title: Heterozygous Ptn E/P deletion from F121-9, ESC status, early S fraction, replicate 2

description:
Library name: D9ESR2_E
nascent DNA from early S fraction


title: white_H3K36me3_D15

status: Public on Feb 01 2026

type: SRA

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Library name: 35-22578_S89

library_source: genomic

data_processing:
FASTQ sequences from H3K27ac, H3K4me3, H3K4me1, H3K27me3, H3K36me3 and H3K9me3 ChIPs  were aligned to hg38 using Bowtie2 v2.4.5
Peaks were detected using MACS2 v2.2.7.1 with default narrow option for H3K4me3 and H3K27ac and broad option for H3K4me1, H3K36me3 and H3K27me3.  H3K9me3 peaks were called using EDD [protocol].
ChIP-seq read counts were normalized to library size using reads per genome coverage (RPGC) method in deepTools.
Assembly: hg38
Supplementary files format and content: narrowPeak, broadPeak are MACS2 output files, whilst _peaks.bed are bed files showing genomic enrichments output by EDD.
Supplementary files format and content: bigwig files are RPGC normalised coverage tracks.

molecule: genomic DNA

organism: Homo sapiens

source_name: subcutaneous abdominal adipose

growth_protocol: Primary ASCs were isolated from subcutaneous fat obtained by liposuction from a female donor (age 45; BMI 20,9 kg/m2). ASCs were cultured in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum and 20 ng/ml basic fibroblast growth factor (proliferation medium).

extract_protocol:
Cells were fixed for 10 min with 1% formaldehyde, lysed in 50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS, protease inhibitors and Na-butyrate, and sonicated in a Picorupter (Diagnode) into ~200 bp fragments. After sedimentation, the supernatant was diluted 10 times in RIPA buffer and incubated with H3K4me3 (Diagenode c15410003), H3K4me1 (Diagenode c15410037) or H3K27ac (Diagenode c15410174) antibodies (each at 2.5 µg/106 cells) coupled to magnetic Dynabeads Protein A/G (Invitrogen) for 2 h at 4°C. ChIP samples were washed, cross-links were reversed and DNA was eluted for 2 h at 68°C in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS and 50 ng/µl Proteinase K. DNA was purified using phenol-chloroform isoamylalcohol and dissolved in H2O. For Day 15 differentiated white and beige adipocytes, cells were trypsinized, resuspended in HBSS, 0.5% BSA, and centrifuged 200g for 5 min to isolate floating mature adipocytes. Purified nuclei were then fixed and processed as cell samples
ChIP-seq libraries were prepared using a Microplex kit (Diagenode) and sequenced with 150-bp paired-end reads on an Illumina NovaSeq.

treatment_protocol: Upon confluency, fibroblast growth factor was removed, and cells cultured for 72 h in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum (basal medium) before induction of differentiation (day 0: D0). For white adipogenic differentiation, ASCs were induced with a cocktail of 0.5 µM 1-methyl-3 isobutyl xanthine, 1 µM dexamethasone, 10 µg/ ml insulin and 200 µM indomethacin in basal medium. Differentiation media was renewed every 3 days until day 9, after which cells were maintained in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum and 10 µg/ ml insulin. For beige adipogenic differentiation, media were supplemented with 1 µM Rosiglitazone (Sigma, R2408) until day 15. Samples were harvested on day (D0), then D1, D3 and D15 after induction.

tag: tissue

value: subcutaneous abdominal adipose

tag: cell type

value: primary adipose stem cells

tag: time

tag: treatment

value: white adipogenic differentiation

tag: chip antibody


title: 113V12PL

city: Dublin

first: Walter

last: Kolch

address: School of Medicine, University College Dublin, Belfield, Dublin 4.

country: Ireland

institute: Systems Biology Ireland

description: Library name: GTG-360-B2-58

library_source: transcriptomic

data_processing:
The reads were aligned and quantified  to the Genome Reference Consortium Human Build 38 using the R package Rsubread with default settings.
Assembly: Assembly: hg38
Supplementary files format and content: Txt file with raw gene counts for each sample

molecule: total RNA

source_name: skin

extract_protocol:
RNA isolation was then performed using a Fibrous RNA isolation kit (Qiagen) following the manufacturer’s instruction.
cDNA was created from 100ng of input RNA using theTruSeq Stranded mRNA input kit, sequencing 50 bp paired end stranded

value: skin

tag: disease

value: Psoriasis

tag: lesional (ls)_or_nonlesional_(nl)

value: NL

tag: batch


title: 112V12PL

description: Library name: 19-508-042


title: beige_H3K9me3_D3

description: Library name: 17-23706_S2

value: beige adipogenic differentiation


title: 112V12L

description: Library name: 19-508-041

value: LS


title: 112V1L

description: Library name: 19-508-043


title: 114V1PL

description: Library name: GTG-360-B1-68


title: 112V1PL

description: Library name: 19-508-044


title: Homozygous Ptn E/P deletion from F121-9, ESC status, early S fraction, replicate 2

city: San Diego

first: David

middle: M

last: Gilbert

state: CA

address: 3525 John Hopkins Ct., Ste. 200

country: USA

institute: San Diego BioMEd

description:
Library name: B8ESR2_E
nascent DNA from early S fraction

data_processing:
Repli-seq and Bru-seq data processing methods have been described in PMC6546437. Basically, sequencing reads were mapped to mm10 then reads for 129 and cas alleles were parsed using SNPsplit.
Assembly: mm10
Supplementary files format and content: bedgraph files, log2(E/L) for each allele (129 or cas), scaled and LOESS smoothed in 300kb bins

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: 2i media for mESC maintenance and RHB-A for NPC differentiation. Both have been described in PMC5991511.

extract_protocol:
Repli-seq and Bru-seq sample extraction methods have been described in PMC6546437.
Repli-seq and Bru-seq library preparation methods have been described in PMC6546437.

treatment_protocol: For tet promoter activation, doxycycline hyclate was added to the culture media (concentration and duration indicated in the file name or figre legends in PMC11838563).

value: embryonic stem cell

tag: cell line

value: biol rep 2


title: 111V1PL

description: Library name: 19-508-040


title: 111V1L

description: Library name: 19-508-039


title: 113V12L

description: Library name: GTG-360-B2-57


title: TRE promoter upstream of Ptn gene, reversal from doxycycline 2000ng/mL doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_Rev_L_Rep2
nascent DNA from late S fraction

value: F121:R26puroR-M2rtTA;  Ptn^TRE


title: beige_H3K9me3_D15

description: Library name: 34-22577_S81


title: 111V12PL

description: Library name: 19-508-038


title: beige_H3K9me3_D1

description: Library name: 11-23700_S20


title: TRE promoter upstream of Ptn gene, reversal from doxycycline 2000ng/mL doxycycline, late S fraction, replicate 3

description:
Library name: TRE_Ptn_Rev_L_Rep3
nascent DNA from late S fraction

value: biol rep 3


title: 111V12L

description: Library name: 19-508-037


title: 110V1PL

description: Library name: GTG-360-B1-64


title: beige_H3K4me3_D3

description: Library name: 13-23702_S15


title: 110V1L

description: Library name: GTG-360-B1-63


title: TRE promoter upstream of Ptn gene, reversal from doxycycline 2000ng/mL doxycycline, early S fraction, replicate 3

description:
Library name: TRE_Ptn_Rev_E_Rep3
nascent DNA from early S fraction


title: 110V12PL

description: Library name: GTG-360-B1-62


title: 109V1PL

description: Library name: 19-508-036


title: 110V12L

description: Library name: GTG-360-B1-61


title: 109V1L

description: Library name: 19-508-035


title: 109V12PL

description: Library name: 19-508-034


title: beige_H3K4me1_D3

description: Library name: 15-23704_S13


title: TRE promoter upstream of Ptn gene, reversal from doxycycline 2000ng/mL doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_Rev_E_Rep2
nascent DNA from early S fraction


title: beige_H3K4me1_D1

description: Library name: 9-23698_S14


title: TRE promoter upstream of Ptn gene, reversal from doxycycline 2000ng/mL doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_Rev_L_Rep1
nascent DNA from late S fraction

value: biol rep 1


title: beige_H3K4me3_D1

description: Library name: 7-23696_S11


title: 109V12L

description: Library name: 19-508-033


title: 108V1PL

description: Library name: GTG-360-B1-60


title: beige_H3K36me3_D3

description: Library name: 18-23707_S10


title: 103V1PL

description: Library name: 20-559-020


title: 108V1L

description: Library name: GTG-360-B1-59


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 24hr, late S fraction, replicate 1

description:
Library name: TRE_Ptn_24h_L_Rep1
nascent DNA from late S fraction


title: 103V1L

description: Library name: 20-559-019


title: 102V1PL

description: Library name: 20-559-016


title: TRE promoter upstream of Ptn gene, reversal from doxycycline 2000ng/mL doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_Rev_E_Rep1
nascent DNA from early S fraction


title: 103V12PL

description: Library name: 20-559-022


title: beige_H3K36me3_D15

description: Library name: 36-22579_S84


title: beige_H3K36me3_D1

description: Library name: 12-23701_S16


title: 103V12L

description: Library name: 20-559-021


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 24hr, early S fraction, replicate 2

description:
Library name: TRE_Ptn_24h_E_Rep2
nascent DNA from early S fraction


title: beige_H3K27me3_D3

description: Library name: 16-23705_S7


title: 102V1L

description: Library name: 20-559-015


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 24hr, late S fraction, replicate 2

description:
Library name: TRE_Ptn_24h_L_Rep2
nascent DNA from late S fraction


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 24hr, early S fraction, replicate 1

description:
Library name: TRE_Ptn_24h_E_Rep1
nascent DNA from early S fraction


title: beige_H3K27ac_D3

description: Library name: 14-23703_S9


title: 102V12L

description: Library name: 20-559-017


title: beige_H3K27me3_D1

description: Library name: 10-23699_S19


title: 101V1PL2

description: Library name: GTG-360-B2-56


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 12hr, late S fraction, replicate 2

description:
Library name: TRE_Ptn_12h_L_Rep2
nascent DNA from late S fraction


title: 101V1L2

description: Library name: GTG-360-B2-54


title: 101V1PL1

description: Library name: GTG-360-B2-55


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 12hr, late S fraction, replicate 1

description:
Library name: TRE_Ptn_12h_L_Rep1
nascent DNA from late S fraction


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 12hr, early S fraction, replicate 2

description:
Library name: TRE_Ptn_12h_E_Rep2
nascent DNA from early S fraction


title: 101V1L1

description: Library name: GTG-360-B2-53


title: beige_H3K27ac_D1

description: Library name: 8-23697_S4


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 12hr, early S fraction, replicate 3

description:
Library name: TRE_Ptn_12h_E_Rep3
nascent DNA from early S fraction


title: 102V12PL

description: Library name: 20-559-018


title: white_D1-rep2

description: Library name: 47-wD1-rep2-23653_S125

data_processing:
RNA-seq reads were filtered to remove low-quality reads using fastp v 0.20.1.
Filtered reads were aligned to the hg38 genome (GENCODE 32 annotation) with hisat2 v2.1.0.
To calculate gene-level counts, featureCounts in Subread v2.0.1 was used with options -M and --fraction.
Coverage tracks at 10 bp binsize were produced with deepTools v3.5.5 from alignments
Assembly: hg38; gencode v32
Supplementary files format and content: bigwig: RNA-seq coverage in 10bp bins
Supplementary files format and content: featureCounts.counts: tab delimited read counts in genes for all samples

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from triplicate experiments using the RNAeasy mini kit (Qiagen).
Sequencing libraries were prepared using the KAPA mRNA HyperPrep kit (Roche) and sequenced on a Novaseq 6000 (Illumina).

