title: iPax3 re-isolated, N1KO, rep3

city: Minneapolis

first: Aline Miyoko

last: Sakaguchi Yamashita

state: Minnesota

address: 2231 6th St SE

department: Department of Medicine

institute: University of Minnesota

data_processing:
Data alignment and comparison of gene expression was analyzed using the CHURP pipeline at the UMGC. 2 x 150bp FASTQ paired-end reads for a total of 26 biological samples (22.8 million reads average per sample) were trimmed using Trimmomatic (v0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample was performed with FastQC. Read mapping was performed via HISAT241 (v2.1.0) using the mouse genome (GRCh39.106) as reference. Gene quantification was done via Feature Counts for raw read counts. Differentially expressed genes were identified using the EdgeR (negative binomial, R programming) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts. We filtered the generated list based on a minimum 2x absolute fold change and FDR-corrected p < 0.05.
Assembly: mm10
Supplementary files format and content: Combined_Notchcorr_cpm_.csv

source_name: re-isolated satellite cells

extract_protocol:
RNA isolation was performed in two different ways. For samples with high input (in vitro cells), iPax3 and iPax3-N1OE myogenic progenitors RNA was extracted using Trizol (Invitrogen) and RNA extraction Kit (Invitrogen) following manufacturer’s instructions. For samples with low input of RNA (in vivo cells, re-isolated donor-derived satellite cells), RNA was extracted using Buffer RLT (QIAGEN) and nucleic acid beads.
For samples with high input (in vitro cells), iPax3 and iPax3-N1OE myogenic progenitors. The total RNA was used to for generate unique dual-indexed (UDI) TruSeq stranded mRNA libraries. For samples with low input (in vivo cells, re-isolated donor-derived satellite cells). The cDNA was synthesized using the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification kit (New England Biolabs) and the libraries were generated with the Nextera XT DNA Library Preparation Kit (Illumina).

value: re-isolated satellite cells

value: iPAX3 cells

value: donor-derived satellite cells

value: Notch1 KO


title: cKO - Nestin-Cre; TDP-43 homozygous conditional knockout mouse, Cortex, ID-154

status: Public on Feb 02 2025

type: SRA

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

description: Library name: CTX_154

library_source: transcriptomic

data_processing:
The RNA-seq reads were pseudoaligned and quantified using kallisto v.46.1 with default parameters and 100 bootstraps.
Assembly: GRCm39 GENCODE vM29 Ensembl 106
Supplementary files format and content: abundance.h5: HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.
Supplementary files format and content: abundance.tsv.gz: plaintext file of the abundance estimates (estimated counts, TPM and effective length of transcript). These files do not contain bootstrap estimates.

molecule: polyA RNA

organism: Mus musculus

source_name: Cortex

growth_protocol: The mice were maintained at C57BL/6J background and housed in groups with individually ventilated cages under a 12:12-hour light/dark cycle and access to food/water ad libitum. Conditional TDP-43 (Tardbp-fl/fl) mice (stock number 017591) and Nestin-Cre (stock number 003771) were purchased from the Jackson Laboratory.

extract_protocol:
Cortex and thalamus tissues were dissected from 14.5 days old embryonic mice brains and flash frozen under liquid nitrogen. The RNA was harvested using Trizol reagent
RNA-Seq libraries were contructed using the Illumina TruSeq Sample Prep Kit

tag: tissue

value: Cortex

tag: strain

tag: genotype

value: Nestin-Cre;TDP-43 f/f

tag: Sex

value: female

tag: age


title: U2OS cells, shPin1#2, biological replicate 3

city: Chengdu

first: Ying

last: Tong

state: Sichuan

address: 29 Wangjiang Road

department: College of life science

country: China

institute: Sichuan University

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data.
Reads mapping to the reference genome: Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCh38/hg38/Ensemble 94
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: bone

growth_protocol: Human pancreatic adenocarcinoma PANC-1 and osteosarcoma U2OS cells were cultured in DMEM with 10% fetal bovine serum in a humidified 37oC incubator under a 5% CO2 atmosphere.

extract_protocol:
5×10^6 cells were collected and RNA was extracted using Trizol reagent. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: bone

tag: cell line

tag: cell type

value: osteosarcoma

value: Pin1 knockdown


title: Mus musculus Microglia Casp8flox/flox Female Young, Replicate 5

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

country: USA

institute: Northwestern University

description:
Library name: Microglia_Y_WT5
C8_Y_F5_MIC

data_processing:
Raw sequencing files were de-multiplexed using bcl2fastq.
Adapter sequences and low-quality bases were trimmed using bbduk.
Trimmed reads were aligned to the mouse genome (mm10) using STAR aligner.
Gene expression counts were quantified using HTSeq with GRCm38 gene reference.
Normalized expression values were calculated as counts per million (CPM).
Assembly: mm10
Supplementary files format and content: tab-delimited table of RNA counts across all samples
Supplementary files format and content: tab-delimited table of CPM values across all samples

source_name: brain

growth_protocol: Mice were housed in a barrier/specific-pathogen-free facility with controlled temperature and humidity. Female mice aged 5-6 months (young cohort) and 11-12 months (old cohort) were used for all experiments.

extract_protocol:
Brain tissues were harvested immediately following perfusion with ice-cold HBSS. Brains were dissociated using a combination of mechanical and enzymatic digestion (Liberase TL and DNase I), and cell populations were sorted by FACS based on surface markers. RNA was extracted from FACS-purified populations using the PicoPure RNA Isolation Kit following the manufacturer’s protocol.
RNA-seq libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina (Lexogen Inc.). Libraries were indexed and amplified according to the manufacturer's instructions. Samples were excluded based on experimental and technical factors that impact their quality.

value: Young:5 - 6 months

value: brain

value: microglia


title: Mus musculus Microglia Casp8flox/flox Female Young, Replicate 7

description:
Library name: Microglia_Y_WT7
C8_Y_F7_MIC


title: iPax3 re-isolated, N1KO, rep2


title: Mus musculus Microglia Casp8flox/flox Female Young, Replicate 2

description:
Library name: Microglia_Y_WT2
C8_Y_F2_MIC


title: cKO - Nestin-Cre; TDP-43 homozygous conditional knockout mouse, Cortex, ID-128

description: Library name: CTX_128

value: male


title: U2OS cells, shPin1#2, biological replicate 2


title: cKO - Nestin-Cre; TDP-43 homozygous conditional knockout mouse, Cortex, ID-108

description: Library name: CTX_108


title: U2OS cells, shPin1#2, biological replicate 1


title: OVCAR3 cells, DMSO treated, 1 hour, batch B, replicate 2

city: Madison

first: Alexander

middle: J

last: Fagan

state: WI

address: 1300 University Ave Room 1220

department: Department of Statistics

institute: UW-Madison

description: Library name: D_1_B_2

data_processing:
Gene expression counts were obtained using RSEM (RRID:SCR_000262) with the STAR aligner (RRID:SCR_004463).
Assembly: GRCh38 release 112
Supplementary files format and content: Tab-delimited text file containing estimated counts for each sample

growth_protocol: OVCAR3 (RRID:CVCL_0465) and OVCAR5 ((RRID:CVCL_1628) cell lines of female biological sex were utilized. Cells were maintained in the recommended culture media and incubated at 37°C in a humidified atmosphere with 5% CO2. Cell lines were used within six months of purchase or validated by Single Tandem Repeat (STR) analysis performed by the Translational Research Initiatives in Pathology (TRIP) laboratory at the University of Wisconsin, Madison. Cell lines were tested for mycoplasma regularly using the MycoscopeTM PCR Mycoplasma Detection

extract_protocol:
RNA extraction was performed using the RNeasy Mini kit from Qiagen.
Library preparation and RNA sequencing were performed by Novogene.

treatment_protocol: OVCAR3 cells were treated with atovaquone and vehicle (DMSO) at the stated concentrations and collected at different time points post-treatment using TRIzol. Three biological replicates were used for each experimental condition.

value: High-grade serous ovarian adenocarcinoma

value: WT

tag: treatment

value: DMSO

tag: time

value: Hour 1

tag: replicate

tag: batch

value: B


title: U2OS cells, shPin1#1, biological replicate 3


title: cKO - Nestin-Cre; TDP-43 homozygous conditional knockout mouse, Cortex, ID-104

description: Library name: CTX_104


title: iPax3 re-isolated, N1OE, rep4

value: re-isolated satellite cells

value: iPAX3 cells

value: donor-derived satellite cells

value: NICD1 overexpression


title: Mus musculus Microglia Casp8flox/flox Female Young, Replicate 1

description:
Library name: Microglia_Y_WT1
C8_Y_F1_MIC


title: iPax3 re-isolated, N1OE, rep3


title: cHet - Nestin-Cre; TDP-43 hemizygous conditional knockout mouse, Cortex, ID-156

description: Library name: CTX_156

value: Cortex

value: Nestin-Cre;TDP-43 f/+


title: U2OS cells, shPin1#1, biological replicate 2

value: bone

value: osteosarcoma


title: WTGFC

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

description:
Library name: SAMPLES 1
10X Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq data were pre-processed and qualitied with Seurat (version 4). We removed the cells that had greater than 15% expression originating from mitochondrial genes as well as expressed less than 200 genes or greater than 6,000 genes to filter out low-quality cells and doublets.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separted values files and matrix files

source_name: gut

extract_protocol:
For the collection of the immune cells in colon, mice were sacrificed by CO2 overdose and colon was removed and placed in ice-cold HBSS (GIBCO) with 5% FBS. Isolated cells were resuspended in 10 ml of the 40% fraction of a 40: 80 Percoll gradient and overlaid on 5 ml of the 80% fraction in a 15 ml Falcon tube. Percoll gradient separation was performed by centrifugation for 20 min at 1,800 rpm at room temperature. lymphocytes were collected at the interphase of the Percoll gradient, washed and resuspended in medium, and then stained for sorting and analyzed by flow cytometry. Dead cells were eliminated through 7-AAD staining.
According to the manufacture’s introduction, single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: gut

value: gut lamina propria


title: 17KO

description:
Library name: SAMPLES 2
10X Genomics

value: LncRNA17Rik knockout


title: iPax3 re-isolated, N1OE, rep2


title: OVCAR3 cells, DMSO treated, 1 hour, batch B, replicate 1

description: Library name: D_1_B_1


title: U2OS cells, shPin1#1, biological replicate 1

value: Pin1 knockdown


title: double negative DRGs

city: La Jolla

first: Yu

last: Wang

state: CA

address: 10550 N. Torrey Pines Rd.

