title: PON1-OE3

city: xi'an

first: Haolin

last: Wei

address: No. 169, Changle West Road

department: Department of Cell Biology

institute: Air Force Medical University

description:
Library name: LM-OE3
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

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
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release115
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: Hepatocyte

value: Stable PON1 overexpression


title: Proximal_colon_TCR_7

status: Public on Jul 01 2026

type: SRA

city: Cambridge

first: Colin

middle: YC

last: Lee

address: Wellcome Genome Campus, Hinxton

country: United Kingdom

institute: Molecular Immunity Unit

description:
Takara Bio SMARTER TCRa/b profiling
I7-c-proximalM7aR6-bR6F10

library_source: transcriptomic

data_processing:
Raw MiSeq reads were filtered for base quality using QUASR.
Data was processed (alignment and clonotype assembly) using MIXCR (v3.0.13), following the 'analyze amplicon' workflow with default settings. Further downstream analysis was performed in vdjtools v1.2.1.
Supplementary files format and content: MIXCR alignment output (.vdjca), tab delimited file
Supplementary files format and content: MIXCR contig/clonotype assembly output (.clns), tab delimited file

molecule: total RNA

organism: Mus musculus

source_name: Proximal colon

extract_protocol:
Tissues were digested and RNA was extracted using the RNA pure link mini kit (Thermo Fisher) as per the manufacturer's instructions.
Libraries were prepared using the Takara Bio mouse TCRa/b profiling kit as per the manufacturer's instructions.

tag: tissue

value: Proximal colon

tag: genotype

tag: treatment

value: DSS


title: immune profiling,sfbneg, class-switched pp b cells, GEX, rep1

city: Bethesda

first: Byunghyun

last: Kang

state: Maryland

address: 9000 Rockville Pike

country: USA

institute: NIAID

description:
Library name: pp_n_1_mRNA
GEX(5' mRNA) library

library_source: transcriptomic single cell

data_processing:
Single-cell immune profiling raw data of sorted IgA⁺, IgG1⁺, and IgG2b⁺ CSB cells, generated using the 5′ Chromium 10X kit, were initially processed using the Cell Ranger Multi pipeline (v7.0.0) with the Cell Ranger V(D)J reference (vdj-GRCm38-alts-ensembl-7.0.0). This initial processing step produced three datasets: gene expression (GEX), antibody-derived tags (ADT), and B-cell receptor (BCR) sequences. A Seurat object was constructed from the 5′ GEX and ADT data using the Seurat package.
The BCR sequencing results generated using cellranger multi were further processed with Dandelion. BCR contigs from 'all_contigs.fasta' and 'all_contig_annotations.csv' were re-annotated using an Immcantation-inspired preprocessing pipeline included in the Dandelion Singularity container (v0.3.0).
Assembly: mm10
Supplementary files format and content: cellranger multi output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: dandelion_singularity out files: AIRR formatted

molecule: polyA RNA

source_name: peyer's patches

extract_protocol:
For PP B cell immune profiling, IgA⁺, IgG1⁺, or IgG2b⁺ class-switched B (CSB) cells (CD45⁺CD19⁺TCRβ⁻Isotype⁺) from SFB-negative and SFB-positive Taconic WT mice (five mice pooled per group) were individually FACS-sorted.
The three isotype-positive CSB populations were then mixed to reflect their natural ratio in PPs from SFB-negative and SFB-positive mice. The sorted and pooled cells were subsequently stained with the following TotalSeqTM C antibodies (BioLegend): IgD (Cat# 405747), IgM (Cat# 406541), CD62L (Cat# 104455), and CD38 (Cat# 102735), and processed using the Chromium Next GEM Single Cell 5′ Library & Gel Bead Kit v2 (10x Genomics) along with the 5′ Feature Barcode Library Kit and Mouse B Cell V(D)J Enrichment Kit, according to the manufacturer’s instructions.

value: peyer's patches

tag: cell type

value: B cells

value: wild type

value: sfb(-)

tag: library type

value: mRNA


title: PON1-OE2

country: China

description:
Library name: LM-OE2
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

organism: Homo sapiens

tag: cell line

value: WT


title: Proximal_colon_TCR_6

description:
Takara Bio SMARTER TCRa/b profiling
I6-c-proximalM6aR6-bR6F9


title: mouse ileal PP,SFB(+),rep5

description: Library name: PP_total10

data_processing:
Extraction of a normalized count matrix from the demultiplexed FASTQ files was performed using Partek Flow (Partek): adaptor sequences (18 bp from the 5′ end) were trimmed, resulting in 151 bp reads with an average quality score above Q35. Reads were aligned to the reference genome (STAR-2.7.3a with mm10) and quantified against the annotation model (mm10_ensembl_release95_v2). The minimally normalized count matrix (with 1.0E−4 added) was used as input for DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts per sample

extract_protocol:
Total RNA was extracted from the harvested PPs using the RNeasy Mini Kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions.
cDNA synthesis and sequencing library preparation were performed using the SMARTer Stranded Total RNA Sample Prep Kit – HI Mammalian (Takara Bio) following the provided protocol. Library fragment size distribution and concentration were evaluated using the Agilent Bioanalyzer 2100 with the High Sensitivity DNA chip.

tag: strain

value: sfb-containing stools


title: Proximal_colon_TCR_5

description:
Takara Bio SMARTER TCRa/b profiling
I5-c-proximalM5aR6-bR6F8


title: PON1-OE1

description:
Library name: LM-OE1
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: Proximal_colon_TCR_4

description:
Takara Bio SMARTER TCRa/b profiling
I4-c-proximalM4aR6-bR6F7


title: Proximal_colon_TCR_3

description:
Takara Bio SMARTER TCRa/b profiling
I3-c-proximalM3aR6-bR6F6


title: PON1-NC3

description:
Library name: LM-NC3
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: NC control


title: Proximal_colon_TCR_2

description:
Takara Bio SMARTER TCRa/b profiling
I2-c-proximalM2aR6-bR6F5


title: mouse ileal PP,SFB(+),rep4

description: Library name: PP_total9


title: PON1-NC2

description:
Library name: LM-NC2
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: Proximal_colon_TCR_1

description:
Takara Bio SMARTER TCRa/b profiling
I1-c-proximalM1aR6-bR6F4


title: Ileum_TCR_9

description:
Takara Bio SMARTER TCRa/b profiling
H8-ileumM9aR6-bR6F3

source_name: Ileum

value: Ileum


title: Ileum_TCR_8

description:
Takara Bio SMARTER TCRa/b profiling
H7-ileumM8aR6-bR6F2


title: mouse ileal PP,SFB(+),rep2

description: Library name: PP_total7


title: mouse ileal PP,SFB(+),rep3

description: Library name: PP_total8


title: PON1-NC1

description:
Library name: LM-NC1
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: mouse ileal PP,SFB(+),rep1

description: Library name: PP_total6


title: Ileum_TCR_7

description:
Takara Bio SMARTER TCRa/b profiling
H6-ileumM7aR6-bR6F1


title: sh3-3

city: Shanghai

first: ye

last: qing

address: Dongchuan road

institute: cancer institute

description:
Library name: Sample6
sh3-3_fpkm

data_processing:
Raw reads were processed with fastp (v0.23.2) for adapter trimming and quality filtering (Q20).
Clean reads were aligned to the reference genome (GRCh38/mm10) using HISAT2 (v2.2.1).
Transcript abundances were quantified via StringTie (v2.2.3).
Assembly: GRCh38
Supplementary files format and content: Processed data files include an Excel file containing gene-level raw read counts, FPKM, and TPM expression values for each sample, along with gene annotations (gene ID, gene name, gene type, and genomic coordinates).

source_name: SW 1990 cells

growth_protocol: SW 1990 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol, total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit.

treatment_protocol: shRNA constructs were cloned into the pLKO.1 vector and packaged into lentiviral particles in 293T cells. Target cells were transduced with lentivirus in the presence of polybrene and selected with puromycin to establish stable knockdown cell lines.

value: SW 1990 cells

value: pancreatic cancer cell

value: LRRC8A knockdown

value: shRNA-mediated knockdown of LRRC8A

tag: batch


title: BCIF30

city: Bundoora

first: Quynh Nhu

last: Dinh

state: VIC

address: Kingsbury Drive & Plenty Rd

country: Australia

institute: La Trobe University

data_processing:
High-throughput sequencing was conducted using the HiSeqTM2500 platform
The results were mapped to the Ensembl-released mouse genome sequence and annotation.
Differential expression analysis was conducted using the DESeq R Package V.1.10.1 and P-values were adjusted using the Banjamini and Hochberg’s approach for controlling the false discovery rate
Genes were considered differentially expressed if the adjusted P-value was less than 0.05.
Supplementary files format and content: tab-delimited text files fpkm gene counts

source_name: Cerebral artery

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene

treatment_protocol: Mice underwent ad libitum eating or intermittant fasting for 3 months. After 3 months, chronic cerebral hypoperfusion was induced by the bilateral carotid arterys stenosis (BCAS) surgery. Control mice underwent sham surgery. Mice were culled at days 1, 14, 21 and 30 days post-surgery and cerebral arteries were collected.

