title: Skin epidermis, Ovol1/2 iDKO, 52 DPI, biological replicate 1

city: Irvine

first: Morgan

last: Dragan

address: D288 Medical Sciences I

department: Biological Chemistry

institute: UC Irvine

data_processing:
Fastqc v 0.11.9; Trimmomatic-0.35; Star v 2.5.2a
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic NexteraPE-PE adapters.
Trimmed sequence reads were mapped to GrCM38/mm10 using start alignment (parameters: chimSegmentMin 15, chimJunctionOverhangMin 15, outFilterMismatchNmax 3, alignEndsType Local, runThreadN 8,  outFilterMultimapNmax 1, outBAMcompression 10, outBAMsortingThreadN 8, quantMode GeneCounts TranscriptomeSAM, quantTranscriptomeBAMcompression 10, outSAMtype BAM, SortedByCoordinate, alignSJDBoverhangMin 6, alignIntronMax 300000
Read count extraction and normalization were performed using STAR 2.5.2a and differential expression was analyzed using DESeq2 version 1.24.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: skin

extract_protocol:
RNA was isolated from skin epidermis using Trizol RNA isolation protocol
RNA libraries for RNA-seq were prepared using Clontech SMART-seq v4 ultra low input Library Prep Kit by UCI Genomic core

value: skin

value: epidermis

value: Ovol1/2 iDKO


title: Placenta, Chlorpyrifos, CPF4-563

status: Public on Apr 06 2023

type: SRA

city: New York

first: Corina

last: Lesseur

state: New York

address: 1428 Madison Ave

department: Environmental Medicine & Public Health

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: MGI Tech

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
RNA-seq reads in the fastq files were characterized with FastQC, MultiQC, the reads were quality‐filtered (90% of bases quality score >20), aligned and quantified using STAR v2.7.5b. Transcript level counts were summarized to the gene level using featureCounts.
Assembly: Gencode release M20; GRCm38.p6
Supplementary files format and content: tab-delimited text files with gene counts aligned wih STAR and summarized with featureCounts

molecule: total RNA

organism: Mus musculus

source_name: Placenta

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. 1 ug was used for RNA-seq libraries)
Libraries were prepared with the RNAse H protocol for rRNA depletion (New England Biolabs (NEB), Ipswich, MA, USA).

tag: tissue

value: Placenta

tag: strain

tag: age

value: Gestational day 17

tag: treatment

value: Chlorpyrifos


title: Skin epidermis, Control, 52 DPI, biological replicate 2

state: CA

tag: cell type

tag: genotype

value: control


title: Skin epidermis, Ovol1/2 iDKO, 52 DPI, biological replicate 2


title: 7009

type: genomic

city: Honolulu

first: Rafael

middle: Aniu

last: Peres-David

state: Hawaii

address: 1800 East-West road

department: Anatomy

institute: University Of Hawaii

description: Normal self-esteem monocyte DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IlluminaInfinium MethylationEPIC v2.0 BeadChip Kit using standard Illumina protocol

scan_protocol: Arrays were imaged using illumina iScan Reader using standard recommended Illumina scanner setting

data_processing: Raw IDAT files were analyzed using R statistical software (v4.1.2) via the RnBeads package (v2.12.2)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic monocyte DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen Allprep DNA/RNA/miRNA Universal Kit according to standard instructions

tag: self-esteem category

value: Normal

value: monocytes


title: CD4 T cell - medium, rep3 [medium_CD4_3]

city: Taipei

first: I-Tsu

last: Chyuan

state: Outside of the US

address: No. 280, Sec. 4, Renai Rd.

department: Internal Medicine

country: Taiwan

institute: Cathay General Hospital

description: CD4+ T cells were cultured in RPMI-1640 medium containing 10% fetal calf serum plus penicillin (10 units/ml) and streptomycin (10 µg/ml) only.

data_processing:
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases (LEADING:20 TRAILING:13 SLIDINGWINDOW:5:20 MINLEN:30).
Trimmed reads were aligned to the reference genome sequence (GRCh38) using HISAT2 v2.1.0 to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Read count extraction and normalization were performed using StringTie v2.1.2.
Differential expression analysis was performed using DESeq2 (for replicate samples) R package v1.28.1 to test for differential expression for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each gene of each Sample

source_name: spleen

growth_protocol: CD4+ T cells were isolated from murine spleens using negative selection kits, EasySep™ Mouse CD4+ T Cell Isolation Kit (StemCell Technologies), and were cultured in RPMI-1640 medium (Invitrogen) containing 10% fetal calf serum (Invitrogen) plus penicillin (10 units/ml) and streptomycin (10 µg/ml) (Invitrogen).