institute: Scripps Research

description: Library name: unlabeled-DRGs

data_processing:
The Cell Ranger pipeline together with the mouse transcriptome mm10 were used to align the reads and to generate the gene-cell matrices.
Assembly: mm10
Supplementary files format and content: tab separated files and matrix file

source_name: Dorsal root ganglia

extract_protocol:
DRG neurons are dissected and dissociated and loaded to FACS sorting. Sorted cells are loadded onto 10x Genomics
Each sample was processed using the Chromium Next GEM Single Cell 3’ Reagent Kits, v3, single index (10x Genomics). Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10x Genomics; PN-1000092), the Chromium Chip B Single Cell Kit (10x Genomics; PN- 1000073), and the Chromium i7 Multiplex Kit v2 (10x Genomics; PN-120262). Briefly, single cells were partitioned into Gel Beads-in-emulsion (GEMS) using the Chromium X instrument (10x Genomics). The presence of poly(dT) primer enabled the creation of full-length cDNA from poly-adenylated mRNA. cDNA was amplified to generate adequate mass for library construction. Sequencing libraries were prepared using end repair, A-tailing, adaptor ligation followed by PCR.

value: Dorsal root ganglia


title: iPax3 re-isolated, N1OE, rep1


title: iPax3 re-isolated, N1KO, rep1

value: Notch1 KO


title: cHet - Nestin-Cre; TDP-43 hemizygous conditional knockout mouse, Cortex, ID-122

description: Library name: CTX_122

value: male


title: iPax3 re-isolated, control, rep9

value: WT


title: U2OS cells, shControl, biological replicate 3


title: U2OS cells, shControl, biological replicate 2


title: iPax3 re-isolated, control, rep8


title: Control - TDP-43 floxed mouse, Thalamus, ID-148

description: Library name: THL_148

source_name: Thalamus

value: Thalamus

value: TDP-43 f/f

value: female


title: U2OS cells, shControl, biological replicate 1


title: 647+ DRGs (CTB647 labeled from eWAT)

description: Library name: eWAT-DRGs


title: Control - TDP-43 floxed mouse, Cortex, ID-147

description: Library name: CTX_147


title: PANC-1 cells, shPin1#2, biological replicate 3

source_name: pancreas

value: pancreas

value: pancreatic adenocarcinoma


title: primary mouse brain microvascular endothelial cells-DTG treated-2

city: Toronto

first: Chang

last: Huang

state: Ontario

address: 386 yonge st, unit4008, unit 4008

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

description:
Library name: Sample 5
MBBB_DTG-2_P4_RM

data_processing:
Qiagen CLC Genomic Workbench v23.0.4 with default parameters
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: primary brain microvascular endothelial cells

growth_protocol: Primary cultures of mouse (C57BL/6) brain microvascular endothelial cells were cultured (passage 2-6) in complete Mouse Endothelial Cell Medium (M1168, Cell Biologics Inc, Chicago, Illinois, USA), supplemented with vascular endothelial growth factor, endothelia cell growth supplements, heparin, epidermal growth factor, hydrocortisone, L-glutamine, antibiotic-Antimycotic Solution, and 5% FBS, and grown on gelatin-coated tissue culture plates. Cell lines were maintained in a humidified incubator at 37 °C with 5% CO2, 95% air with fresh medium replaced every 2-3 days.

extract_protocol:
Total RNA was isolated from cell samples using TRIzol reagent (Invitrogen). A total amount of 2 μg of RNA was used for construction of sequencing libraries
RNA quality was first assessed by Agilent Fragment Analyzer, then was subjected to library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101) according to the manufacturer’s instructions.

treatment_protocol: Confluent monolayers of primary cultures of mouse brain microvascular endothelial cells were treated with DMSO (vehicle control) and DTG (5000 ng/ml) for a period of 24 h at 37 °C.

value: DTG 5000 ng/ml, 24h


title: iPax3 re-isolated, control, rep7

value: re-isolated satellite cells

value: iPAX3 cells

value: donor-derived satellite cells


title: primary mouse brain microvascular endothelial cells-DTG treated-1

description:
Library name: Sample 4
MBBB_DIG-2_P5_RM

value: primary brain microvascular endothelial cells


title: primary mouse brain microvascular endothelial cells-DTG treated-3

description:
Library name: Sample 6
MBBB_DTG-3_P4_RM


title: Control - TDP-43 floxed mouse, Cortex, ID-148

description: Library name: CTX_148

value: Cortex


title: PANC-1 cells, shPin1#2, biological replicate 2


title: cHet - Nestin-Cre; TDP-43 hemizygous conditional knockout mouse, Cortex, ID-127

description: Library name: CTX_127

value: Nestin-Cre;TDP-43 f/+


title: Control - TDP-43 floxed mouse, Cortex, ID-120

description: Library name: CTX_120


title: PANC-1 cells, shPin1#2, biological replicate 1

value: Pin1 knockdown


title: iPax3 re-isolated, control, rep4


title: Control - TDP-43 floxed mouse, Cortex, ID-125

description: Library name: CTX_125


title: iPax3 re-isolated, control, rep6


title: primary mouse brain microvascular endothelial cells-DMSO treated-3

description:
Library name: Sample 3
MBBB_DMSO-3_P5_RM

value: DMSO


title: PANC-1 cells, shPin1#1, biological replicate 3


title: Serum from patients with Healthy controls 4

city: Ningbo

first: Junhong

last: He

state: Zhejiang

address: 1059 Zhongshan East Road

description: Library name: Con4

data_processing:
The raw sequence of each sample was used to evaluate sequencing quality using statistical Q30. The sequencing of miRNA in this study was completed by Aksomics Co., Ltd., Shanghai, China.The miRNA expression threshold was that miRNAs with counts per million (CPM) mean of ≥1 in each group were considered to be expressed in the group and statistically analyzed. The specific calculation formula for CPM is as follows: CPM=(C×〖10〗^6)/N C: The number of reads mapped to a gene. N: The total number of reads mapped to all genes. The differential expression of miRNAs between the groups was analyzed using edgeR (3.18.1) software. The threshold was set to a 1.5-fold difference, P-value < 0.05, and CPM mean within the group >1 to screen for differentially expressed miRNAs. Cluster analysis was performed using the CPM values of the significantly expressed miRNAs obtained from comparisons between groups. Principal component analysis was performed using R software.
Supplementary files format and content: The sequencer generated raw sequencing data in FASTQ format including raw counts for each sample

source_name: Serum

extract_protocol:
The samples were removed from -80°C, thawed, and centrifuged, and the supernatant was collected. TRIzol LS reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) was added to dissociate the nucleic acid-protein complex. Chloroform was then added to the extract, the resulting colorless aqueous phase was removed, and isopropanol was added to precipitate the RNA. Finally, ethanol was used to wash the RNA precipitate, the ethanol was removed, and RNase-free water was added to obtain the RNA solution, which was stored at -70°C. RNA purification and quantification were examined by spectrophotometry (NanoDrop, ND 2000; Wilmington, DE, USA).
Total RNA from each sample was used to prepare the miRNA sequencing libraries. An NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) was used according to the manufacturer's instructions, and included the following steps: 1) 3' adapter ligation; 2) 5' adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Selection of PCR amplified fragments of 135 to 155 bp (corresponding to small RNAs of 15 to 35 nt). The quality and concentration of the sequencing library were evaluated using an Agilent 2100 bioanalyzer (Agilent, Santa Clara, California, USA). The library was denatured into single-stranded DNA molecules using a TruSeq Rapid SR cluster kit (#GD-402-4001, Illumina, San Diego, California, USA), captured on an Illumina Flow cell, amplified in situ into clusters, and sequenced on an Illumina sequencer according to the sequencing instructions.

value: Serum

tag: disease

value: Healthy (Con)


title: primary mouse brain microvascular endothelial cells-DMSO treated-2

description:
Library name: Sample 2
MBBB_DMSO-1_P5_RM

value: WT


title: cHet - Nestin-Cre; TDP-43 hemizygous conditional knockout mouse, Cortex, ID-109

description: Library name: CTX_109


title: iPax3 re-isolated, control, rep3


title: 488+ DRGs (CTB488 labeled from iWAT)

description: Library name: iWAT-DRGs

value: Dorsal root ganglia


title: Serum from patients with Healthy controls 3

description: Library name: Con3


title: primary mouse brain microvascular endothelial cells-DMSO treated-1

description:
Library name: Sample 1
MBBB_DMSO-1_P4_RM


title: Serum from patients with Healthy controls 1

description: Library name: Con1


title: iPax3 re-isolated, control, rep2


title: PANC-1 cells, shPin1#1, biological replicate 1


title: Serum from patients with rheumatoid arthritis 4

description: Library name: RA4

value: Rheumatoid arthritis (RA)


title: PANC-1 cells, shControl, biological replicate 3


title: iPax3 re-isolated, control, rep1


title: kat6a Replicate-3

city: Auckland

first: Jonathan

last: Astin

state: Region

address: 85 Park Road

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

description: Library name: kat6a3 S3

data_processing:
The filtered clean reads were mapped to the Danio rerio reference genome (GRCz10) by HISAT2.
StringTie and the R package Ballgown were used to identify differentially expressed genes (DEGs) with a P value of < 0.01
Assembly: GRCz10
Supplementary files format and content: Excel file includes FPKM values for genes. Each sample (S1-S8) is a separate column

organism: Danio rerio

source_name: Chondrocyte

growth_protocol: Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.

