title: HFF Native DFF-ChIP Exp4 H3K4me3 Rep2

description: Library name: Sample 32

library_source: genomic

data_processing:
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 and FJ616285.1 using bowtie 1.2.2.
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Assembly: hg38, FJ616285.1
Supplementary files format and content: bigwig files containing pileup of DFF ChIP-Seq fragments across whole HCMV genomes.

source_name: HCMV Towne BAC Infected 96 h

extract_protocol:
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described (M. Li et al. 2020). Following DFF digestion, nuclei were lightly sonicated for 20s and the soluble material was immunoprecipitated with antibodies.
Library construction is detailed in the manuscript.

value: HFF

value: Human foreskin fibroblasts

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: serum exosomes, PH133, week 12, 24hr

status: Public on Jul 22 2025

type: SRA

city: Dayton

first: Madhavi

last: Kadakia

state: OH

address: 3640 Colonel Glenn Hwy

department: Biochemistry and Molecular Biology

country: USA

institute: Wright State University

description:
PH133w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

library_source: other

data_processing:
Data processing performed in Partek Flow v10.0.21.0706
Reads were trimmed to a fixed length based on an average PHRED quality score greater than 20.
Trimmed reads were alighed to miRbase v21/hg38 using Bowtie aligner (seed mismatch =1, seed length = 10) and quantitated using miRBase v21.
Reads were normalized using the Trimmed Mean of M values (TMM) normalization method with an offset of 1.0.
Assembly: miRBase v21 of the hg38 (GRCh38) assembly.
Supplementary files format and content: tab-delimited text files listing raw read counts for each sample
Supplementary files format and content: tab-delimited text files listing TMM-normalized read counts for each sample

molecule: other

organism: Homo sapiens

source_name: serum exosomes

extract_protocol:
Muscle: Total RNA isolated using mirVana Paris Kit (Fisher); Serum exosomes: Exosomes isolated using Total Exosome Isolation from Serum Kit (Life Tech) and exosomal RNA purified using the Total Exosome RNA and Protein Isolation Kit (Life Tech).  XX RNA was used for construction of sequencing libraries.
cDNA was barcoded with IonExpress RNA-Seq Barcode 1-16 kit (Life Tech). 7.5picomoles each of 8-10 barcoded libraries were pooled and clonally amplified onto IonSphere Particles and enriched using the OneTouch2 (Life Tech).

treatment_protocol: All participants completed 12 weeks of either TRAD or HITT exercise followed by a 4 week detraining period.

tag: tissue

value: serum exosomes

tag: participant id

tag: treatment

value: HITT

tag: week

value: week 12

tag: time

tag: Sex

value: Male


title: serum exosomes, PH133, week 16, rest

description:
PH133w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: serum exosomes, PH133, week 12, pre

description:
PH133w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: serum exosomes, PH133, week 0, pre

description:
PH133w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: Exp1 D-NT2 WT 12 hpi No Flavo

city: Iowa City

first: Jeffery

middle: L

last: Meier

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

description: Library name: Sample 1

data_processing:
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to concatenated hg38 (human), FJ616285.1 (Towne) and JQCY02.1 (spodoptera) using bowtie 1.2.2.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup).
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Assembly: hg38 (human), FJ616285.1 (Towne) and JQCY02.1 (spodoptera)
Supplementary files format and content: bigwig files containing PRO-Seq pileups
Library strategy: PRO-Seq

source_name: HCMV Towne infected 12h

growth_protocol: Culturing NT2 in DMEM with 10% FBS results in a sizeable proportion of cells expressing HCMV MIE protein within 24 hours of infection. Adding 10 µM retinoic acid (Sigma) further differentiates these cells. For the experiments in differentiated NT2 (D-NT2), the NT2 were cultured with retinoic acid for 10 days. On the day before the infection, the growth medium containing retinoic acid was removed, and the cells were cultured in DMEM with 10% FBS. HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium and grown to confluence for at least one week before infection. All HFF used for these studies were at passage number ≤ 6.

extract_protocol:
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described in Li et. al. (2020, PMID: 32251483).
Library construction is detailed in the manuscript and was carried out as previously described by  Li et. al. (2020, PMID: 32251483), with some modifications.

treatment_protocol: Cells were infected with the indicated virus for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: cell line

tag: cell type

value: neuronal cells


title: 7810920019_R04C02 whole blood

type: genomic

city: Boston

first: Benjamin

middle: A

last: Raby

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Sample collected in EDTA tube, DNA for methylation was extracted

hyb_protocol: Using standard Illumina Infinium Human Methylation 450K BeadChip array hyb protocol.

scan_protocol: Using standard Illumina Infinium Human Methylation 450K BeadChip array scan protocol.

data_processing: Normalization was performed using the within-array combination of Noob (Triche et al. 2013) in R package “minfi” and BMIQ (Teschendorff et al. 2013) in R package “wateRmelon”. The minfi package was used to identify and remove 25,165 probes with SNPs. Sex was imputed by DNA methylation and 23 samples were removed due to mismatch between reported and genetic imputed sex. ComBat (Johnson, 2017) from the sva R package (Leek, 2023) was used for batch effect correction, transforming to m-values, then back transforming to beta-values.

label: Cy3, Cy5

molecule: genomic DNA

source_name: WhiteBloodCells from Purple Top EDTA tubes

label_protocol: Cy3, Cy5

extract_protocol: PureGene Blood Kit (Qiagen, Germantown, Maryland), AllPrep DNA Mini Kit (Qiagen)

tag: sample id

tag: subject id

value: M

tag: age

tag: asthma

value: N


title: Exp1 D-NT2 WT 72 hpi  PFA No Flavo

description: Library name: Sample 5

source_name: HCMV Towne infected 72h

value: Cells were treated with PFA 72h.


title: serum exosomes, PH133, week 12, 3hr

description:
PH133w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH133, week 12, 0hr

description:
PH133w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: HFF Native DFF-ChIP Exp4 H3K4me3 Rep1

description: Library name: Sample 31


title: serum exosomes, PH133, week 0, 24hr

description:
PH133w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920019_R03C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F

value: Y


title: serum exosomes, PH133, week 0, 3hr

description:
PH133w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920019_R02C02 whole blood


title: serum exosomes, PH136, week 0, 24hr

description:
PH136w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: 7810920019_R01C02 whole blood


title: HFF Native DFF-ChIP Exp4 TBP Rep1

description: Library name: Sample 29

value: HFF

value: Human foreskin fibroblasts

value: TBP (Abcam, ab51841)


title: HFF Native DFF-ChIP Exp4 TBP Rep2

description: Library name: Sample 30


title: HFF Native DFF-ChIP Exp4 Pol II Rep2

description: Library name: Sample 28

value: Pol II (Santa Cruz Biotechnology, sc-55492)


title: 7810920019_R06C01 whole blood


title: 7810920019_R05C01 whole blood


title: serum exosomes, PH130, week 16, rest

description:
PH130w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: HITT


title: serum exosomes, PH133, week 0, 0hr

description:
PH133w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: serum exosomes, PH130, week 12, 3hr

description:
PH130w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: serum exosomes, PH130, week 12, 24hr

description:
PH130w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920019_R04C01 whole blood


title: serum exosomes, PH130, week 12, 0hr

description:
PH130w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH130, week 0, pre

description:
PH130w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: pre


title: serum exosomes, PH130, week 0, 3hr

description:
PH130w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH129, week 16, rest

description:
PH129w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 16

value: rest


title: serum exosomes, PH129, week 12, pre

description:
PH129w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D-NT2 Crossing-Link DFF-ChIP Exp4 H3K4me3 Rep1

description: Library name: Sample 25

value: neuronal cells

value: Cells were treated with 16% paraformaldehyde to a final concentration of 1% for 10 min at room temperature. The crosslinking was stopped by adding Tris (pH 7.6) at final concentration 1.33 M.

value: H3K4me3 (Abcam, ab8580)


title: 7810920019_R01C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M

value: Y


title: serum exosomes, PH130, week 12, pre

description:
PH130w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: serum exosomes, PH129, week 12, 3hr

description:
PH129w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920019_R02C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: F

value: N


title: serum exosomes, PH129, week 12, 24hr

description:
PH129w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: 7810920016_R06C02 whole blood


title: D-NT2 Crossing-Link DFF-ChIP Exp4 TBP Rep2

description: Library name: Sample 24

value: TBP (Abcam, ab51841)


title: 7810920019_R03C01 whole blood


title: serum exosomes, PH129, week 0, 3hr

description:
PH129w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: HFF Native DFF-ChIP Exp4 Pol II Rep1

description: Library name: Sample 27

value: HFF

value: Human foreskin fibroblasts

value: Pol II (Santa Cruz Biotechnology, sc-55492)


title: D-NT2 Crossing-Link DFF-ChIP Exp4 TBP Rep1

description: Library name: Sample 23


title: serum exosomes, PH129, week 0, pre

description:
PH129w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 0

value: pre


title: serum exosomes, PH129, week 0, 24hr

description:
PH129w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D-NT2 Crossing-Link DFF-ChIP Exp4 Pol II Rep2

description: Library name: Sample 22

value: neuronal cells

value: Cells were treated with 16% paraformaldehyde to a final concentration of 1% for 10 min at room temperature. The crosslinking was stopped by adding Tris (pH 7.6) at final concentration 1.33 M.


