title: MYC and SMARCD3 overexpression in postnatal day 2 male mouse cerebellum, rep2

description: Library name: MYC_mouse_12


title: human endometrial stromal organoid, co-culture, bio replicate 6

status: Public on Mar 25 2026

type: SRA

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

country: USA

institute: Rutgers University

description:
Library name: U5
Column name in rawCounts_all.csv: U5

library_source: transcriptomic

data_processing:
High-quality, trimmed paired-end reads were processed using Partek Flow software. Potential ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) contaminants were removed using Bowtie 2. The cleaned reads were aligned to the mouse reference genome (mm10) using the HISAT 2 aligner. Raw read counts were generated by mapping aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm, and normalization was performed using the Transcripts Per Million (TPM) method.
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: primary cell derived organoid

extract_protocol:
Arcturus PicoPure RNA Isolation Kit
Total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems), following the manufacturer’s protocol. Library preparation and low-input RNA-seq were conducted on the Illumina NovaSeq 6000 platform by Novogene (Novogene Corporation, Sacramento, CA).

tag: cell type

value: primary cell derived organoid

tag: treatment

value: co-culture with follicle

tag: batch


title: MYC and SMARCD3 overexpression in postnatal day 2 female mouse cerebellum, rep1

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

description: Library name: MYC_mouse_9

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trim Glare (v.0.6.4_dev) and Cutadapt (v.2.6).
Trimmed reads were mapped to mm10 whole genome using Hisat2 (v.2.1.0).
Count matrix was calculated using FeatureCounts (v.1.6.4).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for each sample and gene.

organism: Mus musculus

source_name: Tumor

extract_protocol:
RNeasy Plus Mini Kit (Catlog#74134; Qiagen) was used for RNA extraction.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

tag: tissue

value: Tumor


title: human endometrial stromal organoid, co-culture, bio replicate 4

description:
Library name: U3
Column name in rawCounts_all.csv: U3


title: human endometrial stromal organoid, co-culture, bio replicate 3

description:
Library name: U2
Column name in rawCounts_all.csv: U2


title: MYC and SMARCD3 overexpression in postnatal day 2 female mouse cerebellum, rep2

description: Library name: MYC_mouse_10


title: 2506, Mus musculus, Thymus,Thymus

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

institute: Pfizer

description: Library name: itox002506

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human

source_name: Thymus,Thymus

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

value: Thymus,Thymus


title: MYC overexpression in postnatal day 5 male mouse cerebellum, rep2

description: Library name: MYC_mouse_8


title: human endometrial stromal organoid, co-culture, bio replicate 2

description:
Library name: U1
Column name in rawCounts_all.csv: U1


title: 12280, Sus scrofa, Trachea,Trachea

description: Library name: itox012280

organism: Sus scrofa

source_name: Trachea,Trachea

value: Trachea,Trachea


title: human endometrial stromal organoid, co-culture, bio replicate 1

description:
Library name: E6
Column name in rawCounts_all.csv: E6

value: EPC


title: MYC overexpression in postnatal day 2 male mouse cerebellum, rep2

description: Library name: MYC_mouse_6


title: human endometrial stromal organoid, EPC, bio replicate 5

description:
Library name: E3
Column name in rawCounts_all.csv: E3


title: human endometrial stromal organoid, EPC, bio replicate 6

description:
Library name: E5
Column name in rawCounts_all.csv: E5


title: MYC overexpression in postnatal day 2 male mouse cerebellum, rep1

description: Library name: MYC_mouse_5


title: 2507, Mus musculus, Artery- Aorta (abdominal descending) -Pooled,Artery- Aorta (abdominal descending) -Pooled

description: Library name: itox002507


title: 12281, Sus scrofa, Bladder,Bladder

description: Library name: itox012281

source_name: Bladder,Bladder

value: Bladder,Bladder


title: human endometrial stromal organoid, EPC, bio replicate 2

description:
Library name: E1
Column name in rawCounts_all.csv: E1


title: 2486, Mus musculus, Cecum,Cecum

description: Library name: itox002486

source_name: Cecum,Cecum

value: Cecum,Cecum


title: human endometrial stromal organoid, EPC, bio replicate 3

description:
Library name: E2
Column name in rawCounts_all.csv: E2


title: 12283, Sus scrofa, Uterus,Uterus

description: Library name: itox012283

source_name: Uterus,Uterus

value: Uterus,Uterus


title: 11881, Sus scrofa, Parathyroid Gland,Parathyroid Gland

description: Library name: itox011881

source_name: Parathyroid Gland,Parathyroid Gland

value: Parathyroid Gland,Parathyroid Gland


title: 2487, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002487


title: 12279, Sus scrofa, Tonsil,Tonsil

description: Library name: itox012279

source_name: Tonsil,Tonsil

value: Tonsil,Tonsil


title: 1711, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001711

source_name: Brain-Striatum,Brain-Striatum

value: Brain-Striatum,Brain-Striatum


title: MYC overexpression in postnatal day 5 female mouse cerebellum, rep2

description: Library name: MYC_mouse_4


title: human endometrial stromal organoid, EPC, bio replicate 1

description:
Library name: A5
Column name in rawCounts_all.csv: A5

value: cAMP


title: 2510, Mus musculus, Skin (inguinal),Skin (inguinal)

description: Library name: itox002510

source_name: Skin (inguinal),Skin (inguinal)

value: Skin (inguinal),Skin (inguinal)


title: 11882, Sus scrofa, Pituitary Gland,Pituitary Gland

description: Library name: itox011882

source_name: Pituitary Gland,Pituitary Gland

value: Pituitary Gland,Pituitary Gland


title: MYC overexpression in postnatal day 2 female mouse cerebellum, rep2

description: Library name: MYC_mouse_2


title: 12282, Sus scrofa, Uterus,Uterus

description: Library name: itox012282


title: MYC overexpression in postnatal day 5 female mouse cerebellum, rep1

description: Library name: MYC_mouse_3


title: 2511, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002511


title: MYC overexpression in postnatal day 2 female mouse cerebellum, rep1

description: Library name: MYC_mouse_1


title: 11884, Sus scrofa, Thyroid Gland,Thyroid Gland

description: Library name: itox011884

source_name: Thyroid Gland,Thyroid Gland

value: Thyroid Gland,Thyroid Gland


title: human endometrial stromal organoid, cAMP, bio replicate 3

description:
Library name: A3
Column name in rawCounts_all.csv: A3


title: 11886, Sus scrofa, Heart,Heart

description: Library name: itox011886

source_name: Heart,Heart

value: Heart,Heart


title: 2514, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002514


title: human endometrial stromal organoid, cAMP, bio replicate 4

description:
Library name: A4
Column name in rawCounts_all.csv: A4

value: primary cell derived organoid


title: 11883, Sus scrofa, Salivary Gland,Salivary Gland

description: Library name: itox011883

source_name: Salivary Gland,Salivary Gland

value: Salivary Gland,Salivary Gland


title: 2512, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002512


title: Setd2-ISC-KO2

city: Shanghai

first: Yue

last: Xu

address: 上海市徐汇区华山路

country: China

institute: 上海交通大学

description: Library name: Sample5

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCm38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

source_name: intestine

extract_protocol:
The selected cells were processed for single-cell RNA extraction and reverse transcription within 1 h and were subjected to cDNA amplification and purification.
Single cells were gently transferred into lysis buffer, and reverse transcription was performed using a SMARTer Ultra Low RNA Kit (Clontech) directly in the cell lysate. Single-cell cDNA was amplified using an Advantage 2 PCR Kit (Clontech) according to the manufacturer’s protocol. After cDNA amplification, 50 μl of the sample was subjected to cDNA purification, whereas the remaining sample was kept for single-cell PCR experiments.

value: intestine

value: Intestinal stem cell

tag: genotype


title: Setd2-ISC-KO3

description: Library name: Sample6


title: 2515, Mus musculus, Spleen,Spleen

description: Library name: itox002515

source_name: Spleen,Spleen

value: Spleen,Spleen


title: Setd2-ISC-KO1

description: Library name: Sample4


title: 11887, Sus scrofa, Heart,Heart

description: Library name: itox011887


title: human endometrial stromal organoid, cAMP, bio replicate 1

description:
Library name: A1
Column name in rawCounts_all.csv: A1

source_name: primary cell derived organoid


title: 2516, Mus musculus, Spleen,Spleen

description: Library name: itox002516


title: Setd2-ISC-WT3

description: Library name: Sample3


title: human endometrial stromal organoid, cAMP, bio replicate 2

description:
Library name: A2
Column name in rawCounts_all.csv: A2


title: 11771, Sus scrofa, Artery,Artery

description: Library name: itox011771

source_name: Artery,Artery

value: Artery,Artery


title: 2517, Mus musculus, Spleen,Spleen

description: Library name: itox002517


title: 11868, Sus scrofa, Bone Marrow,Bone Marrow

description: Library name: itox011868

source_name: Bone Marrow,Bone Marrow

value: Bone Marrow,Bone Marrow


title: human endometrial stromal organoid, control, bio replicate 4

description:
Library name: C4
Column name in rawCounts_all.csv: C4

value: vehicle


title: Setd2-ISC-WT1

description: Library name: Sample1


title: human endometrial stromal organoid, control, bio replicate 1

description:
Library name: C1
Column name in rawCounts_all.csv: C1


title: 2513, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002513


title: human endometrial stromal organoid, control, bio replicate 3

description:
Library name: C3
Column name in rawCounts_all.csv: C3


title: 11888, Sus scrofa, Heart,Heart

description: Library name: itox011888


title: 11893, Sus scrofa, Kidney,Kidney

description: Library name: itox011893

source_name: Kidney,Kidney

value: Kidney,Kidney


title: MYC overexpression in postnatal day 5 male mouse cerebellum, rep1

description: Library name: MYC_mouse_7

source_name: Tumor

value: Tumor


title: sh-Cyp4f3b2

city: Kunming

first: xiang

middle: wen

last: lan

address: 300 Bailong Temple, Panlong District, Kunming, Yunnan 650224, China

institute: Southwest Forestry University

description: Library name: sh-2

data_processing:
CLC Genomics Workbench v 11.0.1
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: FPKM values for each Sample

source_name: Gallbladder

extract_protocol:
RNA was extracted using TRIzol Reagent (Ambion).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Gallbladder

tag: cell line

value: GBC-SD

value: Epithelial-like gallbladder carcinoma cell

value: sh-Cyp4f3b (Cyp4f4b knockdown)

