title: HL7702 cells, BPS replicate 2

description:
Library name: HL7702_BPS_2
HL7702 cells treated with BPS at IC01 for 24 h, biological replicate 2


title: HIEC6 cells, DBP replicate 1

status: Public on Jul 01 2026

type: SRA

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

country: South Korea

institute: Pusan National University

description:
Library name: HIEC6_DBP_1
HIEC6 cells treated with DBP at IC01 for 24 h, biological replicate 1

library_source: transcriptomic

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 Plus platform to generate 151 bp paired-end reads.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38(NCBI) whole genome using STAR
Calculation mapped reads using salmon
TMM + CPM calculation using conorm
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files contain Read count values for each sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: HaCaT human keratinocyte cells and HL7702 human hepatic epithelial cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, penicillin (100 U/mL), and streptomycin (100 µg/mL). HIEC-6 human small intestinal epithelial cells were cultured in Opti-MEM supplemented with 10 ng/mL EGF, 4% fetal bovine serum, penicillin (100 U/mL), and streptomycin (100 µg/mL). BEAS-2B human bronchial epithelial cells were cultured in Airway Epithelial Cell Basal Medium supplemented with the Bronchial Epithelial Cell Growth Kit. All cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated using the AccuPrep® Universal RNA Extraction Kit (Bioneer) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: Each cell line was cultured under standard conditions and allowed to attach for 24 h. Cells were then exposed to the indicated hazardous chemicals at cell line–specific IC01 concentrations for 24 h. Following exposure, total RNA was extracted and used for RNA sequencing.

tag: cell line

tag: cell type

value: normal human intestinal epithelial cell lines

tag: genotype

value: WT

tag: treatment

value: DBP (125 μM)

tag: batch


title: HIEC6 cells, AlCl3 replicate 2

description:
Library name: HIEC6_AlCl3_2
HIEC6 cells treated with AlCl3 at IC01 for 24 h, biological replicate 2


title: HL7702 cells, BPA replicate 2

description:
Library name: HL7702_BPA_2
HL7702 cells treated with BPA at IC01 for 24 h, biological replicate 2

value: normal human hepatic epithelium


title: patient244

type: other

city: Memphis

first: Kyle

middle: S

last: Smith

state: TN

address: 262 Danny Thomas Pl

country: USA

institute: St. Jude Children's Research Hospital

description: Brain tumor patient

hyb_protocol: Bisulphite converted DNA was amplified and hybridized to human MethylationHM450 BeadChip

scan_protocol: Array were imaged using BeadArray Reader (HiScan) and standard recommended illumina scanner setting

data_processing: Minfi R package (v1.58)

label: Cy3 and Cy5

molecule: other

source_name: Brain tumor

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from samples using Qiagen Kit according to standard instructions

tag: Sex

value: Male

tag: age

tag: mstage

tag: risk group

value: High

tag: subgroup

tag: g34 subtype

value: VIII

tag: tissue

value: Brain tumor


title: HIEC6 cells, AlCl3 replicate 1

description:
Library name: HIEC6_AlCl3_1
HIEC6 cells treated with AlCl3 at IC01 for 24 h, biological replicate 1


title: patient224

description: Brain tumor patient

value: Average

value: II


title: patient230

description: Brain tumor patient


title: CART19_IL10_Rep2

city: Philadelphia

first: Rawan

last: Shraim

state: PA

address: 3501 Civic Center Blvd

department: Oncology

institute: Children's Hospital of Philadelphia

description: Library name: HTS114_38_G2_CART19_IL10_Rep2_S38

data_processing:
Bulk RNA-sequencing - Fastq files were aligned to the human reference genome (GRCh38) using the STAR aligner (v2.7.11b). Per gene read counts for Ensembl gene annotations were computed using the subread package in R. Gene counts were normalized for library sizes, voom transformed and represented as log2CPM( counts per million)  using the edgeR R package (v 4.2.2).
scRNA-sequencing - Samples were processed using cellranger-7.1.0. For non-multiplexed samples, cellranger count was used to obtain the single-cell matrix and .h5 file. For multiplexed samples, cellranger multi was used in additional to supplementary files corresponding to the sample names. After obtaining the .h5 file, Seurat was used for downstream analyses.
Assembly: HG38
Supplementary files format and content: scRNA-sequencing - Files are in .h5 format and can be read into R using Seurat library.
Supplementary files format and content: Bulk RNA-sequencing - csv files with voom transformed log2 CPM per sample

growth_protocol: Bulk RNA-sequencing - NALM6 or UOCB cell lines transduced to express GFP were co-cultured with CART cells at an effector:target ratio of 1:8 in RPMI supplemented with 20% fetal bovine serum (FBS) and 1% penicillin/streptomycin, 1% HEPES, 1% non-essential amino acids, and 1% L-glutamine.

extract_protocol:
Bulk RNA-sequencing  -  Pellets were transformed to total RNA using Qiagen’s QiaShredder (Cat no. 79656) and RNeasy Mini RNA extraction kit
scRNA-sequencing - Cryopreserved peripheral blood mononuclear cells (PBMCs) or bone marrow mononuclear cells (BMMC) were thawed and resuspended in media. Suspensions were centrifuged at 300 x g for 5 minutes at 4°C and resuspended in Dulbecco's phosphate-buffered saline (DPBS, Gibco, PN 14190-144) with 1% bovine serum albumin (BSA, Miltenyi Biotec, PN 130-091-376). Cell suspensions were then centrifuged at 500 x g for 5 minutes at 4°C and resuspended in 50 µL of cell staining buffer (Biolegend Inc, PN 420201) followed by addition of 5 µL of Human TruStain FcX™ blocking reagent (Biolegend Inc, PN 422301) if the cell count per sample in DPBS + 1% BSA was > 200,000 cells. Cells were incubated in Fc block for 10 minutes at 4°C. During incubation, hashtag antibodies were prepared by adding 2.2 µL (1.5 µg) of each of the TotalSeq™ anti-human Hashtag to 52.8 µL cell staining buffer and centrifuged at 14000 x g for 10 minutes at 4°C. At the end of incubation in Fc block, each cell suspension was labelled with 50 µL TotalSeq™ anti-human Hashtag antibody and incubated for 30 minutes at 4°C. Cells were then washed thrice in cell staining buffer at 500 x g for 5 minutes at 4°C and resuspended in DPBS + 0.04% BSA. If cell counts in DPBS + 1% BSA were < 200, 000 cells, cells were centrifuged at 300 x g for 5 minutes at 4°C and resuspended in DPBS + 0.04% BSA.
Bulk RNA-sequencing - Complementary DNA libraries were prepared with Illumina’s Stranded mRNA poly-A enrichment kit following the standard protocol. Individual library QC was performed on Agilent TapeStation prior to pooling. Pooled libraries were sequenced on NextSeq2000 on a P4 XLEAP SBS flow cell to collect 20 million reads per sample.
scRNA-sequencing - Hashed and pooled cell suspensions or individual cell suspensions were subsequently processed to generate single cell RNA-seq libraries using chromium Next GEM single cell 3’ reagent kits v3.1 Dual Index (10x Genomics, PN-1000268) with 3’ feature barcode technology (10x Genomics, PN-1000262) for cell surface protein using chromium controller as per manufacturer’s instructions. Library fragment size was determined using the Bioanalyzer Agilent 2100 with the High Sensitivity DNA chip (Agilent Technologies, 5067-4626) and libraries were quantified using Kapa qPCR quantification kit (Roche Diagnostics, PN 501965234). After pooling, libraries were sequenced on an Illumina NovaSeq 6000 using sequencing parameters read1: i7: i5: read2 :: 28:10:10:90 bp at an average sequencing depth of 50,000 read pairs per cell.

treatment_protocol: Bulk RNA-sequencing - Cells were incubated with or without IL-10 added at a concentration of 15 ng/mL.

value: with IL10


title: PA_DMSO_rep3

city: Changchun

first: Qi

last: Dandan

address: 吉林省长春市绿园区新竹路1977号吉林大学动物医学学院

country: China

institute: JILIN UNIVERSITY

description: Library name: A3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
RSEM was used to estimate read counts for each gene and transcript in every sample, based on alignments to the reference genome and the corresponding annotation file. The resulting counts were subsequently converted to TPM values to obtain normalized expression levels at both the gene and transcript levels.
Genes differential expression analysis was performed by DESeq2 software between two different groups. The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 1.5 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ARS-UCD2.0
Supplementary files format and content: tab-delimited text files include raw counts and TPM values for each Sample
Supplementary files format and content: tab-delimited text files include results of gene differential expression analysis performed using DESeq2 software

organism: Bos taurus

source_name: Liver

growth_protocol: Hepatocytes were initially cultured in an attachment medium consisting of RPMI-1640 supplemented with 10% FBS, 1×10⁻⁶ mol/L insulin, 1×10⁻⁶ mol/L dexamethasone, and 10 μg/mL vitamin C. After cell attachment, the medium was replaced with growth medium containing RPMI-1640, 10% FBS, and 1% penicillin–streptomycin. The medium was renewed daily, and cells were maintained in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted from bovine hepatocytes using RNAiso Plus (D9108, TaKaRa) according to the manufacturer’s instructions. RNA concentration and purity were determined using a NanoDrop 2000 spectrophotometer, and integrity was assessed by agarose gel electrophoresis. RNA quality was further evaluated using an Agilent 5300 system to obtain the RQN value. Only samples with total RNA ≥ 1 μg, concentration ≥ 30 ng/μL, RQN ≥ 6.5, and an OD260/280 ratio between 1.8 and 2.2 were used for library construction.
mRNA was enriched from total RNA using oligo(dT) magnetic beads and fragmented into ~300 bp fragments. Double-stranded cDNA was generated through reverse transcription and second-strand synthesis. The cDNA fragments were end-repaired, A-tailed, and ligated to adapters, followed by size selection and PCR amplification to construct sequencing libraries. The libraries were sequenced on  Illumina Novaseq X Plus following the vendor's recommended protocol.

treatment_protocol: For the treatment protocol, bovine hepatocytes were treated with 400μmol/L PA  together with either DMSO or 200 μmol/L 3-IAA  to assess the effects of 3-IAA.

value: Liver

value: Primary hepatocytes


title: HIEC6 cells, control replicate 3

description:
Library name: HIEC6_Con_3
HIEC6 cells vehicle control for 24 h, biological replicate 3

value: Vehicle control


title: patient223

description: Brain tumor patient

value: Female

tag: shh subtype


title: patient242

description: Brain tumor patient


title: PA_DMSO_rep2

address: 吉林省长春市绿园区新竹路1977号吉林大学动物医学学院

description: Library name: A2


title: CART19_IL10_Rep1

description: Library name: HTS114_37_G1_CART19_IL10_Rep1_S37


title: patient241

description: Brain tumor patient


title: patient C13, 0 day

city: Daejeon

first: Yoonjung

last: Choi

address: 7-12, Daehak-ro 179beon-gil, Yuseong-gu

institute: Yoonjung

description:
Library name: C13_0M
Column name in processed_data.txt : C13_0M FPKM

data_processing:
Raw FASTQ files were processed through the following pipeline: adapter trimming was performed using Trimmomatic, reads were aligned to the human genome (hg19) using STAR v2.4.0, and gene-level quantification was conducted with HOMER.
Assembly: hg19
Supplementary files format and content: tab-delimitied text file includes FPKM for each Sample