title: serum exosomes, PH129, week 12, 0hr

description:
PH129w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: 7810920016_R05C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M


title: D-NT2 Crossing-Link DFF-ChIP Exp4 Pol II Rep1

description: Library name: Sample 21


title: D-NT2 Native DFF-ChIP Exp4 H3K4me3

description: Library name: Sample 20

value: H3K4me3 (Abcam, ab8580)


title: 7810920016_R03C02 whole blood

value: Y


title: serum exosomes, PH129, week 0, 0hr

description:
PH129w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH119, week 12, pre

description:
PH119w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920016_R02C02 whole blood

value: F


title: D-NT2 Crossing-Link DFF-ChIP Exp4 H3K4me3 Rep2

description: Library name: Sample 26


title: serum exosomes, PH119, week 12, 3hr

description:
PH119w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: serum exosomes, PH119, week 16, rest

description:
PH119w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: D-NT2 Native DFF-ChIP Exp4 TBP

description: Library name: Sample 19

value: TBP (Abcam, ab51841)


title: serum exosomes, PH130, week 0, 24hr

description:
PH130w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: Female


title: 7810920016_R01C02 whole blood


title: serum exosomes, PH119, week 12, 24hr

description:
PH119w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: Male


title: serum exosomes, PH119, week 0, 24hr

description:
PH119w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: serum exosomes, PH119, week 12, 0hr

description:
PH119w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D-NT2 Native DFF-ChIP Exp4 Pol II

description: Library name: Sample 18

value: neuronal cells

value: Pol II (Santa Cruz Biotechnology, sc-55492)


title: D-NT2 Native DFF-ChIP Exp3 IE2 Rep2

description: Library name: Sample 17

value: IE2 ( Millipore sigma, MAB8140)


title: 7810920016_R06C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: serum exosomes, PH119, week 0, 0hr

description:
PH119w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920016_R04C01 whole blood


title: serum exosomes, PH117, week 12, pre

description:
PH117w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12

value: pre


title: D-NT2 Native DFF-ChIP Exp3 H3K27Ac

description: Library name: Sample 15

value: H3K27Ac (Cell Signaling, D5E4)


title: serum exosomes, PH119, week 0, pre

description:
PH119w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920016_R03C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: F

value: Y


title: 7810920016_R05C01 whole blood


title: D-NT2 Native DFF-ChIP Exp3 H3K4me3 Rep2

description: Library name: Sample 14

value: H3K4me3 (Abcam, ab8580)


title: 7810920016_R02C01 whole blood


title: serum exosomes, PH117, week 16, rest

description:
PH117w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: week 16

value: rest


title: serum exosomes, PH117, week 12, 24hr

description:
PH117w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH117, week 12, 3hr

description:
PH117w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D-NT2 Native DFF-ChIP Exp3 IE2 Rep1

description: Library name: Sample 16


title: serum exosomes, PH117, week 0, pre

description:
PH117w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH117, week 0, 3hr

description:
PH117w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920016_R01C01 whole blood

value: N


title: serum exosomes, PH117, week 0, 24hr

description:
PH117w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: serum exosomes, PH119, week 0, 3hr

description:
PH119w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: serum exosomes, PH117, week 0, 0hr

description:
PH117w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: serum exosomes, PH102, week 12, pre

description:
PH102w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D-NT2 Native DFF-ChIP Exp3 TBP Rep1

description: Library name: Sample 11

value: neuronal cells

value: TBP (Abcam, ab51841)


title: D-NT2 Native DFF-ChIP Exp3 H3K4me3 Rep1

description: Library name: Sample 13


title: serum exosomes, PH102, week 12, 3hr

description:
PH102w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D-NT2 Native DFF-ChIP Exp3 TBP Rep2

description: Library name: Sample 12


title: serum exosomes, PH102, week 16, rest

description:
PH102w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920015_R05C02 whole blood


title: serum exosomes, PH102, week 12, 24hr

description:
PH102w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920015_R06C02 whole blood

value: M


title: serum exosomes, PH102, week 0, pre

description:
PH102w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH102, week 0, 3hr

description:
PH102w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH117, week 12, 0hr

description:
PH117w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D-NT2 Native DFF-ChIP Exp2 TBP Rep2

description: Library name: Sample 8


title: serum exosomes, PH102, week 0, 24hr

description:
PH102w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920015_R01C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: WhiteBloodCells from Purple Top EDTA tubes


title: serum exosomes, PH095, week 16, rest

description:
PH095w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH102, week 12, 0hr

description:
PH102w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: serum exosomes, PH102, week 0, 0hr

description:
PH102w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH095, week 12, 3hr

description:
PH095w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D-NT2 Native DFF-ChIP Exp3 Pol II Rep1

description: Library name: Sample 9

value: Pol II (Santa Cruz Biotechnology, sc-55492)


title: serum exosomes, PH095, week 12, 24hr

description:
PH095w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920015_R02C02 whole blood


title: D-NT2 Native DFF-ChIP Exp3 Pol II Rep2

description: Library name: Sample 10


title: D-NT2 Native DFF-ChIP Exp2 Pol II Rep1

description: Library name: Sample 5


title: D-NT2 Native DFF-ChIP Exp2 TBP Rep1

description: Library name: Sample 7


title: serum exosomes, PH095, week 0, pre

description:
PH095w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: serum exosomes, PH095, week 12, pre

description:
PH095w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920015_R04C01 whole blood

value: F


title: 7810920015_R06C01 whole blood


title: D-NT2 Native DFF-ChIP Exp2 Pol II Rep2

description: Library name: Sample 6


title: serum exosomes, PH091, week 12, pre

description:
PH091w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: Female


title: D-NT2 Native DFF-ChIP Exp1 Pol II Rep2

description: Library name: Sample 2


title: 7810920015_R05C01 whole blood

value: Y


title: serum exosomes, PH095, week 12, 0hr

description:
PH095w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: D-NT2 Native DFF-ChIP Exp1 H3K4me3 Rep2

description: Library name: Sample 4

value: H3K4me3 (Abcam, ab8580)


title: 7810920015_R04C02 whole blood


title: 7810920015_R03C02 whole blood


title: D-NT2 Native DFF-ChIP Exp1 Pol II Rep1

description: Library name: Sample 1


title: D-NT2 Native DFF-ChIP Exp1 H3K4me3 Rep1

description: Library name: Sample 3


title: serum exosomes, PH091, week 12, 0hr

description:
PH091w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH091, week 0, pre

description:
PH091w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920014_R05C01 whole blood


title: 7810920015_R03C01 whole blood

value: N


title: serum exosomes, PH091, week 12, 24hr

description:
PH091w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH095, week 0, 0hr

description:
PH095w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: serum exosomes, PH091, week 0, 3hr

description:
PH091w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH095, week 0, 24hr

description:
PH095w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: serum exosomes, PH091, week 12, 3hr

description:
PH091w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920014_R05C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: 7810920015_R02C01 whole blood


title: 7810920014_R06C01 whole blood


title: serum exosomes, PH091, week 0, 24hr

description:
PH091w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: endometrial stromal cells, EE_P55

city: bunnkyo Tokyo

first: Gentaro

last: Izumi

address: 7-3-1 hongo

country: Japan

institute: The university of Tokyo

description: Library name: EE_P55

library_source: transcriptomic

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20
The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0).
The HISAT2-resultant .sam files were converted into .bam files with Samtools (Version 1.9).
The .bam files were used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

source_name: ovarian endometrioma

growth_protocol: Stromal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Medium for estrogen treatment was phenol red-free DMEM/F12 (1:1, vol/vol) medium (0% FBS- DMEM/F12) without FBS and with antibiotic-antifungal mixture solution (1:100, vol/vol). medium) was used; E2(Cayman chemical, Michigan)ethanol solution (10-5 mol/L), E4(Tront Research Chemicals, Canada) ethanol solution (10-3 mol/L) or EE(Pharmaceutical and Medical Device Regulatory Science Society of Japan, Japan) ethanol solution (10-6 mol/L) was diluted in 0% FBS- DMEM/F12 medium to obtain E2 (10-6, 10-8, 10-9, 10-10 mol/L), E4 ( 10-6, 10-8, 10-9, 10-10 mol/L), or EE (10-9, 10-11, 10-12, 10-13 mol/L) medium. The control was 0% FBS- DMEM/F12 medium without estrogen.　 Endometriosis cells were cultured for 3-48 hours in medium for estrogen treatment.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and  NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Endometriosis cells were cultured into 6-well plates at a cell count of 2x105 cells/well and cultured in 5% FBS- DMEM/F12 medium. When cells reached 70-90% confluency, they were replaced with medium for estrogen treatment.