value: Batch 2


title: Setd2-ISC-WT2

description: Library name: Sample2


title: 2605, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002605

source_name: Whole Blood,Whole Blood

value: Whole Blood,Whole Blood


title: 11894, Sus scrofa, Cecum,Cecum

description: Library name: itox011894

source_name: Cecum,Cecum

value: Cecum,Cecum


title: 11895, Sus scrofa, Colon,Colon

description: Library name: itox011895

source_name: Colon,Colon

value: Colon,Colon


title: 11896, Sus scrofa, Rectum,Rectum

description: Library name: itox011896

source_name: Rectum,Rectum

value: Rectum,Rectum


title: 11891, Sus scrofa, Hippocampus,Hippocampus

description: Library name: itox011891

source_name: Hippocampus,Hippocampus

value: Hippocampus,Hippocampus


title: 11897, Sus scrofa, Liver,Liver

description: Library name: itox011897

source_name: Liver,Liver

value: Liver,Liver


title: 2584, Mus musculus, Lung (left lobe),Lung (left lobe)

description: Library name: itox002584

source_name: Lung (left lobe),Lung (left lobe)

value: Lung (left lobe),Lung (left lobe)


title: Setd2-KO-H3K4me1

description: Library name: Sample3

library_source: genomic

data_processing:
CUT&Tag reads were aligned to the mm10 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: GRCm38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
CUT&Tag analysis was performed using the Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) as described by the manufacturers with some modifications. Briefly, nuclei were extracted from the 10,000 fresh cells, and added the ConA beads incubating at room temperature for 10 min. The mixed complexes were the incubated with antibodies with IgG antibody as a control, and the next day, followed by the secondary antibody. A diluted pA-Tn5 adapter complex was then added to the above system and incubated at room temperature for 1 h. After extensive washing, system were subsequently sheared by adding 5 × TTBL. Subsequent proteinase K and DNA extract beads were used for obtaining eluted DNA.
Finally, the sequencing libraries were established after 12 cycles of PCR amplification and sequenced using Illumina Novaseq 6000 with paired-end 2x150 as the sequencing mode.

value: intestine

value: Intestinal stem cell


title: Setd2-WT-H3K4me3

description: Library name: Sample8


title: 2583, Mus musculus, Lung (left lobe),Lung (left lobe)

description: Library name: itox002583


title: sh-Cyp4f3b1

description: Library name: sh-1

value: sh-Cyp4f3b (Cyp4f3b knockdown)


title: human endometrial stromal organoid, control, bio replicate 2

description:
Library name: C2
Column name in rawCounts_all.csv: C2

value: primary cell derived organoid

value: vehicle


title: Setd2-WT-H3K4me1

description: Library name: Sample7


title: 2579, Mus musculus, Ileum,Ileum

description: Library name: itox002579

source_name: Ileum,Ileum

value: Ileum,Ileum


title: sh-Cyp4f3b3

description: Library name: sh-3

value: Gallbladder

value: GBC-SD

value: sh-Cyp4f3b (Cyp4f5b knockdown)


title: 1732, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001732

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: Setd2-KO-H3K27me3

description: Library name: Sample2

source_name: intestine


title: 11867, Sus scrofa, Coronary Artery,Coronary Artery

description: Library name: itox011867

source_name: Coronary Artery,Coronary Artery

value: Coronary Artery,Coronary Artery


title: Setd2-WT-H3K27me3

description: Library name: Sample6


title: 2602, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002602


title: sh-NC3

description: Library name: NC-3

value: Epithelial-like gallbladder carcinoma cell

value: Wild-type

value: sh-NC (control)

value: Batch 1


title: Setd2-KO-H3K4me3

description: Library name: Sample4


title: 2581, Mus musculus, Peripheral Nerve (sciatic)-Pooled,Peripheral Nerve (sciatic)-Pooled

description: Library name: itox002581


title: 2580, Mus musculus, Peripheral Nerve (sciatic)-Pooled,Peripheral Nerve (sciatic)-Pooled

description: Library name: itox002580


title: CB, RNA-seq, R750W, rep2

city: Shimotsuke

first: Kohei

last: Iida

state: Tochigi

address: Yakushiji 3311-1

department: Regenerative medicine

country: Japan

institute: Jichi medical university

description:
Library name: RNA-seq CB 11
Column name in processed data files: R750W_2

data_processing:
The fastq file was uploaded to Galaxy (https://usegalaxy.org) for analysis.
Sequence reads were aligned to the human genome (hg38) using HISAT2(v2.2.1).
Reads were then counted using Feature Count(v2.0.1) and gene expression variations were analyzed using EdgeR(v3.36.0).
The read count data generated by Feature Count were normalized by the TPM method.
Assembly: hg38
Supplementary files format and content: tab-delimited raw read counts for each sample.
Supplementary files format and content: tab-delimited TPM values for each sample.

source_name: umbilical cord blood

growth_protocol: CB CD34+ cells were incubated in StemSpanTM SFEMII supplemented with 50 ng/ml mouse Flt-3, 50 ng/ml human thrombopoietin (TPO), 10 ng/ml human stem cell factor (SCF) and 1% antibiotics with 5% CO2 at 37C.

extract_protocol:
Total RNA was then extracted and purified from the GFP+ cells using the FastGene™ RNA Purification Kit (FastGene, FG-8005).After RNA fragmentation, cDNA was synthesized by random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP.
Following end repair, add A and adapter ligation, the DNA fragments were amplified by PCR. Libraries were sequenced using Illumina Novaseq 6000 with paired-end mode.

treatment_protocol: With pre-cultured human CD34+ umbilical cord blood cells transduced with pMYS-IRE-GFP vector, wild-type MECOM, or mutant MECOM (MECOM-R750 or MECOM-DL/AS), GFP+ cells were sorted 48 hours after transduction, and were cultured for 4 days.

value: umbilical cord blood

value: CD34+ umbilical cord blood cells


title: 11899, Sus scrofa, Mesenteric Lymph Node,Mesenteric Lymph Node

description: Library name: itox011899


title: 11898, Sus scrofa, Lung,Lung

description: Library name: itox011898

source_name: Lung,Lung

value: Lung,Lung


title: sh-NC2

description: Library name: NC-2


title: CB, RNA-seq, R750W, rep3

description:
Library name: RNA-seq CB 12
Column name in processed data files: R750W_3


title: Setd2-WT-H3K27ac

description: Library name: Sample5

value: intestine

value: Intestinal stem cell


title: sh-NC1

description: Library name: NC-1


title: CB, RNA-seq, R750W, rep1

description:
Library name: RNA-seq CB 10
Column name in processed data files: R750W_1


title: ATAC-Setd2-WT2

description: Library name: sample2

data_processing:
ATAC-seq reads were aligned to the mm10 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: GRCm38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

extract_protocol:
The ATAC experiments were performed as described (Buenrostro et al., 2013).
Cells were  vehicle treated and then collected and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen). All samples were then amplified by PCR using NEBNextHigh-Fidelity 2× PCR Master Mix (New Englands Labs) with primers containing a barcode to generate libraries. DNA was again purified using AMPure Beads.DNA libraries for ATAC-seq were prepared using NextEra Library Prep Kit following manufacturer's protocols.


title: 1739, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001739


title: 1712, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001712

source_name: Brain-Striatum,Brain-Striatum

value: Brain-Striatum,Brain-Striatum


title: 11900, Sus scrofa, Skeletal Muscle,Skeletal Muscle

description: Library name: itox011900

source_name: Skeletal Muscle,Skeletal Muscle

value: Skeletal Muscle,Skeletal Muscle


title: 1737, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001737


title: 2586, Mus musculus, Skin (inguinal),Skin (inguinal)

description: Library name: itox002586

source_name: Skin (inguinal),Skin (inguinal)

value: Skin (inguinal),Skin (inguinal)


title: 11902, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox011902

source_name: Peripheral nerve,Peripheral nerve

value: Peripheral nerve,Peripheral nerve


title: ATAC-Setd2-KO2

description: Library name: sample1


title: CB, RNA-seq, DL/AS, rep3

description:
Library name: RNA-seq CB 9
Column name in processed data files: DL/AS_3

value: DL/AS


title: CB, RNA-seq, DL/AS, rep2

description:
Library name: RNA-seq CB 8
Column name in processed data files: DL/AS_2


title: Setd2-KO-H3K27ac

description: Library name: Sample1


title: ATAC-Setd2-KO1

description: Library name: Sample1


title: 2568, Mus musculus, Thymus,Thymus

description: Library name: itox002568

source_name: Thymus,Thymus

value: Thymus,Thymus


title: 2569, Mus musculus, Skin (inguinal),Skin (inguinal)

description: Library name: itox002569


title: 11901, Sus scrofa, Optic Nerve,Optic Nerve

description: Library name: itox011901

source_name: Optic Nerve,Optic Nerve

value: Optic Nerve,Optic Nerve


title: mCherry+SOCS1-24h-rep3

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou National Laboratory

description: Library name: mChe+SOCS1-24h-rep3

data_processing:
Raw sequencing reads were first subjected to basic quality control including removal of potential sequencing adapters, and poor quality bases or reads using TrimGalore (v0.6.10). Then, clean reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.10b) with default arguments, and only uniquely mapped reads were retained. Reads quantification on the gene level was performed using featureCounts (v2.0.6). Genes with a minimal raw count of 10 and detected in at least three samples were retained. Differentially gene expression analysis was conducted using DESeq2 package (v1.40.2, p < 0.05 and fold change > 1.5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: HUVEC

extract_protocol:
HUVECs were collected at 6h and 24h after IVT mRNA transfection. Then, total RNA was extracted using RNeasy Plus Mini Kit (Cat# 74134, QIAGEN).
RNA-seq libraries were prepared according to the standard protocol of VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Cat# NR603).

treatment_protocol: We co-transfected 6μg mCherry mRNA with 1.2μg Luc, M, and SOCS1 mRNA into HUVECs, respectively.