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples were collected from RA patients prior to TNF-α inhibitor treatment and preserved in PAXgene Blood RNA Tubes (PreAnalytiX). Total RNA was extracted according to the manufacturer’s instructions using the PAXgene Blood RNA Kit.
High-quality RNA samples were subjected to DNase I treatment prior to library preparation. Strand-specific libraries were constructed using the NEXTflex Rapid Directional mRNA-Seq Kit (BIOO Scientific), following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq platform with paired-end 150 bp (PE150) reads under strand-specific conditions.

treatment_protocol: This study included patients diagnosed with RA who were prescribed a TNF-α inhibitor for the first time. TNF-α inhibitors used in these patients include adalimumab, golimumab, and infliximab. The exclusion criteria were age under 19 years, a history of malignancy, pregnancy or lactation, and incomplete electronic medical records (EMRs). Patients were followed for six months after the initiation of TNF-α inhibitor therapy.

value: Peripheral blood

tag: disease state

value: rheumatoid arthritis

value: prior to anti-TNF-α inhibitor treatment; baseline


title: HIEC6 cells, control replicate 2

description:
Library name: HIEC6_Con_2
HIEC6 cells vehicle control for 24 h, biological replicate 2

value: normal human intestinal epithelial cell lines

value: WT


title: patient222

description: Brain tumor patient


title: HL7702 cells, AlCl3 replicate 2

description:
Library name: HL7702_AlCl3_2
HL7702 cells treated with AlCl3 at IC01 for 24 h, biological replicate 2

value: normal human hepatic epithelium


title: PA_DMSO_rep1

address: 吉林省长春市绿园区新竹路1977号吉林大学动物医学学院

description: Library name: A1


title: HIEC6 cells, control replicate 1

description:
Library name: HIEC6_Con_1
HIEC6 cells vehicle control for 24 h, biological replicate 1


title: patient221

description: Brain tumor patient

value: Male

value: VII


title: NALM6_Rep3

description: Library name: HTS114_36_F6_NALM6_Rep3_S36

value: without IL10


title: articular cartilage, Y-T3

city: weifang

first: Zhuozheng

last: Li

state: shandong

address: 7166 Baotong West Street

institute: shandong second medical university

description:
Library name: sample12
FPKM

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/) to map reads to the reference genome of homo sapiens Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Data availability statement: Due to institutional data management policies and the lack of appropriate controlled access repositories, the raw RNA-seq data generated in this study cannot be made public. However, the processed data (FPKM expression matrices) that support the findings of this study have been deposited for this submission and are openly accessible.
Assembly: Oryctolagus cuniculus
Supplementary files format and content: csv files include FPKM and count values for each sample

organism: Oryctolagus cuniculus

source_name: articular cartilage

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 400±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ X Plus (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: articular cartilage

value: Articular chondrocytes

value: primary cells

value: Y-T


title: NALM6_Rep2

description: Library name: HTS114_35_F5_NALM6_Rep2_S35


title: patient220

description: Brain tumor patient

value: High

value: VI

value: Brain tumor


title: SEV,HealthyControl,HC1

city: Pavia

first: Rosalinda

last: Di Gerlando

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

description: Library name: HC1

data_processing:
FastQ files were generated via Illumina bcl2fastq2 (Version 2.17.1.14 http://support.illumina.com/downloads/bcl2fastq-conversion-software-v217.html).
Quantification of miRNAs was done as described in the literature [13]. The workflow, including quality control filter, trimming of adapters, and reads mapping against miRNA precursors, is implemented in Docker4Seq package
Assembly: HG19
Supplementary files format and content: fastq.gz

source_name: Small Extracellular Vesicles from plasma

growth_protocol: Venus blood from AD patients, FTD patients and CTRL subjects was collected in sodium citrate tubes and then plasma was retrieved. Differential centrifugation method was applied to separate SEVs from LEVs.

extract_protocol:
RNA was extracted from SEVs fractions using miRNeasy Mini kit (Qiagen, Germany) according to manufacturer’s instructions.
Libraries for miRNA sequencing have been prepared using the Small RNA-Seq Library Prep kit (Lexogen) according to the user manual. Sequencing steps have been carried out on the Illumina NextSeq 500.


title: PBMC, DENV3, P4, biol rep 3

city: Syracuse

first: Celine

last: Hardy

address: 750 East Adams Street

institute: SUNY Upstate Medical University

description: Library name: Sample 21

data_processing:
FASTQs generated using bcl2fastq
Kallisto (v0.46.2) was used to pseudoalign samples to the GRCh38 human transcriptome without bootstraps
Transcript-level counts and abundance data were imported into R using the TxImport package and TMM normalized using the package EdgeR
Assembly: GRCh38
Supplementary files format and content: abundance.tsv file containing transcripts per million (TPM)

source_name: PBMC

extract_protocol:
RNA was extracted with the Qiagen RNeasy Plus Mini kit
RNA quality and quantity were assessed with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit. Sequencing libraries were prepared with the Illumina Stranded Total RNA Ribo-Zero Plus library prep kit, using 20-50ng RNA as input. Libraries were assessed with the D1000 assay on the Agilent 4150 TapeStation and quantified with Qubit dsDNA High Sensitivity assay. A paired end 2x150bp sequencing run was performed on the Illumina NextSeq 2000 instrument.

treatment_protocol: Whole blood was collected from a healthy human donor, from which PBMC were freshly isolated and plated at 100,000 PBMC per well. PBMCs were inoculated with DENV-1 45AZ5 or DENV-3 CH53489 at 0 (uninfected control), 1 X 102, 103, or 104 PFU (triplicate for each condition). Cells were incubated at 37oC , 5% CO2 for 24 hours, following which cells were harvested, washed, and resuspended in RLT plus buffer with b-mercaptoethanol (BMF) and supernatants were discarded.

value: PBMC


title: NALM6_Rep1

description: Library name: HTS114_34_F4_NALM6_Rep1_S34


title: patient219

description: Brain tumor patient

value: Female

value: VIII


title: PBMC, DENV3, P4, biol rep 1

description: Library name: Sample 19


title: UOCB_Rep3

description: Library name: HTS114_33_F3_UOCB_Rep3_S33

source_name: UOCB

value: UOCB


title: patient218

description: Brain tumor patient

value: V


title: articular cartilage, Y3

description:
Library name: sample9
FPKM

value: Y


title: patient217

description: Brain tumor patient

value: Average


title: patient216

description: Brain tumor patient

value: Male


title: PBMC, DENV3, P3, biol rep 2

description: Library name: Sample 17


title: articular cartilage, Y1

description:
Library name: sample7
FPKM


title: NALM6_IL10_Rep3

description: Library name: HTS114_30_E6_NALM6_IL10_Rep3_S30

value: with IL10


title: patient215

description: Brain tumor patient

value: III


title: PBMC, DENV3, P3, biol rep 1

description: Library name: Sample 16


title: articular cartilage, T2

description:
Library name: sample5
FPKM

value: articular cartilage

value: T


title: NALM6_IL10_Rep2

description: Library name: HTS114_29_E5_NALM6_IL10_Rep2_S29


title: patient214

description: Brain tumor patient


title: patient213

description: Brain tumor patient

value: VII


title: NALM6_IL10_Rep1

description: Library name: HTS114_28_E4_NALM6_IL10_Rep1_S28


title: PBMC, DENV3, P2, biol rep 2

description: Library name: Sample 14


title: PBMC, DENV3, P2, biol rep 1

description: Library name: Sample 13


title: UOCB_IL10_Rep3

description: Library name: HTS114_27_E3_UOCB_IL10_Rep3_S27


title: patient212

description: Brain tumor patient


title: PBMC, DENV1, P4, biol rep 3

description: Library name: Sample 12


title: UOCB_IL10_Rep2

description: Library name: HTS114_26_E2_UOCB_IL10_Rep2_S26


title: patient211

description: Brain tumor patient


title: PBMC, DENV1, P4, biol rep 2

description: Library name: Sample 11


title: patient210

description: Brain tumor patient

value: IV


title: articular cartilage, C1

description:
Library name: sample1
FPKM

value: Articular chondrocytes

value: primary cells

value: C


title: NALM6_CART22_Rep3

description: Library name: HTS114_24_D6_NALM6_CART22_Rep3_S24

value: without IL10


title: PBMC, DENV1, P4, biol rep 1

description: Library name: Sample 10

value: PBMC


title: patient209

description: Brain tumor patient

value: High

value: VIII

value: Brain tumor


title: Donkey ovarian tissue

city: Qingda

first: yadan

last: Jin

state: 山东Shandong

address: Qingdao

institute: Qingdao Agricultural University

description: Library name: Samples2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support 10xgenomics. com/single-cel-gene-expression/software/pipelines/latestwhat- is-cel-range)
Assembly: 10mm
Supplementary files format and content: Tab-separated values files and matrix files

organism: Equus asinus

source_name: ovarian tissue

extract_protocol:
The ovary were washed in 1×PBS immediately after dissociation. These samples were stored in MACS Tissue Storage Solution within 48 h (Miltenyi Biotec, Bergisch Gladbach, Germany). It was subsequently transferred to 0.2% collagenase IV and DNase I digestive juices, followed by incubation at 37°C for 15 min. After digestion and mechanical striking into single cells, the cell suspension was filtered through a cell strainer (Solarbio, Beijing, China).
DNBelab C series high-throughput single-cell RNA library preparation kit is based on droplet microfluidic technology and independently designed using MGIC4 droplet generation device, through efficient mRNA capture magnetic beads and droplet recognition microbeads and single-cell RNA library preparation kit The single-cell (nuclear) suspension can be quickly prepared into a dedicated library corresponding to the sequencing platform.