extract_protocol:
At 3 days post fertilisation sox:10:EGFP;col2a1a:mcherry-double expressing chondrocytes were isolated from whole larvae by FACS.
RNA seq libraries were prepared using the Nextflex Rapid directional RNA-Seq kit (Perkin Elmer)

value: Chondrocyte


title: iPax3 myogenic progenitors, N1OE, rep3

source_name: in vitro myogenic progenitors

value: in vitro myogenic progenitors

value: ESC-derived myogenic progenitors


title: iPax3 myogenic progenitors, N1OE, rep2


title: kat6a Replicate-1

description: Library name: kat6a1 S1


title: PANC-1 cells, shControl, biological replicate 1

value: pancreas

value: pancreatic adenocarcinoma


title: kat6a Replicate-2

description: Library name: kat6a2 S2


title: PANC-1 cells, shControl, biological replicate 2


title: Serum from patients with rheumatoid arthritis 2

description: Library name: RA2


title: Granta-519 control rep 1

city: columbus

first: Lalit

last: Sehgal

state: Ohio

department: Hematology

institute: The Ohio State University

data_processing:
Basepair RNA seq pipeline
Assembly: hg19
Supplementary files format and content: tab-delimited text files include expression count

source_name: Peripheral blood

growth_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting for total RNA prepration.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA followed by ribodepletion was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Peripheral blood

value: B cell lymphoma

tag: condition

value: Control


title: iPax3 myogenic progenitors, N1OE, rep1

value: iPAX3 cells


title: Serum from patients with palindromic rheumatism 4

description: Library name: PR4

value: Palindromic rheumatism (PR)


title: WT Replicate-4

description: Library name: WT3 S8

value: Tg(sox10:EGFP); Tg(col2a1a:mcherry)


title: Serum from patients with palindromic rheumatism 3

description: Library name: PR3


title: iPax3 myogenic progenitors, control, rep4


title: Granta-519 control rep 2


title: WT Replicate-3

description: Library name: WT3 S7


title: Serum from patients with palindromic rheumatism 2

description: Library name: PR2


title: iPax3 re-isolated, control, rep5

value: re-isolated satellite cells

value: donor-derived satellite cells


title: iPax3 myogenic progenitors, control, rep3


title: Granta-519 shFGFR1 rep 2


title: Granta-519 shFGFR1 rep 1


title: WT Replicate-2

description: Library name: WT2 S6


title: Serum from patients with palindromic rheumatism 1

description: Library name: PR1

value: Serum


title: iPax3 myogenic progenitors, control, rep2

value: WT


title: Serum from patients with rheumatoid arthritis 3

description: Library name: RA3


title: WT Replicate-1

description: Library name: WT1 S5


title: iPax3 myogenic progenitors, control, rep1


title: MUTZ3 - V5 ChIP-seq - CL14 - no_tx

status: Public on Feb 01 2025

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

description: Library name: MUTZ3_EVI1_V5_AID_GFP_CL14_V5_IP

library_source: genomic

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 for runs sequenced on the Hiseq 2500 and v2.20.422 for runs sequenced on the Novaseq 6000
ChIP-seq reads were aligned to the human reference genome build hg19 with bowtie (v1.1.1)
Peak calling was performed with MACS2 (v 2.1.2), using input sequencing data as controls. For transcription factor ChIP-seq, default settings were employed; for histone marks, the --broad argument was used.
For the histone marks H3K9me3 and H3K27me3, domains were also called with EPIC2
Bigwig files were generated for visualization with deepTools bamCoverage (v3.5.1) and the options  --normalizeUsing RPKM --smoothLength 100 --binSize 20
Assembly: hg19
Supplementary files format and content: bigWig files display signal for genome visualization; peaks.txt contain peaks called by MACS2 with the narrowPeak option; broad_peaks.txt files contain peaks called by MACS2 with the broadPeak option; .tsv files contain peaks called by the EPIC2 algorithm

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: MUTZ3 cells were cultured in Alpha mem medium supplemented with 20% supernatant of urinary bladder carcinoma cell line 5637, and 20% FCS. Medium used was supplemented with 50U/ml penicillin and 50 U/ml streptomycin.

extract_protocol:
Cells were pelleted and resuspended in PBS containing 1% formaldehyde, followed by 3x washing using lysis buffer. Lysates were sonicated on a Biorupter and antibody was added. Nexxt, DNA was eluted, decrosslinked and quantified.
10 ng ChIP DNA was used in library preparation using MicroPlex library preparation kit.

treatment_protocol: MUTZ3 MECOM-V5-AID-T2A-GFP cells were treated with auxin in order to induce degradation of MECOM

value: Bone marrow

value: acute myelomonocytic leukemia

tag: protocol

value: Double-crosslink DSG


title: CAL27, Mock tranfect, repeat1

city: Hangzhou

first: Jiong

last: Lyu

address: Rd.Yuhangtang  866

institute: Zhejiang University

description: Library name: CALM1

data_processing:
Truseq SB Kit v4-HS
Assembly: Hg38
Supplementary files format and content: CSV files

growth_protocol: CAL27 cell line maintain in DMEM/F12 with 10% FBS

extract_protocol:
For RNA-seq RNA was exract with Trizole;
NEBNext Ply(A) mRNA Magnetic Isolation Module

treatment_protocol: Lentivirus transfect with KLF7 or Mock

value: Tongue cancer

value: Mock transfect

value: Lentivirus


title: CAL27, KLF7 tranfect, repeat2

description: Library name: CALK2

value: KLF7 transfect


title: CAL27, KLF7 tranfect, repeat3

description: Library name: CALK3


title: CAL27, Mock tranfect, repeat2

description: Library name: CALM2


title: MUTZ3 - V5 ChIP-seq - CL20 - no_tx

description: Library name: MUTZ3_EVI1_V5_AID_GFP_CL20_V5_IP


title: CAL27, KLF7 tranfect, repeat1

description: Library name: CALK1


title: XX2 hiPSCs RRBS

city: Jerusalem

first: Ithai

last: Waldhorn

address: Kiryat Hadassah

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hebrew University

data_processing:
Quality control measures were applied to FASTQ files, trimming low quality bases (Q<20), residual adapters and filtering out short reads (L<20). These measures were performed with Trim_Galore v0.4.1 wrapper tool (https://github.com/FelixKrueger/TrimGalore) applying rrbs and paired end options. File assessment before and after quality control was performed with FastQC v0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Alignment to the genome, assembly HSA GRCh38, was performed with Bismark - Bisulfite Mapper and Methylation Caller v0.20.1 (https://github.com/FelixKrueger/Bismark). Bismark Alignment was followed by Bismark methylation extractor, coverge2cytosine utility and a final custom script to prepare files for Methylation calling.
Differentially Methylated Regions (DMR) were analyzed with Methylkit, DNA methylation analysis from high-throughput bisulfite sequencing results, v1.8.1. (Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE, 2012. “methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.” Genome Biology, 13(10), R87.). Regions were defined as 100-base tiles with minimum CpG count of 10. DMRs were defined with methylation difference of 30% points minimum and p-Value of 1e-10 maximum.
Regions were annotated with HOMER (Hypergeometric Optimization of Motif Enrichment) and specifically “annotatePeaks.pl” function V4.10.3 (Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432).
Genome_build: HSA GRCh38
Supplementary_files_format_and_content: A table consisting of 536 rows representing DMR regions. DMR coordinates are provided in columns 1-3 followed by genomic and gene annotations in columns 4-7. Columns 8-14 provide nearest gene data including ID aliases and short functional description.

source_name: Human induced pluripotent stem cells

growth_protocol: EBV-immortalized B-cells were reprogrammed using B-cell Nucleofector Kit with 4 plasmids containing the following genes: SOX2, OCT4, KLF4, LIN28, L-MYC, SV40LT, shP53. hiPSCs were cultured on human foreskin fibroblasts with KnockOut medium supplemented with serum replacement and bFGF.

extract_protocol:
Genomic DNA was extracted from hiPSCs by cell lysis, followed by treatment with Proteinase K, phenol:chloroform extraction, and ethanol precipitation. Bisulfite conversion of RRBS library was performed using the EpiTect DNA Bisulfite Kit (Qiagen GmbH)
100 bp paired-end sequencing was carried out using the HighSeq 2500 (Illumina).

value: hiPSCs

tag: sex chromosome complement


title: XX3 hiPSCs RRBS


title: XY2 hiPSCs RRBS


title: kat6a Replicate-4

description: Library name: kat6a4 S4

value: Chondrocyte


title: KO_RS_rep2

city: New York city

first: Feifei

last: Yuan

state: NY

institute: Columbia University

description:
Library name: FF20
bulk RNA-seq

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm10 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.2.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
A tab-delimited matrix file containing FPKM values for RefSeq genes in each sample generated using Cufflinks.
Assembly: mm10
Supplementary files format and content: tab-delimited text file

source_name: testis

extract_protocol:
Total RNA was extracted using Trizol.
RNA-seq library construction was performed at Azenta Life Sciences Inc. with a standard polyA-enrichment protocol.

value: testis

value: spermatid

value: Tex10f/-; Stra8iCre

value: Male

value: 8 weeks


title: XX1 hiPSCs RRBS


title: XY3 hiPSCs RRBS


title: KO_RS_rep1

description:
Library name: FF19
bulk RNA-seq

value: MII spermatocyte


title: KO_sctMI_rep1

description:
Library name: FF15
bulk RNA-seq


title: KO_sctMII_rep1

description:
Library name: FF17
bulk RNA-seq

value: spermatogonia


title: PANC-1 cells, shPin1#1, biological replicate 2

value: pancreas

value: pancreatic adenocarcinoma

value: Pin1 knockdown


title: XY1 hiPSCs RRBS


title: KO_sctMII_rep2

description:
Library name: FF18
bulk RNA-seq

value: MI spermatocyte


title: KO_spg_rep1

description:
Library name: FF13
bulk RNA-seq


title: C_RS_rep2

description:
Library name: FF08
bulk RNA-seq

value: WT


title: C_sctMI_rep2

description:
Library name: FF06
bulk RNA-seq


title: CAL27, Mock tranfect, repeat3

description: Library name: CALM3

value: Tongue cancer

value: Mock transfect


title: C_sctMII_rep2

description:
Library name: FF07
bulk RNA-seq


title: C_spg_rep2

description:
Library name: FF05
bulk RNA-seq


title: C_RS_rep1

description:
Library name: FF04
bulk RNA-seq


title: M_OCT_WAT

city: Nagoya

first: Junfeng

last: Chen

state: 23 - 愛知県

address: Nagoya University

country: Japan

institute: Nagoya University

data_processing:
Mapping and quantification were performed by bowtie (v1.2.3) and RSEM (v1.3.3).
Assembly: Mmul_10
Supplementary files format and content: Excel files include FPM values for each tissue.

organism: Macaca mulatta

source_name: white adipose tissue

growth_protocol: Adult rhesus macaques were kept in an open enclosure  with natural light and temperature at the Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan. Two meals were provided per day at the estimated ad libitum levels and water was always available ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen).
3'RNA-Seq library was prepared by the Lasy-Seq v1.1 protocol (https://sites.google.com/view/lasy-seq/)

treatment_protocol: Macaques were immobilized with  10 mg/kg BW ketamine hydrochloride (intramuscularly), and anaesthesized with 80 mg/kg BW pentobarbital (intravenously), and perfused with ice-cold Ames' medium.