treatment_protocol: Upon confluency, fibroblast growth factor was removed, and cells cultured for 72 h in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum (basal medium) before induction of differentiation (day 0: D0). For white adipogenic differentiation, ASCs were induced with a cocktail of 0.5 µM 1-methyl-3 isobutyl xanthine, 1 µM dexamethasone, 10 µg/ ml insulin and 200 µM indomethacin in basal medium. Differentiation media was renewed every 3 days until day 9 (D9), after which cells were maintained in DMEM/F12 (17.5 mM glucose) with 10% fetal calf serum and 10 µg/ ml insulin. For beige adipogenic differentiation, media were supplemented with 1 µM Rosiglitazone (Sigma, R2408) until day 15 (D15). Samples were harvested 24h (D1) and 72h (D3) after induction.

tag: replicate


title: white_D1-rep3

description: Library name: 48-wD1-rep3-23654_S82


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 12hr, late S fraction, replicate 3

description:
Library name: TRE_Ptn_12h_L_Rep3
nascent DNA from late S fraction


title: CD4+T cells，KO-3

city: shanghai

first: xiaoxue

last: li

country: China

institute: Shanghai Jiao Tong University

description: Library name: sample6

data_processing:
The MACS2 software was used to detect the binding sites of the data after removing duplicates and ribosome sequences, that is, to find the enrichment regions of the reads on the stained surfaces in this experiment as characteristic peaks for subsequent analysis. Annotate the peaks using the R package ChIPseeker
Assembly: mm10
Supplementary files format and content: peak annotations and bw files for each samples

source_name: Spleen

extract_protocol:
1.Lysate the cells to extract the nuclei. 50,000 complete live cells were extracted. The number of live cells was detected using trypan blue, with 0.4% Trypan blue at 1 μ l and 9 μ l Cell suspension, stained for 3-5 minutes, microscopic examination technique.Add 50 μ l of pre-cooled RSB (add 0.1% NP40, 0.1% Tween-20, 0.01% digitalis soap) Invert three times and incubate on ice for 3 minutes.Add 1ml of pre-cooled RSB (add only 0.1% Tween-20), invert three times to mix well, and separate 500xg at 4°C. Wait for 5 minutes and discard the supernatant. 2.Transposase treatment Add 50 μ l of transposition mix, and incubate at 1000RPM at 37° C for 30 minutes using Qiagen MinElute PCR Purification Kit purifies DNA. DNA fragments were purified using the Zymo DNA Clean and Concentrator-5 Kit, with 10 μ l of 10 mm Tris Dissolve in buffer (PH8) and store at -20℃. 3.PCR amplification Search for the optimal number of amplification cycles. DNA fragments were purified using the Zymo DNA Clean and Concentrator-5 Kit, with 10 μ l of 10 mm Tris Dissolve in buffer (PH 8). Store at -20°C. 4. On-machine sequencing The library was sequenced through the illumina HiSeq/NextSeq platform after passing the detection.
(1) clean data was obtained by removing the joint sequences and low-quality sequences using the Trimmomatic[2] program; (2) Use the Fastqc[3] program to count the data volume of clean data;(3) Use the bowtie2[4] program to align the clean data to the reference genome; (4) ATAC-SEQ-related quality control; (5) peak-calling on the genome using MACS2[4]; (6) Use the MEME[5] tool for motif detection of the binding peak; (7) Perform ChIPseeker[6] for peak annotation and screen the genes associated with the binding sites for functional enrichment; (8) Use DiffBind[7] for inter-sample difference analysis.

value: Spleen

value: CD4+T cell

tag: genotype

value: SUB1 knockout

value: EAE model


title: CD4+T cells，KO-2

description: Library name: sample5


title: CD4+T cells，WT-2

description: Library name: sample2

value: WT


title: white_D1-rep1

description: Library name: 46-wD1-rep1-23652_S118

value: subcutaneous abdominal adipose

value: primary adipose stem cells


title: CD4+T cells，KO-1

description: Library name: sample4


title: Supp13 UTUC Sample 112

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description: Library name: UTUC_RNAseq_PT112

data_processing:
RNA-seq sequencing reads were aligned against human genome assembly hg19 by STAR 2-pass alignment. Gene level raw read count values were computed by using the R package GenomicAlignments over aligned reads with UCSC KnownGene in hg19 as the base gene model. The Union counting mode was used and only mapped paired reads after alignment quality filtering were considered. Finally, gene level FPKM (Fragments Per Kilobase Million) and TPM (Transcripts Per Million) values were computed by the R package DESeq2. Batch corrected TPM expression matrix was derived by the ComBat function implemented by the R package sva.
Assembly: hg19
Supplementary files format and content: Compressed Tab-delimited files, including raw count file and batch-corrected log1p(TPM) count file
Supplementary files format and content: Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.log1p_tpm.maskid.txt (batch corrected log1p(TPM) values)

source_name: Upper Tract Urothelial Carcinoma

extract_protocol:
Total RNA from frozen tissue was isolated using Trizol (Thermo Fisher Scientific) and the quantity and quality of the resulting RNA was measured using an Agilent 2100 Bioanalyzer.
The TruSeq RNA Library Prep Kit v2 (Illumina) was used for library preparation, followed by sequencing (55 million paired end reads) on an Illumina HiSeq 2500.

value: Upper Tract Urothelial Carcinoma

value: tissue

tag: io cohort

value: Y

value: BT


title: Supp13 UTUC Sample 111

description: Library name: UTUC_RNAseq_PT111


title: CD4+T cells，WT-1

description: Library name: sample1


title: Supp13 UTUC Sample 110

description: Library name: UTUC_RNAseq_PT110


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 6hr, late S fraction, replicate 3

description:
Library name: TRE_Ptn_06h_L_Rep3
nascent DNA from late S fraction


title: Supp13 UTUC Sample 113

description: Library name: UTUC_RNAseq_PT113

value: S


title: CD4+T cells，WT-3

description: Library name: sample3


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 12hr, early S fraction, replicate 1

description:
Library name: TRE_Ptn_12h_E_Rep1
nascent DNA from early S fraction

value: embryonic stem cell


title: beige_D3-rep3

description: Library name: 45-bD3-rep3-23651_S112

value: beige adipogenic differentiation


title: Supp13 Lung-Met Sample 109

description: Library name: UTUC_RNAseq_PT109

source_name: Lung-Met

value: Lung-Met


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 6hr, late S fraction, replicate 2

description:
Library name: TRE_Ptn_06h_L_Rep2
nascent DNA from late S fraction

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 2


title: beige_D3-rep2

description: Library name: 43-bD3-rep2-23649_S99


title: Supp13 UTUC Sample 108

description: Library name: UTUC_RNAseq_PT108


title: beige_D1-rep3

description: Library name: 44-bD1-rep3-23650_S105


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 6hr, late S fraction, replicate 1

description:
Library name: TRE_Ptn_06h_L_Rep1
nascent DNA from late S fraction

value: biol rep 1


title: Supp13 UTUC Sample 106

description: Library name: UTUC_RNAseq_PT106


title: Supp13 Lung-Met Sample 104

description: Library name: UTUC_RNAseq_PT104


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 6hr, early S fraction, replicate 3

description:
Library name: TRE_Ptn_06h_E_Rep3
nascent DNA from early S fraction

value: biol rep 3


title: beige_D1-rep2

description: Library name: 42-bD1-rep2-23648_S93


title: beige_D1-rep1

description: Library name: 40-bD1-rep1-23646_S81


title: Supp13 UTUC Sample 105

description: Library name: UTUC_RNAseq_PT105


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 6hr, early S fraction, replicate 1

description:
Library name: TRE_Ptn_06h_E_Rep1
nascent DNA from early S fraction


title: Supp13 UTUC Sample 102

description: Library name: UTUC_RNAseq_PT102

value: BA


title: beige_D3-rep1

description: Library name: 41-bD3-rep1-23647_S87


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 6hr, early S fraction, replicate 2

description:
Library name: TRE_Ptn_06h_E_Rep2
nascent DNA from early S fraction


title: MSK100 UTUC Sample 100

description: Library name: UTUC_RNAseq_PT100

value: N


title: Supp13 UTUC Sample 101

description: Library name: UTUC_RNAseq_PT101

value: AV


title: MSK100 UTUC Sample 99

description: Library name: UTUC_RNAseq_PT099


title: Supp13 Lung-Met Sample 103

description: Library name: UTUC_RNAseq_PT103


title: HEK293 POLG-D274A knock-in cell, HTO

city: Berlin

first: Leif

last: Ludwig

address: Hannoversche Str. 28

country: Germany

institute: Berlin Institute for Medical Systems Biology

description:
Library name: HEK293_POLG_D274A _HTO
Hashtag-derived oligonucleotide (HTO)
HTO library: Reads1 contains UMI, Reads2 contains cell barcode, Read3 file contains Hashtag antibodies derived Tag reads

library_source: other

data_processing:
Raw fastq files/sequencing reads were aligned to the mtDNA blacklist modified hg38 reference genome using CellRanger-ATAC count (v2.1.0) to generate possorted_bam.bam, fragments.tsv.gz and filtered_peak_bc_matrix.h5
The cell hashtag tag abundances were quantified using ASAP_to_kite.py (https://github.com/caleblareau/asap_to_kite), followed by the kallisto, bustools, and kite pipeline.
Assembly: hg38
Supplementary files format and content: CellRanger output files: singlecell.csv, fragments.tsv.gz, fragments.tsv.gz.tbi and filtered_peak_bc_matrix.h5
Supplementary files format and content: kb-kite output files: featurecounts.barcodes.txt, featurecounts.genes.txt, and featurecounts.mtx
Library strategy: CITE-seq

molecule: protein

growth_protocol: Control and KI36 HEK293 cell lines were cultured in basal medium Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% [v/v] FBS Standard, 50 µg/L Uridine, and 1 U/ml Pen-Strep. KIA2 HEK293 cell lines were supplemented additionally with 50 µg/ml Hygromycin B, and 15 µg/ml Blasticidin S Hydrochloride without the induction of mitoEagI.

extract_protocol:
Single cells were encapsulated in  Gel-Beads-in emulsion (GEMs) according to the manufacturer’s instructions (CG000209-Rev F) with the Chromium Controller and Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (PN-1000176) with minor modification and sample multiplexing with TotalSeq-A hashtag antibodies.
ASAP-seq libraries were generated as previously described (PMID: 34083792)

value: mixed sample (WT, POLG-D274A)

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0251 anti-human Hashtag 1 Antibody, TotalSeq-B0252 anti-human Hashtag 2 Antibody, TotalSeq-B0253 anti-human Hashtag 3 Antibody


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 3hr, late S fraction, replicate 3

description:
Library name: TRE_Ptn_03h_L_Rep3
nascent DNA from late S fraction


title: MSK100 UTUC Sample 97

description: Library name: UTUC_RNAseq_PT097

value: Upper Tract Urothelial Carcinoma

value: tissue


title: HEK293 POLG-D274A knock-in cell, scATAC

description:
Library name: HEK293_POLG_D274A _mtscATAC
Tn5-derived chromatin accessibity profile
ATAC: Read1 and Read3 files contains  ATAC sequence, Reads2 contains cell barcode

library_source: genomic single cell

data_processing:
Raw fastq files/sequencing reads were aligned to the mtDNA blacklist modified hg38 reference genome using CellRanger-ATAC count (v2.1.0) to generate possorted_bam.bam, fragments.tsv.gz and filtered_peak_bc_matrix.h5
The cell hashtag tag abundances were quantified using ASAP_to_kite.py (https://github.com/caleblareau/asap_to_kite), followed by the kallisto, bustools, and kite pipeline.
Assembly: hg38
Supplementary files format and content: CellRanger output files: singlecell.csv, fragments.tsv.gz, fragments.tsv.gz.tbi and filtered_peak_bc_matrix.h5
Supplementary files format and content: kb-kite output files: featurecounts.barcodes.txt, featurecounts.genes.txt, and featurecounts.mtx

value: ATAC


title: Supp13 UTUC Sample 107

description: Library name: UTUC_RNAseq_PT107

value: Y

value: BT


title: effect of marennine on macrophages D mar

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

description: Library name: P22T044

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using STAR
Assembly: hg38
Supplementary files format and content: Count matrix (raw counts) was obtained using DESeq2. Format is csv.

source_name: macrophages

growth_protocol: Human CD14+ monocytes were cultured in presence of 80 ng/mL of MCSF for 6 days.