value: ovarian endometrioma

value: stromal cell

value: EE


title: serum exosomes, PH095, week 0, 3hr

description:
PH095w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, EE_P54

description: Library name: EE_P54


title: serum exosomes, PH091, week 0, 0hr

description:
PH091w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH087, week 12, 3hr

description:
PH087w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH087, week 16, rest

description:
PH087w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: serum exosomes, PH087, week 12, 0hr

description:
PH087w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: 7810920014_R02C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: serum exosomes, PH087, week 0, pre

description:
PH087w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: endometrial stromal cells, EE_P53

description: Library name: EE_P53


title: 7810920014_R01C01 whole blood

value: M


title: serum exosomes, PH087, week 12, 24hr

description:
PH087w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT


title: 7810920012_R02C02 whole blood

value: F


title: serum exosomes, PH087, week 0, 3hr

description:
PH087w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: endometrial stromal cells, EE_P44

description: Library name: EE_P44


title: serum exosomes, PH084, week 12, pre

description:
PH084w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: 7810920012_R05C01 whole blood

value: Y


title: endometrial stromal cells, E4_P55

description: Library name: E4_P55


title: endometrial stromal cells, E4_P57

description: Library name: E4_P57


title: serum exosomes, PH084, week 12, 3hr

description:
PH084w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH087, week 12, pre

description:
PH087w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920012_R06C01 whole blood


title: serum exosomes, PH087, week 0, 0hr

description:
PH087w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, E4_P53

description: Library name: E4_P53


title: serum exosomes, PH084, week 16, rest

description:
PH084w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, E4_P54

description: Library name: E4_P54


title: 7810920010_R06C02 whole blood


title: serum exosomes, PH084, week 12, 24hr

description:
PH084w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH084, week 0, 3hr

description:
PH084w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920012_R04C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: N


title: endometrial stromal cells, E2_P57

description: Library name: E2_P57


title: serum exosomes, PH084, week 12, 0hr

description:
PH084w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH084, week 0, 24hr

description:
PH084w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH087, week 0, 24hr

description:
PH087w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: 7810920012_R03C02 whole blood


title: serum exosomes, PH130, week 0, 0hr

description:
PH130w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: endometrial stromal cells, E4_P44

description: Library name: E4_P44

value: ovarian endometrioma


title: serum exosomes, PH083, week 16, rest

description:
PH083w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: 7810920010_R05C02 whole blood


title: endometrial stromal cells, E2_P55

description: Library name: E2_P55

value: stromal cell


title: serum exosomes, PH083, week 12, pre

description:
PH083w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH084, week 0, 0hr

description:
PH084w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH083, week 12, 24hr

description:
PH083w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920010_R04C02 whole blood


title: serum exosomes, PH083, week 12, 3hr

description:
PH083w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, E2_P54

description: Library name: E2_P54


title: serum exosomes, PH084, week 0, pre

description:
PH084w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920010_R05C01 whole blood


title: endometrial stromal cells, E2_P53

description: Library name: E2_P53


title: serum exosomes, PH083, week 0, 24hr

description:
PH083w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, C_P57

description: Library name: C_P57

value: control


title: serum exosomes, PH083, week 0, 0hr

description:
PH083w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH083, week 0, pre

description:
PH083w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH083, week 12, 0hr

description:
PH083w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH080, week 12, pre

description:
PH080w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920010_R04C01 whole blood


title: endometrial stromal cells, E2_P44

description: Library name: E2_P44


title: 7810920010_R03C01 whole blood


title: serum exosomes, PH083, week 0, 3hr

description:
PH083w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, C_P55

description: Library name: C_P55


title: endometrial stromal cells, C_P54

description: Library name: C_P54


title: serum exosomes, PH080, week 12, 24hr

description:
PH080w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH080, week 12, 3hr

description:
PH080w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH080, week 12, 0hr

description:
PH080w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920010_R01C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: serum exosomes, PH080, week 16, rest

description:
PH080w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: serum exosomes, PH080, week 0, 3hr

description:
PH080w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, C_P44

description: Library name: C_P44


title: 7810920010_R01C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: 7810920010_R02C01 whole blood


title: 7810920010_R06C01 whole blood


title: serum exosomes, PH080, week 0, pre

description:
PH080w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: 7810920008_R06C02 whole blood


title: serum exosomes, PH080, week 0, 24hr

description:
PH080w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: SUM159_pLVX_POGK_repl3

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

data_processing:
Raw fastq files first had optical duplicates removed using clumpify from the BBTools  suite using the flag “dedupe spany addcount”.  Next, adaptor trimming was performed using bbduk, also from the BBTools suite using the flag “ktrim=l hdist=2”.  Next, reads were quality trimmed with Trimmomatic  in paired end mode with the flags “ILLUMINACLIP: <adapter_path> Truseq3.PE.fa:2:15:4:4:true LEADING:28 TRAILING:28 SLIDINGWINDOW:4:26 MINLEN:20”.  Alignment was performed using STAR  with the flags “--outFilterScoreMinOverLread 0.25 --outFilterMatchNminOverLread 0.25 --outFilterMultimapNmax 5“ with the resultant bam files sorted and indexed using samtools .  BamCoverage was used to generate coverage maps using default parameters. FeatureCounts  was used to generate gene counts values using the flags “-g gene_id --extraAttributes gene_name -p -M -O -f -d 20”.
Assembly: hg38
Supplementary files format and content: tab-delimited txt file containing raw counts combined for all sample including gene annotations
Supplementary files format and content: bigWig coverage file per sample

growth_protocol: SUM159 cells were cultured in Ham’s F12 medium with 5% FBS, 5 μg/ml Insulin and 1 μg/ml Hydrocortisone.

extract_protocol:
Total cellular RNA was extracted using RNEasy (Qiagen, Hilden, Germany) and assessed using NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA). The RNA quantity of A260/A280 is between 1.95 to 2.
Total of 100 ng RNA was further processed for ribosomal RNA removal using the Epicenter rRNA depletion kit. Ribosomal RNA-depleted samples were subsequently used to generate sequencing libraries using Roche Diagnostics KAPA mRNA HyperPrep Kit. RNA Seq performed in Whitehead Institute for Biomedical Research Genome Technology Core using a NovoSeq 6000 (Cambridge, MA). The RNA sequencing data was aligned to human genome hg38.

tag: genotype

value: POGK-overexpressing stable cells


title: 7810920008_R05C02 whole blood


title: serum exosomes, PH080, week 0, 0hr

description:
PH080w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH079, week 16, rest

description:
PH079w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT


title: serum exosomes, PH079, week 12, 24hr

description:
PH079w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: serum exosomes, PH079, week 12, 3hr

description:
PH079w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: SUM159_pLVX_POGK_repl2


title: 7810920008_R04C02 whole blood

value: F


title: SUM159_pLVX_repl3


title: serum exosomes, PH079, week 0, 3hr

description:
PH079w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: serum exosomes, PH079, week 12, pre

description:
PH079w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, C_P53

description: Library name: C_P53


title: 7810920008_R02C02 whole blood

value: M

value: Y


title: 7810920008_R03C02 whole blood


title: serum exosomes, PH079, week 12, 0hr

description:
PH079w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: SUM159_pLVX_POGK_repl1


title: 7810920008_R01C02 whole blood


title: serum exosomes, PH079, week 0, 0hr

description:
PH079w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: serum exosomes, PH078, week 16, rest

description:
PH078w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: SUM159_pLVX_repl1


title: serum exosomes, PH078, week 12, pre

description:
PH078w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: 7810920008_R06C01 whole blood


title: serum exosomes, PH078, week 12, 3hr

description:
PH078w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: endometrial stromal cells, EE_P57

description: Library name: EE_P57

value: ovarian endometrioma

value: stromal cell

value: EE


title: serum exosomes, PH078, week 12, 24hr

description:
PH078w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH078, week 12, 0hr

description:
PH078w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: SUM159_pLVX_FLAG_POGK_repl2, ChIP

description:
pogk_chipseq_broad_all_peaks_calculated.tsv
pogk_chipseq_broad_setting_table.tsv

data_processing:
Raw fq files were processed with ChIP-AP (PMID 34965583) v5.4 with the settings table provided in processed data. With the raw fq files and the settings table, ChIP-AP is able to reproduce the exact same analysis. Briefly though, rawfq files have optical duplicates removed and then undergo adapter and quality trimming. Afterwhich, alignment is performed using bwa against hg38 and peaks called using MACS2, HOMER, Genrich and SICER2. The output of all 4 peak callers is combined and presented as processed data.
Assembly: hg38
Supplementary files format and content: bigWig, ChIP-AP_settings_table.tsv
Supplementary files format and content: tab delimited txt file containing ChIP-AP settings for analysis re-run
Supplementary files format and content: pogk_chipseq_broad_all_peaks_calculated.tsv - complete listing of all peaks output from ChIP-AP

extract_protocol:
Each reaction includes 5X106 cells, initially crosslinked with 1% formaldehyde and subsequently quenched using glycine. The crosslinked cells underwent sonication to achieve DNA fragmentation within the range of 200 to 350 base pairs. Immunoprecipitation of DNA was then conducted utilizing magnetic antibody beads. Following reverse crosslinking, DNA purification was carried out using the Qiagen PCR purification kit. The DNA quantity was validated using the 2100 Bioanalyzer expert High Sensitivity DNA Assay.
Each reaction includes ~50 ng of DNA and undergoes library preparation and sequencing conducted by Azenta NGS laboratory (Waltham, MA) utilizing the Illumina HiSeq platform configured with 2x150 base pairs. The sequencing depth achieves over 20 million reads per sample. The sequencing data are aligned to the human genome hg38 for analysis.


title: 7810920008_R05C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: serum exosomes, PH079, week 0, pre

description:
PH079w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: SUM159_pLVX_FLAG_repl2, Input


title: serum exosomes, PH078, week 0, pre

description:
PH078w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920008_R02C01 whole blood

value: N


title: serum exosomes, PH075, week 16, rest

description:
PH075w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: rhLUM-C