tag: sampling point

value: October, 2019

value: white adipose tissue

value: M


title: C_sctMI_rep1

description:
Library name: FF02
bulk RNA-seq

value: testis


title: C_sctMII_rep1

description:
Library name: FF03
bulk RNA-seq


title: C_spg_rep1

description:
Library name: FF01
bulk RNA-seq


title: M_OCT_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus


title: KO_sctMI_rep2

description:
Library name: FF16
bulk RNA-seq

value: spermatid

value: Tex10f/-; Stra8iCre


title: M_OCT_THA

source_name: thalamus

value: thalamus


title: M_OCT_VIC

source_name: visual cortex

value: visual cortex


title: M_OCT_TON

source_name: tongue

value: tongue


title: D6-OE1

description:
Library name: FF11
bulk RNA-seq

source_name: embryonic stem cell

value: embryonic stem cell

value: Male


title: D6-OE2

description:
Library name: FF12
bulk RNA-seq


title: M_OCT_TES


title: M_OCT_SPL

source_name: spleen

value: spleen


title: D6-EV1

description:
Library name: FF09
bulk RNA-seq


title: M_OCT_THR

source_name: thyroid

value: thyroid


title: D6-EV2

description:
Library name: FF10
bulk RNA-seq


title: D2-dTAG2

description:
Library name: FF08
bulk RNA-seq

value: dTAG13 treatment for 2 days


title: D2-dATG1

description:
Library name: FF07
bulk RNA-seq


title: M_OCT_SON

source_name: supraoptic nucleus

value: supraoptic nucleus


title: M_OCT_SN

source_name: substantia nigra

value: substantia nigra


title: M_OCT_STM

source_name: stomach

value: October, 2019

value: stomach


title: D2-OE2

description:
Library name: FF04
bulk RNA-seq


title: M_OCT_VTA

source_name: ventral tegmental area

value: ventral tegmental area

value: M


title: M_OCT_SKNB

source_name: skin on the back

value: skin on the back


title: M_OCT_SG

source_name: salivary gland

value: salivary gland


title: M_OCT_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: D2-C2

description:
Library name: FF06
bulk RNA-seq

value: DMSO treatment for 2 days


title: D2-EV2

description:
Library name: FF02
bulk RNA-seq


title: D2-EV1

description:
Library name: FF01
bulk RNA-seq


title: M_OCT_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: M_OCT_REC

source_name: rectum

value: rectum


title: M_OCT_RET

source_name: retina

value: retina


title: High dose group rep3

city: Urumqi

first: Binghong

last: Liu

address: No. 567, Shangde North Road, Shuimogou District, Urumqi, Xinjiang Uygur Autonomous Region

department: College of TCM Xinjiang Medical University

institute: Xinjiang Medical University

description:
Library name: sample 9
High dose ZCL treatment group tissue sample

data_processing:
Quality control: Library quality was assessed on Agilent Bioanalyzer 2100 system
Sequencing: Performed on Illumina HiSeq 4000 platform generating 150 bp paired-end reads
Gene expression quantification: FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method was used
Differential expression analysis: Genes with fold change > 1.5 and p < 0.05 were considered differentially expressed
Pathway analysis: GO and KEGG enrichment analyses were performed on differentially expressed genes
Assembly: Reference genome: GRCm38.p5 (mm10), downloaded from NCBI: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.25_GRCm38.p5/GCF_000001635.25_GRCm38.p5_genomic.fna.gz
Supplementary files format and content: Raw sequencing data: Fastq format files
Supplementary files format and content: Expression data: Gene expression values in FPKM format

source_name: aortic arch

growth_protocol: The mice were acclimated for 3 weeks before experiments. C57BL/6J mice were fed standard diet, while ApoE-/- mice were fed high-fat diet for 15 weeks.

extract_protocol:
Total RNA was extracted from aortic arch tissue using TRIzol reagent. Tissue was ground in liquid nitrogen, mixed with TRIzol, and incubated at room temperature for 15 minutes. After chloroform addition and centrifugation, RNA was precipitated with isopropanol, washed with 75% ethanol, and dissolved in RNase-free water.
1.5 μg RNA per sample was used for library preparation using NEBNext® UltraTM RNA Library Prep Kit for Illumina®. mRNA was purified, fragmented, and reverse transcribed to cDNA, followed by second-strand synthesis, end repair, and adaptor ligation. After size selection and USER enzyme treatment, PCR amplification was performed.

treatment_protocol: ApoE-/- mice were randomly divided into 5 groups (n=20): Model group, Atorvastatin group (5 mg/kg/day), Low-Dose group (1.28 g/kg/day ZCL), Medium-Dose group (2.56 g/kg/day ZCL), and High-Dose group (5.12 g/kg/day ZCL). Treatment was administered by gavage for 15 weeks.

value: aortic arch

value: ApoE-/-

value: high-fat diet + ZCL(5.12g/kg/d)


title: M_OCT_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus


title: M_OCT_PUT

source_name: putamen

value: putamen


title: Model group rep3

description:
Library name: sample 6
AS model group tissue sample

value: high-fat diet


title: M_OCT_PT

source_name: pars tuberalis of the pituitary

value: October, 2019

value: pars tuberalis of the pituitary


title: Control group rep3

description:
Library name: sample 3
Control group tissue sample

value: standard diet


title: M_OCT_PIN

source_name: pineal gland

value: pineal gland

value: M


title: Model group rep2

description:
Library name: sample 5
AS model group tissue sample


title: D2-C1

description:
Library name: FF05
bulk RNA-seq

source_name: embryonic stem cell

value: embryonic stem cell

value: Male


title: M_OCT_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: Model group rep1

description:
Library name: sample 4
AS model group tissue sample


title: M_OCT_PRO

source_name: prostate gland

value: prostate gland


title: M_OCT_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: M_OCT_OLB

source_name: olfactory bulb

value: olfactory bulb


title: D2-OE1

description:
Library name: FF03
bulk RNA-seq


title: M_OCT_PAN

source_name: pancreas

value: pancreas


title: Control group rep2

description:
Library name: sample 2
Control group tissue sample

value: aortic arch


title: KO_spg_rep2

description:
Library name: FF14
bulk RNA-seq

source_name: testis

value: testis

value: MI spermatocyte

value: Tex10f/-; Stra8iCre

value: 8 weeks


title: M_OCT_OES

source_name: oesophagus

value: October, 2019

value: oesophagus


title: APCKO_OPC_3

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Raw reads were passed through adapter filtration and process for potential rRNA contaminants clearance
The clean data were then aligned to GRCm38 for genome reference
Normalization of gene expression was performed by transferring the read counts to FPKM values, and both the read counts and FPKM values were used in visualization
Assembly: GRCm38
Supplementary files format and content: csv file includes baseMean, log2Foldchange, lfcSE, p-value, and adjusted p-value as WT vs. APC KO for OPC samples
Supplementary files format and content: excel files includes TPM, FPKM, Read Count and Normalized Read Count for each sample

source_name: Central Nervous System

extract_protocol:
RNA was extracted from the isolated cells by Trizol (Thermo, Cat No. 15596026) according to the manufacturer’s protocol
All EASY-RNAseq libraries were sequenced through the Illumina HiSeq platform with a 150-bp pair-end model.

value: Central Nervous System

value: Primary oligodendrocyte precursor cell culture


title: High dose group rep2

description:
Library name: sample 8
High dose ZCL treatment group tissue sample

value: ApoE-/-

value: high-fat diet + ZCL(5.12g/kg/d)


title: M_OCT_NM

source_name: nasal mucosa

value: nasal mucosa

value: M


title: APCKO_OPC_2


title: M_OCT_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: APCKO_OPC_1


title: WT_OPC_3

value: Apc-fl/fl


title: M_OCT_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: WT_OPC_1


title: M_OCT_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: 3-Tppp3-OE-568-2d

city: Pittsburgh

first: Kun-Che

last: Chang

state: PA

address: 1622 Locust St

department: Department of Ophthalmology

institute: University of Pittsburgh School of Medicine

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench v22 (QIAGEN Digital Insights). Reads were aligned to the GRCm39/mm39 version of the mouse reference genome using default settings
Assembly: mm39
Supplementary files format and content: CSV file-matrix table with total raw counts for every gene and every sample

source_name: Retina

extract_protocol:
Total RNA was extracted from frozen tissue samples using Qiagen RNeasy mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).ERCC RNA Spike-In Mix kit (cat. 4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were clustered on one flowcell lane. After clustering, the flowcell was loaded on the Illumina instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated from the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: To investigate the gene expression profiles, injured mouse retinas treated with either Tppp3 AAV2 OE (n=4) or CMV-control-AAV2 (n=3) werecollected two days after ONC

value: Retina

value: wildtype

value: Tppp3 overexpression AAV2


title: 2-Tppp3-OE-374-2d


title: M_OCT_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: 1-Tppp3-OE-376-2d


title: 4-Control-382-2d

value: Control AAV2


title: M_OCT_LIV

source_name: liver

value: October, 2019

value: liver


title: M_OCT_LUN

source_name: lung

value: lung


title: 2-Control-384-2d


title: High dose group rep1

description:
Library name: sample 7
High dose ZCL treatment group tissue sample

source_name: aortic arch

value: aortic arch


title: M_OCT_KIM

source_name: kidney medulla

value: kidney medulla


title: 1-Control-385-2d


title: GT18-07003_18-chesler-002_PHI6647A225_A1485

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: ribo-minus

data_processing:
Reads were demultiplexed and converted into fastq files with BCL2Fastq (v2.18.0.12)
Raw read files were concatenated by sample using zcat and gzip.
Reads were quality controlled with fastqc (v0.11.3) and MultiQC (v1.2). All read files were of uniformly high quality.
Reads were aligned using the splice-aware STAR aligner (v2.6.1) to the GRCm38 genome with Ensembl v94 transcript annotation (ERCC sequence and annotation information were included in the reference). Quantification was performed using the TranscriptomeSAM method.
Transcript-level quantification was performed by  expectation maximization using RSEM (v1.3.0).
Genome_build: GRCm38 with Ensembl v94 transcript annotation (with ERCC data included)
Supplementary_files_format_and_content: Processed data files contain transcript abundance estimates from RSEM and are in tab-delimited formats with abundances in multiple units. These files are suitable for importation and downstream analysis using tximport.

