-53_TP01_CD3pos_F3


title: 117_Donor-53_TP01_CD3pos_E3


title: 112_Donor-53_TP01_CD3pos_H2


title: 115_Donor-53_TP01_CD3pos_C3


title: 114_Donor-53_TP01_CD3pos_B3


title: 111_Donor-53_TP01_CD3pos_G2


title: 110_Donor-53_TP01_CD3pos_F2


title: 132_Donor-53_TP01_CD3pos_D5


title: 135_Donor-53_TP01_CD3pos_G5


title: 129_Donor-53_TP01_CD3pos_A5


title: 109_Donor-53_TP01_CD3pos_E2


title: 108_Donor-53_TP01_CD3pos_D2


title: 103_Donor-53_TP01_CD3pos_G1


title: 105_Donor-53_TP01_CD3pos_A2


title: 102_Donor-53_TP01_CD3pos_F1


title: 099_Donor-53_TP01_CD3pos_C1


title: 097_Donor-53_TP01_CD3pos_A1


title: 100_Donor-53_TP01_CD3pos_D1


title: 093_Donor-53_TP00_CD3pos_E12

value: Treatment naïve


title: 106_Donor-53_TP01_CD3pos_B2


title: 098_Donor-53_TP01_CD3pos_B1


title: 101_Donor-53_TP01_CD3pos_E1


title: 090_Donor-53_TP00_CD3pos_B12


title: 092_Donor-53_TP00_CD3pos_D12


title: 096_Donor-53_TP00_CD3pos_H12


title: 116_Donor-53_TP01_CD3pos_D3


title: 088_Donor-53_TP00_CD3pos_H11


title: 094_Donor-53_TP00_CD3pos_F12


title: 091_Donor-53_TP00_CD3pos_C12


title: 113_Donor-53_TP01_CD3pos_A3


title: 083_Donor-53_TP00_CD3pos_C11


title: 082_Donor-53_TP00_CD3pos_B11


title: 087_Donor-53_TP00_CD3pos_G11


title: 089_Donor-53_TP00_CD3pos_A12


title: 095_Donor-53_TP00_CD3pos_G12


title: 081_Donor-53_TP00_CD3pos_A11


title: 085_Donor-53_TP00_CD3pos_E11


title: 084_Donor-53_TP00_CD3pos_D11


title: 104_Donor-53_TP01_CD3pos_H1


title: 079_Donor-53_TP00_CD3pos_G10


title: 076_Donor-53_TP00_CD3pos_D10


title: 077_Donor-53_TP00_CD3pos_E10


title: 080_Donor-53_TP00_CD3pos_H10


title: 071_Donor-53_TP00_CD3pos_G9


title: 107_Donor-53_TP01_CD3pos_C2


title: 068_Donor-53_TP00_CD3pos_D9


title: 078_Donor-53_TP00_CD3pos_F10


title: 074_Donor-53_TP00_CD3pos_B10


title: 072_Donor-53_TP00_CD3pos_H9


title: 066_Donor-53_TP00_CD3pos_B9


title: 065_Donor-53_TP00_CD3pos_A9


title: 067_Donor-53_TP00_CD3pos_C9


title: 070_Donor-53_TP00_CD3pos_F9


title: 064_Donor-53_TP00_CD3pos_H8


title: 063_Donor-53_TP00_CD3pos_G8


title: 061_Donor-53_TP00_CD3pos_E8


title: 062_Donor-53_TP00_CD3pos_F8


title: 060_Donor-53_TP00_CD3pos_D8


title: 059_Donor-53_TP00_CD3pos_C8


title: 055_Donor-53_TP00_CD3pos_G7


title: 057_Donor-53_TP00_CD3pos_A8


title: 053_Donor-53_TP00_CD3pos_E7


title: 058_Donor-53_TP00_CD3pos_B8


title: 051_Donor-53_TP00_CD3pos_C7


title: 050_Donor-53_TP00_CD3pos_B7


title: 052_Donor-53_TP00_CD3pos_D7


title: 049_Donor-53_TP00_CD3pos_A7


title: 056_Donor-53_TP00_CD3pos_H7


title: 048_Donor-53_TP00_CD3pos_H6


title: 046_Donor-53_TP00_CD3pos_F6


title: 047_Donor-53_TP00_CD3pos_G6


title: 045_Donor-53_TP00_CD3pos_E6


title: 044_Donor-53_TP00_CD3pos_D6


title: 043_Donor-53_TP00_CD3pos_C6


title: 069_Donor-53_TP00_CD3pos_E9


title: 042_Donor-53_TP00_CD3pos_B6


title: 041_Donor-53_TP00_CD3pos_A6


title: 040_Donor-53_TP00_CD3pos_H5


title: 039_Donor-53_TP00_CD3pos_G5


title: 038_Donor-53_TP00_CD3pos_F5


title: 037_Donor-53_TP00_CD3pos_E5


title: 035_Donor-53_TP00_CD3pos_C5


title: 034_Donor-53_TP00_CD3pos_B5


title: 036_Donor-53_TP00_CD3pos_D5


title: 033_Donor-53_TP00_CD3pos_A5


title: 019_Donor-53_TP00_CD3pos_C3


title: 002_Donor-53_TP00_CD3pos_B1


title: 192_Donor-54_TP01_CD8pos_H12

value: CD14-CD19-CD20-CD45+ live cells CD3+CD8+


title: 191_Donor-54_TP01_CD8pos_G12


title: 014_Donor-53_TP00_CD3pos_F2


title: 007_Donor-53_TP00_CD3pos_G1


title: 011_Donor-53_TP00_CD3pos_C2


title: 006_Donor-53_TP00_CD3pos_F1


title: 005_Donor-53_TP00_CD3pos_E1


title: 009_Donor-53_TP00_CD3pos_A2


title: 015_Donor-53_TP00_CD3pos_G2


title: 018_Donor-53_TP00_CD3pos_B3


title: 010_Donor-53_TP00_CD3pos_B2


title: 001_Donor-53_TP00_CD3pos_A1


title: 017_Donor-53_TP00_CD3pos_A3


title: 187_Donor-54_TP01_CD8pos_C12


title: 188_Donor-54_TP01_CD8pos_D12


title: 190_Donor-54_TP01_CD8pos_F12


title: 027_Donor-53_TP00_CD3pos_C4


title: 189_Donor-54_TP01_CD8pos_E12


title: 179_Donor-54_TP01_CD8pos_C11


title: 185_Donor-54_TP01_CD8pos_A12


title: 184_Donor-54_TP01_CD8pos_H11


title: 161_Donor-54_TP01_CD8pos_A9


title: 166_Donor-54_TP01_CD8pos_F9


title: 180_Donor-54_TP01_CD8pos_D11


title: 168_Donor-54_TP01_CD8pos_H9


title: 183_Donor-54_TP01_CD8pos_G11


title: 182_Donor-54_TP01_CD8pos_F11


title: 172_Donor-54_TP01_CD8pos_D10


title: 173_Donor-54_TP01_CD8pos_E10


title: 162_Donor-54_TP01_CD8pos_B9


title: 177_Donor-54_TP01_CD8pos_A11


title: 169_Donor-54_TP01_CD8pos_A10


title: 178_Donor-54_TP01_CD8pos_B11


title: 181_Donor-54_TP01_CD8pos_E11


title: 170_Donor-54_TP01_CD8pos_B10


title: 186_Donor-54_TP01_CD8pos_B12


title: 167_Donor-54_TP01_CD8pos_G9


title: 165_Donor-54_TP01_CD8pos_E9


title: 174_Donor-54_TP01_CD8pos_F10


title: 163_Donor-54_TP01_CD8pos_C9


title: 160_Donor-54_TP01_CD8pos_H8


title: 176_Donor-54_TP01_CD8pos_H10


title: 164_Donor-54_TP01_CD8pos_D9


title: 175_Donor-54_TP01_CD8pos_G10


title: 157_Donor-54_TP01_CD8pos_E8


title: 158_Donor-54_TP01_CD8pos_F8


title: 159_Donor-54_TP01_CD8pos_G8


title: 171_Donor-54_TP01_CD8pos_C10


title: 156_Donor-54_TP01_CD8pos_D8


title: 154_Donor-54_TP01_CD8pos_B8


title: 150_Donor-54_TP01_CD8pos_F7


title: 151_Donor-54_TP01_CD8pos_G7


title: 149_Donor-54_TP01_CD8pos_E7


title: 153_Donor-54_TP01_CD8pos_A8


title: 138_Donor-54_TP01_CD8pos_B6


title: 145_Donor-54_TP01_CD8pos_A7


title: 142_Donor-54_TP01_CD8pos_F6


title: 143_Donor-54_TP01_CD8pos_G6


title: 147_Donor-54_TP01_CD8pos_C7


title: 146_Donor-54_TP01_CD8pos_B7


title: 152_Donor-54_TP01_CD8pos_H7


title: 136_Donor-54_TP01_CD8pos_H5


title: 134_Donor-54_TP01_CD8pos_F5


title: 135_Donor-54_TP01_CD8pos_G5


title: 132_Donor-54_TP01_CD8pos_D5


title: 141_Donor-54_TP01_CD8pos_E6


title: 144_Donor-54_TP01_CD8pos_H6


title: 139_Donor-54_TP01_CD8pos_C6


title: 137_Donor-54_TP01_CD8pos_A6


title: 155_Donor-54_TP01_CD8pos_C8


title: 130_Donor-54_TP01_CD8pos_B5


title: 140_Donor-54_TP01_CD8pos_D6