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
i. STAR Version 2.7.8: Alignment (https://github.com/alexdobin/STAR). ii.  RSEM Version 1.2.31: Quantify expression (https://deweylab.github.io/RSEM/). iii. EBSeq Version 1.18.0: Identify differentially expressed genes (http://bioconductor.org/packages/release/bioc/html/EBSeq.html)
Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp. Low quality is defined as (i) reads with more than 5% unknown bases, (ii) reads with more than 50% of bases with quality value <=11.
Reads were mapped to the reference genome using STAR (default parameters) with the following exception: twopassMode: Basic
Differentially expression analysis was done using EBSeq.
Assembly: Human Genome GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

source_name: HCC

extract_protocol:
Total RNA was extracted from MHCC97L xenograft using RNAiso Plus (Takara Bio Inc., Kusatsu, Shiga, Japan) according to manufacturer's protocol.
Quality and quantity of total RNA samples were assessed using the RNA 6000 Nano total RNA assay (Agilent) by Agilent 2100 bioanalyzer and Qubit 2.0 Fluorometer, respectively. Qualified RNA (1 μg) samples were subjected to library preparation using KAPA mRNA HyperPrep Kit (KR1352). Poly-A containing mRNA was collected by using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented to 200 – 300bp by incubating at 94oC for 6 min in the presence of magnesium ions. The fragmented mRNA was then applied as template to synthesize the first-strand cDNA by using random hexamer-primer and reverse transcriptase. In the second strand cDNA synthesis, the mRNA template was removed and a replacement strand was generated to form the blunt-end double-stranded (ds) cDNA. The ds cDNA underwent, 3’ adenylation and indexed adaptor ligation. The adaptor-ligated libraries were enriched by 10 cycles of polymerase chain reaction (PCR). The libraries were denatured and diluted to optimal concentration. Illumina NovaSeq 6000 was used for Pair-End 151bp sequencing.

value: HCC

value: rhLUM


title: SUM159_pLVX_FLAG_repl1, Input


title: serum exosomes, PH078, week 0, 0hr

description:
PH078w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH078, week 0, 3hr

description:
PH078w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: SUM159_pLVX_repl2

value: control


title: serum exosomes, PH078, week 0, 24hr

description:
PH078w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: rhLUM-A


title: serum exosomes, PH075, week 12, 3hr

description:
PH075w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: 7810920008_R01C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F


title: 7810920007_R05C02 whole blood


title: 7810920008_R03C01 whole blood

value: M


title: serum exosomes, PH075, week 12, 24hr

description:
PH075w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: serum exosomes, PH075, week 12, 0hr

description:
PH075w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: rhLUM-B


title: serum exosomes, PH072, week 12, pre

description:
PH072w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: serum exosomes, PH075, week 0, 0hr

description:
PH075w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 0


title: serum exosomes, PH072, week 12, 24hr

description:
PH072w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH075, week 0, pre

description:
PH075w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920007_R02C02 whole blood


title: serum exosomes, PH072, week 12, 0hr

description:
PH072w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 240h, RHOG, CART0077_D3

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

data_processing:
Alignment using STAR
Count matrix aggregated using the wrapper from
snakemake-workflows/rna-seq-star-deseq2
Assembly: hg38
Supplementary files format and content: Comma-separated file includes aggregated counts for each sample

growth_protocol: Human primary T cells were isolated from the whole blood of three independent healthy donors. Cells were stimulated with anti-CD3/CD28 reagent. After 2 days, cells were transduced with CROP-seq-CAR lentivirus to deliver the CAR and a library of 8 gRNAs targeting either RHOG or a safe harbor locus. Puromycin was added 2 days later to select for the lentiviral construct. After a total of 7 days from initial stimulation, cells were restimulated with anti-CD3/CD28 reagent. After 2 days, cells were electroporated with synthetic mRNA for Cas9 and blasticidin resistance. Blasticidin was added 24 hours later and kept for 2 days in the culture medium to select for successful electroporation. 6 days later, CRISPR-modified CAR T cells were used for the RNA-seq readout.

extract_protocol:
To isolate pure CD4 or CD8 cells from primary T cell culture and co-culture with irradiated tumor cells, we used the EasySep Human CD4 Positive Selection Kit II (Stemcell #17852) and EasySep Human CD8 Positive Selection Kit II (Stemcell #17853). RNA was isolated using the Monarch Total RNA Miniprep Kit (NEB #T2010S) from at least 200,000 lysed cells and stored at -80 ˚C in 300 µl of Protection Reagent.
Sequencing libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760L).
RNA-seq libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, on the Illumina NovaSeq 6000 platform and the 50 bp paired-end configuration.

treatment_protocol: CAR T cells were repeatedly stimulated with irradiated CD19+ K562 tumor cells at 1:1 ratio and sampled at day 0, 3, 7 and 10.

value: RHOG

tag: treatment hours

tag: donor

value: Male


title: serum exosomes, PH075, week 0, 24hr

description:
PH075w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920007_R06C02 whole blood

value: N


title: SUM159_pLVX_FLAG_POGK_repl1, ChIP

description:
pogk_chipseq_broad_all_peaks_calculated.tsv
pogk_chipseq_broad_setting_table.tsv


title: 7810920007_R01C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: 7810920008_R04C01 whole blood


title: serum exosomes, PH075, week 0, 3hr

description:
PH075w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: Ctrl-C

value: Ctrl


title: 7810920007_R06C01 whole blood

value: Y


title: serum exosomes, PH075, week 12, pre

description:
PH075w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920007_R04C02 whole blood


title: CD8, 240h, RHOG, CART0077_D2

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences


title: serum exosomes, PH091, week 16, rest

description:
PH091w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: week 16

value: rest


title: serum exosomes, PH072, week 16, rest

description:
PH072w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: 7810920007_R05C01 whole blood


title: serum exosomes, PH067, week 16, rest

description:
PH067w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 240h, SafeHarbor, CART0077_D2

value: SafeHarbor


title: serum exosomes, PH079, week 0, 24hr

description:
PH079w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: Ctrl-B

value: HCC


title: 7810920007_R04C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F


title: CD8, 240h, RHOG, CART0077_D1

value: Female


title: 7810920007_R03C01 whole blood

value: M


title: serum exosomes, PH067, week 0, pre

description:
PH067w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: pre


title: CD8, 240h, SafeHarbor, CART0077_D1


title: serum exosomes, PH067, week 0, 3hr

description:
PH067w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: 7810920007_R03C02 whole blood


title: 7810920007_R02C01 whole blood


title: serum exosomes, PH072, week 12, 3hr

description:
PH072w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: Ctrl-A


title: serum exosomes, PH072, week 0, pre

description:
PH072w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH072, week 0, 3hr

description:
PH072w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920007_R01C01 whole blood


title: serum exosomes, PH065, week 16, rest

description:
PH065w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 240h, SafeHarbor, CART0077_D3

value: Male


title: serum exosomes, PH065, week 12, pre

description:
PH065w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH072, week 0, 24hr

description:
PH072w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH065, week 12, 3hr

description:
PH065w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920005_R05C02 whole blood

value: N


title: serum exosomes, PH067, week 12, pre

description:
PH067w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH072, week 0, 0hr

description:
PH072w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH065, week 0, 3hr

description:
PH065w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920005_R03C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: Y


title: serum exosomes, PH067, week 12, 3hr

description:
PH067w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH065, week 0, 0hr

description:
PH065w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT


title: serum exosomes, PH067, week 12, 0hr

description:
PH067w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 240h, RHOG, CART0077_D3

value: RHOG


title: serum exosomes, PH063, week 12, pre

description:
PH063w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH067, week 0, 24hr

description:
PH067w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH067, week 0, 0hr

description:
PH067w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH063, week 12, 24hr

description:
PH063w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 168h, SafeHarbor, CART0077_D3


title: serum exosomes, PH067, week 12, 24hr

description:
PH067w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 240h, SafeHarbor, CART0077_D3


title: serum exosomes, PH063, week 0, pre

description:
PH063w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 168h, RHOG, CART0077_D2


title: CD4, 240h, RHOG, CART0077_D2


title: 7810920005_R06C02 whole blood


title: serum exosomes, PH065, week 12, 24hr

description:
PH065w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 240h, SafeHarbor, CART0077_D2


title: serum exosomes, PH065, week 12, 0hr

description:
PH065w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH063, week 0, 0hr

description:
PH063w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH062, week 16, rest

description:
PH062w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: 7810920005_R04C02 whole blood


title: 7810920005_R02C01 whole blood


title: CD4, 240h, RHOG, CART0077_D1


title: serum exosomes, PH062, week 12, pre

description:
PH062w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: serum exosomes, PH065, week 0, pre

description:
PH065w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH065, week 0, 24hr

description:
PH065w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 240h, SafeHarbor, CART0077_D1

value: SafeHarbor


title: serum exosomes, PH063, week 16, rest

description:
PH063w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 168h, SafeHarbor, CART0077_D1


title: 7810920005_R01C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: WhiteBloodCells from Purple Top EDTA tubes


title: CD4, 168h, RHOG, CART0077_D3


title: 7810920005_R03C01 whole blood


title: 7810920005_R02C02 whole blood

value: F


title: CD8, 168h, RHOG, CART0077_D3


title: 7810920005_R01C02 whole blood


title: CD4, 168h, SafeHarbor, CART0077_D3


title: serum exosomes, PH063, week 12, 3hr

description:
PH063w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920005_R05C01 whole blood