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit (Illumina). 500 ng of RNA was used for each sample. Sequencing was performed on NovaSeq 6000 (Illumina) (100-nt-length reads, paired end).

treatment_protocol: Cells were exposed to marennine (100 microgram/mL) or vehicle (same volume of H2O) for 8h.

value: macrophages

tag: donor

value: D

value: marennine


title: effect of marennine on macrophages D veh

description: Library name: P22T043

value: vehicle


title: MSK100 UTUC Sample 95

description: Library name: UTUC_RNAseq_PT095

value: S


title: MSK100 UTUC Sample 94

description: Library name: UTUC_RNAseq_PT094


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 3hr, early S fraction, replicate 3

description:
Library name: TRE_Ptn_03h_E_Rep3
nascent DNA from early S fraction

value: embryonic stem cell

value: F121:R26puroR-M2rtTA;  Ptn^TRE

value: biol rep 3


title: MSK100 UTUC Sample 98

description: Library name: UTUC_RNAseq_PT098


title: MSK100 UTUC Sample 93

description: Library name: UTUC_RNAseq_PT093

value: N


title: MSK100 UTUC Sample 96

description: Library name: UTUC_RNAseq_PT096


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 3hr, late S fraction, replicate 2

description:
Library name: TRE_Ptn_03h_L_Rep2
nascent DNA from late S fraction

value: biol rep 2


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 3hr, late S fraction, replicate 1

description:
Library name: TRE_Ptn_03h_L_Rep1
nascent DNA from late S fraction

value: biol rep 1


title: effect of marennine on macrophages C veh

description: Library name: P22T041

value: C


title: MSK100 UTUC Sample 91

description: Library name: UTUC_RNAseq_PT091

value: Upper Tract Urothelial Carcinoma


title: MSK100 UTUC Sample 89

description: Library name: UTUC_RNAseq_PT089

value: tissue


title: effect of marennine on macrophages B mar

description: Library name: P22T040

value: B


title: MSK100 UTUC Sample 88

description: Library name: UTUC_RNAseq_PT088


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 3hr, early S fraction, replicate 2

description:
Library name: TRE_Ptn_03h_E_Rep2
nascent DNA from early S fraction


title: TRE promoter upstream of Ptn gene, 16000ng/mL doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_D1600_L_Rep2
nascent DNA from late S fraction


title: MSK100 UTUC Sample 86

description: Library name: UTUC_RNAseq_PT086


title: effect of marennine on macrophages C mar

description: Library name: P22T042


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline 3hr, early S fraction, replicate 1

description:
Library name: TRE_Ptn_03h_E_Rep1
nascent DNA from early S fraction


title: MSK100 UTUC Sample 87

description: Library name: UTUC_RNAseq_PT087


title: TRE promoter upstream of Ptn gene, 16000ng/mL doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_D1600_L_Rep1
nascent DNA from late S fraction


title: MSK100 UTUC Sample 84

description: Library name: UTUC_RNAseq_PT084


title: effect of marennine on macrophages B veh

description: Library name: P22T039


title: MSK100 UTUC Sample 92

description: Library name: UTUC_RNAseq_PT092

value: Y


title: effect of marennine on macrophages A mar

description: Library name: P22T038

value: A


title: MSK100 UTUC Sample 81

description: Library name: UTUC_RNAseq_PT081


title: MSK100 UTUC Sample 82

description: Library name: UTUC_RNAseq_PT082


title: TRE promoter upstream of Ptn gene, 16000ng/mL doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_D1600_E_Rep1
nascent DNA from early S fraction


title: MSK100 UTUC Sample 90

description: Library name: UTUC_RNAseq_PT090

value: AV


title: effect of marennine on macrophages A veh

description: Library name: P22T037

value: macrophages


title: Biopsy collected at 4wks from Pt_13

city: Duarte

first: Jian

last: Ye

address: 1500 E Duarte Rd

department: Department of Medical Oncology and Therapeutics Research

institute: City of Hope National Medical Center

description:
Library name: Biopsy_16
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_16

data_processing:
Raw RNA-seq data were processed using Partek Flow cloud-based bioinformatics platform.
Assembly: Reads were aligned to the hg38 human genome using STAR v2.7.8a with default parameters.
Supplementary files format and content: Gene-level quantification was performed using HTSeq with the annotation file hg38_ensembl_release110_v2_gene_level.transcripts, and duplicate reads were summed.

source_name: Tumor biopsy

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagene)
RNA libraries for RNA-seq were prepared using polyA enrichement protocol by Novogene

value: Tumor biopsy

tag: collection

tag: patient id

tag: best response

value: PD

tag: pfs months


title: MSK100 UTUC Sample 80

description: Library name: UTUC_RNAseq_PT080

tag: tissue

tag: cell type

value: S


title: TRE promoter upstream of Ptn gene, 16000ng/mL doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_D1600_E_Rep2
nascent DNA from early S fraction

value: embryonic stem cell


title: MSK100 UTUC Sample 83

description: Library name: UTUC_RNAseq_PT083

value: BA


title: Biopsy collected at 4wks from Pt_20

description:
Library name: Biopsy_15
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_15

value: SD


title: TRE promoter upstream of Ptn gene, 8000ng/mL doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_D0800_L_Rep2
nascent DNA from late S fraction

value: F121:R26puroR-M2rtTA;  Ptn^TRE


title: MSK100 UTUC Sample 85

description: Library name: UTUC_RNAseq_PT085


title: MSK100 UTUC Sample 76

description: Library name: UTUC_RNAseq_PT076

value: N


title: MSK100 UTUC Sample 77

description: Library name: UTUC_RNAseq_PT077


title: TRE promoter upstream of Ptn gene, 8000ng/mL doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_D0800_L_Rep1
nascent DNA from late S fraction

value: biol rep 1


title: MSK100 UTUC Sample 75

description: Library name: UTUC_RNAseq_PT075


title: MSK100 UTUC Sample 79

description: Library name: UTUC_RNAseq_PT079


title: Biopsy collected at 4wks from Pt_10

description:
Library name: Biopsy_14
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_14


title: MSK100 UTUC Sample 74

description: Library name: UTUC_RNAseq_PT074


title: TRE promoter upstream of Ptn gene, 8000ng/mL doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_D0800_E_Rep2
nascent DNA from early S fraction

value: biol rep 2


title: Biopsy collected at Baseline from Pt_21

description:
Library name: Biopsy_13
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_13

value: Baseline


title: MSK100 UTUC Sample 73

description: Library name: UTUC_RNAseq_PT073

value: Upper Tract Urothelial Carcinoma

value: tissue


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, late S fraction, replicate 5

description:
Library name: TRE_Ptn_D0400_L_Rep5
nascent DNA from late S fraction

value: biol rep 5


title: Biopsy collected at 4wks from Pt_14

description:
Library name: Biopsy_12
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_12


title: TRE promoter upstream of Ptn gene, 8000ng/mL doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_D0800_E_Rep1
nascent DNA from early S fraction


title: MSK100 UTUC Sample 78

description: Library name: UTUC_RNAseq_PT078


title: Biopsy collected at Baseline from Pt_13

description:
Library name: Biopsy_11
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_11


title: MSK100 UTUC Sample 72

description: Library name: UTUC_RNAseq_PT072

value: Y


title: MSK100 UTUC Sample 70

description: Library name: UTUC_RNAseq_PT070


title: MSK100 UTUC Sample 69

description: Library name: UTUC_RNAseq_PT069


title: Biopsy collected at Baseline from Pt_20

description:
Library name: Biopsy_10
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_10


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, late S fraction, replicate 4

description:
Library name: TRE_Ptn_D0400_L_Rep4
nascent DNA from late S fraction

value: biol rep 4


title: MSK100 UTUC Sample 68

description: Library name: UTUC_RNAseq_PT068


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, late S fraction, replicate 3

description:
Library name: TRE_Ptn_D0400_L_Rep3
nascent DNA from late S fraction

value: biol rep 3


title: MSK100 UTUC Sample 67

description: Library name: UTUC_RNAseq_PT067


title: Biopsy collected at Baseline from Pt_10

description:
Library name: Biopsy_08
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_08

value: Tumor biopsy


title: MSK100 UTUC Sample 66

description: Library name: UTUC_RNAseq_PT066


title: MSK100 UTUC Sample 65

description: Library name: UTUC_RNAseq_PT065


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_D0400_L_Rep2
nascent DNA from late S fraction


title: Biopsy collected at 4wks from Pt_7

description:
Library name: Biopsy_07
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_07


title: MSK100 UTUC Sample 71

description: Library name: UTUC_RNAseq_PT071


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_D0400_L_Rep1
nascent DNA from late S fraction


title: MSK100 UTUC Sample 64

description: Library name: UTUC_RNAseq_PT064


title: MSK100 UTUC Sample 63

description: Library name: UTUC_RNAseq_PT063

value: AV


title: Biopsy collected at 4wks from Pt_25

description:
Library name: Biopsy_06
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_06

value: PR


title: MSK100 UTUC Sample 61

description: Library name: UTUC_RNAseq_PT061


title: MSK100 UTUC Sample 58

description: Library name: UTUC_RNAseq_PT058


title: Biopsy collected at Baseline from Pt_14

description:
Library name: Biopsy_05
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_05


title: MSK100 UTUC Sample 59

description: Library name: UTUC_RNAseq_PT059


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, early S fraction, replicate 4

description:
Library name: TRE_Ptn_D0400_E_Rep4
nascent DNA from early S fraction

value: embryonic stem cell


title: Biopsy collected at Baseline from Pt_26

description:
Library name: Biopsy_04
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_04


title: MSK100 UTUC Sample 57

description: Library name: UTUC_RNAseq_PT057


title: MSK100 UTUC Sample 56

description: Library name: UTUC_RNAseq_PT056


title: MSK100 UTUC Sample 62

description: Library name: UTUC_RNAseq_PT062


title: Biopsy collected at Baseline from Pt_25

description:
Library name: Biopsy_03
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_03


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, early S fraction, replicate 3

description:
Library name: TRE_Ptn_D0400_E_Rep3
nascent DNA from early S fraction


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_D0400_E_Rep2
nascent DNA from early S fraction


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, early S fraction, replicate 5

description:
Library name: TRE_Ptn_D0400_E_Rep5
nascent DNA from early S fraction


title: MSK100 UTUC Sample 54

description: Library name: UTUC_RNAseq_PT054


title: MSK100 UTUC Sample 53

description: Library name: UTUC_RNAseq_PT053


title: MSK100 UTUC Sample 60

description: Library name: UTUC_RNAseq_PT060


title: CD8 T cells, collected at 8wks from Pt_23

description: Library name: CD8E_321

data_processing:
Raw RNA-seq data were processed using  Partek Flow cloud-based bioinformatics platform.
Assembly: Reads were aligned to the hg38 human genome using STAR v2.7.8a with default parameters.
Supplementary files format and content: Gene-level quantification was performed using HTSeq with the annotation file hg38_ensembl_release110_v2_gene_level.transcripts, and duplicate reads were summed.