value: Cerebral artery

tag: Sex

value: Male

tag: disease state

value: Chronic cerebral hypoperfusion


title: Ileum_TCR_5

description:
Takara Bio SMARTER TCRa/b profiling
H4-ileumM5aR5-bR5F11

value: DSS


title: Ileum_TCR_6

description:
Takara Bio SMARTER TCRa/b profiling
H5-ileumM6aR5-bR5F12


title: mouse ileal PP,SFB(-),rep4

description: Library name: PP_total5

value: peyer's patches


title: Ileum_TCR_4

description:
Takara Bio SMARTER TCRa/b profiling
H3-ileumM4aR5-bR5F10


title: sh3-2

description:
Library name: Sample5
sh3-2_fpkm


title: CHOP_KO_Con_ATF4_rep1

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

description: Library name: CHOP_KO_Con_ATF4_rep1

library_source: genomic

data_processing:
Paired-end ChIP-seq reads were trimmed using TrimGalore.
Trimmed reads were aligned to the human hg19 reference genome using BWA (v0.7.17) with default parameters.
Low-quality alingments were filtered using SAMtools with the parameters q 30 –F 1804 –f 2, and duplicate reads were marked using Picard (v2.18.23) with MarkDuplicates function. Uniquely mapped reads were normalized to counts per million (CPM) DNA and duplicate reads were then removed using SAMtools.
Uniquely mapped reads were normalize to generate bigwig file.
Peaks were called for each biological replicate using MACS2 (v2.2.7.1) with the parameters callpeak -f BAMPE --nomodel -g hg19 -q 0.001 --narrow.
Assembly: hg19
Supplementary files format and content: narrowPeak, CPM normalized bigwig

molecule: genomic DNA

growth_protocol: The human colorectal cancer cell line HCT116 was cultured in RPMI-1640 medium (Welgene) supplemented with 10% fetal bovine serum (FBS; HyClone) and 1% penicillin–streptomycin (Welgene) at 37 ℃ in a humidified incubator containing 5% CO2. Cells were subcultured every 48–72 h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched using 0.125 M glycine for 5 min, followed by washing with cold PBS. After cell lysis, chromatin was sheared by sonication using a Qsonica sonicator(30 s ON/30 s OFF, 10 cycles, repeated three times). Lysates were pre-cleared by incubation with protein A/G magnetic beads (Invitrogen) prior to immunoprecipitation. Pre-cleared chromatin was incubated overnight at 4 ℃ with the indicated antibodies.
Tagmentation was then performed directly on bead-bound chromatin using the Nextera DNA Library Prep kit (Illumina) followed by two washes to remove excess transposase. Bead-bound chromatin was incubated overnight  for reverse cross-linking, and the recovered DNA was PCR-amplified using Nextera PCR primers. Amplified libraries were size-selected and purified using AMPure XP beads (0.65x–0.9x)

treatment_protocol: Cells were treated with tunicamycin (Sigma-Aldrich) at a final concentration of 0.5 µg ml-1 for 6 h. Cells treated with 0.1% DMSO for the same duration served as vehicle controls.

tag: chip antibody

value: ATF4 (Cell signaling technology, #11815)

value: Human colorectal cancer

value: 0.1% DMSO

tag: time


title: Ileum_TCR_3

description:
Takara Bio SMARTER TCRa/b profiling
H2-ileumM3aR5-bR5F9


title: mouse ileal PP,SFB(-),rep3

description: Library name: PP_total4


title: Ileum_TCR_1

description:
Takara Bio SMARTER TCRa/b profiling
G8-ileumM1aR5-bR5F7


title: sh3-1

description:
Library name: Sample4
sh3-1_fpkm


title: Ileum_TCR_2

description:
Takara Bio SMARTER TCRa/b profiling
H1-ileumM2aR5-bR5F8


title: Duodenum_TCR_9

description:
Takara Bio SMARTER TCRa/b profiling
G7-duodenumM9aR5-bR5F6

source_name: Duodenum

value: Duodenum


title: mouse ileal PP,SFB(-),rep2

description: Library name: PP_total3

value: WT


title: mouse ileal PP,SFB(-),rep1

description: Library name: PP_total2


title: Duodenum_TCR_8

description:
Takara Bio SMARTER TCRa/b profiling
G6-duodenumM8aR5-bR5F5


title: shNC-3

description:
Library name: Sample3
shNC-3_fpkm

value: control

value: non-targeting shRNA


title: Duodenum_TCR_7

description:
Takara Bio SMARTER TCRa/b profiling
G5-duodenumM7aR5-bR5F4


title: Duodenum_TCR_6

description:
Takara Bio SMARTER TCRa/b profiling
G4-duodenumM6aR5-bR5F3


title: shNC-2

description:
Library name: Sample2
shNC-2_fpkm


title: HC_3

city: Jinan

first: Chong

middle: lei

last: Fu

state: Shandong

address: No. 6699, Qingdao Road

institute: Shandong First Medical University

description: Library name: HC_3

library_source: other

data_processing:
Nextera adaptor sequences were trimmed from raw reads using skewer v0.2.2. The trimmed reads were aligned to the reference genome using BWA with standard parameters. Aligned reads were filtered to retain high-quality reads with MAPQ ≥ 13, non-mitochondrial reads, properly paired reads, and reads longer than 18 nt. Peak calling was performed using MACS2 with the command “macs2 callpeak --nomodel --keepdup all --call-summits”. Regions with corrected q value ≤ 0.05 were considered peak regions. Differentially accessible regions between groups were identified using DiffBind v3.2.0 in R v4.3.2. Genomic annotation of differentially accessible regions was performed using ChIPseeker v1.38.0, and downstream Gene Ontology enrichment analysis was performed for genes associated with DAR peaks.
Assembly: Homo sapiens reference genome hg38
Supplementary files format and content: Processed data include peak files in BED/narrowPeak format and/or tab-delimited text files. Peak files contain genomic coordinates of ATAC-seq accessible chromatin regions for each sample, including chromosome, start position, end position, peak name or ID, signal score, strand, enrichment, statistical significance, and summit information when available. Group-level processed files may include a merged peak count matrix containing read counts for each peak across all samples, as well as a table of differentially accessible regions with genomic coordinates, associated genes, fold change, P value, adjusted P value/FDR, and genomic annotation such as promoter, exon, intron, or intergenic region.

molecule: other

source_name: organoids

extract_protocol:
Forebrain organoids were washed three times with PBS. Nuclei were extracted from the samples and resuspended in Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
ATAC-seq libraries were prepared using a Tn5 transposase-based protocol. After transposition, equimolar Adapter 1 and Adapter 2 were added, and PCR amplification was performed to generate sequencing libraries. The amplified libraries were purified using AMPure beads, and library quality was assessed using Qubit. Index-coded libraries were clustered on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS according to the manufacturer’s instructions. After cluster generation, libraries were sequenced on an Illumina HiSeq platform to generate 150 bp paired-end reads.

value: organoids

value: neuron


title: shNC-1

description:
Library name: Sample1
shNC-1_fpkm

value: SW 1990 cells

value: pancreatic cancer cell


title: Duodenum_TCR_4

description:
Takara Bio SMARTER TCRa/b profiling
G2-duodenumM4aR5-bR5F1


title: HC_2

description: Library name: HC_2


title: Duodenum_TCR_5

description:
Takara Bio SMARTER TCRa/b profiling
G3-duodenumM5aR5-bR5F2


title: Duodenum_TCR_3

description:
Takara Bio SMARTER TCRa/b profiling
G1-duodenumM3aR4-bR4F12


title: Duodenum_TCR_2

description:
Takara Bio SMARTER TCRa/b profiling
F8-duodenumM2aR4-bR4F11


title: HC_1

description: Library name: HC_1


title: Rosette, nmotif, SOX2 4C-Seq, Rep 2

city: New York

first: Devin

last: Bready

state: NY

address: Placantonakis Lab, 33rd and East River Drive, Smilow 1306H

department: Neurosurgery

institute: NYU School of Medicine

description: Library name: Rosette nmotif 4C Rep 2

data_processing:
Base calls were performed using bcl2fastq for Novaseq.
4C-sequencing was mapped against a fragment library of the DpnIICsp6I digested genome using 4Cker to generate bigwig files for visualization
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: 4C-Seq

source_name: H9 Derived Rosette NSCs

growth_protocol: H9 (WA09) human embryonic stem cells (hESCs) stably nucleofected with a Hes5::GFP reporter were  cultured as colonies on a layer of mouse embryonic fibroblasts (MEFs, Invitrogen) in hESC medium, consisting of 1:1 DMEM/F12 (Invitrogen), 20% KSR (Invitrogen), 5 ng/mL FGF2 (R&D), 2 mM glutamine (Invitrogen), 0.1 mM non-essential amino acids (Invitrogen), and 0.1 mM β-mercaptoethanol (Invitrogen).

extract_protocol:
Cells were dissociated and counted, and 1x107 cells were crosslinked with 2% methanol-free formaldehyde (Tousimis) in PBS for 10 minutes at RT. The reaction was quenched with glycine to a final concentration of 0.125 M. After centrifugation, the cell pellet was resuspended in 1 mL of lysis buffer (50 mM Tris, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100 and 1X Roche complete protease inhibitor). Cells were incubated on ice for 15 minutes and then centrifuged at 2500 RPM at 4 °C for 5 minutes. Pellets were resuspended in 360 µL of molecular grade H2O, 60 µL of DpnII restriction buffer and 15 µL of 10% SDS. Samples were incubated at 37 °C for 1 hour shaking at 900 RPM. One hundred fifty µL of 10% Triton X-100 was added and samples were further incubated at 37 °C for 1 hour at 900 RPM. A 5 µL sample was taken and stored for comparison with the prepared template. Nuclei were incubated overnight with 200 units of DpnII (New England Biolabs) restriction enzyme. Eighty µL of 10% SDS were added and samples were then incubated at 65 °C for 30 minutes to inactivate the DpnII enzyme. Samples were brought up to 7 mL and proximity-ligated using 4000 units of T4 DNA ligase (NEB) overnight at 16 °C. Crosslinks were reversed by addition of 30 µL of proteinase K and incubation overnight at 65 °C with shaking. Thirty µL of RNase A were then added and samples were incubated at 37 °C to eliminate RNA. Samples were phenol/chloroform/isoamyl alcohol (Sigma)-extracted and DNA was ethanol precipitated. A subsequent restriction digestion was performed in 500 µL total volume using 50 units of Csp6I (Fermentas). Samples were incubated at 65 °C for 30 minutes to inactivate the enzyme and another proximity ligation reaction was performed in 14 mL total volume using 6000 units of T4 DNA ligase (NEB). DNA was again phenol/chloroform-extracted and ethanol precipitated. DNA was resuspended in 10 mM Tris pH 8.0 and purified using QIAquick PCR purification kits. DNA was quantified by Qubit fluorometry.
4C template DNA was PCR-amplified using Expand Long Template PCR System (Roche). 400 ng of template was used as input in 50 µL PCR reactions using single barcode primers containing the SOX2 promoter bait. Libraries were isolated using QIAquick PCR purification (Qiagen) and quantified by Qubit and KAPA qPCR (Roche) prior to sequencing.