title: 7810920004_R05C02 whole blood


title: CD4, 168h, RHOG, CART0077_D2

value: Female


title: CD8, 168h, SafeHarbor, CART0077_D2


title: 7810920005_R04C01 whole blood


title: CD8, 168h, RHOG, CART0077_D1


title: serum exosomes, PH063, week 12, 0hr

description:
PH063w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH058, week 12, pre

description:
PH058w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 168h, SafeHarbor, CART0077_D2


title: serum exosomes, PH062, week 12, 24hr

description:
PH062w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920004_R03C02 whole blood


title: serum exosomes, PH063, week 0, 24hr

description:
PH063w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 168h, RHOG, CART0077_D1


title: serum exosomes, PH062, week 0, pre

description:
PH062w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH062, week 0, 3hr

description:
PH062w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920004_R06C02 whole blood


title: serum exosomes, PH062, week 12, 3hr

description:
PH062w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH058, week 0, pre

description:
PH058w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH062, week 0, 24hr

description:
PH062w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 72h, RHOG, CART0077_D3


title: serum exosomes, PH062, week 0, 0hr

description:
PH062w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920004_R04C02 whole blood

value: M


title: serum exosomes, PH058, week 0, 0hr

description:
PH058w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH058, week 12, 24hr

description:
PH058w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 168h, SafeHarbor, CART0077_D1


title: 7810920004_R02C02 whole blood


title: serum exosomes, PH056, week 12, 3hr

description:
PH056w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: serum exosomes, PH056, week 12, pre

description:
PH056w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: serum exosomes, PH062, week 12, 0hr

description:
PH062w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH058, week 12, 0hr

description:
PH058w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH058, week 0, 3hr

description:
PH058w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: 7810920004_R04C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: serum exosomes, PH058, week 12, 3hr

description:
PH058w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: CD8, 72h, RHOG, CART0077_D2


title: serum exosomes, PH058, week 16, rest

description:
PH058w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH056, week 12, 0hr

description:
PH056w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: 7810920004_R01C02 whole blood

value: N


title: 7810920004_R03C01 whole blood

value: Y


title: serum exosomes, PH058, week 0, 24hr

description:
PH058w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT


title: 7810920004_R06C01 whole blood


title: CD8, 72h, RHOG, CART0077_D1

value: RHOG


title: 7810920004_R02C01 whole blood


title: serum exosomes, PH056, week 16, rest

description:
PH056w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16


title: serum exosomes, PH056, week 0, 0hr

description:
PH056w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 72h, SafeHarbor, CART0077_D3


title: 7810920004_R05C01 whole blood


title: serum exosomes, PH056, week 12, 24hr

description:
PH056w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 72h, SafeHarbor, CART0077_D2


title: CD4, 72h, RHOG, CART0077_D3


title: 7810920004_R01C01 whole blood


title: serum exosomes, PH056, week 0, 3hr

description:
PH056w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH056, week 0, pre

description:
PH056w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH054, week 12, pre

description:
PH054w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH054, week 16, rest

description:
PH054w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: rest


title: serum exosomes, PH056, week 0, 24hr

description:
PH056w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: CD4, 72h, SafeHarbor, CART0077_D3

value: SafeHarbor


title: serum exosomes, PH054, week 12, 3hr

description:
PH054w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 72h, SafeHarbor, CART0077_D1


title: CD4, 72h, RHOG, CART0077_D2


title: 7810920003_R06C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: serum exosomes, PH054, week 0, pre

description:
PH054w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920003_R04C02 whole blood


title: serum exosomes, PH054, week 12, 24hr

description:
PH054w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920003_R05C02 whole blood

value: F


title: serum exosomes, PH054, week 12, 0hr

description:
PH054w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: serum exosomes, PH054, week 0, 24hr

description:
PH054w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH051, week 16, rest

description:
PH051w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH054, week 0, 3hr

description:
PH054w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 72h, RHOG, CART0077_D1


title: CD4, 72h, SafeHarbor, CART0077_D2


title: serum exosomes, PH051, week 12, pre

description:
PH051w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920003_R03C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: 7810920003_R02C02 whole blood


title: CD4, 72h, SafeHarbor, CART0077_D1


title: serum exosomes, PH051, week 12, 3hr

description:
PH051w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920003_R01C02 whole blood

value: M


title: CD8, 24h, RHOG, CART0077_D3


title: CD8, 24h, SafeHarbor, CART0077_D3


title: serum exosomes, PH051, week 0, pre

description:
PH051w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH051, week 12, 24hr

description:
PH051w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH051, week 12, 0hr

description:
PH051w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH051, week 0, 24hr

description:
PH051w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH051, week 0, 3hr

description:
PH051w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH054, week 0, 0hr

description:
PH054w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: 7810920003_R04C01 whole blood


title: serum exosomes, PH050, week 16, rest

description:
PH050w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 24h, RHOG, CART0077_D2


title: serum exosomes, PH051, week 0, 0hr

description:
PH051w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920003_R03C01 whole blood


title: serum exosomes, PH050, week 12, pre

description:
PH050w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: CD8, 24h, RHOG, CART0077_D1


title: serum exosomes, PH050, week 12, 0hr

description:
PH050w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH050, week 0, pre

description:
PH050w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: serum exosomes, PH050, week 0, 3hr

description:
PH050w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920003_R02C01 whole blood


title: CD8, 24h, SafeHarbor, CART0077_D1


title: 6229009043_R06C01 whole blood


title: serum exosomes, PH050, week 0, 0hr

description:
PH050w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920003_R06C01 whole blood


title: serum exosomes, PH050, week 0, 24hr

description:
PH050w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 7810920003_R05C01 whole blood


title: 6229009043_R05C02 whole blood


title: serum exosomes, PH049, week 12, pre

description:
PH049w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: 6229009043_R05C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: serum exosomes, PH049, week 12, 3hr

description:
PH049w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Male


title: CD4, 24h, SafeHarbor, CART0077_D3


title: CD8, 24h, SafeHarbor, CART0077_D2


title: 6229009043_R04C02 whole blood


title: serum exosomes, PH049, week 12, 0hr

description:
PH049w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 24h, SafeHarbor, CART0077_D2


title: serum exosomes, PH050, week 12, 24hr

description:
PH050w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6229009043_R04C01 whole blood


title: serum exosomes, PH049, week 0, pre

description:
PH049w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH049, week 0, 24hr

description:
PH049w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH049, week 0, 3hr

description:
PH049w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH049, week 0, 0hr

description:
PH049w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6229009043_R03C02 whole blood


title: CD4, 24h, RHOG, CART0077_D1


title: CD4, 24h, RHOG, CART0077_D3


title: CD4, 24h, SafeHarbor, CART0077_D1


title: serum exosomes, PH048, week 12, pre

description:
PH048w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6229009043_R03C01 whole blood


title: serum exosomes, PH049, week 16, rest

description:
PH049w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 0h, RHOG, CART0077_D3


title: serum exosomes, PH048, week 12, 3hr

description:
PH048w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH048, week 12, 24hr

description:
PH048w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH049, week 12, 24hr

description:
PH049w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD4, 24h, RHOG, CART0077_D2


title: 6229009043_R02C02 whole blood


title: serum exosomes, PH048, week 12, 0hr

description:
PH048w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH048, week 0, 3hr

description:
PH048w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 0h, SafeHarbor, CART0077_D2


title: serum exosomes, PH048, week 0, 24hr

description:
PH048w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD8, 0h, RHOG, CART0077_D2


title: 6229009043_R02C01 whole blood

value: N


title: serum exosomes, PH048, week 0, 0hr

description:
PH048w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6229009043_R01C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: Y


title: 6229009043_R01C01 whole blood


title: DU145_sPOM121_4

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

data_processing:
The Illumina TruSeq RNA kit was used for 100nt/pair-end reads, 4 samples were run per lane using the standard Truseq indices.  Raw cDNA reads are aligned to the hg38 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Assembly: hg38
Supplementary files format and content: txt format; the read count for each gene

source_name: Prostate cancer

growth_protocol: Prostate cancer DU145 and 22Rv1 were obtained from ATCC and grown in RPMI media with 10% FBS in a humidified 37°C atmosphere with 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy Mini kit (QIAGEN) in accordance with manufacturer’s instructions.
High-quality total RNA samples (RNA Integrity score > 8 by Agilent Bioanalyzer) were subjected to poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer’s protocol. The libraries were sequenced by HiSeq 2500 genome sequencer (Illumina) to generate 100 bp single-end reads.
Hi-Seq, 100nt, Paired-End Read, 4 samples per lane

treatment_protocol: Soluble POM121 (sPOM121) and Control Knockdowns (KD)

value: Prostate cancer

value: sPOM121 KD


title: serum exosomes, PH047, week 12, pre

description:
PH047w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT


title: serum exosomes, PH048, week 16, rest

description:
PH048w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: 6229009036_R06C02 whole blood


title: DU145_sPOM121_3


title: serum exosomes, PH047, week 12, 3hr

description:
PH047w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: CD4, 0h, RHOG, CART0077_D3

value: RHOG


title: DU145_sPOM121_2


title: serum exosomes, PH047, week 12, 0hr

description:
PH047w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6229009036_R05C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F