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagene)
RNA libraries for RNA-seq were prepared using polyA enrichement protocol by Novogene

treatment_protocol: PBMCs were thawed and resuspended in 1640 complete medium. Cells were stained with live/dead dye (L/D Blue, L23104) and TrueStain Fc blocker (1:100), followed by surface marker antibodies, including CD3 (BUV395, UCHT1, BD), CD4 (PerCP-Cy5.5, SK3, BioLegend), CD8 (FITC, SK1, BioLegend), CCR7 (BV421, G043H7, BioLegend), and CD45RA (APC-H7, HI100, BD). Staining was performed on ice for 60 minutes, followed by two washes with FACS buffer. Cells were resuspended in 300 μL FACS buffer, transferred to flow tubes. Sorting was performed on a BD Aria II, gating non-naïve CD4 and CD8 T cells and collecting sorted cells directly into 350 μL RLT buffer for downstream RNA extraction.

tag: group


title: MSK100 UTUC Sample 55

description: Library name: UTUC_RNAseq_PT055


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, late S fraction, replicate 4

description:
Library name: TRE_Ptn_D0200_L_Rep4
nascent DNA from late S fraction


title: MSK100 UTUC Sample 52

description: Library name: UTUC_RNAseq_PT052


title: MSK100 UTUC Sample 50

description: Library name: UTUC_RNAseq_PT050


title: TRE promoter upstream of Ptn gene, 4000ng/mL doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_D0400_E_Rep1
nascent DNA from early S fraction


title: CD8 T cells, collected at 8wks from Pt_16

description: Library name: CD8E_319


title: Biopsy collected at Baseline from Pt_7

description:
Library name: Biopsy_01
Column name in raw_counts_All_samples_RIN_Biopsy.txt: Biopsy_01


title: MSK100 UTUC Sample 49

description: Library name: UTUC_RNAseq_PT049


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, late S fraction, replicate 3

description:
Library name: TRE_Ptn_D0200_L_Rep3
nascent DNA from late S fraction


title: CD8 T cells, collected at 8wks from Pt_29

description: Library name: CD8E_318

value: PD


title: MSK100 UTUC Sample 48

description: Library name: UTUC_RNAseq_PT048

value: AL


title: MSK100 UTUC Sample 47

description: Library name: UTUC_RNAseq_PT047


title: MSK100 UTUC Sample 45

description: Library name: UTUC_RNAseq_PT045


title: MSK100 UTUC Sample 44

description: Library name: UTUC_RNAseq_PT044


title: CD8 T cells, collected at 8wks from Pt_28

description: Library name: CD8E_315


title: MSK100 UTUC Sample 46

description: Library name: UTUC_RNAseq_PT046


title: CD8 T cells, collected at 8wks from Pt_1

description: Library name: CD8E_316


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_D0200_L_Rep1
nascent DNA from late S fraction

value: F121:R26puroR-M2rtTA;  Ptn^TRE


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_D0200_L_Rep2
nascent DNA from late S fraction


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, early S fraction, replicate 4

description:
Library name: TRE_Ptn_D0200_E_Rep4
nascent DNA from early S fraction


title: MSK100 UTUC Sample 43

description: Library name: UTUC_RNAseq_PT043

value: N


title: MSK100 UTUC Sample 42

description: Library name: UTUC_RNAseq_PT042


title: MSK100 UTUC Sample 41

description: Library name: UTUC_RNAseq_PT041


title: MSK100 UTUC Sample 51

description: Library name: UTUC_RNAseq_PT051


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, early S fraction, replicate 3

description:
Library name: TRE_Ptn_D0200_E_Rep3
nascent DNA from early S fraction


title: MSK100 UTUC Sample 39

description: Library name: UTUC_RNAseq_PT039


title: CD8 T cells, collected at 8wks from Pt_13

description: Library name: CD8E_313


title: CD8 T cells, collected at 8wks from Pt_21

description: Library name: CD8E_314


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_D0200_E_Rep2
nascent DNA from early S fraction


title: MSK100 UTUC Sample 40

description: Library name: UTUC_RNAseq_PT040


title: TRE promoter upstream of Ptn gene, 2000ng/mL doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_D0200_E_Rep1
nascent DNA from early S fraction

value: biol rep 1


title: MSK100 UTUC Sample 37

description: Library name: UTUC_RNAseq_PT037


title: CD8 T cells, collected at 8wks from Pt_27

description: Library name: CD8E_311

value: SD


title: MSK100 UTUC Sample 36

description: Library name: UTUC_RNAseq_PT036


title: CD8 T cells, collected at 8wks from Pt_20

description: Library name: CD8E_312


title: MSK100 UTUC Sample 35

description: Library name: UTUC_RNAseq_PT035


title: MSK100 UTUC Sample 34

description: Library name: UTUC_RNAseq_PT034


title: MSK100 UTUC Sample 38

description: Library name: UTUC_RNAseq_PT038


title: CD8 T cells, collected at 8wks from Pt_19

description: Library name: CD8E_309


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, late S fraction, replicate 6

description:
Library name: TRE_Ptn_D0050_L_Rep6
nascent DNA from late S fraction

value: biol rep 6


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, late S fraction, replicate 5

description:
Library name: TRE_Ptn_D0050_L_Rep5
nascent DNA from late S fraction


title: MSK100 UTUC Sample 32

description: Library name: UTUC_RNAseq_PT032

value: Upper Tract Urothelial Carcinoma


title: CD8 T cells, collected at 8wks from Pt_9

description: Library name: CD8E_306


title: CD8 T cells, collected at 8wks from Pt_24

description: Library name: CD8E_305


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, late S fraction, replicate 4

description:
Library name: TRE_Ptn_D0050_L_Rep4
nascent DNA from late S fraction


title: MSK100 UTUC Sample 29

description: Library name: UTUC_RNAseq_PT029

value: tissue


title: MSK100 UTUC Sample 28

description: Library name: UTUC_RNAseq_PT028


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, late S fraction, replicate 3

description:
Library name: TRE_Ptn_D0050_L_Rep3
nascent DNA from late S fraction


title: MSK100 UTUC Sample 33

description: Library name: UTUC_RNAseq_PT033


title: MSK100 UTUC Sample 27

description: Library name: UTUC_RNAseq_PT027


title: CD8 T cells, collected at 8wks from Pt_17

description: Library name: CD8E_304


title: MSK100 UTUC Sample 26

description: Library name: UTUC_RNAseq_PT026


title: MSK100 UTUC Sample 30

description: Library name: UTUC_RNAseq_PT030


title: MSK100 UTUC Sample 31

description: Library name: UTUC_RNAseq_PT031


title: MSK100 UTUC Sample 25

description: Library name: UTUC_RNAseq_PT025


title: MSK100 UTUC Sample 23

description: Library name: UTUC_RNAseq_PT023


title: MSK100 UTUC Sample 24

description: Library name: UTUC_RNAseq_PT024


title: CD8 T cells, collected at 8wks from Pt_10

description: Library name: CD8E_302


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_D0050_L_Rep2
nascent DNA from late S fraction

value: biol rep 2


title: CD8 T cells, collected at 8wks from Pt_6

description: Library name: CD8E_303


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, early S fraction, replicate 6

description:
Library name: TRE_Ptn_D0050_E_Rep6
nascent DNA from early S fraction


title: MSK100 UTUC Sample 22

description: Library name: UTUC_RNAseq_PT022


title: MSK100 UTUC Sample 20

description: Library name: UTUC_RNAseq_PT020


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_D0050_L_Rep1
nascent DNA from late S fraction


title: CD8 T cells, collected at 8wks from Pt_25

description: Library name: CD8E_301


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, early S fraction, replicate 5

description:
Library name: TRE_Ptn_D0050_E_Rep5
nascent DNA from early S fraction

value: biol rep 5


title: MSK100 UTUC Sample 21

description: Library name: UTUC_RNAseq_PT021


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, early S fraction, replicate 4

description:
Library name: TRE_Ptn_D0050_E_Rep4
nascent DNA from early S fraction

value: biol rep 4


title: MSK100 UTUC Sample 19

description: Library name: UTUC_RNAseq_PT019


title: CD8 T cells, collected at 4wks from Pt_2

description: Library name: CD8E_220


title: CD8 T cells, collected at 4wks from Pt_23

description: Library name: CD8E_221


title: MSK100 UTUC Sample 18

description: Library name: UTUC_RNAseq_PT018


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, early S fraction, replicate 3

description:
Library name: TRE_Ptn_D0050_E_Rep3
nascent DNA from early S fraction

value: biol rep 3


title: MSK100 UTUC Sample 17

description: Library name: UTUC_RNAseq_PT017


title: CD8 T cells, collected at 4wks from Pt_16

description: Library name: CD8E_219


title: MSK100 UTUC Sample 16

description: Library name: UTUC_RNAseq_PT016


title: MSK100 UTUC Sample 13

description: Library name: UTUC_RNAseq_PT013


title: MSK100 UTUC Sample 15

description: Library name: UTUC_RNAseq_PT015


title: MSK100 UTUC Sample 14

description: Library name: UTUC_RNAseq_PT014


title: MSK100 UTUC Sample 12

description: Library name: UTUC_RNAseq_PT012


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_D0050_E_Rep2
nascent DNA from early S fraction


title: MSK100 UTUC Sample 9

description: Library name: UTUC_RNAseq_PT009


title: CD8 T cells, collected at 4wks from Pt_12

description: Library name: CD8E_217


title: CD8 T cells, collected at 4wks from Pt_29

description: Library name: CD8E_218


title: TRE promoter upstream of Ptn gene, 500ng/mL doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_D0050_E_Rep1
nascent DNA from early S fraction


title: CD8 T cells, collected at 4wks from Pt_1

description: Library name: CD8E_216


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, late S fraction, replicate 6

description:
Library name: TRE_Ptn_D0025_L_Rep6
nascent DNA from late S fraction


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, late S fraction, replicate 5

description:
Library name: TRE_Ptn_D0025_L_Rep5
nascent DNA from late S fraction


title: CD8 T cells, collected at 4wks from Pt_28

description: Library name: CD8E_215


title: MSK100 UTUC Sample 11

description: Library name: UTUC_RNAseq_PT011


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_D0025_L_Rep2
nascent DNA from late S fraction


title: CD8 T cells, collected at 4wks from Pt_21

description: Library name: CD8E_214


title: MSK100 UTUC Sample 8

description: Library name: UTUC_RNAseq_PT008


title: MSK100 UTUC Sample 7

description: Library name: UTUC_RNAseq_PT007


title: MSK100 UTUC Sample 10

description: Library name: UTUC_RNAseq_PT010


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_D0025_L_Rep1
nascent DNA from late S fraction


title: MSK100 UTUC Sample 5

description: Library name: UTUC_RNAseq_PT005


title: MSK100 UTUC Sample 2

description: Library name: UTUC_RNAseq_PT002


title: MSK100 UTUC Sample 4

description: Library name: UTUC_RNAseq_PT004


title: MSK100 UTUC Sample 3

description: Library name: UTUC_RNAseq_PT003


title: CD8 T cells, collected at 4wks from Pt_13

description: Library name: CD8E_213


title: CD8 T cells, collected at 4wks from Pt_20

description: Library name: CD8E_212


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, early S fraction, replicate 5

description:
Library name: TRE_Ptn_D0025_E_Rep5
nascent DNA from early S fraction