treatment_protocol: To differentiate to rosette NSCs hESCs cells were plated on Geltrex-coated plates at ~50,000 cells/cm2 611 and grown under feeder-free conditions available under aCC-BY-NC-ND 4.0 International license. in Pluristem Human ES Cell Medium (Millipore) until reaching ~80% confluence. Medium was then changed first to KSR medium [Knockout-DMEM, 15% knockout serum replacement (KSR), 2 mM L-glutamine, 1X nonessential amino acids (NEAA), and 0.1% β-mercaptoethanol] supplemented with 10 µM SB-431542 (stemMACS) and 100 nM LDN-193189 (Fisher) to achieve dual SMAD inhibition. KSR concentration was gradually reduced over 10 days in exchange for N2 medium: on day 2, medium was changed to 75% KSR medium + 25% N2 Medium [1:1 DMEM/F12 (Invitrogen), N2 supplement 1X, and 1.6 g/L glucose], again supplemented with SB-431542 and LDN-193189; on days 4, 6, and 8, medium was changed with a 25% decrease in KSR medium composition every two days, until on day 8 the medium consisted of 100% N2 with SB-431542 and LDN-193189.

value: H9 Derived Rosette NSCs

value: Rosette NSCs


title: Duodenum_TCR_1

description:
Takara Bio SMARTER TCRa/b profiling
F7-duodenumM1aR4-bR4F10


title: ATAC-sequencing done on human neural stem cells derived from H9 hESCs

description: Library name: NSC-ATAC-Seq

data_processing:
Base calls were performed using bcl2fastq for Novaseq.
Demultiplexed fastq files were trimmed using Trimmomatic. Trimmed fastq files were aligned against the Hg19 genome assembly using Bowtie2, and processed to BigWigs and Bed files for visualization using Samtools and Deeptools. Reads Per Genomic Content (RPGC)-normalized files
Trimmed fastq files were aligned against the Hg19 genome assembly using Bowtie2, and processed to BigWigs visualization using Samtools and Deeptools with Reads Per Genomic Content (RPGC) normalization.
Assembly: Hg19
Supplementary files format and content: Bigwig

source_name: H9 hESC derived NSCs

growth_protocol: Human ESC-derived NSCs were cultured in DMEM/F12 medium (Thermo) supplemented with N2  supplement 1X (Fisher), B27 supplement 0.1X (Fisher), insulin (Sigma), glucose (1.6 g/L) (Fisher), 20 ng/mL EGF (R&D Systems) and 20 ng/mL FGF2 (R&D Systems). Cells were cultured on plates coated for 24 hours with 0.025% poly-L-ornithine (Gibco) followed by 2 hours of coating with 10 µg/mL of laminin in  PBS (Gibco). Medium was changed every 48 hours.

extract_protocol:
After counting, 100,000 cells were collected, resuspended in 1X cold DPBS (Gibco) and centrifuged at 500xg for 5 min at 4 °C. After centrifugation, the supernatant was removed and the cell pellet resuspended in 500 µL of cold ATAC-seq resuspension buffer 1 (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 and 0.1% Tween-20 in H20). Fifty µL (50,000 cells) were transferred to a new 1.5 ml Eppendorf tube and 0.5 µL 1% Digitonin (Promega) was added by pipetting well a few times. The cell lysis reaction was incubated on ice for 3 min. After lysis, 1 mL of cold ATAC-seq resuspension buffer 2 (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20 in H20) was added. The tube was inverted three times to mix the contents and nuclei were pelleted by centrifugation for 10 min at 500xg at 4 °C.
Nuclei were resuspended in 45 µL of transposition mix [25 µL 2X TD buffer (Illumina), 16.5 µL 1X PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20 and 2.5 µL H2O) by pipetting up and down a few times. Five µL of transposase enzyme (Illumina) was then added and the transposition reaction was incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 rpm. The reaction was cleaned up with MinElute Reaction Cleanup Kit (Qiagen). Transposed DNA fragments were then amplified as described previously in Buenrostro et al 2017. Final libraries were purified with Ampure 698 XP Beads (Beckman), checked by Tapestation High Sensitivity (Agilent) and quantified by Qubit (Life Technologies).

value: H9 hESC derived NSCs


title: BDII_3

description: Library name: BDII_3


title: Rosette, nmotif, SOX2 4C-Seq, Rep 1

description: Library name: Rosette nmotif 4C Rep 1


title: intestinal stem cell 10 day sample4

city: Chengdu

first: Qian

last: Zhang

address: No. 37 Guoxue Lane, Wuhou District, Chengdu, Sichuan Province, China

institute: Sichuan University

description: Library name: Young esgts-lacZ_1

data_processing:
STAR 2.7.1a
reads were aligned to the reference genome (dm6) using STAR
Aligned BAM files were processed with StringTie forFPKM calculation
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

organism: Drosophila melanogaster

source_name: midgut

extract_protocol:
After FACS, sorted Drosophila midgut ISCs were centrifuged at 400×g, resuspended in 500 µL RNA extraction reagents (Vazyme, R701), and immediately frozen using liquid nitrogen.
All samples were then processed for RNA-seq by SEQHEALTH Technology Co., Ltd (China). The sequence platform was based on novaseq 6000 (Illumina, San Diego, US) using a 150 bp paired end run resulting in over 20 million reads per sample.

value: midgut

tag: sample group

value: intestinal stem cell 10 day


title: intestinal stem cell 10 day sample3

description: Library name: Young esgts-lacZ_2


title: intestinal stem cell 10 day sample1

description: Library name: Young esgts-lacZ_4


title: intestinal stem cell 30 day sample3

description: Library name: Old esgts-lacZ_2

value: intestinal stem cell 30 day


title: BDII_1

description: Library name: BDII_1


title: Rosette, ROSA26, SOX2 4C-Seq, Rep 1

description: Library name: Rosette ROSA26 4C Rep 1


title: Rosette, ROSA26, SOX2 4C-Seq, Rep 2

description: Library name: Rosette ROSA26 4C Rep 2


title: intestinal stem cell 30 day sample4

description: Library name: Old esgts-lacZ_1


title: hESC, nmotif, SOX2 4C-Seq, Rep 2

description: Library name: hESC nmotif 4C Rep 2

source_name: H9 hESC

value: H9 hESC

value: hESC


title: intestinal stem cell 30 day sample2

description: Library name: Old esgts-lacZ_3


title: intestinal stem cell 10 day kd ADAR sample4

description: Library name: Young esgts-Adar IR_1

value: intestinal stem cell 10 day kd ADAR


title: intestinal stem cell 30 day sample1

description: Library name: Old esgts-lacZ_4


title: hESC, nmotif, SOX2 4C-Seq, Rep 1

description: Library name: hESC nmotif 4C Rep 1


title: BDI_1

description: Library name: BDI_1


title: intestinal stem cell 10 day kd ADAR sample3

description: Library name: Young esgts-Adar IR_2


title: intestinal stem cell 10 day kd ADAR sample1

description: Library name: Young esgts-Adar IR_4


title: hESC, ROSA26, SOX2 4C-Seq, Rep 2

description: Library name: hESC ROSA26 4C Rep 2


title: patient309

type: other

city: Memphis

first: Kyle

middle: S

last: Smith

state: TN

address: 262 Danny Thomas Pl

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

source_name: Brain tumor

label_protocol: Standard Illumina Protocol

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

value: Male

tag: age

tag: mstage

tag: risk group

value: High

tag: subgroup

tag: g34 subtype

value: II

value: Brain tumor


title: kd Zn72D sample3

description: Library name: Zn72d-IR_1

source_name: whole organism

tag: tissue

value: whole organism

value: kd Zn72D


title: kd Zn72D sample2

description: Library name: Zn72d-IR_2


title: kd Zn72D WT3

description: Library name: WT-Zn72d_1

value: kd Zn72D WT


title: patient308

description: Brain tumor patient

value: Female

value: VII


title: PBMC, pediatric MCD, n=4

first: Chaeyoon

address: 103, Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

institute: Seoul National University

description:
Library name: MCD_PBMC
PBMC from 4 pediatric minimal change disease patients

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Demuxalot and Cell Ranger software v7.1.0. Donor genotype VCF files contain individual-level human variation data and are therefore not provided as public supplementary files; the demultiplexed cell annotations are provided in the processed h5ad object.
Assembly: GRCh38-2024-A
Supplementary files format and content: 10x Genomics feature-barcode matrix files

source_name: peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized whole blood by density-gradient centrifugation using Ficoll-Paque. Whole blood was diluted 1:1 with DPBS and carefully layered onto Ficoll (Ficoll: diluted blood = 15 mL:25 mL in 50 mL tubes, or 5 mL:10 mL in 15 mL tubes). Samples were centrifuged at 2000 rpm for 20 min at 20°C. The PBMC layer at the plasma–Ficoll interface was collected and transferred to pre-warmed DPBS, followed by two washes. Cells were counted, resuspended in cryopreservation medium, aliquoted into cryovials, and cryopreserved using a controlled-rate freezing container before storage at liquid nitrogen. For library preparation, cryopreserved PBMCs were thawed and processed according to the manufacturer's guidelines
Libraries were prepared according to the manufacturer's guidelines  (Chromium Next GEM Single Cell 3' HT, 10x Genomics). Thawed cells were resuspended in the supplied master mix and co-loaded with gel beads and partitioning oil into the microfluidic chip to form GEMs. Each GEM served as an isolated reaction chamber where cells were lysed and polyadenylated transcripts were reverse-transcribed into cDNA. The resulting cDNA molecules were tagged with a 10x cell barcode and UMI, and also contained the Illumina Read 1 priming sequence. Barcoded cDNA was then pooled, the emulsion was removed, and cDNA was cleaned up using Silane DynaBeads prior to PCR amplification. Size selection of amplified cDNA was performed with SPRIselect reagent, and the selected fragments were converted into sequencing libraries by adding the Illumina Read 2 priming sequence, P5/P7 flow-cell adapters, and a sample index for multiplexed paired-end sequencing.

value: peripheral blood

value: Peripheral blood mononuclear cell


title: kd Zn72D sample1

description: Library name: Zn72d-IR_3


title: kd Zn72D WT2

description: Library name: WT-Zn72d_2


title: patient307

description: Brain tumor patient

value: Average

value: VIII


title: kd Zn72D WT1

description: Library name: WT-Zn72d_3


title: U2OS, siORCA, Input, Bmi1, TSA Seq

city: Urbana

first: Supriya

last: Prasanth

state: IL

address: 601 S Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois Urbana Champaign

description: Library name: U2OS_siORCA_Bmi1_Input

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq Conversion Software (Illumina).
Trimming of reads was performed with trimmomatic
All sequencing files were aligned to human genome (T2T-CHM13v2.0) using Bowtie2 (v) and the sam files were converted to bam files using SAMtools (v)
BAM files were further analyzed by using the method here https://github.com/lgchang27/TSA-Seq-2020v2/tree/master
Assembly: T2T-CHM13v2.0
Supplementary files format and content: bigwig files

source_name: Bone

growth_protocol: DMEM, 5% Fetal Bowin serum, 1X Penicillin and Streptomycin. Cells were cultured at 37 C at 5% CO2

extract_protocol:
Genomic DNA was isolated using Phenol Cholorofrom method and sonicated.
Sequencing libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina, IP-202-1012) as per manufacturer’s protocol.

