title: st8-E2F1&OTX1-double MO-rep2

data_processing:
CANTAC-seq reads were trimmed with fastp with parameters --length_required 20 -q 30.
The reads were then aligned to Xenopus Tropocalis v10.0 genome using bowtie2 2.4.5.
Duplicates were removed with sambamba version 0.7.0.
Peaks were called using MACS2 version 2.2.7.1 with parameters -g 1.435e9 --keep-dup all -q 0.01.
bigwig files were generated using deepTools bamCoverage with parameters -normalizeUsing CPM -bs 5.
Counts matrix were obtained with featureCounts v2.0.1 -p -BC -O -F SAF.
Assembly: xenopus tropocalis v10.0
Supplementary files format and content: Counts matrix contain counts for promoters of the genes.
Supplementary files format and content: bigwig files were used for visualization using the Integrative Genome Viewer ver 2.16.0
Library strategy: CANTAC-seq (similar to ATAC-seq)

extract_protocol:
X. tropicalis embryos were collected and homogenized with a P20 pipette tip. The nuclei were captured using ConA beads, followed by washing and lysing in 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) for 3 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD501)
PCR was then performed to amplify the library for 12-18 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s followed by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 40s, and finally 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2 ×DNA clean beads (Vazyme Biotech, N411)

value: Stage 8

value: E2F1&OTX1-double MO


title: AGS cells, PI103, 1

status: Public on Sep 03 2025

type: SRA

city: Trondheim

first: Åsmund

last: Flobak

state: Norway

address: Prinsesse Kristinas gt 1, Gastrosenteret

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology - NTNU

description: Library name: af02

library_source: transcriptomic

data_processing:
The final libraries were purified using the AMPure XP (Beckman Coulter, Inc., Indianapolis, IN, USA), quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., Wilmington, MA, USA), and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were quantified (KAPA Library Quantification Kit (Illumina/ABI Prism), normalized and pooled.
Quantitated libraries were further diluted to 2.5 nM and subject to clustering by a cBot Cluster Generation System on four HiSeq2000 flow cells (Illumina Inc. San Diego, CA, USA), according to the manufacturer's instructions.
Assembly: GRCh38
Supplementary files format and content: csv file with gene counts (HGNC, rows) per sample (sample_id, column)
Supplementary files format and content: all_samples_gene_counts.csv

molecule: total RNA

organism: Homo sapiens

source_name: stomach

growth_protocol: AGS (human gastric adenocarcinoma, ATCC, Rockville, MD) were grown in Ham’s F12 medium (Invitrogen, Carlsbad, CA) supplemented with 5% fetal calf serum (FCS; Euroclone, Devon, UK), and 10 U/ml penicillin-streptomycin (Invitrogen).

extract_protocol:
RNA was harvested using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). 0.8 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep Ligation Kit following manufacturer’s protocols.

treatment_protocol: Inhibitors (5Z)-7-oxozeaenol (0.5 µM), PD0325901 (0.035 µM), and PI103 (0.7 µM) were added (single or in combination) to be incubated in AGS cells for 24 hours. Combinatorial treatments were administered using half their full concentration. All inhibitors were obtained from Merck.

tag: tissue

value: stomach

tag: cell line

value: AGS

tag: genotype

value: WT

tag: treatment

tag: batch


title: siControl Poly N3

city: Kingston

first: Mark

middle: L.

last: Ormiston

state: Ontario

address: 18 Stuart Street

country: Canada

institute: Queen's University

data_processing:
Reads were trimmed and filtered for quality by Trimmomatic, and were aligned to the Human reference genome (GRCh38) using STAR. The abundance of each transcript was estimated using FeatureCounts.
Assembly: GrCH38
Supplementary files format and content: .csv file containing raw counts for each sample

molecule: polyA RNA

source_name: HPAECs

growth_protocol: Primary HPAECs were maintained in EGM2 (containing 2% FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was isolated from sucrose using overnight ethanol precipitation, and pellets were subsequently subject to TRIzol/chloroform extraction.
mRNA stranded RNA

treatment_protocol: siRNA mediated knockdown of linear BMPR2 mRNAs, circ5078, both, or a control were performed on cells plated in 15cm dishes. The following day, cells were harvested, and lysates separated on 10-45% sucrose gradients. Input RNA was sequenced alongside RNA isolated from heavily translated fractions (8-13)

value: HPAECs

tag: cell type

value: primary pulmonary artery endothelial cells

value: siControl

value: Polysome Fraction


title: siLinear Poly N3

value: siLinear


title: si5078 Poly N3


title: CD4, NRIP1 WT, wRA, replicate 1, scATACseq

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute of MIT and Harvard

description: 10X Genomics

library_source: genomic

data_processing:
10X multiome data was processed using Cell Ranger ARC mkfastq (v2.0.1) from 10x Genomics via the cumulus workflow.
Peaks were called using MACS2 (v2.2.7.1) with default parameters
Assembly: mm10
Supplementary files format and content: Fragment files in tab-separated values format and tabix indexed files in tbi format
Supplementary files format and content: Called peaks in narrowPeak format

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Mouse splenic naïve CD4+ T cells were purified using EasySep™ Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL). Cells were then stimulated by plates coated with 2μg/ml anti-mouse CD3e and 2μg/ml anti-mouse CD28 antibodies, with or without 100nM atRA supplement in full RPMI 1640 medium
Samples were prepared according to the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing protocol and Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression User Guide.

value: spleen

value: NRIP1 WT

value: with atRA


title: AGS cells, control, 1

description: Library name: af01


title: st8-OTX1-MO-CANTAC-rep2

city: ShenZhen

first: Luming

last: Zhang

state: Guangdong

address: 1088 Xueyuan Avenue

department: School of Life Sciences

country: China

institute: Southern University of Science and Technology

organism: Xenopus tropicalis

source_name: Embryos

value: Embryos

tag: developmental stage

value: OTX1 MO


title: CD4, NRIP1 WT, wRA, replicate 2, scATACseq

description: 10X Genomics


title: CD4, NRIP1 KO, woRA, replicate 2, scATACseq

description: 10X Genomics

value: NRIP1 KO

value: without atRA


title: st8-OTX1-MO-CANTAC-rep1

value: Stage 8


title: st8-E2F1&OTX1-double MO-CANTAC-rep1

value: E2F1&OTX1-double MO


title: si5078 Poly N2


title: CD4, NRIP1 KO, woRA, replicate 3, scATACseq

description: 10X Genomics


title: F-3

city: shenzhen

last: Li

state: guangdong

address: A16, Life Science Valley, Jinye Avenue

department: Institute of Shenzhen Respiratory Diseases

institute: Shenzhen People's Hospital

description: Library name: wt-Mab-oua33

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.23.0. (parameter:-l 50; -n 5; -q 20;-W 4;-M 20) ；
Assembly: Trimmed sequencereads were mapped to GRCm39 using hisat2 v2-2.1.0 (paramtrer:-p 8;-5 5;-3 5;--min-intronlen 20;--max-intronlen 500000;-k 3;--phred33)
Supplementary files format and content: Read count extraction and normaliation were performed using Htseq v2.0.1 (paramtrer:-s no;-a 10;-m union;-i gene_name;--nonunique none)

source_name: lung

extract_protocol:
RNA was extrated by Trizol
Samples were ground under liquid nitrogen in a mortar and pestle, and the resulting powder dissolved in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA), then extracted total RNA. 2） The quality and purity of RNA were examined by a NanoDrop™ One/OneC spectrophotometer (Thermo Scientific, Waltham, MA, USA) and Life Invitrogen Qubit RNA BR (Broad-Range) Assay Kit. RNA integrity was analyzed using Agilent 4200 TapeStation system (Agilent, Santa Clara, CA, USA)

treatment_protocol: Fresh lung tissues of C57BL/6J mice with M. abscessus infected and Ouabain treatment were selected for RNA sequencing.

value: lung

value: M. abscessus infected animals and intraperitoneal injection with ouabain


title: CD4, NRIP1 KO, woRA, replicate 1, scATACseq

description: 10X Genomics


title: st7-E2F1&OTX1-double MO-CANTAC-rep2

value: Stage 7


title: AGS cells, PI103+(5Z)-7-oxozeaenol, 1

description: Library name: af05

value: stomach

value: AGS

value: WT

value: PI103 + (5Z)-7-oxozeaenol


title: siLinear Poly N2

value: HPAECs

value: primary pulmonary artery endothelial cells

value: siLinear

value: Polysome Fraction


title: F-2

description: Library name: wt-Mab-oua32


title: st7-E2F1&OTX1-double MO-CANTAC-rep1

value: Embryos


title: CD4, NRIP1 WT, woRA, replicate 3, scATACseq

description: 10X Genomics

value: spleen

value: NRIP1 WT


title: siControl Poly N2

value: siControl


title: F-1

description: Library name: wt-Mab-oua31


title: CD4, NRIP1 WT, woRA, replicate 2, scATACseq

description: 10X Genomics

value: without atRA


title: siLinear+5078 Poly N2


title: C-3

description: Library name: wt-Mab48

value: animals infected with M. abscessus and intraperitoneally injected with saline


title: C-2

description: Library name: wt-Mab47

value: lung


title: st7-OTX1-MO-CANTAC-rep2

value: OTX1 MO


title: si5078 Poly N1


title: mouse skeletal muscle CTX-D10  Rep2

city: Guangzhou

first: TAN

last: YEYA

address: Jinsui Road, Tianhe District, Guangzhou City, Guangdong Province

department: Guangzhou Women and Children's Medical Center

institute: Guangzhou Medical University

description: Library name: CTX-D10  Rep2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: skeletal muscle

growth_protocol: The mouse skeletal myoblast C2C12  cells were cultured in growth medium, which consisted of high-glucose Dulbecco's modified Eagle's medium supplemented with 10% FBS and 1% penicillin/streptomycin, at 37 °C in 5% CO2. The cells were plated and cultured to 100% confluence and then transferred to differentiation medium consisting of DMEM containing 2% horse serum and 1% penicillin/streptomycin for further culture.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent following the manufacturer’s procedure. The RNA integrity was assessed with a Bioanalyzer 2100 with a RIN > 7.0 and confirmed by electrophoresis with a denaturing agarose gel.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: skeletal muscle


title: st7-OTX1-MO-CANTAC-rep1

value: Stage 7


title: mouse skeletal muscle CTX-D10  Rep1

description: Library name: CTX-D10  Rep1


title: MES-CANTAC

data_processing:
CANTAC-seq reads were trimmed for adaptor sequences using fastp with parametes -a CTGTCTCTTATA --detect_adapter_for_pe --length_required 20 -q 30.
The reads were then aligned to Xenopus Tropocalis v10.0 genome using bowtie2 2.4.5 with parameters -X 2000.
Duplicates were removed with sambamba version 0.7.0.
Peaks were called using MACS2 version 2.2.7.1 with parameters -g 1.435e9 --keep-dup all -q 0.05 --slocal 10000 --nomodel --nolambda -B --SPMR.
bigwig files were generated using deepTools bamCoverage with parameters -normalizeUsing CPM -bs 5.
Assembly: xenopus tropocalis v10.0
Supplementary files format and content: Counts matrix contain counts for known genes
Supplementary files format and content: bigwig files were used for visualization using the Integrative Genome Viewer ver 2.16.0

source_name: MES

extract_protocol:
X. tropicalis embryos were collected and homogenized with a P20 pipette tip. The nuclei were captured using ConA beads, followed by washing and lysing in 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) for 3 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD501)
PCR was then performed to amplify the library for 12-18 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s followed by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 40s, and finally 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2 ×DNA clean beads (Vazyme Biotech, N411)
CANTAC-seq (similar to ATAC-seq)

value: MES

value: stem cell


title: LJ mouse male rep19, d120 irrad

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (version 0.44.0).
We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: Mouse: GRCm38

source_name: Whole blood

extract_protocol:
Blood samples were collected by cheek bleeds/tail vein and added to 4X volume of PAX solution (Becton Dickinson, NJ) and inverted 10X before freezing at − 80 °C. After overnight freezing, the samples were thawed at room temperature and left for > 2 h before processing for total RNA isolation using the PAXgene® Blood RNA kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Isolated RNA was quantified using the Nanodrop One spectrophotometer (Thermofisher) and A260/ 280 ratios recorded.
RNA sequencing analysis for gene expression was performed according to standard RNA-seq pipeline at the Columbia University Medical Center Genome Center. We used the RIBOZERO workflow in which ribosomal depletion was performed to remove rRNAs from globin cleared total RNA. RINs of globin cleared RNA (catalog number AM1981 from Thermofisher) were in the acceptable range for 40-million reads RNAseq (75% of samples had RIN values >7.5).
After rRNA depletion, library construction was performed using Illumina TruSeq Stranded Total RNA kit.