source_name: striatum

growth_protocol: Mice from the following strains were surveyed in these experiments: A/J (JAX stock #000646), C57BL/6J (JAX stock #000664), 129S1/SvImJ (JAX stock #002448), NOD/ShiLtJ (JAX stock #001976), NZO/HlLtJ (JAX stock #002105), CAST/EiJ (JAX stock #000928), PWK/PhJ (JAX stock #003715), and WSB/EiJ (JAX stock #001145). These strains are the founders of the Diversity Outbred heterogeneous stock and Collaborative Cross recombinant inbred strains. Surveys of these eight strains can demonstrate statistical heritability patterns that justify further dissection using the derived resources. The mice used in the Chesler Lab at The Jackson Laboratory came from breeding colonies maintained in the Chesler Lab. These colonies were derived from production colonies at The Jackson Laboratory and breeders were replaced with animals from The Jackson Laboratory’s production colony at least every five generations. All procedures were approved by the Jackson Laboratory of Mammalian Genetics institutional animal care and use committee. Mice were housed according to the CSNA animal housing SOP (https://www.jax.org/-/media/jaxweb/files/research-and-faculty/tools-and-resources/system-neurogenetics/csna-animal-housing.pdf).

extract_protocol:
Total RNA was isolated from striatum samples by The Jackson Laboratory's Genome Technologies core using a MagMAX mirVana Total RNA Isolation Kit according to manufacturer's specifications.
After sample QC for RNA integrity, total RNA libraries were constructed using rRNA depletion…

treatment_protocol: Mice from each strain went through the CSNA cocaine locomotor sensitization pipeline and were exposed to either saline (sham) or cocaine. Exposure to cocaine followed the CSNA SOP for cocaine locomotor sensitization (https://www.jax.org/-/media/jaxweb/files/research-and-faculty/tools-and-resources/system-neurogenetics/cocaine-locomotor-sensitization-assay.pdf?la=en&hash=9E5D4C248C3BCCAD947C164AE81663C13A77EB0D). Brains were extracted and striatum tissue dissected approximately 24 hours after the final exposure (day 19).

value: WSB/EiJ

tag: subspecies

value: domesticus

tag: injection

value: sham


title: GT18-07009_18-chesler-002_PHI6647A231_A386

description: ribo-minus

tag: strain

value: F

value: cocaine


title: M_OCT_KIC

source_name: kidney cortex

tag: tissue

value: kidney cortex

value: M


title: M_OCT_LC

source_name: locus coeruleus

value: locus coeruleus

tag: Sex


title: M_OCT_MUA

source_name: abdominal muscle

value: abdominal muscle


title: GT18-06988_18-chesler-002_PHI6647A210_A1480

description: ribo-minus


title: M_OCT_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: GT18-06980_18-chesler-002_PHI6647A202_A1038

description: ribo-minus


title: M_OCT_JEJ

source_name: jejunum

value: jejunum


title: GT18-06981_18-chesler-002_PHI6647A203_A1048

description: ribo-minus


title: GT18-06978_18-chesler-002_PHI6647A200_A383

description: ribo-minus


title: M_OCT_IRI

source_name: iris

value: iris


title: M_OCT_mPFC

source_name: medial prefrontal cortex

value: October, 2019

value: medial prefrontal cortex


title: M_OCT_ILE

source_name: ileum

value: ileum


title: M_OCT_HEA

source_name: heart

value: heart


title: M_OCT_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: M_OCT_HAB

source_name: habenula

value: habenula


title: GT18-06968_18-chesler-002_PHI6647A190_A1481

description: ribo-minus

value: WSB/EiJ

value: domesticus


title: M_OCT_GUM

source_name: gum

value: gum


title: M_OCT_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: M_OCT_GAL

source_name: gallbladder

value: gallbladder


title: M_OCT_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment

value: M


title: GT18-06962_18-chesler-002_PHI6647A184_A1047

description: ribo-minus

value: F

value: sham


title: GT18-06943_18-chesler-002_PHI6647A165_A1050

description: ribo-minus


title: GT18-06955_18-chesler-002_PHI6647A177_A1484

description: ribo-minus


title: GT18-06925_18-chesler-002_PHI6647A147_A379

description: ribo-minus

value: cocaine


title: 3-Control-383-2d

source_name: Retina

value: Retina

tag: genotype

value: wildtype

value: Control AAV2


title: M_OCT_FOV

source_name: fovea centralis

value: October, 2019

value: fovea centralis


title: M_OCT_EPI

source_name: epididymis

value: epididymis


title: GT18-06920_18-chesler-002_PHI6647A142_A1486

description: ribo-minus

source_name: striatum


title: Control group rep1

description:
Library name: sample 1
Control group tissue sample

source_name: aortic arch

value: aortic arch

value: standard diet


title: GT18-06926_18-chesler-002_PHI6647A148_A1482

description: ribo-minus

value: WSB/EiJ

value: domesticus


title: M_OCT_DRN

source_name: dorsal raphe

value: dorsal raphe


title: M_OCT_DUO

source_name: duodenum

value: duodenum


title: GT18-06915_18-chesler-002_PHI6647A137_A1483

description: ribo-minus


title: GT18-06994_18-chesler-002_PHI6647A216_A1404

description: ribo-minus

value: PWK/PhJ

value: musculus


title: GT18-06911_18-chesler-002_PHI6647A133_A387

description: ribo-minus

value: M


title: M_OCT_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: GT18-06909_18-chesler-002_PHI6647A131_A1049

description: ribo-minus

value: sham


title: M_OCT_CRB

source_name: cerebellum

value: cerebellum


title: GT18-07019_18-chesler-002_PHI6647A241_A557

description: ribo-minus

value: cocaine


title: GT18-06997_18-chesler-002_PHI6647A219_A559

description: ribo-minus


title: M_OCT_COL

source_name: colon

value: colon


title: M_OCT_CEC

source_name: cecum

value: October, 2019

value: cecum


title: GT18-06977_18-chesler-002_PHI6647A199_A554

description: ribo-minus

value: F


title: M_OCT_BON

source_name: bone

value: bone


title: GT18-06976_18-chesler-002_PHI6647A198_A1358

description: ribo-minus


title: M_OCT_BRO

source_name: bronchus

value: bronchus


title: M_OCT_BOM

source_name: bone marrow

value: bone marrow


title: GT18-07020_18-chesler-002_PHI6647A242_A1113

description: ribo-minus


title: M_OCT_COR

source_name: cornea

value: cornea


title: GT18-06944_18-chesler-002_PHI6647A166_A1111

description: ribo-minus


title: GT18-06937_18-chesler-002_PHI6647A159_A1357

description: ribo-minus


title: M_OCT_BLA

source_name: urinary bladder

value: urinary bladder


title: GT18-06993_18-chesler-002_PHI6647A215_A1110

description: ribo-minus


title: M_OCT_CAT

source_name: cartilage

value: cartilage


title: GT18-06990_18-chesler-002_PHI6647A212_A1106

description: ribo-minus

value: PWK/PhJ


title: M_OCT_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: M_OCT_CA1

source_name: hippocampus CA1

value: hippocampus CA1

value: M


title: GT18-06982_18-chesler-002_PHI6647A204_A1109

description: ribo-minus

value: musculus


title: M_OCT_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: GT18-06972_18-chesler-002_PHI6647A194_A1554

description: ribo-minus

source_name: striatum

value: cocaine


title: M_OCT_AXL

source_name: axillary lymph node

value: axillary lymph node


title: GT18-06929_18-chesler-002_PHI6647A151_A1406

description: ribo-minus


title: GT18-06933_18-chesler-002_PHI6647A155_A1356

description: ribo-minus

value: sham


title: M_OCT_AOR

source_name: aorta

value: October, 2019

value: aorta


title: M_OCT_ARC

source_name: arcuate nucleus

value: arcuate nucleus


title: M_OCT_ANU

source_name: anus

value: anus


title: M_OCT_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: GT18-07021_18-chesler-002_PHI6647A243_A1398

description: ribo-minus

value: NZO/HlLtJ

value: domesticus

value: F


title: GT18-06940_18-chesler-002_PHI6647A162_A1103

description: ribo-minus

value: PWK/PhJ


title: GT18-06936_18-chesler-002_PHI6647A158_A1359

description: ribo-minus


title: M_OCT_CAU

source_name: caudate nucleus

value: caudate nucleus


title: M_OCT_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: GT18-07012_18-chesler-002_PHI6647A234_14414

description: ribo-minus

value: M


title: GT18-06992_18-chesler-002_PHI6647A214_11464

description: ribo-minus


title: GT18-06991_18-chesler-002_PHI6647A213_14400

description: ribo-minus


title: M_OCT_ADG

source_name: adrenal gland

value: adrenal gland


title: GT18-06963_18-chesler-002_PHI6647A185_14412

description: ribo-minus


title: M_JUN_WAT

source_name: white adipose tissue

value: white adipose tissue


title: GT18-06974_18-chesler-002_PHI6647A196_14398

description: ribo-minus

value: cocaine


title: M_JUN_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: GT18-06958_18-chesler-002_PHI6647A180_11465

description: ribo-minus

value: sham


title: M_JUN_TON

source_name: tongue

value: tongue


title: M_JUN_VIC

source_name: visual cortex

value: visual cortex


title: M_JUN_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus


title: GT18-07034_18-chesler-002_PHI6647A256_12089

description: ribo-minus


title: GT18-06942_18-chesler-002_PHI6647A164_14413

description: ribo-minus


title: M_JUN_THA

source_name: thalamus

value: thalamus


title: M_JUN_THR

source_name: thyroid

value: thyroid


title: GT18-07028_18-chesler-002_PHI6647A250_14401

description: ribo-minus

value: NZO/HlLtJ


title: GT18-06931_18-chesler-002_PHI6647A153_14408

description: ribo-minus

value: domesticus


title: M_JUN_TES

source_name: testis

value: testis


title: GT18-06927_18-chesler-002_PHI6647A149_14397

description: ribo-minus

source_name: striatum

value: F


title: M_OCT_AMYC

source_name: amygdala central nucleus

value: October, 2019

value: amygdala central nucleus


title: M_JUN_SPL

source_name: spleen

value: spleen

value: M


title: M_JUN_STM

source_name: stomach

value: stomach


title: GT18-06921_18-chesler-002_PHI6647A143_12090

description: ribo-minus

value: cocaine


title: GT18-06918_18-chesler-002_PHI6647A140_A1134

description: ribo-minus


title: M_JUN_SON

source_name: supraoptic nucleus

value: supraoptic nucleus


title: GT18-07031_18-chesler-002_PHI6647A253_11303

description: ribo-minus

value: NOD/ShiLtJ

value: sham


title: GT18-07030_18-chesler-002_PHI6647A252_11308

description: ribo-minus


title: M_JUN_SN

source_name: substantia nigra

value: substantia nigra


title: M_JUN_SKNB

source_name: skin on the back

value: skin on the back


title: M_JUN_SG

source_name: salivary gland

value: salivary gland


title: GT18-06999_18-chesler-002_PHI6647A221_11312

description: ribo-minus


title: GT18-07006_18-chesler-002_PHI6647A228_A1211

description: ribo-minus


title: M_JUN_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: GT18-06985_18-chesler-002_PHI6647A207_11306