treatment_protocol: Cells were transfected with control (gl3) or siORCA or siEZH2.

value: Bone

value: Osteosarcoma

tag: treatment

value: siORCA

value: Batch 2


title: OE E374A Drosophila melanogaster sample3

description: Library name: E374A-OE_1

value: OE E374A Drosophila melanogaster


title: patient306

description: Brain tumor patient

value: Male

value: High


title: OE E374A Drosophila melanogaster sample2

description: Library name: E374A-OE_2


title: U2OS, Control, Input, Bmi1, TSA Seq

description: Library name: U2OS_Control_Bmi1_Input

tag: cell type


title: OE E374A Drosophila melanogaster sample1

description: Library name: E374A-OE_3


title: OE E374A Drosophila melanogaster WT3

description: Library name: WT-E374A_1

value: OE E374A Drosophila melanogaster WT


title: patient305

description: Brain tumor patient

value: VI

value: Brain tumor


title: U2OS, siORCA, Bmi1, Replicate2, TSA Seq

description: Library name: U2OS_siORCA_Bmi1_2


title: OE E374A Drosophila melanogaster WT2

description: Library name: WT-E374A_2

value: whole organism


title: patient304

description: Brain tumor patient


title: OE E374A Drosophila melanogaster WT1

description: Library name: WT-E374A_3


title: U2OS, siORCA, Bmi1, Replicate1, TSA Seq

description: Library name: U2OS_siORCA_Bmi1_1


title: patient303

description: Brain tumor patient


title: tex_SBI_3

city: Bilthoven

first: Els

last: Alsema

address: Antonie van Leeuwenhoeklaan 9

department: Centre for Health Protection

country: Netherlands

institute: RIVM

description: Library name: S48

data_processing:
Raw bcl files were demultiplexed using bcl2fastq (Illumina, version v2.19.0.316).
The resulting FASTQ files were subjected to a quality control procedure using FastQC (version 0.11.5).
Reads were mapped to the human genome (Ensembl GRCh38, release 90) using STAR (version 2.5.3a).
The number of mapped reads were counted for each gene and compiled into an expression matrix using featureCounts (version 1.6.0).
Further statistical data analysis and visualization was conducted in R statistical software (version 4.4.0).
Assembly: Ensembl GRCh38, release 90
Supplementary files format and content: RawCounts.txt: count data per sample plus gene annotation

growth_protocol: THP-1 monocytes (TIB-202, lot 70025047) were purchased from ATCC and maintained in complete medium, consisting of RPMI GlutaMAX medium (72400-021, Gibco) supplemented with 1% penicillin/streptomycin (10,000 U/ml, 15140-122, Gibco) and 10% heat-inactivated FBS (A5256801, Gibco). Cells were passaged every 3-4 days by centrifugation at 130 x g for 5 minutes, followed by resuspension at 2 x 105 cells/ml. Cell density of the cultures were checked before passaging, to ensure it did not exceed 1 x 106 cells/ml. Cells were used for experiments between passage 11 to 15.

extract_protocol:
Cell culture medium was removed from the wells 24 hours after PMA removal and the cells were disrupted by adding buffer RLT (79216, Qiagen), containing 1% 2-mercaptoethanol (63689, Sigma-Aldrich), onto the cells (1200 μL for breast implant surfaces in 12-well plates, 300 μL for PAA gels and surgical meshes, 350 µL for other materials in 24-well plates). Cells were resuspended by vigorous pipetting, vortexing for 1 minute and transferred to polypropylene vials (DNA LoBind tubes, 0030108051, Eppendorf). Vials were immediately stored at -80 °C until further processing. For the surgical meshes, 300 μL of lysate from 2 wells was pooled into one vial, creating a total of 3 samples from 6 wells. For the PAA gels, 300 µL buffer was added for 10 minutes on ice, followed by vigorous pipetting and transferral to vials. Subsequently, this procedure was repeated on the same well with another 300 µl of RLT buffer to retrieve RNA absorbed into the gel. Total RNA extraction was performed using the RNeasy Mini Kit (74104, Qiagen), in combination with a QIAshredder homogenisation (79656, Qiagen) and DNase digestion step (79254, Qiagen), following the manufacturer’s protocol. The RNA concentration was determined using the Qubit RNA HS assay (Q32852, Invitrogen) on a Qubit 3 fluorometer (Invitrogen). RNA quality was analysed using the 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano kit (5067-1511, Agilent Technologies). All RNA samples had an RNA Integrity Number (RIN) of 9.5 or higher and were considered of sufficient quality for sequencing.
Three samples of each experimental group were further processed for Next Generation Sequencing using the TruSeq Stranded mRNA kit (20020594, Illumina), following the Low Sample Protocol. Briefly, samples were enriched for poly-A RNA, after which first-strand cDNA synthesis was performed using SuperScript™ II Reverse Transcriptase (18064014, Thermo Fisher Scientific). TruSeq RNA Single Indexes Set A and B (20020492 and 20020493, Illumina) were used for sample indexing. AMPure XP beads (A63881, Beckman Coulter) were used for all purification steps during the library preparation. Size and purity of the libraries were assessed using a 2100 Bioanalyzer with the DNA 1000 Kit (5067-1504, Agilent Technologies). Sequencing libraries were normalised based on KAPA qPCR quantification (7960140001, Roche Diagnostics) using a QuantStudio 6 Flex Real-Time PCR System (ThermoFisher Scientific) to ensure equal amounts of DNA before pooling. Sequencing was performed on a NextSeq 550 System (Illumina) using the NextSeq 500/550 High Output Kit v2.5 (75 cycles) in three runs, with 16 libraries per run.

treatment_protocol: Prior to cell seeding, all materials were coated with a 34 µg/ml fibronectin solution (33010-018, Gibco) in DPBS for 45 minutes to enhance cell attachment. THP1 monocytes were then seeded onto the coated surfaces at a density of 1.56 E5 cells/cm2 in complete RPMI medium, supplemented with 50 ng/ml PMA (tlrl-pma, Invivogen) to induce differentiation into macrophages. For surgical meshes, a higher density of 1.74 E5 cells/cm2 was used to compensate for lower seeding efficiency. After 16 hours, cells were washed once with DPBS to remove PMA and non-adherent cells, and fresh medium was added. For the surgical mesh materials, O-rings were removed after the 16 hour PMA treatment and meshes were transferred to new wells using sterile forceps. For all subsequent medium changes or washes, meshes were again transferred to new wells, in order to eliminate cells attaching to the well bottom instead of the meshes. Culture on the materials was done in 24-well plates, except for SBI surfaces which were tested in 12-well plates.

value: macrophage

tag: material variant

value: SBI-Tex (microtextured breast implant shell)

tag: material group

value: M-SBI

tag: sequencing run


title: tex_SBI_2

description: Library name: S47

tag: cell line


title: U2OS, Control, Bmi1, Replicate2, TSA Seq

description: Library name: U2OS_Control_Bmi1_2

value: Control

tag: batch


title: tex_SBI_1

description: Library name: S46


title: sm_SBI_3

description: Library name: S45

value: SBI-Sm (smooth breast implant shell)


title: sm_SBI_2

description: Library name: S44


title: patient302

description: Brain tumor patient

tag: Sex

value: Female

value: Average


title: U2OS, Control, Bmi1, Replicate1, TSA Seq

description: Library name: U2OS_Control_Bmi1_1

value: Bone

value: Osteosarcoma


title: patient301

description: Brain tumor patient

value: VIII


title: sm_SBI_1

description: Library name: S43


title: U2OS, siEZH2, Input, TSA Seq

description: Library name: U2OS_siEZH2_Input

value: Batch 2


title: patient300

description: Brain tumor patient

value: Male

tag: shh subtype


title: 50kPA_PAA_3

description: Library name: S42

value: STIFF-50 (50kPa polyacrylamide gel)

value: M-STIFF


title: 50kPA_PAA_2

description: Library name: S41


title: U2OS, siEZH2, Replicate 2, TSA Seq

description: Library name: U2OS_siEZH2_2


title: 50kPA_PAA_1

description: Library name: S40


title: U2OS, siEZH2, Replicate1, TSA Seq

description: Library name: U2OS_siEZH2_1


title: 1kPA_PAA_3

description: Library name: S39

value: STIFF-1 (1kPa polyacrylamide gel)


title: 1kPA_PAA_2

description: Library name: S38


title: patient299

description: Brain tumor patient

value: Brain tumor


title: intestinal stem cell 10 day sample2

description: Library name: Young esgts-lacZ_3

value: midgut

value: intestinal stem cell 10 day


title: patient298

description: Brain tumor patient

value: I


title: BDII_2

description: Library name: BDII_2

value: organoids

value: neuron

tag: genotype


title: HMC3, FLAG-3

city: Guangzhou

first: Wang

last: Yinglun

address: 15th Floor, School of Basic Medical Sciences

institute: Southern Medical University

description:
Library name: Sample 6
Column name in raw_counts_all_samples_and_degs.csv: Ctrl-3

data_processing:
We used FastQC (v0.11.9) to assess the sequencing quality of the FASTQ files and ensure that all samples exhibited high quality. Illumina adapter sequences were trimmed using Trim galore (v0.6.7). The 150 bp paired-end reads were then aligned to the human reference genome (GRCh38) using the Hisat2 (v2.2.1) method. A comparative analysis of differentially expressed genes based on reads was performed using DEseq2 (v1.40.2).
Assembly: GRCh38
Supplementary files format and content: xlsx files include raw counts from each sample and DEGs result

source_name: brain

growth_protocol: Human microglial cell line HMC3 cells were cultured in MEM medium supplemented with 10% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol:
total RNA was extracted using the RNeasy Mini Kit (Qiagen).
1 μg total RNA was used for following library preparation.  The poly(A) mRNA isolation was performed using Oligo(dT) beads.  The mRNA fragmentation was performed using divalent cations and high temperature.  Priming was performed using Random Primers.  First strand cDNA and the second-strand cDNA were synthesized.  The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends.  Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads.  Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: HMC3 microglial cells were treated with the C1s-CM, and the changes in gene expression were analyzed using high-throughput RNA sequencing (RNA-seq)