extract_protocol:
Total RNA extraction was performed using TRIzol (Invitrogen) following the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Agilent SureSelect XT HS2 mRNA Library Prep Kit following manufacturer's instructions.

treatment_protocol: The CD4+ T cells stimulated with anti-CD3 (3 µg/ml) and anti-CD28 (2 µg/ml) antibodies (BioLegend) in the presence or absence of TRAIL (10 µg/ml)(GenScript) for 24 hours.

value: spleen

value: wild type


title: 7000

description: Normal self-esteem monocyte DNA


title: Placenta, Deltamethrin, DM-4-531

description: MGI Tech

value: Deltamethrin


title: Vehicle control Female

city: Bangkok

first: Tewarit

last: Sarachana

address: 154 Rama 1 Rd. Wangmai Pathumwan

country: Thailand

institute: Chulalongkorn University

data_processing:
The library is sequenced using Illumina HiSeq 4000.
Raw reads were filtered by removing the adaptors, sequences with more than 5% of unknown bases(N), and low quality reads to get clean reads. The clean reads were used to perform genome mapping with rn6 genome using HISAT version: v0.1.6-beta with parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
The clean reads were mapped to reference genome using  Bowtie2, version: v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200, and then calculate gene expression level with software package RSEM version: v1.2.12.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: frontal cortex

extract_protocol:
Neonatal rat frontal cortex tissues were quickly removed in cold buffer and collected in RNAlater until use. RNA was extracted using mirVana miRNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
To isolate mRNA, total RNA was treated with DNase I, and Oligo(dT) was used. The mRNA was then mixed with a fragmentation buffer, resulting in the fragmentation of the mRNA. cDNA was synthesized using the mRNA fragments as templates, and the resulting short fragments were purified and resolved with an EB buffer for end reparation and the addition of a single nucleotide A (adenine). The short fragments were then connected with adapters, and suitable fragments were selected for PCR amplification. During the quality control (QC) steps, the sample library was quantified and qualified using the Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System.

treatment_protocol: Pregnant female rat at gestation day 1 (GD1) were daily treated with 5,000 microgram/kilogram of maternal body weight or vehicle control until parturition.

value: Wistar

tag: Sex

value: female

value: prenatally exposed to vehicle (control)

value: postnatal day 1

value: frontal cortex


title: Placenta, Chlorpyrifos, CPF1-561

description: MGI Tech


title: 6258

description: Normal self-esteem monocyte DNA


title: Skin epidermis, Control, 25 DPI, biological replicate 2

value: skin


title: Skin epidermis, Control, 25 DPI, biological replicate 1

value: epidermis


title: Skin epidermis, Ovol1/2 iDKO, 25 DPI, biological replicate 1

value: Ovol1/2 iDKO


title: Fetal Brain, Control, CTL18-554

description: MGI Tech

source_name: Fetal Brain

value: Fetal Brain

value: Control


title: ST2ko_neg BSSE_QGF_179019

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Reads were aligned to the mouse UCSC mm10 genome using STAR (version 2.7.0c) and setting options for multi-mapping reads to ‘--outFilterMultimapNmax 10 --outSAMmultNmax 1’.
All further analysis was performed within the R/Bioconductor framework. Gene expression was quantified with featureCounts (RSubread package) using extra options `allowMultiOverlap=TRUE, read2pos=5, countMultiMappingReads=TRUE, primaryOnly=TRUE, strandSpecific=0` and relied on gene annotation from Ensembl version 102.
Assembly: mm10

molecule: polyA RNA

source_name: CD 8 T Cells

growth_protocol: d0, P14 WT Tcf7gpf cells and  P14 ST2-/- Tcf7gpf cell transfer and LCMV Cl13 high dose infection, analysis d4 p.i.