value: ovarian tissue

value: single

value: germ cells


title: PBMC, DENV1, P3, biol rep 3

description: Library name: Sample 9


title: Mesonephric tissue and gonadal tissue of donkey

description: Library name: Samples1

source_name: Mesonephric tissue and gonadal tissue

value: Mesonephric tissue and gonadal tissue


title: patient208

description: Brain tumor patient

value: Female

value: V


title: NALM6_CART22_Rep1

description: Library name: HTS114_22_D4_NALM6_CART22_Rep1_S22


title: exp_HL215

city: Wuhan

first: Lintong

last: Men

address: Huazhong University of Science and Technology  1095 Jiefang Avenue

institute: Tongji Hospital Tongji Medical College

description:
Library name: Sample10
cardiac

data_processing:
The boxplot can show the distribution of gene expression levels of each sample, and is an effective visual representation of both central tendency and dispersionot.
To visualize the number of genes in different FPKM range of each sample, we performed statistics on the number of genes in three situations of FPKM (FPKM <= 1, FPKM 1 ~ 10, FPKM> = 10).
In order to reflect the correlation of gene expression between samples, the Pearson correlation coefficients of all gene expression between each two samples were calculated, and these coefficients were reflected in the form of a heatmap. The correlation coefficients can reflect the similar situation of the overall gene expression between each sample. The higher the correlation coefficient is, the more similar the gene expression level is
Biological experiments generally have biological replicates. Biological replicates generally occurs in biological experiment, and the multiple samples of biological replicates shall be classified into one group. The following table is the grouping of samples used in analysis
One of the key analytic points of small RNA sequencing is the comparison of the differences in gene expression.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: gene_expression.xls

organism: Mus musculus

source_name: heart

extract_protocol:
Mouse cardiac tissue was minced to 1×1×1 mm pieces and digested in DMEM (Wuhan Promoter Biological CO., LTD, Cat#KGL1211-500) containing Type II collagenase (Biosharp, Cat#9001-12-1) at 37°C in a constant temperature water bath for 1 hour. All tissue fragments with supernatants were centrifuged at 300 g for 10 minutes. The supernatants centrifugation at 2000 g for 20 minutes, and then collected and filtered through a 0.22 μm filter (Merck, Cat#SLGP033R), followed by ultracentrifugation (Optima XPN-100, Beckman Coulter, Brea, CA, USA) at 10000 g for 30 minutes. Next, the collected supernatants ultracentrifuged at 100000 g for 70 minutes. The sEVs were washed in 56 mL of sterile PBS and re-centrifuged at 100000 g for another 70 minutes. The final pellet was resuspended in 100 µL of sterile PBS. Similarly, the supernatants from HL-1 cells with or without Palmitic acid (PA, 100 μM, Kunchuang Biotechnology, Cat#KC002) were collected and sEVs were isolated following the above centrifugation steps. sEVs were lysed in 10×cell lysis buffer (Antgene, Cat#ANT071) and the amount of sEVs proteins recovered was quantified by a BCA assay (Wuhan Promoter Biological CO., LTD, Cat#P5026). The morphology and size of the isolated sEVs were determined using electron microscopy according to the manufacturer's instructions. A total of 20 μg sEVs were used for Western blot experiments. Exosomes were verified by using primary antibodies such as HSP70 (HUABIO, Cat#ET1601-11, RRID: AB_3069593, 1:1000 dilution), TSG101 (HUABIO, Cat#T1701-59, RRID: AB_3068599, 1:1000 dilution) and CD9 (HUABIO, Cat#ET1601-9, RRID: AB_3069620, 1:1000 dilution). Flow NanoAnalyzer (N30E, NANOFCM, Medical sub-center of Analytical and Testing Center, Huazhong University of Science and Technology) was used for concentration of sEVs derived from mice myocardial tissue.
Library preparation is performed using MGIEasy Small RNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA is ligated 3’ and 5’ adaptors sequentially in two reaction systems for adaptors ligation. After adaptor ligation, RNA is reverse transcribed into cDNA and PCR amplified. The library is fragment size selected by polyacrylamide gel electrophoresis and subjected to quality control.Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and sequencing reads of SE50 bases length are generated on G400 platform (BGI-Shenzhen, China).

value: heart

value: HFD plus L-NAME


title: NALM6_CART19_Rep3

description: Library name: HTS114_21_D3_NALM6_CART19_Rep3_S21


title: PBMC, DENV1, P3, biol rep 1

description: Library name: Sample 7


title: exp_HL205

description:
Library name: Sample9
cardiac


title: NALM6_CART19_Rep2

description: Library name: HTS114_20_D2_NALM6_CART19_Rep2_S20


title: patient205

description: Brain tumor patient

value: Average


title: exp_HL203

description:
Library name: Sample8
cardiac


title: NALM6_CART19_Rep1

description: Library name: HTS114_19_D1_NALM6_CART19_Rep1_S19


title: PBMC, DENV1, P2, biol rep 2

description: Library name: Sample 5


title: patient206

description: Brain tumor patient

value: Male

value: VI


title: exp_HL202

description:
Library name: Sample7
cardiac


title: patient204

description: Brain tumor patient


title: PBMC, DENV1, P2, biol rep 3

description: Library name: Sample 6


title: PBMC, DENV1, P2, biol rep 1

description: Library name: Sample 4


title: NALM6_CART22_IL10_Rep3

description: Library name: HTS114_18_C6_NALM6_CART22_IL10_Rep3_S18

value: with IL10


title: patient203

description: Brain tumor patient


title: NALM6_CART22_IL10_Rep2

description: Library name: HTS114_17_C5_NALM6_CART22_IL10_Rep2_S17


title: exp_HL201

description:
Library name: Sample6
cardiac


title: articular cartilage, Y-T2

description:
Library name: sample11
FPKM

value: articular cartilage

value: Articular chondrocytes

value: primary cells

value: Y-T


title: PBMC, Control, P0, biol rep 3

description: Library name: Sample 3

value: PBMC


title: PBMC, DENV3, P4, biol rep 2

description: Library name: Sample 20


title: articular cartilage, Y-T1

description:
Library name: sample10
FPKM


title: PBMC, DENV3, P3, biol rep 3

description: Library name: Sample 18


title: patient202

description: Brain tumor patient

value: High

value: VIII

value: Brain tumor


title: exp_CON230

description:
Library name: Sample5
cardiac

value: chow diet


title: UOCB_Rep2

description: Library name: HTS114_32_F2_UOCB_Rep2_S32

value: UOCB

value: without IL10


title: articular cartilage, Y2

description:
Library name: sample8
FPKM

value: Y


title: UOCB_Rep1

description: Library name: HTS114_31_F1_UOCB_Rep1_S31


title: NALM6_CART22_IL10_Rep1

description: Library name: HTS114_16_C4_NALM6_CART22_IL10_Rep1_S16


title: PBMC, Control, P0, biol rep 2

description: Library name: Sample 2


title: PBMC, DENV3, P2, biol rep 3

description: Library name: Sample 15


title: patient201

description: Brain tumor patient

value: Female

value: IV


title: articular cartilage, T3

description:
Library name: sample6
FPKM

value: T


title: exp_CON227

description:
Library name: Sample4
cardiac

value: heart


title: NALM6_CART19_IL10_Rep3

description: Library name: HTS114_15_C3_NALM6_CART19_IL10_Rep3_S15

value: with IL10


title: patient200

description: Brain tumor patient

value: Male

value: Average


title: articular cartilage, T1

description:
Library name: sample4
FPKM

value: articular cartilage

value: Articular chondrocytes

value: primary cells


title: PBMC, Control, P0, biol rep 1

description: Library name: Sample 1

value: PBMC


title: exp_CON223

description:
Library name: Sample3
cardiac


title: patient199

description: Brain tumor patient

value: I


title: NALM6_CART19_IL10_Rep2

description: Library name: HTS114_14_C2_NALM6_CART19_IL10_Rep2_S14


title: PEB_AL#6_d28_hemanoids

city: Graz

first: Afrim

last: Avdili

address: Auenbruggerplatz 48

department: Blood Group Serology and Transfusion Medicine

country: Austria

institute: Medicl University of Graz

description:
Library name: 240906_PEB_EB_d28
FFPE spatial transcriptomics

data_processing:
Raw sequencing data were processed using the 10x genomics space ranger pipeline  to produce fastaq files
Assembly: GRCh38 (human genome assembly)
Supplementary files format and content: barcodes.tsv.gz: the list of psecial barcodes
Supplementary files format and content: features.tsc.gz: the list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: scalefactors_json.json:  sclae factors in json format
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: spatial_enrichment.csv: Region-specific gene enrichment
Supplementary files format and content: tissue_hires_image.png: high resolution of tissue image
Supplementary files format and content: tissue_lowres_image.png: low resolution tissue image
Supplementary files format and content: tissue_positions.csv: Spatial spot coordinates
Library strategy: Spatial Transcriptomics

source_name: iPSC derived organoids

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) hemanoids were sectioned at a thickness of 5 µm using a microtome
Sequencing libraries were prepared with the 10xGenomics Visium Spatial Gene Expresion Slides & reagent kitt sccording to the manufacturer instructions

treatment_protocol: iPSCs differentiation protocol

value: iPSC derived organoids

value: iPSCs

tag: time point

value: day 28


title: exp_CON222

description:
Library name: Sample2
cardiac

value: chow diet


title: patient198

description: Brain tumor patient

value: High

value: Brain tumor


title: NALM6_CART19_IL10_Rep1

description: Library name: HTS114_13_C1_NALM6_CART19_IL10_Rep1_S13


title: PEB_AL#6_d16_hemanoids

description:
Library name: 240905_PEB_EB_d16
FFPE spatial transcriptomics

value: day 16


title: exp_CON221

description:
Library name: Sample1
cardiac


title: articular cartilage, C3

description:
Library name: sample3
FPKM

value: C


title: UOCB_CART22_Rep3

description: Library name: HTS114_12_B6_UOCB_CART22_Rep3_S12

value: without IL10


title: Pat6_rep1_urine_VDJ

city: Berlin

first: Christopher

middle: Mark

last: Skopnik

address: Charitéplatz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

description:
Library name: Sample26
10X Genomics

data_processing:
For gene expression (GEX): Initial FASTQ files were generated from base call files with cellranger mkfastq. From fastq files, GEX reads were mapped against human reference genome as provided by 10X Genomics (GRCh38-2020-A) using cellranger count from Cell Ranger v7.1.0 with default settings but exclusion of intronic reads (--include-introns=false). This generated the files filtered_feature_bc_matrix.h5 and raw_feature_bc_matrix.h5 with respective sample prefixes.
From resulting BAM files, anonymized (bamboozled) versions were generated with the python tool BAMboozle (v.0.5.0) (https://pypi.org/project/BAMboozle/) with default settings. The bamboozled BAM files were converted back to fastq files with cellranger bamtofastq. Bamboozled fastq files were deposited at the Sequencing read archive (SRA).
For T cell receptors (VDJ): TCR reads of VDJ libraries were mapped against GRCh38-alts-ensembl-2.0.0 as provided by 10X Genomics using cellranger vdj with default settings. Here, Cell Ranger v3.0.2 and v5.0.0 were used for Pat2 (replicate one), Pat3, Pat4 and Pat2 (replicate two), Pat5, Pat6, respectively. This generated all_contig_annotations.csv, clonotypes.csv, consensus_annotations.csv, filtered_contig_annotations.csv.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5 and raw_feature_bc_matrix.h5 contain unique molecular identifier (UMI) count matrices for GEX. all_contig_annotations.csv, clonotypes.csv, consensus_annotations.csv, filtered_contig_annotations.csv contain TCR chain callings and clonotype annotation for cellular barcodes; all as inferred from VDJ libraries. See 10X Genomics’ documentation for exact file description.

