title: CD4+ CD25hi Tregs Gene Expression (oVAT)

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: Library name: ERa-Tregs_GEX

data_processing:
Demultiplexing, barcode processing, gene, HTO and VDJ-TCR counting was done with Cellranger 9.0.1 into a single set of files.
Assembly: mm10, refdata-gex-mm10-2020-A, refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: Tab separated values and matrix files, and comma delimited TCR abundance estimation file with annotation as well as read and umi counts.

source_name: oVAT

extract_protocol:
oVAT tissues were isolated. FACS sorted Tregs were pooled and loaded into a 10X Genomics Chromium Controller system in conjunction with the Chromium NextGEM Single Cell 5’ Library and Gel Beads v2 kit.
After subsequent reverse transcription, cDNA libraries were generated for gene expression, TCR sequences, and feature barcodes.

value: oVAT

value: CD4+ CD25hi Tregs

value: mixed sample Era+/+ or Era-/-

value: mixed sample NCD/HFD

tag: library type

value: mRNA


title: PC9/cDDPr rep1

status: Public on Feb 13 2026

type: SRA

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

country: China

institute: China Pharmaceutical University

description:
Library name: Sample 11
PC9_DDPR1
PC9_counts.xlsx

library_source: transcriptomic

data_processing:
Raw transcriptome sequencing data were first subjected to quality control using FastQC and summarized with MultiQC. Low-quality bases and residual adapter sequences were then removed using TrimGalore (https://github.com/FelixKrueger/TrimGalore). The cleaned reads were aligned to the human reference genome (GRCh38, Ensembl release) using Hisat2. Gene-level read counts were quantified with FeatureCounts. Differential expression analysis was performed using DESeq2. Genes with an absolute log2 fold change (|log2FC|) > 1 and a p-value < 0.05 were considered significantly differentially expressed.
Assembly: GRCh38
Supplementary files format and content: Excel (.xlsx) files containing processed gene expression count matrices. Each file includes genes in rows and samples in columns. Values represent raw counts per gene.

molecule: total RNA

organism: Homo sapiens

source_name: lung

growth_protocol: All cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. To maintain the resistant phenotype, H226/cDDPr, H460/cDDPr and PC9/cDDPr cells were routinely cultured with 1 µM, 0.83 µM and 6.6 µM cisplatin, respectively. Cells were switched to drug free medium for one week prior to experiments. All cultures were maintained at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cells at 70–80% confluence using TRIzol reagent according to the manufacturer’s instructions.
Libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform.

tag: tissue

value: lung

tag: cell line

tag: cell type

value: Non-Small Cell Lung Cancer

tag: treatment

value: cisplatin-resistant


title: CD4+ CD25hi Tregs Surface Protein (oVAT)

country: USA

description: Library name: ERa-Tregs_CITE

library_source: other

data_processing:
Demultiplexing, barcode processing, gene, HTO and VDJ-TCR counting was done with Cellranger 9.0.1 into a single set of files.
Assembly: mm10, refdata-gex-mm10-2020-A, refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: Tab separated values and matrix files, and comma delimited TCR abundance estimation file with annotation as well as read and umi counts.
Library strategy: CITE-seq

molecule: protein

organism: Mus musculus

tag: genotype

value: HTO


title: CD4+ CD25hi Tregs TCR (oVAT)

description: Library name: ERa-Tregs_VDJ

data_processing:
Demultiplexing, barcode processing, gene, HTO and VDJ-TCR counting was done with Cellranger 9.0.1 into a single set of files.
Assembly: mm10, refdata-gex-mm10-2020-A, refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: Tab separated values and matrix files, and comma delimited TCR abundance estimation file with annotation as well as read and umi counts.
Library strategy: TCR-Seq

molecule: polyA RNA

value: TCR


title: T4

city: Zhengzhou City

first: Yang

last: Bai

state: Henan Province

address: 1 Jianshe Dong Road, Erqi District, Zhengzhou City, Henan Pr

institute: Zhengzhou University

description:
Library name: I/R4
T4

data_processing:
Data quality control of raw data with fastp software; Removal of primers and adapter sequences (Adaptor)
Remove sequences with fragment length < 50 bp;
Remove N bases to a certain percentage of reads (default is set to 5 bp)
Removal of low-quality bases with mass values less than 20;
Calculate the base average mass value with a 4 base window, and excise it if the base average mass value is less than 20
Assembly: mm10

source_name: kidney

growth_protocol: After detissue, store in liquid nitrogen

extract_protocol:
Trizol (Invitrogen) method was used to extract total RNA from tissues
Trizol (Invitrogen) method was used to extract total RNA from tissues

treatment_protocol: We randomly assigned C57BL/6N mice to sham-operated (Sham, n=6) or I/R (n=6) groups. The I/R group received pentobarbital sodium anesthesia followed by renal pedicle occlusion. After 60 minutes of ischemia, we restored blood flow for 6h reperfusion before euthanasia and sample collection

value: kidney

value: WT

value: I/R


title: H460/cDDPr rep2

description:
Library name: Sample 8
H460_DDPR2
H460_counts.xlsx


title: FK3

city: Bad Nauheim

first: Pieterjan

last: Dierickx

state: Hessen

address: Parkstrasse 1

department: Circadian Regulation of Cardiometabolism

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: Library name: FK3

data_processing:
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Besides one global GFM index, HISAT2 also includes a large set of small GFM indexes that collectively cover the whole genome. These small indexes (local indexes), combined with multiple alignment strategies, enabled effective alignment of RNA-seq reads, particularly, reads spanning multiple exons.
The abundance of transcripts reflects gene expression level directly. In RNA-seq experiments, gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon(Goldstein et al., 2016). Read counts is proportional to gene expression level, gene length and sequencing depth(Liao et al., 2014). FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)(Trapnell, Cole, et al., 2010) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al., 2008).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

source_name: Heart

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.
RNA sequencing via Illumina platforms, based on the mechanism of SBS (sequencing by synthesis), offers a wide range of benefits on high throughput and high accuracy out of low sample requirements. This technical method can be a powerful tool for researching RNA transcriptional activity.

value: Heart

value: Cardiomyocyte


title: T2

description:
Library name: I/R2
T2


title: PC9/Nor rep1

description:
Library name: Sample 9
PC9_NR1
PC9_counts.xlsx


title: H460/cDDPr rep1

description:
Library name: Sample 7
H460_DDPR1
H460_counts.xlsx


title: C5

description:
Library name: sham5
C5

value: Sham


title: C3

description:
Library name: sham3
C3


title: H460/Nor rep1

description:
Library name: Sample 5
H460_NR1
H460_counts.xlsx


title: H460/Nor rep2

description:
Library name: Sample 6
H460_NR2
H460_counts.xlsx


title: C2

description:
Library name: sham2
C2


title: C1

description:
Library name: sham1
C1


title: T1

description:
Library name: I/R1
T1


title: C4

description:
Library name: sham4
C4


title: H226/cDDPr rep1

description:
Library name: Sample 3
H226N-CDDP1
H226_counts.xlsx


title: H226/Nor rep2

description:
Library name: Sample 2
H226N2
H226_counts.xlsx


title: hFOB cells, Day 10, replicate 4

city: Toronto

first: John

middle: A

last: Morris

state: Ontario

address: 160 College Street

department: Donnelly Centre for Cellular and Biomolecular Research

country: Canada

institute: University of Toronto

description:
Library name: 16_day10D
hFOB_day10_peaks.hg38.narrowPeak

library_source: genomic

data_processing:
Sequencing reads were aligned to the hg38 reference genome using Bowtie2.
Consensus peaks for a given day of osteogenic differentiation were called using Genrich (github.com/jsh58/Genrich).
Assembly: hg38
Supplementary files format and content: NarrowPeak files containing consensus ATAC-seq peak coordinates (hg38) for replicates from a given day of osteogenic differentiation.Columns include: chromosome, start coordinate, end coordinate, peak identifier, score (0–1000), strand, signal value, −log10(p-value), −log10(q-value), and distance from the start coordinate to the peak summit.

molecule: genomic DNA

source_name: hFOB 1.19

growth_protocol: hFOB 1.19 cells (ATCC #CRL-11372) were cultured at 34°C in minimal essential media (MEM; Gibco #10370‐021) supplemented with 10% fetal bovine serum (FBS; Atlantic Biologicals #S12450), 1% Glutamax (Gibco #35050‐061), and 1% Pen Strep (Gibco #15140‐122), following ATCC recommendations.

extract_protocol:
Nuclei were isolated from ~100,000 undifferentiated or osteoblast-differentiated hFOB 1.19 cells following cell detachment using sequential collagenase and trypsin treatment.
ATAC-seq libraries were constructed using the Active Motif ATAC-seq kit (Active Motif #53150) according to the manufacturer’s protocol.

treatment_protocol: Osteogenic differentiation was induced (Day 0) by culturing hFOB 1.19 cells at 39.5°C in MEM alpha (Gibco #12571‐063) supplemented with 10% FBS, 1% Glutamax, 1% Pen Strep, 50 μg/μL Ascorbic Acid (Sigma‐Aldrich #A4544‐25G), 10mM beta‐Glycerophosphate (Sigma‐Aldrich #G9422‐100G), and 10nM Dexamethasone (Sigma‐Aldrich #D4902‐25MG).

value: hFOB 1.19

value: human fetal osteoblasts

tag: time

value: Day 10

value: osteogenic differentiation

tag: replicate


title: Retinal vascular cells isolated from P6 Tspan12 KO mice.

city: Chengdu

first: Shujin

last: Li

state: Sichuan

address: Chengdu, Sichuan province, China, first-ring road, No.34

institute: Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences

description: Library name: P6 Tspan12 KO

library_source: transcriptomic single cell

data_processing:
Under sterile conditions, the freshly collected retinas were washed twice with pre-cooled RPMI 1640 medium containing 0.04% BSA. The tissues were then mechanically dissociated into approximately 0.5 mm³ fragments using surgical scissors and transferred into freshly prepared enzymatic digestion solution. The digestion mixture contained RPMI 1640 (Conring, cat.no. 10-040-CVR), 0.04% BSA (MACS, cat.no. 1000076), and 0.2% collagenase II (Gibco, cat.no. 17101015). The samples were incubated at 37°C for 30-60 minutes with gentle inversion every 5-10 minutes. The digested cell suspension was filtered through a BD 40 μm cell strainer (Falcon, cat.no. 352340) 1-2 times. The filtrate was centrifuged at 300 × g for 5 minutes at 4°C. The cell pellet was resuspended in appropriate medium, mixed with an equal volume of red blood cell lysis buffer (Miltenyi, cat.no. 130-094-183), and incubated at 4°C for 10 minutes. After centrifugation at 300 × g for 5 minutes, the supernatant was discarded. The pellet was washed once with medium followed by another centrifugation at 300 × g for 5 minutes, and the final supernatant was removed. CD31+/CD11b vascular cells were enriched using Mouse CD31 MicroBeads (Miltenyi) and mouse CD11b MicroBeads (Miltenyi） accordding to the manufacturer’s protocol. Finally，the cells were re-suspended with 1ml RPMI 1640 medium (Conring, cat.no.10-040-CVR) with 0.04% BSA added. Single-cell suspension concentration and cell viability were then evaluated by Luna-FL cell counter (Logos Biosystems，Korea) or Trypan Blue staining method.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: retinal