title: 129_Donor-54_TP01_CD8pos_A5


title: 128_Donor-54_TP01_CD8pos_H4


title: 127_Donor-54_TP01_CD8pos_G4


title: 148_Donor-54_TP01_CD8pos_D7


title: 131_Donor-54_TP01_CD8pos_C5


title: 133_Donor-54_TP01_CD8pos_E5


title: 123_Donor-54_TP01_CD8pos_C4


title: 122_Donor-54_TP01_CD8pos_B4


title: 126_Donor-54_TP01_CD8pos_F4


title: 121_Donor-54_TP01_CD8pos_A4


title: 124_Donor-54_TP01_CD8pos_D4


title: 120_Donor-54_TP01_CD8pos_H3


title: 118_Donor-54_TP01_CD8pos_F3


title: 117_Donor-54_TP01_CD8pos_E3


title: 114_Donor-54_TP01_CD8pos_B3


title: 116_Donor-54_TP01_CD8pos_D3


title: 119_Donor-54_TP01_CD8pos_G3


title: 112_Donor-54_TP01_CD8pos_H2


title: 111_Donor-54_TP01_CD8pos_G2


title: 106_Donor-54_TP01_CD8pos_B2


title: 115_Donor-54_TP01_CD8pos_C3


title: 109_Donor-54_TP01_CD8pos_E2


title: 110_Donor-54_TP01_CD8pos_F2


title: 099_Donor-54_TP01_CD8pos_C1


title: 105_Donor-54_TP01_CD8pos_A2


title: 107_Donor-54_TP01_CD8pos_C2


title: 103_Donor-54_TP01_CD8pos_G1


title: 104_Donor-54_TP01_CD8pos_H1


title: 102_Donor-54_TP01_CD8pos_F1


title: 101_Donor-54_TP01_CD8pos_E1


title: 100_Donor-54_TP01_CD8pos_D1


title: 125_Donor-54_TP01_CD8pos_E4


title: 098_Donor-54_TP01_CD8pos_B1


title: 095_Donor-54_TP00_CD3pos_G12


title: 094_Donor-54_TP00_CD3pos_F12


title: 093_Donor-54_TP00_CD3pos_E12


title: 092_Donor-54_TP00_CD3pos_D12


title: 090_Donor-54_TP00_CD3pos_B12


title: 108_Donor-54_TP01_CD8pos_D2


title: 086_Donor-54_TP00_CD3pos_F11


title: 084_Donor-54_TP00_CD3pos_D11


title: 083_Donor-54_TP00_CD3pos_C11


title: 087_Donor-54_TP00_CD3pos_G11


title: 079_Donor-54_TP00_CD3pos_G10


title: 078_Donor-54_TP00_CD3pos_F10


title: 081_Donor-54_TP00_CD3pos_A11


title: 085_Donor-54_TP00_CD3pos_E11


title: 082_Donor-54_TP00_CD3pos_B11


title: 088_Donor-54_TP00_CD3pos_H11


title: 089_Donor-54_TP00_CD3pos_A12


title: 077_Donor-54_TP00_CD3pos_E10


title: 073_Donor-54_TP00_CD3pos_A10


title: 069_Donor-54_TP00_CD3pos_E9


title: 068_Donor-54_TP00_CD3pos_D9


title: 067_Donor-54_TP00_CD3pos_C9


title: 066_Donor-54_TP00_CD3pos_B9


title: 065_Donor-54_TP00_CD3pos_A9


title: 071_Donor-54_TP00_CD3pos_G9


title: 091_Donor-54_TP00_CD3pos_C12


title: 063_Donor-54_TP00_CD3pos_G8


title: 064_Donor-54_TP00_CD3pos_H8


title: 080_Donor-54_TP00_CD3pos_H10


title: 062_Donor-54_TP00_CD3pos_F8


title: 061_Donor-54_TP00_CD3pos_E8


title: 060_Donor-54_TP00_CD3pos_D8


title: 070_Donor-54_TP00_CD3pos_F9


title: 059_Donor-54_TP00_CD3pos_C8


title: 058_Donor-54_TP00_CD3pos_B8


title: 055_Donor-54_TP00_CD3pos_G7


title: 056_Donor-54_TP00_CD3pos_H7


title: 052_Donor-54_TP00_CD3pos_D7


title: 051_Donor-54_TP00_CD3pos_C7


title: 050_Donor-54_TP00_CD3pos_B7


title: 057_Donor-54_TP00_CD3pos_A8


title: 054_Donor-54_TP00_CD3pos_F7


title: 047_Donor-54_TP00_CD3pos_G6


title: 046_Donor-54_TP00_CD3pos_F6


title: 072_Donor-54_TP00_CD3pos_H9


title: 045_Donor-54_TP00_CD3pos_E6


title: 044_Donor-54_TP00_CD3pos_D6


title: 043_Donor-54_TP00_CD3pos_C6


title: 042_Donor-54_TP00_CD3pos_B6


title: 041_Donor-54_TP00_CD3pos_A6


title: 040_Donor-54_TP00_CD3pos_H5


title: 039_Donor-54_TP00_CD3pos_G5


title: 037_Donor-54_TP00_CD3pos_E5


title: 036_Donor-54_TP00_CD3pos_D5


title: 038_Donor-54_TP00_CD3pos_F5


title: 033_Donor-54_TP00_CD3pos_A5


title: 034_Donor-54_TP00_CD3pos_B5


title: 035_Donor-54_TP00_CD3pos_C5


title: 049_Donor-54_TP00_CD3pos_A7


title: 053_Donor-54_TP00_CD3pos_E7


title: 031_Donor-54_TP00_CD3pos_G4


title: 029_Donor-54_TP00_CD3pos_E4


title: 028_Donor-54_TP00_CD3pos_D4


title: 027_Donor-54_TP00_CD3pos_C4


title: 026_Donor-54_TP00_CD3pos_B4


title: 030_Donor-54_TP00_CD3pos_F4


title: 048_Donor-54_TP00_CD3pos_H6


title: 025_Donor-54_TP00_CD3pos_A4


title: 021_Donor-54_TP00_CD3pos_E3


title: 023_Donor-54_TP00_CD3pos_G3


title: 022_Donor-54_TP00_CD3pos_F3


title: 020_Donor-54_TP00_CD3pos_D3


title: 019_Donor-54_TP00_CD3pos_C3


title: 018_Donor-54_TP00_CD3pos_B3


title: 015_Donor-54_TP00_CD3pos_G2


title: 014_Donor-54_TP00_CD3pos_F2


title: 032_Donor-54_TP00_CD3pos_H4


title: 013_Donor-54_TP00_CD3pos_E2


title: 012_Donor-54_TP00_CD3pos_D2


title: 011_Donor-54_TP00_CD3pos_C2


title: 010_Donor-54_TP00_CD3pos_B2


title: 009_Donor-54_TP00_CD3pos_A2


title: 007_Donor-54_TP00_CD3pos_G1


title: 006_Donor-54_TP00_CD3pos_F1


title: 024_Donor-54_TP00_CD3pos_H3


title: 001_Donor-54_TP00_CD3pos_A1


title: TIL_2_NON-TRM

description: 3' Transcriptome sequencing (10X genomics)

data_processing:
Reads from single-cell RNA-seq were aligned and collapsed into unique molecular identifier (UMI) counts using 10x genomics’s cell-ranger software (version 2.0.2)
Counts were normalized across libraries with the aggregate function from cellranger
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Tumor

growth_protocol: CD8 cell types were isolated from human tissue and directly sorted by Flow cytometry into 50% FBS. No particular cell growth procedure was required.

extract_protocol:
Single-cell RNA-seq using 10X genomics platform was performed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol (Zheng et. al., 2017).
Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol
Libraries were sequenced on HiSeq2500/4000 platform to obtain 100 and 32-bp paired end reads using the following read length; read 1, 26 cycles, read 2, 98 cycles and i7 index, 8 cycles.

value: lymphocytes

tag: subject #

value: Pool of 6 donors


title: TIL_2_TRMPos


title: TIL_1_TRMPos


title: TIL_1_NON-TRM


title: Lung_TRM

source_name: Human Lung


title: 9_SCT13_Donor-40_CD103pos_TIL_N718_S513

description: Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)

data_processing:
Single-cell RNA–seq data were mapped against the human hg19 reference genome using TopHat
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Clarke_SC_raw_counts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Clarke_SC_TPM.txt contains contains Transcript per Million normalized counts