source_name: urine

extract_protocol:
Paired samples of heparinized venous blood and freshly voided non-morning urine (usually 2nd urine of the day; processed less than one-hour post excretion) were collected from patients who were hospitalized at the Charité - Universitätsmedizin Berlin due to acute lupus flares with renal involvement. After dipstick analysis to exclude urinary tract infection urine was diluted 1:2 in Annexin binding buffer (ABB) with 1 % BSA and 2 µg/ml Actinomycin D (ActD). Peripheral blood was treated with 2 µg/ml ActD and both body fluids were incubated for 30 min on ice. ActD should preserve transcriptomes from alteration ex vivo. Urine pellets from centrifugation (300 g, 7 min, 4 °C) and PBMC isolated by density gradient centrifugation (600 g, 20 min, 25 °C) with Ficoll-Paque were subjected to red blood cell lysis with ammonium chloride buffer when necessary. Subsequent to 20 min incubation on ice with AnnexinV-FITC (Biolegend, 640906 or Miltenyi, 130-093-060), FCγR blocking reagent and fluorochrome conjugated mAb against human CD3 (APC-eFluor780, SK7, eBioscience, 47-0036-42), CD4 (PE-Vio770, REA623, Miltenyi, 130-113-227) and CD8 (PE or APC, GN11/134D7, DRFZ in-house) cell pellets were filtered through 30 µm mesh, washed at least 10X volume of ABB, resuspended in 2 ng/ml DAPI -containing ABB and sorted by FACS on machines from BD (FACSAria or FACSAriaII) with 70 µm nozzles for DAPI- AnnexinV- CD3+ and CD4+ or CD8+ events. Cell sorters were maintained by the FCCF at DRFZ in Berlin. Events from urine were sorted into one tube. CD4+ or CD8+ T cell events from blood were sorted separately for and mixed subsequently at the CD4-to-CD8 ratio equivalent to that from paired urine samples. ScRNA-seq was conducted subsequently when absolute sorted event count from urine was 3000 or above.
Library construction was conducted according to protocols Chromium Single Cell 3’ Library and Gel Bead Kit v2 (PN-120267) for Pat0 and Pat1, Chromium Single Cell 5' Library and Gel Bead Kit v1 (PN-1000014) for Pat2 (replicate one) and Pat3 5, Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1 (PN-1000167) for Pat2 (replicate two) and Pat6. Libraries of Pat2 6 were split and separately processed for sequencing of gene expression (GEX) and immune receptors V(D)J, here T cell receptor (TCR). Intermediate and final library quantity and quality was assessed with Qubit and Bioanalyzer2100 (Agilent).

value: urine

value: T lymphocyte

tag: replicate

tag: patient sex

value: female

tag: patient age

tag: sort date

tag: 10x library_version

tag: library type

value: T cell receptor (VDJ)


title: patient197

description: Brain tumor patient

value: Female

value: Average


title: UOCB_IL10_Rep1

description: Library name: HTS114_25_E1_UOCB_IL10_Rep1_S25

tag: cell line

value: UOCB

tag: treatment

value: with IL10


title: [Mouse kidney tissue][Control_3]

city: WuHan

first: Zhipu

last: Qian

address: DongHu road ,No.115

institute: WuHan university

description: Library name: Sample 9

data_processing:
Preparation of single-cell suspension fluid
capture the single-cell and prepare library construction
Sequencing data processing and analysis
data visualization, and generation of the final report
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: one sample from kidney tissue of the control group

extract_protocol:
The single cells were mixed with oil droplets using the DNBelab C-TaiM4 instrument, then homogenized. The cells were lysed and the released primers contained poly(dT) reverse transcription primers, thereby capturing RNA with polyA tails.
The captured RNA will have the process of reverse transcription, released, purified by magnetic beads,produce more cDNA by PCR,and then fragmented, end-repaired, ligated with adapters, and finally, a cDNA library and oligo library containing P5 and P7 adapters are constructed by PCR method.

value: kidney tissue


title: UOCB_CART22_Rep2

description: Library name: HTS114_11_B5_UOCB_CART22_Rep2_S11


title: Pat6_rep1_blood_VDJ

description:
Library name: Sample25
10X Genomics

source_name: peripheral blood

value: peripheral blood

tag: cell type


title: articular cartilage, C2

description:
Library name: sample2
FPKM

value: articular cartilage

value: Articular chondrocytes

value: primary cells


title: patient196

description: Brain tumor patient

tag: Sex

value: Male

tag: age

tag: mstage

value: Brain tumor


title: [Mouse kidney tissue][Control_2]

description: Library name: Sample 8


title: patient195

description: Brain tumor patient

tag: risk group

tag: subgroup

tag: g34 subtype

value: VII


title: Pat2_rep2_urine_VDJ

description:
Library name: Sample18
10X Genomics

tag: tissue


title: UOCB_CART19_Rep3

description: Library name: HTS114_09_B3_UOCB_CART19_Rep3_S9

value: without IL10


title: Pat2_rep2_blood_VDJ

description:
Library name: Sample17
10X Genomics


title: [Mouse kidney tissue][Control_1]

description: Library name: Sample 7


title: [Mouse kidney tissue][CKD_EGT_3]

description: Library name: Sample 6

source_name: one sample from kidney tissue of the EGT group


title: G401-i cells, SMARCB1-reexpression, day 10, rep2

city: Paris

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Library name: G401_SMARCB1_J10_2
Column name in raw counts and TPM matrixes : P118T553
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on GRCh39/hg19 reference genome were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and then removed
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: a single tab-delimited text file includes matrix of TPM values with sample in columns and genes on rows

growth_protocol: I2A cells were maintained in RPMI containing 10% fetal bovine serum (FBS) and supplemented with 50 ng/mL doxycycline, 50 μg/mL hygromycin B and 300 μg/mL geneticin. G401-i cells were maintained in RPMI containing 10% FBS and supplemented with 50 ng/mL doxycycline. For both inducible cell lines, medium was changed every 3-4 days to renew drugs and cells were washed three times in Phosphate Buffer Saline (PBS) to completely remove doxycycline in order to induce SMARCB1 expression.

extract_protocol:
Total RNAs from cell line samples were extracted using the Nucleospin II kit (Macherey-Nagel). Total RNAs from frozen human tumors were extracted using the QIAamp RNAeasy kit (Qiagen)
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.,).

treatment_protocol: For low-dose decitabine (DAC) experiments, I2A cells were treated with DAC at 100 nM or DMSO as a control for 21 days.

value: Rhabdoid tumor cells

tag: genotype


title: Pat6_rep1_urine_GEX

description:
Library name: Sample14
10X Genomics

value: urine

value: T lymphocyte

tag: replicate

value: gene expression (GEX)


title: patient193

description: Brain tumor patient

value: High

tag: shh subtype


title: Pat6_rep1_blood_GEX

description:
Library name: Sample13
10X Genomics

tag: patient sex

value: female

tag: patient age


title: G401-i cells, SMARCB1-reexpression, day 10, rep1

description:
Library name: G401_SMARCB1_J10_1
Column name in raw counts and TPM matrixes : P118T552
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt


title: [Mouse kidney tissue][CKD_EGT_1]

description: Library name: Sample 4


title: patient191

description: Brain tumor patient

value: Female

value: IV


title: G401-i cells, SMARCB1-reexpression, day 7, rep3

description:
Library name: G401_SMARCB1_J7_3
Column name in raw counts and TPM matrixes : P118T551
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt


title: Pat2_rep2_urine_GEX

description:
Library name: Sample6
10X Genomics

tag: sort date

tag: 10x library_version


title: [Mouse kidney tissue][CKD_3]

description: Library name: Sample 3

source_name: one sample from kidney tissue of the AKI-to-CKD group

value: kidney tissue


title: patient190

description: Brain tumor patient

value: Average

value: III


title: [Mouse kidney tissue][CKD_2]

description: Library name: Sample 2


title: G401-i cells, SMARCB1-reexpression, day 7, rep1

description:
Library name: G401_SMARCB1_J7_1
Column name in raw counts and TPM matrixes : P118T549
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt

tag: cell line


title: [Mouse kidney tissue][CKD_1]

description: Library name: Sample 1


title: SCC154-hfm HPV-positive post-hypoxic replicate 5

city: Leuven

first: Sandra

last: Nuyts

address: Herestraat 49

country: Belgium

institute: KU Leuven

description: Library name: GC166356

data_processing:
Sequencing reads were quality-checked with FastQC v0.11.9; trimmed with Trimmomatic v0.39; aligned to hg38 using HISAT2 v2.2.1; deduplicated with UMI-tools v1.1.5; and assigned to genes using featureCounts v1.5.1. Count matrices were generated and used for normalization and differential expression analysis with DESeq2.
Assembly: hg38
Supplementary files format and content: text file containg raw counts

growth_protocol: Hfm-spheroids from HPV-negative FADU-hfm and HPV-positive SCC154-hfm were created using 96-well ultra-low attachment (ULA) plates (Corning). Medium containing 20% FBS and 1% penicillin-streptomycin (Thermo Fisher Scientific) was refreshed biweekly. Hfm spheroids were treated with 1.25% Trypsin (T1426, Sigma-Aldrich) for 1 hour at 37°C to isolate post-hypoxic (GFP-positive) and non-hypoxic (DsRed-positive) cell populations using fluorescence-activated cell sorting (BD Influx, BD Biosciences) to obtain clearly defined post-hypoxic and non-hypoxic FADU-hfm and SCC154-hfm cells. These cells were cultured at 37°C and passaged via trypsinization.

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen)
RNA-sequencing libraries were prepared with the QuantSeq 3′ mRNA-Seq V2 Library Prep Kit (Lexogen)

value: Head and neck squamous cell carcinoma cell line

value: hypoxia-fate mapped GFP-positive


title: G401-i cells, day 0, rep3

description:
Library name: G401_J0_3
Column name in raw counts and TPM matrixes : P118T545
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt


title: SCC154-hfm HPV-positive non-hypoxic replicate 5

description: Library name: GC166355

value: hypoxia-fate mapped DsRED-positive


title: patient188

description: Brain tumor patient

value: Male

value: V

value: Brain tumor


title: white adipose tissue,rebound sleep,rep#5

city: Beijing

first: Hong

last: Jiang

address: No. 38, Xueyuan Road, Haidian District, Beijing

institute: School of Basic Medical Sciences Peking University

description:
Library name: male-WATSD5
Column name in merged.gene_count_matrix.xlsx : male-WATSD5

data_processing:
Preprocessing and Quality Control:Raw FASTQ files were performed data filtering and quality control using fastp, which included quality control of raw reads to assess sequencing quality and remove low-quality bases or adapter sequences.
Gene-Level Quanitification:And then aligned to the Ensembl GRCm39 reference genome using STAR. Using StringTie to assemble the reads on the alignment to create all the transcripts present in all samples. Per-gene transcripts were quantified with StringTie to produce a raw gene expression matrix and use the FPKM value (Fragments Per Kilobase Million) to evaluate the correlation of gene expression characteristics within and between groups.
Differential Gene Expression Analysis:  For the differential gene expression analysis, the DESeq2 package, version 1.38.3,42 implemented in R, was employed. Raw counts were normalized, and statistical models were applied to identify differentially expressed genes across experimental conditions.
Enrichment Analysis: Differentially expressed genes from the RS vs Control genes (adjusted p value<0.05) were filtered to retain only those enriched in  based on the enrichment criteria.
Assembly: GRCm39 reference genome
Supplementary files format and content: Supplementary files format and content: merged.gene_count_matrix.xlsx :Gene Counts
Supplementary files format and content: Supplementary files format and content: deseq2_and_GO_results_combined.xlsx :DESeq2 results

source_name: white adipose tissue

extract_protocol:
The WAT tissues were collected during rebound sleep stage in the dark phase (ZT16). The WAT tissues RNA concentration was measured by Qubit 4.0 and diluted to a final concentration of 200-250 ng/ml. RNA integrity number (RIN) was analyzed with the Agilent RNA 6000 Nano Kit (5067-1511, Agilent Technologies) and the Agilent 2100 Bioanalyzer. All samples displayed a RIN of >8.
RNA libraries were prepared with 1 mg of total RNA using the Illumina TruSeq mRNA stranded sample preparation Kit. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperatures. The RNA fragments underwent reverse transcription using random primers. This is followed by second-strand cDNA synthesis with DNA Polymerase I and RNaseH. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of the library were pooled. The pool was quantified by using Agilent 2100 DNA 1000 kit. The pool was sequenced for 37.5 million reads using an DNBSEQ-T7/Gene+Seq-2000 instrument and a PE100 sequencing protocol.