extract_protocol:
Cells were sorted on a FACSAria II (BectonDickinson), collected directly into Trizol LS (Sigma-Aldrich) and stored at -80°C until RNA extraction. RNA was extracted using the Direct-zolTM RNA MicroPrep kit (Zymo research). RNA from samples  were quality-checked on the Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Pico Chip (Agilent, Cat# 5067-1513) and quantified by Fluorometry using the QuantiFluor RNA System (Cat# E3310, Promega, Madison, WI, USA).
Library preparation was performed, starting from 4.5ng total RNA, using the SMART-Seq v4 PLUS Kit (Cat# R400753, Takara Bio). Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical) revealing excellent quality of libraries (average concentration was 31±5 nmol/L and average library size was 508±27 base pairs). Samples were pooled to equal molarity. The pool was quantified by Fluorometry using the QuantiFluor ONE dsDNA System (Cat# E4871, Promega, Madison, WI, USA). Libraries were sequenced Paired-End 51 bases (in addition: 8 bases for index 1 and 8 bases for index 2) using the NovaSeq 6000 instrument (Illumina) and the SP Flow-Cell loaded at a final concentration in Flow-Lane of 400pM and including 1% PhiX. Primary data analysis was performed with the Illumina RTA version 3.4.4. On average per sample: 32.2±2.8 millions pass-filter reads were collected on 1 SP Flow-Cell.

treatment_protocol: For the assessment of the transcriptome accessibility of P14 WT Tcf7gpf cells and of P14 ST2-/- Tcf7gpf cells on day 4 after LCMV infection, we single transferred 106 MACS-purified cells of either type (Miltenyi Biotec naïve CD8 T cell isolation kit, mouse) into WT recipients. Tcf7gpf+ and Tcf7gpf- were FACS-sorted on day 4 after LCMV infection and were processed for RNAseq.  Single cell suspensions of spleens were prepared by mechanical disruption using a metal mesh. Surface stain was performed at 4°C in the dark for 30 mins. Red blood cell lysis prior to sorting. Cells have been sorted in Trizol-LS.