value: brain

value: Human microglia cell

value: WT

value: CM without C1s


title: 1kPA_PAA_1

description: Library name: S37

value: macrophage


title: patient297

description: Brain tumor patient

value: Female

value: High

value: II


title: PVDF_mesh_3

description: Library name: S27

value: MESH-PVDF (PVDF surgical mesh)

value: M-MESH


title: PVDF_mesh_2

description: Library name: S26


title: HMC3, FLAG-2

description:
Library name: Sample 5
Column name in raw_counts_all_samples_and_degs.csv: Ctrl-2


title: BDI_2

description: Library name: BDI_2


title: PVDF_mesh_1

description: Library name: S25


title: patient296

description: Brain tumor patient

value: Male

value: Average


title: intestinal stem cell 10 day kd ADAR sample2

description: Library name: Young esgts-Adar IR_3

value: midgut

tag: sample group

value: intestinal stem cell 10 day kd ADAR


title: PP_mesh_2

description: Library name: S23

value: MESH-PP (polypropylene surgical mesh)


title: HMC3, FLAG-1

description:
Library name: Sample 4
Column name in raw_counts_all_samples_and_degs.csv: Ctrl-1


title: PP_mesh_3

description: Library name: S24


title: patient295

description: Brain tumor patient

tag: age

value: Brain tumor


title: PP_mesh_1

description: Library name: S22


title: patient310

description: Brain tumor patient

tag: mstage

value: VII


title: C301coated_silicone_3

description: Library name: S21

value: CHEM-C301 (C301-coated silicone)

value: M-CHEM


title: HMC3, C1s-CM3

description:
Library name: Sample 3
Column name in raw_counts_all_samples_and_degs.csv: C1S-CM3

value: brain

value: Human microglia cell

value: WT

value: CM with C1S


title: patient294

description: Brain tumor patient

tag: risk group


title: HMC3, C1s-CM2

description:
Library name: Sample 2
Column name in raw_counts_all_samples_and_degs.csv: C1S-CM2


title: C301coated_silicone_2

description: Library name: S20

value: macrophage


title: hESC, ROSA26, SOX2 4C-Seq, Rep 1

description: Library name: hESC ROSA26 4C Rep 1

value: H9 hESC

value: hESC


title: patient293

description: Brain tumor patient

value: High

tag: subgroup

value: VI


title: C301coated_silicone_1

description: Library name: S19


title: C170coated_silicone_3

description: Library name: S18

value: CHEM-C170 (C170-coated silicone)


title: patient292

description: Brain tumor patient

value: Female

value: Average

tag: g34 subtype


title: C170coated_silicone_1

description: Library name: S16


title: con3

city: Shijiangzhuang

first: li

last: Zheng

address: 河北省石家庄市中山东路361号

institute: Hebei Medical University

description:
Library name: Sample 6
con3-FPKM
Non-induced HepG2 cells.Sex:Male.Cultivar:MEM medium89%,Fetal Bovine Serum10%,Non-Essential Amino Acids solution1%.Disease:Hepatocellular carcinoma.Time:36h.

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm38
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA purity and concentration were determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

tag: tissue

value: Liver

value: hepatocyte

value: Non-induced HepG2 cells


title: C170coated_silicone_2

description: Library name: S17


title: uncoated_silicone_3

description: Library name: S15

value: CHEM-Unc (uncoated silicone)


title: patient291

description: Brain tumor patient

value: VII

value: Brain tumor


title: uncoated_silicone_2

description: Library name: S14

value: M-CHEM


title: HMC3, C1s-CM1

description:
Library name: Sample 1
Column name in raw_counts_all_samples_and_degs.csv: C1S-CM1

value: brain

value: Human microglia cell

value: WT

tag: treatment

value: CM with C1s


title: uncoated_silicone_1

description: Library name: S13

tag: cell type

value: macrophage


title: patient290

description: Brain tumor patient

value: Male

value: High

value: II


title: con2

address: 河北省石家庄市中山东路361号

description:
Library name: Sample 5
con2-FPKM
Non-induced HepG2 cells.Sex:Male.Cultivar:MEM medium89%,Fetal Bovine Serum10%,Non-Essential Amino Acids solution1%.Disease:Hepatocellular carcinoma.Time:36h.


title: con1

address: 河北省石家庄市中山东路361号

description:
Library name: Sample 4
con1-FPKM
Non-induced HepG2 cells.Sex:Male.Cultivar:MEM medium89%,Fetal Bovine Serum10%,Non-Essential Amino Acids solution1%.Disease:Hepatocellular carcinoma.Time:36h.


title: topo990_SIBS_2

description: Library name: S11

tag: material variant

value: SIBS-Topo (990)

value: M-TOPO


title: patient289

description: Brain tumor patient

value: Female

value: Average


title: T3

address: 河北省石家庄市中山东路361号

description:
Library name: Sample 3
T3-FPKM
Maturation and differentiation of HepG2 cells were induced by high-temperature TSN.Sex:Male.Cultivar:MEM medium89%,Fetal Bovine Serum10%,Non-Essential Amino Acids solution1%.Disease:Hepatocellular carcinoma.Time:36h.

value: Liver

value: hepatocyte


title: topo990_SIBS_1

description: Library name: S10

tag: material group


title: topo990_SIBS_3

description: Library name: S12

tag: sequencing run


title: patient288

description: Brain tumor patient

value: VIII


title: T2

address: 河北省石家庄市中山东路361号

description:
Library name: Sample 2
T2-FPKM
Maturation and differentiation of HepG2 cells were induced by high-temperature TSN.Sex:Male.Cultivar:MEM medium89%,Fetal Bovine Serum10%,Non-Essential Amino Acids solution1%.Disease:Hepatocellular carcinoma.Time:36h.

tag: cell line


title: flat_SIBS_2

description: Library name: S08

value: SIBS-Flat


title: flat_SIBS_3

description: Library name: S09


title: flat_SIBS_1

description: Library name: S07


title: patient287

description: Brain tumor patient

value: Brain tumor


title: 30um_PP_3

description: Library name: S06

value: PORE-30 (30um polypropylene membrane)

value: M-PORE


title: T1

address: 河北省石家庄市中山东路361号

description:
Library name: Sample 1
T1-FPKM
Maturation and differentiation of HepG2 cells were induced by high-temperature TSN.Sex:Male.Cultivar:MEM medium89%,Fetal Bovine Serum10%,Non-Essential Amino Acids solution1%.Disease:Hepatocellular carcinoma.Time:36h.

value: WT


title: 30um_PP_2

description: Library name: S05


title: patient286

description: Brain tumor patient


title: 30um_PP_1

description: Library name: S04


title: NSCLC, Pretreatment, mEGFR, Ph22_35

city: Pathumwan

first: Chanida

last: Vinayanuwattikun

state: Bangkok

address: Phayathai Road

department: Department of Medicine

country: Thailand

institute: Chulalongkorn University

description: Library name: Ph22_35

data_processing:
Sequencing was performed using the NovaSeq, generating 150 paired-end reads, each at least 60 million reads
RNA data is aligned to the human reference genome (GRCh37) employing the STAR aligner 2.6.1
Gene expression counts are quantified using Salmon 1.4.058, through the bcbio-nextgen pipeline (version 1.2.9)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumor tissue (FFPE)

extract_protocol:
RNA was extracted from paraffin-embedded tissue using High Pure RNA Paraffin Kit. Total RNA was used for the construction of sequencing libraries.
the samples proceeded to library construction using Agilent SureSelect XT HS2 Human All Exon V8 library preparation and target enrichment (San Diego, CA, USA).

value: Tumor tissue (FFPE)

value: NSCLC

value: mEGFR

value: Afatinib


title: 0.6um_PP_3

description: Library name: S03

value: macrophage

value: PORE-0.6 (0.6um polypropylene membrane)


title: NSCLC, Pretreatment, mEGFR, Ph22_27

description: Library name: Ph22_27

value: Erlotinib


title: 0.6um_PP_1

description: Library name: S01


title: 0.6um_PP_2

description: Library name: S02


title: patient285

description: Brain tumor patient

value: Female

value: VII


title: patient284

description: Brain tumor patient

value: Average

value: III


title: HaCaT cells, PFTeDA replicate 3

city: Busan

first: BuHyun

last: Youn

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

department: Biological Sciences

institute: Pusan National University

description:
Library name: HaCaT_PFTeDA_3
HaCaT cells treated with PFTeDA at IC01 for 24 h, biological replicate 3

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.

source_name: HaCaT

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.

value: HaCaT

value: norma human keratinocyte

value: PFTeDA (20.41 μM)

tag: batch


title: NSCLC, Pretreatment, mEGFR, Ph22_25

description: Library name: Ph22_25

value: Osimertinib


title: NSCLC, Pretreatment, mEGFR, Ph22_18

description: Library name: Ph22_18

value: Dacomitinib


title: HaCaT cells, PFTeDA replicate 2

description:
Library name: HaCaT_PFTeDA_2
HaCaT cells treated with PFTeDA at IC01 for 24 h, biological replicate 2

value: WT


title: patient282

description: Brain tumor patient

tag: Sex

value: High

value: II

value: Brain tumor


title: HaCaT cells, PFOA replicate 3

description:
Library name: HaCaT_PFOA_3
HaCaT cells treated with PFOA at IC01 for 24 h, biological replicate 3


title: HaCaT cells, PFOA replicate 2

description:
Library name: HaCaT_PFOA_2
HaCaT cells treated with PFOA at IC01 for 24 h, biological replicate 2


title: HaCaT cells, PFOA replicate 1

description:
Library name: HaCaT_PFOA_1
HaCaT cells treated with PFOA at IC01 for 24 h, biological replicate 1


title: patient283

description: Brain tumor patient


title: HaCaT cells, PFTeDA replicate 1

description:
Library name: HaCaT_PFTeDA_1
HaCaT cells treated with PFTeDA at IC01 for 24 h, biological replicate 1


title: patient281

description: Brain tumor patient

value: Male


title: HaCaT cells, NiCl2 replicate 3

description:
Library name: HaCaT_NiCl2_3
HaCaT cells treated with NiCl2 at IC01 for 24 h, biological replicate 3

value: NiCl2 (407 μM)


title: NSCLC, Pretreatment, mEGFR, Ph22_15

description: Library name: Ph22_15

value: Tumor tissue (FFPE)