value: Whole blood

value: LJ

value: 11.35 Gy upper body irradiation

tag: group

value: Live

tag: time

value: Day 120


title: XT-st7-E2F1-OTX1-MO-RNA_rep2

data_processing:
RNA-seq reads adaptors were trimmed by fastp with parameters -a AGATCGGAAGAGC --detect_adapter_for_pe -w 12 --length_required 30 -q 20.
Reads were mapped to the genome by STAR ver 2.7.0e.
Counts for known genes were obtained by featureCounts ver2.0.1 with parameters -s 2 -p -BC.
bigwig files were generated using deepTools bamCoverage with the following configurations --normalizeUsing RPKM -bs 5
Assembly: xenopus tropicalis v10.0
Supplementary files format and content: Counts matrix contain counts for known genes
Supplementary files format and content: bigwig files were used for visualization using the Integrative Genome Viewer ver 2.16.0

extract_protocol:
Total RNA was isolated using RNA Isolator Total RNA Extraction Reagent (Vazyme) followed by isopropanol precipitation according to standard protocols.
Libraries were prepared using standard protocol provided by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme).

value: Embryos

value: E2F1-OTX1 double MO

value: E2F1-OTX1 MO injected


title: siLinear Poly N1

value: HPAECs

value: primary pulmonary artery endothelial cells

value: siLinear

value: Polysome Fraction


title: MES-ATAC

value: WT


title: siLinear+5078 Input N3

value: Input Fraction


title: XT-st8-E2F1-OTX1-MO-RNA_rep1

value: Stage 8


title: XT-st8-E2F1-OTX1-MO-RNA_rep2


title: mouse skeletal muscle CTX-D5  Rep2

description: Library name: CTX-D5  Rep2

value: skeletal muscle


title: LJ mouse male rep18, d120 irrad


title: XT-st7-E2F1-OTX1-MO-RNA_rep1

value: Stage 7


title: siControl Poly N1

value: siControl


title: si5078 Input N3


title: mouse skeletal muscle CTX-D5  Rep1

description: Library name: CTX-D5  Rep1


title: LJ mouse male rep17, d120 irrad

value: Whole blood

value: LJ


title: siLinear Input N3


title: XT-st8-OTX1-MO-RNA_rep2

value: OTX1 MO

value: OTX1 MO injected


title: siLinear+5078 Poly N1


title: CD4, NRIP1 WT, woRA, replicate 1, scATACseq

description: 10X Genomics

value: spleen

value: NRIP1 WT

value: without atRA


title: mouse skeletal muscleCTX-D3  Rep2

description: Library name: CTX-D3  Rep2


title: LJ mouse male rep16, d120 irrad

value: 11.35 Gy upper body irradiation

value: Die

value: Day 120


title: XT-st8-OTX1-MO-RNA_rep1

value: Embryos


title: siControl Input N3

value: HPAECs

value: primary pulmonary artery endothelial cells


title: mouse skeletal muscleCTX-D3  Rep1

description: Library name: CTX-D3  Rep1


title: LJ mouse male rep15, d120 irrad


title: XT-st7-OTX1-MO-RNA_rep2


title: siLinear+5078 Input N2

value: Input Fraction


title: LJ mouse male rep14, d120 irrad


title: LJ mouse male rep13, d120 irrad

value: Live


title: si5078 Input N2


title: XT-st7-OTX1-MO-RNA_rep1

value: Stage 7


title: mouse skeletal muscle CTX-D1  Rep1

description: Library name: CTX-D1  Rep1

value: skeletal muscle


title: XT-st8-E2F1-Rescue-RNA_rep2

value: Stage 8

value: E2F1 Rescue

value: E2F1 mRNA and MO injected


title: siLinear Input N2

value: siLinear


title: LJ mouse male rep12, d120 irrad

value: Whole blood

value: LJ


title: XT-st8-E2F1-Rescue-RNA_rep1


title: mouse skeletal muscle CTX-D0  Rep1

description: Library name: CTX-D0  Rep1


title: mouse skeletal muscle CTX-D0  Rep2

description: Library name: CTX-D0  Rep2


title: XT-st7-E2F1-Rescue-RNA_rep2


title: siControl Input N2

value: siControl


title: LJ mouse male rep11, d120 irrad

value: 11.35 Gy upper body irradiation


title: siLinear+5078 Input N1


title: LJ mouse male rep10, d120 irrad

value: Die


title: XT-st7-E2F1-Rescue-RNA_rep1


title: si5078 Input N1


title: XT-st6-E2F1-Rescue-RNA_rep2

value: Stage 6


title: LJ mouse male rep9, d120 irrad

value: Day 120


title: C2C12 myoblasts-Cas9M3-D3 Rep1

description: Library name: Cas9M3-D3 Rep1

source_name: C2C12 myoblasts

value: C2C12 myoblasts

value: mouse C2C12 myoblasts


title: siLinear Input N1

value: HPAECs

value: primary pulmonary artery endothelial cells

value: Input Fraction


title: C2C12 myoblasts-Cas9M3-D0 Rep2

description: Library name: Cas9M3-GM Rep2


title: mouse skeletal muscle CTX-D1  Rep2

description: Library name: CTX-D1  Rep2

value: skeletal muscle


title: LJ mouse male rep8, d120 irrad

value: Live


title: siControl Input N1


title: stage7 cdknla rep2

value: Embryos

value: Stage 7

value: Cdkn1a mRNA

value: Cdkn1a mRNA injected


title: XT-st6-E2F1-Rescue-RNA_rep1

value: E2F1 Rescue

value: E2F1 mRNA and MO injected


title: LJ mouse male rep7, d120 irrad

value: Whole blood

value: LJ

value: 11.35 Gy upper body irradiation


title: HPAECs, siBMPR2, BMP9, N3

data_processing:
Reads were trimmed and filtered for quality by Trimmomatic, and were aligned to the Human reference genome (GRCh38) using STAR. The abundance of each transcript was estimated using HT-Seq Count.
Assembly: GRCh38
Supplementary files format and content: .csv file with raw count data for each sample

extract_protocol:
Cells were harvested in TRIzol and total RNA was purified using Direct-zol RNA Miniprep columns
rRNA depleted stranded total RNA was sequenced

treatment_protocol: siRNA mediated knockdown was performed the day following plating of cells in 6-well plate. The next day, cells were quiesced in EBM2 (with 2% FBS) for 4 hours, and subsequently returned to EGM2 media +/- 1ng/mL BMP9 for 24 hours.


title: XT-st8-E2F1-MO-RNA_rep1

value: Stage 8

value: E2F1 MO

value: E2F1 MO injected


title: LJ mouse male rep6, d120 irrad

value: Day 120


title: C2C12 myoblasts-CTRL-D3 Rep1

description: Library name: Ctrl-D3 Rep1

value: C2C12 myoblasts

value: mouse C2C12 myoblasts


title: XT-st8-E2F1-MO-RNA_rep2


title: C2C12 myoblasts-CTRL-D3 Rep2

description: Library name: Ctrl-D3 Rep2


title: HPAECs, siControl, BMP9, N3

value: HPAECs

value: primary pulmonary artery endothelial cells

value: siControl


title: C2C12 myoblasts-CTRL-D0 Rep2

description: Library name: Ctrl-GM Rep2


title: C2C12 myoblasts-Cas9M3-D3 Rep2

description: Library name: Cas9M3-D3 Rep2


title: LJ mouse male rep4, d120 irrad

value: Die


title: XT-st7-E2F1-MO-RNA_rep2

value: Embryos

value: Stage 7


title: XT-st7-E2F1-MO-RNA_rep1


title: XT-st6-E2F1-MO-RNA_rep2

value: Stage 6


title: C2C12 myoblasts-CTRL-D0 Rep1

description: Library name: Ctrl-GM Rep1


title: C2C12 myoblasts-GFP-D4 Rep2

description: Library name: C2-GFP-D4 Rep2


title: XT-st6-E2F1-MO-RNA_rep1


title: LJ mouse male rep3, d120 irrad


title: LJ mouse male rep2, d120 irrad


title: C2C12 myoblasts-GFP-D4 Rep1

description: Library name: C2-GFP-D4 Rep1


title: HPAECs, siBMPR2, BMP9, N2


title: C2C12 myoblasts-Cas9M3-D0 Rep1

description: Library name: Cas9M3-GM Rep1


title: HPAECs, siBMPR2, NS, N2

value: NS


title: XT-16cell-E2F1-MO-RNA-rep2

value: Stage 5


title: LJ mouse male rep1, d120 irrad

value: Whole blood

value: LJ

value: Live


title: HPAECs, siControl, BMP9, N2


title: LJ mouse male rep10, d120 control

value: sham irradiation


title: C2C12 myoblasts-GFP-D0 Rep2

description: Library name: C2-GFP-D0 Rep2


title: HPAECs, siBMPR2, NS, N3


title: XT-16cell-E2F1-MO-RNA-rep1

value: E2F1 MO

value: E2F1 MO injected


title: LJ mouse male rep5, d120 irrad

value: 11.35 Gy upper body irradiation

value: Day 120


title: C2C12 myoblasts-GFP-D0 Rep1

description: Library name: C2-GFP-D0 Rep1

value: C2C12 myoblasts

value: mouse C2C12 myoblasts


title: XT-8cell-E2F1-MO-RNA-rep2

value: Stage 4


title: C2C12 myoblasts-M3-D4 Rep2

description: Library name: C2-M3-D4 Rep2


title: LJ mouse male rep8, d120 control


title: HPAECs, siBMPR2, BMP9, N1

value: HPAECs

value: primary pulmonary artery endothelial cells


title: XT-8cell-E2F1-MO-RNA-rep1

value: Embryos


title: HPAECs, siControl, NS, N3

value: siControl


title: C2C12 myoblasts-M3-D4 Rep1

description: Library name: C2-M3-D4 Rep1


title: HPAECs, siBMPR2, NS, N1

value: NS


title: LJ mouse male rep7, d120 control


title: XT-4cell-E2F1-MO-RNA-rep2

value: Stage 3


title: LJ mouse male rep6, d120 control

value: Whole blood


title: XT-4cell-E2F1-MO-RNA-rep1


title: C2C12 myoblasts-M3-D0 Rep1

description: Library name: C2-M3-D0 Rep1


title: LJ mouse male rep5, d120 control

value: LJ


title: HPAECs, siControl, NS, N1


title: XT-st13-WT-RNA-rep2

value: Stage 13

value: WT


title: LJ mouse male rep4, d120 control

value: sham irradiation

value: Live


title: K562-CANTAC

value: lymphoblastoid


title: LJ mouse male rep3, d120 control

value: Day 120


title: K562-ATAC


title: XT-st10-WT-RNA-rep2

value: Stage 10


title: EVs, hBM-MSC-derived EVs, Smase-treated, rep3

city: Atlanta

first: Daniel

middle: C

last: Shah

state: Ga

address: 315 Ferst Dr.