title: 017_Donor-54_TP00_CD3pos_A3

tag: tissue


title: 016_Donor-54_TP00_CD3pos_H2


title: 9_SCT12_Donor-39_CD103pos_TIL_N702_S502


title: 9_SCT10_Donor-37_CD103pos_TIL_N702_S513


title: 9_SCT11_Donor-38_CD103pos_TIL_N718_S502


title: Lung_NON-TRM


title: 92_SCT10_Donor-37_CD103pos_TIL_N715_S517


title: 92_SCT12_Donor-39_CD103pos_TIL_N715_S506


title: 91_SCT12_Donor-39_CD103pos_TIL_N715_S505


title: 91_SCT11_Donor-38_CD103pos_TIL_N729_S505


title: 008_Donor-54_TP00_CD3pos_H1


title: 91_SCT10_Donor-37_CD103pos_TIL_N715_S516


title: 92_SCT13_Donor-40_CD103pos_TIL_N729_S517


title: 90_SCT13_Donor-40_CD103pos_TIL_N729_S515


title: 90_SCT11_Donor-38_CD103pos_TIL_N729_S503


title: 8_SCT13_Donor-40_CD103pos_TIL_N716_S522


title: 8_SCT10_Donor-37_CD103pos_TIL_N701_S522


title: 8_SCT12_Donor-39_CD103pos_TIL_N701_S511


title: 8_SCT11_Donor-38_CD103pos_TIL_N716_S511


title: 90_SCT10_Donor-37_CD103pos_TIL_N715_S515


title: 92_SCT11_Donor-38_CD103pos_TIL_N729_S506


title: 89_SCT12_Donor-39_CD103pos_TIL_N715_S502


title: 91_SCT13_Donor-40_CD103pos_TIL_N729_S516


title: 89_SCT11_Donor-38_CD103pos_TIL_N729_S502


title: 88_SCT12_Donor-39_CD103pos_TIL_N714_S511


title: 88_SCT11_Donor-38_CD103pos_TIL_N728_S511


title: 90_SCT12_Donor-39_CD103pos_TIL_N715_S503


title: 87_SCT10_Donor-37_CD103pos_TIL_N714_S521


title: 87_SCT13_Donor-40_CD103pos_TIL_N728_S521


title: 86_SCT13_Donor-40_CD103pos_TIL_N728_S520


title: 88_SCT10_Donor-37_CD103pos_TIL_N714_S522


title: 87_SCT12_Donor-39_CD103pos_TIL_N714_S510


title: 85_SCT12_Donor-39_CD103pos_TIL_N714_S507


title: 89_SCT13_Donor-40_CD103pos_TIL_N729_S513


title: 86_SCT11_Donor-38_CD103pos_TIL_N728_S508


title: 87_SCT11_Donor-38_CD103pos_TIL_N728_S510


title: 85_SCT11_Donor-38_CD103pos_TIL_N728_S507


title: 86_SCT10_Donor-37_CD103pos_TIL_N714_S520


title: 84_SCT12_Donor-39_CD103pos_TIL_N714_S506


title: 83_SCT13_Donor-40_CD103pos_TIL_N728_S516


title: 84_SCT10_Donor-37_CD103pos_TIL_N714_S517


title: 86_SCT12_Donor-39_CD103pos_TIL_N714_S508


title: 85_SCT13_Donor-40_CD103pos_TIL_N728_S518


title: 83_SCT12_Donor-39_CD103pos_TIL_N714_S505


title: 83_SCT11_Donor-38_CD103pos_TIL_N728_S505


title: 84_SCT13_Donor-40_CD103pos_TIL_N728_S517


title: 83_SCT10_Donor-37_CD103pos_TIL_N714_S516


title: 82_SCT13_Donor-40_CD103pos_TIL_N728_S515


title: 82_SCT12_Donor-39_CD103pos_TIL_N714_S503


title: 82_SCT10_Donor-37_CD103pos_TIL_N714_S515


title: 81_SCT13_Donor-40_CD103pos_TIL_N728_S513


title: 81_SCT12_Donor-39_CD103pos_TIL_N714_S502


title: 89_SCT10_Donor-37_CD103pos_TIL_N715_S513


title: 88_SCT13_Donor-40_CD103pos_TIL_N728_S522


title: 85_SCT10_Donor-37_CD103pos_TIL_N714_S518


title: 80_SCT12_Donor-39_CD103pos_TIL_N712_S511


title: 81_SCT10_Donor-37_CD103pos_TIL_N714_S513


title: 7_SCT12_Donor-39_CD103pos_TIL_N701_S510


title: 80_SCT11_Donor-38_CD103pos_TIL_N727_S511


title: 80_SCT13_Donor-40_CD103pos_TIL_N727_S522


title: 79_SCT11_Donor-38_CD103pos_TIL_N727_S510


title: 80_SCT10_Donor-37_CD103pos_TIL_N712_S522


title: 82_SCT11_Donor-38_CD103pos_TIL_N728_S503


title: 79_SCT10_Donor-37_CD103pos_TIL_N712_S521


title: 79_SCT13_Donor-40_CD103pos_TIL_N727_S521


title: 77_SCT11_Donor-38_CD103pos_TIL_N727_S507


title: 7_SCT10_Donor-37_CD103pos_TIL_N701_S521


title: 78_SCT11_Donor-38_CD103pos_TIL_N727_S508


title: 7_SCT13_Donor-40_CD103pos_TIL_N716_S521


title: 77_SCT10_Donor-37_CD103pos_TIL_N712_S518


title: 76_SCT13_Donor-40_CD103pos_TIL_N727_S517


title: 78_SCT13_Donor-40_CD103pos_TIL_N727_S520


title: 79_SCT12_Donor-39_CD103pos_TIL_N712_S510


title: 78_SCT12_Donor-39_CD103pos_TIL_N712_S508


title: 75_SCT13_Donor-40_CD103pos_TIL_N727_S516


title: 75_SCT12_Donor-39_CD103pos_TIL_N712_S505


title: 78_SCT10_Donor-37_CD103pos_TIL_N712_S520


title: 75_SCT11_Donor-38_CD103pos_TIL_N727_S505


title: 7_SCT11_Donor-38_CD103pos_TIL_N716_S510


title: 77_SCT12_Donor-39_CD103pos_TIL_N712_S507


title: 74_SCT12_Donor-39_CD103pos_TIL_N712_S503


title: 77_SCT13_Donor-40_CD103pos_TIL_N727_S518


title: 81_SCT11_Donor-38_CD103pos_TIL_N728_S502


title: 76_SCT10_Donor-37_CD103pos_TIL_N712_S517


title: 75_SCT10_Donor-37_CD103pos_TIL_N712_S516


title: 73_SCT13_Donor-40_CD103pos_TIL_N727_S513


title: 74_SCT13_Donor-40_CD103pos_TIL_N727_S515


title: 73_SCT12_Donor-39_CD103pos_TIL_N712_S502


title: 76_SCT12_Donor-39_CD103pos_TIL_N712_S506


title: 73_SCT11_Donor-38_CD103pos_TIL_N727_S502


title: 72_SCT11_Donor-38_CD103pos_TIL_N726_S511


title: 73_SCT10_Donor-37_CD103pos_TIL_N712_S513


title: 76_SCT11_Donor-38_CD103pos_TIL_N727_S506


title: 74_SCT11_Donor-38_CD103pos_TIL_N727_S503


title: 72_SCT10_Donor-37_CD103pos_TIL_N711_S522


title: 74_SCT10_Donor-37_CD103pos_TIL_N712_S515


title: 72_SCT13_Donor-40_CD103pos_TIL_N726_S522


title: 72_SCT12_Donor-39_CD103pos_TIL_N711_S511


title: 71_SCT12_Donor-39_CD103pos_TIL_N711_S510


title: 71_SCT13_Donor-40_CD103pos_TIL_N726_S521


title: 71_SCT10_Donor-37_CD103pos_TIL_N711_S521


title: 70_SCT13_Donor-40_CD103pos_TIL_N726_S520


title: 71_SCT11_Donor-38_CD103pos_TIL_N726_S510


title: 70_SCT12_Donor-39_CD103pos_TIL_N711_S508


title: 70_SCT11_Donor-38_CD103pos_TIL_N726_S508


title: 70_SCT10_Donor-37_CD103pos_TIL_N711_S520


title: 6_SCT12_Donor-39_CD103pos_TIL_N701_S508


title: 6_SCT11_Donor-38_CD103pos_TIL_N716_S508


title: 6_SCT13_Donor-40_CD103pos_TIL_N716_S520


title: 69_SCT11_Donor-38_CD103pos_TIL_N726_S507


title: 6_SCT10_Donor-37_CD103pos_TIL_N701_S520


title: 69_SCT12_Donor-39_CD103pos_TIL_N711_S507


title: 69_SCT13_Donor-40_CD103pos_TIL_N726_S518


title: 69_SCT10_Donor-37_CD103pos_TIL_N711_S518


title: 68_SCT13_Donor-40_CD103pos_TIL_N726_S517


title: 68_SCT11_Donor-38_CD103pos_TIL_N726_S506


title: 67_SCT10_Donor-37_CD103pos_TIL_N711_S516


title: 68_SCT12_Donor-39_CD103pos_TIL_N711_S506


title: 66_SCT10_Donor-37_CD103pos_TIL_N711_S515


title: 67_SCT13_Donor-40_CD103pos_TIL_N726_S516


title: 66_SCT12_Donor-39_CD103pos_TIL_N711_S503


title: 67_SCT12_Donor-39_CD103pos_TIL_N711_S505


title: 68_SCT10_Donor-37_CD103pos_TIL_N711_S517


title: 66_SCT11_Donor-38_CD103pos_TIL_N726_S503


title: 66_SCT13_Donor-40_CD103pos_TIL_N726_S515


title: 65_SCT13_Donor-40_CD103pos_TIL_N726_S513