value: NSCLC

value: mEGFR

value: Gefitinib


title: patient280

description: Brain tumor patient

value: Female

value: Average


title: HaCaT cells, NiCl2 replicate 2

description:
Library name: HaCaT_NiCl2_2
HaCaT cells treated with NiCl2 at IC01 for 24 h, biological replicate 2

value: HaCaT


title: NSCLC, Pretreatment, mEGFR, Ph22_12

description: Library name: Ph22_12

value: Erlotinib


title: HaCaT cells, NiCl2 replicate 1

description:
Library name: HaCaT_NiCl2_1
HaCaT cells treated with NiCl2 at IC01 for 24 h, biological replicate 1

value: norma human keratinocyte


title: HaCaT cells, DINCH replicate 3

description:
Library name: HaCaT_DINCH_3
HaCaT cells treated with DINCH at IC01 for 24 h, biological replicate 3

value: DINCH (2.137 μM)


title: patient279

description: Brain tumor patient

value: VII


title: HaCaT cells, DINCH replicate 2

description:
Library name: HaCaT_DINCH_2
HaCaT cells treated with DINCH at IC01 for 24 h, biological replicate 2

value: WT


title: NSCLC, Pretreatment, mEGFR, Ph22_06

description: Library name: Ph22_06

value: Osimertinib


title: HaCaT cells, DINCH replicate 1

description:
Library name: HaCaT_DINCH_1
HaCaT cells treated with DINCH at IC01 for 24 h, biological replicate 1


title: HaCaT cells, DEHP replicate 3

description:
Library name: HaCaT_DEHP_3
HaCaT cells treated with DEHP at IC01 for 24 h, biological replicate 3

value: DEHP (4110 μM)


title: HaCaT cells, DEHP replicate 2

description:
Library name: HaCaT_DEHP_2
HaCaT cells treated with DEHP at IC01 for 24 h, biological replicate 2


title: HaCaT cells, DEHP replicate 1

description:
Library name: HaCaT_DEHP_1
HaCaT cells treated with DEHP at IC01 for 24 h, biological replicate 1


title: NSCLC, Pretreatment, mEGFR, Ph22_05

description: Library name: Ph22_05


title: patient278

description: Brain tumor patient

value: I

value: Brain tumor


title: NSCLC, Pretreatment, mEGFR, Ph21_176

description: Library name: Ph21_176


title: patient276

description: Brain tumor patient

value: Male

value: III


title: HaCaT cells, DBP replicate 3

description:
Library name: HaCaT_DBP_3
HaCaT cells treated with DBP at IC01 for 24 h, biological replicate 3

value: DBP (1.2 μM)


title: HaCaT cells, DBP replicate 2

description:
Library name: HaCaT_DBP_2
HaCaT cells treated with DBP at IC01 for 24 h, biological replicate 2


title: patient277

description: Brain tumor patient


title: NSCLC, Pretreatment, mEGFR, Ph21_68

description: Library name: Ph21_68

value: Tumor tissue (FFPE)

value: NSCLC

value: mEGFR


title: HaCaT cells, DBP replicate 1

description:
Library name: HaCaT_DBP_1
HaCaT cells treated with DBP at IC01 for 24 h, biological replicate 1


title: patient275

description: Brain tumor patient

value: Female

value: High


title: HaCaT cells, BPS replicate 3

description:
Library name: HaCaT_BPS_3
HaCaT cells treated with BPS at IC01 for 24 h, biological replicate 3

value: HaCaT

value: BPS (158 μM)


title: NSCLC, Pretreatment, mEGFR, Ph21_60

description: Library name: Ph21_60


title: patient274

description: Brain tumor patient

value: Average


title: HaCaT cells, BPS replicate 2

description:
Library name: HaCaT_BPS_2
HaCaT cells treated with BPS at IC01 for 24 h, biological replicate 2

value: norma human keratinocyte


title: HaCaT cells, BPS replicate 1

description:
Library name: HaCaT_BPS_1
HaCaT cells treated with BPS at IC01 for 24 h, biological replicate 1

value: WT


title: patient273

description: Brain tumor patient

value: VII


title: HaCaT cells, BPA replicate 2

description:
Library name: HaCaT_BPA_2
HaCaT cells treated with BPA at IC01 for 24 h, biological replicate 2


title: HaCaT cells, BPA replicate 1

description:
Library name: HaCaT_BPA_1
HaCaT cells treated with BPA at IC01 for 24 h, biological replicate 1


title: patient272

description: Brain tumor patient


title: HaCaT cells, AlCl3 replicate 3

description:
Library name: HaCaT_AlCl3_3
HaCaT cells treated with AlCl3 at IC01 for 24 h, biological replicate 3


title: NSCLC, Pretreatment, mEGFR, Ph21_57

description: Library name: Ph21_57

value: Erlotinib


title: NSCLC, Pretreatment, mEGFR, Ph21_59

description: Library name: Ph21_59


title: HaCaT cells, BPA replicate 3

description:
Library name: HaCaT_BPA_3
HaCaT cells treated with BPA at IC01 for 24 h, biological replicate 3


title: HaCaT cells, AlCl3 replicate 2

description:
Library name: HaCaT_AlCl3_2
HaCaT cells treated with AlCl3 at IC01 for 24 h, biological replicate 2


title: NSCLC, Pretreatment, mEGFR, Ph21_43

description: Library name: Ph21_43


title: NSCLC, Pretreatment, mEGFR, Ph21_39

description: Library name: Ph21_39


title: patient271

description: Brain tumor patient


title: HaCaT cells, control replicate 2

description:
Library name: HaCaT_Con_2
HaCaT cells vehicle control for 24 h, biological replicate 2

value: Vehicle control


title: HaCaT cells, control replicate 3

description:
Library name: HaCaT_Con_3
HaCaT cells vehicle control for 24 h, biological replicate 3


title: NSCLC, Pretreatment, mEGFR, Ph21_34

description: Library name: Ph21_34

value: Osimertinib


title: patient270

description: Brain tumor patient

value: Male

value: Brain tumor


title: HaCaT cells, control replicate 1

description:
Library name: HaCaT_Con_1
HaCaT cells vehicle control for 24 h, biological replicate 1


title: patient269

description: Brain tumor patient

value: II


title: BEAS2B cells, PFTeDA replicate 3

description:
Library name: BEAS2B_PFTeDA_3
BEAS-2B cells treated with PFTeDA at IC01 for 24 h, biological replicate 3

value: normal human bronchial epithelial cell

value: PFTeDA (6160 μM)


title: BEAS2B cells, PFTeDA replicate 2

description:
Library name: BEAS2B_PFTeDA_2
BEAS-2B cells treated with PFTeDA at IC01 for 24 h, biological replicate 2


title: NSCLC, Pretreatment, mEGFR, Ph21_31

description: Library name: Ph21_31

value: Tumor tissue (FFPE)

value: NSCLC

value: mEGFR

value: Gefitinib


title: patient268

description: Brain tumor patient


title: BEAS2B cells, PFTeDA replicate 1

description:
Library name: BEAS2B_PFTeDA_1
BEAS-2B cells treated with PFTeDA at IC01 for 24 h, biological replicate 1


title: BEAS2B cells, PFOA replicate 3

description:
Library name: BEAS2B_PFOA_3
BEAS-2B cells treated with PFOA at IC01 for 24 h, biological replicate 3


title: patient267

description: Brain tumor patient

value: VI


title: NSCLC, Pretreatment, mEGFR, Ph21_30

description: Library name: Ph21_30


title: BEAS2B cells, PFOA replicate 2

description:
Library name: BEAS2B_PFOA_2
BEAS-2B cells treated with PFOA at IC01 for 24 h, biological replicate 2


title: NSCLC, Pretreatment, mEGFR, Ph21_27

description: Library name: Ph21_27


title: patient266

description: Brain tumor patient

value: Average

tag: shh subtype


title: BEAS2B cells, PFOA replicate 1

description:
Library name: BEAS2B_PFOA_1
BEAS-2B cells treated with PFOA at IC01 for 24 h, biological replicate 1

tag: genotype


title: NSCLC, Pretreatment, mEGFR, Ph21_12

description: Library name: Ph21_12


title: BEAS2B cells, NiCl2 replicate 3

description:
Library name: BEAS2B_NiCl2_3
BEAS-2B cells treated with NiCl2 at IC01 for 24 h, biological replicate 3


title: BEAS2B cells, NiCl2 replicate 2

description:
Library name: BEAS2B_NiCl2_2
BEAS-2B cells treated with NiCl2 at IC01 for 24 h, biological replicate 2


title: patient265

description: Brain tumor patient

value: Female


title: BEAS2B cells, NiCl2 replicate 1

description:
Library name: BEAS2B_NiCl2_1
BEAS-2B cells treated with NiCl2 at IC01 for 24 h, biological replicate 1

value: WT


title: NSCLC, Pretreatment, mEGFR, Ph21_08

description: Library name: Ph21_08


title: BEAS2B cells, DINCH replicate 3

description:
Library name: BEAS2B_DINCH_3
BEAS-2B cells treated with DINCH at IC01 for 24 h, biological replicate 3

value: DINCH (2500 μM)


title: patient264

description: Brain tumor patient

value: High

value: VIII


title: BEAS2B cells, DINCH replicate 2

description:
Library name: BEAS2B_DINCH_2
BEAS-2B cells treated with DINCH at IC01 for 24 h, biological replicate 2


title: NSCLC, Pretreatment, mEGFR, Ph21_06

description: Library name: Ph21_06

value: Erlotinib


title: BEAS2B cells, DINCH replicate 1

description:
Library name: BEAS2B_DINCH_1
BEAS-2B cells treated with DINCH at IC01 for 24 h, biological replicate 1


title: BEAS2B cells, DEHP replicate 3

description:
Library name: BEAS2B_DEHP_3
BEAS-2B cells treated with DEHP at IC01 for 24 h, biological replicate 3

value: DEHP (12.5 μM)


title: NSCLC, Pretreatment, mEGFR, Ph21_03

description: Library name: Ph21_03


title: patient262

description: Brain tumor patient

value: Male

value: VII

value: Brain tumor


title: BEAS2B cells, DEHP replicate 2

description:
Library name: BEAS2B_DEHP_2
BEAS-2B cells treated with DEHP at IC01 for 24 h, biological replicate 2

value: normal human bronchial epithelial cell


title: BEAS2B cells, DEHP replicate 1

description:
Library name: BEAS2B_DEHP_1
BEAS-2B cells treated with DEHP at IC01 for 24 h, biological replicate 1