department: Biomedical Engineering

institute: Georgia Institute of Technology

description:
Library name: Sample 12
column name in Raw Counts_All EVs: EV_S3

data_processing:
RNA-seq Analysis Portal 5.0 (https://rnaportal.qiagen.com)
Sequence reads were aligned and mapped to the homo sapiens reference miRbase_v22 using RNA Analysis Portal.
Read count and CMP was generated using RNA-seq Analysis Portal 5.0
Assembly: Total RNA (EVs = ~6-30 ng and MSCs =100 ng) was used to construct the sequence libraries.
Supplementary files format and content: csv files including read counts for each sample

source_name: Bone Marrow

growth_protocol: BM-MSC donor RB183 was cultured and maintained in RoosterNourish media containing RoosterBooster in humidified conditions with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using miRNeasy tissue/cell advanced mini kit (Qiagen).
Libraries for miRNA-seq was consructed using QIAseq miRNA library kit following the manufactureer's protocol.

treatment_protocol: Once sub-passaged cells were ~80% confluent, they were switched to Rooster Collect-EV and treated with or without 0.3 U/mL of filter sterilized sphingomyelinase.

value: Bone Marrow

value: Mesenchymal Stromal cells

value: SMase-treated


title: XT-st13-WT-RNA-rep1


title: EVs, hBM-MSC-derived EVs, Smase-treated, rep1

description:
Library name: Sample 10
column name in Raw Counts_All EVs: EV_S1


title: LJ mouse male rep9, d120 control


title: HPAECs, siControl, NS, N2

value: HPAECs

value: primary pulmonary artery endothelial cells


title: digested dental pulp single-cell suspensions

city: Shanghai

first: Lingyong

last: Jiang

state: Shanghai

address: No.639, zhi zao ju road

institute: Shanghai jiao tong University

description: BD Rhapsody

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: Single cell matrix files

source_name: dental pulp

extract_protocol:
In brief, dental pulp tissues and periodontal ligament were removed from teeth, minced, and digested in a solution of 3mg/mL collagenase type I and 4mg/mL dispase (Sigma-Aldrich, St.Louis, MO) for 30–60 min at 37°C.
cDNA synthesis was performed using the BD Rhapsody Express Single-Cell Analysis System, and gene expression libraries were prepared using Whole Transcriptome Analysis Amplification Kit (all from BD Biosciences).Whole Transcriptome Analysis Amplification Kit (all from BD Biosciences).

value: dental pulp

tag: Sex

value: male

tag: age


title: EVs, hBM-MSC-derived EVs, untreated, rep3

description:
Library name: Sample 9
column name in Raw Counts_All EVs: EV_UT3


title: digested periodontal ligament single-cell suspensions

description: BD Rhapsody

source_name: periodontal ligament

value: periodontal ligament


title: XT-st10-WT-RNA-rep1

value: Embryos


title: XT-st9-WT-RNA-rep2

value: Stage 9


title: LJ mouse male rep1, d120 control

value: Whole blood

value: LJ


title: LJ mouse male rep2, d120 control

value: sham irradiation


title: RNA-Seq - Patient_20

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: RNA-sequencing

data_processing:
The expression levels for each gene were quantified from the sequencing data using Kallisto software.
The tximport package (ver. 1.18.0) was used to summarize the data.
Assembly: GRCh38
Supplementary files format and content: tab-separated values file includes TPM values for each sample

source_name: ovarian cancer

extract_protocol:
Total RNA was extracted from fresh-frozen samples using an miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Library construction and pair-end sequencing were conducted by Novogene, Inc. (Beijing, China).

value: ovarian cancer

tag: Stage

tag: neoajuvant chemotherapy

value: Yes

value: PR

tag: surgical outcome

value: complete

tag: 1st tfip


title: Aged_bulk-HSCs_rep3

city: Kobe

first: Katsuyuki

last: Nishi

state: Hyogo

address: 1-5-6 Minatojima-minamimachi, Chuo-ku

institute: Kobe University Graduate School of Medicine

data_processing:
Raw transcriptome sequence data were mapped to the genome (mm10) using HISAT2 (ver 65 2.1.0).
Sam files were converted to bam files using Samtools (ver 1.7).
Alignments were then passed to StringTie (ver 1.3.4d), which was used to assemble and quantify transcripts in each sample.
Assembly: mm10
Supplementary files format and content: Comma-separated values file including read count matrix.

extract_protocol:
RNA was harvested using RNeasy MinElute columns (Qiagen).
cDNA libraries were prepared from bulk-HSCs, ST-HSCs and LT-HSCs using a KAPA RNA HyperPrep kit with RiboErase (HMR).


title: C2C12 myoblasts-M3-D0 Rep2

description: Library name: C2-M3-D0 Rep2

value: C2C12 myoblasts

value: mouse C2C12 myoblasts


title: XT-st9-WT-RNA-rep1

value: WT


title: HPAECs, siControl, BMP9, N1

value: HPAECs

value: siControl


title: EVs, hBM-MSC-derived EVs, untreated, rep1

description:
Library name: Sample 7
column name in Raw Counts_All EVs: EV_UT1

value: Bone Marrow

value: Mesenchymal Stromal cells


title: RNA-Seq - Patient_18

description: RNA-sequencing

value: Complete


title: Cells, hBM-MSCs, SMase-treated, rep3

description:
Library name: Sample 6
column name in Raw Counts_All MSCs: MSC_S3

value: SMase-treated


title: XT-st8-WT-RNA-rep2

value: Embryos

value: Stage 8


title: RNA-Seq - Patient_19

description: RNA-sequencing

value: No

value: Optimal


title: Aged_bulk-HSCs_rep2


title: Aged_ST-HSCs_rep3


title: EVs, hBM-MSC-derived EVs, Smase-treated, rep2

description:
Library name: Sample 11
column name in Raw Counts_All EVs: EV_S2


title: Aged_bulk-HSCs_rep1


title: Cells, hBM-MSCs, untreated, rep3

description:
Library name: Sample 3
column name in Raw Counts_All MSCs: MSC_UT3


title: Aged_ST-HSCs_rep2


title: XT-st6-WT-RNA-rep2

value: Stage 6


title: XT-st8-WT-RNA-rep1


title: Aged_ST-HSCs_rep1


title: RNA-Seq - Patient_16

description: RNA-sequencing

value: ovarian cancer

value: Suboptimal


title: XT-st6-WT-RNA-rep1


title: Aged_LT-HSCs_rep3


title: RNA-Seq - Patient_12

description: RNA-sequencing

value: Yes

value: PR


title: RNA-Seq - Patient_17

description: RNA-sequencing


title: EVs, hBM-MSC-derived EVs, untreated, rep2

description:
Library name: Sample 8
column name in Raw Counts_All EVs: EV_UT2


title: Control_5_Ascites-miRNA

description: Small RNA-sequencing

data_processing:
The CLC Genomics Workbench version 9.5.3 program (Qiagen) was used for data analysis.
Adaptor sequences were trimmed and sequences between 15 and 35 bps were counted.
The trimmed data were mapped to the miRbase 21 database, allowing up to two mismatches.
The data was normalized with reads per million mapped reads.
Assembly: miRbase 21
Supplementary files format and content: tab-delimited text file includes RPM values for each sample

source_name: Ascites EV

extract_protocol:
Total RNA was extracted from fresh-frozen samples using an miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Small RNA libraries was prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA)

treatment_protocol: Ascites samples were centrifuged at 10,000 × g for 40 min at 4°C (Kubota 3520). The supernatant was filtered using a 0.22 μm filter, and ultracentrifuged at 110,000 × g for 70 min at 4°C using a TLA55 rotor (Beckman Coulter Inc., USA). The pellet was washed with PBS, ultracentrifuged under the same conditions, and resuspended in PBS to extract the sEVs.

value: Ascites EV

tag: diagnosis

value: ovarian fibroma


title: Cells, hBM-MSCs, SMase-treated, rep1

description:
Library name: Sample 4
column name in Raw Counts_All MSCs: MSC_S1

value: WT


title: XT-st7-WT-RNA-rep1

value: Stage 7


title: RNA-Seq - Patient_14

description: RNA-sequencing

value: CR


title: Cells, hBM-MSCs, untreated, rep2

description:
Library name: Sample 2
column name in Raw Counts_All MSCs: MSC_UT2

value: Bone Marrow

value: Mesenchymal Stromal cells


title: XT-16cell-WT-RNA-rep1

value: Stage 5


title: RNA-Seq - Patient_13

description: RNA-sequencing


title: Cells, hBM-MSCs, untreated, rep1

description:
Library name: Sample 1
column name in Raw Counts_All MSCs: MSC_UT1


title: XT-16cell-WT-RNA-rep2

value: Embryos


title: RNA-Seq - Patient_15

description: RNA-sequencing


title: Aged_LT-HSCs_rep1


title: XT-st7-WT-RNA-rep2


title: Cells, hBM-MSCs, SMase-treated, rep2

description:
Library name: Sample 5
column name in Raw Counts_All MSCs: MSC_S2

value: SMase-treated


title: RNA-Seq - Patient_11

description: RNA-sequencing

value: No


title: Young_bulk-HSCs_rep2


title: Control_4_Ascites-miRNA

description: Small RNA-sequencing

value: uterine leiomyoma


title: XT-8cell-WT-RNA-rep2

value: Stage 4


title: Aged_LT-HSCs_rep2


title: Control_3_Ascites-miRNA

description: Small RNA-sequencing

value: ovarian mucinous cystadenoma


title: RNA-Seq - Patient_9

description: RNA-sequencing

value: ovarian cancer

value: Optimal


title: Control_2_Ascites-miRNA

description: Small RNA-sequencing


title: XT-8cell-WT-RNA-rep1


title: Young_bulk-HSCs_rep1


title: XT-4cell-WT-RNA-rep2

value: Stage 3


title: RNA-Seq - Patient_8

description: RNA-sequencing

value: Yes

value: PR


title: Young_ST-HSCs_rep3


title: XT-4cell-WT-RNA-rep1

value: WT


title: RNA-Seq - Patient_7

description: RNA-sequencing


title: Young_bulk-HSCs_rep3


title: Young_LT-HSCs_rep3


title: RNA-Seq - Patient_6

description: RNA-sequencing

value: Complete


title: OTX1-ChIP-st8-rep2

data_processing:
ChIP-seq reads were trimmed for adaptor sequences using fastp with parameters --length_required 20 -q 30, and then aligned to Xenopus Tropocalis v10.0 genome using bowtie2 2.4.5 with parameters --very-sensitive.
Duplicates were removed with sambamba version 0.7.0.
Peaks were called using MACS2 version 2.2.7.1 with parameters -g 1.435e9 --keep-dup all -q 0.01.
bigwig files were generated using deepTools bamCoverage with parameters -normalizeUsing CPM -bs 5.
Assembly: xenopus tropocalis v10.0
Supplementary files format and content: bigwig files were used for visualization using the Integrative Genome Viewer ver 2.16.0

extract_protocol:
The ChIP assay was performed according to the standard protocol provided by SimpleChIP Plus Sonication Chromatin IP Kit (CST)
Libraries were prepared using standard protocol provided by VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme)

value: Stage 8

value: OTX1 Rescue

value: OTX1 mRNA and MO injected

tag: chip antibody

value: Myc-Tag (CST, #2276)


title: RNA-Seq - Patient_10

description: RNA-sequencing

tag: tissue


title: Young_ST-HSCs_rep2


title: Patient_19_Ascites-miRNA

description: Small RNA-sequencing

value: Ascites EV


title: RNA-Seq - Patient_5

description: RNA-sequencing


title: Young_LT-HSCs_rep2


title: RNA-Seq - Patient_4

description: RNA-sequencing


title: E2F1-ChIP-st8-rep2

value: Embryos

value: E2F1 Rescue

value: E2F1 mRNA and MO injected

value: HA (Sigma, H6908)


title: OTX1-ChIP-st8-rep1


title: Patient_18_Ascites-miRNA

description: Small RNA-sequencing


title: Patient_17_Ascites-miRNA

description: Small RNA-sequencing

value: No


title: Patient_16_Ascites-miRNA

description: Small RNA-sequencing

value: ovarian cancer

value: Suboptimal


title: E2F1-ChIP-st8-rep1


title: Young_LT-HSCs_rep1


title: RNA-Seq - Patient_3

description: RNA-sequencing


title: RNA-Seq - Patient_2

description: RNA-sequencing

value: Optimal


title: Control_1_Ascites-miRNA

description: Small RNA-sequencing

value: uterine leiomyoma


title: Patient_15_Ascites-miRNA

description: Small RNA-sequencing


title: Pool_18_TGCATGTTAC-TCTCTGTTAG

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description:
Library name: Sample 12
Column name in raw_counts_All Samples.txt: Pool_18_TGCATGTTAC-TCTCTGTTAG

data_processing:
The libraries were sequenced from both ends of the fragments for a total of 150bp per end, to a total depth of at least 2 million reads per sample. The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA). The quality of the demultiplexed fastq files were evaluated with the FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), which generates reports with the quality scores, base composition, k-mer, GC and N contents, sequence duplication levels and overrepresented sequences.
Assembly: S. salar reference genome (Ssal_v3.1)
Supplementary files format and content: Matrix data from DEseq2 analysis

organism: Salmo salar

source_name: Skin

extract_protocol:
Total RNA was obtained by homogenized the tissue with Trisure.1 μg of total RNA was used for the construction of sequencing libraries. Three pools were used for each condition and season, consisting of five fish each.
RNA libraries for RNA-seq were preapred using TruSeq Stranted Total RNA Sample Prep Kit following manufacter's protocols.