title: CD4, 0h, SafeHarbor, CART0077_D3

value: SafeHarbor


title: CD8, 0h, SafeHarbor, CART0077_D3


title: DU145_sPOM121_1


title: 6229009036_R04C02 whole blood

value: M


title: serum exosomes, PH047, week 0, pre

description:
PH047w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre


title: DU145_ctrl_4

value: control


title: CD4, 0h, RHOG, CART0077_D2

value: Female


title: CD4, 0h, SafeHarbor, CART0077_D2


title: 6229009036_R04C01 whole blood


title: serum exosomes, PH047, week 0, 3hr

description:
PH047w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: Male


title: 6229009036_R03C02 whole blood

value: Y


title: DU145_ctrl_3

value: Prostate cancer


title: serum exosomes, PH047, week 0, 24hr

description:
PH047w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: DU145_ctrl_2


title: CD4, 0h, RHOG, CART0077_D1


title: 6229009036_R05C02 whole blood

value: N


title: 6229009036_R03C01 whole blood


title: serum exosomes, PH047, week 0, 0hr

description:
PH047w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT


title: DU145_ctrl_1


title: CD4, 0h, SafeHarbor, CART0077_D1


title: 6229009036_R02C02 whole blood


title: 6229009036_R02C01 whole blood


title: serum exosomes, PH045, week 12, pre

description:
PH045w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 12


title: 6229009036_R01C02 whole blood


title: 22Rv1_sPOM121_4

value: sPOM121 KD


title: D13_Untransduced_DN3

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

data_processing:
The fastq files were assessed for initial quality using FastQC v0.11.8, trimmed for adapter sequences using TrimGalore v0.6.0  and aligned to GRCh38.p13 (Gencode release 35) with STAR aligner (v2.6.0c) using twopassMode.
Transcript abundance was estimated using RSEM v1.3.0 and imported into R v3.5.1 using txImport v1.10.1 and then processed using DESeq2 v1.22.2, generating VST transformed data.
Assembly: GRCh38.p13 (Gencode release 35)
Supplementary files format and content: tab-delimited text files with DESeq2 VST log2 values for each Sample

source_name: Peripheral blood

extract_protocol:
Cells were counted and lysed with 800 µl to 1 ml TRIzol (15596026, ambion) reagent, incubated for 10 minutes at RT and stored at -80 °C. Chloroform (C2432-26ML, Honeywell) was added at 160 µl or 200 µl respectively, to defrosted samples followed by vigorous shake for 15 seconds and 3 minutes at RT incubation. A centrifugation step at 11,000 rpm for 15 minutes at 4 °C was followed by collection of the aqueous phase. 400 µl isopropanol and 10 µl glycogen (AM9510, Invitrogen) were added and the mixture was incubated for 10 minutes at RT. Samples were centrifuged at 11,000 rpm for 10 minutes at 4 °C and the pellet was washed three times with 75% ethanol followed by a centrifugation step at 9,000 rpm for 5 minutes at 4 °C. RNA pellets were air dried for 10 minutes and dissolved in 30 µl RNase free water. RNA was incubated at 55 °C for 10 minutes, treated with DNases for genomic DNA removal (AM1906, Invitrogen) and stored at -20 °C.
Sequencing libraries and sequencing were carried out by Novogene.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by Lymphoprep density gradient, 2000 rpm centrifugation for 20 minutes at room temperature (RT). PBMCs were washed with phosphate saline buffer (PBS), counted, and labelled appropriately, based on a human memory B cells isolation kit (130-093-546, Miltenyi Biotec), with B cell biotin antibody cocktail for 20 minutes at 4 °C. Magnetic isolation of total B cells was performed upon incubation for 20 minutes at 4 °C with anti-biotin beads. Following the previously established in vitro plasma cell differentiation method, memory B cells were isolated following magnetic labeling with anti-CD23 beads (130-094-510, Miltenyi Biotec) and co-cultured in a 24 well-plate format at 2x10^5 cells/ml with 2x10^4 cells/ml CD40L-L stromal cells in IMDM CM containing IL-2 (40 U/ml), IL-21 (100 ng/ml) and F(ab’)2 fragments goat anti-human IgG, IgM and IgA (20 µg/ml) (109-006-064, Jackson Immunoresearch). At day 3 of B cell differentiation in vitro, activated B cells were seeded without CD40L-L stromal cells in a new 24 well-plate at 0.33x10^5 cells/ml for the T58I-t2A-BCL2, WT-t2A-BCL2 and ΔΜΒΙ-t2A-BCL2 conditions and at 1x10^5 cells/ml for the rest of the conditions, in IMDM CM containing IL-2 (20 U/ml), IL-21 (50 ng/ml) and supplements (lipid mixture 1; chemically defined (200X) and MEM amino acids solution (50X)). At day 6, the T58I-t2A-BCL2, WT-t2A-BCL2 and ΔΜΒΙ-t2A-BCL2 cells were re-seeded at 0.66x10^5 cells/ml, and the rest of the conditions at 2x10^6 cells/ml in IMDM CM containing APRIL (100 ng/ml), IL-21 (10 ng/ml), IL-6 (10 ng/ml) and supplements at 1 ml final volume per well. At day 9, the T58I-t2A-BCL2, WT-t2A-BCL2 and ΔΜΒΙ-t2A-BCL2 cells were splitted following a 1:2 ratio, and appropriate volume of the day 6 complete medium was added to all the conditions aiming at a final volume of 2 ml per well. At day 13 onwards, the T58I-t2A-BCL2, WT-t2A-BCL2 and ΔΜΒΙ-t2A-BCL2 cells were re-seeded at 0.33x10^5 cells/ml, and the rest of the conditions at 1x10^6 cells/ml in IMDM CM containing APRIL (100 ng/ml), IL-6 (10 ng/ml) and supplements at 2 ml final volume per well.

value: Peripheral blood

value: plasma-cell


title: 22Rv1_sPOM121_3


title: D13_Untransduced_DN2


title: 22Rv1_sPOM121_2


title: serum exosomes, PH047, week 16, rest

description:
PH047w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: week 16

value: rest


title: 6229009036_R01C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M


title: serum exosomes, PH045, week 12, 3hr

description:
PH045w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH045, week 12, 0hr

description:
PH045w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 22Rv1_sPOM121_1


title: CD8, 0h, RHOG, CART0077_D1

value: RHOG

value: Female


title: 22Rv1_ctrl_4

value: control


title: serum exosomes, PH063, week 0, 3hr

description:
PH063w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: Male


title: 6229009034_R06C01 whole blood

value: Y


title: CD8, 0h, SafeHarbor, CART0077_D1

value: SafeHarbor


title: 22Rv1_ctrl_3

value: Prostate cancer


title: D13_MYC.WT-BCL2_DN3


title: serum exosomes, PH045, week 0, pre

description:
PH045w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: pre


title: D13_MYC.WT-BCL2_DN1

value: Peripheral blood


title: 6229009034_R06C02 whole blood


title: 22Rv1_ctrl_2


title: 6229009034_R05C02 whole blood


title: D13_MYC.MBIIW135A-BCL2_DN3

value: plasma-cell


title: serum exosomes, PH045, week 0, 24hr

description:
PH045w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: 6229009034_R04C02 whole blood


title: D13_MYC.MBIIW135A-BCL2_DN2


title: serum exosomes, PH044, week 16, rest

description:
PH044w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: week 16


title: 6229009034_R03C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: WhiteBloodCells from Purple Top EDTA tubes

value: F


title: 6229009034_R05C01 whole blood

value: M

value: N


title: 22Rv1_ctrl_1

value: control


title: D13_Untransduced_DN1


title: D13_MYC.MBII4aamut-BCL2_DN3


title: 6229009034_R03C01 whole blood


title: serum exosomes, PH045, week 12, 24hr

description:
PH045w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: serum exosomes, PH045, week 0, 0hr

description:
PH045w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: Male


title: serum exosomes, PH045, week 0, 3hr

description:
PH045w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: ChIPseq_DU145_SMARCA5_Input

data_processing:
The Illumina TruSeq DNA kit was used for 100nt/single end reads, 4 samples were run per lane using the standard Truseq indices.  Reads are aligned to the hg38 reference with the aligner BWA followed by peak calling via macs2.
Assembly: hg38
Supplementary files format and content: big wig format; -log10 pvalues by comparing IP with input DNA

extract_protocol:
Cells were crosslinked and DNA sheared and processed for ChIP sequencing acording to standard protocols
Hi-Seq, 100nt, Single-End Read, 4 samples per lane

treatment_protocol: No treatments

value: input


title: D13_MYC.WT-BCL2_DN2


title: ChIPseq_DU145_SMARCA5_IP_2

value: Prostate cancer

value: IP


title: serum exosomes, PH044, week 12, pre

description:
PH044w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: pre

value: Female


title: D13_MYC.MBIIW135A-BCL2_DN1

value: Peripheral blood

value: plasma-cell


title: 6229009034_R02C01 whole blood

value: Y


title: D13_MYC.MBII4aamut-BCL2_DN2


title: serum exosomes, PH044, week 12, 3hr

description:
PH044w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: HITT


title: ChIPseq_DU145_SMARCA5_IP_1


title: 6229009034_R01C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F


title: ChIPseq_22Rv1_SMARCA5_Input


title: ChIPseq_22Rv1_SMARCA5_IP_2


title: D13_MYC.delMBII-BCL2_DN3


title: serum exosomes, PH044, week 12, 0hr

description:
PH044w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: ChIPseq_22Rv1_SMARCA5_IP_1