description: ribo-minus


title: M_JUN_RET

source_name: retina

value: retina


title: M_JUN_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: GT18-06941_18-chesler-002_PHI6647A163_14409

description: ribo-minus

value: NZO/HlLtJ

value: domesticus


title: M_JUN_PUT

source_name: putamen

value: putamen


title: GT18-06969_18-chesler-002_PHI6647A191_11305

description: ribo-minus

value: F


title: M_JUN_REC

source_name: rectum

value: rectum


title: M_JUN_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus

value: M


title: M_JUN_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: GT18-06957_18-chesler-002_PHI6647A179_11462

description: ribo-minus


title: GT18-06961_18-chesler-002_PHI6647A183_A1212

description: ribo-minus


title: GT18-06934_18-chesler-002_PHI6647A156_A1210

description: ribo-minus

value: cocaine


title: GT18-07010_18-chesler-002_PHI6647A232_11309

description: ribo-minus

value: NOD/ShiLtJ


title: GT18-06930_18-chesler-002_PHI6647A152_11310

description: ribo-minus


title: M_JUN_PIN

source_name: pineal gland

value: pineal gland


title: GT18-06951_18-chesler-002_PHI6647A173_A1214

description: ribo-minus

value: sham


title: GT18-06949_18-chesler-002_PHI6647A171_11311

description: ribo-minus


title: GT18-06917_18-chesler-002_PHI6647A139_11307

description: ribo-minus


title: GT18-06914_18-chesler-002_PHI6647A136_A1142

description: ribo-minus


title: M_JUN_PAN

source_name: pancreas

value: pancreas


title: GT18-07007_18-chesler-002_PHI6647A229_A1217

description: ribo-minus

source_name: striatum


title: M_JUN_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: M_JUN_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: GT18-06912_18-chesler-002_PHI6647A134_A1143

description: ribo-minus


title: M_JUN_OVI

source_name: oviduct

value: oviduct


title: GT18-07033_18-chesler-002_PHI6647A255_A1316

description: ribo-minus

value: CAST/EiJ

value: castaneus


title: GT18-07029_18-chesler-002_PHI6647A251_A1321

description: ribo-minus


title: GT18-07022_18-chesler-002_PHI6647A244_12126

description: ribo-minus


title: M_JUN_PRO

source_name: prostate gland

value: prostate gland


title: M_JUN_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: GT18-07016_18-chesler-002_PHI6647A238_A1395

description: ribo-minus


title: M_JUN_NM

source_name: nasal mucosa

value: nasal mucosa


title: GT18-07008_18-chesler-002_PHI6647A230_A1322

description: ribo-minus


title: M_JUN_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: M_JUN_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: GT18-06966_18-chesler-002_PHI6647A188_A716

description: ribo-minus

value: F


title: GT18-06959_18-chesler-002_PHI6647A181_A1319

description: ribo-minus


title: M_JUN_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node

value: M


title: GT18-06965_18-chesler-002_PHI6647A187_A1247

description: ribo-minus


title: GT18-06979_18-chesler-002_PHI6647A201_A1396

description: ribo-minus


title: M_JUN_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: GT18-06986_18-chesler-002_PHI6647A208_A1315

description: ribo-minus

value: cocaine


title: M_JUN_MUA

source_name: abdominal muscle

value: abdominal muscle


title: GT18-06947_18-chesler-002_PHI6647A169_A720

description: ribo-minus


title: M_JUN_OLB

source_name: olfactory bulb

value: olfactory bulb


title: M_JUN_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: GT18-06946_18-chesler-002_PHI6647A168_A1393

description: ribo-minus

value: sham


title: GT18-06967_18-chesler-002_PHI6647A189_12127

description: ribo-minus


title: M_JUN_LUN

source_name: lung

value: lung


title: GT18-06948_18-chesler-002_PHI6647A170_12122

description: ribo-minus

value: CAST/EiJ


title: M_JUN_LC

source_name: locus coeruleus

value: locus coeruleus


title: M_JUN_OES

source_name: oesophagus

value: oesophagus


title: GT18-07027_18-chesler-002_PHI6647A249_A1076

description: ribo-minus

source_name: striatum

value: domesticus


title: GT18-06928_18-chesler-002_PHI6647A150_A1394

description: ribo-minus

value: castaneus


title: GT18-07013_18-chesler-002_PHI6647A235_11301

description: ribo-minus


title: M_JUN_ILE

source_name: ileum

value: ileum


title: M_JUN_KIC

source_name: kidney cortex

value: kidney cortex


title: GT18-06923_18-chesler-002_PHI6647A145_A719

description: ribo-minus


title: M_JUN_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: M_JUN_JEJ

source_name: jejunum

value: jejunum


title: M_JUN_IRI

source_name: iris

value: iris

value: M


title: M_JUN_HEA

source_name: heart

value: heart


title: M_JUN_HAB

source_name: habenula

value: habenula


title: GT18-07011_18-chesler-002_PHI6647A233_11297

description: ribo-minus


title: M_JUN_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: GT18-06938_18-chesler-002_PHI6647A160_11295

description: ribo-minus

value: F


title: GT18-07004_18-chesler-002_PHI6647A226_11299

description: ribo-minus

value: sham


title: M_JUN_LIV

source_name: liver

value: liver


title: GT18-06984_18-chesler-002_PHI6647A206_11279

description: ribo-minus

value: cocaine


title: M_JUN_FOV

source_name: fovea centralis

value: fovea centralis


title: M_JUN_EPI

source_name: epididymis

value: epididymis


title: M_JUN_DUO

source_name: duodenum

value: duodenum


title: M_JUN_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: GT18-06954_18-chesler-002_PHI6647A176_A1075

description: ribo-minus

value: domesticus


title: GT18-07000_18-chesler-002_PHI6647A222_11292

description: ribo-minus


title: M_JUN_GUM

source_name: gum

value: gum


title: GT18-07026_18-chesler-002_PHI6647A248_A1080

description: ribo-minus


title: M_JUN_GAL

source_name: gallbladder

value: gallbladder


title: M_JUN_DRN

source_name: dorsal raphe

value: dorsal raphe


title: M_JUN_KIM

source_name: kidney medulla

value: kidney medulla


title: GT18-06983_18-chesler-002_PHI6647A205_11293

description: ribo-minus

source_name: striatum


title: GT18-06907_18-chesler-002_PHI6647A129_11298

description: ribo-minus

value: M


title: GT18-06908_18-chesler-002_PHI6647A130_11296

description: ribo-minus


title: M_JUN_CRB

source_name: cerebellum

value: cerebellum


title: M_JUN_COR

source_name: cornea

value: cornea


title: M_JUN_CEC

source_name: cecum

value: cecum


title: GT18-07025_18-chesler-002_PHI6647A247_11281

description: ribo-minus

value: A/J

value: F


title: GT18-06924_18-chesler-002_PHI6647A146_A1081

description: ribo-minus

value: sham


title: GT18-06919_18-chesler-002_PHI6647A141_11291

description: ribo-minus


title: GT18-06916_18-chesler-002_PHI6647A138_11300

description: ribo-minus

value: cocaine


title: GT18-07023_18-chesler-002_PHI6647A245_11280

description: ribo-minus


title: M_JUN_CAU

source_name: caudate nucleus

value: caudate nucleus


title: GT18-07017_18-chesler-002_PHI6647A239_A1089

description: ribo-minus


title: M_JUN_CAT

source_name: cartilage

value: cartilage


title: GT18-06910_18-chesler-002_PHI6647A132_11294

description: ribo-minus


title: GT18-07032_18-chesler-002_PHI6647A254_A1086

description: ribo-minus


title: GT18-07002_18-chesler-002_PHI6647A224_A532

description: ribo-minus


title: GT18-07001_18-chesler-002_PHI6647A223_11283

description: ribo-minus


title: GT18-06996_18-chesler-002_PHI6647A218_11408

description: ribo-minus


title: M_JUN_COL

source_name: colon

value: colon


title: M_JUN_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: M_JUN_BLA

source_name: urinary bladder

value: urinary bladder


title: GT18-07015_18-chesler-002_PHI6647A237_A666

description: ribo-minus

value: domesticus


title: M_JUN_CA1

source_name: hippocampus CA1

value: hippocampus CA1


title: M_JUN_BRO

source_name: bronchus

value: bronchus


title: M_JUN_AXL

source_name: axillary lymph node

value: axillary lymph node


title: M_JUN_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus

value: M


title: GT18-06998_18-chesler-002_PHI6647A220_11290

description: ribo-minus


title: M_JUN_BOM

source_name: bone marrow

value: bone marrow


title: GT18-06939_18-chesler-002_PHI6647A161_11284

description: ribo-minus


title: M_JUN_AOR

source_name: aorta

value: aorta


title: GT18-07024_18-chesler-002_PHI6647A246_11271

description: ribo-minus


title: M_JUN_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: GT18-06987_18-chesler-002_PHI6647A209_11285

description: ribo-minus

value: A/J


title: GT18-06973_18-chesler-002_PHI6647A195_A1473

description: ribo-minus


title: M_JUN_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: GT18-06964_18-chesler-002_PHI6647A186_A1088

description: ribo-minus

source_name: striatum

value: sham


title: GT18-06945_18-chesler-002_PHI6647A167_A535

description: ribo-minus


title: GT18-07014_18-chesler-002_PHI6647A236_11267

description: ribo-minus

value: F


title: M_JUN_ARC

source_name: arcuate nucleus

value: arcuate nucleus


title: M_JUN_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: M_FEB_VMH

source_name: ventromedial  hypothalamic nucleus

value: February, 2020

value: ventromedial  hypothalamic nucleus


title: M_JUN_BON

source_name: bone

value: bone


title: M_JUN_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: GT18-07018_18-chesler-002_PHI6647A240_11269