value: HUVEC


title: CB, RNA-seq, WT, rep3

description:
Library name: RNA-seq CB 6
Column name in processed data files: WT_3

value: WT


title: 11903, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox011903


title: ATAC-Setd2-WT1

description: Library name: Sample2


title: 2593, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002593

source_name: Whole Blood,Whole Blood

value: Whole Blood,Whole Blood


title: 12147, Sus scrofa, Liver,Liver

description: Library name: itox012147

value: Liver,Liver


title: mCherry+SOCS1-24h-rep1

description: Library name: mChe+SOCS1-24h-rep1


title: CB, RNA-seq, WT, rep1

description:
Library name: RNA-seq CB 4
Column name in processed data files: WT_1


title: 2594, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002594


title: CB, RNA-seq, DL/AS, rep1

description:
Library name: RNA-seq CB 7
Column name in processed data files: DL/AS_1


title: 12148, Sus scrofa, Lung,Lung

description: Library name: itox012148


title: mCherry+SOCS1-24h-rep2

description: Library name: mChe+SOCS1-24h-rep2


title: CB, RNA-seq, Empty Vector, rep3

description:
Library name: RNA-seq CB 3
Column name in processed data files: control_3

value: Empty vector


title: mCherry+SOCS1-6h-rep3

description: Library name: mChe+SOCS1-6h-rep3


title: 1740, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001740

value: Eye (minus lens),Eye (minus lens)


title: 2592, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002592


title: CB, RNA-seq, Empty Vector, rep2

description:
Library name: RNA-seq CB 2
Column name in processed data files: control_2

value: umbilical cord blood

value: CD34+ umbilical cord blood cells


title: 12150, Sus scrofa, Skeletal Muscle,Skeletal Muscle

description: Library name: itox012150


title: 12145, Sus scrofa, Large Intestine,Large Intestine

description: Library name: itox012145

source_name: Large Intestine,Large Intestine

value: Large Intestine,Large Intestine


title: 12149, Sus scrofa, Lymph Node,Lymph Node

description: Library name: itox012149

source_name: Lymph Node,Lymph Node

value: Lymph Node,Lymph Node


title: mCherry+SOCS1-6h-rep1

description: Library name: mChe+SOCS1-6h-rep1


title: 1713, Mus musculus, Peripheral Nerve (sciatic),Peripheral Nerve (sciatic)

description: Library name: itox001713


title: 1750, Mus musculus, Mammary Gland/Tissue (female only),Mammary Gland/Tissue (female only)

description: Library name: itox001750


title: 12152, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox012152


title: mCherry+Mpro-24h-rep3

description: Library name: mChe+M-24h-rep3


title: CB, RNA-seq, WT, rep2

description:
Library name: RNA-seq CB 5
Column name in processed data files: WT_2


title: CB, RNA-seq, Empty Vector, rep1

description:
Library name: RNA-seq CB 1
Column name in processed data files: control_1


title: 1765, Mus musculus, Oviduct (Fallopian tube),Oviduct (Fallopian tube)

description: Library name: itox001765


title: mCherry+Mpro-24h-rep2

description: Library name: mChe+M-24h-rep2


title: 1770, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001770

source_name: Ovary (left),Ovary (left)

value: Ovary (left),Ovary (left)


title: HEK293T, ChIP-seq, WT, AM tag

description: Library name: ChIP-seq HEK293T WT

data_processing:
The fastq file was uploaded to Galaxy (https://usegalaxy.org) for analysis and mapped to the human genome (hg38) using Bowtie2 (v2.4.2).
MACS2 (Galaxy Version 2.1.1.20160309.6) was used for peak calling.
ChIPseeker (v1.18.0) was used for peak annotation.
BamCoverage (v3.3.2.0.0), computeMatrix (v3.5.1.0.0) and plotHeatmap (v3.5.1.0.1) were used for sequence depth visualization.
The IGV tool (v2.8.12) was used to visualize sequence reads
Homer (v4.10) was used to identify de novo motifs. The size of the region used for motif discovery is 100 bp.
Assembly: hg38
Supplementary files format and content: CSV file

growth_protocol: HEK293T cells were incubated in DMEM supplemented with 10% fetal bovine serum (FBS)and 1% antibiotics with 5% CO2 at 37C.

extract_protocol:
HEK293T cells transfected with pMYS-IG vector, MECOM-WT or MECOM-R750W with AM tag were fixed with 1% formaldehyde (Sigma) and then quenched with glycine. After washing and cell lysis, the chromatin was fragmented with 0.75 µl micrococcal nuclease (MNase) at 37 C for 15–20 min and nuclei were completely lysed by sonication. Chromatin was then harvested, immunoprecipitated, and DNA purified using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling, #9003). Anti-AM tag (active motif, catalog #91112) was used as the antibody for immunoprecipitation overnight at 4C with rotation.
Add A and adapter ligation to purified DNA, the DNA fragments were amplified by PCR.ChIP-seq libraries were sequenced using Illumina Novaseq 6000 with paired-end mode.

value: human embryonic kidney cells


title: 12151, Sus scrofa, Optic Nerve,Optic Nerve

description: Library name: itox012151


title: HEK293T, ChIP-seq, R750W, AM tag

description: Library name: ChIP-seq HEK293T R750W


title: 12157, Sus scrofa, Pancreas,Pancreas

description: Library name: itox012157

source_name: Pancreas,Pancreas

value: Pancreas,Pancreas


title: 1773, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001773


title: mCherry+Mpro-24h-rep1

description: Library name: mChe+M-24h-rep1


title: mCherry+Mpro-6h-rep2

description: Library name: mChe+M-6h-rep2


title: 12130, Sus scrofa, Adrenal Gland,Adrenal Gland

description: Library name: itox012130

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: Lung, Stable disease, Post-treatment initiation, TMRE High, Patient 2

city: Nashville

first: John

last: Karijolich

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description: Library name: 9341-ML-19

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were performed with CellRanger (version 7.0.0) (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: matrix files

source_name: peripheral blood

extract_protocol:
Kidney and lung cancer patient peripheral blood was collected in mononuclear cell preparation tubes (BD Biosciences, 362761) and processed according to manufacturer protocol. Healthy donor PBMCs were isolated by density gradient centrifugation using Ficoll-Paque (Cytiva,17144002) in SepMate-50 tubes (STEMCELL Technologies, 85450) following manufacturer protocols. For single cell experiments, kidney and lung patient PBMCs were FACS sorted using BD FACS Aria II at the Vanderbilt Flow Cytometry Shared Resource by cell singlets (FSC-A vs FSC-H and SSC-A vs SSC-H), lymphocytes, viable, CD3+, TMRElow and TMREhigh. TMRElow and hi populations were separated based on TMRE modal distributions.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5’ v2 platform (P/N: 1000263; 10x Genomics, Inc.) according to the manufacturer’s protocol.  FACS-sorted CD3+ TMRE low and CD3+ TMRE high T cells from patient PBMCs were used as input for scRNA-seq library preparation were loaded into each channel of the Chromium X controller to achieve the target cell recover of ~5,000 cells.  Cells were partitioned into Gel Bead Emulsion (GEMs), where cell lysis and barcoded reverse transcription of the RNA occurred, followed by cDNA amplification.  Amplified cDNA was purified using SPRI beads and dual indexed libraries were constructed by fragmentation, end repair, A-tailing, adapter ligation, and PCR amplification. The library quality was assessed using a Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument. Prepared libraries were pooled in equimolar ratios, and the resulting pool was subjected to cluster generation using the NovaSeq 6000 System, following the manufacturer's protocols. 150 bp paired-end sequencing was performed on the NovaSeq 6000 platform targeting 50,000 reads per cell.  Raw sequencing data (FASTQ files) obtained from the NovaSeq 6000 was subjected to quality control analysis, including read quality assessment. Real Time Analysis Software (RTA) and NovaSeq Control Software (NCS) (1.8.0; Illumina) were used for base calling. MultiQC (v1.7; Illumina) was used for data quality assessments.

value: peripheral blood

value: CD3+ T cells


title: 12156, Sus scrofa, Fallopian tube,Fallopian tube

description: Library name: itox012156

source_name: Fallopian tube,Fallopian tube

value: Fallopian tube,Fallopian tube


title: 1772, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001772


title: 1797, Mus musculus, Trachea,Trachea

description: Library name: itox001797

source_name: Trachea,Trachea

value: Trachea,Trachea


title: HEK293T, ChIP-seq, Vector, AM tag

description: Library name: ChIP-seq HEK293T Vector

value: Vector


title: 12158, Sus scrofa, Cerebral cortex,Cerebral cortex

description: Library name: itox012158

source_name: Cerebral cortex,Cerebral cortex

value: Cerebral cortex,Cerebral cortex


title: Lung, Stable disease, Post-treatment initiation, TMRE low, Patient 2

description: Library name: 9341-ML-20


title: mCherry+Mpro-6h-rep1

description: Library name: mChe+M-6h-rep1

value: HUVEC


title: Lung, Stable disease, Pre-treatment, TMRE low, Patient 2

description: Library name: 9341-ML-18


title: 12159, Sus scrofa, Skin,Skin

description: Library name: itox012159

source_name: Skin,Skin

value: Skin,Skin


title: mCherry+SOCS1-6h-rep2

description: Library name: mChe+SOCS1-6h-rep2


title: mCherry+Mpro-6h-rep3

description: Library name: mChe+M-6h-rep3


title: 1798, Mus musculus, Trachea,Trachea

description: Library name: itox001798


title: 1718, Mus musculus, Peripheral Nerve (sciatic),Peripheral Nerve (sciatic)