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: retinal

tag: age

value: vascular cells

value: Tspan12 KO


title: H226/cDDPr rep2

description:
Library name: Sample 4
H226N-CDDP2
H226_counts.xlsx

value: lung

value: Non-Small Cell Lung Cancer


title: hFOB cells, Day 10, replicate 3

description:
Library name: 15_day10C
hFOB_day10_peaks.hg38.narrowPeak


title: Retinal vascular cells isolated from P6 mice with EC-specific deletion of Ctnnb1, driven by the Pdgfb-iCreERT.

description: Library name: P6 Ctnnb1 cKO


title: H226/Nor rep1

description:
Library name: Sample 1
H226N1
H226_counts.xlsx


title: RT, 3

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

country: Japan

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

description: Library name: Sample 7

data_processing:
Adapter sequences and low-quality bases at read ends were removed using Trimmomatic (version 0.38).
Trimmed reads were aligned to the GRCh38 reference genome with HISAT2 (version 2.1.0).
Transcripts were assembled using StringTie (version 2.1.3b). After assembly, the abundance of gene/transcript is calculated in the read count and normalized values as TPM (Transcripts Per Kilobase Million) for a sample.
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: palatine tonsils

extract_protocol:
Total RNA was extracted from sorted IF-Tfh cells with TRIzol reagent (Thermo Fisher Scientific).
RNA sequencing libraries were generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: Single-cell suspensions were generated from tonsillar tissues by passing cells through a 70-µm cell strainer (Corning), followed by density-gradient centrifugation with Lympholyte-H cell separation reagent (Cedarlane). Cells were stained on ice for 1 hour with fluorochrome-conjugated monoclonal antibodies diluted in FACS buffer (PBS containing 0.5% bovine serum albumin and 2 mM EDTA). After washing, cells were sorted on a FACS Aria III (BD Biosciences).

value: palatine tonsils


title: pool1_ADT

city: Portland

first: Timothy

middle: J

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

description:
Library name: pool1_ADT
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

data_processing:
cellranger v7.0.0 used to count and map reads and assign to cells.
Assembly: mm10-2020-A cellranger referenc3
Supplementary files format and content: filtered feature matrix output from cellranger in HDF5 file format.
Supplementary files format and content: Feature barcode matrix used as input for cellranger to assign ADT and HTO reads.
Library strategy: CITE-seq

source_name: Small intestine

extract_protocol:
Epithelial fractions were isolated from mouse small intestine and cells were stained with fluorescent antibodies followed by enrichment of CD45-positive cells with magnetic microbeads. MIxed myeloid cells were isolated based on lack of CD3 stain and presence of CD11b and/or CD11c antibody stains. In addition to fluorescent antibodies used for FACS, cells were stained with antibody-derived tags (ADT) and  cells from each mouse were stained with a different hashtag oligonucleotide (HTO).
Library was constructed using 10x genomics single cell 3' v3  reagents according to manufacturers protocol

value: Small intestine

value: Myeloid

tag: strain

value: C57BL/6J WT

value: ADT

tag: hto

value: TotalSeq-A0568 anti-mouse/rat XCR1, TotalSeq-A0014 anti-mouse/human CD11b, TotalSeq-A0103 anti-mouse/human CD45R/B220, TotalSeq-A0849 anti-mouse CD80, TotalSeq-A0002 anti-mouse CD8a, TotalSeq-A0013 anti-mouse Ly-6C, TotalSeq-A0015 anti-mouse Ly-6G, TotalSeq-A0093 anti-mouse CD19, TotalSeq-A0098 anti-mouse CD135, TotalSeq-A0105 anti-mouse CD115, TotalSeq-A0106 anti-mouse CD11c, TotalSeq-A0117 anti-mouse I-A/I-E, TotalSeq-A0200 anti-mouse CD86, TotalSeq-A0201 anti-mouse CD103, TotalSeq-A0212 anti-mouse CD24, TotalSeq-A0422 anti-mouse CD172a, TotalSeq-A0563 anti-mouse CX3CR1, TotalSeq-A0811 anti-mouse CD317, TotalSeq-A0903 anti-mouse CD40, TotalSeq-A0981 anti-mouse TCR Vα2, TotalSeq-A1010 anti-mouse CD205


title: RT, 4

description: Library name: Sample 8


title: hFOB cells, Day 4, replicate 3

description:
Library name: 11_day4C
hFOB_day4_peaks.hg38.narrowPeak

value: WT

value: Day 4


title: hFOB cells, Day 10, replicate 2

description:
Library name: 14_day10B
hFOB_day10_peaks.hg38.narrowPeak

value: hFOB 1.19


title: Retinal vascular cells isolated from P6 WT mice.

description: Library name: P6 WT


title: hFOB cells, Day 4, replicate 1

description:
Library name: 9_day4A
hFOB_day4_peaks.hg38.narrowPeak

value: human fetal osteoblasts


title: hFOB cells, Day 10, replicate 1

description:
Library name: 13_day10A
hFOB_day10_peaks.hg38.narrowPeak

value: Day 10


title: pool1_HTO

description:
Library name: pool1_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: HTO

value: TotalSeq-A0301 anti-mouse hashtag 1 (Male1), TotalSeq-A0302 anti-mouse hashtag 2 (Female1), TotalSeq-A0303 anti-mouse hashtag 3 (Male2), TotalSeq-A0304 anti-mouse hashtag 4 (Female2), TotalSeq-A0305 anti-mouse hashtag 5 (Male3), TotalSeq-A0306 anti-mouse hashtag 6 (Female3), TotalSeq-A0307 anti-mouse hashtag 7 (Male4), TotalSeq-A0308 anti-mouse hashtag 8 (Female8)


title: hFOB cells, Day 4, replicate 2

description:
Library name: 10_day4B
hFOB_day4_peaks.hg38.narrowPeak

value: osteogenic differentiation


title: pool1_GEX

description:
Library name: pool1_GEX
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript sequence

data_processing:
cellranger v7.0.0 used to count and map reads and assign to cells.
Assembly: mm10-2020-A cellranger referenc3
Supplementary files format and content: filtered feature matrix output from cellranger in HDF5 file format.
Supplementary files format and content: Feature barcode matrix used as input for cellranger to assign ADT and HTO reads.

value: mRNA


title: hFOB cells, Day 2, replicate 4

description:
Library name: 8_day2D
hFOB_day2_peaks.hg38.narrowPeak

value: Day 2


title: hFOB cells, Day 2, replicate 2

description:
Library name: 6_day2B
hFOB_day2_peaks.hg38.narrowPeak


title: RT, 1

description: Library name: Sample 5


title: RT, 2

description: Library name: Sample 6


title: hFOB cells, Day 4, replicate 4

description:
Library name: 12_day4D
hFOB_day4_peaks.hg38.narrowPeak


title: hFOB cells, Day 2, replicate 3

description:
Library name: 7_day2C
hFOB_day2_peaks.hg38.narrowPeak


title: Spleen_4

description: Library name: Spleen_4

data_processing:
Sequencing data was processed using the NextFlow NF-Core ATAC-Seq pipeline
Assembly: mm10
Supplementary files format and content: bigWig files for each sample

source_name: Spleen

extract_protocol:
Epithelial fractions were isolated from mouse small intestine and splenocytes were isolated from spleens. Cells were stained with fluorescent antibodies followed by enrichment of CD45-positive cells with magnetic microbeads. Plasmacytoid dendritic cells (pDC) were sorted from live CD45-positive cells based on lack of staining for CD3 or CD11b and expression of CD11c, Ly6C, and Siglech.
Sorted cells were fixed and preparted as ATACseq libraries using a kit from Active Motif (cat #53151).

value: Spleen

value: pDC

value: ATAC


title: IgAN, 4

description: Library name: Sample 4

value: palatine tonsils


title: hFOB cells, Day 2, replicate 1

description:
Library name: 5_day2A
hFOB_day2_peaks.hg38.narrowPeak


title: hFOB cells, Day 0, replicate 4

description:
Library name: 4_day0D
hFOB_day0_peaks.hg38.narrowPeak

value: Day 0


title: IgAN, 3

description: Library name: Sample 3


title: Spleen_3

description: Library name: Spleen_3

value: C57BL/6J WT


title: hFOB cells, Day 0, replicate 3

description:
Library name: 3_day0C
hFOB_day0_peaks.hg38.narrowPeak


title: hFOB cells, Day 0, replicate 1

description:
Library name: 1_day0A
hFOB_day0_peaks.hg38.narrowPeak


title: IgAN, 1

description: Library name: Sample 1


title: Spleen_2

description: Library name: Spleen_2


title: Spleen_1

description: Library name: Spleen_1


title: Isogenic control iPS-derived endothelial cell rep2

city: Cambridge

first: Tatsuya

last: Osaki

state: MA

address: 43 Vassar street, 46-6227

department: Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

description:
Library name: mRNA-microRNA-iEC-WT-2
Colume name in raw_counts_all_samples.csv: WT-EC-Rep2

data_processing:
Fastq files were combined and aligned with STAR 2.0.4b Gene counts derived with Subread:featureCount 1.45. RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: GRCh37/hg19
Supplementary files format and content: Raw counts matrix

growth_protocol: Genome-edited iPS cells (ETV2-iPS cells), carrying either MECP2[R306C] or MECP2[R168X] mutations were plated onto Matrigel-coated 6-well plates and cultured until the cells reached 70%–80% confluence. At day 0, the cells were treated with 1 ml of Accutase and incubated for 4 min, then 1 mL of mTeSR plus was added for neuralization. Collected cells were further dissociated by pipetting up and down 10 times with a 1 ml pipette tip to obtain single cells. Then, the cells were re-plated to Matrigel-coated 6-well plates at 250,000–350,000 cells/well in mTeSR plus medium and 10 μM Y-23632. The next day, the culture medium was replaced with mesoderm differentiation medium (DMEM/F12 supplemented with 1% GlutaMAX, 60 µg/ml of L-ascorbic acid, 6 µM of CHIR99021(GSK3 Inhibitor/WNT Activator, STEMCELL Technologies)) and cultured for 2 days with a daily medium change. Then, the culture medium was replaced with endothelial differentiation medium (DMEM/F12 supplemented with 1% GlutaMAX, 60 µg/ml of L-ascorbic acid, 50 ng/ml of VEGF-A, 50 ng/mL of bFGF2, 10 ng/mL of EGF, and 10 µM of SB431542 (Activin/BMP/TGF-beta inhibitor, STEMCELL Technologies)) and 3 µg/ml of DOX. The next day, the medium was changed to the same endothelial differentiation medium but without DOX. At day 5, differentiated iECs were seeded to a T150 culture flask for expansion using a Vasculife VEGF Endothelial Medium Complete Kit (Lifeline cell technology, LL-0003) supplemented with 10% fetal bovine serum (FBS) and 10 µM of SB431542.

extract_protocol:
Total RNA was isolated from the cells from 2D culture using RNAeasy Mini Kit (Qiagen) following manufacture protocol.
NA libraries for RNA sequencing were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin library prep kit according to the manufacturer’s instructions.