title: 65_SCT11_Donor-38_CD103pos_TIL_N726_S502


title: 64_SCT12_Donor-39_CD103pos_TIL_N710_S511


title: 65_SCT10_Donor-37_CD103pos_TIL_N711_S513


title: 63_SCT13_Donor-40_CD103pos_TIL_N724_S521


title: 64_SCT13_Donor-40_CD103pos_TIL_N724_S522


title: 64_SCT11_Donor-38_CD103pos_TIL_N724_S511


title: 84_SCT11_Donor-38_CD103pos_TIL_N728_S506


title: 63_SCT10_Donor-37_CD103pos_TIL_N710_S521


title: 64_SCT10_Donor-37_CD103pos_TIL_N710_S522


title: 63_SCT11_Donor-38_CD103pos_TIL_N724_S510


title: 63_SCT12_Donor-39_CD103pos_TIL_N710_S510


title: 67_SCT11_Donor-38_CD103pos_TIL_N726_S505


title: 62_SCT11_Donor-38_CD103pos_TIL_N724_S508


title: 62_SCT12_Donor-39_CD103pos_TIL_N710_S508


title: 62_SCT10_Donor-37_CD103pos_TIL_N710_S520


title: 62_SCT13_Donor-40_CD103pos_TIL_N724_S520


title: 61_SCT13_Donor-40_CD103pos_TIL_N724_S518


title: 65_SCT12_Donor-39_CD103pos_TIL_N711_S502


title: 61_SCT10_Donor-37_CD103pos_TIL_N710_S518


title: 61_SCT11_Donor-38_CD103pos_TIL_N724_S507


title: 61_SCT12_Donor-39_CD103pos_TIL_N710_S507


title: 60_SCT12_Donor-39_CD103pos_TIL_N710_S506


title: 60_SCT11_Donor-38_CD103pos_TIL_N724_S506


title: 5_SCT11_Donor-38_CD103pos_TIL_N716_S507


title: 60_SCT10_Donor-37_CD103pos_TIL_N710_S517


title: 5_SCT12_Donor-39_CD103pos_TIL_N701_S507


title: 5_SCT13_Donor-40_CD103pos_TIL_N716_S518


title: 5_SCT10_Donor-37_CD103pos_TIL_N701_S518


title: 59_SCT12_Donor-39_CD103pos_TIL_N710_S505


title: 59_SCT13_Donor-40_CD103pos_TIL_N724_S516


title: 59_SCT11_Donor-38_CD103pos_TIL_N724_S505


title: 58_SCT11_Donor-38_CD103pos_TIL_N724_S503


title: 59_SCT10_Donor-37_CD103pos_TIL_N710_S516


title: 58_SCT10_Donor-37_CD103pos_TIL_N710_S515


title: 58_SCT13_Donor-40_CD103pos_TIL_N724_S515


title: 57_SCT13_Donor-40_CD103pos_TIL_N724_S513


title: 60_SCT13_Donor-40_CD103pos_TIL_N724_S517


title: 57_SCT10_Donor-37_CD103pos_TIL_N710_S513


title: 57_SCT11_Donor-38_CD103pos_TIL_N724_S502


title: 56_SCT13_Donor-40_CD103pos_TIL_N723_S522


title: 57_SCT12_Donor-39_CD103pos_TIL_N710_S502


title: 56_SCT11_Donor-38_CD103pos_TIL_N723_S511


title: 56_SCT10_Donor-37_CD103pos_TIL_N707_S522


title: 55_SCT13_Donor-40_CD103pos_TIL_N723_S521


title: 55_SCT10_Donor-37_CD103pos_TIL_N707_S521


title: 56_SCT12_Donor-39_CD103pos_TIL_N707_S511


title: 55_SCT12_Donor-39_CD103pos_TIL_N707_S510


title: 55_SCT11_Donor-38_CD103pos_TIL_N723_S510


title: 54_SCT12_Donor-39_CD103pos_TIL_N707_S508


title: 54_SCT11_Donor-38_CD103pos_TIL_N723_S508


title: 54_SCT13_Donor-40_CD103pos_TIL_N723_S520


title: 54_SCT10_Donor-37_CD103pos_TIL_N707_S520


title: 53_SCT11_Donor-38_CD103pos_TIL_N723_S507


title: 53_SCT10_Donor-37_CD103pos_TIL_N707_S518


title: 53_SCT12_Donor-39_CD103pos_TIL_N707_S507


title: 58_SCT12_Donor-39_CD103pos_TIL_N710_S503


title: 52_SCT13_Donor-40_CD103pos_TIL_N723_S517


title: 52_SCT11_Donor-38_CD103pos_TIL_N723_S506


title: 52_SCT10_Donor-37_CD103pos_TIL_N707_S517


title: 51_SCT13_Donor-40_CD103pos_TIL_N723_S516


title: 51_SCT11_Donor-38_CD103pos_TIL_N723_S505


title: 52_SCT12_Donor-39_CD103pos_TIL_N707_S506


title: 50_SCT13_Donor-40_CD103pos_TIL_N723_S515


title: 50_SCT11_Donor-38_CD103pos_TIL_N723_S503


title: 50_SCT12_Donor-39_CD103pos_TIL_N707_S503


title: 4_SCT12_Donor-39_CD103pos_TIL_N701_S506


title: 4_SCT10_Donor-37_CD103pos_TIL_N701_S517


title: 4_SCT11_Donor-38_CD103pos_TIL_N716_S506


title: 4_SCT13_Donor-40_CD103pos_TIL_N716_S517


title: 49_SCT10_Donor-37_CD103pos_TIL_N707_S513


title: 49_SCT11_Donor-38_CD103pos_TIL_N723_S502


title: 48_SCT13_Donor-40_CD103pos_TIL_N722_S522


title: 53_SCT13_Donor-40_CD103pos_TIL_N723_S518


title: 49_SCT12_Donor-39_CD103pos_TIL_N707_S502


title: 47_SCT12_Donor-39_CD103pos_TIL_N706_S510


title: 48_SCT12_Donor-39_CD103pos_TIL_N706_S511


title: 47_SCT11_Donor-38_CD103pos_TIL_N722_S510


title: 46_SCT12_Donor-39_CD103pos_TIL_N706_S508


title: 47_SCT10_Donor-37_CD103pos_TIL_N706_S521


title: 46_SCT13_Donor-40_CD103pos_TIL_N722_S520


title: 51_SCT10_Donor-37_CD103pos_TIL_N707_S516


title: 49_SCT13_Donor-40_CD103pos_TIL_N723_S513


title: 47_SCT13_Donor-40_CD103pos_TIL_N722_S521


title: 50_SCT10_Donor-37_CD103pos_TIL_N707_S515


title: 46_SCT10_Donor-37_CD103pos_TIL_N706_S520


title: 45_SCT13_Donor-40_CD103pos_TIL_N722_S518


title: 46_SCT11_Donor-38_CD103pos_TIL_N722_S508


title: 45_SCT11_Donor-38_CD103pos_TIL_N722_S507


title: 48_SCT10_Donor-37_CD103pos_TIL_N706_S522


title: 45_SCT12_Donor-39_CD103pos_TIL_N706_S507


title: 45_SCT10_Donor-37_CD103pos_TIL_N706_S518


title: 48_SCT11_Donor-38_CD103pos_TIL_N722_S511


title: 44_SCT13_Donor-40_CD103pos_TIL_N722_S517


title: 51_SCT12_Donor-39_CD103pos_TIL_N707_S505


title: 43_SCT11_Donor-38_CD103pos_TIL_N722_S505


title: 43_SCT12_Donor-39_CD103pos_TIL_N706_S505


title: 44_SCT12_Donor-39_CD103pos_TIL_N706_S506


title: 43_SCT13_Donor-40_CD103pos_TIL_N722_S516


title: 43_SCT10_Donor-37_CD103pos_TIL_N706_S516


title: 42_SCT13_Donor-40_CD103pos_TIL_N722_S515


title: 42_SCT12_Donor-39_CD103pos_TIL_N706_S503


title: 44_SCT11_Donor-38_CD103pos_TIL_N722_S506


title: 42_SCT11_Donor-38_CD103pos_TIL_N722_S503


title: 41_SCT13_Donor-40_CD103pos_TIL_N722_S513


title: 42_SCT10_Donor-37_CD103pos_TIL_N706_S515


title: 40_SCT13_Donor-40_CD103pos_TIL_N721_S522


title: 40_SCT12_Donor-39_CD103pos_TIL_N705_S511


title: 41_SCT10_Donor-37_CD103pos_TIL_N706_S513


title: 3_SCT13_Donor-40_CD103pos_TIL_N716_S516


title: 40_SCT11_Donor-38_CD103pos_TIL_N721_S511


title: 41_SCT11_Donor-38_CD103pos_TIL_N722_S502


title: 3_SCT11_Donor-38_CD103pos_TIL_N716_S505


title: 40_SCT10_Donor-37_CD103pos_TIL_N705_S522


title: 3_SCT12_Donor-39_CD103pos_TIL_N701_S505


title: 3_SCT10_Donor-37_CD103pos_TIL_N701_S516


title: 39_SCT11_Donor-38_CD103pos_TIL_N721_S510


title: 38_SCT13_Donor-40_CD103pos_TIL_N721_S520


title: 38_SCT11_Donor-38_CD103pos_TIL_N721_S508


title: 39_SCT12_Donor-39_CD103pos_TIL_N705_S510


title: 39_SCT13_Donor-40_CD103pos_TIL_N721_S521


title: 38_SCT10_Donor-37_CD103pos_TIL_N705_S520


title: 37_SCT13_Donor-40_CD103pos_TIL_N721_S518


title: 39_SCT10_Donor-37_CD103pos_TIL_N705_S521


title: 38_SCT12_Donor-39_CD103pos_TIL_N705_S508


title: 44_SCT10_Donor-37_CD103pos_TIL_N706_S517