description: Library name: itox001718


title: mCherry+Luc-24h-rep2

description: Library name: mChe+Luc-24h-rep2


title: Lung, Stable disease, Pre-treatment, TMRE high, Patient 2

description: Library name: 9341-ML-17


title: 12160, Sus scrofa, Small Intestine,Small Intestine

description: Library name: itox012160

source_name: Small Intestine,Small Intestine

value: Small Intestine,Small Intestine


title: mCherry+Luc-24h-rep3

description: Library name: mChe+Luc-24h-rep3


title: 12179, Sus scrofa, Eye,Eye

description: Library name: itox012179

source_name: Eye,Eye

value: Eye,Eye


title: Lung, Partial disease, Post-treatment initiation, TMRE low, Patient 2

description: Library name: 9341-ML-16


title: 12161, Sus scrofa, Small Intestine,Small Intestine

description: Library name: itox012161


title: mCherry+Luc-24h-rep1

description: Library name: mChe+Luc-24h-rep1


title: 1800, Mus musculus, Trechea,Trechea

description: Library name: itox001800

source_name: Trechea,Trechea

value: Trechea,Trechea


title: mCherry+Luc-6h-rep3

description: Library name: mChe+Luc-6h-rep3


title: Lung, Partial disease, Pre-treatment, TMRE low, Patient 2

description: Library name: 9341-ML-14


title: mCherry+Luc-6h-rep2

description: Library name: mChe+Luc-6h-rep2


title: 12182, Sus scrofa, Adrenal Gland,Adrenal Gland

description: Library name: itox012182


title: 1803, Mus musculus, Trachea,Trachea

description: Library name: itox001803


title: mCherry+Luc-6h-rep1

description: Library name: mChe+Luc-6h-rep1


title: 1802, Mus musculus, Trachea,Trachea

description: Library name: itox001802


title: 12162, Sus scrofa, Small Intestine,Small Intestine

description: Library name: itox012162


title: 1804, Mus musculus, Trachea,Trachea

description: Library name: itox001804


title: 12163, Sus scrofa, Spinal Cord,Spinal Cord

description: Library name: itox012163

source_name: Spinal Cord,Spinal Cord

value: Spinal Cord,Spinal Cord


title: 1805, Mus musculus, Trachea,Trachea

description: Library name: itox001805


title: mCherry-24h-rep3

description: Library name: mChe-24h-rep3


title: 12164, Sus scrofa, Spleen,Spleen

description: Library name: itox012164

source_name: Spleen,Spleen

value: Spleen,Spleen


title: Lung, Progressive disease, Post-treatment initiation, TMRE low

description: Library name: 9341-ML-12


title: 1801, Mus musculus, Trachea,Trachea

description: Library name: itox001801


title: 12165, Sus scrofa, Stomach,Stomach

description: Library name: itox012165

source_name: Stomach,Stomach

value: Stomach,Stomach


title: 1806, Mus musculus, Trachea,Trachea

description: Library name: itox001806


title: Lung, Progressive disease, Post-treatment initiation, TMRE high

description: Library name: 9341-ML-11


title: mCherry-24h-rep1

description: Library name: mChe-24h-rep1

source_name: HUVEC


title: Lung, Partial disease, Pre-treatment, TMRE high, Patient 2

description: Library name: 9341-ML-13


title: 1807, Mus musculus, Trachea,Trachea

description: Library name: itox001807


title: Lung, Partial disease, Post-treatment initiation, TMRE high, Patient 2

description: Library name: 9341-ML-15


title: 12166, Sus scrofa, Adipose,Adipose

description: Library name: itox012166

source_name: Adipose,Adipose

value: Adipose,Adipose


title: Lung, Progressive disease, Pre-treatment, TMRE low

description: Library name: 9341-ML-10


title: Lung, Stable disease, Post-treatment initiation, TMRE low, Patient 1

description: Library name: 9341-ML-8


title: mCherry-6h-rep2

description: Library name: mChe-6h-rep2


title: 12186, Sus scrofa, Salivary Gland,Salivary Gland

description: Library name: itox012186

source_name: Salivary Gland,Salivary Gland

value: Salivary Gland,Salivary Gland


title: 12167, Sus scrofa, Adipose,Adipose

description: Library name: itox012167


title: 12216, Sus scrofa, Testis,Testis

description: Library name: itox012216

source_name: Testis,Testis

value: Testis,Testis


title: Lung, Stable disease, Post-treatment initiation, TMRE high, Patient 1

description: Library name: 9341-ML-7

value: peripheral blood


title: 1792, Mus musculus, Trachea,Trachea

description: Library name: itox001792


title: mCherry-6h-rep1

description: Library name: mChe-6h-rep1


title: 1808, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001808

source_name: Urinary Bladder,Urinary Bladder

value: Urinary Bladder,Urinary Bladder


title: Lung, Progressive disease, Pre-treatment, TMRE high

description: Library name: 9341-ML-9

value: CD3+ T cells


title: mCherry-24h-rep2

description: Library name: mChe-24h-rep2


title: Lung, Partial disease, Post-treatment initiation, TMRE low, Patient 1

description: Library name: 9341-ML-4


title: 1794, Mus musculus, Trachea,Trachea

description: Library name: itox001794

value: Trachea,Trachea


title: CT-6h-rep3

description: Library name: CT-6h-rep3


title: 12217, Sus scrofa, Thalamus,Thalamus

description: Library name: itox012217

source_name: Thalamus,Thalamus

value: Thalamus,Thalamus


title: Lung  Stable disease, Pre-treatment, TMRE low, Patient 1

description: Library name: 9341-ML-6

source_name: peripheral blood


title: Lung, Stable disease, Pre-treatment, TMRE high, Patient 1

description: Library name: 9341-ML-5


title: 12215, Sus scrofa, Stomach,Stomach

description: Library name: itox012215


title: 1793, Mus musculus, Trachea,Trachea

description: Library name: itox001793


title: Lung, Partial disease, Post-treatment initiation, TMRE high, Patient 1

description: Library name: 9341-ML-3


title: 12240, Sus scrofa, Parathyroid Gland,Parathyroid Gland

description: Library name: itox012240

source_name: Parathyroid Gland,Parathyroid Gland

value: Parathyroid Gland,Parathyroid Gland


title: 1809, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001809


title: p30_sham_4

first: zheng

last: sixie

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong Univerisity School of Medicine

description: Library name: Sample 9

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38(mm10)
Supplementary files format and content: FPKM

source_name: lung

growth_protocol: The postnatal  mice were breastfed by the motherand were housed in groups of 5-6 per cage, fed under the same conditions with free access to food and water, maintained in the 12h: 12h day: night cycle.

extract_protocol:
Lung tissue  was rapidly removed from executed mice and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The P7 mice were anesthetized using 4% isoflurane, then were performed with a midline laparotomy to expose the abdominal aorta (AA) and inferior vena cava (IVC). After puncturing through the AA into the IVC with a needle of 11-0 nylon thread, a hemostatic compression for 2 min with the surrounding connective tissue was performed. At last, the abdominal wall was closed, and the pups were returned to their mother.  The mice in Sham group underwent the same procedure except for the puncture step.

value: lung

value: WT

value: Sham operated


title: p30_sham_5

description: Library name: Sample 10


title: 12238, Sus scrofa, Adrenal Gland,Adrenal Gland

description: Library name: itox012238

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: 1726, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001726

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: CT-6h-rep1

description: Library name: CT-6h-rep1

value: HUVEC


title: 12241, Sus scrofa, Pituitary Gland,Pituitary Gland

description: Library name: itox012241

source_name: Pituitary Gland,Pituitary Gland

value: Pituitary Gland,Pituitary Gland


title: 2518, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002518


title: Lung, Partial disease, Pre-treatment, TMRE high, Patient 1

description: Library name: 9341-ML-1


title: 1851, Mus musculus, Seminal Vesicles,Seminal Vesicles

description: Library name: itox001851

source_name: Seminal Vesicles,Seminal Vesicles

value: Seminal Vesicles,Seminal Vesicles


title: CT-6h-rep2

description: Library name: CT-6h-rep2


title: Kidney, Partial disease Pre-treatment, Progressive disease Post-treatment initiation, TMRE high

description: Library name: 8418-ML-10


title: 2519, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002519


title: 12243, Sus scrofa, Thyroid Gland,Thyroid Gland

description: Library name: itox012243

source_name: Thyroid Gland,Thyroid Gland

value: Thyroid Gland,Thyroid Gland


title: p30_sham_3

description: Library name: Sample 8


title: p30_sham_1

description: Library name: Sample 6


title: 12244, Sus scrofa, Heart,Heart

description: Library name: itox012244

source_name: Heart,Heart

value: Heart,Heart


title: Lung, Partial disease, Pre-treatment, TMRE low, Patient 1

description: Library name: 9341-ML-2


title: p30_sham_2

description: Library name: Sample 7


title: 2521, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox002521

source_name: Heart - Atrium,Heart - Atrium

value: Heart - Atrium,Heart - Atrium


title: Kidney, Partial disease Pre-treatment, Progressive disease Post-treatment initiation, TMRE low

description: Library name: 8418-ML-9

value: peripheral blood


title: 12242, Sus scrofa, Salivary Gland,Salivary Gland

description: Library name: itox012242

value: Salivary Gland,Salivary Gland


title: 2520, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002520


title: 2522, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox002522


title: Kidney, Mixed disease, Partial disease, Post-treatment initiation, TMRE high

description: Library name: 8418-ML-8

value: CD3+ T cells


title: 12245, Sus scrofa, Heart,Heart

description: Library name: itox012245


title: Kidney, Mixed disease, Partial disease, Post-treatment initiation, TMRE low

description: Library name: 8418-ML-7


title: p30_ipf_5

description: Library name: Sample 5

value: fistula surgery


title: p30_ipf_4

description: Library name: Sample 4


title: 12246, Sus scrofa, Heart,Heart

description: Library name: itox012246


title: Kidney, Mixed disease, Progressive disease, Pre-treatment, TMRE high

description: Library name: 8418-ML-6


title: 2542, Mus musculus, Colon (mid),Colon (mid)

description: Library name: itox002542

source_name: Colon (mid),Colon (mid)

value: Colon (mid),Colon (mid)


title: p30_ipf_3

description: Library name: Sample 3


title: Kidney, Mixed disease, Progressive disease, Pre-treatment, TMRE low

description: Library name: 8418-ML-5


title: 12247, Sus scrofa, Heart,Heart

description: Library name: itox012247


title: 2523, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox002523


title: p30_ipf_2

description: Library name: Sample 2


title: 12248, Sus scrofa, Heart,Heart

description: Library name: itox012248


title: 2524, Mus musculus, Thymus,Thymus

description: Library name: itox002524

source_name: Thymus,Thymus

value: Thymus,Thymus


title: p30_ipf_1

description: Library name: Sample 1

value: lung


title: KO 4 Treg

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: University of Cologne

description: Library name: Sample 8

data_processing:
RNA‐seq data were analyzed using the Cologne Center for Genomics’ in‐house pipeline for RNA‐Seq analysis based on the nextflow DSL (version 20.01.0 build 5264)
Assembly: GRCm38
Supplementary files format and content: countTables.xlsx (including raw counts, FPKM, DeSEQ2 normalized counts)

source_name: CD4 T cells

growth_protocol: CD4+ T cell were cultured in RPMI medium + 10%FCS supplemented with 100 U/mL human recombinant IL-2 (10ngr/mL) (PeproTech, Cat# 200-02), TGF-β (10ngr/mL) (Thermo Fisher Scientific,  Cat#100-21-100UG), anti-IFNγ (4mg/mL) (Bio X Cell, Cat#BP0055), anti-IL4 (mg/mL) (Bio X Cell, Cat# BP0045)

extract_protocol:
RNA was extracted using Rneasy mini kit (qiagen)
Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation Kit. Library preparation started with 500ng total RNA. After poly-A selection (poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This was followed by second-strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (15 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent Tape Station), equimolar amounts of the library were pooled. The pools were quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced on an Illumina NovaSeq6000 sequencing instrument with a PE100 protocol.

treatment_protocol: no treatment

value: CD4 T cells

value: KO


title: 12250, Sus scrofa, Kidney,Kidney

description: Library name: itox012250

source_name: Kidney,Kidney

value: Kidney,Kidney


title: 12249, Sus scrofa, Hippocampus,Hippocampus

description: Library name: itox012249

source_name: Hippocampus,Hippocampus

value: Hippocampus,Hippocampus


title: 2525, Mus musculus, Thymus,Thymus

description: Library name: itox002525


title: Kidney, Progessive disease, Stable disease, Pre-treatment, TMRE high

description: Library name: 8418-ML-2


title: 1731, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001731

value: Eye (minus lens),Eye (minus lens)


title: KO 3 Treg

description: Library name: Sample 7


title: Kidney, Progessive disease, Stable disease, Post-treatment initiation, TMRE high

description: Library name: 8418-ML-4


title: KO 2 Treg

description: Library name: Sample 6


title: 2509, Mus musculus, Skin (inguinal),Skin (inguinal)

description: Library name: itox002509

source_name: Skin (inguinal),Skin (inguinal)

value: Skin (inguinal),Skin (inguinal)


title: 2508, Mus musculus, Artery- Aorta (abdominal descending) -Pooled,Artery- Aorta (abdominal descending) -Pooled

description: Library name: itox002508


title: 12252, Sus scrofa, Cecum,Cecum

description: Library name: itox012252

source_name: Cecum,Cecum

value: Cecum,Cecum


title: 10xMultiome, PF-EPN brain tumor, PF10

city: Memphis

first: Stephen

middle: C.