treatment_protocol: Before RNA extraction, skin samples were stripped of scales and muscle.

value: Skin

value: Autumn-Non-infested


title: XT_E2F1_MO_st8_CANTAC_rep1

value: E2F1 MO


title: RNA-Seq - Patient_1

description: RNA-sequencing

value: Yes

value: PR


title: Patient_14_Ascites-miRNA

description: Small RNA-sequencing

value: CR

value: Complete


title: Pool_17_GAATGTGTTG-ACGGAGATGG

description:
Library name: Sample 11
Column name in raw_counts_All Samples.txt: Pool_17_GAATGTGTTG-ACGGAGATGG


title: Patient_20_Ascites-miRNA

description: Small RNA-sequencing

value: Ascites EV

value: complete


title: XT_E2F1_MO_st7_CANTAC_rep2

value: Embryos

value: Stage 7


title: Pool_16_ATAGGACACA-AAGACGTCAA

description:
Library name: Sample 10
Column name in raw_counts_All Samples.txt: Pool_16_ATAGGACACA-AAGACGTCAA


title: Patient_13_Ascites-miRNA

description: Small RNA-sequencing


title: XT_E2F1_MO_st7_CANTAC_rep1


title: H4K12ac ChIP, Control RNAi, IgG antibody for ChIP, Replicate 1

city: Planegg-Martinsried

first: Zivkos

last: Apostolou

address: Großhaderner Strasse 9

country: Germany

institute: Biomedical Center Munich, LMU

description: Library name: H4K12ac-ChIP_Ctrl-RNAi_IgG_Rep1

data_processing:
Raw reads from FASTQ files were first trimmed to remove sequencing adaptors using cutadapt (v1.16).
Trimmed reads were then aligned to the Drosophila melanogaster reference genome (Ensembl BDGP6.46) using Bowtie2, followed by processing with SAMtools (v1.9) to filter alignments with a mapping quality of at least 2 (-q 2), and BEDTools (v2.28.0).
BigWig files were generated using bamCompare (deepTools v3.5.0), normalizing each CUT&RUN sample to its corresponding IgG control (for H2A.V and H2A.Vac) or pre-immune serum (for Tip60), while also adjusting for sequencing depth. ChIP-seq samples were normalized to its corresponding input control, while also adjusting for sequencing length.
For each condition, biological replicates were averaged according to the number of mapped reads using bigwigAverage (deepTools v3.5.6).
Peak calling for Tip60 was performed independently in each replicate with MACS2 (v2.1.2) using the parameters: --qvalue 0.05 --fe-cutoff 2, and only peaks present in all three replicates were retained.
Assembly: Drosophila melanogaster reference genome (Ensembl BDGP6.46)
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

growth_protocol: Drosophila embryonic Kc167 and S2 cells were obtained from Drosophila Genomic Resource Center. Cells were cultured at 26°C in Schneider’s Drosophila Medium (Thermo-Fischer, Cat. No. 21720024) supplemented with 10% FBS (Capricorn, Cat. No. FBS-12A) and 1% Penicillin-Streptomycin solution (PenStrep; Sigma-Aldrich, Cat. No. P-4333).

extract_protocol:
CUT&RUN was performed as previously described (Meers M.P. et.al., 2019. DOI: 10.7554/eLife.46314). Briefly, Concanavalin-A magnetic beads (10 μl of slurry/reaction) were pre-activated by washing 2 times with Binding Buffer (BB: 20 mM Hepes pH 7.5 (NaOH), 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 106 Kc167 cells per condition were bound to the beads, and washed twice with Wash Buffer (WB: 20 mM Hepes pH 7.5 (NaOH), 150 mM NaCl, 0.5 mM spermidine, 1x cOmplete EDTA-free Protease inhibitor). Cells were permeabilized using 150 μl of Antibody Buffer (AB: 20 mM Hepes, pH 7.5 (NaOH), 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin, 2 mM EDTA, 0.5 mM Na-butyrate). Antibodies were mixed into AB at the indicated dilutions. Samples were put on a nutator at RT for 2 hours, and washed twice with Dig-Wash Buffer (Dig-WB: 20 mM Hepes, pH 7.5 (NaOH), 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin, 1x cOmplete EDTA-free Protease inhibitor). pAG/MNase protein (700 ng/ml) was mixed into 150 μl of Dig-WB and samples were placed on a nutator at 4°C for 1 hour, and then washed twice with Dig-WB. Chromatin digestion was performed by the addition of 2 mM (f.c.) CaCl2 into 100 μl of Dig-WB and incubated at 4°C for 30 min. The reaction was stopped by adding 100 μl of 2x STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 μg/ml RNase A, 50 μg/ml glycogen) and the chromatin fragments were released from insoluble nuclear chromatin by incubating at 37°C for 30 min. Samples were collected by a quick spin and placed on a magnet stand to concentrate the magnetic beads with bound chromatin fragments. Chromatin was digested with 0.25 mg/ml Proteinase K/ 0.1% SDS, and DNA was purified by phenol/chloroform extraction. DNA concentrations were determined using Qubit (Thermo Fisher).                                    ChIP-seq was performed using 70 million S2 cells fixed with 2.2 ml 10x Fixing Solution (0.1 M NaCl, 50 mM Hepes pH 7.6, 1 mM EDTA, 0.5 mM EGTA, 10% methanol-free formaldehyde) for 8 min at RT. Fixation was quenched with 125 mM glycine for 10 min on ice, cells were pelleted (1500 rpm, 10 min, 4°C), and washed twice with 10 ml ice-cold PBS. Nuclei were isolated in 1 ml 0.5% Triton/PBS supplemented with 1x cOmplete EDTA-free protease inhibitors and 2 mM Na-butyrate (rotate 15 min, 4°C), centrifuged (3000 rpm, 10 min), and washed once with PBS. Pellets were resuspended in 1 ml RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.1% SDS, 1% Triton X-100) supplemented with 2 mM CaCl2, 1x cOmplete EDTA-free protease inhibitors, 1 mM PMSF, and 2 mM Na-butyrate. Lysates of 1 ml were digested with 0.6 U MNase (Sigma–Aldrich), was resuspended in EX-50 (50 mM KCl, 10 mM HEPES, pH 7.6, 1.5 mM MgCl2, 0.5 mM EGTA, 10% glycerol) at 0.6 U/μl, at 37°C for 35 min and stopped with 22 μl 0.5 M EGTA on ice. Chromatin was mildly sheared with a Covaris AFA S220 (50 W peak power, 200 cycles/burst, 20% duty factor, 8 min, 4°C), centrifuged (16,000 g, 20 min, 4°C), and supernatant was pre-cleared with 10 μl Protein A+G beads per 100 μl chromatin (1 h, 4°C). Beads were removed (3000 rpm, 3 min), and 50 μl input was collected. For IP, 200 μl chromatin were diluted to 500 μl in RIPA, incubated overnight at 4°C with antibody or IgG control, and captured with 40 μl Protein A+G beads (3 h, 4°C). Beads were washed 5× with 1 ml RIPA, resuspended in 100 μl TE (10 mM Tris pH 8.0, 1 mM EDTA), and inputs adjusted to equal volume. Decrosslinking was performed with RNase A (50 μg/ml, 30 min, 37°C), followed by Proteinase K (0.5 mg/ml) and SDS (0.6%) at 68°C for 2 h. DNA was purified using AMPure XP beads. To 100 μl sample, 200 μl beads (1:1 dilution) were added, mixed by pipetting, and incubated 5 min at RT. Tubes were placed on a magnetic stand for ≥2 min, supernatant removed, and beads washed twice with 200 μl 80% ethanol. After a brief spin, residual ethanol was removed on the magnetic stand and beads were air-dried for 2 min. DNA was eluted in 30 μl TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0) by pipetting, incubated 2 min at RT, and collected after 1 min on the magnetic stand.
For ChIP-seq samples, libraries were prepared using NEB Next Ultra II DNA Library (New England Biolabs) according to the manufacturer's instructions. For CUT&RUN, sequencing libraries were prepared as described (25). All libraries were sequenced on an Illumina NextSeq1000/2000 sequencer at the Laboratory of Functional Genomic Analysis (LAFUGA, Gene Center Munich, LMU). For CUT&RUN about 5x106 paired-end reads were sequenced per sample for each of the biological replicates.

treatment_protocol: Double-stranded RNA (dsRNA) targeting the desired sequences was generated by in vitro transcription using the HiScribe T7 High Yield RNA Synthesis Kit (NEB, Cat. No. E2040S). For CUT&RUN, the cells underwent two consecutive rounds of RNAi. In brief, 6 μg of dsRNA was added to 10⁶ Kc167 cells in 0.5 ml of serum-free medium. Following a 1-hour incubation at 26°C, an equal volume of medium containing 20% fetal bovine serum (FBS) and 2% PenStrep was added, resulting in final concentrations of 10% FBS and 1% PenStrep. Cells were incubated in 12-well plates at 26°C for 3 days. On day 4, cells were split, counted and 0.8×10⁶ RNAi-treated cells of each condition was used for the second round of RNAi.

tag: cell line

tag: cut&run antibody

value: IgG (Cell Signaling, #2729S)

value: Ctrl-RNAi


title: H4K12ac ChIP, Control RNAi, H4K12ac antibody for ChIP, Replicate 1

description: Library name: H4K12ac-ChIP_Ctrl-RNAi_H4K12ac_Rep1

value: H4K12ac (Sigma-Aldrich, #07-595)

tag: treatment


title: Patient_12_Ascites-miRNA

description: Small RNA-sequencing

value: ovarian cancer

value: Suboptimal


title: H4K12ac ChIP, Control RNAi, Input, Replicate 1

description: Library name: H4K12ac-ChIP_Ctrl-RNAi_Input_Rep1


title: Young_ST-HSCs_rep1


title: XT_st13_CANTAC_rep2

value: Stage 13

tag: genotype

value: WT


title: Patient_10_Ascites-miRNA

description: Small RNA-sequencing

value: Optimal


title: Patient_11_Ascites-miRNA

description: Small RNA-sequencing

value: No


title: Pool_13_ACTTAACACC-TGCTATCTAG

description:
Library name: Sample 7
Column name in raw_counts_All Samples.txt: Pool_13_ACTTAACACC-TGCTATCTAG

value: Skin

value: Autumn-Infested


title: XT_st13_CANTAC_rep1


title: XT_st10_CANTAC_rep2

value: Stage 10


title: Colon content KO DSS, rep 3

city: Wuerzburg

first: Natalie

last: Burkard

address: Oberduerrbacherstr. 6

department: Experimentelle Viszeralchirurgie

institute: Universitätsklinikum Würzburg

data_processing:
library strategy: 16s rRNA gene seq
Demultiplexed FASTQ files were generated with bcl-convert v4.0.3
Raw sequence data were processed using the QIIME2 pipeline
Paired-end reads were quality filtered, trimmed, and merged using the DADA2 plugin, chimeric sequences were removed during this step
The 'feature table.csv' shows abundance data for amplicon sequence variants (ASVs) for each individual sample. The raw data were processed using a denoising filter (DADA2). The identifiers (in the feature table.csv) are 'names' for the ASVs, which were randomly generated by the algorithm.
Assembly: not provided
Supplementary files format and content: abundance data for amplicon sequence variants (ASVs) for each individual sample

source_name: colon content

extract_protocol:
Total genomic DNA was extracted using the QIAmp PowerFecal Pro DNA Kit, 10 ng of DNA was used for library preparation
Sequencing of pooled libraries, spiked with 10% PhiX control library, was performed at 600 K reads/sample in paired-end mode with 2x150 nt read length on the MiniSeq platform (Illumina). For this, custom primers were spiked into the Illumina primers for both, normal and index reads.