title: 37_SCT11_Donor-38_CD103pos_TIL_N721_S507


title: 41_SCT12_Donor-39_CD103pos_TIL_N706_S502


title: 37_SCT10_Donor-37_CD103pos_TIL_N705_S518


title: 36_SCT11_Donor-38_CD103pos_TIL_N721_S506


title: 37_SCT12_Donor-39_CD103pos_TIL_N705_S507


title: 36_SCT10_Donor-37_CD103pos_TIL_N705_S517


title: 35_SCT13_Donor-40_CD103pos_TIL_N721_S516


title: 36_SCT13_Donor-40_CD103pos_TIL_N721_S517


title: 36_SCT12_Donor-39_CD103pos_TIL_N705_S506


title: 35_SCT10_Donor-37_CD103pos_TIL_N705_S516


title: 35_SCT12_Donor-39_CD103pos_TIL_N705_S505


title: 35_SCT11_Donor-38_CD103pos_TIL_N721_S505


title: 34_SCT13_Donor-40_CD103pos_TIL_N721_S515


title: 34_SCT12_Donor-39_CD103pos_TIL_N705_S503


title: 34_SCT11_Donor-38_CD103pos_TIL_N721_S503


title: 32_SCT13_Donor-40_CD103pos_TIL_N720_S522


title: 33_SCT13_Donor-40_CD103pos_TIL_N721_S513


title: 32_SCT12_Donor-39_CD103pos_TIL_N704_S511


title: 33_SCT12_Donor-39_CD103pos_TIL_N705_S502


title: 33_SCT10_Donor-37_CD103pos_TIL_N705_S513


title: 34_SCT10_Donor-37_CD103pos_TIL_N705_S515


title: 32_SCT11_Donor-38_CD103pos_TIL_N720_S511


title: 32_SCT10_Donor-37_CD103pos_TIL_N704_S522


title: 31_SCT13_Donor-40_CD103pos_TIL_N720_S521


title: 31_SCT12_Donor-39_CD103pos_TIL_N704_S510


title: 31_SCT11_Donor-38_CD103pos_TIL_N720_S510


title: 31_SCT10_Donor-37_CD103pos_TIL_N704_S521


title: 30_SCT13_Donor-40_CD103pos_TIL_N720_S520


title: 2_SCT12_Donor-39_CD103pos_TIL_N701_S503


title: 30_SCT12_Donor-39_CD103pos_TIL_N704_S508


title: 2_SCT10_Donor-37_CD103pos_TIL_N701_S515


title: 2_SCT11_Donor-38_CD103pos_TIL_N716_S503


title: 29_SCT12_Donor-39_CD103pos_TIL_N704_S507


title: 29_SCT13_Donor-40_CD103pos_TIL_N720_S518


title: 30_SCT10_Donor-37_CD103pos_TIL_N704_S520


title: 2_SCT13_Donor-40_CD103pos_TIL_N716_S515


title: 29_SCT11_Donor-38_CD103pos_TIL_N720_S507


title: 29_SCT10_Donor-37_CD103pos_TIL_N704_S518


title: 33_SCT11_Donor-38_CD103pos_TIL_N721_S502


title: 28_SCT12_Donor-39_CD103pos_TIL_N704_S506


title: 27_SCT13_Donor-40_CD103pos_TIL_N720_S516


title: 28_SCT13_Donor-40_CD103pos_TIL_N720_S517


title: 27_SCT12_Donor-39_CD103pos_TIL_N704_S505


title: 28_SCT10_Donor-37_CD103pos_TIL_N704_S517


title: 27_SCT11_Donor-38_CD103pos_TIL_N720_S505


title: 27_SCT10_Donor-37_CD103pos_TIL_N704_S516


title: 30_SCT11_Donor-38_CD103pos_TIL_N720_S508


title: 26_SCT10_Donor-37_CD103pos_TIL_N704_S515


title: 25_SCT13_Donor-40_CD103pos_TIL_N720_S513


title: 25_SCT12_Donor-39_CD103pos_TIL_N704_S502


title: 28_SCT11_Donor-38_CD103pos_TIL_N720_S506


title: 25_SCT10_Donor-37_CD103pos_TIL_N704_S513


title: 24_SCT10_Donor-37_CD103pos_TIL_N703_S522


title: 24_SCT11_Donor-38_CD103pos_TIL_N719_S511


title: 24_SCT12_Donor-39_CD103pos_TIL_N703_S511


title: 23_SCT12_Donor-39_CD103pos_TIL_N703_S510


title: 23_SCT13_Donor-40_CD103pos_TIL_N719_S521


title: 26_SCT12_Donor-39_CD103pos_TIL_N704_S503


title: 23_SCT11_Donor-38_CD103pos_TIL_N719_S510


title: 26_SCT13_Donor-40_CD103pos_TIL_N720_S515


title: 22_SCT11_Donor-38_CD103pos_TIL_N719_S508


title: 22_SCT13_Donor-40_CD103pos_TIL_N719_S520


title: 26_SCT11_Donor-38_CD103pos_TIL_N720_S503


title: 21_SCT11_Donor-38_CD103pos_TIL_N719_S507


title: 22_SCT12_Donor-39_CD103pos_TIL_N703_S508


title: 22_SCT10_Donor-37_CD103pos_TIL_N703_S520


title: 25_SCT11_Donor-38_CD103pos_TIL_N720_S502


title: 21_SCT12_Donor-39_CD103pos_TIL_N703_S507


title: 21_SCT13_Donor-40_CD103pos_TIL_N719_S518


title: 21_SCT10_Donor-37_CD103pos_TIL_N703_S518


title: 20_SCT12_Donor-39_CD103pos_TIL_N703_S506


title: 20_SCT10_Donor-37_CD103pos_TIL_N703_S517


title: 20_SCT11_Donor-38_CD103pos_TIL_N719_S506


title: 1_SCT11_Donor-38_CD103pos_TIL_N716_S502


title: 23_SCT10_Donor-37_CD103pos_TIL_N703_S521


title: 1_SCT12_Donor-39_CD103pos_TIL_N701_S502


title: 24_SCT13_Donor-40_CD103pos_TIL_N719_S522


title: 1_SCT13_Donor-40_CD103pos_TIL_N716_S513


title: 19_SCT12_Donor-39_CD103pos_TIL_N703_S505


title: 18_SCT12_Donor-39_CD103pos_TIL_N703_S503


title: 19_SCT11_Donor-38_CD103pos_TIL_N719_S505


title: 19_SCT13_Donor-40_CD103pos_TIL_N719_S516


title: 20_SCT13_Donor-40_CD103pos_TIL_N719_S517


title: 19_SCT10_Donor-37_CD103pos_TIL_N703_S516


title: 18_SCT13_Donor-40_CD103pos_TIL_N719_S515


title: 18_SCT11_Donor-38_CD103pos_TIL_N719_S503


title: 17_SCT11_Donor-38_CD103pos_TIL_N719_S502


title: 16_SCT13_Donor-40_CD103pos_TIL_N718_S522


title: 16_SCT10_Donor-37_CD103pos_TIL_N702_S522


title: 17_SCT12_Donor-39_CD103pos_TIL_N703_S502


title: 17_SCT10_Donor-37_CD103pos_TIL_N703_S513


title: 16_SCT12_Donor-39_CD103pos_TIL_N702_S511


title: 17_SCT13_Donor-40_CD103pos_TIL_N719_S513


title: 16_SCT11_Donor-38_CD103pos_TIL_N718_S511


title: 1_SCT10_Donor-37_CD103pos_TIL_N701_S513


title: 18_SCT10_Donor-37_CD103pos_TIL_N703_S515


title: 15_SCT13_Donor-40_CD103pos_TIL_N718_S521


title: 15_SCT12_Donor-39_CD103pos_TIL_N702_S510


title: 15_SCT11_Donor-38_CD103pos_TIL_N718_S510


title: 15_SCT10_Donor-37_CD103pos_TIL_N702_S521


title: 14_SCT10_Donor-37_CD103pos_TIL_N702_S520


title: 14_SCT12_Donor-39_CD103pos_TIL_N702_S508


title: 13_SCT13_Donor-40_CD103pos_TIL_N718_S518


title: 13_SCT10_Donor-37_CD103pos_TIL_N702_S518


title: 12_SCT13_Donor-40_CD103pos_TIL_N718_S517


title: 12_SCT11_Donor-38_CD103pos_TIL_N718_S506


title: 13_SCT11_Donor-38_CD103pos_TIL_N718_S507


title: 12_SCT12_Donor-39_CD103pos_TIL_N702_S506


title: 12_SCT10_Donor-37_CD103pos_TIL_N702_S517


title: 11_SCT13_Donor-40_CD103pos_TIL_N718_S516


title: 13_SCT12_Donor-39_CD103pos_TIL_N702_S507


title: 11_SCT11_Donor-38_CD103pos_TIL_N718_S505


title: 10_SCT12_Donor-39_CD103pos_TIL_N702_S503


title: 10_SCT10_Donor-37_CD103pos_TIL_N702_S515


title: 96_Donor-40_CD103Pos_96


title: 14_SCT13_Donor-40_CD103pos_TIL_N718_S520


title: 9_Donor-40_CD103Pos_9


title: 10_SCT11_Donor-38_CD103pos_TIL_N718_S503


title: 11_SCT10_Donor-37_CD103pos_TIL_N702_S516


title: 95_Donor-40_CD103Pos_95


title: 14_SCT11_Donor-38_CD103pos_TIL_N718_S508


title: 97_Donor-40_CD103neg_1


title: 92_Donor-40_CD103Pos_92


title: 93_Donor-40_CD103Pos_93


title: 10_SCT13_Donor-40_CD103pos_TIL_N718_S515


title: 91_Donor-40_CD103Pos_91


title: 90_Donor-40_CD103Pos_90