value: white adipose tissue

tag: treatment

value: rebound sleep and control sleep conditions


title: G401-i cells, day 0, rep2

description:
Library name: G401_J0_2
Column name in raw counts and TPM matrixes : P118T544
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt

tag: cell type

value: Rhabdoid tumor cells


title: white adipose tissue,rebound sleep,rep#4

description:
Library name: male-WATSD4
Column name in merged.gene_count_matrix.xlsx : male-WATSD4


title: patient187

description: Brain tumor patient

source_name: Brain tumor

tag: Sex


title: SCC154-hfm HPV-positive post-hypoxic replicate 4

description: Library name: GC166352


title: I2A cells, DAC treatment, 100 nM, 21 days, rep3

description:
Library name: I2Ap_Decitabine_100n_21d_3
Column name in raw counts and TPM matrixes : I2Ap_Decitabine_100n_21d_3
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: Decitabine


title: SCC154-hfm HPV-positive non-hypoxic replicate 4

description: Library name: GC166351


title: patient185

description: Brain tumor patient

tag: age

value: II


title: white adipose tissue,rebound sleep,rep#2

description:
Library name: male-WATSD2
Column name in merged.gene_count_matrix.xlsx : male-WATSD2


title: I2A cells, DAC treatment, 100 nM, 21 days, rep2

description:
Library name: I2Ap_Decitabine_100n_21d_2
Column name in raw counts and TPM matrixes : I2Ap_Decitabine_100n_21d_2
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: FADU-hfm HPV-negative post-hypoxic replicate 4

description: Library name: GC166350

source_name: FADU

value: FADU


title: patient184

description: Brain tumor patient

tag: mstage

value: VIII


title: white adipose tissue,rebound sleep,rep#1

description:
Library name: male-WATSD1
Column name in merged.gene_count_matrix.xlsx : male-WATSD1


title: I2A cells, DAC treatment, 100 nM, 21 days, rep1

description:
Library name: I2Ap_Decitabine_100n_21d_1
Column name in raw counts and TPM matrixes : I2Ap_Decitabine_100n_21d_1
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: FADU-hfm HPV-negative non-hypoxic replicate 4

description: Library name: GC166349


title: patient183

description: Brain tumor patient

tag: risk group


title: white adipose tissue,control sleep,rep#3

description:
Library name: male-WATC5
Column name in merged.gene_count_matrix.xlsx :  male-WATC5


title: SCC154-hfm HPV-positive post-hypoxic replicate 3

description: Library name: GC166348


title: patient182

description: Brain tumor patient

value: High

tag: subgroup


title: SCC154-hfm HPV-positive non-hypoxic replicate 3

description: Library name: GC166347


title: patient181

description: Brain tumor patient

tag: g34 subtype


title: I2A cells, DMSO treatment, 21 days, rep1

description:
Library name: I2Ap_DMSO_1
Column name in raw counts and TPM matrixes : I2Ap_DMSO_1
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: DMSO


title: white adipose tissue,control sleep,rep#2

description:
Library name: male-WATC4
Column name in merged.gene_count_matrix.xlsx :  male-WATC4

tag: tissue


title: I2A cells, DMSO treatment, 21 days, rep2

description:
Library name: I2Ap_DMSO_2
Column name in raw counts and TPM matrixes : I2Ap_DMSO_2
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

tag: genotype


title: patient180

description: Brain tumor patient

value: Average


title: white adipose tissue,control sleep,rep#1

description:
Library name: male-WATC2
Column name in merged.gene_count_matrix.xlsx :  male-WATC2


title: Stereo-CITE-seq, mouse thymus, Protein

city: Singapore

first: Shibo

last: Liu

address: 12 Science Drive 2

country: Singapore

institute: National University of Singapore

description: Library name: A02677B5_v7.1_mouse_thymus_Stereo-CITE_ADT

library_source: other

data_processing:
The fastq files from Stereo-seq were processed following the standard pipeline (https://github.com/STOmics/SAW).
Assembly: mm10
Supplementary files format and content: The .tissue.gef.h5 data is the tissue bin resolution and the .cellbin.gef.h5 data is the cellbin resolution.

molecule: protein

source_name: thymus

extract_protocol:
Prior to the experiment, all solutions were freshly prepared and maintained on ice. Blocking Buffer (50 µl per sample) was composed of 3x SSC, 0.1% Triton-X-100, 10% serum, 1 µg/µl sheared salmon sperm DNA, 2.5 µl TruStain FcX PLUS (anti-mouse CD16/32) antibody (BioLegend, Cat. No. 156604), 5% RNase inhibitor (RI), and 5 µM 32-nt Poly A. The Wash Buffer consisted of 3x SSC with 5% RI. Cryosectioned OCT-embedded tissue, cut to 10 µm thick, was carefully transferred onto the Stereo-seq chip. These chips, now bearing tissue sections, were immediately warmed to 37℃ for 1 minute using a thermocycler adaptor. Tissues were then fixed by placing the chips in pre-chilled methanol at -20℃ for 30 minutes. Following fixation, blocking was performed by incubating the tissue with Blocking Buffer for 20 minutes, after which the sections were exposed to the TotalSeqTM-A antibody mix in Blocking Buffer for 45 minutes at room temperature. The tissue sections on chips were then washed three times with Wash Buffer, each for 30 seconds. After DAPI staining, the tissue sections were mounted with glycerol and imaged. Subsequent processing followed the Stereo-seq Transcriptomics T Kit protocol with minor adjustments. Briefly, the sections were permeabilized with Permeabilization Mix for an optimized duration, as recommended in the Stereo-seq Permeabilization Kit instructions. After reverse transcription, cDNA and antibody-derived tag (ADT) products were released from the chips using Release Enzyme Mix and collected. Separation of the cDNA fraction from the ADT library was achieved via a 0.8X bead selection, followed by preparation of the cDNA sequencing library in accordance with the Stereo-seq Transcriptomics T Kit. The ADT product in the supernatant was purified using a 2.0X (0.8X + 1.2X) bead selection, then amplified with Protein PCR Primer Mix.
Both ADT and cDNA libraries were sequenced using MGI DNBSEQ-T7 sequencing platforms.

value: thymus


title: FADU-hfm HPV-negative non-hypoxic replicate 3

description: Library name: GC166345

value: Head and neck squamous cell carcinoma cell line


title: I2A cells, DNMT3A-knockout cells, clone 1D1

description:
Library name: I2Ap_DNMT3aKO_1D1
Column name in raw counts and TPM matrixes : I2Ap_DNMT3aKO_1D1
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: SMARCB1-negative DNMT3A knockout


title: patient179

description: Brain tumor patient

value: VII


title: FADU-hfm HPV-negative post-hypoxic replicate 3

description: Library name: GC166346

value: hypoxia-fate mapped GFP-positive


title: Stereo-CITE-seq, mouse thymus, GEX

description: Library name: A02677B5_v7.1_mouse_thymus_Stereo-CITE_mRNA


title: I2A cells, DNMT3A-knockout cells, clone 1C12

description:
Library name: I2Ap_DNMT3aKO_1C12
Column name in raw counts and TPM matrixes : I2Ap_DNMT3aKO_1C12
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: SCC154-hfm HPV-positive post-hypoxic replicate 2

description: Library name: GC166344


title: UOCB_CART22_Rep1

description: Library name: HTS114_10_B4_UOCB_CART22_Rep1_S10

value: without IL10


title: patient178

description: Brain tumor patient

value: Female

value: Brain tumor


title: patient194

description: Brain tumor patient


title: [Mouse kidney tissue][CKD_EGT_2]

description: Library name: Sample 5

value: kidney tissue


title: I2A cells, DNMT3A-knockout cells, clone 1C10

description:
Library name: I2Ap_DNMT3aKO_1C10
Column name in raw counts and TPM matrixes : I2Ap_DNMT3aKO_1C10
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: Rhabdoid tumor cells


title: scRNA_E7.5

city: Shanghai

first: Qing

state: Shanghai

address: Xuhui Yueyang road 320, ShangHai, China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

data_processing:
Raw RNA-seq reads were cleaned using fastp (v0.20.0) program, aligned to mm10 using STAR (v2.7.3a)
Only unique mapped reads were kept and counted by featureCounts (v2.0.0)
FPKM and TPM were calculated by stringtie (v2.0)
Genome coverage was counted by bamCoverage (v3.3.1). Differential gene expression was carried out using DESeq2 (v1.30.0), and clusterProfiler (v3.18.1) was used for GO and KEGG analysis in R
Assembly: mm10
Supplementary files format and content: For deep-seq, tale-delimited text file includes number of different reads for each sample. For RNA-seq, tab-delimited text file includes RPKM values for each sample. For WGBS, bed file includes the average methylation sites per 200bp in the genome. For scRNA-seq of E7.5 embryos, cellfocus file includes the representation matrix of different cells.

source_name: embryos

extract_protocol:
For deep-seq, The genomic DNA of various tissues (brain, heart, liver, testis, and tail) from wild-type mice and Gjb235delG/35delG mice derived from diploid compensation, was isolated using the TIANamp Genomic DNA Kit (TIANGEN). This was followed by PCR amplification for Sanger sequencing. Target sites were amplified from the extracted genomic DNA using Phanta® Max Super-Fidelity DNA Polymerase (Vazyme)For RNA-seq, single cells were picked using a Piezo-drill micromanipulator and transferred into a 200 µl tube containing 1.2 µl of lysis buffer. The lysate underwent cDNA amplification with the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712)
For deep-seq,  the PCR products were then ligated with different barcodes and pooled together. Libraries were generated from adapter-modified PCR products. For RNA-seq, the RNA-seq library was prepared using the TruePrep DNA Library Prep Kit V2 (Vazyme, Cat#TD503) for Illumina sequencing
Libraries of deep-seq and RNA-seq subjected to deep sequencing on Illumina NovaSeq6000 platform following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads by Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: embryos

tag: strain

tag: genetic modification

value: Actin-RFP and Actin-GRP transgene

tag: time


title: patient192

city: Memphis

first: Kyle

institute: St. Jude Children's Research Hospital

description: Brain tumor patient

data_processing: Minfi R package (v1.58)

extract_protocol: DNA was extracted from samples using Qiagen Kit according to standard instructions

value: Male


title: patient177

description: Brain tumor patient

tag: shh subtype


title: SCC154-hfm HPV-positive non-hypoxic replicate 2

description: Library name: GC166343

value: hypoxia-fate mapped DsRED-positive


title: PTX-anti-VEGF-no2

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

country: Japan

institute: Okayama University Hospital

description: Library name: Sample 8

data_processing:
CLC Genomics Workbench (version 22.0.2) was used for RNA-seq Analysis pipeline (version 2.6). GRCm38.p6 was used for reference genome. TPM was calculated for expression value.
Assembly: GRCm38.p6
Supplementary files format and content: Excel file format

source_name: Lung tumor

growth_protocol: Female C57BL/6J mice (7 weeks old) were maintained under pathogen-free conditions. Subcutaneous tumors were established by inoculating 7-8×10^5 Egfr-mutant lung cancer cells suspended in 50% Matrigel solution.