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

description:
Library name: PF10
10xGenomics

library_source: other

data_processing:
The CellRanger-arc count pipelines (v2.0.2, 10X Genomics) were used to process sequenced 10xMultiome data. The CellRanger-arc pipeline performs filtering and alignment of  snATAC-seq/snRNA reads and identifies the transposase cut sites for snATAC.
Assembly: GRCh38 (refdata-cellranger-arc-GRCh38-2020-A-2.0.0)
Supplementary files format and content: filtered_feature_bc_matrix.h5: the file includes barcodes,  gene IDs, peak regions, gene expression, and atac count data
Supplementary files format and content: atac_fragments.tsv.gz: snATAC fragment data
Supplementary files format and content: atac_fragments.tsv.gz.tbi: snATAC fragment index data

molecule: other

source_name: PF-EPN brain tumor

extract_protocol:
10-30mg of tissue was cut from tumors and was input into the 10x Nuclei Isolation Kit (PN-1000494). Kit instructions were followed but lysis buffer incubation time was increased to 15 minutes to isolate quality nuclei. Nuclei were resuspended in nuclei buffer supplied in the 10x Chromium Next GEM Single Cell Multiome Kit, counted via hemocytometer, and 10,000 were loaded onto the 10x Chromium Chip.
Libraries were constructed using the 10x Chromium Next GEM Single Cell Multiome Kit and assessed via Agilent High Sensitivity D5000 TapeStation. They were then sent for sequencing at St. Jude’s Hartwell Center on a NovaSeq 6000. Gene Expression libraries had 400 million reads with a 28-10-10-90 cycle configuration and ATAC libraries had 500 million reads with a 50-8-24-49 cycle configuration.

value: PF-EPN brain tumor


title: KO 1 Treg

description: Library name: Sample 5


title: 10xMultiome, PF-EPN brain tumor, PF9

description:
Library name: PF9
10xGenomics


title: Kidney, Progessive disease, Stable disease, Post-treatment initiation, TMRE low

description: Library name: 8418-ML-3

source_name: peripheral blood


title: 12253, Sus scrofa, Colon,Colon

description: Library name: itox012253

source_name: Colon,Colon

value: Colon,Colon


title: 12254, Sus scrofa, Rectum,Rectum

description: Library name: itox012254

source_name: Rectum,Rectum

value: Rectum,Rectum


title: 2530, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002530


title: Wt 3 Treg

description: Library name: Sample 3

value: Wt


title: 12251, Sus scrofa, Kidney,Kidney

description: Library name: itox012251


title: Kidney, Progessive disease, Stable disease, Pre-treatment, TMRE low

description: Library name: 8418-ML-1

value: peripheral blood


title: 10xMultiome, PF-EPN brain tumor, PF7

description:
Library name: PF7
10xGenomics


title: 10xMultiome, PF-EPN brain tumor, PF8

description:
Library name: PF8
10xGenomics


title: 2531, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002531


title: 2532, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002532


title: 12236, Sus scrofa, Frontal Lobe,Frontal Lobe

description: Library name: itox012236

source_name: Frontal Lobe,Frontal Lobe

value: Frontal Lobe,Frontal Lobe


title: Wt 2 Treg

description: Library name: Sample 2


title: 10xMultiome, PF-EPN brain tumor, PF6

description:
Library name: PF6
10xGenomics


title: Wt 1 Treg

description: Library name: Sample 1


title: Wt 4 Treg

description: Library name: Sample 4


title: 11722, Sus scrofa, Adipose,Adipose

description: Library name: itox011722

source_name: Adipose,Adipose

value: Adipose,Adipose


title: 2533, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002533


title: 10xMultiome, PF-EPN brain tumor, PF5

description:
Library name: PF5
10xGenomics


title: 2534, Mus musculus, Spleen,Spleen

description: Library name: itox002534

source_name: Spleen,Spleen

value: Spleen,Spleen


title: 10xMultiome, PF-EPN brain tumor, PF4

description:
Library name: PF4
10xGenomics


title: Liver from WT mice, rep 2

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Liver_WT2

data_processing:
Libraries were sequenced by the Illumina Novaseq 6000 using SP mode 100 cycles kit (Illumina)
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154))
Reads were trimmed using cutadapt (DOI:10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
The remaining reads were mapped to the genome using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Assembly: mm10
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

source_name: Liver

growth_protocol: Mice were grown in normal conditions

extract_protocol:
RNA was extracted using TRI reagent (Sigma), following standard extraction protocol.
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

treatment_protocol: Otub2 knock-out and WT mice were sacrificed by cervical dislocation. Pancreas and livers were removed by standard protocols

value: Liver

value: OTUB2 +/+


title: 11723, Sus scrofa, Adipose,Adipose

description: Library name: itox011723


title: 12235, Sus scrofa, Retina,Retina

description: Library name: itox012235

source_name: Retina,Retina

value: Retina,Retina


title: 2535, Mus musculus, Spleen,Spleen

description: Library name: itox002535


title: 2536, Mus musculus, Spleen,Spleen

description: Library name: itox002536


title: 10xMultiome, PF-EPN brain tumor, PF3

description:
Library name: PF3
10xGenomics


title: Liver from WT mice, rep 1

description: Library name: Liver_WT1


title: 11724, Sus scrofa, Artery,Artery

description: Library name: itox011724

source_name: Artery,Artery

value: Artery,Artery


title: 11729, Sus scrofa, Corpus Callosum,Corpus Callosum

description: Library name: itox011729

source_name: Corpus Callosum,Corpus Callosum

value: Corpus Callosum,Corpus Callosum


title: 10xMultiome, PF-EPN brain tumor, PF2

description:
Library name: PF2
10xGenomics


title: 2537, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox002537

source_name: Stomach (glandular),Stomach (glandular)

value: Stomach (glandular),Stomach (glandular)


title: 11731, Sus scrofa, Epididymis,Epididymis

description: Library name: itox011731

source_name: Epididymis,Epididymis

value: Epididymis,Epididymis


title: 11730, Sus scrofa, Dorsal Root Ganglion,Dorsal Root Ganglion

description: Library name: itox011730


title: 10xMultiome, PF-EPN brain tumor, PF1

description:
Library name: PF1
10xGenomics


title: 1734, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001734

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: Liver from Heterozygote mice, rep 3

description: Library name: Liver_HET3

value: OTUB2 +/-


title: 10xMultiome, ZFTA-RELA fusion EPN brain tumor, ZR6

description:
Library name: ZR6
10xGenomics

source_name: ZFTA-RELA fusion EPN brain tumor

value: ZFTA-RELA fusion EPN brain tumor


title: 2538, Mus musculus, Cecum,Cecum

description: Library name: itox002538

value: Cecum,Cecum


title: 2539, Mus musculus, Cecum,Cecum

description: Library name: itox002539


title: 10xMultiome, ZFTA-RELA fusion EPN brain tumor, ZR5

description:
Library name: ZR5
10xGenomics


title: 11732, Sus scrofa, Esophagus,Esophagus

description: Library name: itox011732

source_name: Esophagus,Esophagus

value: Esophagus,Esophagus


title: 11733, Sus scrofa, Eye,Eye

description: Library name: itox011733

source_name: Eye,Eye

value: Eye,Eye


title: Liver from Heterozygote mice, rep 2

description: Library name: Liver_HET2


title: 10xMultiome, ZFTA-RELA fusion EPN brain tumor, ZR4

description:
Library name: ZR4
10xGenomics


title: Liver from Heterozygote mice, rep 1

description: Library name: Liver_HET1


title: Pancreas from WT mice, male, rep 12

description: Library name: Pancreas_WT_M_12

source_name: Pancreas

value: Pancreas


title: Liver from Heterozygote mice, rep 4

description: Library name: Liver_HET4


title: 2540, Mus musculus, Colon (mid),Colon (mid)

description: Library name: itox002540

source_name: Colon (mid),Colon (mid)

value: Colon (mid),Colon (mid)


title: 10xMultiome, ZFTA-RELA fusion EPN brain tumor, ZR3

description:
Library name: ZR3
10xGenomics


title: CRISPR

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

description:
Library name: M13-CRISPR
Filtered feature-barcode matrix

data_processing:
Single-cell RNA-seq outputs were processed using the Cell Ranger (10X Genomics). Raw reads were mapped to a merged and modified genome of hg 38.
Secondary analysis was conducted using the Seurat 4.0.5 package in R version 4.1
Assembly: hg38
Supplementary files format and content: Filtered feature-barcode matrix

growth_protocol: MOLM-13 cells were cultured in DMEM medium supplement with 10% FBS and 1% Penstrep.

extract_protocol:
BFP positive cells were counted to ~3X104 cells for each sample and subjected for cell sorting followed by single cell capture was performed at UAB Single Cell Sequencing core facility using 10x Genomics platform.
RNA libraries were prepared by Single Cell 3’ v3.1 kit (10xGenomics) according to the manufacturer’s manual.

value: WT


title: Liver from Heterozygote mice, rep 5

description: Library name: Liver_HET5


title: Pancreas from WT mice, male, rep 11

description: Library name: Pancreas_WT_M_11


title: Pancreas from WT mice, female, rep 16

description: Library name: Pancreas_WT_F_16


title: 2604, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002604

source_name: Whole Blood,Whole Blood

value: Whole Blood,Whole Blood


title: VTP_WM119 Replicate 2

description:
Library name: VTP_WM119 Replicate 2
Column name in Read counts.csv: VTP_WM119_R2

data_processing:
The paired-end reads were mapped to the human genome (hg38) using STAR (v2.5.1b) with default parameters.
DESeq2 was used to identify differentially identified genes between comparision groups.
Assembly: hg38
Supplementary files format and content: csv file including raw counts for each samples.

source_name: Cell line

extract_protocol:
Total RNA was isolated using TRI Reagent and Direct-zol RNA Miniprep Kits (Zymo Research, R2053).
Sequencing libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina.