title: 89_Donor-40_CD103Pos_89


title: 88_Donor-40_CD103Pos_88


title: 94_Donor-40_CD103Pos_94


title: 85_Donor-40_CD103Pos_85


title: 84_Donor-40_CD103Pos_84


title: 86_Donor-40_CD103Pos_86


title: 11_SCT12_Donor-39_CD103pos_TIL_N702_S505


title: 82_Donor-40_CD103Pos_82


title: 83_Donor-40_CD103Pos_83


title: 81_Donor-40_CD103Pos_81


title: 80_Donor-40_CD103Pos_80


title: 98_Donor-40_CD103neg_2


title: 7_Donor-40_CD103Pos_7


title: 77_Donor-40_CD103Pos_77


title: 78_Donor-40_CD103Pos_78


title: 8_Donor-40_CD103Pos_8


title: 71_Donor-40_CD103Pos_71


title: 75_Donor-40_CD103Pos_75


title: 6_Donor-40_CD103Pos_6


title: 73_Donor-40_CD103Pos_73


title: 74_Donor-40_CD103Pos_74


title: 70_Donor-40_CD103Pos_70


title: 65_Donor-40_CD103Pos_65


title: 63_Donor-40_CD103Pos_63


title: 68_Donor-40_CD103Pos_68


title: 62_Donor-40_CD103Pos_62


title: 69_Donor-40_CD103Pos_69


title: 66_Donor-40_CD103Pos_66


title: 61_Donor-40_CD103Pos_61


title: 59_Donor-40_CD103Pos_59


title: 5_Donor-40_CD103Pos_5


title: 60_Donor-40_CD103Pos_60


title: 58_Donor-40_CD103Pos_58


title: 79_Donor-40_CD103Pos_79


title: 56_Donor-40_CD103Pos_56


title: 55_Donor-40_CD103Pos_55


title: 57_Donor-40_CD103Pos_57


title: 76_Donor-40_CD103Pos_76


title: 54_Donor-40_CD103Pos_54


title: 52_Donor-40_CD103Pos_52


title: 53_Donor-40_CD103Pos_53


title: 72_Donor-40_CD103Pos_72


title: 51_Donor-40_CD103Pos_51


title: 4_Donor-40_CD103Pos_4


title: 48_Donor-40_CD103Pos_48


title: 46_Donor-40_CD103Pos_46


title: 50_Donor-40_CD103Pos_50


title: 64_Donor-40_CD103Pos_64


title: 47_Donor-40_CD103Pos_47


title: 44_Donor-40_CD103Pos_44


title: 40_Donor-40_CD103Pos_40


title: 41_Donor-40_CD103Pos_41


title: 42_Donor-40_CD103Pos_42


title: 3_Donor-40_CD103Pos_3


title: 45_Donor-40_CD103Pos_45


title: 43_Donor-40_CD103Pos_43


title: 38_Donor-40_CD103Pos_38


title: 37_Donor-40_CD103Pos_37


title: 381_Donor-39_CD103neg_93


title: 380_Donor-39_CD103neg_92


title: 39_Donor-40_CD103Pos_39


title: 377_Donor-39_CD103neg_92


title: 378_Donor-39_CD103neg_93


title: 373_Donor-39_CD103neg_88


title: 374_Donor-39_CD103neg_89


title: 372_Donor-39_CD103neg_87


title: 376_Donor-39_CD103neg_91


title: 375_Donor-39_CD103neg_90


title: 371_Donor-39_CD103neg_86


title: 367_Donor-39_CD103neg_82


title: 370_Donor-39_CD103neg_85


title: 365_Donor-39_CD103neg_80


title: 36_Donor-40_CD103Pos_36


title: 368_Donor-39_CD103neg_83


title: 369_Donor-39_CD103neg_84


title: 364_Donor-39_CD103neg_79


title: 379_Donor-39_CD103neg_91


title: 363_Donor-39_CD103neg_78


title: 361_Donor-39_CD103neg_76


title: 360_Donor-39_CD103neg_75


title: 357_Donor-39_CD103neg_72


title: 354_Donor-39_CD103neg_69


title: 35_Donor-40_CD103Pos_35


title: 359_Donor-39_CD103neg_74


title: 353_Donor-39_CD103neg_68


title: 358_Donor-39_CD103neg_73


title: 350_Donor-39_CD103neg_65


title: 355_Donor-39_CD103neg_70


title: 349_Donor-39_CD103neg_64


title: 362_Donor-39_CD103neg_77


title: 352_Donor-39_CD103neg_67


title: 347_Donor-39_CD103neg_62


title: 34_Donor-40_CD103Pos_34


title: 366_Donor-39_CD103neg_81


title: 346_Donor-39_CD103neg_61


title: 356_Donor-39_CD103neg_71


title: 345_Donor-39_CD103neg_60


title: 344_Donor-39_CD103neg_59


title: 342_Donor-39_CD103neg_57


title: 343_Donor-39_CD103neg_58


title: 341_Donor-39_CD103neg_56


title: 338_Donor-39_CD103neg_53


title: 33_Donor-40_CD103Pos_33


title: 340_Donor-39_CD103neg_55


title: 335_Donor-39_CD103neg_50


title: 336_Donor-39_CD103neg_51


title: 337_Donor-39_CD103neg_52


title: 333_Donor-39_CD103neg_48


title: 331_Donor-39_CD103neg_46


title: 32_Donor-40_CD103Pos_32


title: 332_Donor-39_CD103neg_47


title: 348_Donor-39_CD103neg_63


title: 329_Donor-39_CD103neg_44


title: 334_Donor-39_CD103neg_49


title: 330_Donor-39_CD103neg_45


title: 326_Donor-39_CD103neg_41


title: 328_Donor-39_CD103neg_43


title: 324_Donor-39_CD103neg_39


title: 325_Donor-39_CD103neg_40


title: 323_Donor-39_CD103neg_38


title: 31_Donor-40_CD103Pos_31


title: 320_Donor-39_CD103neg_35


title: 321_Donor-39_CD103neg_36


title: 318_Donor-39_CD103neg_33


title: 317_Donor-39_CD103neg_32


title: 316_Donor-39_CD103neg_31


title: 314_Donor-39_CD103neg_29


title: 312_Donor-39_CD103neg_27


title: 315_Donor-39_CD103neg_30


title: 30_Donor-40_CD103Pos_30


title: 311_Donor-39_CD103neg_26


title: 309_Donor-39_CD103neg_24


title: 313_Donor-39_CD103neg_28


title: 307_Donor-39_CD103neg_22


title: 306_Donor-39_CD103neg_21


title: 308_Donor-39_CD103neg_23


title: 300_Donor-39_CD103neg_15


title: 304_Donor-39_CD103neg_19


title: 2_Donor-40_CD103Pos_2


title: 322_Donor-39_CD103neg_37


title: 302_Donor-39_CD103neg_17


title: 299_Donor-39_CD103neg_14


title: 303_Donor-39_CD103neg_18


title: 301_Donor-39_CD103neg_16


title: 29_Donor-40_CD103Pos_29


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title: 293_Donor-39_CD103neg_8


title: 294_Donor-39_CD103neg_9


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title: 287_Donor-39_CD103neg_2


title: 283_Donor-39_CD103Pos_94


title: 282_Donor-39_CD103Pos_93


title: 28_Donor-40_CD103Pos_28


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title: 27_Donor-40_CD103Pos_27


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title: 273_Donor-39_CD103Pos_84


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title: 268_Donor-39_CD103Pos_79


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title: 260_Donor-39_CD103Pos_71


title: 257_Donor-39_CD103Pos_68


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title: 258_Donor-39_CD103Pos_69


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title: 23_Donor-40_CD103Pos_23


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title: 245_Donor-39_CD103Pos_56


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title: 227_Donor-39_CD103Pos_38


title: 22_Donor-40_CD103Pos_22


title: 237_Donor-39_CD103Pos_48


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title: 1_Donor-40_CD103Pos_1


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title: 194_Donor-39_CD103Pos_5


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title: 195_Donor-39_CD103Pos_6