tag: Sex

value: Female

value: Endothelial cells

value: biol rep2


title: Isogenic control iPS-derived endothelial cell rep1

description:
Library name: mRNA-microRNA-iEC-WT-1
Colume name in raw_counts_all_samples.csv: WT-EC-Rep1

value: WT

value: biol rep1


title: Rett syndrome iPS-derived endothelial cell rep1

description:
Library name: mRNA-microRNA-iEC-RTT-1
Colume name in raw_counts_all_samples.csv: RTT-EC-Rep1


title: Gut_4

description: Library name: Gut_4

value: Small intestine


title: IgAN, 2

description: Library name: Sample 2


title: LPS_1ug_per_mL_PM_Neuts_027

city: La Jolla

first: Sonia

last: Sharma

state: CA

address: 9420 Athena Cir

department: Center for Autoimmunity and Inflammation

institute: La Jolla Institute of Immunology

description:
Library name: PM_Neuts_027
LPS_1ug_per_mL

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2 (-S --fr)
Filtered reads were mapped against the human GRCh38 reference using STAR(v 2.6.1c )
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ-lite v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5)  and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: count matrix with rows as genes and columns as samples

source_name: Human primary neutrophils

extract_protocol:
Total RNA was extracted from 1.5 million cells using Direct-zol RNA Miniprep Kit (Zymo Research). Libraries were prepared using the NEB Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module (supplier info). 20 ng total RNA was used for each sample and libraries underwent 16 cycles of PCR amplification. Agilent Universal Human Reference RNA was prepared as a process control. Libraries were sequenced on the Novaseq 6000 using a 50x50 run configuration at a targeted depth of 25M (50M paired-end) reads.
RNA-seq 50 x 50 Paired-end sequencing reads

treatment_protocol: Cells were seeded in deep-well 96-well plates at a density of 2 × 10⁶ cell in 1ml  of FBS-free RPMI media, with or without test compounds (LPC 16:0 or LPC 18:2 at 10uM), and incubated at 37°C for 2 hours.

value: Human primary neutrophils


title: hFOB cells, Day 0, replicate 2

description:
Library name: 2_day0B
hFOB_day0_peaks.hg38.narrowPeak

value: hFOB 1.19

value: human fetal osteoblasts


title: BMD STING-seq pilot GDO 2

description: Library name: Pilot-GDO-2

data_processing:
We generated UMI count matrices for all single-cell sequencing libraries using 10X Cell Ranger v8.0.1. We produced cDNA UMI count matrices aligned to hg38 (refdata-gex-GRCh38-2024-A), gRNA UMI count matrices, and hashtag UMI count matrices for the pilot and full experiments.
Assembly: hg38
Supplementary files format and content: UMI count matrices before quality control

molecule: other

source_name: Human fetal osteoblast 1.19, hFOB, expressing KRAB-dCas9-MeCP2

extract_protocol:
We performed single-cell RNA-seq using 10X Genomics Chromium Next GEM Single Cell 5′ Reagent Kits v2 (dual index) on cells detached from culture plates. We labeled cells from each state with different hashtag antibodies targeting cell surface proteins (BioLegend TotalSeq 394661, 394663, 394665, 394667) following the manufacturer’s recommendations. We then pooled equal numbers of cells from each state into a single sample and aliquoted them into as many reactions as needed to capture approximately 200,000 cells in total. We used 2 microfluidics channels for the pilot experiment and 6 channels for the full experiment.
We constructed sequencing libraries for the three different barcoded nucleic acids for each reaction according to 10X Genomics protocols and pooled them disproportionately so that mRNA-derived cDNA libraries represented ~90% of the sample, with gRNA and hashtag libraries comprising the remaining 10%. We sequenced the pooled library to a depth of approximately 20,000 mRNA/cDNA reads per cell on an Illumina NextSeq 500 sequencing platform for the pilot experiment and on an Illumina NovaSeq X for the full experiment.


title: LPS_1ug_per_mL_PM_Neuts_026

description:
Library name: PM_Neuts_026
LPS_1ug_per_mL


title: Rett syndrome iPS-derived endothelial cell rep2

description:
Library name: mRNA-microRNA-iEC-RTT-2
Colume name in raw_counts_all_samples.csv: RTT-EC-Rep2


title: Gut_3

description: Library name: Gut_3


title: BMD STING-seq pilot HTO 2

description: Library name: Pilot-HTO-2

data_processing:
We generated UMI count matrices for all single-cell sequencing libraries using 10X Cell Ranger v8.0.1. We produced cDNA UMI count matrices aligned to hg38 (refdata-gex-GRCh38-2024-A), gRNA UMI count matrices, and hashtag UMI count matrices for the pilot and full experiments.
Assembly: hg38
Supplementary files format and content: UMI count matrices before quality control
Library strategy: CITE-seq

value: Human fetal osteoblast 1.19, hFOB, expressing KRAB-dCas9-MeCP2


title: BMD STING-seq pilot cDNA 2

description: Library name: Pilot-cDNA-2


title: BMD STING-seq pilot HTO 1

description: Library name: Pilot-HTO-1


title: Gut_2

description: Library name: Gut_2


title: LPS_1ug_per_mL_PM_Neuts_025

description:
Library name: PM_Neuts_025
LPS_1ug_per_mL


title: BMD STING-seq pilot cDNA 1

description: Library name: Pilot-cDNA-1


title: Gut_1

description: Library name: Gut_1


title: 3mM_Stauro_PM_Neuts_024

description:
Library name: PM_Neuts_024
3mM_Stauro


title: SAM24489675

city: South San Francisco

first: Jackson

last: Liang

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

description: Library name: LIB6266424

data_processing:
MACS2 peak calling (ENCODE ChIP pipeline)
Assembly: GRCh38
Supplementary files format and content: narrowPeak
Supplementary files format and content: bigWig

source_name: T47D Parental

growth_protocol: Cells were cultured in in DMEM/F12 media + 10% FBS.

extract_protocol:
Cross linked DNA
Ovation Ultralow Library System V2 (ChIP-seq)

treatment_protocol: Cells were treated with 100nM giredestrant for specified times.

value: T47D Parental

value: Breast

tag: chip antibody

value: Input


title: BMD STING-seq pilot GDO 1

description: Library name: Pilot-GDO-1


title: SAM24489673

description: Library name: LIB6266422

source_name: MCF7 GiredR

value: MCF7 GiredR


title: 4dpi_RNA

city: Calgary

first: Arshad

last: Ayyaz

state: Alberta

address: BI238D, 507 Campus Dr nw

institute: University of Calgary

description:
Library name: A12_RNA
10x Genomics Multiome

data_processing:
All demultiplexing, barcode analysis, gene aggregation and counting were done using Cell Ranger version 2.1.1
Assembly: mm39
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Small Intestine

extract_protocol:
Small intestines were removed from mice and flushed with ice-cold PBS. Intestines were cut into 2mm pieces and washed with ice-cold PBS, and incuabted in 2mM EDTA solution for 40 minutes at 4℃ while on a shaker. Following whole intestinal fragments were shaken vigoursouly in ice-cold PBS to isolate epithelial segments. Solution was then enriched for crypts by passing liquid through a 70 µm strainer. 10X genomics Single Cell Multiome (ATAC + Gene Expression)
10X genomics Multiome ATAC + Gene Expression kit was used and manufactures instructions were followed

value: Small Intestine

value: 12Gy irridation (96hr)


title: 3mM_Stauro_PM_Neuts_022

description:
Library name: PM_Neuts_022
3mM_Stauro


title: 3mM_Stauro_PM_Neuts_023

description:
Library name: PM_Neuts_023
3mM_Stauro


title: SAM24489668

description: Library name: LIB6266417

source_name: T47D GiredR

value: T47D GiredR


title: SAM24489677

description: Library name: LIB6266426


title: LPC_16_0_10uM_PM_Neuts_021

description:
Library name: PM_Neuts_021
LPC_16_0_10uM


title: SAM24489667

description: Library name: LIB6266416


title: 1dpi_ATAC

description:
Library name: A10_ATAC
10x Genomics Multiome

library_source: genomic single cell

value: 12Gy irridation (24hr)


title: SAM24489663

description: Library name: LIB6266412


title: SAM24489664

description: Library name: LIB6266413


title: CKO3

city: Changsha

first: Mengdi

last: Zhang

state: Hunan

address: 139 Middle Renmin Road, Furong District

department: National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology

institute: The Second Xiangya Hospital of Central South University

description: Library name: SAMPLE6

data_processing:
Raw sequencing reads were first processed using fastp (https://github.com/OpenGene/fastp) with default parameters to remove adapter sequences, low-quality bases, and undetermined bases. Sequence quality was assessed using fastp-generated quality control reports.
Clean reads were then aligned to the Mus musculus reference genome GRCm38 using HISAT2 (https://ccb.jhu.edu/software/hisat2), applying default alignment parameters. The resulting mapped reads for each sample were assembled into transcripts using StringTie(https://ccb.jhu.edu/software/stringtie). Subsequently, transcript assemblies from all samples were merged into a unified transcriptome annotation using gffcompare (https://github.com/gpertea/gffcompare/).
Following transcriptome reconstruction, StringTie was used to estimate transcript abundance and calculate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for each gene. Differentially expressed mRNAs were identified using the edgeR package (https://bioconductor.org/packages/release/bioc/html/edgeR.html) in R. Genes with a fold change > 2 or < 0.5 and a p-value < 0.05 based on a parametric F-test comparing nested linear models were considered significantly differentially expressed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw read counts per gene for each sample (gene_count_matrix.txt)
Supplementary files format and content: tab-delimited text file contains FPKM values per gene for each sample (1_genes_fpkm_expression.txt)

source_name: Thymus

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Thymus

value: Thymocytes

value: USP10 knockout


title: CKO4

description: Library name: SAMPLE7


title: SAM24489671

description: Library name: LIB6266420

source_name: MCF7 Parental

value: MCF7 Parental


title: LPC_16_0_10uM_PM_Neuts_020

description:
Library name: PM_Neuts_020
LPC_16_0_10uM


title: SAM24489660

description: Library name: LIB6266409


title: LPC_16_0_10uM_PM_Neuts_019

description:
Library name: PM_Neuts_019
LPC_16_0_10uM


title: CKO2

description: Library name: SAMPLE5


title: SAM24489655

description: Library name: LIB6266404


title: SAM24489659

description: Library name: LIB6266408


title: CKO1

description: Library name: SAMPLE4


title: LPC_16_0_1uM_PM_Neuts_018

description:
Library name: PM_Neuts_018
LPC_16_0_1uM


title: SAM24489652

description: Library name: LIB6266401


title: 4dpi_ATAC

description:
Library name: A12_ATAC
10x Genomics Multiome


title: SAM24489656

description: Library name: LIB6266405


title: SAM24489648

description: Library name: LIB6266397


title: LPC_16_0_1uM_PM_Neuts_017

description:
Library name: PM_Neuts_017
LPC_16_0_1uM


title: LPC_16_0_1uM_PM_Neuts_016

description:
Library name: PM_Neuts_016
LPC_16_0_1uM


title: WT2

description: Library name: SAMPLE2

value: wild type


title: SAM24489644

description: Library name: LIB6266393


title: LPC_18_0_10uM_PM_Neuts_015

description:
Library name: PM_Neuts_015
LPC_18_0_10uM

value: Human primary neutrophils


title: WT1

description: Library name: SAMPLE1


title: SAM24489640

description: Library name: LIB6266389


title: WT3

description: Library name: SAMPLE3


title: LPC_18_0_10uM_PM_Neuts_014

description:
Library name: PM_Neuts_014
LPC_18_0_10uM


title: SAM24489647

description: Library name: LIB6266396


title: LPC_18_0_10uM_PM_Neuts_013

description:
Library name: PM_Neuts_013
LPC_18_0_10uM


title: ACLF_84h_4

city: Shanghai

first: Yun

last: Song

address: 1111 Xianxia Road, Shanghai 200336, China

institute: shanghai jiao tong university

description: Library name: Sample76

data_processing:
RNA-seq
Assembly: hg19/mm10
Supplementary files format and content: tab-delimited text fles include raw count values for each Sample

source_name: liver

extract_protocol:
RNA was hanested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing librares.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit folowing manufacturer's protocols.