title: D13_MYC.delMBII-BCL2_DN2


title: serum exosomes, PH044, week 0, pre

description:
PH044w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496039_R06C02 whole blood

value: N


title: ChIPseq_DU145_sPOM121_Input


title: D13_MYC.delMBII-BCL2_DN1


title: serum exosomes, PH044, week 0, 3hr

description:
PH044w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: ChIPseq_DU145_sPOM121_IP_2


title: ChIPseq_DU145_sPOM121_IP_1


title: serum exosomes, PH044, week 0, 24hr

description:
PH044w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496039_R05C01 whole blood


title: 6264496039_R05C02 whole blood


title: serum exosomes, PH044, week 12, 24hr

description:
PH044w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH044, week 0, 0hr

description:
PH044w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: ChIPseq_22Rv1_sPOM121_Input


title: D13_MSCV-backbone_DN2


title: 6229009034_R01C01 whole blood


title: D13_MYC.MBII4aamut-BCL2_DN1


title: 6264496039_R04C01 whole blood


title: D13_MSCV-backbone_DN1


title: ChIPseq_22Rv1_sPOM121_IP_2


title: D13_Untransduced_DN4

tag: time point


title: 6264496039_R03C02 whole blood


title: serum exosomes, PH043, week 16, rest

description:
PH043w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: week 16

value: rest


title: serum exosomes, PH043, week 12, pre

description:
PH043w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: ChIPseq_22Rv1_sPOM121_IP_1


title: D13_Untransduced_DN3


title: 6264496039_R03C01 whole blood

value: M


title: ATACseq_DU145_SMARCA5_KD_2

data_processing:
The Illumina TruSeq DNA kit was used for 100nt/single end reads, 4 samples were run per lane using the standard Truseq indices.  Reads are aligned to the hg38 reference with the aligner BWA followed by peak calling via macs2.
Assembly: hg38
Supplementary files format and content: big wig format; -log10 pvalues by comparing sPOM121/SMARCA5 KD with control

extract_protocol:
Cells were processed for ATAC sequencing acording to standard protocols
Hi-Seq, 100nt, Single-End Read, 4 samples per lane

treatment_protocol: Soluble POM121 (sPOM121), SMARCA5 and Control Knockdowns (KD)

value: Prostate cancer

value: SMARCA5 KD


title: D13_Untransduced_DN2


title: D13_MSCV-backbone_DN3


title: 6264496039_R04C02 whole blood


title: serum exosomes, PH043, week 12, 24hr

description:
PH043w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496039_R02C02 whole blood


title: ATACseq_DU145_SMARCA5_KD_1


title: 6264496039_R02C01 whole blood


title: D13_Untransduced_DN1


title: ATACseq_DU145_SMARCA5_Cont

value: control


title: serum exosomes, PH043, week 12, 0hr

description:
PH043w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: 6264496039_R01C01 whole blood


title: D13_MYC.WT-BCL2_DN4

value: Peripheral blood


title: ATACseq_22Rv1_SMARCA5_KD_2


title: serum exosomes, PH043, week 0, pre

description:
PH043w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

value: pre


title: 6264496037_R06C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: serum exosomes, PH043, week 0, 3hr

description:
PH043w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: D13_MYC.WT-BCL2_DN2

value: plasma-cell


title: serum exosomes, PH043, week 0, 24hr

description:
PH043w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D13_MYC.WT-BCL2_DN1


title: 6264496037_R06C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: Y


title: D13_MYC.WT-BCL2_DN3


title: 6264496037_R05C02 whole blood


title: ATACseq_DU145_sPOM121_KD_2

value: sPOM121 KD


title: D13_MYC.delMBII-BCL2_DN4


title: serum exosomes, PH043, week 0, 0hr

description:
PH043w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: serum exosomes, PH042, week 16, rest

description:
PH042w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16


title: 6264496037_R05C01 whole blood

value: F

value: N


title: ATACseq_DU145_sPOM121_KD_1


title: 6264496037_R04C02 whole blood


title: D13_MYC.delMBII-BCL2_DN3


title: ATACseq_DU145_sPOM121_Cont


title: D13_MYC.delMBII-BCL2_DN2


title: 6264496037_R04C01 whole blood

value: M


title: ATACseq_22Rv1_SMARCA5_Cont

value: Prostate cancer


title: ATACseq_22Rv1_SMARCA5_KD_1

value: SMARCA5 KD


title: ATACseq_22Rv1_sPOM121_KD_2


title: serum exosomes, PH042, week 12, 24hr

description:
PH042w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: 6264496037_R03C02 whole blood


title: D13_MYC.delMBII-BCL2_DN1


title: D13_MYC.delMBI-BCL2_DN4


title: 6264496037_R03C01 whole blood


title: serum exosomes, PH042, week 0, pre

description:
PH042w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: serum exosomes, PH042, week 12, 0hr

description:
PH042w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: ATACseq_22Rv1_sPOM121_KD_1


title: 6264496037_R02C02 whole blood


title: ATACseq_22Rv1_sPOM121_Cont

value: control


title: 6264496037_R02C01 whole blood


title: serum exosomes, PH043, week 12, 3hr

description:
PH043w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: serum exosomes, PH042, week 0, 3hr

description:
PH042w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: in vivo, Palbociclib+Telaglenestat, 4

city: Barcelona

first: Míriam

last: Tarrado-Castellarnau

address: Av. Diagonal 643

country: Spain

institute: Universitat de Barcelona

data_processing:
FastQ files for each sample were obtained using CASAVA v1.8 software
Reads were aligned to the Ensembl reference genome and converted to reads per gene with the STAR software.
Assembly: hg38
Supplementary files format and content: Coma-delimited text file with raw counts for each sample.

molecule: polyA RNA

source_name: Residual xenograft tumor

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions and including a DNase (Qiagen) digestion step.
RNA-Seq libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina. Poly A+ RNA was purified using poly-T oligo-attached magnetic beads.

value: Residual xenograft tumor

value: Palbociclib+Telaglenestat


title: serum exosomes, PH042, week 12, pre

description:
PH042w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: pre


title: in vivo, Palbociclib+Telaglenestat, 3


title: serum exosomes, PH042, week 12, 3hr

description:
PH042w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D13_MYC.delMBI-BCL2_DN1

value: Peripheral blood

value: plasma-cell


title: serum exosomes, PH042, week 0, 24hr

description:
PH042w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD


title: 6264496037_R01C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: 6264496037_R01C01 whole blood


title: serum exosomes, PH041, week 16, rest

description:
PH041w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: week 16

value: rest


title: in vivo, Palbociclib+Telaglenestat, 1


title: serum exosomes, PH042, week 0, 0hr

description:
PH042w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D13_MYC.delMBI-BCL2_DN3


title: in vivo, Telaglenestat, 4

value: Telaglenestat


title: D13_MYC.delMB0-BCL2_DN2


title: serum exosomes, PH041, week 12, pre

description:
PH041w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D13_MYC.delMBI-BCL2_DN2


title: in vivo, Telaglenestat, 3


title: D13_MYC.delMB0-BCL2_DN1


title: serum exosomes, PH041, week 12, 3hr

description:
PH041w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496023_R05C02 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: F

value: Y


title: D13_MSCV-backbone_DN4


title: in vivo, Telaglenestat, 2


title: 6264496023_R05C01 whole blood


title: serum exosomes, PH041, week 12, 24hr

description:
PH041w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12

value: Female


title: in vivo, Telaglenestat, 1


title: serum exosomes, PH041, week 12, 0hr

description:
PH041w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496023_R04C02 whole blood

value: N


title: D13_MSCV-backbone_DN3


title: in vivo, Palbociclib, 5

value: Residual xenograft tumor

value: Palbociclib


title: 6264496023_R06C02 whole blood


title: D13_MSCV-backbone_DN2


title: serum exosomes, PH041, week 0, pre

description:
PH041w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: week 0


title: in vivo, Palbociclib+Telaglenestat, 2

value: Palbociclib+Telaglenestat


title: D13_MYC.delMB0-BCL2_DN4

value: Peripheral blood

value: plasma-cell


title: D13_MSCV-backbone_DN1


title: in vivo, Palbociclib, 4


title: serum exosomes, PH041, week 0, 3hr

description:
PH041w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496023_R04C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: 6264496023_R03C02 whole blood


title: serum exosomes, PH047, week 12, 24hr

description:
PH047w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: Male


title: in vivo, Palbociclib, 3


title: D06_Untransduced_DN4

value: plasmablast


title: 6264496023_R03C01 whole blood


title: serum exosomes, PH041, week 0, 24hr

description:
PH041w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D06_Untransduced_DN3


title: in vivo, Palbociclib, 2


title: serum exosomes, PH041, week 0, 0hr

description:
PH041w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496023_R02C02 whole blood


title: in vivo, Palbociclib, 1


title: D06_Untransduced_DN2


title: 6264496023_R02C01 whole blood


title: serum exosomes, PH039, week 16, rest

description:
PH039w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: in vivo, control, 3