title: 10xMultiome, PLAG/L fusion brain tumor, PLAG/L5

description:
Library name: PLAG/L5
10xGenomics

source_name: PLAG/L fusion brain tumor

value: PLAG/L fusion brain tumor


title: Gene Expression

description:
Library name: M13-Gene Expression
Filtered feature-barcode matrix


title: 11734, Sus scrofa, Eye,Eye

description: Library name: itox011734


title: 10xMultiome, ZFTA-RELA fusion EPN brain tumor, ZR1

description:
Library name: ZR1
10xGenomics


title: Pancreas from Homozygote mice, male, rep 10

description: Library name: Pancreas_HOM_M_10

value: OTUB2 -/-


title: Pancreas from Homozygote mice, male, rep 21

description: Library name: Pancreas_HOM_M_21


title: Pancreas from Heterozygote mice, male, rep 16

description: Library name: Pancreas_HET_M_16


title: WM119 Replicate 1

description:
Library name: WM119 Replicate 1
Column name in Read counts.csv: WM119_R1


title: 10xMultiome, ZFTA-RELA fusion EPN brain tumor, ZR2

description:
Library name: ZR2
10xGenomics


title: 1741, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001741


title: WM119 Replicate 2

description:
Library name: WM119 Replicate 2
Column name in Read counts.csv: WM119_R2


title: Pancreas from Homozygote mice, male, rep 19

description: Library name: Pancreas_HOM_M_19


title: 10xMultiome, PLAG/L fusion brain tumor, PLAG/L3

description:
Library name: PLAG/L3
10xGenomics


title: 10xMultiome, PLAG/L fusion brain tumor, PLAG/L4

description:
Library name: PLAG/L4
10xGenomics


title: VTP Replicate 2

description:
Library name: VTP Replicate 2
Column name in Read counts.csv: VTP_R2


title: VTP_WM119 Replicate 1

description:
Library name: VTP_WM119 Replicate 1
Column name in Read counts.csv: VTP_WM119_R1


title: Pancreas from Heterozygote mice, male, rep 15

description: Library name: Pancreas_HET_m_15


title: 2608, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002608


title: Pancreas from Heterozygote mice, male, rep 10

description: Library name: Pancreas_HET_M_10


title: 2609, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002609


title: 2607, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002607


title: 10xMultiome, PLAG/L fusion brain tumor, PLAG/L2

description:
Library name: PLAG/L2
10xGenomics


title: 2606, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002606


title: 2603, Mus musculus, Spleen,Spleen

description: Library name: itox002603

value: Spleen,Spleen


title: 10xMultiome, PLAG/L fusion brain tumor, PLAG/L1

description:
Library name: PLAG/L1
10xGenomics


title: 2590, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002590


title: DMSO Replicate 2

description:
Library name: DMSO Replicate 2
Column name in Read counts.csv: DMSO_R2

value: DMSO


title: ATACseq_HG03464_rep3

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: Library name: Sample23

data_processing:
10X linked-reads: 10X linked-reads were mapped to the hg38-based reference genome (refdata-GRCh38-2.1.0) provided by 10X Genomics using the Long Ranger pipeline v2.2.2 with the “--precalled” parameter to specify a VCF file containing variant data from the 1000 Genomes Project.
Hi-C: Hi-C reads were mapped to the hg38 human reference genome assembly using bwa mem with the Open2C distiller-nf pipeline. Mapped reads were parsed using pairtools with the walks-policy parameter set to mask and the max_mismatch_bp parameter set to 1. Read pairs were then binned into Hi-C contact matrices. Iterative correction of the matrices and removal of low coverage bins was performed using the "balance" function from cooler.!Sample_data_processing = ATAC-seq: ATAC-seq reads were mapped to the hg38 reference human genome and both haplotypes 1 and 2 of the personal genome using bwa v0.7.17-r1188. Uniquely mapped reads that were not mapped to mitochondrial DNA and had MAPQ > 10 were selected using SAMtools v1.6. Duplicate reads were filtered out using the Picard v2.27.4 “MarkDuplicates” function. Peak calling was performed using MACS2 v2.2.6.
TT-seq: TT-seq reads were mapped using STAR v2.7.10a with the “--outFilterMultimapNmax” set to 20, the “--alignSJoverhangMin” set to 999, the “--alignSJDBoverhangMin” set to 1, the “--outFilterMismatchNmax” set to 999, the “--outFilterMismatchNoverReadLmax” set to 0.04. Uniquely mapped reads with MAPQ>10 were selected using SAMtools v1.6. Duplicate reads were filtered out using the Picard v2.27.4 “MarkDuplicates” function. Gene counts were obtained using the ”htseq-count” function from HTSeq v0.13.5.
Assembly: hg38
Supplementary files format and content: ATAC-seq: normalized signal tracks in bigWig format; peaks in BED format; peak counts in TXT format. TT-seq: normalized signal tracks in bigWig format; read counts in TXT format. Hi-C: contact matrices in MCOOL format.

source_name: HG03464 lymphoblastoid cell line

growth_protocol: Lymphoblastoid cell lines were cultured in suspension in 80% RPMI-1640 media (Gibco) supplemented with 20% fetal bovine serum, 2 mM L-glutamine, and 1X penicillin/streptomycin.

extract_protocol:
10X linked-reads: Linked-reads data generation was outsourced to NGX Bio. For each sample, 3 million cells were harvested in PBS and the frozen cell pellets were sent to NGX Bio for processing. The resulting high molecular weight DNA was extracted using the MagAttract HMW DNA Extraction Kit (Qiagen). The quality of the DNA was assessed using the TapeStation system (Agilent Technologies).
Hi-C: Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Haarhuis et al., 2017). Cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI (NEB), and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down.
ATAC-seq: Cells were washed in cold PBS and subjected to lysis using a 2x lysis buffer. Subsequently, the cells were centrifuged, and the resulting pellet was treated with 2xTD buffer and 2 uL of transposon mix.
TT-seq: Libraries for TTchem-seq were prepared following a published protocol (Gregersen et al., 2020). Cells were labelled with 2 mM of the uridine analog 4-thiouridine (4sU) for 10 min. Total RNA was isolated and fragmented. The 4sU-biotin labelled RNA was enriched using µMacs Streptavidin Kit (Miltenyi).
10X linked-reads: Libraries were prepared using the 10X Genomics GemCode platform with reagents from 10X Genomics and the KAPA Hyper Prep Kit (Roche).
Hi-C: Hi-C libraries were prepared using a standard end-repair and A-tailing method.
ATAC-seq: PCR amplification was conducted using KAPA HiFi HotStart ReadyMix (Roche). Fragments ranging from 200 to 700 bp were purified utilising AMPure XP beads (Beckman Coulter).
TT-seq: Libraries were prepared using KAPA RNA HyperPrep and KAPA Dual-Indexed Adapter kits (Roche) using dual indexing adapters.

value: HG03464 lymphoblastoid cell line

value: B-Lymphocyte


title: 1742, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001742


title: 2591, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002591


title: Pancreas from Heterozygote mice, female, rep 9

description: Library name: Pancreas_HET_f9


title: 866, Homo sapiens, AoEC,AoEC

description: Library name: itox000866

source_name: AoEC,AoEC

value: AoEC,AoEC


title: Pancreas from Heterozygote mice, female, rep 11

description: Library name: Pancreas_HET_f11


title: 867, Homo sapiens, LMVEC,LMVEC

description: Library name: itox000867

source_name: LMVEC,LMVEC

value: LMVEC,LMVEC


title: CRC2899_N

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

description: Library name: Sample 73

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads preprocessing was performed by Trim_galore with default parameters.
Mapping of RNA-seq reads was done using bowtie2 with default parameters for paired  RNA-seq data.
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Assembly: hg19
Supplementary files format and content: txt format; processed counts, TPM (Transcripts Per Kilobase Million).

source_name: matched normal

extract_protocol:
RNA was isolated using EZNA total RNA Kit (Omega #R6834-02) according to manufacturer’s instructions.
The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: matched normal


title: ATACseq_HG03464_rep2

description: Library name: Sample22


title: DMSO Replicate 1

description:
Library name: DMSO Replicate 1
Column name in Read counts.csv: DMSO_R1


title: muscle_bcy_rep2

city: Carlsbad

first: Juliana

middle: S

last: Capitanio

state: CA

address: 2855 Gazelle Court

institute: Ionis Pharmaceuticals

description: 10x genomics

data_processing:
Fastq files were processed with 10x Genomics Cell Ranger 7.2.0 to align reads and generate feature-barcode matrices. Data QC was performed using the Seurat (v4) package, and it involved ambient RNA removal and filtering of low-quality cells, which were identified by mitochondrial RNA above 5%, number of detected gene above 3,000 or below 350, unique molecular identifier (UMI) counts above 10,000 or below 500, or complexity below 0.8. Non-expressed genes and genes expressed by less than 10 cells were removed from the analysis. Data normalization and variance stabilization were performed using SCTransform, and data integration was performed using Harmony. After dimensionality reduction (UMAP, resolutions between 0.2 and 1.2) and clustering (shared nearest neighbor modularity optimization), cell types present in each cluster were identified based on the expression of curated marker genes.
Assembly: mm10
Supplementary files format and content: tsv and mtx files

molecule: nuclear RNA

source_name: muscle-gastrocnemius

extract_protocol:
Muscle nuclei were isolated using a modified version of the 10x Genomics Chromium Nuclei Isolation Kit for Single Cell Multiome ATAC + Gene Expression. In brief, approximately 50 mg of flash frozen gastrocnemius muscle were pulverized in Covaris tissueTUBE TT2 with one pulse of the CP02 cryoPREP Automated Dry pulverizer at the highest impact setting. Pulverized samples were transferred to pre-chilled sample dissociation tubes provided in the 10x Genomics Nuclei Isolation Kit, and nuclei were isolated as directed in the manufacturer’s instructions. Nuclei suspensions were diluted to 1,000 nuclei/l using fluorescent nucleic acid staining (AOPI), and nuclei quality was confirmed under 40x magnification.
The single nuclei suspension was loaded onto Chromium X (10x Genomics) for targeting of 6,000 nuclei, according to the manufacturer's instructions. Libraries were constructed using Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics). Quantity and quality of cDNA and indexed libraries were determined with Qubit 1X dsDNA HS Assay Kit (Thermo Fisher Scientific) and High Sensitivity DNA ScreenTape Analysis (Agilent).