value: liver


title: SAM24489651

description: Library name: LIB6266400


title: SAM24489639

description: Library name: LIB6266388


title: SAM24489643

description: Library name: LIB6266392


title: ACLF_84h_3

description: Library name: Sample75


title: Lung adenocarcinoma, adjacent non-tumor tissues, patients#1

first: Bo

last: Zeng

address: No.4, Section 2, North Jianshe Road, Chengdu

department: school of medicine

institute: University of Electronic Science and Technology of China

description:
Library name: LN_1
10 x Genomics

data_processing:
preprocessing of scRNA-seq data, integration, dimensionality reduction and clustering were performed by Capital Bio-Tech (Beijing, China)
Assembly: Homo sapiens
Supplementary files format and content: .fastq

source_name: adjacent non-tumor tissue

extract_protocol:
Tissues were rinsed with ice-cold PBS three times to remove blood clots and then minced on ice. The tissue block was incubated with a digestion solution made of 0.25% trypsin and 10 µg/mL DNase I, at 37°C with a shaking speed of 50 rpm or 30 min. Cell suspensions were filtered using a 70-μm cell strainer and then through a 40-μm strainer again, and the filtrate was collected into a new centrifuge tube. The cell pellet was resuspended in 3 ml of red blood cell lysis solution and incubated on ice for 5 min. Then, 10 ml of precooled PBS was added and centrifuged at 250 × g for 5 min. The cell pellet was resuspended in PBS containing 0.5% FBS. Cells were stained with 0.4% AO/PI to evaluate cell viability.
10 × Genomics single-cell capture, Illumina library construction were performed by Capital Bio-Tech (Beijing, China).

value: para-tumor normal tissue

tag: tumor stage

value: male

value: untreated


title: Lung adenocarcinoma, tumor tissues, patients#1

description:
Library name: LT_1
10 x Genomics

source_name: tumor tissue

value: tumor


title: LPC_18_0_1uM_PM_Neuts_012

description:
Library name: PM_Neuts_012
LPC_18_0_1uM


title: Lung adenocarcinoma, adjacent non-tumor tissues, patients#2

description:
Library name: LN_2
10 x Genomics

value: female


title: LPC_18_0_1uM_PM_Neuts_011

description:
Library name: PM_Neuts_011
LPC_18_0_1uM


title: ACLF_84h_1

description: Library name: Sample73


title: ACLF_84h_2

description: Library name: Sample74


title: SAM24456533

description: Library name: LIB6236573

data_processing:
MACS2 peak calling (ENCODE ATAC pipeline)
Assembly: GRCh38
Supplementary files format and content: narrowPeak

extract_protocol:
Performed as described in Corces, et al. 'Omni-ATAC-seq: Improved ATAC-seq'. (2017)
ATAC-seq

value: Breast

value: Untreated


title: SAM24456532

description: Library name: LIB6236572


title: LPC_18_0_1uM_PM_Neuts_010

description:
Library name: PM_Neuts_010
LPC_18_0_1uM


title: SAM24456530

description: Library name: LIB6236570


title: ACLF_72h_5

description: Library name: Sample72


title: SAM24456531

description: Library name: LIB6236571


title: ACLF_72h_4

description: Library name: Sample71


title: LPC_18_2_10uM_PM_Neuts_009

description:
Library name: PM_Neuts_009
LPC_18_2_10uM


title: Lung adenocarcinoma, tumor tissues, patients#2

description:
Library name: LT_2
10 x Genomics


title: SAM24456534

description: Library name: LIB6236574


title: ACLF_72h_3

description: Library name: Sample70


title: SAM24456528

description: Library name: LIB6236568

value: 4 months, 100nM giredestrant


title: SAM24456526

description: Library name: LIB6236566


title: LPC_18_2_10uM_PM_Neuts_008

description:
Library name: PM_Neuts_008
LPC_18_2_10uM


title: SAM24456527

description: Library name: LIB6236567


title: LPC_18_2_10uM_PM_Neuts_007

description:
Library name: PM_Neuts_007
LPC_18_2_10uM


title: SAM24456524

description: Library name: LIB6236564

value: 2 months, 100nM giredestrant


title: SAM24456525

description: Library name: LIB6236565


title: SAM24456523

description: Library name: LIB6236563


title: ACLF_72h_2

description: Library name: Sample69


title: SAM24456529

description: Library name: LIB6236569


title: LPC_18_2_1uM_PM_Neuts_006

description:
Library name: PM_Neuts_006
LPC_18_2_1uM


title: ACLF_72h_1

description: Library name: Sample68


title: LPC_18_2_1uM_PM_Neuts_005

description:
Library name: PM_Neuts_005
LPC_18_2_1uM


title: SAM24456520

description: Library name: LIB6236560


title: ACLF_60h_5

description: Library name: Sample67


title: LPC_18_2_1uM_PM_Neuts_004

description:
Library name: PM_Neuts_004
LPC_18_2_1uM


title: SAM24456518

description: Library name: LIB6236558


title: SAM24456521

description: Library name: LIB6236561


title: SAM24456517

description: Library name: LIB6236557


title: ACLF_60h_4

description: Library name: Sample66


title: Unstim_PM_Neuts_003

description:
Library name: PM_Neuts_003
Unstim


title: V9

city: Valencia

first: Patricia

last: Diaz-Gimeno

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

country: Spain

institute: IIS La Fe / IVIRMA Global Research Alliance

description: Library name: V9_run3

data_processing:
Raw data were evaluated using FastQC. STAR was employed to align high-quality data using GRCh37/hg19 as a reference. Gene counts obtained using featureCounts.
Assembly: GRCh37/hg19
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Endometrium

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Samples were sequenced using the AmpliSeq for Illumina® Transcriptome Human Gene Expression Panel23 in a NextSeq 500/550 system.

value: Endometrium

tag: batch


title: SAM24456522

description: Library name: LIB6236562


title: SAM24456519

description: Library name: LIB6236559


title: V72

description: Library name: V72_run4


title: V71

description: Library name: V71_run4


title: Unstim_PM_Neuts_002

description:
Library name: PM_Neuts_002
Unstim


title: Unstim_PM_Neuts_001

description:
Library name: PM_Neuts_001
Unstim


title: V7

description: Library name: V7_run4


title: ACLF_60h_1

description: Library name: Sample63


title: V68

description: Library name: V68_run2


title: ACLF_60h_3

description: Library name: Sample65


title: V67

description: Library name: V67_run4


title: SUM149_SphC

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

description:
Library name: SUM149_Sphere
10x Genomics

data_processing:
Data analysis was processed using the 10x Genomics cellranger pipeline (v4.0.0) to demultiplex reads and then align reads to hg38 reference (Refdata-gex-GRCh38-2020-A) and to generate a single cell barcode and gene expression matrix that was used for downstream analysis.
Assembly: human hg38
Supplementary files format and content: Tab separated valude file and count matrix files

growth_protocol: SUM149 and IBC-3 cells were cultured in 2D, "emboli" culture (EmC) or mammosphere culture (SphC) for 3 days.

extract_protocol:
RNA was extracted using GeneJET RNA purification kit (Thermo Scientific, #K0732)
10x Genomics Single Cell Chromium 3' Gene Expression Protocol

value: breast cancer cell

value: Inflammatory Breast Cancer


title: ACLF_48h_5

description: Library name: Sample62


title: V65

description: Library name: V65_run5


title: V70

description: Library name: V70_run4


title: ACLF_48h_4

description: Library name: Sample61


title: ACLF_60h_2

description: Library name: Sample64


title: V66

description: Library name: V66_run5


title: SUM149_EmC

description:
Library name: SUM149_Emboli
10x Genomics


title: V62

description: Library name: V62_run5


title: ACLF_48h_3

description: Library name: Sample60


title: V61

description: Library name: V61_run5


title: V64

description: Library name: V64_run4


title: ACLF_48h_2

description: Library name: Sample59


title: V63

description: Library name: V63_run2


title: SUM149_2D

description:
Library name: SUM149_2D
10x Genomics


title: IBC3_EmC

description:
Library name: IBC_Emboli
10x Genomics


title: IBC3_SphC

description:
Library name: IBC_Sphere
10x Genomics


title: IBC3_2D

description:
Library name: IBC_2D
10x Genomics


title: V56

description: Library name: V56_run0


title: V59

description: Library name: V59_run3


title: Fibrosis_4

description: Library name: Sample57


title: ACLF_48h_1

description: Library name: Sample58


title: BW092-001T0036, H9WAO9, IL-4+IL-13

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

description: Library name: Sample24

data_processing:
Library preparation was checked by calculating ribosomal (and globin) content.
Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA).
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30.
Assembly: To align the reads of each sample, the  human reference GRCh38.p14 was used. Data was analyzed with DESEQ2 package in R studio
Supplementary files format and content: Tab delimited txt

source_name: Stem cells

growth_protocol: H9WAO9 cells were differentated in a 12 day protocol towards vagal neural crest cells, froim these spheroids were formed in 4 days and these vagal neural crest precursor spheroids were then differentiated to sensory neurons for 6 days, followed by 2-3 weeks of maturation, and subsequent treatment.

extract_protocol:
Total RNA was isolated using the RNA purification NucleoSpin RNA XS kit (#740902 Macherey-Nagel, Germany) according to the manufacturer’s guide. The yield of the isolated RNA was then measured using the NanoDrop 1000 spectrophotometer.
RNA-seq was conducted using the Illumina NovaSeq 6000 sequencer by BMK (https://www.bmkgene.com/). The procedure included data quality control, adapter trimming, alignment of short reads and feature counting. Library preparation was checked by calculating ribosomal (and globin) content. Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA). Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. To align the reads of each sample, the the  mouse reference GRCh38.p14 was used. Data was analyzed with DESEQ2 in R studio

treatment_protocol: Mature hPSC-derived sensory neurons were treated for 5 days with TGF-β (2 ng/ml) or IL-4 (10 ng/ml) + IL-13 (3 ng/ml), all dissolved in PBS with 0.1% bovine serum albumin (BSA). Control samples received the same amount of a 0.1% BSA in PBS solution.