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, early S fraction, replicate 6

description:
Library name: TRE_Ptn_D0025_E_Rep6
nascent DNA from early S fraction


title: IBD_308858, colon

city: Chapel Hill

first: Terrence

last: Furey

state: North Carolina

address: 120 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: Library name: IBD_308858

data_processing:
A decoy-aware index was built using a concatenated transcriptome of GENCODE v39 and the predicted lncRNAs using salmon index (salmon v.1.6.0)
RNA-seq data was quantified using salmon quant (salmon v.1.6.0) in mapping-based mode.
Assembly: hg38; reads were assembled with GENCODE v39, concatenated with the set of predicted lncRNAs (coordinates are in supplementary GTF file)
Supplementary files format and content: Tab-delimited text file includes raw count data for each sample from Salmon quantification
Supplementary files format and content: Tab-delimited text file includes TPM-normalized count data for each sample from Salmon quantification
Supplementary files format and content: GTF file includes transcript and exon feature annotations for the predicted lncRNA set

source_name: colon

extract_protocol:
Samples were collected and stored in RNA-later from macroscopically non-inflamed sections of colonic mucosa for patients undergoing colonoscopy or surgical resection. RNA was isolated using the Qiagen RNeasy Mini Kit.
Total RNA libraries were constructed with the Kapa Total RNA Stranded with Ribo Erase; PolyA libraries were constructed with the Illumina TruSeq polyA+ Sample Prep Kit

value: colon

value: E

tag: inflammation

value: uninflamed

tag: disease status

value: CD

tag: Sex

value: Male


title: IBD_627183, colon

description: Library name: IBD_627183

tag: batch

value: Female


title: MSK100 UTUC Sample 6

description: Library name: UTUC_RNAseq_PT006

value: AL


title: IBD_995536, colon

description: Library name: IBD_995536


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_D0025_E_Rep2
nascent DNA from early S fraction

value: embryonic stem cell

tag: cell line

value: F121:R26puroR-M2rtTA;  Ptn^TRE


title: MSK100 UTUC Sample 1

description: Library name: UTUC_RNAseq_PT001

value: N


title: CD8 T cells, collected at 4wks from Pt_4

description: Library name: CD8E_210

value: SD


title: CD8 T cells, collected at 4wks from Pt_27

description: Library name: CD8E_211


title: IBD_417916, colon

description: Library name: IBD_417916


title: IBD_654735, colon

description: Library name: IBD_654735


title: IBD_440319, colon

description: Library name: IBD_440319


title: IBD_605981, colon

description: Library name: IBD_605981

value: NIBD


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, late S fraction, replicate 6

description:
Library name: TRE_Ptn_D0010_L_Rep6
nascent DNA from late S fraction

value: biol rep 6


title: CD8 T cells, collected at 4wks from Pt_22

description: Library name: CD8E_208

value: PD


title: CD8 T cells, collected at 4wks from Pt_8

description: Library name: CD8E_207


title: IBD_787025, colon

description: Library name: IBD_787025


title: IBD_991887, colon

description: Library name: IBD_991887


title: TRE promoter upstream of Ptn gene, 250ng/mL doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_D0025_E_Rep1
nascent DNA from early S fraction

value: biol rep 1


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, late S fraction, replicate 4

description:
Library name: TRE_Ptn_D0010_L_Rep4
nascent DNA from late S fraction

value: biol rep 4


title: Post-ischemia sample of left ventricle sample from patient 50V, surgery in morning

city: Houston

first: Holger

middle: K.

last: Eltzschig

state: TX

department: Department of Anesthesiology

institute: The University of Texas Health Science Center at Houston

data_processing:
Alignment of RNA sequencing tags was restricted to those mapping to the same DNA strand as annotated in the GRCm38 reference genome, utilizing the STAR software. Quantification of transcripts was conducted by calculating the fragments per kilobase of transcript per million mapped reads (FPKM) values, along with transcript counts. In the preprocessing step of mRNA analysis, any gene identified as non-expressed, defined as having an FPKM expression level less than 1 in more than 80% of samples, was excluded. The normalized expression profiles of these mRNAs were then subjected to PCA for quality control and to evaluate sample similarity. Differential expression analysis was executed using the DESeq2 pipeline, with DEGs being identified based on a threshold of 1.5-fold change and an adjusted p-value below 0.05, as determined by the Benjamini-Hochberg method
Assembly: GRCm38
Supplementary files format and content: Gene quantification and differential expression

source_name: Left ventricle

extract_protocol:
The AAR of the heart was harvested following 2h of reperfusion from the C57BL/6J mice subjected to myocardial IRI at either ZT8 or ZT20.
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and employed to construct RNA-Seq libraries

value: Left ventricle

value: AM

tag: treatment

value: Post-ischemia


title: Post-ischemia sample of left ventricle sample from patient 47V, surgery in morning


title: CD8 T cells, collected at 4wks from Pt_24

description: Library name: CD8E_205


title: Pre-ischemia sample of left ventricle sample from patient 50V, surgery in morning

value: Pre-ischemia


title: CD8 T cells, collected at 4wks from Pt_6

description: Library name: CD8E_203

value: PR


title: CD8 T cells, collected at 4wks from Pt_9

description: Library name: CD8E_206


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, late S fraction, replicate 3

description:
Library name: TRE_Ptn_D0010_L_Rep3
nascent DNA from late S fraction

value: biol rep 3


title: Post-ischemia sample of left ventricle sample from patient 138V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 32V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 47V, surgery in morning


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_D0010_L_Rep1
nascent DNA from late S fraction


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, early S fraction, replicate 6

description:
Library name: TRE_Ptn_D0010_E_Rep6
nascent DNA from early S fraction


title: CD8 T cells, collected at 4wks from Pt_19

description: Library name: CD8E_209


title: Pre-ischemia sample of left ventricle sample from patient 138V, surgery in morning


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_D0010_L_Rep2
nascent DNA from late S fraction

value: biol rep 2


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, late S fraction, replicate 5

description:
Library name: TRE_Ptn_D0010_L_Rep5
nascent DNA from late S fraction

value: biol rep 5


title: CD8 T cells, collected at 4wks from Pt_17

description: Library name: CD8E_204


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, early S fraction, replicate 4

description:
Library name: TRE_Ptn_D0010_E_Rep4
nascent DNA from early S fraction

value: embryonic stem cell


title: Pre-ischemia sample of left ventricle sample from patient 71V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 32V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 71V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 68V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 78V, surgery in afternoon

value: PM


title: Pre-ischemia sample of left ventricle sample from patient 68V, surgery in morning


title: CD8 T cells, collected at Baseline from Pt_2

description: Library name: CD8E_120

value: Baseline


title: Post-ischemia sample of left ventricle sample from patient 78V, surgery in afternoon


title: CD8 T cells, collected at 4wks from Pt_25

description: Library name: CD8E_201


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, early S fraction, replicate 5

description:
Library name: TRE_Ptn_D0010_E_Rep5
nascent DNA from early S fraction

value: F121:R26puroR-M2rtTA;  Ptn^TRE


title: CD8 T cells, collected at Baseline from Pt_23

description: Library name: CD8E_121

value: SD


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, early S fraction, replicate 3

description:
Library name: TRE_Ptn_D0010_E_Rep3
nascent DNA from early S fraction


title: Post-ischemia sample of left ventricle sample from patient 102V, surgery in morning


title: CD8 T cells, collected at Baseline from Pt_16

description: Library name: CD8E_119


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_D0010_E_Rep2
nascent DNA from early S fraction


title: Post-ischemia sample of left ventricle sample from patient 110V, surgery in morning


title: CD8 T cells, collected at 4wks from Pt_10

description: Library name: CD8E_202


title: TRE promoter upstream of Ptn gene, 100ng/mL doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_D0010_E_Rep1
nascent DNA from early S fraction


title: Post-ischemia sample of left ventricle sample from patient 159V, surgery in afternoon


title: TRE promoter upstream of Ptn gene, no doxycycline, late S fraction, replicate 5

description:
Library name: TRE_Ptn_D0000_L_Rep5
nascent DNA from late S fraction


title: Pre-ischemia sample of left ventricle sample from patient 102V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 103V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 159V, surgery in afternoon


title: Pre-ischemia sample of left ventricle sample from patient 110V, surgery in morning


title: CD8 T cells, collected at Baseline from Pt_12

description: Library name: CD8E_117


title: CD8 T cells, collected at Baseline from Pt_29

description: Library name: CD8E_118


title: Pre-ischemia sample of left ventricle sample from patient 103V, surgery in morning


title: TRE promoter upstream of Ptn gene, no doxycycline, late S fraction, replicate 3

description:
Library name: TRE_Ptn_D0000_L_Rep3
nascent DNA from late S fraction


title: Post-ischemia sample of left ventricle sample from patient 150V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 150V, surgery in morning


title: CD8 T cells, collected at Baseline from Pt_28

description: Library name: CD8E_115


title: CD8 T cells, collected at Baseline from Pt_1

description: Library name: CD8E_116


title: TRE promoter upstream of Ptn gene, no doxycycline, late S fraction, replicate 2

description:
Library name: TRE_Ptn_D0000_L_Rep2
nascent DNA from late S fraction


title: Post-ischemia sample of left ventricle sample from patient 34V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 135V, surgery in morning


title: CD8 T cells, collected at Baseline from Pt_13

description: Library name: CD8E_113


title: TRE promoter upstream of Ptn gene, no doxycycline, late S fraction, replicate 1

description:
Library name: TRE_Ptn_D0000_L_Rep1
nascent DNA from late S fraction


title: MCF-7 cells treated with HOXB2-specific siRNA_replicate 2

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

description: Library name: Hoxb2_2

data_processing:
FastQC Version 0.11.9
Trimmomatic Version 0.39
FastQC Version 0.11.9
STAR Aligner Version 2.7.11b
featureCounts
Assembly: Ensemble Homo sapiens GRCh38 genome
Supplementary files format and content: .bam files for the alignment output

growth_protocol: MCF-7 cells were grown in a humidified chamber maintained at 37°C and 5% CO2. The cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM), supplemented with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin (M1 medium).

extract_protocol:
Total RNA was isolated using RNA extraction reagent prepared in-house as per Chomczynski and Sacchi (2006).
After mRNA enrichment with NEB Magnetic mRNA Isolation Kit, libraries were prepared with the NEB Ultra II RNA Library Prep Kit.

treatment_protocol: MCF-7 cells were treated with scrambled or HOXB2 specific siRNA using Lipofectamine RNAiMax. Thereafter cells were shifted to charcoal-stripped serum-containing, phenol red free DMEM for 72 h before isolation of total RNA.