description: ribo-minus

value: domesticus

value: cocaine


title: M_FEB_TON

source_name: tongue

value: tongue


title: GT18-06960_18-chesler-002_PHI6647A182_A1526

description: ribo-minus

value: M


title: M_FEB_WAT

source_name: white adipose tissue

value: white adipose tissue


title: M_JUN_ADG

source_name: adrenal gland

value: adrenal gland


title: GT18-06932_18-chesler-002_PHI6647A154_11289

description: ribo-minus


title: M_FEB_THR

source_name: thyroid

value: thyroid


title: GT18-06971_18-chesler-002_PHI6647A193_11278

description: ribo-minus

value: A/J


title: GT18-07005_18-chesler-002_PHI6647A227_11277

description: ribo-minus


title: GT18-06956_18-chesler-002_PHI6647A178_11272

description: ribo-minus


title: M_FEB_TES

source_name: testis

value: testis


title: GT18-06975_18-chesler-002_PHI6647A197_A1597

description: ribo-minus


title: GT18-06952_18-chesler-002_PHI6647A174_11496

description: ribo-minus

value: sham


title: GT18-06995_18-chesler-002_PHI6647A217_11266

description: ribo-minus

value: F


title: GT18-06989_18-chesler-002_PHI6647A211_11270

description: ribo-minus


title: M_FEB_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: M_FEB_STM

source_name: stomach

value: stomach


title: GT18-06970_18-chesler-002_PHI6647A192_11268

description: ribo-minus


title: M_JUN_ANU

source_name: anus

value: anus


title: GT18-06950_18-chesler-002_PHI6647A172_11274

description: ribo-minus


title: M_FEB_SON

source_name: supraoptic nucleus

value: February, 2020

value: supraoptic nucleus


title: M_FEB_SPL

source_name: spleen

value: spleen


title: M_FEB_THA

source_name: thalamus

value: thalamus


title: GT18-06935_18-chesler-002_PHI6647A157_A1600

description: ribo-minus

source_name: striatum

value: domesticus

value: cocaine


title: GT18-06922_18-chesler-002_PHI6647A144_11500

description: ribo-minus

value: M


title: GT18-06913_18-chesler-002_PHI6647A135_A1523

description: ribo-minus


title: M_FEB_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: M_FEB_VIC

source_name: visual cortex

value: visual cortex


title: GT18-06953_18-chesler-002_PHI6647A175_11275

description: ribo-minus


title: M_FEB_SN

source_name: substantia nigra

value: substantia nigra


title: M_FEB_SG

source_name: salivary gland

value: salivary gland


title: HEK293T_PRCCTFE3_2

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome hg19 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 75.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Assembly: hg19
Supplementary files format and content: Excel file containing raw read counts, normalized counts (by sequencing depth and median gene length) and log2(fold-change) with adjusted p-values for comparisons of interest. The file contains two distinct sheets for LoF experiments in tRCC cell lines and GoF experiments in HEK293T.

source_name: Human cell line HEK293T expressing PRCC-TFE3 fusion protein

growth_protocol: The embryonic kidney HEK293T cell line and the derived lines expressing ectopic TFE3 fusions cells were grown in DMEM medium supplemented with glucose (1g/L).

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
Total mRNA isolation was performed using Trizol (TR 118) and isopropanol precipitation. RNA was then treated with DNAseI following the TurboDNAse kit instructions (AM1907 – ThermoFisher) and 1µg of RNA was reversed transcribed using SuperScript IV (18090050 – ThermoFisher) following manufacturer instructions.

treatment_protocol: TFE3, NONO-TFE3 and PRCC-TFE3 cDNAs were synthesized by GenScript and subsequently cloned into the all-in-one doxycycline inducible lentiviral pCW57-GFP-P2A-MCS vector (Addgene plasmid #71783) in place of GFP. Lentiviral particles were produced to express independently each of the 3 genes of interest or GFP control by transfection of HEK293T cells with packaging plasmids. Lentiviral particles were purified by filtration and ultracentrifugation and resuspended in PBS. After titration, HEK293T cells were infected at MOI of 1 using polybrene and selected by puromycin addition to the media (1µg/mL). After establishment of the stable cell lines, expression of the proteins of interest was induced by adding of Doxycycline (Dox) in the medium (10µg/mL).

value: Embryonic Kidney

tag: cell line

value: Doxycycline

tag: library strandedness

value: Unstranded


title: HEK293T_PRCCTFE3_1

tag: treatment


title: M_FEB_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: HEK293T_NONOTFE3_2

source_name: Human cell line HEK293T expressing NONO-TFE3 fusion protein


title: M_FEB_RET

source_name: retina

value: retina


title: HEK293T_NONOTFE3_1


title: M_FEB_SKNB

source_name: skin on the back

value: skin on the back


title: M_FEB_REC

source_name: rectum

value: February, 2020

value: rectum


title: M_FEB_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: HEK293T_TFE3_2

source_name: Human cell line HEK293T expressing TFE3


title: HEK293T_TFE3_3


title: M_FEB_PUT

source_name: putamen

value: putamen


title: M_FEB_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: HEK293T_TFE3_1


title: M_FEB_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: HEK293T_GFP_3

source_name: Human cell line HEK293T expressing GFP


title: HEK293T_GFP_2


title: M_FEB_PRO

source_name: prostate gland

value: prostate gland

value: M


title: M_FEB_PIN

source_name: pineal gland

value: pineal gland


title: M_FEB_PAN

source_name: pancreas

value: pancreas


title: HEK293T_GFP_1


title: M_FEB_OLB

source_name: olfactory bulb

value: olfactory bulb


title: HEK293T_NONOTFE3_3

value: Embryonic Kidney


title: UOK146_siTFE3_1

source_name: Human cell line UOK146 treated with TFE3 siRNA

growth_protocol: These cell lines were grown in DMEM medium supplemented with glucose (4.5g/L), 10% heat-inactivated Foetal Calf Serum (FCS), Non-essential amino acid (AANE) and 1% penicillin/streptomycin.

treatment_protocol: Cells were cultured in 10cm petri dish 18 hours before transfection. Transfection was performed in OPTI-MEM medium using lipofectamine RNAiMAX (13778150 – Invitrogen) with 25nM siRNA (mix of 3 individual siRNA for knockdown of TFE3 – J-009363 -06, -08, -09 ; with a pool of 4 non-targeting siRNA as control – D-0018-10 – Dharmacon). After 7h of incubation, OPTI-MEM was replaced by complete medium.

value: Adult Kidney


title: UOK146_siCtrl_3

source_name: Human cell line UOK146 treated with Control siRNA

value: siCtrl

value: Unstranded


title: M_FEB_OES

source_name: oesophagus

value: oesophagus


title: M_FEB_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: UOK146_siCtrl_1


title: M_FEB_NM

source_name: nasal mucosa

value: February, 2020

value: nasal mucosa


title: M_FEB_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: TF1_siTFE3_3

source_name: Human cell line TF1 treated with TFE3 siRNA

extract_protocol:
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
Total mRNA isolation was performed using Trizol (TR 118) and isopropanol precipitation. RNA was then treated with DNAseI following the TurboDNAse kit instructions (AM1907 – ThermoFisher) and 1µg of RNA was reversed transcribed using SuperScript IV (18090050 – ThermoFisher) following manufacturer instructions.

value: Stranded (negative)


title: TF1_siTFE3_2


title: M_FEB_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus


title: M_FEB_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: TF1_siTFE3_1


title: TF1_siCtrl_3

source_name: Human cell line TF1 treated with Control siRNA


title: M_FEB_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: UOK146_siTFE3_3


title: TF1_siCtrl_2


title: M_FEB_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node

value: M


title: M_FEB_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: UOK109_siTFE3_3

source_name: Human cell line UOK109 treated with TFE3 siRNA


title: M_FEB_LUN

source_name: lung

value: lung


title: M_FEB_LIV

source_name: liver

value: liver


title: TF1_siCtrl_1

value: Adult Kidney


title: UOK146_siTFE3_2


title: UOK109_siTFE3_2


title: UOK109_siCtrl_3

source_name: Human cell line UOK109 treated with Control siRNA

value: siCtrl


title: HEK293T_PRCCTFE3_3

source_name: Human cell line HEK293T expressing PRCC-TFE3 fusion protein

value: Embryonic Kidney

value: Doxycycline

value: Unstranded


title: M_FEB_LC

source_name: locus coeruleus

value: February, 2020

value: locus coeruleus


title: UOK109_siCtrl_2


title: M_FEB_KIM

source_name: kidney medulla

value: kidney medulla


title: UOK109_siCtrl_1

value: Stranded (negative)


title: M_FEB_JEJ

source_name: jejunum

value: jejunum


title: M_FEB_MUA

source_name: abdominal muscle

value: abdominal muscle


title: UOK120_siTFE3_2

source_name: Human cell line UOK120 treated with TFE3 siRNA


title: UOK120_siTFE3_3


title: M_FEB_IRI

source_name: iris

value: iris


title: M_FEB_KIC

source_name: kidney cortex

value: kidney cortex


title: UOK120_siTFE3_1


title: M_FEB_ILE

source_name: ileum

value: ileum

value: M


title: UOK120_siCtrl_3

source_name: Human cell line UOK120 treated with Control siRNA


title: UOK120_siCtrl_2


title: M_FEB_HEA

source_name: heart

value: heart


title: M_FEB_GUM

source_name: gum

value: gum


title: M_FEB_HAB

source_name: habenula

value: habenula


title: UOK120_siCtrl_1

value: Adult Kidney

value: siCtrl


title: UOK146_siCtrl_2

source_name: Human cell line UOK146 treated with Control siRNA


title: M_FEB_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: UOK146_H3K27ac

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1 with the "--broad" parameter for H3K27ac and the “-f BAMPE” parameter for TFE3.
Assembly: hg19
Supplementary files format and content: Peak coordinates called by MACS2 in BED format (chromosome/start/end/name/score).

source_name: Adult Kidney

growth_protocol: Cells were grown in DMEM medium supplemented with glucose (4.5g/L), 10% heat-inactivated Foetal Calf Serum (FCS), Non-essential amino acid (AANE) and 1% penicillin/streptomycin.