value: colon content

value: DSS


title: Pool_14_GCCAAGGAGT-TAAGGTCCAA

description:
Library name: Sample 8
Column name in raw_counts_All Samples.txt: Pool_14_GCCAAGGAGT-TAAGGTCCAA


title: XT_E2F1_MO_st8_CANTAC_rep2

value: Stage 8

value: E2F1 MO


title: Patient_8_Ascites-miRNA

description: Small RNA-sequencing

value: Ascites EV

value: Yes

value: PR


title: XT_st10_CANTAC_rep1

value: Embryos


title: Patient_7_Ascites-miRNA

description: Small RNA-sequencing

value: ovarian cancer


title: Pool148_10_11_1

description:
Library name: Sample 6
Column name in raw_counts_All Samples.txt: Pool148_10_11_1

value: Spring-infested


title: Pool131_4_7_1

description:
Library name: Sample 5
Column name in raw_counts_All Samples.txt: Pool131_4_7_1


title: Colon content WT basal, rep 2

value: Jupfl/fl

value: basal


title: Patient_6_Ascites-miRNA

description: Small RNA-sequencing

value: Complete


title: XT_st9_CANTAC_rep2

value: Stage 9

value: WT


title: Colon content WT basal, rep 1


title: Pool1213_15_1

description:
Library name: Sample 4
Column name in raw_counts_All Samples.txt: Pool1213_15_1

value: Skin

value: Spring-Non-infested


title: Pool_15_GCAAGGTTCC-CTGTGCTACA

description:
Library name: Sample 9
Column name in raw_counts_All Samples.txt: Pool_15_GCAAGGTTCC-CTGTGCTACA

value: Autumn-Infested


title: XT_st9_CANTAC_rep1


title: Colon content KO basal, rep 1

value: colon content


title: Pool1110_12_1

description:
Library name: Sample 3
Column name in raw_counts_All Samples.txt: Pool1110_12_1


title: Patient_5_Ascites-miRNA

description: Small RNA-sequencing

value: Optimal


title: XT_st8_CANTAC_rep2

value: Stage 8


title: Patient_4_Ascites-miRNA

description: Small RNA-sequencing

value: Ascites EV


title: Colon content WT DSS, rep 2

value: DSS


title: Patient_2_Ascites-miRNA

description: Small RNA-sequencing

value: Yes

value: PR


title: Pool102_8_9_1

description:
Library name: Sample 2
Column name in raw_counts_All Samples.txt: Pool102_8_9_1


title: Patient_3_Ascites-miRNA

description: Small RNA-sequencing

value: ovarian cancer

value: No


title: Colon content KO DSS, rep 1


title: Patient_1_Ascites-miRNA

description: Small RNA-sequencing

value: Suboptimal


title: XT_st8_CANTAC_rep1

value: Embryos


title: Colon content KO basal, rep 2

value: basal


title: FMD+VC 46

status: Public on Sep 02 2025

city: Los Angeles

first: Valter

middle: D

last: Longo

state: CA

address: 3715 McClintock Avenue

institute: USC

description: Mouse 46

data_processing:
After initial quality check RNA-Seq reads were mapped to the mouse GRCm38 references using HISAT2 (2.1.0) with default parameter.
The resulting mapped reads of each sample are stored in a binary format file (.bam).  Gene counts were obtained by counting the number of sequencing reads overlapping each of the genes (HTSeq v0.6.1)
Gene annotations (ENSEMBL GRCh38, gtf format) were downloaded from www.ensembl.org. The script htseq-count is supplied with the GTF file with gene models and a bam file containing the mapped reads.   The script generates individual gene counts by examining the read overlap with the genes.
A conservative setting (--mode=intersection-strict) was chosen to handle reads overlapping more than one feature. Thus, reads overlapping several genes simultaneously are marked as reads with no feature and excluded from consideration.  Gene counts from every sample are used to determine genes differentially expressed across the conditions (DeSeq2 with default parameters).  DeSeq2 models read counts as a negative binomial distribution and uses shrinkage estimation for dispersions and fold changes.
Within-group variability (variability between replicates) is used to determine if the observed difference between the conditions may be attributed to the experimental conditions and not to the biological variance.  FDR corrected p-values are used to control the number of false positives.
Supplementary files format and content: excel file include normalized RLD counts for each sample

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (QIAGEN) followed by on-column DNase I digestion as per manufacturer's instructions. RNA integrity was verified with a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA was quantified with the Qubit fluorometer (Invitrogen), and 1 µg of purified RNA was utilized as starting material for library construction
RNA libraries for RNA-seq were prepared using the KAPA RNA HyperPrep Kit with RiboErase (KAPA BIOSYSTEM KK8560) as per manufacturer's instructions

value: spleen

tag: strain

value: C57BL/6J mice

value: male

value: 20 weeks old

tag: disease

value: B-ALL

value: FMD+vincristine


title: Colon content KO DSS, rep 2

value: colon content


title: Pool1512_13_15_1

description:
Library name: Sample 1
Column name in raw_counts_All Samples.txt: Pool1512_13_15_1

value: Skin

value: Spring-infested


title: XT_st7_CANTAC_rep1

tag: developmental stage

value: Stage 7

value: WT


title: FMD+VC 21

description: Mouse 21


title: Colon content WT DSS, rep 1

value: Jupfl/fl

value: DSS


title: HUCCT1-Con2

first: Zhanfeng

last: Gu

state: Guangzhou

address: No. 183, Zhongshan Avenue West

department: Department of Hepatobiliary surgery

institute: The Third Affiliated Hospital of Southern Medical University

description:
Library name: Sample3
3_fpkm

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2. HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz. The CIRCexplorer program (v2.3.8) was used to identify both the circularizing junction and the spliced sequence of circRNAs. All circRNA candidates with junction reads less than 2 were discarded. The remaining circRNA candidates were considered bonafide circRNAs.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs between tumor and non-tumor samples, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Assembly: hg38
Supplementary files format and content: zip file include FPKM values for each Sample

growth_protocol: HUCCT-1 cells were cultured in RPMI1640 medium.All culture media were supplemented with 10% fetal bovine serum (Exocell) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
samples:Total RNA was isolated using TRIzol reagent according to the manufacturer’s instruction (15596026, Invitrogen, USA).
The RNA library was constructed using the KAPA mRNA HyperPrep Kit (Roche), following the standard protocol of poly(A) selection for mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: HUCCT-1 cells were treated with vehicle, GSK805 or XY101 (5 µM) for 48 hours.

tag: cell type

value: tumor cells


title: HUCCT1-XY101

description:
Library name: Sample4
4_fpkm


title: XT_st7_CANTAC_rep2


title: FMD+VC 30

description: Mouse 30

tag: Sex


title: K562 and NIH/3T3 cell mixture

city: Vilnius

first: Denis

last: Baronas

address: Saulėtekio al. 7

country: Lithuania

institute: Vilnius University

description:
Library name: species-mixing
CapSeq of species-mixing experiment of K562 and NIH/3T3

library_source: transcriptomic single cell

data_processing:
The STARsolo wrapper pipeline (https://github.com/jsimonas/solo-in-drops) was used to process the sequencing data and to obtain cell ⨉ gene count matrices. Shortly, barcode ligation linker sequences were removed from the read1 the and read1 was reassembled to have a structure of BC3[8nt]BC2[10nt]BC1[8nt] UMI[8nt]. Next, STAR(https://doi.org/10.1101/2021.05.05.442755) (version 2.7.10a) was run with the following parameters: --soloUMIdedup Exact, --soloFeatures GeneFull, --soloType CB_UMI_Complex, --soloCBposition 0_0_0_7 0_8_0_17 0_18_0_25, --soloUMIposition 0_26_0_33, --soloCBmatchWLtype EditDist_2. The reads were aligned to either the human GRCh38 genome (GENCODE v41) or the mouse GRCm39 genome (GENCODE M30).
Assembly: GRCh38
Assembly: GRCm39
Supplementary files format and content: Matrix files of gene expression raw count data in _matrix.mtx
Supplementary files format and content: Tab separated files of barcodes in _barcodes.tsv
Supplementary files format and content: Tab separated files of genes in _features.tsv
Supplementary files format and content: AnnData files in _adata.h5ad
Supplementary files format and content: Excel files of metadata containing barcode information linked to patient code or condition in _metadata.xlsx

organism:
Homo sapiens
Mus musculus

source_name: cell mixture

extract_protocol:
White blood cells were prepared by removing red blood cells (RBC) in the following manner. Peripheral blood was collected within the last 2 hours into a K2EDTA vacutainer and stored on wet ice. Subsequently, 10 µL of 0.5 M EDTA (Invitrogen, cat. no. 15575-038) was added per 1 mL of peripheral blood. In 2 mL Protein LoBind tube (Eppendorf, cat. no. 0030108132) 1800 µL of RBC lysis buffer (R7757, Sigma-Aldrich) was combined with 200 µL of peripheral blood. Cells with RBC lysis buffer were incubated for 5 min at room temperature and the tube was gently inverted every 5 s. Next, cells were centrifuged for 10 min at 300g and 4 °C using a swinging-bucket rotor. After discarding the supernatant, the pellet was gently resuspended with 2 mL RBC lysis buffer. The tube was incubated for 3 min at room temperature and gently inverted every 5 s. Then the cells were centrifuged for 5 min at 300g and 4 °C using a swinging-bucket rotor, and supernatant was discarded. Additional wash in RBC lysis buffer was performed if very bright red color was still visible on the pellet. Finally, the pellet was resuspended to the final volume of 100 µL with ice cold 1X DPBS. Cells were fixed by slowly adding 900 µL of ice-cold methanol into the 100 µL of cell suspension in 2 mL Protein LoBind tube. To avoid cell clumping the first 500 µL of the methanol was added drop by drop (3-5 drops per 1 s) and the remaining volume was added more quickly (in 1-2 s). After methanol was added, the tube was gently inverted 10-times. Next, the tube with methanol-fixed cells was incubated on ice for 15-30 min and transferred at -20 °C (for short period <6 months) or at -80 °C (for longer period >6 months). The fixed cells from the freezer were initially incubated on ice for 15-30 min followed by centrifugation for 5 min at 1000g and 4 °C using a swinging-bucket rotor. Next, the methanol was removed, and the cell pellet was resuspended in 1 mL of rehydration buffer (RB; 1X SSC, 2 M NaCl, 0.1% BSA) and transferred to a new 1.5 mL tube. The resuspended cells were then subjected to an additional centrifugation step for 5 min at 1000g and 4 °C. Subsequently, the supernatant was discarded, and the cells were subjected to an identical wash procedure using 1 mL of RB. A 10 µL aliquot of the cell suspension was utilized to determine the cell concentration using a hemocytometer. Following removal of the supernatant, the cell pellet was resuspended to achieve a final volume corresponding to 3 million cells per milliliter.
Illumina sequencing libraries were prepared for each amplified cDNA aliquot with NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (NEB, cat. no. E7805S) according to the instructions in the manual, with minor changes. In particular, 5-10 ng of amplified cDNA was used for cDNA fragmentation and transferred to a PCR tube. Nuclease-free water was added to reach the final volume on 13 µL. Fragmentation reaction was assembled on ice by adding 3.5 µL of NEBNext® Ultra™ II FS Reaction Buffer followed by 1 µL of NEBNext® Ultra™ II FS Enzyme Mix. Reaction mix was vortexed and spun-down for 3-5 seconds. The fragmentation was performed for 8 minutes at 37 °C, followed by end-repair and dA tailing for 30 min at 65 °C (lid was set at 75 °C). Fragmented cDNA was purified with 0.6X-0.8X double-size selection using SPRIselect beads and eluted in 17.5 µL with nuclease-free water. Then, 1.5 µM ligation adapter was prepared in advance by mixing 1.5 µL of forward ligation primer (100 µM, /5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC; HPLC purification, IDT) and 1.5 µL of reverse ligation primer (/5AmMC6/GCTCTTCCGATCT; HPLC purification, IDT) with 97 µL of water. To anneal oligos, the solution was heated to 95 °C for 2 min (lid at 100 °C) and cooled at room temperature for 5 min. Next, purified fragmented cDNA was mixed with 15 µL of NEBNext® Ultra™ II Ligation Master Mix, 1.25 µL of ligation adapter and 0.5 µL of NEBNext® Ligation Enhancer. Reaction solution was well mixed by pipetting and incubated for 15 min at 20 °C (lid set at 37 °C). The ligation product was diluted to 100 µL with nuclease-free water, followed by a 0.8X SPRI size selection procedure and eluted in 40 µL with nuclease-free water. Finally, the ligation product was amplified by 12-cyles of PCR: 95 ºC for 3 min, 12-cycles [98 ºC for 20 s, 54 ºC for 30 s, 72 ºC for 20 s], and 72 ºC for 60 s. PCR mix was prepared by mixing 20 µL of ligation product, 2.5 µL of forward indexing primer (Table  S25), 2.5 µL of reverse indexing primer (Table S25) and 25 µL of 2X KAPA HiFi HotStart ReadyMix. Amplified sequencing libraries were purified with 0.6X-0.8X double-size selection using SPRIselect beads and eluted in 20 µL with nuclease-free water.