value: Breast cancer cells

tag: genotype

value: Wild type

value: Treated with HOXB2-specific siRNA for 24 h


title: TRE promoter upstream of Ptn gene, no doxycycline, early S fraction, replicate 3

description:
Library name: TRE_Ptn_D0000_E_Rep3
nascent DNA from early S fraction


title: TRE promoter upstream of Ptn gene, no doxycycline, early S fraction, replicate 5

description:
Library name: TRE_Ptn_D0000_E_Rep5
nascent DNA from early S fraction


title: MCF-7 cells treated with scrambled siRNA_replicate 2

description: Library name: Scr_2

value: Treated with scrambled (control) siRNA for 24 h


title: MCF-7 cells treated with HOXB2-specific siRNA_replicate 1

description: Library name: Hoxb2_1


title: CD8 T cells, collected at Baseline from Pt_20

description: Library name: CD8E_112


title: CD8 T cells, collected at Baseline from Pt_4

description: Library name: CD8E_110


title: TRE promoter upstream of Ptn gene, no doxycycline, early S fraction, replicate 1

description:
Library name: TRE_Ptn_D0000_E_Rep1
nascent DNA from early S fraction

value: biol rep 1


title: Pre-ischemia sample of left ventricle sample from patient 98V, surgery in morning

value: Left ventricle

value: AM


title: MCF-7 cells treated with scrambled siRNA_replicate 1

description: Library name: Scr_1


title: Pre-ischemia sample of left ventricle sample from patient 34V, surgery in morning

value: Pre-ischemia


title: Post-ischemia sample of left ventricle sample from patient 92V, surgery in morning

value: Post-ischemia


title: CD8 T cells, collected at Baseline from Pt_21

description: Library name: CD8E_114

value: PD


title: Pre-ischemia sample of left ventricle sample from patient 92V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 98V, surgery in morning


title: CD8 T cells, collected at Baseline from Pt_27

description: Library name: CD8E_111


title: Post-ischemia sample of left ventricle sample from patient 162V, surgery in afternoon


title: TRE promoter upstream of Ptn gene, no doxycycline, early S fraction, replicate 2

description:
Library name: TRE_Ptn_D0000_E_Rep2
nascent DNA from early S fraction

value: biol rep 2


title: CD8 T cells, collected at Baseline from Pt_19

description: Library name: CD8E_109


title: CD8 T cells, collected at Baseline from Pt_22

description: Library name: CD8E_108


title: MOLM13_DNp73_OE ChIP DNp73ab

city: Groningen

first: Diego A

last: Pereira-Martins

state: Groningen

address: Hanzeplein 1

department: Hematology

country: Netherlands

institute: University Medical Center Groningen

description: Library name: MOLM13_DNp73_OE_DNp73ab

data_processing:
Sequenced reads were trimmed for adapter sequences. Data analysis was done as described in Orlando et al. 2014. In short, metagenome was generated for human hg38. Paired-end reads were aligned to the reference metagenome using BWA with default settings. Bigwig files were generated using BEDTools and BedGrapToBigWig from UCSC Peaks were called using MACS2 with the estimated fragment size using narrow peak settings
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak

source_name: Bone marrow

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes, followed by quenching and cell lysis. Next, cells were sonicated using a Bioruptor (Diagenode).
ChIP-Seq

value: Bone marrow

value: AML cell line


title: MOLM13_DNp73_OE ChIP TP53ab

description: Library name: MOLM13_DNp73_OE_TP53ab


title: MOLM13_EV ChIP TAp73ab

description: Library name: MOLM13_EV_TAp73ab


title: MOLM13_DNp73_OE ChIP TAp73ab

description: Library name: MOLM13_DNp73_OE_TAp73ab


title: non-activated TRE promoter upstream of Ptn gene, late S fraction, replicate 2

description:
Library name: TRE_Ptn_L_Rep2
nascent DNA from late S fraction

value: embryonic stem cell


title: Pre-ischemia sample of left ventricle sample from patient 162V, surgery in afternoon

value: PM


title: non-activated TRE promoter upstream of Ptn gene, early S fraction, replicate 2

description:
Library name: TRE_Ptn_E_Rep2
nascent DNA from early S fraction

value: F121:R26puroR-M2rtTA;  Ptn^TRE


title: MOLM13_EV ChIP TP53ab

description: Library name: MOLM13_EV_TP53ab


title: non-activated TRE promoter upstream of Ptn gene, late S fraction, replicate 1

description:
Library name: TRE_Ptn_L_Rep1
nascent DNA from late S fraction


title: MOLM13 KO 2

description: Library name: MOLM13 KO_2


title: Pre-ischemia sample of left ventricle sample from patient 66V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 66V, surgery in morning


title: activated TRE promoter upstream of Ptn gene, late S fraction, replicate 1

description:
Library name: TRE_Ptn_Dox_L_Rep1
nascent DNA from late S fraction

value: doxycycline


title: MOLM13 KO 1

description: Library name: MOLM13 KO_1


title: CD8 T cells, collected at Baseline from Pt_6

description: Library name: CD8E_103

value: Baseline

value: PR


title: CD8 T cells, collected at Baseline from Pt_24

description: Library name: CD8E_105

value: SD


title: MOLM13 DNp73-OE 2

description: Library name: MOLM13 DNp73_2


title: CD8 T cells, collected at Baseline from Pt_17

description: Library name: CD8E_104


title: MOLM13 DNp73-OE 1

description: Library name: MOLM13 DNp73_1


title: Post-ischemia sample of left ventricle sample from patient 106V, surgery in afternoon


title: activated TRE promoter upstream of Ptn gene, early S fraction, replicate 2

description:
Library name: TRE_Ptn_Dox_E_Rep2
nascent DNA from early S fraction


title: activated TRE promoter upstream of Ptn gene, late S fraction, replicate 2

description:
Library name: TRE_Ptn_Dox_L_Rep2
nascent DNA from late S fraction


title: CD8 T cells, collected at Baseline from Pt_10

description: Library name: CD8E_102


title: CD8 T cells, collected at Baseline from Pt_9

description: Library name: CD8E_106


title: CD8 T cells, collected at Baseline from Pt_25

description: Library name: CD8E_101


title: Pre-ischemia sample of left ventricle sample from patient 130V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 130V, surgery in morning


title: non-activated TRE promoter upstream of Ptn gene, early S fraction, replicate 1

description:
Library name: TRE_Ptn_E_Rep1
nascent DNA from early S fraction


title: mPGK promoter upstream of Ptn gene, late S fraction, replicate 2

description:
Library name: mPGK_Ptn_L_Rep2
nascent DNA from late S fraction

value: F121:R26puroR-M2rtTA;  Ptn^mPGK


title: Pre-ischemia sample of left ventricle sample from patient 106V, surgery in afternoon


title: Post-ischemia sample of left ventricle sample from patient 52V, surgery in morning


title: activated TRE promoter upstream of Ptn gene, early S fraction, replicate 1

description:
Library name: TRE_Ptn_Dox_E_Rep1
nascent DNA from early S fraction

value: biol rep 1


title: MOLM13 empty vector 1

description: Library name: MOLM13 EV_1


title: mPGK promoter upstream of Ptn gene, early S fraction, replicate 2

description:
Library name: mPGK_Ptn_E_Rep2
nascent DNA from early S fraction


title: CD4 T cells, collected at 8wks from Pt_16

description: Library name: CD4E_319


title: white_Input_D3

description: Library name: 34-20266_S10

value: subcutaneous abdominal adipose

value: primary adipose stem cells

tag: time

value: white adipogenic differentiation

tag: chip antibody

value: Input


title: MOLM13 empty vector 2

description: Library name: MOLM13 EV_2


title: white_Input_D1

description: Library name: 35-20267_S11


title: Pre-ischemia sample of left ventricle sample from patient 52V, surgery in morning

value: Left ventricle

value: AM

value: Pre-ischemia


title: CD4 T cells, collected at 8wks from Pt_29

description: Library name: CD4E_318

value: PD


title: CD4 T cells, collected at 8wks from Pt_23

description: Library name: CD4E_321


title: mPGK promoter upstream of Ptn gene, late S fraction, replicate 1

description:
Library name: mPGK_Ptn_L_Rep1
nascent DNA from late S fraction

value: embryonic stem cell


title: mPGK promoter upstream of Ptn gene, early S fraction, replicate 1

description:
Library name: mPGK_Ptn_E_Rep1
nascent DNA from early S fraction


title: Pre-ischemia sample of left ventricle sample from patient 153V, surgery in morning


title: CD4 T cells, collected at 8wks from Pt_21

description: Library name: CD4E_314


title: white_H3K9me3_D1

description: Library name: 15-21349_S20


title: white_H3K9me3_D3

description: Library name: 16-21350_S17


title: Pre-ischemia sample of left ventricle sample from patient 157V, surgery in morning


title: CD4 T cells, collected at 8wks from Pt_13

description: Library name: CD4E_313


title: hPGK promoter upstream of Ptn gene, late S fraction, replicate 2

description:
Library name: hPGK_Ptn_L_Rep2
nascent DNA from late S fraction

value: F121:R26puroR-M2rtTA;  Ptn^hPGK

value: biol rep 2


title: white_H3K4me3_D1

description: Library name: 7-20239_S7


title: CD4 T cells, collected at 8wks from Pt_28

description: Library name: CD4E_315


title: hPGK promoter upstream of Ptn gene, late S fraction, replicate 1

description:
Library name: hPGK_Ptn_L_Rep1
nascent DNA from late S fraction


title: hPGK promoter upstream of Ptn gene, early S fraction, replicate 2

description:
Library name: hPGK_Ptn_E_Rep2
nascent DNA from early S fraction


title: Post-ischemia sample of left ventricle sample from patient 23V, surgery in morning

value: Post-ischemia


title: white_H3K4me3_D3

description: Library name: 6-20238_S6


title: Post-ischemia sample of left ventricle sample from patient 157V, surgery in morning


title: CD4 T cells, collected at 8wks from Pt_1

description: Library name: CD4E_316


title: Post-ischemia sample of left ventricle sample from patient 153V, surgery in morning


title: hPGK promoter upstream of Ptn gene, early S fraction, replicate1

description:
Library name: hPGK_Ptn_E_Rep1
nascent DNA from early S fraction


title: Pre-ischemia sample of left ventricle sample from patient 23V, surgery in morning


title: white_H3K4me1_D1

description: Library name: 28-20260_S4


title: Post-ischemia sample of left ventricle sample from patient 140V, surgery in afternoon

value: PM


title: CD4 T cells, collected at 8wks from Pt_4

description: Library name: CD4E_310


title: CD4 T cells, collected at 8wks from Pt_27

description: Library name: CD4E_311


title: white_H3K36me3_D3

description: Library name: 8-21342_S15


title: white_H3K4me1_D3

description: Library name: 27-20259_S3


title: CD4 T cells, collected at 8wks from Pt_20

description: Library name: CD4E_312


title: CD4 T cells, collected at 8wks from Pt_19

description: Library name: CD4E_309


title: CAG promoter upstream of Ptn gene, early S fraction, replicate1

description:
Library name: CAG_Ptn_E_Rep1
nascent DNA from early S fraction

value: F121:R26puroR-M2rtTA;  Ptn^CAG


title: white_H3K36me3_D1

description: Library name: 7-21341_S2


title: CAG promoter upstream of Ptn gene, early S fraction, replicate 2

description:
Library name: CAG_Ptn_E_Rep2
nascent DNA from early S fraction


title: CD4 T cells, collected at 8wks from Pt_9

description: Library name: CD4E_306

value: PR


title: Wild type F121-9, early S fractioon, replicate 2

description:
Library name: TRIP_WT_E_Rep2
nascent DNA from early S fraction


title: CAG promoter upstream of Ptn gene, late S fraction, replicate1

description:
Library name: CAG_Ptn_L_Rep1
nascent DNA from late S fraction


title: Post-ischemia sample of left ventricle sample from patient 57V, surgery in morning


title: CAG promoter upstream of Ptn gene, late S fraction, replicate 2

description:
Library name: CAG_Ptn_L_Rep2
nascent DNA from late S fraction


title: Wild type F121-9, late S fractioon, replicate 2

description:
Library name: TRIP_WT_L_Rep2
nascent DNA from late S fraction


title: Pre-ischemia sample of left ventricle sample from patient 140V, surgery in afternoon


title: white_H3K27me3_D1

description: Library name: 21-20253_S9


title: white_H3K27me3_D3

description: Library name: 20-20252_S8


title: Pre-ischemia sample of left ventricle sample from patient 57V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 118V, surgery in morning


title: CD4 T cells, collected at 8wks from Pt_17

description: Library name: CD4E_304


title: CD4 T cells, collected at 8wks from Pt_10

description: Library name: CD4E_302

value: SD


title: CD4 T cells, collected at 8wks from Pt_24

description: Library name: CD4E_305


title: Pre-ischemia sample of left ventricle sample from patient 118V, surgery in morning