tag: replicate

tag: tcf

value: neg


title: Skin epidermis, Ovol1/2 iDKO, 25 DPI, biological replicate 2


title: 7001

description: Normal self-esteem monocyte DNA


title: ST2ko_pos BSSE_QGF_179018

value: pos


title: Skin epidermis, Control, 52 DPI, biological replicate 1

value: control


title: 6255

description: Normal self-esteem monocyte DNA

value: Normal

value: monocytes


title: 6251

description: Low self-esteem monocyte DNA

value: Low


title: 6252

description: Normal self-esteem monocyte DNA


title: 6253

description: Normal self-esteem monocyte DNA


title: ST2ko_neg BSSE_QGF_179017


title: ST2ko_pos BSSE_QGF_179016


title: Placenta, Control, CTL17-581

description: MGI Tech

value: Placenta

value: Gestational day 17


title: Placenta, Deltamethrin, DM-13-525

description: MGI Tech

value: Deltamethrin


title: Placenta, Chlorpyrifos, CPF12-566

description: MGI Tech

value: Chlorpyrifos


title: Placenta, Control, CTL-1-518

description: MGI Tech


title: Fetal Brain, Deltamethrin, DM-1-511

description: MGI Tech


title: Fetal Brain, Control, CTL-2-594

description: MGI Tech


title: Fetal Brain, Deltamethrin, DM-7-507

description: MGI Tech


title: ST2ko_neg BSSE_QGF_179015


title: Placenta, Deltamethrin, DM-7-541

description: MGI Tech


title: 6244

description: Normal self-esteem monocyte DNA


title: 6248

description: Normal self-esteem monocyte DNA


title: ST2ko_pos BSSE_QGF_179014


title: 6242

description: Normal self-esteem monocyte DNA


title: 6247

description: Low self-esteem monocyte DNA


title: ST2ko_neg BSSE_QGF_179013


title: Placenta, Control, CTL16-578

description: MGI Tech


title: 6249

description: Low self-esteem monocyte DNA


title: 6240

description: Low self-esteem monocyte DNA


title: ST2ko_pos BSSE_QGF_179012


title: Fetal Brain, Control, CTL17-556

description: MGI Tech


title: 6220

description: Normal self-esteem monocyte DNA


title: Placenta, Chlorpyrifos, CPF11-573

description: MGI Tech


title: 6218

description: Normal self-esteem monocyte DNA


title: 6213

description: Normal self-esteem monocyte DNA


title: Placenta, Control, CTL-6-521

description: MGI Tech


title: Placenta, Deltamethrin, DM-8-535

description: MGI Tech


title: ST2ko_neg BSSE_QGF_179011


title: 6212

description: Low self-esteem monocyte DNA


title: Fetal Brain, Deltamethrin, DM-4-513

description: MGI Tech


title: ST2ko_pos BSSE_QGF_179010


title: Fetal Brain, Control, CTL15-552

description: MGI Tech


title: WT_neg BSSE_QGF_179007

value: WT


title: 6200

description: Low self-esteem monocyte DNA


title: 6191

description: Normal self-esteem monocyte DNA


title: WT_neg BSSE_QGF_179005


title: WT_pos BSSE_QGF_179006


title: 6195

description: Normal self-esteem monocyte DNA


title: Placenta, Chlorpyrifos, CPF9-565

description: MGI Tech


title: 6189

description: Normal self-esteem monocyte DNA


title: Fetal Brain, Chlorpyrifos, CPF13-546

description: MGI Tech


title: Placenta, Deltamethrin, DM-9-529

description: MGI Tech


title: WT_pos BSSE_QGF_179002


title: 6188

description: Normal self-esteem monocyte DNA


title: Placenta, Control, CTL-10-519

description: MGI Tech


title: WT_neg BSSE_QGF_179001


title: 6176

description: Low self-esteem monocyte DNA


title: Placenta, Chlorpyrifos, CPF3-570

description: MGI Tech


title: 6162

description: Normal self-esteem monocyte DNA


title: WT_pos BSSE_QGF_179000


title: 6147

description: Normal self-esteem monocyte DNA


title: WT_pos BSSE_QGF_179004


title: Placenta, Chlorpyrifos, CPF16-560

description: MGI Tech


title: WT_neg BSSE_QGF_178999


title: Placenta, Chlorpyrifos, CPF15-558

description: MGI Tech


title: WT_pos BSSE_QGF_178998


title: 6144

description: Normal self-esteem monocyte DNA


title: Fetal Brain, Control, CTL-7-595

description: MGI Tech


title: 6136

description: Normal self-esteem monocyte DNA


title: 6145

description: Low self-esteem monocyte DNA


title: Fetal Brain, Control, CTL14-551

description: MGI Tech


title: WT_D BSSE_QGF_142334

library_source: genomic

data_processing:
Paired-end reads were aligned to the UCSC mm10 genome using bowtie2 (version 2.4.2) with parameter settings "-maxins 2000 -no-mixed -no-discordant -local" and resulting BAM files were sorted and indexed with samtools (version 1.11).
For each group of biological replicates, regions of accessible chromation where called with macs2 (version 2.1.2.1) using the option '-f BAM -g 2652783500 --nomodel --shift -100 --extsize 200 --broad --keep-dup all --qvalue 0.05'.
The resulting peak lists were cleaned from peaks called in mitochondria, chrX and chrY, and ENCODE blacklist regions. Additionally, we applied a log-fold-change > 1.5 and FDR < 0.05 filter.
Genotype-specfic peak lists were combined into one list where peaks regions in a distance less than 250 based were merged using functions from the GenomicRanges package (R version 4.1.1, Bioconductor version 3.14.0).
Assembly: mm10
Supplementary files format and content: bed file with peaks merged across genotypes

source_name: CD8 T cells

growth_protocol: d0, P14 WT Tcf7gpf cells and of P14 ST2-/- Tcf7gpf cell transfer and LCMV Cl13 high dose infection, analysis d4 p.i.

extract_protocol:
20 000 Tcf7gpf+ (P14 WT or P14 ST2ko) were FACS-sorted on day 4 after LCMV infection into 500 µl of lymphocytic medium and were processed for ATAC-seq.
Library preparation for sequencing was performed as described (Corces et al., 2017). Briefly, sorted cells were lysed and tagmentated for 30 min at 37°C using the Illumina Tagment DNA Enzyme and Buffer Kit. DNA was purified with the Zymo DNA Clean and Concentrator Kit and amplified for five cycles using the NEBNext® High-Fidelity 2X PCR Master Mix and Custom Nextera Index Primers (Illumina). The number of additional cycles was determined by Real-time PCR as the number of cycles needed to reach ¼ of maximum fluorescent intensity. After the second amplification step, DNA was cleaned up using AMpure XP beads and sequenced on an Illumina NexSeq 50 machine using 41-bp paired-end run.

treatment_protocol: For ATAC-seq analysis of P14 WT Tcf7gpf+ cells and of P14 ST2-/- Tcf7gpf+ cells on day 4 after LCMV infection, we individually transferred 106 MACS-purified cells of either genotype (Miltenyi Biotec naïve CD8 T cell isolation kit, mouse) into WT recipients.