value: cell mixture

value: K562 and NIH/3T3


title: FMD+VC 29

description: Mouse 29

tag: age


title: FMD 26

description: Mouse 26

value: fasting mimicking diet FMD+vehicle


title: FMD+VC 45

description: Mouse 45

value: spleen


title: FMD 34

description: Mouse 34

value: C57BL/6J mice


title: FMD+VC 42

description: Mouse 42

value: male


title: FMD 11

description: Mouse 11

value: 20 weeks old


title: FMD 9

description: Mouse 9

value: B-ALL


title: FMD 8

description: Mouse 8


title: FMD 7

description: Mouse 7


title: VC 41

description: Mouse 41

value: vincristine


title: VC 14

description: Mouse 14


title: CTRL 33

description: Mouse 33

value: ad lib+ vehicle


title: VC 13

description: Mouse 13


title: CTRL 6

description: Mouse 6


title: ac_PBL3, PBLs cocultured with hAMSCs, Test

city: Zunyi

first: Yi

last: Luo

address: 149 Dalian Road, Huichuan District

institute: Affiliated Hospital of Zunyi Medical University

description: Library name: Sample 6

data_processing:
CLC Genomics Workbenchv11.0.1
Sequence reads were trimmed for adaptor sequence/low quality sequence using genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameter-mismath cost: 2 insertion cost: 3 length fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Blood

extract_protocol:
RNA was using Rnease mini plus kit, 1.3 ug of total RNA was used for the construction  of sequencing librarie
RNA libraries for RNA-seq were prepared using SMARTER mRNA seq Library Prep kit followingmanufacturer'sprotocols.

value: Blood

value: Primary cells

value: Lymphocyte

value: Normal culture


title: CTRL 25

description: Mouse 25


title: PBL3, PBLs, Control

description: Library name: Sample 3

value: WT


title: ac_PBL1, PBLs cocultured with hAMSCs, Test

description: Library name: Sample 4


title: CTRL 32

description: Mouse 32


title: PBL2, PBLs, Control

description: Library name: Sample 2


title: CTRL 3

description: Mouse 3


title: PBL1, PBLs, Control

description: Library name: Sample 1


title: ac_PBL2, PBLs cocultured with hAMSCs, Test

description: Library name: Sample 5


title: P10-3, hAMSCs, Control

description: Library name: Sample 3

source_name: Amniotic membrane

value: Amniotic membrane

value: Mesenchymal stem cells


title: PBL-P10-3, hAMSCs cocultured with PBL, Test

description: Library name: Sample 6


title: VC 18

description: Mouse 18

source_name: spleen


title: P10-2, hAMSCs, Control

description: Library name: Sample 2


title: CTRL 2

description: Mouse 2


title: CAR_Dd_1

city: Ribeirão Preto

first: Matheus

middle: Henrique

last: dos Santos

state: SP

address: R. Ten. Catão Roxo, 2501

department: Oncology

country: Brazil

institute: University of Sao Paulo

description:
Library name: LCS10338_CAR_Dd_1_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_Dd_1

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Assembly: Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Supplementary files format and content: xlsm file include FPKM value for each sample

source_name: cell line

growth_protocol: CAR-NK cells were cultivated in X-VIVO suplemented with 10% fetal bovine serum and 200U of IL-2/mL. NALM-6 cells were cultivated in RPMI 10% fetal bovine sereum. The cell were co-cultured in X-VIVO 10% FBS.

extract_protocol:
RNA was extracted using RNAeasy mini kit (QIAGEN)
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip

treatment_protocol: After co-culture, CAR-labelled NK cells were separeted from target cells using magnetic columns.

value: cell line

value: Lentivirally transduced

value: no-treatment


title: P10-1, hAMSCs, Control

description: Library name: Sample 1


title: PBL-P10-1, hAMSCs cocultured with PBL, Test

description: Library name: Sample 4


title: PBL-P10-2, hAMSCs cocultured with PBL, Test

description: Library name: Sample 5


title: VC 17

description: Mouse 17

value: spleen


title: SALL4_ChIP-seq

city: Kumamoto

first: Hiroaki

last: Okae

address: 2-2-1 Honjo, Chuo-ku

department: Department of Trophoblast Research

institute: Kumamoto University

description: Library name: SALL4_ChIP-seq

data_processing:
Reads were trimmed using TrimGalore and aligned to the reference genome (UCSC hg38) using Bowtie 2 v2.2.5. SALL4-binding sites were identified using MACS2 v2.2.7.2.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Placenta

extract_protocol:
hTSCs were transduced with FLAG-SALL4 using lentivirus. ChIP was performed using ChIP Reagents (#318-07131; Nippon Gene, Tokyo, Japan) and an anti-FLAG antibody (1:100; #F3165; Sigma-Aldrich, St. Louis, MO, USA). Briefly, IP was performed in buffer containing 400 mM NaCl instead of 150 mM to reduce the background signal.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645; New England Biolabs, Ipswich, MA, USA) and sequenced on an Illumina NovaSeq 6000 platform.

value: Placenta

value: Human trophoblast stem cell


title: CAR_Ad_2

description:
Library name: LCS10338_CAR_Ad_2_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_Ad_2


title: CAR_Cd_2

description:
Library name: LCS10338_CAR_Cd_2_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_Cd_2


title: CAR_Ad_1

description:
Library name: LCS10338_CAR_Ad_1_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_Ad_1


title: CAR_Cd_1

description:
Library name: LCS10338_CAR_Cd_1_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_Cd_1


title: VC 37

description: Mouse 37

value: C57BL/6J mice

value: male

value: 20 weeks old


title: CAR_Dd_2

description:
Library name: LCS10338_CAR_Dd_2_Clean_Data1.fq.gz
Column name in 4_genes_fpkm_expression.xlsx: CAR_Dd_2


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 11

city: Ithaca

first: Praveen

last: Sethupathy

address: 618 Tower Rd

institute: Cornell University

description: Library name: SubLib11

data_processing:
Adapter and quality trimming was performed using Trim Galore with parameters --paired --cores 16 --fastqc.
Reads were processed using Parse Biosciences split-pipe in --mode all with --chemistry v3.
Reads were aligned to the human genome (GRCh38/hg38) using the split-pipe integrated STAR aligner.
Unique molecular identifiers (UMIs) were collapsed to generate per-gene expression counts per nucleus.
Downstream quality control, normalization, clustering, and differential expression were performed using Scanpy in Python.
Assembly: GRCh38 (hg38)
Supplementary files format and content: For each sublibrary, three files are provided: (1) count matrix (.mtx), (2) per-cell metadata (.csv), and (3) gene annotations (.csv).
Supplementary files format and content: We additionally supply combined cohort-level files (all_sample_count_matrix.mtx, all_sample_cell_metadata.csv, and all_sample_all_genes.csv) and a final .h5ad object containing clustering and cell-type annotations.

source_name: liver

extract_protocol:
Fresh-frozen tumor and adjacent tissues were cryopreserved, mechanically dissociated, and processed to isolate nuclei. Nuclei were purified and counted according to the Parse Biosciences Evercode WT v3 protocol.
Single-nucleus RNA-seq libraries were prepared using the Parse Biosciences Evercode WT v3 kit, which employs combinatorial barcoding of fixed nuclei. Libraries were pooled into sublibraries according to manufacturer’s instructions and sequenced (paired-end, 150 bp) on an Illumina NovaSeq 6000.

value: liver


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 9

description: Library name: SubLib9


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 4

description: Library name: SubLib4


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 6

description: Library name: SubLib6


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 7

description: Library name: SubLib7


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 2

description: Library name: SubLib2


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 8

description: Library name: SubLib8


title: RNA seq of Epithelial cells treated with control siRNA (Control)_2

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon GU

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences

description: Library name: Consi_NoIR_4

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 (hg38) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38 (hg38)
Supplementary files format and content: Read count values for each Sample

source_name: lung epithelial cell

growth_protocol: Mice were maintained on a 12-hour light/dark cycle and allowed free access to food and water.

extract_protocol:
Total RNA was extracted from the cells with the use of an RNeasy Mini Kit (Qiagen) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The mice were subjected to restraint using 50 mL tubes for 3 hours every 4 days.

value: lung epithelial cell

value: control siRNA (Control)

tag: replication


title: RNA seq of Epithelial cells treated with control siRNA (Control)_1

description: Library name: Consi_NoIR_3


title: TM-1

city: Chengde

first: Miao

last: Liu

address: Nanyingzi Street

department: Department of Oncology

institute: Affiliated Hospital of Chengde Medical University

description: Library name: Sample 4

data_processing:
The quality and concentration of the sequencing libraries were assessed using the Agilent 2100 Bioanalyzer.
After quality control and preprocessing (removing adapter sequences and overly short fragments from the reads), the resulting trimmed data were aligned to the reference genome.
Gene-level and transcript-level quantification were performed by first using StringTie to calculate transcript abundance from the alignment results against the reference transcriptome, followed by Ballgown to derive the final expression values.
The expression levels were reported in FPKM. A gene or transcript was considered expressed if its FPKM value exceeded 0.5. Within each group, genes or transcripts with a mean FPKM > 0.5 were regarded as expressed and included in the statistical analysis.
Assembly: GRCh37
Supplementary files format and content: XLS files include FPKM values for each Sample.