title: NSCLC, Pretreatment, mEGFR, Ph21_02

description: Library name: Ph21_02

value: Tumor tissue (FFPE)


title: NSCLC, Pretreatment, mEGFR, Ph22_17

description: Library name: Ph22_17

value: NSCLC


title: patient261

description: Brain tumor patient


title: BEAS2B cells, DBP replicate 3

description:
Library name: BEAS2B_DBP_3
BEAS-2B cells treated with DBP at IC01 for 24 h, biological replicate 3

value: DBP (49 μM)


title: NSCLC, Pretreatment, mEGFR, Ph20_167

description: Library name: Ph20_167

value: mEGFR


title: BEAS2B cells, DBP replicate 2

description:
Library name: BEAS2B_DBP_2
BEAS-2B cells treated with DBP at IC01 for 24 h, biological replicate 2


title: patient260

description: Brain tumor patient


title: BEAS2B cells, DBP replicate 1

description:
Library name: BEAS2B_DBP_1
BEAS-2B cells treated with DBP at IC01 for 24 h, biological replicate 1


title: BEAS2B cells, BPS replicate 3

description:
Library name: BEAS2B_BPS_3
BEAS-2B cells treated with BPS at IC01 for 24 h, biological replicate 3


title: NSCLC, Pretreatment, mEGFR, Ph20_166

description: Library name: Ph20_166

value: Gefitinib


title: BEAS2B cells, BPS replicate 2

description:
Library name: BEAS2B_BPS_2
BEAS-2B cells treated with BPS at IC01 for 24 h, biological replicate 2


title: patient263

description: Brain tumor patient

value: Average


title: BEAS2B cells, BPS replicate 1

description:
Library name: BEAS2B_BPS_1
BEAS-2B cells treated with BPS at IC01 for 24 h, biological replicate 1


title: patient259

description: Brain tumor patient


title: patient258

description: Brain tumor patient

value: Female

value: V


title: BEAS2B cells, BPA replicate 3

description:
Library name: BEAS2B_BPA_3
BEAS-2B cells treated with BPA at IC01 for 24 h, biological replicate 3

value: WT


title: BEAS2B cells, BPA replicate 2

description:
Library name: BEAS2B_BPA_2
BEAS-2B cells treated with BPA at IC01 for 24 h, biological replicate 2


title: NSCLC, Pretreatment, mEGFR, Ph20_151

description: Library name: Ph20_151


title: patient257

description: Brain tumor patient


title: BEAS2B cells, BPA replicate 1

description:
Library name: BEAS2B_BPA_1
BEAS-2B cells treated with BPA at IC01 for 24 h, biological replicate 1


title: BEAS2B cells, AlCl3 replicate 3

description:
Library name: BEAS2B_AlCl3_3
BEAS-2B cells treated with AlCl3 at IC01 for 24 h, biological replicate 3


title: NSCLC, Pretreatment, mEGFR, Ph20_149

description: Library name: Ph20_149


title: NSCLC, Pretreatment, mEGFR, Ph20_158

description: Library name: Ph20_158


title: patient256

description: Brain tumor patient

value: High

value: III


title: BEAS2B cells, AlCl3 replicate 2

description:
Library name: BEAS2B_AlCl3_2
BEAS-2B cells treated with AlCl3 at IC01 for 24 h, biological replicate 2


title: BEAS2B cells, AlCl3 replicate 1

description:
Library name: BEAS2B_AlCl3_1
BEAS-2B cells treated with AlCl3 at IC01 for 24 h, biological replicate 1


title: NSCLC, Pretreatment, mEGFR, Ph20_147

description: Library name: Ph20_147


title: BEAS2B cells, control replicate 3

description:
Library name: BEAS2B_Con_3
BEAS-2B cells vehicle control for 24 h, biological replicate 3

value: Vehicle control


title: patient255

description: Brain tumor patient


title: BEAS2B cells, control replicate 2

description:
Library name: BEAS2B_Con_2
BEAS-2B cells vehicle control for 24 h, biological replicate 2


title: NSCLC, Pretreatment, mEGFR, Ph20_141

description: Library name: Ph20_141


title: patient254

description: Brain tumor patient

value: VIII


title: BEAS2B cells, control replicate 1

description:
Library name: BEAS2B_Con_1
BEAS-2B cells vehicle control for 24 h, biological replicate 1


title: HL7702 cells, PFTeDA replicate 3

description:
Library name: HL7702_PFTeDA_3
HL7702 cells treated with PFTeDA at IC01 for 24 h, biological replicate 3

value: normal human hepatic epithelium

value: PFTeDA (20.41 μM)


title: NSCLC, Pretreatment, mEGFR, Ph20_133

description: Library name: Ph20_133


title: patient253

description: Brain tumor patient

value: Male

value: Brain tumor


title: HL7702 cells, PFTeDA replicate 2

description:
Library name: HL7702_PFTeDA_2
HL7702 cells treated with PFTeDA at IC01 for 24 h, biological replicate 2


title: NSCLC, Pretreatment, mEGFR, Ph20_128

description: Library name: Ph20_128

value: Tumor tissue (FFPE)

value: Erlotinib


title: patient252

description: Brain tumor patient


title: HL7702 cells, PFOA replicate 3

description:
Library name: HL7702_PFOA_3
HL7702 cells treated with PFOA at IC01 for 24 h, biological replicate 3

value: PFOA (346 μM)


title: NSCLC, Pretreatment, mEGFR, Ph20_065

description: Library name: Ph20_065

value: NSCLC

value: mEGFR

value: Osimertinib


title: HL7702 cells, PFOA replicate 2

description:
Library name: HL7702_PFOA_2
HL7702 cells treated with PFOA at IC01 for 24 h, biological replicate 2


title: HL7702 cells, PFTeDA replicate 1

description:
Library name: HL7702_PFTeDA_1
HL7702 cells treated with PFTeDA at IC01 for 24 h, biological replicate 1


title: HL7702 cells, PFOA replicate 1

description:
Library name: HL7702_PFOA_1
HL7702 cells treated with PFOA at IC01 for 24 h, biological replicate 1


title: patient251

description: Brain tumor patient

value: Female


title: NSCLC, Pretreatment, mEGFR, Ph20_063

description: Library name: Ph20_063

value: Gefitinib


title: patient250

description: Brain tumor patient

value: Average


title: HL7702 cells, NiCl2 replicate 3

description:
Library name: HL7702_NiCl2_3
HL7702 cells treated with NiCl2 at IC01 for 24 h, biological replicate 3

value: WT


title: HL7702 cells, NiCl2 replicate 1

description:
Library name: HL7702_NiCl2_1
HL7702 cells treated with NiCl2 at IC01 for 24 h, biological replicate 1


title: NSCLC, Pretreatment, mEGFR, Ph20_055

description: Library name: Ph20_055


title: HL7702 cells, DINCH replicate 3

description:
Library name: HL7702_DINCH_3
HL7702 cells treated with DINCH at IC01 for 24 h, biological replicate 3

value: DINCH (3.63 μM)


title: patient249

description: Brain tumor patient


title: HL7702 cells, DINCH replicate 2

description:
Library name: HL7702_DINCH_2
HL7702 cells treated with DINCH at IC01 for 24 h, biological replicate 2


title: NSCLC, Pretreatment, mEGFR, Ph20_018

description: Library name: Ph20_018


title: HL7702 cells, DINCH replicate 1

description:
Library name: HL7702_DINCH_1
HL7702 cells treated with DINCH at IC01 for 24 h, biological replicate 1


title: NSCLC, Pretreatment, mEGFR, MLC21_27

description: Library name: MLC21_27

source_name: Tumor tissue (Fresh)

value: Tumor tissue (Fresh)


title: HL7702 cells, DEHP replicate 2

description:
Library name: HL7702_DEHP_2
HL7702 cells treated with DEHP at IC01 for 24 h, biological replicate 2


title: patient247

description: Brain tumor patient

value: I


title: HL7702 cells, DEHP replicate 3

description:
Library name: HL7702_DEHP_3
HL7702 cells treated with DEHP at IC01 for 24 h, biological replicate 3

value: normal human hepatic epithelium


title: HL7702 cells, DEHP replicate 1

description:
Library name: HL7702_DEHP_1
HL7702 cells treated with DEHP at IC01 for 24 h, biological replicate 1


title: patient248

description: Brain tumor patient

value: High

value: IV


title: NSCLC, Pretreatment, mEGFR, MLC21_08

description: Library name: MLC21_08


title: HL7702 cells, DBP replicate 3

description:
Library name: HL7702_DBP_3
HL7702 cells treated with DBP at IC01 for 24 h, biological replicate 3


title: HL7702 cells, DBP replicate 2

description:
Library name: HL7702_DBP_2
HL7702 cells treated with DBP at IC01 for 24 h, biological replicate 2


title: patient245

description: Brain tumor patient

value: Male

value: Brain tumor


title: NSCLC, Pretreatment, mEGFR, MLC21_05

description: Library name: MLC21_05

value: Erlotinib


title: HL7702 cells, DBP replicate 1

description:
Library name: HL7702_DBP_1
HL7702 cells treated with DBP at IC01 for 24 h, biological replicate 1


title: HTPC_24h_control

city: Planegg-Martinsried

first: Artur

last: Mayerhofer

address: Großhadernerstr. 9

department: Biomedical Center

country: Germany

institute: LMU Munich

description:
Library name: sample 3
10x Genomics

data_processing:
Quality control and filtering steps: ~ 12,000 cells were selected, with at least 6,000 UMI counts, 1,600 detected genes and mitochondrial gene counts are lower than 10%.
Doublets were removed using the Scrublet framework.
Normalization and log transformation with scran.
5000 highly variable genes per group were selected using Cell Ranger flavor with fault parametrization.
SCANPY was used for cell count normalization, Scanorama for integration. Unsupervised clustering was done with the Leiden or Louvain algorithm.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: testis

extract_protocol:
HTPCs were derived from small testicular samples of one donor, with non-obstructive azoospermia and normal spermatogenesis, and were isolated using tissue-explant culture.
In a concentration of ~1,100 cells/µl, 10,000 cells were processed using the Single-Cell 3’ Reagent Kits v2 from 10xGenomics according to the manufacturer´s instructions. This was followed by GEM generation and barcoding, post-GEM-RT cleanup, cDNA amplification, library construction and quality assessment with the Bioanalyzer (Agilent).