extract_protocol:
Subcutaneous tumors harvested on day 8 post-treatment were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted using the RNeasy Mini Kit or AllPrep DNA/RNA Mini Kit (Qiagen). RNA concentration and quality were assessed using Qubit (Thermo Fisher Scientific) and RNA ScreenTape Analysis (Agilent).
Following rRNA depletion using the NEBNext rRNA Depletion Kit v2 (New England Biolabs), cDNA libraries were prepared using the MGIEasy RNA Directional Library Prep Set (MGI Tech Japan). RNA-sequencing was performed on a DNBSEQ-G400RS sequencer using the DNBSEQ-G400RS High-throughput Sequencing Set with a 150-base paired-end setting.

treatment_protocol: When average tumor volumes reached approximately 150 mm3, mice were randomized and administered vehicle (PBS), paclitaxel (20 mg/kg, once a week, intraperitoneally), low-dose anti-VEGFA antibody (1 mg/kg, twice weekly, intraperitoneally), or a combination of both. Tumors were harvested on day 8 post-treatment.

value: Lung tumor

value: PTX+anti-VEGF


title: G401-i cells, SMARCB1-reexpression, day 7, rep2

description:
Library name: G401_SMARCB1_J7_2
Column name in raw counts and TPM matrixes : P118T550
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt


title: I2A cells, DNMT3A-knockout cells, clone 1C5

description:
Library name: I2Ap_DNMT3aKO_1C5
Column name in raw counts and TPM matrixes : I2Ap_DNMT3aKO_1C5
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: Pat2_rep2_blood_GEX

description:
Library name: Sample5
10X Genomics

value: peripheral blood

value: T lymphocyte

tag: replicate

tag: patient sex

value: female

tag: patient age

tag: sort date

tag: library type

value: gene expression (GEX)


title: FADU-hfm HPV-negative post-hypoxic replicate 2

description: Library name: GC166342

tag: cell line

value: FADU

tag: cell type

value: Head and neck squamous cell carcinoma cell line


title: patient176

last: Smith

address: 262 Danny Thomas Pl

description: Brain tumor patient

tag: Sex

tag: age

tag: mstage

value: Average

value: VII


title: patient189

description: Brain tumor patient

tag: risk group

tag: subgroup

tag: g34 subtype

value: I

value: Brain tumor


title: FADU-hfm HPV-negative non-hypoxic replicate 2

description: Library name: GC166341

tag: genotype


title: I2A cells, DNMT3A-knockout cells, clone 1C1

description:
Library name: I2Ap_DNMT3aKO_1C1
Column name in raw counts and TPM matrixes : I2Ap_DNMT3aKO_1C1
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: Rhabdoid tumor cells

value: SMARCB1-negative DNMT3A knockout


title: patient175

description: Brain tumor patient

value: High

tag: tissue


title: PTX-anti-VEGF-no1

description: Library name: Sample 7

tag: treatment


title: anti-VEGF-no2

description: Library name: Sample 6

value: anti-VEGF


title: patient174

description: Brain tumor patient

value: Female

value: V


title: I2A cells, DNMT3A-knockout cells, clone 1B12

description:
Library name: I2Ap_DNMT3aKO_1B12
Column name in raw counts and TPM matrixes : I2Ap_DNMT3aKO_1B12
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: SCC154-hfm HPV-positive non-hypoxic replicate 1

description: Library name: GC166339

value: hypoxia-fate mapped DsRED-positive


title: anti-VEGF-no1

description: Library name: Sample 5

value: Lung tumor


title: I2A cells, SMARCB1-reexpression, day 7, rep6

description:
Library name: I2Am7d_6
Column name in raw counts and TPM matrixes : I2Am7d_6
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: FADU-hfm HPV-negative post-hypoxic replicate 1

description: Library name: GC166338

value: hypoxia-fate mapped GFP-positive


title: FADU-hfm HPV-negative post-hypoxic replicate 5

description: Library name: GC166354


title: patient173

description: Brain tumor patient


title: PTX-no2

description: Library name: Sample 4

value: PTX


title: I2A cells, SMARCB1-reexpression, day 7, rep5

description:
Library name: I2Am7d_5
Column name in raw counts and TPM matrixes : I2Am7d_5
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: FADU-hfm HPV-negative non-hypoxic replicate 1

description: Library name: GC166337


title: G401-i cells, day 0, rep1

description:
Library name: G401_J0_1
Column name in raw counts and TPM matrixes : P118T543
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt


title: patient186

description: Brain tumor patient

value: VIII


title: white adipose tissue,rebound sleep,rep#3

description:
Library name: male-WATSD3
Column name in merged.gene_count_matrix.xlsx : male-WATSD3

value: white adipose tissue

value: rebound sleep and control sleep conditions


title: patient172

description: Brain tumor patient

value: Male

value: III


title: I2A cells, SMARCB1-reexpression, day 7, rep4

description:
Library name: I2Am7d_4
Column name in raw counts and TPM matrixes : I2Am7d_4
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: TatNull+Stim_RNA_rep2

city: Jupiter

first: CHUAN

last: LI

state: FL

address: 130 Scripps Way

institute: University of Florida

description:
Library name: 909_16
RNA-seq of Jurkat T cell population infected with TatNull HIVgko under stimulated condition

data_processing:
Raw sequencing reads of ChIP_seq were quality-checked and adapter-trimmed prior to alignment. Reads were aligned to a combined human (hg38) and HIV reference genome, filtered to remove low-quality and duplicate reads, and normalized coverage tracks were generated. Processed data files consist of normalized bigWig signal tracks used for visualization and quantitative analyses. Raw sequencing reads of RNA_seq were quality-checked and adapter-trimmed prior to quantification. Reads were pseudo-aligned to a combined human (hg38) and HIV reference transcriptome using Salmon, and transcript-level abundances were summarized to gene-level counts using tximport. Raw gene counts and DESeq2-normalized counts were generated for downstream analyses and deposited as processed data files.
Assembly: Sequencing reads were processed using a combined reference consisting of the human genome assembly GRCh38 (hg38) and the HIV-1 proviral sequence corresponding to the integrated HIVGKO construct.
Supplementary files format and content: Processed ChIP-sequencing data are provided as normalized genome-wide signal tracks in bigWig format. Files contain read coverage normalized to counts per million (CPM) across the human (hg38) and HIV reference genomes and are suitable for visualization and quantitative analysis. Processed ChIP-sequencing data are provided as normalized genome-wide signal tracks in bigWig format. Files contain read coverage normalized to counts per million (CPM) across the human (hg38) and HIV reference genomes and are suitable for visualization and quantitative analysis.

source_name: Cell line

growth_protocol: Jurkat CD4⁺ T cells were maintained in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) and penicillin-streptomycin-glutamine (100 U/mL penicillin, 100 µg/mL streptomycin, 2 mM L-glutamine) at 37 °C in a humidified incubator with 5% CO₂. Cells were routinely tested and confirmed negative for mycoplasma contamination.

extract_protocol:
Cells were crosslinked with formaldehyde, chromatin was fragmented by sonication, and immunoprecipitated DNA was purified following reversal of crosslinks prior to sequencing library preparation. Total RNA was isolated from harvested cells using a commercial silica column–based RNA purification kit according to the manufacturer’s instructions. RNA quality and concentration were assessed prior to RNA-sequencing library preparation.
Sequencing libraries were prepared using a commercial library preparation kit from New England Biolabs (NEB) according to the manufacturer’s instructions.

treatment_protocol: Jurkat HIVGKO-infected cells were maintained under basal (non-stimulated) conditions or stimulated to induce Tat accumulation and HIV transcription. For stimulated conditions, cells were treated with phorbol 12-myristate 13-acetate (PMA) and trichostatin A (TSA) for the indicated duration prior to harvesting. Non-stimulated controls were cultured in parallel under identical conditions without stimulation.

value: Cell line

value: Jurkat T

value: T cell

value: TatNull

value: Stimulation (PMA+TSA)


title: patient171

description: Brain tumor patient

value: High

value: Brain tumor


title: I2A cells, DNMT3B-knockout cells, clone G3

description:
Library name: I2Ap_DNMT3bKO_G3
Column name in raw counts and TPM matrixes : I2Ap_DNMT3bKO_G3
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: Rhabdoid tumor cells

value: SMARCB1-negative DNMT3B knockout


title: Control-no2

description: Library name: Sample 2

value: Lung tumor

value: Control


title: PTX-no1

description: Library name: Sample 3

value: PTX


title: TatNull_RNA_rep2

description:
Library name: 909_15
RNA-seq of Jurkat T cell population infected with TatNull HIVgko under basal condition

value: Non-stimulation


title: patient170

description: Brain tumor patient


title: Control-no1

description: Library name: Sample 1


title: I2A cells, DNMT3B-knockout cells, clone B5

description:
Library name: I2Ap_DNMT3bKO_B5
Column name in raw counts and TPM matrixes : I2Ap_DNMT3bKO_B5
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: TatWT+Stim_RNA_rep2

description:
Library name: 909_14
RNA-seq of Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: TatWT


title: patient169

description: Brain tumor patient

value: Female


title: Stereo-CITE-seq, mouse spleen, Protein

description:
Library name: B05050G1_mouse_spleen_Stereo-CITE_ADT
B05050G1_SC_20241202_172705_4.1.0.tar.gz
B05050G1.barcodeToPos.h5

source_name: spleen

extract_protocol:
Prior to the experiment, all solutions were freshly prepared and maintained on ice. Blocking Buffer (50 µl per sample) was composed of 3x SSC, 0.1% Triton-X-100, 10% serum, 1 µg/µl sheared salmon sperm DNA, 2.5 µl TruStain FcX PLUS (anti-mouse CD16/32) antibody (BioLegend, Cat. No. 156604), 5% RNase inhibitor (RI), and 5 µM 32-nt Poly A. The Wash Buffer consisted of 3x SSC with 5% RI. Cryosectioned OCT-embedded tissue, cut to 10 µm thick, was carefully transferred onto the Stereo-seq chip. These chips, now bearing tissue sections, were immediately warmed to 37℃ for 1 minute using a thermocycler adaptor. Tissues were then fixed by placing the chips in pre-chilled methanol at -20℃ for 30 minutes. Following fixation, blocking was performed by incubating the tissue with Blocking Buffer for 20 minutes, after which the sections were exposed to the TotalSeqTM-A antibody mix in Blocking Buffer for 45 minutes at room temperature. The tissue sections on chips were then washed three times with Wash Buffer, each for 30 seconds. After DAPI staining, the tissue sections were mounted with glycerol and imaged. Subsequent processing followed the Stereo-seq Transcriptomics T Kit protocol with minor adjustments. Briefly, the sections were permeabilized with Permeabilization Mix for an optimized duration, as recommended in the Stereo-seq Permeabilization Kit instructions. After reverse transcription, cDNA and antibody-derived tag (ADT) products were released from the chips using Release Enzyme Mix and collected. Separation of the cDNA fraction from the ADT library was achieved via a 0.8X bead selection, followed by preparation of the cDNA sequencing library in accordance with the Stereo-seq Transcriptomics T Kit. The ADT product in the supernatant was purified using a 2.0X (0.8X + 1.2X) bead selection, then amplified with Protein PCR Primer Mix.
Both ADT and cDNA libraries were sequenced using MGI DNBSEQ-G400 sequencing platforms.