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were obtained from our laboratory collection. Cells were cultured in RPMI-1640 medium, supplemented with 1% Penicillin-Streptomycin Solution and 10% FBS. The cultures were incubated at 37℃ in an atmosphere containing 5% CO2.

extract_protocol:
RNA was extracted from transfected cells using the Total RNA Extraction Kit (Omega, USA). 1–2 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the KAPA stranded RNA-seq library Prep kit (Roche, Switzerland) following manufacturer's protocols.

treatment_protocol: Cells were transfected with pcDNA3.1-TM-his or the control plasmid using Attractene transfection reagent (QIAGEN, German) in accordance with the provided instructions.

value: MCF-7 cells

value: breast cancer cells

value: tropomyosin overexpression


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 5

description: Library name: SubLib5


title: TM-2

description: Library name: Sample 5


title: NC3

description: Library name: Sample 3

value: tropomyosin without overexpression


title: RNA seq of Epithelial cells treated with control siRNA and irradiation_1

description: Library name: Consi_IR_3

value: control siRNA and irradiation


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 12

description: Library name: SubLib12


title: NC2

description: Library name: Sample 2


title: RNA seq of Epithelial cells treated with control siRNA and irradiation_2

description: Library name: Consi_IR_4


title: TM-3

description: Library name: Sample 6


title: RNA seq of Epithelial cells treated with control siRNA and cytokine_2

description: Library name: Consi_Cyto_4

value: control siRNA and cytokine


title: NC1

description: Library name: Sample 1


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 10

description: Library name: SubLib10


title: RNA seq of Epithelial cells treated with control siRNA and cytokine_1

description: Library name: Consi_Cyto_3


title: RNA seq of Epithelial celsl treated with Erbb3 siRNA and cytokine_1

description: Library name: 3si_Cyto_3

value: Erbb3 siRNA and cytokine


title: RNA seq of Epithelial cells treated with EGFR siRNA and irradiation_1

description: Library name: 1si_IR_3

value: EGFR siRNA and irradiation


title: RNA seq of Epithelial cells treated with EGFR siRNA and irradiation_2

description: Library name: 1si_IR_4


title: RNA seq of Epithelial cells treated with Erbb3 siRNA and irradiation_1

description: Library name: 3si_IR_3

value: Erbb3 siRNA and irradiation


title: RNA seq of Epithelial cells treated with Erbb3 siRNA and irradiation_2

description: Library name: 3si_IR_4


title: FLC pooled nuclei, Parse Evercode snRNA-seq sublibrary 1

description: Library name: SubLib1


title: RNA seq of Epithelial cells treated with EGFR siRNA and cytokine_2

description: Library name: 1si_Cyto_4

value: EGFR siRNA and cytokine


title: RNA seq of Epithelial cells treated with EGFR siRNA and cytokine_1

description: Library name: 1si_Cyto_3


title: SNU1, 2D, R2

city: Hong Kong

first: Alan Siu Lun

last: Wong

address: Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description:
Library name: Sample 14
Column name in analysis_BC_RNAseq_table.txt: SNU1-C32-R2_1.fastq.gz.subread.BAM

data_processing:
The sequence reads were aligned to the reference human genome (hg19) using the Rsubread package.
Only genes with > 0.5 counts-per-million in at least half of the samples were included in the differential expression analysis, which was performed using edgeR and limma packages.
Assembly: hg19
Supplementary files format and content: txt files with RNA-seq raw counts

extract_protocol:
RNA from all samples  were extracted by MiniBEST Universal RNA Extraction Kit (TaKaRa) according to manufacturer’s instruction.
Qualified RNA samples were proceeded using KAPA mRNA HyperPrep Kit (Kapa Biosystems) to prepare for the cDNA library according to manufacturer’s instruction.


title: SNU1, in vivo tumor, R2

description:
Library name: Sample 16
Column name in analysis_BC_RNAseq_table.txt: SNU1-Tumour-Mice-Gp2-R1L1-WT_1.fastq.gz.subread.BAM

source_name: SNU1-derived tumor

value: SNU1-derived tumor


title: GX049, indirect coculture, R2

description:
Library name: Sample 10
Column name in 049_single_end_RNAseq_countbook.txt: 049-4_1.fastq.gz.subread.BAM


title: SNU1, 2D, R1

description:
Library name: Sample 13
Column name in analysis_BC_RNAseq_table.txt: SNU1-C32-R1_1.fastq.gz.subread.BAM


title: RNA seq of Epithelial cells treated with Erbb3 siRNA and cytokine_2

description: Library name: 3si_Cyto_4


title: GX049, control, R2

description:
Library name: Sample 8
Column name in 049_single_end_RNAseq_countbook.txt: 049-6_1.fastq.gz.subread.BAM


title: GX117, control, R1

description:
Library name: Sample 1
Column name in 117_single_end_RNA_seq_countbook.txt: RP-1_1.fastq.gz.subread.BAM


title: GX049, indirect coculture, R1

description:
Library name: Sample 9
Column name in 049_single_end_RNAseq_countbook.txt: 049-3_1.fastq.gz.subread.BAM


title: SNU1, in vivo tumor, R1

description:
Library name: Sample 15
Column name in analysis_BC_RNAseq_table.txt: SNU1-Mice-Tumour-WT-Gp1-L2_1.fastq.gz.subread.BAM


title: GX049, control, R1

description:
Library name: Sample 7
Column name in 049_single_end_RNAseq_countbook.txt: 049-5_1.fastq.gz.subread.BAM


title: GX117, direct coculture, R3

description:
Library name: Sample 6
Column name in 117_single_end_RNA_seq_countbook.txt: RP-6_1.fastq.gz.subread.BAM


title: GX049, direct coculture, R2

description:
Library name: Sample 12
Column name in 049_single_end_RNAseq_countbook.txt: 049-2_1.fastq.gz.subread.BAM


title: GX049, direct coculture, R1

description:
Library name: Sample 11
Column name in 049_single_end_RNAseq_countbook.txt: 049-1_1.fastq.gz.subread.BAM


title: 036_PBMC_GEX

city: Durham

first: Peter

last: Allen

state: NC

address: 203 Research Dr., MSRB1 Rm. 475

department: Surgery

institute: Duke Medical Center

description: Library name: 036_PBMC_GEX

data_processing:
FASTQs were run through the cellranger (v7.1.0) pipeline.Chemistry was autodetected for Single Cell 5' R2-only. Introns were not included.
Genes were aligned using the human genome reference file GRCh38-2020-A
Assembly: GRCh38-2020-A
Supplementary files format and content: .csv files contain filtered TCR contigs matching the GEX samples
Supplementary files format and content: .h5 files contain the filtered feature matrices for each GEX sample

extract_protocol:
Tissues were digested into single cells and flow sorted for CD45+ cells. PBMCs were isolated via Ficoll separation and sorted for CD45+ cells.
For each sample, up to 10,000 cells were loaded onto the Chromium Next GEM Chip K per the 10x Genomics Single Cell 5’ Reagent Kits v2 protocol.  Gene expression (GEX) and TCR libraries were generated according to the 10x protocol.

value: Blood

value: female

value: Pancreatic Ductal Adenocarcinoma

tag: Stage

value: T2N2 (Stage III)

tag: batch


title: GX117, direct coculture, R1

description:
Library name: Sample 4
Column name in 117_single_end_RNA_seq_countbook.txt: RP-4_1.fastq.gz.subread.BAM


title: 036_PBMC_TCR

description: Library name: 036_PBMC_TCR

data_processing:
FASTQs were run through the cellranger (v7.1.0) pipeline.Chemistry was autodetected for Single Cell 5' R2-only. Introns were not included.
Genes were aligned using the human genome reference file GRCh38-2020-A
Assembly: GRCh38-2020-A
Supplementary files format and content: .csv files contain filtered TCR contigs matching the GEX samples
Supplementary files format and content: .h5 files contain the filtered feature matrices for each GEX sample
Library strategy: TCR-Seq


title: RNA-seq of A375SM cells expressing shEmpty

first: Hyeon Ho

last: Heo

address: 209 Neungdong-ro, Gwangjin-gu

department: Department of Integrative Bioscience and Biotechnology

institute: Sejong University

description:
Library name: lib_shEmpty
shEmpty

data_processing:
Raw reads were subjected to quality control using FastQC.
Low-quality reads and adapter sequences were trimmed using BBDuk.
High-quality reads were aligned to the human reference genome (hg19, UCSC) using TopHat.
Gene expression levels were quantified as FPKM values using Cufflinks.
Differential expression analysis was performed using EdgeR.
Assembly: hg19 (UCSC, Human reference genome build GRCh37)
Supplementary files format and content: A tab-delimited counts matrix (.txt) containing RNA-seq read counts. Each row corresponds to a gene, and each column represents raw counts from A375SM melanoma cells stably expressing shPRAME, shBAP1, or shEmpty (non-targeting control).

source_name: skin

growth_protocol: A375SM melanoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Antibiotic-Antimycotic (Gibco) at 37 °C in a humidified 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNA libraries were constructed using the NEBNext Ultra II Directional RNA-Seq Kit (New England Biolabs) following the manufacturer’s instructions. Briefly, mRNA was purified, fragmented, and reverse-transcribed to generate cDNA. After end repair, adaptor ligation, and PCR amplification, the libraries were subjected to quality control using the Bioanalyzer 2100 system. Sequencing was performed on an Illumina NovaSeq 6000 platform to generate paired-end 100 bp reads.

treatment_protocol: A375SM melanoma cells were infected with lentiviruses carrying LV-GFP based shRNA vectors (shPRAME, shBAP1, shEmpty). GFP-positive cells were selected to establish stable populations, which were subsequently used for experiments.

value: skin

value: melanoma cell

value: WT


title: GX117, indirect coculture, R2

description:
Library name: Sample 3
Column name in 117_single_end_RNA_seq_countbook.txt: RP-3_1.fastq.gz.subread.BAM


title: 036_LiverC_TCR

description: Library name: 036_LiverC_TCR

source_name: Liver

value: Liver


title: 036_LiverB_GEX

description: Library name: 036_LiverB_GEX


title: RNA-seq of A375SM cells expressing shBAP1

description:
Library name: lib_shBAP1
shBAP1

value: BAP1 knockdown


title: GX117, indirect coculture, R1

description:
Library name: Sample 2
Column name in 117_single_end_RNA_seq_countbook.txt: RP-2_1.fastq.gz.subread.BAM


title: RNA-seq of A375SM cells expressing shPRAME

description:
Library name: lib_shPRAME
shPRAME

value: PRAME knockdown


title: GX117, direct coculture, R2

description:
Library name: Sample 5
Column name in 117_single_end_RNA_seq_countbook.txt: RP-5_1.fastq.gz.subread.BAM


title: 036_Panc_CD45Pos_TCR

description: Library name: 036_Panc_CD45Pos_TCR

source_name: Pancreas

value: Pancreas


title: 036_LiverA_GEX

description: Library name: 036_LiverA_GEX


title: 036_Panc_CD45Pos_GEX

description: Library name: 036_Panc_CD45Pos_GEX


title: 036_LiverB_TCR

description: Library name: 036_LiverB_TCR


title: 036_LiverC_GEX

description: Library name: 036_LiverC_GEX


title: 036_LiverA_TCR

description: Library name: 036_LiverA_TCR


title: 037_PBMC_GEX

description: Library name: 037_PBMC_GEX

value: T2N1 (Stage IIB)


title: 037_LiverCcryo_TCR

description: Library name: 037_LiverCcryo_TCR


title: 037_LiverB_TCR

description: Library name: 037_LiverB_TCR


title: 037_Panc_CD45Pos_GEX

description: Library name: 037_Panc_CD45Pos_GEX


title: 037_LiverB_GEX

description: Library name: 037_LiverB_GEX


title: 037_PBMC_TCR

description: Library name: 037_PBMC_TCR


title: 037_Panc_CD45Pos_TCR

description: Library name: 037_Panc_CD45Pos_TCR


title: 037_LiverA_GEX

description: Library name: 037_LiverA_GEX


title: PBMC_TCR

description: Library name: PBMC_TCR


title: 037_LiverCcryo_GEX

description: Library name: 037_LiverCcryo_GEX


title: Liver_3_GEX

description: Library name: Liver_3_GEX


title: Liver_3_TCR

description: Library name: Liver_3_TCR


title: Liver_2_TCR

description: Library name: Liver_2_TCR


title: Pancreas_CD45Pos_live_TCR

description: Library name: Pancreas_CD45Pos_live_TCR


title: Liver_2_GEX

description: Library name: Liver_2_GEX


title: Liver_1_GEX

description: Library name: Liver_1_GEX


title: Br2743_VSPG (ST)