value: Control


title: D06_Untransduced_DN1


title: serum exosomes, PH039, week 12, pre

description:
PH039w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12

value: pre


title: 6264496023_R01C02 whole blood

value: M

value: Y


title: in vivo, control, 2

value: Residual xenograft tumor


title: serum exosomes, PH039, week 12, 3hr

description:
PH039w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: Female


title: 6264496023_R01C01 whole blood

value: F


title: D06_MYC.WT-BCL2_DN4

value: Peripheral blood


title: in vivo, control, 1


title: serum exosomes, PH039, week 12, 24hr

description:
PH039w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496019_R06C02 whole blood


title: D06_MYC.WT-BCL2_DN3


title: ex vivo,  Palbociclib+Telaglenestat, 3

source_name: Cell culture

value: Cell culture

value: Palbociclib+Telaglenestat


title: 6264496019_R06C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: ex vivo,  Palbociclib+Telaglenestat, 2


title: D06_MYC.WT-BCL2_DN1


title: serum exosomes, PH039, week 0, pre

description:
PH039w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

value: week 0


title: 6264496019_R05C02 whole blood

value: N


title: ex vivo, Palbociclib+Telaglenestat, 1


title: D06_MYC.delMBII-BCL2_DN4

value: plasmablast


title: serum exosomes, PH039, week 0, 3hr

description:
PH039w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D06_MYC.delMBII-BCL2_DN3


title: serum exosomes, PH039, week 0, 24hr

description:
PH039w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496019_R04C02 whole blood


title: serum exosomes, PH039, week 0, 0hr

description:
PH039w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D06_MYC.delMBII-BCL2_DN2


title: ex vivo, Telaglenestat, 2

value: Telaglenestat


title: 6264496019_R03C02 whole blood


title: ex vivo, Telaglenestat, 1


title: serum exosomes, PH038, week 16, rest

description:
PH038w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 16

value: rest


title: serum exosomes, PH038, week 12, pre

description:
PH038w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12

value: pre


title: D06_MYC.delMBI-BCL2_DN4


title: ex vivo, Palbociclib, 3

value: Palbociclib


title: ex vivo, Palbociclib, 2


title: 6264496019_R05C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted

value: M


title: D06_MYC.delMBI-BCL2_DN3


title: ex vivo, Telaglenestat, 3


title: 6264496019_R02C01 whole blood


title: ex vivo, Palbociclib, 1


title: 6264496019_R01C02 whole blood


title: D06_MYC.delMBI-BCL2_DN2


title: serum exosomes, PH039, week 12, 0hr

description:
PH039w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

value: Female


title: D06_MYC.WT-BCL2_DN2

value: Peripheral blood


title: ex vivo, control, 3

value: Cell culture

value: Control


title: serum exosomes, PH045, week 16, rest

description:
PH045w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: TRAD

value: Male


title: 6264496019_R01C01 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: F


title: ex vivo, control, 2


title: D06_MYC.delMB0-BCL2_DN4

value: plasmablast


title: 6264496019_R02C02 whole blood

value: N


title: D06_MYC.delMBII-BCL2_DN1


title: serum exosomes, PH038, week 12, 0hr

description:
PH038w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT


title: serum exosomes, PH038, week 0, pre

description:
PH038w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0


title: 6264496009_R06C02 whole blood

value: Y


title: ex vivo, control, 1


title: 6264496009_R06C01 whole blood


title: serum exosomes, PH038, week 0, 3hr

description:
PH038w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D06_MYC.delMB0-BCL2_DN3


title: serum exosomes, PH038, week 12, 3hr

description:
PH038w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12


title: D06_MYC.delMB0-BCL2_DN2


title: serum exosomes, PH038, week 12, 24hr

description:
PH038w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496009_R05C02 whole blood


title: serum exosomes, PH038, week 0, 24hr

description:
PH038w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: CD226- CD8 T cells replicate-1

city: Worcester

first: Tomoyo

last: Shinkawa

address: 55 N Lake Ave

institute: UMass Chan Medical School

description:
Library name: Sample4
L1CD226neg

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1. UMI-based de-duplication was performed using fastp (v.0.23.1) simultaneously. Trimmed and de-duplicated reads were then mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner (v.2.5.2b). Normalization and differential gene expression analysis were performed using DESeq2 R package (v1.38.3).
Assembly: GRCm38
Supplementary files format and content: csv files include normalized counts for each sample

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was extracted from sorted cells stored in RNAprotect (QIAGEN) using Direct-zol RNA Microprep kit (Zymo research) according to the manufacturer’s instructions.
RNA sequencing with poly(A) selection and library construction were performed by Azenta (AZENTA life sciences).

value: Lung

tag: strain

value: C57BL/6 mice infected with M. tuberculosis for 24-28 weeks

value: CD8 T cells

value: CD226- CD8 T cells


title: D06_MYC.delMBI-BCL2_DN1

tag: tissue

value: Peripheral blood


title: CD226- CD8 T cells replicate-3

description:
Library name: Sample6
L3CD226neg


title: serum exosomes, PH034, week 16, rest

description:
PH034w16rst_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes

tag: participant id

value: week 16

value: rest

value: Female


title: CD226- CD8 T cells replicate-2

description:
Library name: Sample5
L2CD226neg


title: 6264496009_R04C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes


title: CD226+ CD8 T cells replicate-3

description:
Library name: Sample3
L3CD226pos

value: CD226+ CD8 T cells


title: D06_MSCV-backbone_DN4

value: plasmablast


title: serum exosomes, PH034, week 12, pre

description:
PH034w12pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

tag: treatment

value: pre


title: D06_MSCV-backbone_DN3


title: 6264496009_R04C01 whole blood

value: F

value: N


title: D06_MSCV-backbone_DN2


title: CD226+ CD8 T cells replicate-2

description:
Library name: Sample2
L2CD226pos


title: 6264496009_R03C01 whole blood


title: CD226+ CD8 T cells replicate-1

description:
Library name: Sample1
L1CD226pos


title: serum exosomes, PH034, week 12, 3hr

description:
PH034w12h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: HITT

tag: week


title: 6264496009_R05C01 whole blood


title: D06_MYC.delMB0-BCL2_DN1


title: 6264496009_R02C02 whole blood


title: serum exosomes, PH038, week 0, 0hr

description:
PH038w0h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 0

tag: time


title: serum exosomes, PH034, week 12, 24hr

description:
PH034w12h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: week 12

tag: Sex


title: D06_MSCV-backbone_DN1


title: serum exosomes, PH034, week 12, 0hr

description:
PH034w12h0_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: D20_Untransduced_DN1

value: plasma-cell


title: SVF, KO, Input, ChIP_2

city: Taipei

first: Chung-Lin

last: Jiang

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description: Library name: p21iWAT_SVF_KO_input_2_ChIPseq

data_processing:
All ChIP-seq FASTQ reads were trimmed for the adapter and low-quality bases using Trim-galore tools (v0.6.7), then followed by alignment to mouse GRCm38/mm10 genome using Bowtie2 aligner (v2.4.2) with the default setting. BAM files were sorted and deduplicated by SAMTools (v1.13). Significant H3K9ac, H3K14ac, and H3K9bhb peaks were generated using MACS2 (v2.2.9.1) peak caller with a cutoff value: -p-value < 0.05. MACS2-identified peaks were subjected to BEDtools (v2.3.0) to determine overlapping regions of two interested data and Annotation analysis provided by HomerTools (v4.1) to evaluate ChIP enrichment on genomic features. Bigwig files were generated by DeepTools (v3.3.1) bamcoverage, and these were visualized in Integrative Genomics Viewer (IGV, v2.17). The differential coverages were normalized to input coverage by subtraction, and the comparison between treatment and control coverage was conducted by log2 foldchange using DeepTools bamCompare with the following parameters: –operation subtract, –centerReads, –normalizeUsing CPM, –scaleFactorsMethod None. Both ChIP-seq and differential coverages were subjected to DeepTools computeMatrix and plotHeatmap for generating heatmap.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: inguinal white adipose tissue

extract_protocol:
Cross-linked with 1% formaldehyde for 5 min at 37°C, and quenched with 125 mM glycine for 5 min at 37°C.  After cell lysis, chromatin was sonicated using a Bioruptor (1.5 mL tube)
Sequencing libraries were constructed using a NEBNext Ultra II DNA Library Prep kit (New England Biolabs, MA, USA).

value: inguinal white adipose tissue

value: stromal vascular fraction

value: wild type


title: D20_T58I-t2A-BCL2_DN4

value: Peripheral blood


title: 6264496009_R02C01 whole blood


title: 6264496009_R01C02 whole blood


title: serum exosomes, PH034, week 0, pre

description:
PH034w0pre_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: serum exosomes


title: D20_T58I-t2A-BCL2_DN3


title: SVF, KO, H3K9bhb, ChIP_2

description: Library name: p21iWAT_SVF_KO_H3K9bhb_2_ChIPseq


title: 6264496023_R06C01 whole blood

description: Sample collected in EDTA tube, DNA for methylation was extracted


title: 6264496009_R01C01 whole blood

value: Y


title: serum exosomes, PH034, week 0, 3hr

description:
PH034w0h3_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt

value: Female


title: D20_T58I-t2A-BCL2_DN1


title: serum exosomes, PH034, week 0, 24hr

description:
PH034w0h24_se
serum_exosomes_raw_counts.txt
serum_exosomes_TMM_counts.txt


title: 6264496006_R06C02 whole blood

value: WhiteBloodCells from Purple Top EDTA tubes

value: M