title: Wild type F121-9, late S fractioon, replicate 1

description:
Library name: TRIP_WT_L_Rep1
nascent DNA from late S fraction

value: biol rep 1


title: Clone CM1420 with PiggyBAC vector expressing GFP from the hPGK promoter, late S fraction, replicate 2

description:
Library name: CM1420_L_Rep2
nascent DNA from late S fraction


title: white_H3K27ac_D3

description: Library name: 13-20245_S1

value: subcutaneous abdominal adipose


title: CD4 T cells, collected at 8wks from Pt_6

description: Library name: CD4E_303


title: white_H3K27ac_D1

description: Library name: 14-20246_S2

value: primary adipose stem cells


title: H3K9me3_D0

description: Library name: 14-21348_S12

value: uninduced


title: Pre-ischemia sample of left ventricle sample from patient 51V, surgery in morning


title: Post-ischemia sample of left ventricle sample from patient 51V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 48V, surgery in morning


title: Input_D0

description: Library name: 33-20265_S9

value: Input


title: Wild type F121-9, early S fractioon, replicate 1

description:
Library name: TRIP_WT_E_Rep1
nascent DNA from early S fraction


title: Clone CM1420 with PiggyBAC vector expressing GFP from the hPGK promoter, late S fraction, replicate 1

description:
Library name: CM1420_L_Rep1
nascent DNA from late S fraction


title: H3K4me3_D0

description: Library name: 5-20237_S5


title: CD4 T cells, collected at 4wks from Pt_23

description: Library name: CD4E_221


title: CD4 T cells, collected at 4wks from Pt_2

description: Library name: CD4E_220


title: Post-ischemia sample of left ventricle sample from patient 33V, surgery in morning

value: Left ventricle


title: Clone CM1420 with PiggyBAC vector expressing GFP from the hPGK promoter, early S fraction, replicate 1

description:
Library name: CM1420_E_Rep1
nascent DNA from early S fraction


title: Pre-ischemia sample of left ventricle sample from patient 33V, surgery in morning

value: AM


title: Clone CM1420 with PiggyBAC vector expressing GFP from the hPGK promoter, early S fraction, replicate 2

description:
Library name: CM1420_E_Rep2
nascent DNA from early S fraction


title: CD4 T cells, collected at 4wks from Pt_16

description: Library name: CD4E_219


title: CD4 T cells, collected at 4wks from Pt_29

description: Library name: CD4E_218


title: Clone CM1417 withPiggyBAC vector expressing GFP from the hPGK promoter, late S fraction, replicate 2

description:
Library name: CM1417_L_Rep2
nascent DNA from late S fraction


title: Post-ischemia sample of left ventricle sample from patient 65V, surgery in morning


title: H3K36me3_D0

description: Library name: 6-21340_S8


title: Clone CM1417 with PiggyBAC vector expressing GFP from the hPGK promoter, early S fraction, replicate 2

description:
Library name: CM1417_E_Rep2
nascent DNA from early S fraction


title: H3K27ac_D0

description: Library name: 12-20244_S12


title: CD4 T cells, collected at 8wks from Pt_25

description: Library name: CD4E_301


title: H3K27me3_D0

description: Library name: 19-20251_S7


title: Post-ischemia sample of left ventricle sample from patient 107V, surgery in morning


title: CD4 T cells, collected at 4wks from Pt_12

description: Library name: CD4E_217


title: Clone CM1417 with PiggyBAC vector expressing GFP from the hPGK promoter, late S fraction, replicate 1

description:
Library name: CM1417_L_Rep1
nascent DNA from late S fraction


title: Pre-ischemia sample of left ventricle sample from patient 65V, surgery in morning

value: Pre-ischemia


title: H3K4me1_D0

description: Library name: 26-20258_S2


title: CD4 T cells, collected at 4wks from Pt_1

description: Library name: CD4E_216

value: PD


title: Pre-ischemia sample of left ventricle sample from patient 107V, surgery in morning


title: CD4 T cells, collected at 4wks from Pt_28

description: Library name: CD4E_215


title: Clone CM1417 with PiggyBAC vector expressing GFP from the hPGK promoter, early S fraction, replicate 1

description:
Library name: CM1417_E_Rep1
nascent DNA from early S fraction

value: embryonic stem cell


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE not activated, early S fraction, replicate 2

description:
Library name: TRE_HTK_E_Rep2
nascent DNA from early S fraction

value: F121:R26puroR-M2rtTA;  Ptn^TRE-Hyg-TK/+


title: CD4 T cells, collected at 4wks from Pt_13

description: Library name: CD4E_213


title: CD4 T cells, collected at 4wks from Pt_21

description: Library name: CD4E_214


title: THP-1 macrophage cells treated with csep1 protein_replicate 3

city: Sydney

first: Li

last: Zhang

state: NSW

address: Botany Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

data_processing:
Quality was checked using FastQC (v 0.11.8)
Trimmomatic (v 0.38) was used to trim Illumina adapter sequences and filter the raw reads
The quality filtered reads were mapped to the reference human genome GRCh38.p14 using HISAT2 (v 2.1.0)
The Subread package Featurecount (v 2.0.1) was used to generate a set of per-gene read counts for each sample using default options
The count data files were loaded into R and analyzed with DESeq2 (v 1.36.0)
Assembly: Reference human genome GRCh38.p14
Supplementary files format and content: Tab-delimited text files of raw counts

extract_protocol:
Total RNA was extracted using the Isolate II RNA minikit (Bioline)
Libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) and sequenced on Illumina’s NextSeq 500

value: macrophage-like


title: Post-ischemia sample of left ventricle sample from patient 35V, surgery in afternoon

value: Post-ischemia


title: THP-1 macrophage cells treated with csep1 protein_replicate 2


title: THP-1 macrophage cells treated with csep1 protein_replicate 1


title: Pre-ischemia sample of left ventricle sample from patient 35V, surgery in afternoon

value: PM


title: Post-ischemia sample of left ventricle sample from patient 64V, surgery in morning


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE not activated, late S fraction, replicate 2

description:
Library name: TRE_HTK_L_Rep2
nascent DNA from late S fraction

value: biol rep 2


title: THP-1 macrophage cells without treatment, control for csep1 treated cells_replicate 3


title: CD4 T cells, collected at 4wks from Pt_20

description: Library name: CD4E_212


title: THP-1 macrophage cells without treatment, control for csep1 treated cells_replicate 2


title: CD4 T cells, collected at 4wks from Pt_27

description: Library name: CD4E_211


title: Post-ischemia sample of left ventricle sample from patient 160V, surgery in morning


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE activated, late S fraction, replicate 2

description:
Library name: TRE_HTK_Dox_L_Rep2
nascent DNA from late S fraction

value: doxycycline


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE not activated, early S fraction, replicate 1

description:
Library name: TRE_HTK_E_Rep1
nascent DNA from early S fraction


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE not activated, late S fraction, replicate 1

description:
Library name: TRE_HTK_L_Rep1
nascent DNA from late S fraction


title: THP-1 macrophage cells without treatment, control for csep1 treated cells_replicate 1


title: CD4 T cells, collected at 4wks from Pt_4

description: Library name: CD4E_210

value: SD


title: IMR32_DMSO_Rep1 (RNAseq)

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

data_processing:
Quality control of the FASTQ files was done using FastQC version 0.11.7.
FASTQ files were aligned and reads were counted using STAR version 2.7.2b.
Counts were normalized using edgeR version 3.36.0 and differential expression analysis was performed using Limma-Voom version 3.50.3 in R.
Assembly: GRCh38.96
Supplementary files format and content: Tab-delimited text file include STAR counts on the reverse strand per sample

source_name: Brain

growth_protocol: The neuroblastoma cell lines were seeded in a T-75 flask at density of 2 x 106 cells per flask.

extract_protocol:
RNA extraction was performed practicing the manufacturer’s instructions of miRNeasy kit (Qiagen) including on-column DNase treatment and nanodrop (Thermo Scientific) was used to determine the concentration. RNA quality was determined with the Experion automated electrophoresis system (BioRad) prior to profiling.
250 ng of RNA-seq isolated from cell line IMR32 upon 6h time point of CR31B treatment was used as input for library preparation with the TruSeq small RNA library Kit from Illumina. During library preparation 15 PCR cycles were used. qPCR quantification of the libraries using the illumine Kapa library quantification kit (Lightcycler 480 qPCR mix Kapa). RNA-seq libraries were sequenced on the NextSeq 500 platform (Illumina) using the Nextseq 500 High Output kit V2 75 cycles paired-end (Illumina).

treatment_protocol: Cells were allowed to adhere for 48 hours, after which the medium was replaced by fresh medium and the treatment was added. CR31B condition, the IC50 concentration was added and 0.1% of DMSO was added to the vehicle condition.

value: Brain

value: neuroblast

value: WT

value: DMSO


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE activated, early S fraction, replicate 2

description:
Library name: TRE_HTK_Dox_E_Rep2
nascent DNA from early S fraction


title: CD4 T cells, collected at 4wks from Pt_19

description: Library name: CD4E_209


title: IMR32_CR31B_Rep1 (RNAseq)


title: Post-ischemia sample of left ventricle sample from patient 136V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 64V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 160V, surgery in morning


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE activated, late S fraction, replicate 1

description:
Library name: TRE_HTK_Dox_L_Rep1
nascent DNA from late S fraction

value: biol rep 1


title: HygTK expression cassette with TRE promoter at Ptn locus, TRE activated, early S fraction, replicate 1

description:
Library name: TRE_HTK_Dox_E_Rep1
nascent DNA from early S fraction


title: CD4 T cells, collected at 4wks from Pt_9

description: Library name: CD4E_206

value: PR


title: CD4 T cells, collected at 4wks from Pt_8

description: Library name: CD4E_207


title: IMR32_DMSO_Rep3 (RNAseq)

data_processing:
Quality control of the FASTQ files was done using FastQC version 0.11.7.
FASTQ files were aligned and reads were counted using STAR version 2.7.2b.
Counts were normalized using edgeR version 3.36.0 and differential expression analysis was performed using Limma-Voom version 3.50.3 in R.
Assembly: GRCh38.96
Supplementary files format and content: Tab-delimited text file include STAR counts per sample

extract_protocol:
RNA extraction was performed practicing the manufacturer’s instructions of miRNeasy kit (Qiagen) including on-column DNase treatment and nanodrop (Thermo Scientific) was used to determine the concentration. RNA quality was determined with the Experion  automated electrophoresis system (BioRad) prior to profiling.
250 ng of RNA-seq  isolated from cell line IMR32 upon 6h time point of CR31B treatment was used as input for library preparation with the TruSeq small RNA library Kit from Illumina. During library preparation 15 PCR cycles were used.  qPCR quantification of the libraries using the illumine Kapa library quantification kit (Lightcycler 480 qPCR mix Kapa). RNA-seq libraries were sequenced on the NextSeq 500 platform (Illumina) using the Nextseq 500 High Output kit V2 75 cycles single-end (Illumina).