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

description: Library name: Br2743_VSPG

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: spatial transcriptomics

source_name: brain (dACC)

extract_protocol:
dACC was dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

value: brain (dACC)


title: Br8492_VSPG (ST)

description: Library name: Br8492_VSPG


title: PBMC_GEX

description: Library name: PBMC_GEX


title: 037_LiverA_TCR

description: Library name: 037_LiverA_TCR


title: Br8667_V12Y31-080_B1 (ST)

description: Library name: Br8667_V12Y31-080_B1


title: Br8492_V12N28-334_B1 (ST)

description: Library name: Br8492_V12N28-334_B1


title: Br6471_V12N28-332_C1 (ST)

description: Library name: Br6471_V12N28-332_C1


title: Br6522_V12N28-332_D1 (ST)

description: Library name: Br6522_V12N28-332_D1


title: Pancreas_CD45Pos_live_GEX

description: Library name: Pancreas_CD45Pos_live_GEX


title: Br8325_V12Y31-080_C1 (ST)

description: Library name: Br8325_V12Y31-080_C1


title: Br6423_VSPG (ST)

description: Library name: Br6423_VSPG


title: Liver_1_TCR

description: Library name: Liver_1_TCR


title: Br3942_VSPG (ST)

description: Library name: Br3942_VSPG


title: Br6471_V12N28-331_C1 (ST)

description: Library name: Br6471_V12N28-331_C1


title: Br6471_V12J03-002_C1 (ST)

description: Library name: Br6471_V12J03-002_C1


title: Br6432_V12N28-332_B1 (ST)

description: Library name: Br6432_V12N28-332_B1


title: Br6432_V12N28-331_B1 (ST)

description: Library name: Br6432_V12N28-331_B1


title: Br6432_V12J03-002_B1 (ST)

description: Library name: Br6432_V12J03-002_B1


title: Br6423_V12N28-334_D1 (ST)

description: Library name: Br6423_V12N28-334_D1


title: Br8667-10c_dACC (snRNA-seq)

description: Library name: 10c_dACC

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each donor.

extract_protocol:
dACC was dissected from fresh frozen postmortem human tissue. 100 micron coronal sections of dACC from fresh frozen postmortem human tissue were obtained by cryosectioning. Nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.


title: Br2720_V12N28-331_A1 (ST)

description: Library name: Br2720_V12N28-331_A1


title: Br8325-8c_dACC (snRNA-seq)

description: Library name: 8c_dACC


title: Br2743_V12N28-334_C1 (ST)

description: Library name: Br2743_V12N28-334_C1


title: Br6522_V12N28-331_D1 (ST)

description: Library name: Br6522_V12N28-331_D1


title: G918_TP186_control_P6_3

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

description: Library name: G918_TP186_control_P6_3

data_processing:
Raw reads were aligned to Mmul_10 using the STAR aligner (version 2.7.0e)
Assembly: Mmul_10
Supplementary files format and content: comma-seperated file containing the raw couts of all samples

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
RNA was extracted from whole blood. The quality of the recovered RNA was determined using a LabChip GX (PerkinElmer) instrument.
Sequencing libraries were generating following globin depletion (KAPPA).

value: Whole blood

value: control

tag: animal id

tag: timepoint

tag: vaccine route

tag: number of_challenges_to_infection


title: G923_TP186_control_P8_2

description: Library name: G923_TP186_control_P8_2

tag: tissue


title: G921_TP186_control_P7_3

description: Library name: G921_TP186_control_P7_3


title: G920_TP186_control_P7_2

description: Library name: G920_TP186_control_P7_2


title: G924_TP186_control_P8_3

description: Library name: G924_TP186_control_P8_3


title: G922_TP186_control_P8_1

description: Library name: G922_TP186_control_P8_1


title: Br8492-9c_dACC (snRNA-seq)

description: Library name: 9c_dACC


title: G919_TP186_control_P7_1

description: Library name: G919_TP186_control_P7_1


title: G917_TP186_control_P6_2

description: Library name: G917_TP186_control_P6_2


title: G915_TP186_control_P5_3

description: Library name: G915_TP186_control_P5_3


title: G916_TP186_control_P6_1

description: Library name: G916_TP186_control_P6_1


title: G914_TP186_control_P5_2

description: Library name: G914_TP186_control_P5_2


title: G913_TP186_control_P5_1

description: Library name: G913_TP186_control_P5_1


title: Br3942_V12N28-334_A1 (ST)

description: Library name: Br3942_V12N28-334_A1


title: G909_TP186_control_P3_3

description: Library name: G909_TP186_control_P3_3


title: G912_TP186_control_P4_3

description: Library name: G912_TP186_control_P4_3


title: Br2720_V12N28-332_A1 (ST)

description: Library name: Br2720_V12N28-332_A1


title: G910_TP186_control_P4_1_mRNA

description: Library name: G910_TP186_control_P4_1_mRNA


title: G911_TP186_control_P4_2

description: Library name: G911_TP186_control_P4_2


title: G908_TP186_control_P3_2

description: Library name: G908_TP186_control_P3_2


title: G907_TP186_control_P3_1

description: Library name: G907_TP186_control_P3_1


title: G906_TP186_control_P2_3

description: Library name: G906_TP186_control_P2_3


title: G905_TP186_control_P2_2

description: Library name: G905_TP186_control_P2_2


title: G904_TP186_control_P2_1_mRNA

description: Library name: G904_TP186_control_P2_1_mRNA


title: G903_TP186_control_P1_3_mRNA

description: Library name: G903_TP186_control_P1_3_mRNA


title: G466_TP186_JF94_B_EP6wk21

description: Library name: G466_TP186_JF94_B_EP6wk21

value: DNA+gp120 protein

value: Separate legs, SubQ


title: G902_TP186_control_P1_2_mRNA

description: Library name: G902_TP186_control_P1_2_mRNA


title: G461_TP186_GM52_B_EP6wk21

description: Library name: G461_TP186_GM52_B_EP6wk21

value: ND


title: G463_TP186_IJ26_B_EP6wk21

description: Library name: G463_TP186_IJ26_B_EP6wk21


title: G459_TP186_GJ04_B_EP6wk21

description: Library name: G459_TP186_GJ04_B_EP6wk21


title: G456_TP186_JE99_B_EP6wk21

description: Library name: G456_TP186_JE99_B_EP6wk21

value: Both legs, SubQ


title: G458_TP186_GH35_B_EP6wk21

description: Library name: G458_TP186_GH35_B_EP6wk21


title: G462_TP186_GN03_B_EP6wk21

description: Library name: G462_TP186_GN03_B_EP6wk21


title: G457_TP186_GC03_B_EP6wk21

description: Library name: G457_TP186_GC03_B_EP6wk21


title: G455_TP186_JC25_B_EP6wk21

description: Library name: G455_TP186_JC25_B_EP6wk21


title: G452_TP186_GI46_B_EP6wk21

description: Library name: G452_TP186_GI46_B_EP6wk21


title: G454_TP186_IA36_B_EP6wk21

description: Library name: G454_TP186_IA36_B_EP6wk21


title: G451_TP186_GI36_B_EP6wk21

description: Library name: G451_TP186_GI36_B_EP6wk21


title: G450_TP186_GI29_B_EP6wk21

description: Library name: G450_TP186_GI29_B_EP6wk21


title: G453_TP186_IA21_B_EP6wk21

description: Library name: G453_TP186_IA21_B_EP6wk21


title: G449_TP186_GH90_B_EP6wk21

description: Library name: G449_TP186_GH90_B_EP6wk21


title: G446_TP186_JB44_B_EP6wk21

description: Library name: G446_TP186_JB44_B_EP6wk21


title: G445_TP186_IV92_B_EP6wk21

description: Library name: G445_TP186_IV92_B_EP6wk21


title: G448_TP186_GB06_B_EP6wk21

description: Library name: G448_TP186_GB06_B_EP6wk21


title: G447_TP186_FG06_B_EP6wk21

description: Library name: G447_TP186_FG06_B_EP6wk21


title: G444_TP186_IC95_B_EP6wk21

description: Library name: G444_TP186_IC95_B_EP6wk21


title: G901_TP186_control_P1_1

description: Library name: G901_TP186_control_P1_1


title: G441_TP186_GM62_B_EP6wk21

description: Library name: G441_TP186_GM62_B_EP6wk21


title: G465_TP186_JC52_B_EP6wk21

description: Library name: G465_TP186_JC52_B_EP6wk21


title: G439_TP186_GH91_B_EP6wk21

description: Library name: G439_TP186_GH91_B_EP6wk21


title: G442_TP186_HE88_B_EP6wk21

description: Library name: G442_TP186_HE88_B_EP6wk21


title: G438_TP186_EE71_B_EP6wk21

description: Library name: G438_TP186_EE71_B_EP6wk21


title: G440_TP186_GK91_B_EP6wk21

description: Library name: G440_TP186_GK91_B_EP6wk21


title: G460_TP186_GM41_B_EP6wk21

description: Library name: G460_TP186_GM41_B_EP6wk21


title: G464_TP186_JC12_B_EP6wk21

description: Library name: G464_TP186_JC12_B_EP6wk21


title: G437_TP186_JE14_B_EP6wk21

description: Library name: G437_TP186_JE14_B_EP6wk21


title: G433_TP186_GM40_B_EP6wk21

description: Library name: G433_TP186_GM40_B_EP6wk21


title: G434_TP186_HF57_B_EP6wk21

description: Library name: G434_TP186_HF57_B_EP6wk21


title: G436_TP186_IN66_B_EP6wk21

description: Library name: G436_TP186_IN66_B_EP6wk21


title: G431_TP186_GM16_B_EP6wk21

description: Library name: G431_TP186_GM16_B_EP6wk21


title: G430_TP186_GI26_B_EP6wk21

description: Library name: G430_TP186_GI26_B_EP6wk21


title: G429_TP186_EI94_B_EP6wk21

description: Library name: G429_TP186_EI94_B_EP6wk21


title: G428_TP186_EE32_B_EP6wk21

description: Library name: G428_TP186_EE32_B_EP6wk21


title: G427_TP186_JF94_B_EP6d024h1

description: Library name: G427_TP186_JF94_B_EP6d024h1


title: G425_TP186_JC12_B_EP6d024h1

description: Library name: G425_TP186_JC12_B_EP6d024h1


title: G426_TP186_JC52_B_EP6d024h1

description: Library name: G426_TP186_JC52_B_EP6d024h1


title: G423_TP186_GN03_B_EP6d024h1

description: Library name: G423_TP186_GN03_B_EP6d024h1


title: G443_TP186_HV65_B_EP6wk2c

description: Library name: G443_TP186_HV65_B_EP6wk2c


title: G422_TP186_GM52_B_EP6d024h1

description: Library name: G422_TP186_GM52_B_EP6d024h1


title: G419_TP186_GH35_B_EP6d024h1

description: Library name: G419_TP186_GH35_B_EP6d024h1


title: G421_TP186_GM41_B_EP6d024h1

description: Library name: G421_TP186_GM41_B_EP6d024h1


title: G420_TP186_GJ04_B_EP6d024h1

description: Library name: G420_TP186_GJ04_B_EP6d024h1


title: G418_TP186_GC03_B_EP6d024h1

description: Library name: G418_TP186_GC03_B_EP6d024h1


title: G416_TP186_JC25_B_EP6d024h1

description: Library name: G416_TP186_JC25_B_EP6d024h1


title: G415_TP186_IA36_B_EP6d024h1

description: Library name: G415_TP186_IA36_B_EP6d024h1


title: G432_TP186_GM22_B_EP6wk21

description: Library name: G432_TP186_GM22_B_EP6wk21


title: G411_TP186_GI29_B_EP6d024h1_mRNA

description: Library name: G411_TP186_GI29_B_EP6d024h1_mRNA


title: G407_TP186_JF94_B_EP6d04h1

description: Library name: G407_TP186_JF94_B_EP6d04h1


title: G412_TP186_GI36_B_EP6d024h1

description: Library name: G412_TP186_GI36_B_EP6d024h1


title: G410_TP186_GH90_B_EP6d024h1

description: Library name: G410_TP186_GH90_B_EP6d024h1