value: Stem cells

value: WT

value: Batch 6


title: V6

description: Library name: V6_run3


title: V54

description: Library name: V54_run2


title: V51

description: Library name: V51_run4


title: Fibrosis_3

description: Library name: Sample56


title: V57

description: Library name: V57_run4


title: BW092-001T0035, H9WAO9, IL-6

description: Library name: Sample23


title: V48

description: Library name: V48_run2


title: V49

description: Library name: V49_run3


title: V46

description: Library name: V46_run3


title: Fibrosis_1

description: Library name: Sample54


title: V53

description: Library name: V53_run2


title: V45

description: Library name: V45_run0


title: BW092-001T0034, H9WAO9, TGF-β

description: Library name: Sample22

value: TGF-β


title: HC_4

description: Library name: Sample53

value: liver


title: V42

description: Library name: V42_run5


title: Fibrosis_2

description: Library name: Sample55


title: BW092-001T0033, H9WAO9, Vehicle

description: Library name: Sample21

value: Vehicle


title: V43

description: Library name: V43_run5


title: V41

description: Library name: V41_run4


title: BW092-001T0032, H9WAO9, IL-4+IL-13

description: Library name: Sample20

value: Batch 5


title: V40

description: Library name: V40_run4


title: BW092-001T0031, H9WAO9, IL-6

description: Library name: Sample19


title: HC_3

description: Library name: Sample52


title: HC_2

description: Library name: Sample51


title: V38

description: Library name: V38_run2


title: V39

description: Library name: V39_run5


title: BW092-001T0030, H9WAO9, TGF-β

description: Library name: Sample18


title: V37_2

description: Library name: V37_2_run4


title: V36

description: Library name: V36_run4


title: HC_1

description: Library name: Sample50


title: BW092-001T0029, H9WAO9, Vehicle

description: Library name: Sample17


title: CD4+ CD25hi Tregs TCR

city: Atlanta

first: Gregory

last: Tharp

address: 954 Gatewood Dr

institute: Yerkes National Primate Research Center

description: Library name: ERa-Tregs_VDJ

data_processing:
Demultiplexing, barcode processing, gene, HTO and VDJ-TCR counting was done with Cellranger 7.1.0 into a single set of files.
Assembly: mm10, refdata-gex-mm10-2020-A, refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: Tab separated values and matrix files, and comma delimited TCR abundance estimation file with annotation as well as read and umi counts.
Library strategy: scTCR-Seq

source_name: mixed sample oVAT/Spleen

extract_protocol:
Spleen and oVAT tissues were isolated. FACS sorted Tregs were pooled and loaded into a 10X Genomics Chromium Controller system in conjunction with the Chromium NextGEM Single Cell 5’ Library and Gel Beads v2 kit.
After subsequent reverse transcription, cDNA libraries were generated for gene expression, TCR sequences, and feature barcodes.

value: mixed sample oVAT/Spleen

value: CD4+ CD25hi Tregs

value: mixed sample Era+/+ or Era-/-

value: mixed sample NCD/HFD

value: TCR


title: BW092-001T0028, H9WAO9, IL-4+IL-13

description: Library name: Sample16

value: Batch 4


title: V33

description: Library name: V33_run0


title: BW092-001T0027, H9WAO9, IL-6

description: Library name: Sample15


title: CD4+ CD25hi Tregs Gene Expression

description:
Library name: ERa-Tregs_GEX
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Demultiplexing, barcode processing, gene, HTO and VDJ-TCR counting was done with Cellranger 7.1.0 into a single set of files.
Assembly: mm10, refdata-gex-mm10-2020-A, refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: Tab separated values and matrix files, and comma delimited TCR abundance estimation file with annotation as well as read and umi counts.

value: mRNA


title: V3

description: Library name: V3_run3

value: Endometrium


title: V32

description: Library name: V32_run2


title: CD4+ CD25hi Tregs Surface Protein

description:
Library name: ERa-Tregs_CITE
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Demultiplexing, barcode processing, gene, HTO and VDJ-TCR counting was done with Cellranger 7.1.0 into a single set of files.
Assembly: mm10, refdata-gex-mm10-2020-A, refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: Tab separated values and matrix files, and comma delimited TCR abundance estimation file with annotation as well as read and umi counts.
Library strategy: CITE-seq

value: HTO


title: V29

description: Library name: V29_run2


title: BW092-001T0026, H9WAO9, TGF-β

description: Library name: Sample14


title: V30

description: Library name: V30_run0


title: V26

description: Library name: V26_run2


title: V27

description: Library name: V27_run2


title: BW092-001T0025, H9WAO9, Vehicle

description: Library name: Sample13


title: V23

description: Library name: V23_run0


title: V34

description: Library name: V34_run0


title: BW092-001T0024, H9WAO9, IL-4+IL-13

description: Library name: Sample12

value: Batch 3


title: Hippocampus, female, Dp1Tyb;AppKO, 877917

city: London

first: Frances

last: Wiseman

address: Queen Square House

country: United Kingdom

institute: University College London

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s BCL Convert Software v3.75
Data were analysed using the nf-core/rnaseq pipeline ver 3.12.0 https://nf-co.re/rnaseq/3.12.0. Within this pipeline we used the STAR to align the data to the GRCm38 reference genome followed by UMI tools for deduplication
Salmon was used to count the transcripts across the genome.
We used the package SARTools version 1.8.1 in R to quantify the differences within groups using DESeq2 as the base. https://github.com/PF2-pasteur-fr/SARTools.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Hippocampus

growth_protocol: Not applicable

extract_protocol:
RNA was prepared using the NEB Monarch Total RNA Miniprep kit (T2010S).  For each sample, 200ng of total RNA was used.
Library was prepared using the KAPA mRNA HyperPrep Kit (Roche p/n KK8580) according to manufacturer’s instructions.

treatment_protocol: Not applicable

value: Hippocampus

value: female


title: Hippocampus, female, Dp1Tyb;AppKO, 877756


title: Hippocampus, female, Dp1Tyb, 871874


title: V2

description: Library name: V2_run4


title: V20

description: Library name: V20_run4


title: V19

description: Library name: V19_run4


title: BW092-001T0023, H9WAO9, IL-6

description: Library name: Sample11

value: Stem cells

value: WT


title: V15

description: Library name: V15_run3


title: BW092-001T0022, H9WAO9, TGF-β

description: Library name: Sample10

value: TGF-β


title: V13

description: Library name: V13_run1


title: Hippocampus, female, Dp1Tyb;AppKO, 870400


title: Hippocampus, female, WT, 870238


title: BW092-001T0021, H9WAO9, Vehicle

description: Library name: Sample9

value: Vehicle


title: V17

description: Library name: V17_run3


title: BW092-001T0020, H9WAO9, IL-4+IL-13

description: Library name: Sample8

value: Batch 2


title: Hippocampus, female, Dp1Tyb;AppKO, 870234


title: V11

description: Library name: V11_run0


title: V1

description: Library name: V1_run5


title: P95

description: Library name: P95_run4


title: P97

description: Library name: P97_run5


title: Hippocampus, male, Dp1Tyb;AppKO, 869031

value: male


title: P99

description: Library name: P99_run4


title: V10

description: Library name: V10_run2


title: BW092-001T0019, H9WAO9, IL-6

description: Library name: Sample7


title: Hippocampus, male, WT, 869030


title: P93

description: Library name: P93_run5


title: Hippocampus, female, WT, 870233


title: BW092-001T0018, H9WAO9, TGF-β

description: Library name: Sample6


title: BW092-001T0017, H9WAO9, Vehicle

description: Library name: Sample5


title: P91

description: Library name: P91_run5


title: P92

description: Library name: P92_run4


title: P94

description: Library name: P94_run4


title: Hippocampus, female, Dp1Tyb, 869028


title: P9

description: Library name: P9_run4


title: P89

description: Library name: P89_run5


title: BW092-001T0016, H9WAO9, IL-4+IL-13

description: Library name: Sample4

value: Batch 1


title: Hippocampus, male, Dp1Tyb;AppKO, 868749


title: BW092-001T0015, H9WAO9, IL-6

description: Library name: Sample3


title: P86

description: Library name: P86_run3


title: P88

description: Library name: P88_run2


title: Hippocampus, female, WT, 868748


title: BW092-001T0014, H9WAO9, TGF-β

description: Library name: Sample2


title: BW092-001T0013, H9WAO9, Vehicle

description: Library name: Sample1


title: Hippocampus, female, Dp1Tyb, 868747


title: P80

description: Library name: P80_run3


title: Hippocampus, female, WT, 868026


title: P8

description: Library name: P8_run0


title: P79

description: Library name: P79_run3


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for KIF11)-replication 3

description: Library name: KIF11_control_3

data_processing:
Data quality control was performed using fastp to remove reads with adapters.Paired reads were removed under the following conditions:when the the number of N in any sequencing read exceeded 10%of the length of that read,and when any sequencing read contained low-quality bases(Q<=20) exceeding 50% of the length of that read.Subsequent analyses were based on clean reads. The reference genome and its annotation files were downloaded from a specified website. HISAT was used to build an index,and clean reads were aligned to the reference genome. Gene expression levels were quantified using feature Counts to calculate gene alignment statistics. Subsequently, FPKM (Fragments Per Kilobase Million) values for each gene were computed based on gene length. FPKM is currently the most used method for estimating gene expression levels.
Assembly: GRCh38.109.
Supplementary files format and content: FPKM for beta-catenin signaling.txt contains fpkm values for each gene of biosample SAMN50221966-SAMN50221980.
Supplementary files format and content: KIF11_KD_symbol_fpkm.txt contains fpkm values for each gene of biosample SAMN50221981-SAMN50221986.
Supplementary files format and content: PRDX1_KD_symbol_fpkm.txt contains fpkm values for each gene of biosample SAMN50221987-SAMN50221992.

source_name: retina

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions(Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNAqualitywas determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDropTechnologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.
mRNA is enriched by Oligo(dT) magnetic beads to selectively capture mRNAs with poly(A) tails. A fragmentation buffer is then added to shear the RNA into short fragments. Using these fragments as a template, first-strand cDNA is synthesized with random hexamers. Subsequently, a buffer, dNTPs, and DNA polymerase are added for second-strand cDNA synthesis, and the resulting double-stranded cDNA is purified using DNA purification magnetic beads. The purified double-stranded cDNA then undergoes end repair, A-tailing, and adapter ligation. Following these steps, DNA purification magnetic beads are used for fragment size selection, and the final cDNA library is obtained through PCR enrichment. The experimental workflow is shown in the figure below.