value: muscle-gastrocnemius

value: BCY17901-Malat1 ASO -3mpk


title: S1 25DIV iPSC-Derived Microglia

city: Braine L'Alleud

first: Jan

middle: R

last: Detrez

address: Chemin du Foriest 1

country: Belgium

institute: UCB

description: Library name: S1

data_processing:
Raw bcl files were converted to FASTQ by 10X’s tool cellranger mkfastq v.7.1, Followed by creation of gene expression matrices by cellranger count v.7.1 using the provided merged GRCh38 and mm10 genome. Samples were pre-filtered during import in R with Seurat::CreateSeuratObject  set to filter keeping a minimum of 10 cells per gene and 200 genes per cell. Following visualisation of the distribution of features, samples were additionally filtered, keeping cells with more than 2000 genes per cell and less than 10% mitochondrial genes. Normalisation was done using Seurat::SCTransform using glmGamPoi, regressing out the cell cycle gene score, the percentage of mitochondrial genes, the processing batch, number of features, and the original identity. Multi-resolution clustering was performed initially, and an appropriate resolution was chosen based on its alignment with the biology. A processing batch effect was observed between subsequent 10X chip runs, and harmony:: RunHarmony was performed, effectively mering separated clusters. Automated cluster annotation was performed by ScType 39, followed by manual curation of the clusters based on canonical marker expression. Cluster pseudo-bulk differential gene expression (DEG) analysis was done by aggregating the count matrix to sample levels, followed by re-clustering of the raw count matrix per cluster and DESeq2::DESeq analysis and visualisation in volcano plots with cut-offs for false discovery rate (FDR) corrected p-values at 0.05 and an absolute log10 fold change (FC) at 1. All figures were generated by pseudo-bulk clustering, unless indicated otherwise. Gene enrichment was done through fgsea::fgsea, using GO database m5.all.v2022.1.Mm.
Assembly: refdata-gex-GRCh38-and-mm10-2020
Supplementary files format and content: delimited file containing aligned cellular barcodes

molecule: polyA RNA

extract_protocol:
Mice were perfused with ice-cold 1X HBSS with 10 U/ml heparin, together with transcriptional inhibitors were added actinomycin D (5 µg/ml), triptolide (10 µM) as was done in other studies 12. Samples were collected on ice in 1X HBSS that contained anisomycin (27.1 µg/ml) as a third transcription inhibitor, as well as RNase Inhibitor (0.2 U/μl) and DTT (1 mM). All compounds were used in all subsequent solutions at the same concentrations, together with and sample were kept at 4°C throughout the process. Brain dissociations were performed based on an adapted protocol previously described for CyTOF tissue processing. Brains were dissociated using a papain-based dissociation kit at 37 C and 5% CO2 for 30 min (according to the manufacturer’s instructions) with gentle titurations using 10 and 5 ml serological pipettes in 10 min intervals. Papain was inhibited by albumin-ovomucoid solution mixed with DNAse. Single cell suspensions were filtered through a 40 µm cell strainer and resuspended in Myelin Removal Beads II solution according to manufacturer’s instructions. Dynamag magnets were used to remove myelin from the solution. For cell culture cells, cells were detached using 37°C PBS and a cell scraper. After passing through a 40 µm cell strainer, cell suspensions were spun at 300 g for 5 min and resuspended in 1X PBS with 0.1% before loading on the Chromium device.
10X single-cell libraries were prepared following the manufacturer’s guidelines per mouse, without pooling. As 10X chips are limited to 8 samples per run, some experiments were run in multiple processing batches.

value: iPSC-derived Microglia


title: VTP Replicate 1

description:
Library name: VTP Replicate 1
Column name in Read counts.csv: VTP_R1


title: ATACseq_HG03464_rep1

description: Library name: Sample21


title: muscle_bcy_rep3

description: 10x genomics


title: 2611, Homo sapiens, Monocytes,Monocytes

description: Library name: itox002611

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human

source_name: Monocytes,Monocytes

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

value: Monocytes,Monocytes


title: ATACseq_HG02601_rep2

description: Library name: Sample19

source_name: HG02601 lymphoblastoid cell line

value: HG02601 lymphoblastoid cell line


title: 2612, Homo sapiens, T Lymphocytes CD4,T Lymphocytes CD4

description: Library name: itox002612

source_name: T Lymphocytes CD4,T Lymphocytes CD4

value: T Lymphocytes CD4,T Lymphocytes CD4


title: CRC2821_N_2

description: Library name: Sample 71


title: CRC2841_N_1

description: Library name: Sample 72


title: CRC2817_N

description: Library name: Sample 70


title: muscle_bcy_rep1

description: 10x genomics


title: ATACseq_HG02601_rep3

description: Library name: Sample20


title: muscle_unc_rep2

description: 10x genomics

value: Unconjugated Malat1 ASO -3mpk


title: ATACseq_HG01241_rep3

description: Library name: Sample17

source_name: HG01241 lymphoblastoid cell line

value: HG01241 lymphoblastoid cell line


title: ATACseq_HG02601_rep1

description: Library name: Sample18


title: 2613, Homo sapiens, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002613

source_name: T Lymphocytes CD8,T Lymphocytes CD8

value: T Lymphocytes CD8,T Lymphocytes CD8


title: CRC2816_N

description: Library name: Sample 69


title: CRC2811_N

description: Library name: Sample 68


title: ATACseq_HG01241_rep1

description: Library name: Sample15


title: 2615, Homo sapiens, B Cells,B Cells

description: Library name: itox002615

source_name: B Cells,B Cells

value: B Cells,B Cells


title: CRC2810_N

description: Library name: Sample 67


title: 2614, Homo sapiens, NK Cells,NK Cells

description: Library name: itox002614

source_name: NK Cells,NK Cells

value: NK Cells,NK Cells


title: muscle_PBS_rep2

description: 10x genomics

value: PBS


title: ATACseq_HG01241_rep2

description: Library name: Sample16


title: muscle_PBS_rep1

description: 10x genomics


title: 2616, Homo sapiens, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002616


title: ATACseq_NA18983_rep3

description: Library name: Sample14

source_name: GM18983 lymphoblastoid cell line

value: GM18983 lymphoblastoid cell line


title: 2617, Homo sapiens, Monocytes,Monocytes

description: Library name: itox002617


title: CRC2803_N

description: Library name: Sample 66


title: ATACseq_NA18983_rep2

description: Library name: Sample13

value: B-Lymphocyte


title: bTBL_R_1

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

description: 10x Genomics

data_processing:
FASTQ files were aligned to the GRCm39 mouse genome with Ensembl release 110 annotations to which the PhageP1_CRE gene was added. Pre-processing was performed with CellRanger software v7.1.0 (10x Genomics) for downstream analyses.
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreatic islets

extract_protocol:
For each sample, 150 islets were pooled and dissociated using TrypLE Express (Gibco) for 20 minutes at 37 °C. Cells were then washed with PBS containing 2% FBS, filtered through a 40 μm Flowmi™ Cell Strainer (Bel-Art) and diluted to a final concentration of ~1000 cells/µl in PBS containing 2% FBS. The cell suspension was immediately used for scRNA-seq library preparation with a target recovery of 10000 cells.
Libraries were prepped using the Chromium Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics, 1000268) according to the manufacturer’s instructions.

treatment_protocol: Isolated pancreatic islets were cultured in RPMI-1680 supplemented with 10% FBS and 1% pen/strep at 37°C overnight

value: pancreatic islets

value: TBL/RBKO

tag: age

value: 5 weeks


title: CRC2801_N

description: Library name: Sample 65

value: matched normal


title: 2619, Homo sapiens, T Lymphocytes CD4,T Lymphocytes CD4

description: Library name: itox002619


title: ATACseq_NA18983_rep1

description: Library name: Sample12


title: CRC2795_N

description: Library name: Sample 64


title: Mouse IUE2 ZFTA-RELA EPN10xMultiome - ATAC

data_processing:
The CellRanger-arc count pipelines (v2.0.1, 10X Genomics) were used to process sequenced 10xMultiome data. The CellRanger-arc pipeline performs filtering and alignment of  snATAC-seq/snRNA reads and identifies the transposase cut sites for snATAC.
Assembly: mm10 (10x Genomics, refdata-cellranger-arc-mm10-2020-A-2.0.0)
Supplementary files format and content: filtered_feature_bc_matrix.h5: the file includes barcodes,  gene IDs, peak regions, gene expression, and atac count data
Supplementary files format and content: atac_fragments.tsv.gz: snATAC fragment data
Supplementary files format and content: atac_fragments.tsv.gz.tbi: snATAC fragment index data
Library strategy: 10xMultiome (snATAC+snRNA)

source_name: Supratentorial ependymomas (with ZFTA-RELA fusion)

extract_protocol:
10-30mg of tissue was cut from tumors and was input into the 10x Nuclei Isolation Kit (PN-1000494). Kit instructions were followed but lysis buffer incubation time was increased to 15 minutes to isolate quality nuclei. Mouse embryonic forebrain was isolated with the 10x Demonstrated Protocol CG000366 RevD, but lysis buffer incubation was decreased to 2 minutes. Nuclei were resuspended in nuclei buffer, counted via hemocytometer, and 10,000 were loaded onto the 10x Chromium Chip.
Libraries were assessed via Agilent TapeStation and sent for sequencing at St. Jude’s Hartwell Center on a NovaSeq 6000. Gene Expression libraries had 400 million reads with a 28-10-10-90 cycle configuration and ATAC libraries had 500 million reads with a 50-8-24-49 cycle configuration.


title: 2618, Homo sapiens, NK Cells,NK Cells

description: Library name: itox002618


title: Ctr_1

description: 10x Genomics

value: wildtype


title: CRC2794_N

description: Library name: Sample 63


title: ATACseq_NA12878_rep3

description: Library name: Sample11

source_name: GM12878 lymphoblastoid cell line

value: GM12878 lymphoblastoid cell line


title: 2620, Homo sapiens, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002620


title: muscle_unc_rep1

description: 10x genomics

value: muscle-gastrocnemius


title: CRC2787_N

description: Library name: Sample 62


title: Mouse IUE0 ZFTA-RELA EPN,10xMultiome - ATAC

value: Supratentorial ependymomas (with ZFTA-RELA fusion)


title: 868, Homo sapiens, LSEC,LSEC

description: Library name: itox000868

source_name: LSEC,LSEC

value: LSEC,LSEC


title: 2621, Homo sapiens, NK Cells,NK Cells

description: Library name: itox002621


title: Mouse IUE1 ZFTA-RELA EPN,10xMultiome - ATAC


title: CRC2783_N

description: Library name: Sample 60


title: 2622, Homo sapiens, B Cells,B Cells

description: Library name: itox002622


title: Model_3

city: Dongtai

first: Hui

last: Sun

state: Jiangsu

address: No. 2 Kangfu West Road

department: Medical Laboratory Department

institute: Affiliated Dongtai Hospital of Nantong University

description:
Library name: sample 6
FABP4 si267 group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to the human reference genome GRCh38 (hg38) using CLC genomic benchwork (parameters: mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: cell culture