title: Post-ischemia sample of left ventricle sample from patient 112V, surgery in morning

value: Left ventricle

value: AM


title: CD4 T cells, collected at 4wks from Pt_24

description: Library name: CD4E_205


title: Pre-ischemia sample of left ventricle sample from patient 136V, surgery in morning

value: Pre-ischemia


title: HygTK expression cassette with mouse PGK promoter at Ptn locus, late S fraction, replicate 2

description:
Library name: mPGK_HTK_L_Rep2
nascent DNA from late S fraction

value: embryonic stem cell


title: Pre-ischemia sample of left ventricle sample from patient 112V, surgery in morning


title: HygTK expression cassette with mouse PGK promoter at Ptn locus, early S fraction, replicate 2

description:
Library name: mPGK_HTK_E_Rep2
nascent DNA from early S fraction


title: IMR32_CR31B_Rep4 (RNAseq)


title: IMR32_DMSO_Rep4 (RNAseq)


title: IMR32_CR31B_Rep3 (RNAseq)


title: HygTK expression cassette with mouse PGK promoter at Ptn locus, late S fraction, replicate 1

description:
Library name: mPGK_HTK_L_Rep1
nascent DNA from late S fraction


title: Post-ischemia sample of left ventricle sample from patient 99V, surgery in morning


title: CD4 T cells, collected at 4wks from Pt_17

description: Library name: CD4E_204


title: CD4 T cells, collected at 4wks from Pt_6

description: Library name: CD4E_203


title: HygTK expression cassette with mouse PGK promoter at Ptn locus, early S fraction, replicate 1

description:
Library name: mPGK_HTK_E_Rep1
nascent DNA from early S fraction


title: IMR32_DMSO_Rep2 (RNAseq)


title: Pre-ischemia sample of left ventricle sample from patient 99V, surgery in morning


title: CD4 T cells, collected at 4wks from Pt_10

description: Library name: CD4E_202


title: IMR32_CR31B_Rep2 (RNAseq)


title: HygTK expression cassette with human PGK promoter at Ptn locus, late S fraction, replicate 2

description:
Library name: hPGK_HTK_L_Rep2
nascent DNA from late S fraction


title: CD4 T cells, collected at 4wks from Pt_25

description: Library name: CD4E_201


title: CD4 T cells, collected at Baseline from Pt_23

description: Library name: CD4E_121

value: Baseline


title: IMR32_DMSO_Rep4 (RIBOseq)

data_processing:
Adaptor sequence (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) were trimmed from RiboSeq reads using the cutadapt 3.2 with parameters (-j 10 -m 20 --discard-untrimmed).
rRNA-derived reads were identified and discarded by bowtie 2.3.4.1 with default settings.
The genes reads count were computed by RSEM v1.2.28 with default settings except using STAR 2.7.1a aligner for mapping. The reference transcripts were generated using hg38 as reference genome and GENCODE v37 as gene annotation.
Differential analysis was performed using the R package DESeq2 1.32.0.
Assembly: GRCh38
Supplementary files format and content: Transcripts Per Million (TPM) normalized counts
Library strategy: Ribo-Seq

growth_protocol: Cells were grown in complete RPMI 1640 medium (Fisher scientific, 52400041).

extract_protocol:
15µg of the lysates were treated with 7,5 units RNase I, purified with the Microspin S-400 columns and the Zymo RNA clean and concentrator kit (Zymo research, ZY-R1015). The eluted samples were size selected (28-30 nt) on a 15% PAGE urea gels.
Samples were 3' dephosphorylated with T4 PNK followed by library prep using the Small RNA library prep kit (Lexogen, 052.96). rRNA was blocked with LNA probes during the cDNA synthesis step of the library prep using the FastSelect H/M/R kit from Qiagen. Library amplification was done according to Lexogen small RNA kit. The PCR products were purified using Ampure XP beads. Library quality control was done on a DNA high sensitivity chip (BioAnalyzer Agilent, 5067-4626). Library concentrations were measured with qPCR according to Illumina's protocol. Libraries were sequenced on 2 NextSeq500 high output runs with 76bp single reads.

treatment_protocol: Cells treated with CR31B (silvestrol analog) and DMSO as control samples. After 6h, cells were treated with CHX before harvesting. Cell lysis of the cell pellets was performed using Mammalian Polysome buffer with CHX. The homogenized cell lysates were incubated for 10-30 min on ice before centrifugation (10 min, 18000g, 4°C). The cleared supernatant was recovered. The lysates were quantified using the Qubit RNA High sensitivity kit (Fisher scientific, 10034622).

tag: target

value: ribosome protected fragments


title: HygTK expression cassette with human PGK promoter at Ptn locus, early S fraction, replicate 2

description:
Library name: hPGK_HTK_E_Rep2
nascent DNA from early S fraction

data_processing:
Repli-seq and Bru-seq data processing methods have been described in PMC6546437. Basically, sequencing reads were mapped to mm10 then reads for 129 and cas alleles were parsed using SNPsplit.
Assembly: mm10
Supplementary files format and content: bedgraph files, log2(E/L) for each allele (129 or cas), scaled and LOESS smoothed in 300kb bins


title: Pre-ischemia sample of left ventricle sample from patient 141V, surgery in afternoon


title: Post-ischemia sample of left ventricle sample from patient 141V, surgery in afternoon

value: Post-ischemia


title: IMR32_CR31B_Rep4 (RIBOseq)


title: IMR32_DMSO_Rep3 (RIBOseq)


title: CD4 T cells, collected at Baseline from Pt_2

description: Library name: CD4E_120

tag: collection


title: Pre-ischemia sample of left ventricle sample from patient 109V, surgery in afternoon

value: PM


title: Pre-ischemia sample of left ventricle sample from patient 61V, surgery in afternoon


title: Post-ischemia sample of left ventricle sample from patient 109V, surgery in afternoon


title: CD4 T cells, collected at Baseline from Pt_16

description: Library name: CD4E_119

tag: patient id


title: IMR32_DMSO_Rep2 (RIBOseq)


title: CD4 T cells, collected at Baseline from Pt_29

description: Library name: CD4E_118

tag: best response

value: PD


title: HygTK expression cassette with human PGK promoter at Ptn locus, early S fraction, replicate 1

description:
Library name: hPGK_HTK_E_Rep1
nascent DNA from early S fraction


title: HygTK expression cassette with CAG promoter at Ptn locus, early S fraction, replicate 2

description:
Library name: CAG_HTK_E_Rep2
nascent DNA from early S fraction

value: F121:R26puroR-M2rtTA;  Ptn^CAG-Hyg-TK/+

value: biol rep 2


title: IMR32_CR31B_Rep2 (RIBOseq)

value: Brain


title: HygTK expression cassette with human PGK promoter at Ptn locus, late S fraction, replicate 1

description:
Library name: hPGK_HTK_L_Rep1
nascent DNA from late S fraction


title: CD4 T cells, collected at Baseline from Pt_12

description: Library name: CD4E_117

value: SD

tag: pfs months


title: HygTK expression cassette with CAG promoter at Ptn locus, late S fraction, replicate 1

description:
Library name: CAG_HTK_L_Rep1
nascent DNA from late S fraction

tag: tissue


title: Post-ischemia sample of left ventricle sample from patient 129V, surgery in morning

tag: cell type


title: Pre-ischemia sample of left ventricle sample from patient 129V, surgery in morning


title: IMR32_DMSO_Rep1 (RIBOseq)

value: neuroblast

value: WT


title: HygTK expression cassette with CAG promoter at Ptn locus, late S fraction, replicate 2

description:
Library name: CAG_HTK_L_Rep2
nascent DNA from late S fraction


title: IMR32_CR31B_Rep1 (RIBOseq)


title: HygTK expression cassette with CAG promoter at Ptn locus, early S fraction, replicate1

description:
Library name: CAG_HTK_E_Rep1
nascent DNA from early S fraction

value: biol rep 1


title: Post-ischemia sample of left ventricle sample from patient 143V, surgery in morning


title: Pre-ischemia sample of left ventricle sample from patient 143V, surgery in morning


title: Lung, high dose group -4

city: Beijing

first: Jiahua

last: Wang

address: No. 16 South Xiaojie, Dongzhimennei, Dongcheng District,

department: Experimental Research Center

institute: China Academy of Chinese Medical Sciences

description:
Library name: Sample 8
QM_4

data_processing:
total RNA was extracted from the tissue samples. The concentration and purity of the RNA were detected by Nanodrop2000, the integrity of the RNA was detected by agarose gel electrophoresis, and the RIN value was determined by Agilent2100. A single library construction required a total amount of RNA ≥1ug, a concentration ≥35ng/μL, an OD260/280≥1.8, and an OD260/230≥1.0
The 3 'end of eukaryotic mRNA has the structure of ployA tail. By using magnetic beads with Oligo (dT) and ployA A-T base pairing, mRNA can be isolated from total RNA for transcriptome analysis. The next-generation high-throughput sequencing platform is designed to sequence short sequence fragments, and the enriched mRNA is a complete RNA sequence with an average length of several kb, so it needs to be interrupted randomly. With the addition of fragmentation buffer, the mRNA can be randomly broken, and small fragments of about 300bp can be separated by magnetic bead screening. Under the action of reverse transcriptase, random hexamers were added, and mRNA was used as a template to reverse synthesize one-strand cDNA, followed by two-strand synthesis to form a stable double-stranded structure. The double-stranded cDNA had A sticky End, which was complemented to a flat end by adding End Repair Mix, and then an "A" base was added to the 3 'end to connect the Y-shaped linker. The second generation high-throughput sequencing platform platform sequencing.
Assembly: mm39
Supplementary files format and content: tab-delimited text fle includes raw counts for each Samplecsvfles include FPKM values for each Sample

source_name: lung tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: lung tissue

value: MLF

value: Mouse lung fibroblasts


title: Post-ischemia sample of left ventricle sample from patient 154V, surgery in afternoon

value: Left ventricle


title: Heterozygous Ptn E/P deletion from F121-9, NPC status, replicate 2

description:
Library name: D9_NPC_R2
nascent RNA

data_processing:
Repli-seq and Bru-seq data processing methods have been described in PMC6546437. Basically, sequencing reads were mapped to mm10 then reads for 129 and cas alleles were parsed using SNPsplit.
Assembly: mm10
Supplementary files format and content: bedgraph files, featureCounts output for each allele (129 or cas)
Library strategy: BRU-Seq

source_name: neural precursor cell

extract_protocol:
Repli-seq and Bru-seq sample extraction methods have been described in PMC6546437.
Repli-seq and Bru-seq library preparation methods have been described in PMC6546437.

value: neural precursor cell


title: CD4 T cells, collected at Baseline from Pt_21

description: Library name: CD4E_114

tag: group

value: Baseline


title: Heterozygous Ptn E/P deletion from F121-9, NPC status, replicate 3

description:
Library name: D9_NPC_R3
nascent RNA

value: biol rep 3


title: Pre-ischemia sample of left ventricle sample from patient 154V, surgery in afternoon

value: Pre-ischemia


title: Lung, high dose group -3

description:
Library name: Sample 7
QM_3


title: Homozygous Ptn E/P deletion from F121-9, NPC status,  replicate 3

description:
Library name: B8_NPC_R3
nascent RNA


title: CD4 T cells, collected at Baseline from Pt_13

description: Library name: CD4E_113


title: Lung, high dose group -1

description:
Library name: Sample 5
QM_1


title: Lung, high dose group -2

description:
Library name: Sample 6
QM_2


title: Homozygous Ptn E/P deletion from F121-9, NPC status,  replicate 2

description:
Library name: B8_NPC_R2
nascent RNA


title: Pre-ischemia sample of left ventricle sample from patient 80V, surgery in morning

value: AM


title: CD4 T cells, collected at Baseline from Pt_28

description: Library name: CD4E_115

value: PD


title: CD4 T cells, collected at Baseline from Pt_27

description: Library name: CD4E_111


title: CD4 T cells, collected at Baseline from Pt_4

description: Library name: CD4E_110


title: Lung, model group-4

description:
Library name: Sample 4
QH_4


title: CD4 T cells, collected at Baseline from Pt_20

description: Library name: CD4E_112