title: 190_Donor-39_CD103Pos_1


title: 212_Donor-39_CD103Pos_23


title: 189_Donor-40_CD103neg_93


title: 191_Donor-39_CD103Pos_2


title: 188_Donor-40_CD103neg_92


title: 187_Donor-40_CD103neg_91


title: 205_Donor-39_CD103Pos_16


title: 202_Donor-39_CD103Pos_13


title: 186_Donor-40_CD103neg_90


title: 185_Donor-40_CD103neg_89


title: 183_Donor-40_CD103neg_87


title: 182_Donor-40_CD103neg_86


title: 181_Donor-40_CD103neg_85


title: 198_Donor-39_CD103Pos_9


title: 17_Donor-40_CD103Pos_17


title: 179_Donor-40_CD103neg_83


title: 196_Donor-39_CD103Pos_7


title: 178_Donor-40_CD103neg_82


title: 177_Donor-40_CD103neg_81


title: 176_Donor-40_CD103neg_80


title: 192_Donor-39_CD103Pos_3


title: 18_Donor-40_CD103Pos_18


title: 173_Donor-40_CD103neg_77


title: 170_Donor-40_CD103neg_74


title: 167_Donor-40_CD103neg_71


title: 169_Donor-40_CD103neg_73


title: 174_Donor-40_CD103neg_78


title: 171_Donor-40_CD103neg_75


title: 165_Donor-40_CD103neg_69


title: 172_Donor-40_CD103neg_76


title: 168_Donor-40_CD103neg_72


title: 16_Donor-40_CD103Pos_16


title: 184_Donor-40_CD103neg_88


title: 164_Donor-40_CD103neg_68


title: 166_Donor-40_CD103neg_70


title: 163_Donor-40_CD103neg_67


title: 180_Donor-40_CD103neg_84


title: 161_Donor-40_CD103neg_65


title: 162_Donor-40_CD103neg_66


title: 158_Donor-40_CD103neg_62


title: 151_Donor-40_CD103neg_55


title: 160_Donor-40_CD103neg_64


title: 159_Donor-40_CD103neg_63


title: 15_Donor-40_CD103Pos_15


title: 150_Donor-40_CD103neg_54


title: 14_Donor-40_CD103Pos_14


title: 155_Donor-40_CD103neg_59


title: 152_Donor-40_CD103neg_56


title: 149_Donor-40_CD103neg_53


title: 154_Donor-40_CD103neg_58


title: 141_Donor-40_CD103neg_45


title: 147_Donor-40_CD103neg_51


title: 146_Donor-40_CD103neg_50


title: 157_Donor-40_CD103neg_61


title: 175_Donor-40_CD103neg_79


title: 156_Donor-40_CD103neg_60


title: 148_Donor-40_CD103neg_52


title: 153_Donor-40_CD103neg_57


title: 144_Donor-40_CD103neg_48


title: 142_Donor-40_CD103neg_46


title: 145_Donor-40_CD103neg_49


title: 203_Donor-39_CD103Pos_14


title: 13_Donor-40_CD103Pos_13


title: 138_Donor-40_CD103neg_42


title: 135_Donor-40_CD103neg_39


title: 134_Donor-40_CD103neg_38


title: 140_Donor-40_CD103neg_44


title: 133_Donor-40_CD103neg_37


title: 132_Donor-40_CD103neg_36


title: 131_Donor-40_CD103neg_35


title: 130_Donor-40_CD103neg_34


title: 12_Donor-40_CD103Pos_12


title: 143_Donor-40_CD103neg_47


title: 139_Donor-40_CD103neg_43


title: 125_Donor-40_CD103neg_29


title: 129_Donor-40_CD103neg_33


title: 128_Donor-40_CD103neg_32


title: 127_Donor-40_CD103neg_31


title: 123_Donor-40_CD103neg_27


title: 137_Donor-40_CD103neg_41


title: 126_Donor-40_CD103neg_30


title: 124_Donor-40_CD103neg_28


title: 121_Donor-40_CD103neg_25


title: 136_Donor-40_CD103neg_40


title: 120_Donor-40_CD103neg_24


title: 116_Donor-40_CD103neg_20


title: 119_Donor-40_CD103neg_23


title: 122_Donor-40_CD103neg_26


title: 117_Donor-40_CD103neg_21


title: 118_Donor-40_CD103neg_22


title: 115_Donor-40_CD103neg_19


title: 114_Donor-40_CD103neg_18


title: 113_Donor-40_CD103neg_17


title: 10_Donor-40_CD103Pos_10


title: 111_Donor-40_CD103neg_15


title: 109_Donor-40_CD103neg_13


title: 108_Donor-40_CD103neg_12


title: 112_Donor-40_CD103neg_16


title: 105_Donor-40_CD103neg_9


title: 106_Donor-40_CD103neg_10


title: 11_Donor-40_CD103Pos_11


title: 104_Donor-40_CD103neg_8


title: 103_Donor-40_CD103neg_7


title: 102_Donor-40_CD103neg_6


title: 101_Donor-40_CD103neg_5


title: 100_Donor-40_CD103neg_4


title: Clarke_Bulk-Stim_Donor-36_SN_CD103neg

description: Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)

data_processing:
Bulk RNA–seq data were mapped against the human hg19 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Clarke_Bulk_raw-counts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Clarke_Bulk_TPM.txt contains Transcript per Million normalized counts

source_name: non-involved lung tissue - 4 hours ex-vivo stimulation

growth_protocol: Cell types were isolated from tissue samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.

extract_protocol:
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method  with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were sonstructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
DNA sequencing - Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).

treatment_protocol: Were noted samples were stimulated with 4 hours of PMA/ionomycine treatment, otherwise sampled were directly ex-vivo

value: Lymphocyte

tag: donor #


title: Clarke_Bulk-Stim_Donor-33_N_CD103neg

source_name: non-involved lung tissue


title: Clarke_Bulk-Stim_Donor-35_N_CD103neg


title: Clarke_Bulk-Stim_Donor-36_N_CD103neg


title: Clarke_Bulk-Stim_Donor-36_ST_CD103neg

source_name: Tumor tissue - 4 hours ex-vivo stimulation


title: Clarke_Bulk-Stim_Donor-35_SN_CD103neg


title: Clarke_Bulk-Stim_Donor-36_T_CD103neg

source_name: Tumor tissue


title: Clarke_Bulk-Stim_Donor-35_T_CD103neg


title: Clarke_Bulk-Stim_Donor-34_SN_CD103neg


title: Clarke_Bulk-Stim_Donor-35_ST_CD103neg


title: 107_Donor-40_CD103neg_11


title: Clarke_Bulk-Stim_Donor-34_T_CD103neg


title: Clarke_Bulk-Stim_Donor-33_T_CD103neg


title: Clarke_Bulk-Stim_Donor-33_SN_CD103neg


title: Clarke_Bulk-Stim_Donor-33_ST_CD103neg


title: Clarke_Bulk-Stim_Donor-31_N_CD103neg


title: Clarke_Bulk-Stim_Donor-34_ST_CD103neg


title: Arabidopsis_thaliana_WS_Rep3_120

city: East Lansing

first: Kevin

last: Childs

state: MI

address: 612 Wilson Rd, Room S108, Plant Biology Laboratories

institute: Michigan State University

data_processing:
Sequencing adapters and low quality bases were trimmed from sequencing reads using Trimmomatic version 0.32.
Cleaned reads were examined using FASTQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for quality evaluation.
Reads were aligned to the reference genome, A. thaliana TAIR10, using the STAR (2.3.0e) alignment program.
The featureCounts function in the Rsubread (version 3) package for R was used to calculate read counts for each gene, and data were normalized as reads per kilobase of transcript per million mapped reads (RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file with RPKM values, Genes as rows, Samples as columns (sample names match "Sample name" entry in "SAMPLE" section of this file).

organism: Arabidopsis thaliana

source_name: fully expanded leaf

growth_protocol: Wild-type Arabidopsis thaliana ecotype Columbia-0 (WT Col) and Wassilewskija (WT WS) were used. Plants were grown in a fluorescently lit growth chamber under a 12 h photoperiod with a photosynthetically active radiation (PAR) of 120 µmol m-2 s-1 until high light treatment when light was changed to 500 µmol m-2 s-1. The daytime temperature was 23°C and the nighttime temperature was 20°C. Humidity was held at a minimum of 60% relative humidity.

extract_protocol:
RNA was extracted using a Qiagen RNeasy Plant Mini Kit according to the manufacturer’s directions.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA) following the manufacturer's recommendations.

treatment_protocol: High light treatment consisted of changing light levels from 120 µmol m-2 s-1 to 500 µmol m-2 s-1.

value: fully expanded leaf

tag: hours high intensity light

tag: ecotype

value: Wassilewskija

tag: replicate


title: Arabidopsis_thaliana_WS_Rep3_15


title: Arabidopsis_thaliana_WS_Rep3_30


title: Arabidopsis_thaliana_WS_Rep3_240


title: Clarke_TCRseq_Beta_Donor-8_Tumor_CD8+_CD103neg

description:
UMI-based TCR-seq(Shugay et. al., 2014)
lymphocytes isolated from human tumor samples

data_processing:
The sequencing data was mapped and analyzed using MIGEC software ( version 1.2.7) with default settings.
Sample fastq were obtained with command Checkout (parameters -cute) from MIGEC software.
Histogram, AssembleBatch, CdrBlastBatch and FilterCDRBlastResultsBatch functions from MIGEC were used to define TCR sequences.
Downstream analysis was performed using V(D)J tools with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: TCR beta chain reconstruction in 10 donors from TCR-seq analysis.

growth_protocol: Tissue samples were immuno stained and FACS sorted into Trizol for RNA isolation no growth protocol was used

extract_protocol:
TCR-seq was performed as described previously by Shugay et al., 2014  with 1ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
TCR-seq was performed as described previously by Shugay et al., 2014  with 1ng of total RNA.
DNA sequencing - libraries were prepared using True-seq nano DNA library kit (Illumina). Libraries were pooled and sequenced on the MiSeq Illumina platform

treatment_protocol: Tissue samples were immuno stained and FACS sorted into Trizol for RNA isolation no treatment protocol was used