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture

value: FABP4 si267


title: Mouse IUE GBM10xMultiome - ATAC

source_name: Glioma brain tumor

value: Glioma brain tumor


title: E14.5 healthy forebrain10xMultiome - ATAC

source_name: Healthy forebrain

value: Healthy forebrain


title: CRC2899_Inv_2

description: Library name: Sample 59

source_name: colorectal tumor

value: colorectal tumor


title: CRC2899_Inv_1

description: Library name: Sample 58


title: Model_2

description:
Library name: sample 5
FABP4 si267 group, replicate biosample 2


title: Mouse IUE1 ZFTA-RELA EPN,10xMultiome - GEX


title: Mouse IUE2 ZFTA-RELA EPN,10xMultiome - GEX


title: 2623, Homo sapiens, Monocytes,Monocytes

first: Darien

last: Capunitan

address: 255 Shennecossett Rd

institute: Pfizer

description: Library name: itox002623

value: Monocytes,Monocytes


title: Control_3

description:
Library name: sample 3
control group, replicate biosample 3

value: wt


title: ATACseq_NA12878_rep1

description: Library name: Sample9

value: B-Lymphocyte


title: Model_1

description:
Library name: sample 4
FABP4 si267 group, replicate biosample 1


title: 2624, Homo sapiens, Monocytes,Monocytes

description: Library name: itox002624


title: CRC2899_core_2

description: Library name: Sample 57


title: ATACseq_NA12878_rep2

description: Library name: Sample10


title: Mouse IUE0 ZFTA-RELA EPN,10xMultiome - GEX


title: CRC2899_core_1

description: Library name: Sample 56


title: Control_2

description:
Library name: sample 2
control group, replicate biosample 2


title: muscle_unc_rep3

description: 10x genomics

source_name: muscle-gastrocnemius

value: Unconjugated Malat1 ASO -3mpk


title: Mouse IUE GBM,10xMultiome - GEX


title: 2625, Homo sapiens, B Cells,B Cells

description: Library name: itox002625

value: B Cells,B Cells


title: CRC2786_N

description: Library name: Sample 61

source_name: matched normal


title: 2627, Homo sapiens, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002627

value: T Lymphocytes CD8,T Lymphocytes CD8


title: Control_1

description:
Library name: sample 1
control group, replicate biosample 1


title: 2626, Homo sapiens, T Lymphocytes CD4,T Lymphocytes CD4

description: Library name: itox002626

value: T Lymphocytes CD4,T Lymphocytes CD4


title: CRC2841_Inv_3

description: Library name: Sample 55


title: E14.5 healthy forebrain,10xMultiome - GEX


title: CRC2841_core_1

description: Library name: Sample 54


title: A549, shRRM1, Decitabine treatment, bio rep2

city: Hangzhou

last: Jiang

state: Zhejiang

address: Yuhangtang Road No.866

institute: Zhejiang university

description: Library name: RRM1-KD-DAC-2

data_processing:
HTSEQ (V0.6.1)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes RPKM value for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The RNA-seq libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, catalog no. NR605-02).

value: non-small cell lung cancer cell line


title: 2628, Homo sapiens, NK Cells,NK Cells

city: Groton

description: Library name: itox002628

value: NK Cells,NK Cells


title: CRC2817_core_2

description: Library name: Sample 52


title: CRC2821_core_4

description: Library name: Sample 53


title: 2630, Homo sapiens, T Lymphocytes CD4,T Lymphocytes CD4

description: Library name: itox002630


title: 2629, Homo sapiens, B Cells,B Cells

description: Library name: itox002629


title: CD8 positive sorted CAR T-cell (Replicate 5), irradiated (RT, 8 Gy) from mouse Lung tumor

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

data_processing:
RNA-seq data was performed by nf-core/rnaseq pipeline (version 3.9).
In brief, adapters and low quality reads were filtered by trimgalore (0.6.6). Cleaned reads were aligned to the mouse reference genome with STAR and genes were quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Comma separated tables containing Salmon quantified raw gene counts for each sample. CPM values were created using EdgeR's cpm function.

source_name: Lung

extract_protocol:
Total RNA was extracted from cells following the Trizol Reagent User Guide (Thermo Fischer Scientific). Extracted RNA were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked using Qubit 2.0 Fluorometer.
SMARTSeq HT Ultra Low Input Kit was used for full-length cDNA synthesis and amplification, and Illumina Nextera XT library was used for library preparation.
Low count RNA-seq

value: Lung

value: CAR T cells

tag: cell subset

value: CD8 positive

value: 8 Gy


title: CD8 positive sorted CAR T-cell (Replicate 2), irradiated (RT, 8 Gy) from mouse Lung tumor


title: A549, shRRM1, Decitabine treatment, bio rep1

description: Library name: RRM1-KD-DAC-1


title: 2631, Homo sapiens, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002631


title: A549, shRRM1, DMSO treatment, bio rep3

description: Library name: RRM1-KD-3


title: CD8 positive sorted CAR T-cell (Replicate 3), irradiated (RT, 8 Gy) from mouse Lung tumor


title: CD8 positive sorted CAR T-cell (Replicate 4), irradiated (RT, 8 Gy) from mouse Lung tumor


title: CRC2816_Inv_2

description: Library name: Sample 51


title: CD8 positive sorted CAR T-cell (Replicate 1), irradiated (RT, 8 Gy) from mouse Lung tumor


title: 2632, Homo sapiens, Monocytes,Monocytes

description: Library name: itox002632

source_name: Monocytes,Monocytes


title: A549, shRRM1, DMSO treatment, bio rep1

description: Library name: RRM1-KD-1


title: CD8 positive sorted CAR T-cell (Replicate 5), unirradiated (NRT, 0 Gy) from mouse Lung tumor

value: 0 Gy


title: A549, shRRM1, DMSO treatment, bio rep2

description: Library name: RRM1-KD-2


title: 2466, Homo sapiens, Eye-Cornea,Eye-Cornea

description: Library name: itox002466

source_name: Eye-Cornea,Eye-Cornea

value: Eye-Cornea,Eye-Cornea


title: A549, shCtrl, Decitabine treatment, bio rep2

description: Library name: DAC-2


title: A549, shCtrl, Decitabine treatment, bio rep1

description: Library name: DAC-1


title: CD8 positive sorted CAR T-cell (Replicate 4), unirradiated (NRT, 0 Gy) from mouse Lung tumor


title: 2634, Homo sapiens, B Cells,B Cells

description: Library name: itox002634


title: CRC2811_core_1

description: Library name: Sample 49


title: 2633, Homo sapiens, NK Cells,NK Cells

description: Library name: itox002633


title: A549, shRRM1, Decitabine treatment, bio rep3

description: Library name: RRM1-KD-DAC-3


title: CRC2803_core_2

description: Library name: Sample 47


title: CRC2810_Inv_2

description: Library name: Sample 48


title: CRC2801_Inv_1

description: Library name: Sample 46


title: CRC2816_core_2

description: Library name: Sample 50


title: CD8 positive sorted CAR T-cell (Replicate 3), unirradiated (NRT, 0 Gy) from mouse Lung tumor


title: CRC2795_core_2

description: Library name: Sample 45


title: CD8 positive sorted CAR T-cell (Replicate 2), unirradiated (NRT, 0 Gy) from mouse Lung tumor


title: A549, shCtrl, DMSO treatment, bio rep3

description: Library name: Ctrl-3


title: 2635, Homo sapiens, T Lymphocytes CD4,T Lymphocytes CD4

description: Library name: itox002635

source_name: T Lymphocytes CD4,T Lymphocytes CD4


title: CRC2794_core_2

description: Library name: Sample 44


title: 2636, Homo sapiens, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002636

source_name: T Lymphocytes CD8,T Lymphocytes CD8


title: CD8 positive sorted CAR T-cell (Replicate 1), unirradiated (NRT, 0 Gy) from mouse Lung tumor


title: A549, shCtrl, DMSO treatment, bio rep2

description: Library name: Ctrl-2


title: A549, shCtrl, DMSO treatment, bio rep1

description: Library name: Ctrl-1


title: CRC2787_core_1

description: Library name: Sample 43


title: MKN45 cells, Negative control -3

city: Ji'nan

first: Shi

last: Duanbo

state: Shandong

address: wenhua xi road 44#

institute: Shandong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: ab-delimited text flies include RPKM values for each Sample

source_name: stomach

growth_protocol: MKN45 cells were supplemented with 10% fetal bovine serum (FBS) in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB #E7530S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: INHBA was overexpressed in MKN45 cells by transfecting LV-GV493-IHNBA, while the other cells was transfected with LV-GV493-Negative control as control group. All the cells were cultrued for 48 hours.

value: stomach

value: gastric cancer cell line

value: Negative control

value: MKN45 cells transfected with LV-GV493-Negative contol


title: CRC2786_Inv_1

description: Library name: Sample 42

value: colorectal tumor


title: 2638, Homo sapiens, NK Cells,NK Cells

description: Library name: itox002638

source_name: NK Cells,NK Cells


title: 2639, Homo sapiens, Blood,Blood

description: Library name: itox002639

source_name: Blood,Blood

value: Blood,Blood


title: MKN45 cells, Negative control -2


title: CRC2783_Inv_2

description: Library name: Sample 41


title: Mouse_cerebellum_E18_male_replicate2

city: Toronto

first: Michael

middle: D.

last: Taylor

state: Ontario

address: 555 University Ave

department: DSCB

country: Canada

institute: The Hospital for Sick Children

description: 10x Genomics

data_processing:
Cell Ranger software v.3.0.2 default pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebellum

extract_protocol:
Hindbrain structures were dissected from mice, dissociated into single cell suspensions using papain and were run on the 10X Genomics Chromium Controller using the Chromium Single Cell 3' Solution V3 protocols
10x Genomics Chromium Single Cell 3' Solution V3 protocols

value: cerebellum

tag: developmental stage

value: Embryonic day 18.5

tag: Sex

value: male

tag: strain

value: wild type


title: MKN45 cells, INHBA overexpressing -3

value: INHBA overexpressing

value: MKN45 cells transfected with LV-GV493-INHBA


title: CD4 positive sorted CAR T-cell (pooled from 5 mice), irradiated (RT, 8 Gy) from mouse Lung tumor

value: Lung

value: CAR T cells

value: CD4 positive


title: CV40_T

description: Library name: Sample 40


title: 2467, Homo sapiens, Eye-Retina,Eye-Retina

description: Library name: itox002467

source_name: Eye-Retina,Eye-Retina

value: Eye-Retina,Eye-Retina


title: 2637, Homo sapiens, Monocytes,Monocytes

description: Library name: itox002637

value: Monocytes,Monocytes