value: testis

value: primary human testicular peritubular cells (HTPCs)

value: no FCS for 24h


title: HL7702 cells, BPA replicate 3

description:
Library name: HL7702_BPA_3
HL7702 cells treated with BPA at IC01 for 24 h, biological replicate 3


title: HTPC_48h_1mM-adenosine

description:
Library name: sample 2
10x Genomics

value: 1 mM adenosine


title: HL7702 cells, BPS replicate 1

description:
Library name: HL7702_BPS_1
HL7702 cells treated with BPS at IC01 for 24 h, biological replicate 1


title: HL7702 cells, BPA replicate 1

description:
Library name: HL7702_BPA_1
HL7702 cells treated with BPA at IC01 for 24 h, biological replicate 1


title: HL7702 cells, AlCl3 replicate 1

description:
Library name: HL7702_AlCl3_1
HL7702 cells treated with AlCl3 at IC01 for 24 h, biological replicate 1


title: HL7702 cells, control replicate 3

description:
Library name: HL7702_Con_3
HL7702 cells vehicle control for 24 h, biological replicate 3

value: Vehicle control


title: patient240

description: Brain tumor patient

value: VIII


title: patient A30, 0 day

city: Daejeon

first: Yoonjung

last: Choi

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

institute: Yoonjung

description:
Library name: A30_0M
Column name in processed_data.txt : A30_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

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: HL7702 cells, control replicate 2

description:
Library name: HL7702_Con_2
HL7702 cells vehicle control for 24 h, biological replicate 2

value: WT


title: HL7702 cells, control replicate 1

description:
Library name: HL7702_Con_1
HL7702 cells vehicle control for 24 h, biological replicate 1


title: patient239

description: Brain tumor patient

tag: age

value: Average

value: I


title: HIEC6 cells, PFTeDA replicate 3

description:
Library name: HIEC6_PFTeDA_3
HIEC6 cells treated with PFTeDA at IC01 for 24 h, biological replicate 3

value: normal human intestinal epithelial cell lines

value: PFTeDA (1.647 μM)


title: patient A28, 0 day

description:
Library name: A28_0M
Column name in processed_data.txt : A28_0M FPKM


title: HIEC6 cells, PFTeDA replicate 2

description:
Library name: HIEC6_PFTeDA_2
HIEC6 cells treated with PFTeDA at IC01 for 24 h, biological replicate 2


title: patient238

description: Brain tumor patient

value: Male

tag: mstage


title: HIEC6 cells, PFTeDA replicate 1

description:
Library name: HIEC6_PFTeDA_1
HIEC6 cells treated with PFTeDA at IC01 for 24 h, biological replicate 1


title: HL7702 cells, BPS replicate 3

description:
Library name: HL7702_BPS_3
HL7702 cells treated with BPS at IC01 for 24 h, biological replicate 3

value: normal human hepatic epithelium


title: patient A12, 0 day

description:
Library name: A12_0M
Column name in processed_data.txt : A12_0M FPKM


title: patient243

description: Brain tumor patient

value: Female

tag: risk group

value: Brain tumor


title: HTPC_48h_control

description:
Library name: sample 1
10x Genomics

value: testis

value: primary human testicular peritubular cells (HTPCs)

value: no FCS for 48h


title: HIEC6 cells, PFOA replicate 3

description:
Library name: HIEC6_PFOA_3
HIEC6 cells treated with PFOA at IC01 for 24 h, biological replicate 3


title: HL7702 cells, AlCl3 replicate 3

description:
Library name: HL7702_AlCl3_3
HL7702 cells treated with AlCl3 at IC01 for 24 h, biological replicate 3


title: HIEC6 cells, PFOA replicate 2

description:
Library name: HIEC6_PFOA_2
HIEC6 cells treated with PFOA at IC01 for 24 h, biological replicate 2


title: patient A10, 0 day

description:
Library name: A10_0M
Column name in processed_data.txt : A10_0M FPKM


title: patient A33, 0 day

description:
Library name: A33_0M
Column name in processed_data.txt : A33_0M FPKM


title: patient236

description: Brain tumor patient

tag: subgroup


title: HIEC6 cells, PFOA replicate 1

description:
Library name: HIEC6_PFOA_1
HIEC6 cells treated with PFOA at IC01 for 24 h, biological replicate 1


title: HIEC6 cells, NiCl2 replicate 3

description:
Library name: HIEC6_NiCl2_3
HIEC6 cells treated with NiCl2 at IC01 for 24 h, biological replicate 3


title: HIEC6 cells, NiCl2 replicate 2

description:
Library name: HIEC6_NiCl2_2
HIEC6 cells treated with NiCl2 at IC01 for 24 h, biological replicate 2


title: patient A5, 0 day

description:
Library name: A5_0M
Column name in processed_data.txt : A5_0M FPKM


title: HaCaT cells, AlCl3 replicate 1

description:
Library name: HaCaT_AlCl3_1
HaCaT cells treated with AlCl3 at IC01 for 24 h, biological replicate 1

value: HaCaT

value: norma human keratinocyte


title: patient235

description: Brain tumor patient

tag: g34 subtype

value: II


title: HIEC6 cells, NiCl2 replicate 1

description:
Library name: HIEC6_NiCl2_1
HIEC6 cells treated with NiCl2 at IC01 for 24 h, biological replicate 1


title: patient A1, 0 day

description:
Library name: A1_0M
Column name in processed_data.txt : A1_0M FPKM

tag: tissue

value: Peripheral blood

value: rheumatoid arthritis


title: patient234

description: Brain tumor patient

value: High

value: VIII


title: HIEC6 cells, DINCH replicate 2

description:
Library name: HIEC6_DINCH_2
HIEC6 cells treated with DINCH at IC01 for 24 h, biological replicate 2

value: WT

tag: treatment

value: DINCH (3.8 μM)


title: CART22_Rep3

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_48_H6_CART22_Rep3_S48

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: without IL10


title: HIEC6 cells, DINCH replicate 1

description:
Library name: HIEC6_DINCH_1
HIEC6 cells treated with DINCH at IC01 for 24 h, biological replicate 1

tag: cell type

value: normal human intestinal epithelial cell lines


title: patient233

description: Brain tumor patient

value: Male

value: Average


title: HIEC6 cells, DEHP replicate 2

description:
Library name: HIEC6_DEHP_2
HIEC6 cells treated with DEHP at IC01 for 24 h, biological replicate 2

value: DEHP (8500 μM)


title: HIEC6 cells, DEHP replicate 3

description:
Library name: HIEC6_DEHP_3
HIEC6 cells treated with DEHP at IC01 for 24 h, biological replicate 3


title: CART22_Rep2

description: Library name: HTS114_47_H5_CART22_Rep2_S47


title: patient232

description: Brain tumor patient

value: Brain tumor


title: HIEC6 cells, DEHP replicate 1

description:
Library name: HIEC6_DEHP_1
HIEC6 cells treated with DEHP at IC01 for 24 h, biological replicate 1


title: CART22_Rep1

description: Library name: HTS114_46_H4_CART22_Rep1_S46


title: HIEC6 cells, DBP replicate 3

description:
Library name: HIEC6_DBP_3
HIEC6 cells treated with DBP at IC01 for 24 h, biological replicate 3

value: DBP (125 μM)


title: patient231

description: Brain tumor patient

value: Female

value: III


title: HIEC6 cells, BPS replicate 3

description:
Library name: HIEC6_BPS_3
HIEC6 cells treated with BPS at IC01 for 24 h, biological replicate 3


title: HIEC6 cells, BPS replicate 2

description:
Library name: HIEC6_BPS_2
HIEC6 cells treated with BPS at IC01 for 24 h, biological replicate 2


title: CART19_Rep2

description: Library name: HTS114_44_H2_CART19_Rep2_S44


title: patient237

description: Brain tumor patient


title: patient229

description: Brain tumor patient

value: VII


title: HIEC6 cells, BPS replicate 1

description:
Library name: HIEC6_BPS_1
HIEC6 cells treated with BPS at IC01 for 24 h, biological replicate 1


title: CART19_Rep1

description: Library name: HTS114_43_H1_CART19_Rep1_S43


title: HIEC6 cells, BPA replicate 3

description:
Library name: HIEC6_BPA_3
HIEC6 cells treated with BPA at IC01 for 24 h, biological replicate 3


title: patient228

description: Brain tumor patient


title: HIEC6 cells, BPA replicate 2

description:
Library name: HIEC6_BPA_2
HIEC6 cells treated with BPA at IC01 for 24 h, biological replicate 2


title: CART22_IL10_Rep3

description: Library name: HTS114_42_G6_CART22_IL10_Rep3_S42

value: with IL10


title: HIEC6 cells, BPA replicate 1

description:
Library name: HIEC6_BPA_1
HIEC6 cells treated with BPA at IC01 for 24 h, biological replicate 1


title: HIEC6 cells, DINCH replicate 3

description:
Library name: HIEC6_DINCH_3
HIEC6 cells treated with DINCH at IC01 for 24 h, biological replicate 3


title: patient227

description: Brain tumor patient

value: VI


title: HL7702 cells, NiCl2 replicate 2

description:
Library name: HL7702_NiCl2_2
HL7702 cells treated with NiCl2 at IC01 for 24 h, biological replicate 2

value: normal human hepatic epithelium


title: CART22_IL10_Rep2

description: Library name: HTS114_41_G5_CART22_IL10_Rep2_S41


title: PA_3-IAA_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

institute: JILIN UNIVERSITY

description: Library name: B3

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

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, AlCl3 replicate 3

description:
Library name: HIEC6_AlCl3_3
HIEC6 cells treated with AlCl3 at IC01 for 24 h, biological replicate 3

value: WT


title: patient226

description: Brain tumor patient


title: HIEC6 cells, DBP replicate 2

description:
Library name: HIEC6_DBP_2
HIEC6 cells treated with DBP at IC01 for 24 h, biological replicate 2


title: CART19_Rep3

description: Library name: HTS114_45_H3_CART19_Rep3_S45


title: CART22_IL10_Rep1

description: Library name: HTS114_40_G4_CART22_IL10_Rep1_S40


title: PA_3-IAA_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: B2


title: CART19_IL10_Rep3

description: Library name: HTS114_39_G3_CART19_IL10_Rep3_S39


title: patient246

description: Brain tumor patient


title: PA_3-IAA_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: B1


title: patient225

description: Brain tumor patient

value: High

value: II