value: retina


title: P75

description: Library name: P75_run3


title: Hippocampus, female, WT, 866987


title: P82

description: Library name: P82_run3


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for KIF11)-replication 2

description: Library name: KIF11_control_2


title: Hippocampus, male, WT, 866742


title: P73

description: Library name: P73_run5


title: P72

description: Library name: P72_run4


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for KIF11)-replication 1

description: Library name: KIF11_control_1


title: P76

description: Library name: P76_run3


title: P70

description: Library name: P70_run3


title: RNA-Seq of HRECs transduced with a KIF11-targeting shRNA lentivirus-replication 2

description: Library name: KIF11_KD_2


title: P68

description: Library name: P68_run0


title: P67

description: Library name: P67_run0


title: Hippocampus, female, Dp1Tyb, 866740


title: P71

description: Library name: P71_run2


title: P66

description: Library name: P66_run3


title: Hippocampus, male, WT, 866741


title: Hippocampus, female, Dp1Tyb;AppKO, 866736


title: RNA-Seq of HRECs transduced with a KIF11-targeting shRNA lentivirus-replication 3

description: Library name: KIF11_KD_3


title: P60

description: Library name: P60_run3


title: RNA-Seq of HRECs transduced with a KIF11-targeting shRNA lentivirus-replication 1

description: Library name: KIF11_KD_1


title: P6

description: Library name: P6_run1


title: P58

description: Library name: P58_run4


title: P54

description: Library name: P54_run3


title: Hippocampus, male, WT, 866735


title: P53

description: Library name: P53_run5


title: Hippocampus, male, Dp1Tyb;AppKO, 866734


title: P62

description: Library name: P62_run0


title: Hippocampus, female, Dp1Tyb;AppKO, 866737


title: HEK293T cells, RNU2-1 harboring C28U bio rep 3

city: Santa Cruz

first: Melissa

last: Jurica

address: 1156 High Street

institute: University of California Santa Cruz

description: Library name: W2-3

data_processing:
Raw fastq read quality was assessed using FastQC (v0.12.1) and trim_galore (v0.6.10) was run to automatically detect and remove remaining illumina adaptors and low-quality reads.
Trimmed reads were then aligned to gencode human reference genome release 47 primary comprehensive gene annotation (GRCh38) using STAR (v2.7.11b) with the following options: --outFilterMultimapNmax 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --alignSJDBoverhangMin 1, --limitSjdbInsertNsj 2000000, --outSAMattributes NH HI AS nM jM, --alignIntronMin 20, --outSAMtype BAM SortedByCoordinate, --twopassMode Basic, and --quantMode TranscriptomeSAM GeneCounts.
Bam files were indexed using samtools (v1.21 with htslib 1.21) and bigwig files were created for the forward and reverse reads using deeptools (v3.5.6). Read counts were normalized using the inverse of the DEseq2 size factors.
Assembly: GRCh38
Supplementary files format and content: bigwig files of normalized read counts

growth_protocol: HEK293T cells were cultured at 37ºC, 5% CO2 in Dulbecco’s Modified Eagle Medium (Gibco,cat 12100061) supplemented with 10% FBS (Hyclone, cat SH3054103).

extract_protocol:
total RNA was isolated by Trizol extraction (Invitrogen, cat 15596018) and ethanol precipitation. Total RNA was treated with RQ1 DNase (Promega, cat M6101) followed by phenol:chloroform:iso-amyl alcohol (25:24:1) extraction, chloroform:iso-amyl alcohol (24:1) extraction and ethanol precipitation.
UC Davis DNA Technologies and Expression Analysis Core Laboratory prepared poly-A strand specific libraries

value: embryonic kidney cells

value: U2 snRNA mutant


title: HEK293T cells, RNU2-1 harboring C28U bio rep 2

description: Library name: W2-2


title: HEK293T cells, RNU2-1 harboring C28U bio rep 1

description: Library name: W2-1


title: P56

description: Library name: P56_run0


title: P52

description: Library name: P52_run3


title: Hippocampus, male, Dp1Tyb, 866733


title: P50

description: Library name: P50_run3


title: Hippocampus, male, WT, 866732


title: P5

description: Library name: P5_run5


title: P48

description: Library name: P48_run5


title: HEK293T cells, RNU2-1 harboring TAG36ACT bio rep 2

description: Library name: UCA-2


title: P47

description: Library name: P47_run5


title: Hippocampus, male, Dp1Tyb;AppKO, 865982


title: P46

description: Library name: P46_run3


title: P81

description: Library name: P81_run5


title: P44

description: Library name: P44_run3


title: HEK293T cells, RNU2-1 harboring TAG36ACT bio rep 3

description: Library name: UCA-3


title: Hippocampus, male, Dp1Tyb;AppKO, 865981


title: Hippocampus, male, Dp1Tyb;AppKO, 865979


title: HEK293T cells, parental cell line control

description: Library name: HT-3


title: P42

description: Library name: P42_run0


title: P4

description: Library name: P4_run2


title: P37

description: Library name: P37_run0


title: P38

description: Library name: P38_run4


title: Hippocampus, female, Dp1Tyb, 865978


title: HEK293T cells, RNU2-1 harboring TAG36ACT bio rep 1

description: Library name: UCA-1


title: HEK293T cells, empty vector control bio rep 2

description: Library name: 783-2


title: P45

description: Library name: P45_run3


title: HEK293T cells, empty vector control bio rep 3

description: Library name: 783-3


title: Hippocampus, male, Dp1Tyb, 863786


title: P34

description: Library name: P34_run2


title: P33

description: Library name: P33_run5


title: HEK293T cells, empty vector control bio rep 1

description: Library name: 783-1


title: Hippocampus, male, Dp1Tyb, 863785


title: P3

description: Library name: P3_run2


title: ACLF22-1

description: Library name: Sample49

value: liver


title: P28

description: Library name: P28_run4


title: P27

description: Library name: P27_run2


title: Hippocampus, male, Dp1Tyb, 863784


title: P31

description: Library name: P31_run1


title: P26

description: Library name: P26_run0


title: P25

description: Library name: P25_run3


title: Hippocampus, female, Dp1Tyb, 863780


title: Hippocampus, female, WT, 863781


title: ACLF20-1

description: Library name: Sample47


title: ACLF19-1

description: Library name: Sample46


title: P21

description: Library name: P21_run0


title: Hippocampus, male, Dp1Tyb, 863179


title: P22

description: Library name: P22_run1


title: ACLF21-1

description: Library name: Sample48


title: P20

description: Library name: P20_run2


title: ACLF18-1

description: Library name: Sample45


title: P2

description: Library name: P2_run5


title: P18

description: Library name: P18_run0


title: P17

description: Library name: P17_run3


title: ACLF17

description: Library name: Sample44


title: P16

description: Library name: P16_run5


title: P19

description: Library name: P19_run5


title: P15

description: Library name: P15_run2


title: Hippocampus, female, Dp1Tyb, 860935


title: ACLF14

description: Library name: Sample42


title: P14

description: Library name: P14_run4


title: Hippocampus, male, Dp1Tyb, 860937


title: Hippocampus, male, Dp1Tyb;AppKO, 860938


title: Hippocampus, female, WT, 860934


title: P12

description: Library name: P12_run2


title: P13

description: Library name: P13_run4


title: ACLF11

description: Library name: Sample40


title: ACLF13

description: Library name: Sample41


title: P11

description: Library name: P11_run2


title: ACLF9

description: Library name: Sample39


title: P108

description: Library name: P108_run4


title: P112

description: Library name: P112_run5


title: Hippocampus, female, WT, 860800


title: Hippocampus, female, Dp1Tyb, 860799


title: P110

description: Library name: P110_run5


title: Hippocampus, male, Dp1Tyb, 860801


title: P105

description: Library name: P105_run5


title: P104

description: Library name: P104_run4


title: P101

description: Library name: P101_run5


title: Hippocampus, male, WT, 860737


title: ACLF7

description: Library name: Sample37


title: P100

description: Library name: P100_run5


title: Hippocampus, male, WT, 860736


title: P1

description: Library name: P1_run4


title: ACLF5

description: Library name: Sample35


title: M8

description: Library name: M8_run2


title: Hippocampus, male, Dp1Tyb, 860735


title: Hippocampus, male, WT, 860734


title: ACLF3

description: Library name: Sample34


title: ACLF6

description: Library name: Sample36


title: ACLF2

description: Library name: Sample33


title: M40

description: Library name: M40_run2


title: M37

description: Library name: M37_run5


title: ACLF8-1

description: Library name: Sample38


title: M9

description: Library name: M9_run1


title: M35

description: Library name: M35_run5


title: M6

description: Library name: M6_run0


title: PP126: Calvaria_Mutant_3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Prx1-Cre;Pth1rfl/fl craniums_3

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: Prx1-Cre;Pth1rfl/fl craniums_3

extract_protocol:
Total RNA was then extracted with an miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Dissected craniums were efficiently homogenized by a bead lysis kit (Tomy Seiko Co., Tokyo, JAPAN) in Trizol solution (Ambion, Austin, TX, USA).

value: Calvaria

tag: genotype/variation


title: M33

description: Library name: M33_run2

value: Endometrium


title: Hippocampus, male, Dp1Tyb;AppKO, 860733


title: M30

description: Library name: M30_run1


title: PP125: Calvaria_Mutant_2

description: Prx1-Cre;Pth1rfl/fl craniums_2

source_name: Prx1-Cre;Pth1rfl/fl craniums_2


title: ACLF1

description: Library name: Sample32


title: CLD16

description: Library name: Sample31


title: M28

description: Library name: M28_run3


title: M3

description: Library name: M3_run1


title: CLD15

description: Library name: Sample30


title: M25

description: Library name: M25_run5


title: Pretreatment whole blood RNA-seq, Sample25

status: Public on Feb 14 2026

city: tsukuba

first: Satoka

last: Kinase

address: tenoudai 1-1-1

institute: University of tsukuba

description: Library name: Sample25

data_processing:
Raw sequencing reads were processed using standard RNA-seq analysis pipelines. Reads were quality-controlled, aligned to the human reference genome, and gene-level counts were generated.
Assembly: Human reference genome GRCh38 (hg38)
Supplementary files format and content: GEO_raw_counts_SampleID.csv (Processed gene expression count matrices containing raw read counts for all samples.)

source_name: Whole blood

growth_protocol: Peripheral blood was collected from patients prior to treatment.

extract_protocol:
Total RNA from whole-blood samples was isolated using a PAXgene Blood RNA kit (PreAnalytix) according to the manufacturer’s instructions. Globin RNA was removed from total RNA using a GLOBINclear-Human Kit (Thermo Fisher Scientific). For RNA sequencing, 500 ng total RNA were rRNA depleted using an NEBNext rRNA Depletion Kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s instructions. Library preparation was performed using an NEBNext Ultra-Directional RNA Library Prep Kit (New England Biolabs). Libraries were validated via Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to determine size distribution and concentration. Validated libraries were then sequenced at Tsukuba i-Laboratory LLP (Tsukuba, Japan) on a NextSeq500 (Illumina, San Diego, CA, USA) with the paired-end, 36-base read option.
RNA-seq libraries were prepared using a poly(A)-selected library preparation kit and sequenced on an Illumina platform.

treatment_protocol: No treatment was applied prior to sample collection.