extract_protocol:
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 0.7 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 3cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.
Crosslinked ChIP was performed according standard protocols (see Strub et al, 2011).

tag: antibody

value: H3K27ac (Active motif 39133)

tag: chip-seq/c&t condition

value: Crosslinked


title: UOK120_H3K27ac


title: TF1_H3K27ac


title: M_FEB_GPe

source_name: globus pallidus external segment

value: February, 2020

value: globus pallidus external segment


title: M_FEB_GAL

source_name: gallbladder

value: gallbladder


title: M_FEB_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: M_FEB_FOV

source_name: fovea centralis

value: fovea centralis


title: UOK109_siTFE3_1

source_name: Human cell line UOK109 treated with TFE3 siRNA

value: Stranded (negative)


title: UOK109_H3K27ac


title: M_FEB_DUO

source_name: duodenum

value: duodenum


title: Input


title: M_FEB_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: M_FEB_EPI

source_name: epididymis

value: epididymis

value: M


title: liver_ATAC_798_l3_s1

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
798_peaks.narrowPeak.gz
798_scaled.bw

data_processing:
Raw sequence reads were trimmed for adapters and low quality bases using cutadapt with parameters -q 20 --minimum-length 36. Reads were aligned to the GRCh38 version of the genome using bowtie2 with parameters --minins 36 --maxins 1000 --no-mixed --no-discordant --no-unal. Reads overlapping ENCODE exclusion regions were removed with BEDTools pairToBed. Reads on primary nuclear chromosomes (chr 1-22, X, Y) with mapq > 20 were selected with samtools. Duplicate alignments were removed using picard MarkDuplicates.
We converted BAM files to BED files using BEDTools and called peaks on each ATAC-seq library separately using MACS2 with parameters -q 0.05 –nomodel –shift -100 –extsize 200 –keep-dup all.
For each individual, we merged the BAM files of the high-quality libraries and removed duplicates using Picard MarkDuplicates because some libraries for the same donor represent re-sequencing of the same library preparation. We then called peaks on merged libraries per individual using the same procedure that we used for single libraries. We merged peaks across individuals using BEDTools and retained merged peaks found in at least 7 individuals (5% of 138). Merging peaks across individuals can result in wide peak boundaries and concatenation of multiple nearby accessible chromatin regions into one peak. Therefore, we developed a procedure to refine the boundaries of the merged peaks found in at least 7 individuals. We first calculated the number of individuals that had a peak overlapping each base of each merged peak, which we define as coverage, using BEDTools coverage. We converted the output of BEDTools coverage into a matrix of coverage values with peak IDs as rows and peak bases as columns. For each peak, we identified all local minima in coverage; peaks that contain only one peak should have only two local minima, whereas peaks containing multiple sub-peaks will have 3 or more local minima. To prevent classifying small fluctuations in coverage as sub-peaks, we only retained adjacent pairs of minima if the distance between them was at least 200 basepairs (bp) and if the maximum coverage between them was both greater than 7 and greater than twice the maximum of the two minima. To define consensus peak boundaries, we identified the position between the two local minima with maximum coverage and extended in both directions until we reached the outermost positions that had half of the maximum coverage. This is similar to the full width at half maximum procedure used to identify boundaries of DNase peaks in ENCODE.
Assembly: GRCh38
Supplementary files format and content: The bigWig (.bw) files contain ATAC-seq signal normalized by reads per million.
Supplementary files format and content: The narrowPeak files contain peaks called on individual donors and are in standard narrowPeak format from macs2. The consensus peaks bed file contains the genomic coordinates of the consensus peaks in bed4 format, with columns chr, start, stop, and peakID.

source_name: liver tissue

extract_protocol:
We pulverized 50-mg pieces of frozen human liver tissue in liquid nitrogen using a Cell Crusher (CellCrusher), homogenized the tissue powder in ice-cold nuclei isolation buffer (NIB: 20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol [pH 7.5]) using a 1-mL dounce for 40 strokes, and rotated for 5 min at 4°C. We filtered the solution through a Miracloth (Calbiochem), centrifuged at 1,100 × g for 10 min at 4°C, washed the pellet with 250 μL NIB containing 0.5% Triton-X, centrifuged at 500 × g for 5 min at 4°C, and resuspended the pellet in 250 μL of resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 [pH 7.4]). After counting isolated nuclei, we pelleted 50,000 nuclei at 500 × g for 5 min at 4°C
We prepared ATAC-seq libraries using the omni-ATAC protocol with 5 ul Tn5 transposase per reaction, cleaned the transposase reaction and final libraries with Zymo DNA Clean and Concentrator (D4029), visualized and quantified the libraries using a TapeStation, and sequenced 150-bp paired-end reads on either an Illumina HiSeq 4000 or HiSeq X ten.

value: liver tissue


title: liver_ATAC_798_l2_s1


title: liver_ATAC_798_l1_s1


title: M_FEB_DRN

source_name: dorsal raphe

value: dorsal raphe


title: M_FEB_COR

source_name: cornea

value: cornea


title: M_FEB_COL

source_name: colon

value: colon


title: M_FEB_CRB

source_name: cerebellum

value: cerebellum


title: liver_ATAC_796_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
796_peaks.narrowPeak.gz
796_scaled.bw


title: liver_ATAC_796_l1_s1


title: M_FEB_CEC

source_name: cecum

value: cecum


title: liver_ATAC_791_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
791_peaks.narrowPeak.gz
791_scaled.bw


title: M_FEB_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: M_FEB_CA1

source_name: hippocampus CA1

value: February, 2020

value: hippocampus CA1


title: M_FEB_BRO

source_name: bronchus

value: bronchus


title: M_FEB_BON

source_name: bone

value: bone


title: M_FEB_CAU

source_name: caudate nucleus

value: caudate nucleus


title: liver_ATAC_783_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
783_peaks.narrowPeak.gz
783_scaled.bw


title: liver_ATAC_783_l1_s1


title: liver_ATAC_780_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
780_peaks.narrowPeak.gz
780_scaled.bw


title: liver_ATAC_783_l3_s1


title: M_FEB_BOM

source_name: bone marrow

value: bone marrow


title: M_FEB_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: liver_ATAC_780_l1_s1


title: M_FEB_BLA

source_name: urinary bladder

value: urinary bladder


title: liver_ATAC_796_l3_s1


title: M_FEB_AXL

source_name: axillary lymph node

value: axillary lymph node


title: M_FEB_ARC

source_name: arcuate nucleus

value: arcuate nucleus

value: M


title: liver_ATAC_791_l2_s1

value: liver tissue


title: M_FEB_CAT

source_name: cartilage

value: cartilage


title: liver_ATAC_791_l1_s1

source_name: liver tissue


title: M_FEB_AOR

source_name: aorta

value: aorta


title: liver_ATAC_778_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
778_peaks.narrowPeak.gz
778_scaled.bw


title: liver_ATAC_778_l1_s1


title: liver_ATAC_778_l5_s1


title: liver_ATAC_775_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
775_peaks.narrowPeak.gz
775_scaled.bw


title: liver_ATAC_779_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
779_peaks.narrowPeak.gz
779_scaled.bw


title: M_FEB_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: liver_ATAC_775_l1_s1


title: M_FEB_ADG

source_name: adrenal gland

value: adrenal gland


title: liver_ATAC_773_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
773_peaks.narrowPeak.gz
773_scaled.bw


title: liver_ATAC_773_l2_s1


title: M_DEC_VMH

source_name: ventromedial  hypothalamic nucleus

value: December, 2019

value: ventromedial  hypothalamic nucleus


title: liver_ATAC_773_l1_s1


title: liver_ATAC_779_l3_s1


title: liver_ATAC_770_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
770_peaks.narrowPeak.gz
770_scaled.bw


title: M_DEC_TON

source_name: tongue

value: tongue


title: M_DEC_VIC

source_name: visual cortex

value: visual cortex


title: liver_ATAC_780_l2_s1


title: liver_ATAC_779_l1_s1


title: liver_ATAC_770_l2_s1


title: liver_ATAC_765_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
765_peaks.narrowPeak.gz
765_scaled.bw


title: M_DEC_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: M_DEC_THR

source_name: thyroid

value: thyroid


title: liver_ATAC_770_l1_s1


title: M_DEC_STM

source_name: stomach

value: stomach


title: liver_ATAC_765_l3_s1


title: M_FEB_BAT

source_name: brown adipose tissue

value: February, 2020

value: brown adipose tissue


title: M_FEB_ANU

source_name: anus

value: anus


title: liver_ATAC_755_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
755_peaks.narrowPeak.gz
755_scaled.bw


title: M_FEB_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: M_DEC_TES

source_name: testis

value: testis

value: M


title: liver_ATAC_755_l2_s1

value: liver tissue


title: liver_ATAC_755_l1_s1


title: liver_ATAC_775_l2_s1


title: liver_ATAC_751_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
751_peaks.narrowPeak.gz
751_scaled.bw


title: M_DEC_SPL

source_name: spleen

value: spleen


title: M_DEC_SG

source_name: salivary gland

value: salivary gland


title: M_DEC_WAT

source_name: white adipose tissue

value: white adipose tissue


title: M_DEC_SKNB

source_name: skin on the back

value: December, 2019

value: skin on the back


title: liver_ATAC_751_l3_s1

source_name: liver tissue


title: M_DEC_THA

source_name: thalamus

value: thalamus


title: M_DEC_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: liver_ATAC_751_l1_s1


title: M_DEC_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: M_DEC_RET

source_name: retina

value: retina


title: liver_ATAC_750_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
750_peaks.narrowPeak.gz
750_scaled.bw


title: liver_ATAC_750_l1_s1


title: liver_ATAC_744_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
744_peaks.narrowPeak.gz
744_scaled.bw


title: liver_ATAC_750_l3_s1


title: M_DEC_SN

source_name: substantia nigra

value: substantia nigra


title: M_DEC_REC

source_name: rectum

value: rectum


title: liver_ATAC_744_l3_s1


title: M_DEC_PUT

source_name: putamen

value: putamen


title: liver_ATAC_741_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
741_peaks.narrowPeak.gz
741_scaled.bw


title: M_DEC_PIN

source_name: pineal gland

value: pineal gland


title: liver_ATAC_741_l3_s1


title: M_DEC_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: M_DEC_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: liver_ATAC_741_l2_s1