tag: longitudinal visit

tag: cell type surface markers

tag: cell type


title: Arabidopsis_thaliana_WS_Rep3_60


title: Arabidopsis_thaliana_WS_Rep3_0


title: Clarke_TCRseq_Beta_Donor-8_Tumor_CD8+_CD103pos

tag: donor


title: Clarke_Bulk-Stim_Donor-34_N_CD103neg


title: Clarke_Bulk-Stim_Donor-32_N_CD103neg


title: Arabidopsis_thaliana_WS_Rep2_240


title: Clarke_Bulk-Stim_Donor-32_T_CD103neg


title: Clarke_TCRseq_Beta_Donor-5_Tumor_CD8+_CD103neg


title: Arabidopsis_thaliana_WS_Rep2_30


title: Arabidopsis_thaliana_WS_Rep2_120


title: Arabidopsis_thaliana_WS_Rep2_15


title: Clarke_TCRseq_Beta_Donor-5_Tumor_CD8+_CD103pos


title: Clarke_Bulk-Stim_Donor-32_SN_CD103neg


title: Clarke_TCRseq_Beta_Donor-1_Tumor_CD8+_CD103pos


title: Clarke_TCRseq_Beta_Donor-7_Tumor_CD8+_CD103neg


title: Arabidopsis_thaliana_WS_Rep2_60


title: Clarke_Bulk-Stim_Donor-32_ST_CD103neg


title: Clarke_TCRseq_Beta_Donor-7_Tumor_CD8+_CD103pos


title: Arabidopsis_thaliana_WS_Rep2_0


title: Clarke_Bulk-Stim_Donor-31_ST_CD103neg


title: Clarke_TCRseq_Beta_Donor-24_Tumor_CD8+_CD103neg


title: Clarke_TCRseq_Beta_Donor-24_Tumor_CD8+_CD103pos


title: Clarke_Bulk-Stim_Donor-31_SN_CD103neg


title: Arabidopsis_thaliana_WS_Rep1_120


title: Arabidopsis_thaliana_WS_Rep1_60


title: Clarke_TCRseq_Beta_Donor-26_Tumor_CD8+_CD103neg


title: Clarke_TCRseq_Beta_Donor-3_Tumor_CD8+_CD103pos


title: Clarke_Bulk-Stim_Donor-31_T_CD103neg


title: Clarke_TCRseq_Beta_Donor-1_Tumor_CD8+_CD103neg


title: Clarke_TCRseq_Beta_Donor-26_Tumor_CD8+_CD103pos


title: Arabidopsis_thaliana_WS_Rep1_240


title: Clarke_TCRseq_Beta_Donor-21_Tumor_CD8+_CD103neg


title: Clarke_TCRseq_Beta_Donor-20_Tumor_CD8+_CD103neg


title: Clarke_Bulk-Stim_Donor-36_SN_CD103pos


title: Clarke_Bulk-Stim_Donor-36_T_CD103pos


title: Clarke_TCRseq_Beta_Donor-21_Tumor_CD8+_CD103pos


title: Arabidopsis_thaliana_WS_Rep1_30


title: Arabidopsis_thaliana_WS_Rep1_15


title: Clarke_TCRseq_Beta_Donor-20_Tumor_CD8+_CD103pos


title: Clarke_TCRseq_Beta_Donor-6_Tumor_CD8+_CD103neg


title: Clarke_Bulk-Stim_Donor-36_ST_CD103pos


title: Clarke_TCRseq_Beta_Donor-3_Tumor_CD8+_CD103neg


title: Clarke_Bulk-Stim_Donor-35_N_CD103pos


title: Arabidopsis_thaliana_WS_Rep1_0


title: Clarke_TCRseq_Beta_Donor-6_Tumor_CD8+_CD103pos


title: MS8345 PBT2 1

city: Brisbane

first: David

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

data_processing:
HiSeq 2500 ultra-high-throughput sequencing system was used for base-calling
Samples were uploaded to the Galaxy web platform (public server at usegalaxy.org), trimmed and mapped to the reference genome (K. pneumoniae MS6671 accession number: LN824133; E. coli accession number: CP025401.1) using bowtie2 with default parameters
Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0
Genome_build: LN824133; CP025401.1
Supplementary_files_format_and_content: Text files for each sample

organism: Escherichia coli

source_name: Bacteria

growth_protocol: Bacteria were grown in cation-adjusted Mueller-Hinton broth (CA-MHB) as per CLSI guidelines at 37°C under aerobic conditions.

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to OD600 of 0.5 in CA-MHB in the presence or absence of PBT2. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions. To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNASeq analysis was performed at the Australian Genome Research Facility. The cDNA library was prepared using a Ribo-zero stranded protocol. In brief, rRNA was depleted with Ribo Zero, RNA was fragmented (heat and divalent cations) and 1st strand cDNA synthesis was done with SuperScript II Reverse Transcriptase (Invitrogen). For the 2nd strand cDNA synthesis, the strand was “marked” with dUTP.  A 3’ adenylation of DNA fragments was performed followed by sequencing adapter ligation (utilizing T-A pairing of adapter and DNA fragments). The library was amplified by PCR (amplification of “unmarked” 1st strand only). Libraries were assessed using either Agilent’s Bioanalyzer DNA 1000 chip or TapeStation D1K TapeScreen system. qPCR was used to quantify individual libraries before normalizing (2 nM) and pooling. Libraries were pooled and clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents followed by sequencing on the Illumina HiSeq 2500 system with TruSeq SBS Kit v3 reagents with 110 (101 read 1, 9 cycles index read). Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 50-base-single end reads. An average of 30 million reads per sample were generated, uploaded to the Galaxy web platform (public server at usegalaxy.org), and mapped to the reference genome (K. pneumoniae MS6671 accession number: LN824133; E. coli accession number: CP025401.1) using bowtie2 with default parameters. Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0. Figures were generated using ggplot2 and ggpubr packages in R-studio

treatment_protocol: Bacteria were grown to  OD600 of 0.5 in CA-MHB in the presence or absence of PBT2 (7 µM for E. coli and 64 µM for K. pneumoniae).

tag: strain


title: MS8345 PBT2 3


title: MS8345 PBT2 2


title: Arabidopsis_thaliana_COL_Rep3_240


title: Clarke_Bulk-Stim_Donor-35_SN_CD103pos


title: Clarke_Bulk-Stim_Donor-36_N_CD103pos


title: MS8345 Control 3


title: Arabidopsis_thaliana_COL_Rep3_120


title: Clarke_Bulk-Stim_Donor-35_T_CD103pos


title: MS8345 Control 2


title: Arabidopsis_thaliana_COL_Rep3_60


title: MS8345 Control 1


title: Clarke_Bulk-Stim_Donor-35_ST_CD103pos


title: Arabidopsis_thaliana_COL_Rep3_30


title: Clarke_Bulk-Stim_Donor-34_N_CD103pos


title: Arabidopsis_thaliana_COL_Rep3_15


title: Clarke_Bulk-Stim_Donor-34_SN_CD103pos


title: Clarke_Bulk-Stim_Donor-34_T_CD103pos


title: ChIPseq_H2B_KO2

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
mapping of the reads to reference genome
filter for mapping quality < 37
merge BAM files of replicate samples
extend each read with 150 bp
normalize for sequencing depth
convert to bigwig
Genome_build: R64-2-1
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae BY4741

growth_protocol: Yeast strains were grown in YEPD.

extract_protocol:
Cells were cross-linked for 20 min with of the volume of freshly prepared Fix Solution containing 1% formaldehyde. Cells were washed once in cold TBS with 0.2 mM PMSF and lysed by bead beating in 200 μl breaking buffer with Zirconia/silica beads. The lysate was washed twice in FA buffer and sonicated using the Bioruptor PICO for 10 min.
Libraries were prepared using the KAPA HTP Library Preparation Kit (Illumina), using Illumina-provided adapters at 200nM. After eleven PCR cycles, cleanup and pooling was as described above. After 11 PCR cycles, a size selection cleanup was performed using 0.5X Agencourt AMPure XP PCR Purification beads to get rid of large fragments due to crosslinking DNA. The supernatant of the 0.5X cleanup was used to catch the smaller fragments; this supernatant was cleaned up 2 times with 1X beads to remove primers present in the libraries.

tag: antibody


title: ChIPseq_H2B_KO1


title: Arabidopsis_thaliana_COL_Rep3_0


title: Arabidopsis_thaliana_COL_Rep2_240


title: ChIPseq_H2B_WT2


title: Arabidopsis_thaliana_COL_Rep2_120


title: ChIPseq_H2Bub_KO2


title: Clarke_Bulk-Stim_Donor-33_N_CD103pos


title: Clarke_Bulk-Stim_Donor-34_ST_CD103pos


title: Arabidopsis_thaliana_COL_Rep2_60


title: ChIPseq_H2Bub_KO1


title: N2 wild type worms grown whole life on control L4440 plates biological rep 3

type: RNA

city: Cologne

first: Aleksandra

last: Trifunovic

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases

description: Gene expression data from N2 wild type worms grown whole life on control L4440 plates

hyb_protocol: Reversely transcribed RNAs were hybridized to Affymetrix EleGene 1.0 ST microarrays, according to the manufacturer's instructions.

scan_protocol: The scan protocol for the samples was the  library files EleGene-1_0-st.

data_processing:
CEL files were processed by the Affymetrix Power Tools, version 1.15.2 , and RMA normalization.
Analysis of differentially regulated genes was carried out using the R language for statistical computing, version 3.0.2.

label: Biotin

organism: Caenorhabditis elegans

label_protocol: Fragmenting and Labeling was done with the Encore Biotin Module ( Nugen).

growth_protocol: Worms were grown on RNAi plates from egg stage until fifth day of adulthood. Wild type N2 and isp-1(qm150);ctb-1(qm189) were grown on control L4440 plates as control. isp-1(qm150);ctb-1(qm189) was also grown on klf-1 RNAi plates until larval L4 stage and then switched to L4440 plates, or switched at L4 larval stage to klf-1 RNAi plates from control L4440 plates.

extract_protocol: RNA was isolated using Rneasy Mini Kit (QIAGEN) according to manufacturors protocol. The samples were amplified with the NuGen Applause WT-Amp Plus ST Kit.

treatment_protocol: Worms were washed in M9 buffer.

tag: Stage

value: fifth day of adulthood


title: isp-1(qm150);ctb-1(qm189) grown whole life on control L4440 plates biological rep 2

description: Gene expression data from isp-1(qm150);ctb-1(qm189) mutant grown whole life on control L4440 plates