value: Whole blood

tag: disease state

value: metastatic renal cell carcinoma

value: nivolumab plus ipilimumab

tag: timepoint

value: pretreatment

tag: irae status

value: Yes


title: PP124: Calvaria_Mutant_1

description: Prx1-Cre;Pth1rfl/fl craniums_1

source_name: Prx1-Cre;Pth1rfl/fl craniums_1

tag: tissue


title: M2

description: Library name: M2_run3


title: M21

description: Library name: M21_run2


title: CLD14

description: Library name: Sample28


title: PP122: Calvaria_Flox_control_3

description: Pth1rfl/fl craniums_3

source_name: Pth1rfl/fl craniums_3


title: CLD14-1

description: Library name: Sample29


title: M22

description: Library name: M22_run2


title: M19

description: Library name: M19_run1


title: PP120: Calvaria_Flox_control_1

description: Pth1rfl/fl craniums_1

source_name: Pth1rfl/fl craniums_1


title: PP121: Calvaria_Flox_control_2

description: Pth1rfl/fl craniums_2

source_name: Pth1rfl/fl craniums_2


title: M17

description: Library name: M17_run1


title: M18

description: Library name: M18_run0


title: CLD13

description: Library name: Sample27


title: M20

description: Library name: M20_run2


title: M16

description: Library name: M16_run0


title: Brain myeloid cells, Infected+Morphine-treated, GEX, rep4

city: Omaha

first: Howard

middle: S

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

description: Library name: 122T_GEX

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger arc software v2.0.2
Assembly: Mmul10, NCBI RefSeq assembly plus SIVmac251 sequence (Gene bank assession number: PP236443)
Supplementary files format and content: Fragment file contains reference genome chromosome of fragment, ajusted start and end position of fragment on chromosome, cell barcode, and total number of read pairs associated with this fragment
Supplementary files format and content: Gene expression matrix file contain cell barcodes and RNA count matrix
Supplementary files format and content: Seurat (.rds) object comprising the combined, processed gene expression count matrix for brain myeloid cells. The dataset integrates snRNA-seq data derived from snMultiome (snATAC-seq + snRNA-seq) and standalone snRNA-seq across four brain regions (Frontal Orbital Gyrus, Anterior Cingulate Gyrus, and Middle Frontal Gyrus, as well as frontal white matter). The object includes raw count matrix, metadata annotations, and cell-type classifications used in the associated analysis.

organism: Macaca mulatta

source_name: Brain

extract_protocol:
Animals were deeply anesthetized with ketamine plus xylazine, and blood was cleared from the brain and other organs by intracardial perfusion with sterile PBS containing 1 U/ml heparin. Brains were harvested, and approximately half of the brain was taken for microglia/macrophage isolation. Briefly, the brain was minced and homogenized in cold Hank’s Balanced Salt Solution (HBSS, Invitrogen, Carlsbad, CA). After being centrifuged, the brain tissue was digested at 37° C in HBSS containing 28 U/ml DNase I and 8 U/ml papain for 30 minutes. After digestion, the enzymes were inactivated by adding 2.5% FBS, and the cells were centrifuged and resuspended in cold HBSS. The cell suspension was mixed with 90% Percoll (GE HealthCare, Pittsburg, PA) to a final concentration of 20% Percoll and centrifuged at 4° C for 15 minutes at 550 x g. The microglia/macrophage pallet at the bottom was resuspended in HBSS and passed through a 40 μm strainer to remove cell clumps and aggregates. Cells were again pelleted by centrifugation and resuspended in RBC lysis buffer for 3 minutes to eliminate contaminating red blood cells. A final wash was performed before the resulting cells were quantified on a hemocytometer and Coulter Counter Z1. The cells were resuspended in 10% DMSO and 90% fetal bovine serum and subjected to slow controlled freezing followed by storage in liquid N2. Nuclei were isolated from the cells and permeabilized as the 10XGenomics protocol. Cryopreserved cell isolates were rapidly thawed in a 37° C water bath. After the recovery, cells were washed and counted by Coulter Counter Z1. Once cell concentration was known, cells were transferred to ice-cold PBS and stained with CD11b (Biolegend 101257) and UV-blue live/dead (Invitrogen L23105). Cells were washed, resuspended in flow cytometry staining buffer (e-bioscience), and sorted on an Aria2 flow cytometer (BD Biosciences, San Jose, CA, USA).
Nuclei were then quantified on a hemocytometer and concentrated to approximately 2200-2400 nuclei per µL. Based on 10× Genomics parameters targeting 8000 nuclei, the ideal volume of cells was loaded onto the 10× Genomics (Pleasanton, CA, USA) Chromium Next GEM Chip J and placed into the Chromium Controller for nuclei capturing and library preparation. The prepared libraries were sequenced using Illumina (San Diego, CA, USA) Novaseq6000 sequencers.

treatment_protocol: The animals in Morphine and MorphineSIV groups were intramuscularly injected with morphine for 9 weeks. The animals in SalineSIV and MorphineSIV groups were inoclulated with SIVmac251 and five weeks post-inoclulation, they were treated with antiretroviral therapy (ART).

value: Brain

tag: cell type

value: CD11b positive cells

value: Infected+Morphine-treated


title: CLD12

description: Library name: Sample26


title: M38

description: Library name: M38_run1


title: M14

description: Library name: M14_run2


title: M15

description: Library name: M15_run1


title: CLD11

description: Library name: Sample25


title: M12

description: Library name: M12_run1


title: Brain myeloid cells, Infected+Morphine-treated, GEX, rep3

description: Library name: 117T_GEX

tag: treatment


title: Brain myeloid cells, Infected+Morphine-treated, GEX, rep2

description: Library name: 114T_GEX


title: Brain myeloid cells, Infected+Morphine-treated, GEX, rep1

description: Library name: 107T_GEX


title: M11

description: Library name: M11_run5


title: CLD10

description: Library name: Sample24


title: CLD9

description: Library name: Sample23


title: BI9

description: Library name: BI9_run1


title: M10

description: Library name: M10_run1


title: Brain myeloid cells, Morphine-treated, GEX, rep4

description: Library name: 116T_GEX

value: Morphine-treated


title: BI7

description: Library name: BI7_run2


title: M1

description: Library name: M1_run1


title: CLD8

description: Library name: Sample22


title: Brain myeloid cells, Morphine-treated, GEX, rep3

description: Library name: 115T_GEX


title: CLD7

description: Library name: Sample21


title: BI6

description: Library name: BI6_run1


title: BI4

description: Library name: BI4_run1


title: Brain myeloid cells, Morphine-treated, GEX, rep2

description: Library name: 110T_GEX


title: BI31

description: Library name: BI31_run1


title: Brain myeloid cells, Morphine-treated, GEX, rep1

description: Library name: 105T_GEX


title: BI30

description: Library name: BI30_run2


title: CLD6

description: Library name: Sample20


title: BI5

description: Library name: BI5_run4


title: BI32

description: Library name: BI32_run4


title: BI3

description: Library name: BI3_run0


title: CLD5

description: Library name: Sample19


title: Brain myeloid cells, Infected, GEX, rep4

description: Library name: 121T_GEX

value: Infected


title: BI29

description: Library name: BI29_run1


title: Brain myeloid cells, Infected, GEX, rep3

description: Library name: 113T_GEX


title: CLD4-1

description: Library name: Sample18


title: CLD3

description: Library name: Sample17


title: BI24

description: Library name: BI24_run5


title: BI22

description: Library name: BI22_run1


title: BI20

description: Library name: BI20_run0


title: BI26

description: Library name: BI26_run3


title: CLD2

description: Library name: Sample16


title: BI2

description: Library name: BI2_run0


title: BI19

description: Library name: BI19_run2


title: Brain myeloid cells, Infected, GEX, rep2

description: Library name: 109T_GEX


title: BI17

description: Library name: BI17_run0


title: CLD1

description: Library name: Sample15


title: Brain myeloid cells, Infected, GEX, rep1

description: Library name: 108T_GEX


title: Brain myeloid cells, Uninfected, GEX, rep4

description: Library name: 120T_GEX

value: Uninfected


title: BI16

description: Library name: BI16_run2


title: Brain myeloid cells, Uninfected, GEX, rep3

description: Library name: 111T_GEX


title: BI14

description: Library name: BI14_run1


title: HC14-1

description: Library name: Sample13


title: BI10

description: Library name: BI10_run0


title: BI12

description: Library name: BI12_run1


title: HC15-1

description: Library name: Sample14


title: Brain myeloid cells, Uninfected, GEX, rep2

description: Library name: 106T_GEX


title: HC13-1

description: Library name: Sample12


title: B8

description: Library name: B8_run5


title: Brain myeloid cells, Uninfected, GEX, rep1

description: Library name: 104T_GEX


title: BI1

description: Library name: BI1_run1


title: B7

description: Library name: B7_run3


title: Brain myeloid cells, Infected+Morphine-treated, ATAC, rep4

description: Library name: 122T_ATAC


title: B4

description: Library name: B4_run3


title: HC11-1

description: Library name: Sample10


title: HC12-1

description: Library name: Sample11


title: B38

description: Library name: B38_run4


title: B35

description: Library name: B35_run3


title: B5

description: Library name: B5_run5


title: HC10-1

description: Library name: Sample9


title: Brain myeloid cells, Infected+Morphine-treated, ATAC, rep3

description: Library name: 117T_ATAC


title: B34

description: Library name: B34_run0


title: HC9-1

description: Library name: Sample8


title: B31

description: Library name: B31_run3


title: B32

description: Library name: B32_run1


title: Brain myeloid cells, Infected+Morphine-treated, ATAC, rep1

description: Library name: 107T_ATAC


title: B3

description: Library name: B3_run5


title: Brain myeloid cells, Infected+Morphine-treated, ATAC, rep2

description: Library name: 114T_ATAC


title: Brain myeloid cells, Morphine-treated, ATAC, rep4

description: Library name: 116T_ATAC


title: B30

description: Library name: B30_run3


title: HC7

description: Library name: Sample6


title: B28

description: Library name: B28_run1


title: B29

description: Library name: B29_run1


title: Brain myeloid cells, Morphine-treated, ATAC, rep3

description: Library name: 115T_ATAC


title: HC6

description: Library name: Sample5


title: B24

description: Library name: B24_run0


title: HC8-1

description: Library name: Sample7


title: Brain myeloid cells, Morphine-treated, ATAC, rep2

description: Library name: 110T_ATAC


title: B22

description: Library name: B22_run1


title: B2

description: Library name: B2_run1


title: HC4-1

description: Library name: Sample4


title: Brain myeloid cells, Morphine-treated, ATAC, rep1

description: Library name: 105T_ATAC


title: HC3

description: Library name: Sample3


title: B15

description: Library name: B15_run1


title: B16

description: Library name: B16_run0


title: B13

description: Library name: B13_run1


title: HC2

description: Library name: Sample2


title: B19

description: Library name: B19_run1


title: Brain myeloid cells, Infected, ATAC, rep4

description: Library name: 121T_ATAC


title: B11

description: Library name: B11_run1


title: B1

description: Library name: B1_run1


title: B17

description: Library name: B17_run1


title: Brain myeloid cells, Infected, ATAC, rep2

description: Library name: 109T_ATAC


title: T. cruzi trypomastigotes Control T7/Cas9

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

description:
Library name: Sample 5
Column name in raw_counts_allsamples.txt: T_cruzi_T7C9_TCT

data_processing:
Raw sequencing  data .fastq files were preprocessed using the software fastp (version 0.20.1). The trimmed files were then mapped to the CL Brener Non Esmeraldo Like genome sequence (release 68), obtained from the TriTrypDB database (Aslett et al., 2009) using the bowtie2 software. The .bam files were processed with featureCounts software (version 2.0.3) to quantify gene abundance
Assembly: T. cruzi CL Brener Non Esmeraldo Like genome sequence (release 68)
Supplementary files format and content: raw counts of gene expression obtained with featureCounts software (version 2.0.3), in comma-separated values (CSV) format

organism: Trypanosoma cruzi

source_name: unicellular organism

growth_protocol: T. cruzi epimastigote forms (CL Brener strain) were cultured at 27 °C in liver-infusion tryptose (LIT) medium supplemented with 10% fetal bovine serum (FBS) (Cultilab) and 1% (v/v) antibiotic solution (streptomycin/penicillin). T,cruzi trypomastigote forms were obtained by infecting LLCMK2 cells with purified T. cruzi metacyclic forms (MOI 10:1). After 120 h of invasion, T. cruzi  trypomastigotes egressed from the LLCMK2 cells and were collected by centrifugation (1000 g, 5 min).