value: spleen


title: TatWT_RNA_rep2

description:
Library name: 909_13
RNA-seq of Jurkat T cell population infected with TatWT HIVgko under basal condition


title: I2A cells, day 0, rep6

description:
Library name: I2Ap_6
Column name in raw counts and TPM matrixes : I2Ap_6
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: patient168

description: Brain tumor patient

value: Average


title: Stereo-CITE-seq, mouse spleen, GEX

description:
Library name: B05050G1_mouse_spleen_Stereo-CITE_mRNA
B05050G1_SC_20241202_172705_4.1.0.tar.gz
B05050G1.barcodeToPos.h5


title: I2A cells, day 0, rep5

description:
Library name: I2Ap_5
Column name in raw counts and TPM matrixes : I2Ap_5
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: patient167

description: Brain tumor patient

value: Male

tag: shh subtype


title: TatNull+Stim_RNA_rep1

description:
Library name: 909_12
RNA-seq of Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: Cell line

value: Jurkat T


title: I2A cells, day 0, rep4

description:
Library name: I2Ap_4
Column name in raw counts and TPM matrixes : I2Ap_4
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: TatNull_RNA_rep1

description:
Library name: 909_11
RNA-seq of Jurkat T cell population infected with TatNull HIVgko under basal condition

value: T cell

value: TatNull


title: patient166

description: Brain tumor patient

value: VII


title: TatWT+Stim_RNA_rep1

description:
Library name: 909_10
RNA-seq of Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: Stimulation (PMA+TSA)


title: Sample-98-10

city: Cologne

first: Philipp

last: Antczak

address: Robert-Koch-Strasse 21

department: Center for Molecular Medicine Cologne

institute: University Hospital Cologne

description: Library name: S98_10

data_processing:
STAR v.2.7.5b with sjdbOverhang 100
Assembly: Ensembl Daphnia magna v2.4
Supplementary files format and content: CountData_Complete.csv was generated by compiling the count information from the STAR run and combining it with gene information from Ensembl Daphnia Magna v 2.4

organism: Daphnia magna

source_name: whole organism

growth_protocol: We followed the methods outlined in ref. (Mathews et al., 2020) with a few differences. Every sampling day, we measured the length of each daphnid and noted the reproductive status (counts of eggs or embryos in the brood pouch and all free-swimming neonates) using a Leica dissecting scope (Leica M80), and we sacrificed individuals for transcriptomic analysis throughout the experiment.

extract_protocol:
We removed Daphnia for transcriptomic analyses from their treatments without being measured to minimize stress. We stored them individually in 500 μL of RNAlater and immediately flash froze them in liquid nitrogen. We then stored them at -80o F until RNA extraction. We extracted RNA from individual Daphnia using a RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions and the extracted RNA was stored in -80o F until sequencing by RNA-seq. The rRNA depletion procedure was used in RNA-Seq library preparation for total of 84 daphnia RNA samples.
Seven hundred ng of total RNA from each sample was subjected to library preparation using NEBNext Ultra II Directional RNA Library Prep with NEBNext rRNA Depletion Kit (New England Biolab, NEB, Ipswich, MA, USA) followed by the manufacturer’s protocol. Each library sample (total of 84) was individually barcoded with NEBNext Dual Index Primers (NEB, Ipswich, MA, USA). The QC of each library was validated by using Qubit fluorometer with Qubit dsDNA HS Assay Kit (Life Technologies, Grand Island, NY) and the Agilent Bioanalyzer 2100 system with Agilent DNA 1000 kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: We chose coal ash mixture exposure concentrations based on previous work (Mathews et al., 2020): 0.015, 0.06, 0.12, 0.25, 1.00, 4.00 nM Hg/L. We define the different concentrations in terms of their Hg concentration for simplicity; however, these concentrations represent a suite of coal ash constituents (Mathews et al., 2020). Similar to ref. (Mathews et al., 2020), we exposed the D. magna to coal ash through a dietary exposure route, since previous work found that coal ash is more toxic to zooplankton through a dietary exposure route compared to aqueous. We conducted dietary exposure by first exposing C. reinhardtii to the exposure concentrations of coal ash for two hours prior to feeding and then feeding the D. magna 25,000 cells/mL/day (0.026 mg C/individual/day).

value: whole organism

tag: day

tag: concentration

value: coal ash


title: patient165

description: Brain tumor patient

value: High

value: VI

value: Brain tumor


title: Sample-95-24

description: Library name: S95_24


title: I2A cells, DNMT3B-knockout cells, clone D11

description:
Library name: I2Ap_DNMT3bKO_D11
Column name in raw counts and TPM matrixes : I2Ap_DNMT3bKO_D11
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: Rhabdoid tumor cells

value: SMARCB1-negative DNMT3B knockout


title: I2A cells, DNMT3B-knockout cells, clone E9

description:
Library name: I2Ap_DNMT3bKO_E9
Column name in raw counts and TPM matrixes : I2Ap_DNMT3bKO_E9
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: TatWT_RNA_rep1

description:
Library name: 909_9
RNA-seq of Jurkat T cell population infected with TatWT HIVgko under basal condition

value: TatWT

value: Non-stimulation


title: patient164

description: Brain tumor patient

value: Average

value: II


title: I2A cells, DNMT3B-knockout cells, clone F2

description:
Library name: I2Ap_DNMT3bKO_F2
Column name in raw counts and TPM matrixes : I2Ap_DNMT3bKO_F2
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: patient163

description: Brain tumor patient

value: Female


title: Sample-93-17

description: Library name: S93_17


title: I2A cells, DMSO treatment, 21 days, rep3

description:
Library name: I2Ap_DMSO_3
Column name in raw counts and TPM matrixes : I2Ap_DMSO_3
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: DMSO


title: I2A cells, SMARCB1-reexpression, day 7, rep3b

description:
Library name: I2Am7d_3
Column name in raw counts and TPM matrixes : I2Am7d_3
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: TatNull+Stim_RNAPII-ChIP_rep2

description:
Library name: 893_40
ChIP-seq analysis of RNAPII in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

library_source: genomic

molecule: genomic DNA

value: Cell line

value: Jurkat T

value: T cell


title: patient162

description: Brain tumor patient

value: Male

value: VII


title: Sample-90-6

description: Library name: S90_6

value: whole organism

value: coal ash


title: TatNull+Stim_RNAPII-ChIP_rep1

description:
Library name: 893_39
ChIP-seq analysis of RNAPII in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: TatNull

value: Stimulation (PMA+TSA)


title: I2A cells, SMARCB1-reexpression, day 7, rep1b

description:
Library name: I2Am7d_1
Column name in raw counts and TPM matrixes : I2Am7d_1
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt

value: Rhabdoid tumor cells


title: TatNull_RNAPII-ChIP_rep2

description:
Library name: 893_38
ChIP-seq analysis of RNAPII in Jurkat T cell population infected with TatNull HIVgko under basal condition


title: Sample-91-10

description: Library name: S91_10


title: patient161

description: Brain tumor patient

value: Brain tumor


title: I2A cells, day 0, rep3b

description:
Library name: I2Ap_3
Column name in raw counts and TPM matrixes : I2Ap_3
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: patient160

description: Brain tumor patient

value: III


title: TatNull_RNAPII-ChIP_rep1

description:
Library name: 893_37
ChIP-seq analysis of RNAPII in Jurkat T cell population infected with TatNull HIVgko under basal condition

value: Non-stimulation


title: Sample-9-10

description: Library name: S9_10


title: I2A cells, day 0, rep3

description:
Library name: I2A_DOX+J0_3
Column name in raw counts and TPM matrixes : I2A_DOX+J0_3
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt


title: Sample-86-17

description: Library name: S86_17


title: patient159

description: Brain tumor patient

value: Average


title: TatWT+Stim_RNAPII-ChIP_rep1

description:
Library name: 893_35
ChIP-seq analysis of RNAPII in Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: TatWT


title: I2A cells, day 0, rep1b

description:
Library name: I2Ap_1
Column name in raw counts and TPM matrixes : I2Ap_1
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt


title: patient158

description: Brain tumor patient

value: Female


title: Sample-88-24

description: Library name: S88_24


title: I2A cells, day 0, rep2

description:
Library name: I2A_DOX+J0_2
Column name in raw counts and TPM matrixes : I2A_DOX+J0_2
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt


title: Sample-83-6

description: Library name: S83_6


title: TatWT+Stim_RNAPII-ChIP_rep2

description:
Library name: 893_36
ChIP-seq analysis of RNAPII in Jurkat T cell population infected with TatWT HIVgko under stimulated condition


title: TatWT_RNAPII-ChIP_rep2

description:
Library name: 893_34
ChIP-seq analysis of RNAPII in Jurkat T cell population infected with TatWT HIVgko under basal condition


title: patient157

description: Brain tumor patient


title: Sample-83-24

description: Library name: S83_24


title: I2A cells, day 0, rep1

description:
Library name: I2A_DOX+J0_1
Column name in raw counts and TPM matrixes : I2A_DOX+J0_1
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt


title: TatWT_RNAPII-ChIP_rep1

description:
Library name: 893_33
ChIP-seq analysis of RNAPII in Jurkat T cell population infected with TatWT HIVgko under basal condition


title: I2A cells, SMARCB1-reexpression, day 14, rep3

description:
Library name: I2A_DOX+J14_3
Column name in raw counts and TPM matrixes : I2A_DOX+J14_3
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt


title: patient155

description: Brain tumor patient

value: High

value: VIII


title: patient156

description: Brain tumor patient


title: Sample-8-6

description: Library name: S8_6


title: TatNull+Stim_CDK9-ChIP_rep2

description:
Library name: 893_32
ChIP-seq analysis of CDK9 in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: Cell line

value: Jurkat T


title: Sample-81-24

description: Library name: S81_24


title: Sample-97-6

description: Library name: S97_6


title: I2A cells, SMARCB1-reexpression, day 14, rep2

description:
Library name: I2A_DOX+J14_2
Column name in raw counts and TPM matrixes: I2A_DOX+J14_2
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt


title: patient154

description: Brain tumor patient

value: Male

value: IV


title: Sample-79-17

description: Library name: S79_17

value: whole organism


title: TatNull+Stim_CDK9-ChIP_rep1

description:
Library name: 893_31
ChIP-seq analysis of CDK9 in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: T cell


title: I2A cells, SMARCB1-reexpression, day 14, rep1

description:
Library name: I2A_DOX+J14_1
Column name in raw counts and TPM matrixes : I2A_DOX+J14_1
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt


title: TatNull_CDK9-ChIP_rep2

description:
Library name: 893_30
ChIP-seq analysis of CDK9 in Jurkat T cell population infected with TatNull HIVgko under basal condition

value: TatNull


title: patient153

description: Brain tumor patient

value: V


title: Sample-77-10

description: Library name: S77_10

value: coal ash


title: I2A cells, SMARCB1-reexpression, day 7, rep3

description:
Library name: I2A_DOX+J7_3
Column name in raw counts and TPM matrixes : I2A_DOX+J7_3
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt

value: Rhabdoid tumor cells


title: patient152

description: Brain tumor patient

value: VII

value: Brain tumor


title: TatNull_CDK9-ChIP_rep1

description:
Library name: 893_29
ChIP-seq analysis of CDK9 in Jurkat T cell population infected with TatNull HIVgko under basal condition

value: Non-stimulation


title: patient151

description: Brain tumor patient

value: VI


title: Sample-73-10

description: Library name: S73_10


title: TatWT+Stim_CDK9-ChIP_rep2

description:
Library name: 893_28
ChIP-seq analysis of CDK9 in Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: TatWT

value: Stimulation (PMA+TSA)


title: I2A cells, SMARCB1-reexpression, day 7, rep2

description:
Library name: I2A_DOX+J7_2
Column name in raw counts and TPM matrixes: I2A_DOX+J7_2
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt


title: I2A cells, SMARCB1-reexpression, day 7, rep1

description:
Library name: I2A_DOX+J7_1
Column name in raw counts and TPM matrixes: I2A_DOX+J7_1
raw_counts_I2A_RNAseq.txt
TPM_I2A_RNAseq.txt
raw_counts_I2A_kinetic_RNAseq.txt
TPM_I2A_kinetic_RNAseq.txt


title: TatWT+Stim_CDK9-ChIP_rep1

description:
Library name: 893_27
ChIP-seq analysis of CDK9 in Jurkat T cell population infected with TatWT HIVgko under stimulated condition


title: Sample-71-17

description: Library name: S71_17


title: Sample-70-24

description: Library name: S70_24


title: patient150

description: Brain tumor patient

value: Female

value: High


title: HC_4

city: Jinan

first: Chong

middle: lei

last: Fu

state: Shandong

address: No. 6699, Qingdao Road

institute: Shandong First Medical University

description: Library name: FRAS210119096-1r

data_processing:
Raw reads in FASTQ format were processed using in-house Perl scripts to remove reads containing adapters, reads containing poly-N, and low-quality reads. Q20, Q30, and GC content were calculated for the clean reads. Clean paired-end reads were aligned to the reference genome using HISAT2 v2.0.5. Mapped reads from each sample were assembled using StringTie v1.3.3b in a reference-based approach. Gene-level read counts were generated using featureCounts v1.5.0-p3, and FPKM values were calculated based on gene length and the number of reads mapped to each gene. Differential expression analysis between groups was performed using the DESeq2 R package, and genes with |log2FoldChange| ≥ 1 and padj ≤ 0.05 were considered differentially expressed. Gene Ontology and KEGG pathway enrichment analyses were performed using the clusterProfiler R package.
Assembly: Homo sapiens reference genome GRCh38/hg38
Supplementary files format and content: Gene expression count matrix: Contains raw read counts for all protein-coding genes across all samples. Rows = genes (Ensembl ID + Gene Symbol), columns = samples.Differential expression tables: Separate files for each pairwise comparison (BDI vs HC, BDII vs HC, BDI vs BDII). Columns include log2FoldChange, p-value, and FDR-adjusted p-value (padj) calculated by DESeq2 (v1.20.0). Genes with |log2FoldChange| ≥ 1 and padj ≤ 0.05 were defined as differentially expressed genes (DEGs).

source_name: Organoids

extract_protocol: Total RNA was isolated from iPSC-derived forebrain organoids using TRIzol reagent. RNA integrity was assessed using the RNA Nano 6000 Assay Kit on an Agilent Bioanalyzer 2100 system.

value: Organoids

value: neuron

tag: sample group

value: HC


title: TatWT_CDK9-ChIP_rep2

description:
Library name: 893_26
ChIP-seq analysis of CDK9 in Jurkat T cell population infected with TatWT HIVgko under basal condition

value: Cell line

value: Jurkat T


title: patient149

description: Brain tumor patient

value: Male


title: Sample-66-10

description: Library name: S66_10

value: whole organism


title: HC_15

description: Library name: FRAS210119098-1r


title: TatNull+Stim_RNAPII-Ser5p-ChIP_rep2

description:
Library name: 893_24
ChIP-seq analysis of RNAPII-Ser5p in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: T cell

value: TatNull


title: patient148

description: Brain tumor patient

value: Average

value: V


title: TatWT_CDK9-ChIP_rep1

description:
Library name: 893_25
ChIP-seq analysis of CDK9 in Jurkat T cell population infected with TatWT HIVgko under basal condition

value: Non-stimulation


title: Sample-65-6

description: Library name: S65_6

value: coal ash


title: Sample-61-17

description: Library name: S61_17


title: patient146

description: Brain tumor patient

value: Brain tumor


title: TatNull+Stim_RNAPII-Ser5p-ChIP_rep1

description:
Library name: 893_23
ChIP-seq analysis of RNAPII-Ser5p in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: Stimulation (PMA+TSA)


title: BDI_6

description: Library name: FRAS210119100-1r

value: BDI


title: Sample-58-6

description: Library name: S58_6


title: HC_13

description: Library name: FRAS210119097-1r


title: BDI_5

description: Library name: FRAS210119099-1r


title: TatNull_RNAPII-Ser5p-ChIP_rep2

description:
Library name: 893_22
ChIP-seq analysis of RNAPII-Ser5p in Jurkat T cell population infected with TatNull HIVgko under basal condition


title: patient145

description: Brain tumor patient


title: Sample-56-24

description: Library name: S56_24


title: BDI_17

description: Library name: FRAS210119101-1r


title: patient144

description: Brain tumor patient

value: Female


title: TatNull_RNAPII-Ser5p-ChIP_rep1

description:
Library name: 893_21
ChIP-seq analysis of RNAPII-Ser5p in Jurkat T cell population infected with TatNull HIVgko under basal condition


title: Sample-54-17

description: Library name: S54_17


title: BDII_18

description: Library name: FRAS210119103-1r

value: Organoids

value: BDII


title: TatWT+Stim_RNAPII-Ser5p-ChIP_rep2

description:
Library name: 893_20
ChIP-seq analysis of RNAPII-Ser5p in Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: TatWT


title: patient143

description: Brain tumor patient

value: I


title: Sample-52-10

description: Library name: S52_10


title: TatWT+Stim_RNAPII-Ser5p-ChIP_rep1

description:
Library name: 893_19
ChIP-seq analysis of RNAPII-Ser5p in Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: Cell line

value: Jurkat T


title: patient142

description: Brain tumor patient

value: High


title: Sample-51-6

description: Library name: S51_6

value: whole organism


title: BDII_12

description: Library name: FRAS210119105-1r

value: neuron


title: BDII_11

description: Library name: FRAS210119104-1r


title: TatWT_RNAPII-Ser5p-ChIP_rep2

description:
Library name: 893_18
ChIP-seq analysis of RNAPII-Ser5p in Jurkat T cell population infected with TatWT HIVgko under basal condition

value: T cell


title: Sample-50-24

description: Library name: S50_24


title: patient141

description: Brain tumor patient

value: Male

value: Average

value: VII


title: BDII_10

description: Library name: FRAS210119102-1r


title: TatWT_RNAPII-Ser5p-ChIP_rep1

description:
Library name: 893_17
ChIP-seq analysis of RNAPII-Ser5p in Jurkat T cell population infected with TatWT HIVgko under basal condition

value: Non-stimulation


title: patient140

description: Brain tumor patient

value: V

value: Brain tumor


title: Sample-49-17

description: Library name: S49_17

value: coal ash


title: A549-WT replicate 3

city: Liège

first: Morgane

last: Paque

address: Quartier Hôpital, avenue de l'Hôpital 1

department: University of Liège

institute: GIGA Institute

description: Library name: 3-A549-WT

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 97.
Assembly: Assembly: GRCh38
Supplementary files format and content: tab-delimited tsv file include raw counts for annotations for all Sample

source_name: Lung

growth_protocol: A549 cells were maintained in RPMI (Biowest) supplemented with 10% fetal bovie serum (FBS, Gibco), 1% L-glutamine (Gibco) and 1% antibiotics (Gibco) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested from WT or HIF1b overexpressing A549 cells using the TriPure isolation method (ref. 11667165001, Roche).
RNA was subjected to library preparation using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit (Cat# 20040525, Illumina) according to the manufacturer's protocols.

treatment_protocol: Transfection

value: Lung

value: Lung cancer cell

value: Wild type

tag: batch

value: Replicate 3


title: TatNull+Stim_RNAPII-Ser2p-ChIP_rep2

description:
Library name: 903_20
ChIP-seq analysis of RNAPII-Ser2p in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: Cell line

value: TatNull

value: Stimulation (PMA+TSA)


title: patient139

description: Brain tumor patient


title: Sample-48-10

description: Library name: S48_10

value: whole organism


title: A549-OE-HIF1b replicate 3

description: Library name: 3-A549-OE-HIF1b

value: HIF1B overexpression


title: TatNull+Stim_RNAPII-Ser2p-ChIP_rep1

description:
Library name: 893_16
ChIP-seq analysis of RNAPII-Ser2p in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: Jurkat T

value: T cell


title: patient138

description: Brain tumor patient

value: Female

value: High

value: I


title: A549-WT replicate 2

description: Library name: 2-A549-WT

value: Replicate 2


title: TatNull_RNAPII-Ser2p-ChIP_rep2

description:
Library name: 903_19
ChIP-seq analysis of RNAPII-Ser2p in Jurkat T cell population infected with TatNull HIVgko under basal condition

value: Non-stimulation


title: patient137

description: Brain tumor patient

value: Male

value: Average

value: VII

value: Brain tumor


title: Sample-47-6

description: Library name: S47_6

value: coal ash


title: Sample-43-17

description: Library name: S43_17


title: A549-OE-HIF1b replicate 2

description: Library name: 2-A549-OE-HIF1b

value: Lung

value: Lung cancer cell


title: patient136

description: Brain tumor patient

value: VIII


title: TatNull_RNAPII-Ser2p-ChIP_rep1

description:
Library name: 893_13
ChIP-seq analysis of RNAPII-Ser2p in Jurkat T cell population infected with TatNull HIVgko under basal condition

value: Cell line

value: TatNull


title: A549-WT replicate 1

description: Library name: 1-A549-WT

value: Wild type

value: Replicate 1


title: Sample-41-10

description: Library name: S41_10

value: whole organism


title: TatWT+Stim_RNAPII-Ser2p-ChIP_rep2

description:
Library name: 893_12
ChIP-seq analysis of RNAPII-Ser2p in Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: Jurkat T

value: T cell

value: TatWT

value: Stimulation (PMA+TSA)


title: patient135

description: Brain tumor patient

value: Female

value: High

value: III


title: Sample-40-6

description: Library name: S40_6


title: A549-OE-HIF1b replicate 1

description: Library name: 1-A549-OE-HIF1b

value: HIF1B overexpression


title: patient134

description: Brain tumor patient

value: Male

value: Average

value: Brain tumor


title: TatWT+Stim_RNAPII-Ser2p-ChIP_rep1

description:
Library name: 903_18
ChIP-seq analysis of RNAPII-Ser2p in Jurkat T cell population infected with TatWT HIVgko under stimulated condition


title: Sample-4-17

description: Library name: S4_17

value: coal ash