extract_protocol:
Total RNA from each sample analyzed were isolated using the RNeasy Mini Kit (Qiagen) and treated with RNAse-free DNAse I (Qiagen). RNA samples were quantified and evaluated for integrity using the fluorometer Qubit 4 (Thermo Scientific). All samples showed an A260/A280 ratio close do 2.0.
Poly-A + RNA was selected by oligo-dT chromatography and used to generate cDNA libraries for massive sequencing using the TruSeq RNA Sample Prep Kit (Illumina) following manufacturer's protocols.

value: unicellular organism

tag: cell line

value: CL Brener

value: protozoan parasite

tag: genotype

value: Parental T7/Cas9

value: 120 h after infection


title: HC1

description: Library name: Sample1

source_name: liver

value: liver


title: T. cruzi trypomastigotes IP6K-/+

description:
Library name: Sample 6
Column name in raw_counts_allsamples.txt: T_cruzi_IP6K_TCT

value: IP6K knockout


title: Brain myeloid cells, Infected, ATAC, rep1

description: Library name: 108T_ATAC


title: SAM24456550

description: Library name: LIB6236486

data_processing:
HTSeqGenie pipeline
Assembly: GRCh38
Supplementary files format and content: TAB (Raw counts and rpkm per gene)

extract_protocol:
RNA was isolated from cultured cells via Qiagen Rneasy Plus kit.
Libraries were prepared from cDNA using the Nextera XT DNA Sample Preparation kit.

value: Breast

value: Untreated


title: T. cruzi epimastigotes Control T7/Cas9 - replicate 2

description:
Library name: Sample 2
Column name in raw_counts_allsamples.txt: T_cruzi_T7C9 - rep2

value: exponential phase


title: Brain myeloid cells, Infected, ATAC, rep3

description: Library name: 113T_ATAC


title: T. cruzi epimastigotes IP6K-/+ - replicate 2

description:
Library name: Sample 4
Column name in raw_counts_allsamples.txt: T_cruzi_IP6K - rep2


title: SAM24456548

description: Library name: LIB6236485


title: Brain myeloid cells, Uninfected, ATAC, rep4

description: Library name: 120T_ATAC


title: T. cruzi epimastigotes Control T7/Cas9 - replicate 1

description:
Library name: Sample 1
Column name in raw_counts_allsamples.txt: T_cruzi_T7C9 - rep1


title: SAM24456551

description: Library name: LIB6236487


title: Brain myeloid cells, Uninfected, ATAC, rep3

description: Library name: 111T_ATAC


title: SAM24456547

description: Library name: LIB6236484


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for PRDX1)-replication 1

city: Chengdu

first: Shujin

last: Li

address: Chengdu, Sichuan province, China, first-ring road, No.34

institute: Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences

description: Library name: PRDX1_control_1

value: retina


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for PRDX1)-replication 2

description: Library name: PRDX1_control_2


title: RNA-Seq of HRECs transduced with a PRDX1-targeting shRNA lentivirus-replication 3

description: Library name: PRDX1_KD_3


title: Brain myeloid cells, Uninfected, ATAC, rep2

description: Library name: 106T_ATAC

value: Brain


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for PRDX1)-replication 3

description: Library name: PRDX1_control_3


title: T. cruzi epimastigotes IP6K-/+ - replicate 1

description:
Library name: Sample 3
Column name in raw_counts_allsamples.txt: T_cruzi_IP6K - rep1


title: RNA-Seq of HRECs transduced with a PRDX1-targeting shRNA lentivirus-replication 2

description: Library name: PRDX1_KD_2


title: RNA-Seq of HRECs transduced with a PRDX1-targeting shRNA lentivirus-replication 1

description: Library name: PRDX1_KD_1


title: RNA-Seq of HRECs transduced with a LRP5-targeting shRNA lentivirus-replication 3

description: Library name: LRP5_KD_3


title: SAM24456544

description: Library name: LIB6236482

value: 4 months, 100nM giredestrant


title: SAM24456545

description: Library name: LIB6236483


title: Brain myeloid cells, Uninfected, ATAC, rep1

description: Library name: 104T_ATAC

value: CD11b positive cells


title: si-dnmt + TNF + IFN, biological replicate 3

city: Charlottesville

first: Andrew

middle: C

last: Dudley

state: VA

address: 1340 Jefferson Park Avenue

department: Dept. of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

description: Library name: H3

data_processing:
cutadapt/4.9:  Trim adapters (P5, P7, and universal Illumina motif). P5 adapter：P5→P7’(5’→3 ’)
AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT
P7 adapter：P5→P7’(5’→3’)
GATCGGAAGAGCACACGTCTGAACTCCAGTCAC[i7]ATCTCGTATGCCGTCTTCTGCTTG
fastqc/0.12.1
multiqc/1.27.1
Assembly: star/2.7.11b followed by featureCounts, and the DESeq2

source_name: Veravec

growth_protocol: Mouse lung ECs were seeded at 1×105 cells/mL in 6-well plates and cultured overnight at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was isolated using a column-based RNA extraction kit (Zymo Research) according to the manufacturer’s instructions.
Libraries were prepared and sequenced by Novogene for bulk RNA-seq analysis.

treatment_protocol: The next day, cells were transfected with either control siRNA or DNMT1-targeting siRNA (BLOCK-iT oligos; Invitrogen) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM I Reduced Serum Medium for 4 h, following the manufacturer’s instructions. A BLOCK-iT Alexa Fluor Red fluorescent oligo (Invitrogen) was used in parallel wells to monitor transfection efficiency. After 4 hrs, the transfection medium was replaced with growth medium containing 20% serum, and the cells were cultured for 24 hrs at 37 °C, humidified 5% CO₂. A second siRNA transfection was performed 24 h later to reinforce the knockdown. Cells were then treated with TNFa (10 ng/mL) or IFNg (1,000 U/mL) for 16 hrs.

value: Veravec

value: lung endothelial cells

value: si-dnmt + TNF + IFN


title: RNA-Seq of HRECs transduced with a TSPAN12-targeting shRNA lentivirus-replication 3

description: Library name: TSPAN12_KD_3


title: si-dnmt + TNF + IFN, biological replicate 2

description: Library name: H2


title: RNA-Seq of HRECs transduced with a LRP5-targeting shRNA lentivirus-replication 1

description: Library name: LRP5_KD_1


title: SAM24456539

first: Jackson

last: Liang

address: 1 DNA Way

institute: Genentech

description: Library name: LIB6236479


title: SAM24456542

description: Library name: LIB6236481

value: 2 months, 100nM giredestrant


title: si-dnmt + TNF + IFN, biological replicate 1

description: Library name: H1


title: RNA-Seq of HRECs transduced with a TSPAN12-targeting shRNA lentivirus-replication 1

description: Library name: TSPAN12_KD_1


title: SAM24456538

description: Library name: LIB6236478


title: SAM24456541

description: Library name: LIB6236480


title: RNA-Seq of HRECs transduced with a FZD4-targeting shRNA lentivirus-replication 1

description: Library name: FZD4_KD_1


title: RNA-Seq of HRECs transduced with a FZD4-targeting shRNA lentivirus-replication 3

description: Library name: FZD4_KD_3


title: RNA-Seq of HRECs transduced with a TSPAN12-targeting shRNA lentivirus-replication 2

description: Library name: TSPAN12_KD_2


title: RNA-Seq of HRECs transduced with a FZD4-targeting shRNA lentivirus-replication 2

description: Library name: FZD4_KD_2


title: si-dnmt + IFN, biological replicate 3

description: Library name: G3

value: si-dnmt + IFN


title: RNA-Seq of HRECs transduced with a CTNNB1-targeting shRNA lentivirus-replication 3

description: Library name: CTNNB1_KD_3


title: SAM24456536

description: Library name: LIB6236477


title: si-dnmt + IFN, biological replicate 4

description: Library name: G4


title: RNA-Seq of HRECs transduced with a CTNNB1-targeting shRNA lentivirus-replication 1

description: Library name: CTNNB1_KD_1


title: RNA-Seq of HRECs transduced with a CTNNB1-targeting shRNA lentivirus-replication 2

description: Library name: CTNNB1_KD_2


title: si-dnmt + IFN, biological replicate 2

description: Library name: G2


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for beta-catenin siganling group)-replication 3

description: Library name: Ctrl_3


title: si-dnmt + TNF + IFN, biological replicate 4

description: Library name: H4


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for beta-catenin siganling group)-replication 2

description: Library name: Ctrl_2


title: si-dnmt + IFN, biological replicate 1

description: Library name: G1


title: Thy6-Sur

city: Chicago

first: Erin

last: Adams

state: IL

institute: University of Chicago

description:
10X Genomics
Thy6_barcodes.tsv.gz
Thy6_features.tsv.gz
Thy6_matrix.mtx.gz
Thy6_ADT

data_processing:
Sequences were deconvoluted using Cellranger software v.7.1 and imported into R. Initial QC and gene expression and clustering analysis was conducted using the standard Seurat v5 pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Vδ1 thymocytes

extract_protocol:
Thymic fragments were incubated in DMEM-F12 with rotation for 20min and thymocytes were collected from supernatant.Dead cells were separated using Ficoll density gradient and thymocytes were counted and frozen in FBS + 10% DMSO until thawing for staining and sequencing.
Samples were processed for sequencing using the 10X Genomics 5’ Single Cell Immune Profiling workflow. γδ TCR libraries were generated using the 10X universal forward primers and nested custom reverse primers (TRG outer Reverse: AGTCTTCATGGTGTTCCCCTCC, TRG inner Reverse: AAAATAGTGGGCTTGGGGGA, TRD outer Reverse GTCGTGTTGAACTGAACATGTCAC, TRD inner Reverse CAGACAAGCGACATTTGTTCCA). Libraries for all samples were pooled and sequenced on a NovaSeq6000 or NovaX (Illumina) and resultant FASTQs were demultiplexed by the University of Chicago Genomics Facility.
scRNA-seq, CITE-seq, and VDJ libraries

value: thymus

value: F

tag: library type

value: ADT

value: 4 day

tag: adt


title: SAM24456535

city: South San Francisco

description: Library name: LIB6236476


title: si-dnmt + TNF, biological replicate 4

description: Library name: F4

value: si-dnmtl + TNF


title: RNA-Seq of HRECs transduced with a non-targeting control lentivirus (for beta-catenin siganling group)-replication 1

description: Library name: Ctrl_1