tag: recipient

value: D


title: ST2ko_C BSSE_QGF_142333

value: C


title: 6131

description: Normal self-esteem monocyte DNA


title: WT_neg BSSE_QGF_179003


title: Fetal Brain, Deltamethrin, DM-5-504

description: MGI Tech


title: Placenta, Deltamethrin, DM-5-532

description: MGI Tech


title: Placenta, Control, CTL14-574

description: MGI Tech


title: ST2ko_B BSSE_QGF_142331

value: B


title: 6135

description: Normal self-esteem monocyte DNA


title: ST2ko_D BSSE_QGF_142335


title: 6130

description: Normal self-esteem monocyte DNA


title: WT_C BSSE_QGF_142332


title: WT_B BSSE_QGF_142330


title: 6125

description: Low self-esteem monocyte DNA


title: Placenta, Deltamethrin, DM-12-530

description: MGI Tech


title: Placenta, Chlorpyrifos, CPF13-571

description: MGI Tech


title: ST2ko_A BSSE_QGF_142329

value: A


title: 6121

description: Normal self-esteem monocyte DNA


title: 6119

description: Normal self-esteem monocyte DNA


title: WT_A BSSE_QGF_142328


title: Fetal Brain, Deltamethrin, DM-3-505

description: MGI Tech

value: Fetal Brain


title: ND_thyroid-mouse-WT-hmod-input

city: Research Triangle Park

first: Hong Soon

last: Kang

state: NC

address: 111 T.W. Alexander Dr.

department: IIDL

institute: NIH/NIEHS

description: input for H3K4me3 and H3K27me3 ChIPs

data_processing:
Reads were filtered to require on a mean base quality score >20.
Adapter trimming was performed via Cutadapt v1.12 (parameters -a AGATCGGAAGAG -O 5 -q 0), followed by removal of reads less than 30bp in length.
Filtered and trimmed reads were aligned against the mm10 or rn6 reference genome via Bowtie v1.2 with parameter '-m 1'.  For samples with multiple sequencing runs, files were combined with MergeSamFiles (Picard tools v1.110).
Mapped reads were deduplicated via MarkDuplicates.jar (Picard tools v1.110).
Coverage tracks were generated by extending each uniquely-mapped non-duplicate read to the estimated average fragment size of 150bp, depth normalizing to 30 million reads (for histone marks and associated inputs) or 5 million reads (for transcription factors and associated inputs), followed by conversion to bedGraph format with BEDtools v2.24.0 genomeCoverageBed and then to bigWig format with UCSC utility bedGraphToBigWig.
TF peak calls were made by HOMER v4.10.3 with parameters "-style factor", followed by re-sizing to 300bp centered on the called peak midpoint. H3K4me3 peak calls were made by HOMER v4.10.3 with parameters "-region -size 500 -minDist 1000 -L 0".  H3K27me3 peak calls were made by HOMER v4.10.3 with parameters "-region -size 1000 -minDist 2500 -L 0".
Unified peak calls per histone mark were made by collapsing peaks from individual samples via BEDtools v2.24.0 mergeBed.
Assembly: mm10,rn6
Supplementary files format and content: peaks calls in BED format
Supplementary files format and content: depth-normalized coverage tracks in bigWig format

source_name: thyroid

growth_protocol: ChIP was performed with thryoid gland from mice or  rat thyrocyte cell line PCCL3.

extract_protocol:
Immunoprecipitated chromatin was washed and ChIPed-DNA was eluted, reverse cross-linked, and DNA fragments purified using PCR purification kit form Qiagen.
NEXTflex DNA-Seq kit from PerkinElmer was used.

value: thyroid

value: 1 month

tag: diet

value: NIH-31, normal diet


title: 6115

description: Normal self-esteem monocyte DNA


title: Placenta, Control, CTL-5-522

description: MGI Tech

value: Control


title: Placenta, Deltamethrin, DM-10-534

description: MGI Tech


title: 6109

description: Normal self-esteem monocyte DNA

value: Normal


title: 6106

description: Low self-esteem monocyte DNA

value: monocytes


title: ND_thyroid-mouse-KO-hmod-input

description: input for H3K4me3 and H3K27me3 ChIPs


title: ND_thyroid-mouse-WT-H3K27me3-IP

description: mouse_thyroid-H3K27me3.ChIP_unified_peaks.bed.gz

tag: antibody

value: H3K27me3, Abcam, ab6002


title: 6097

description: Normal self-esteem monocyte DNA


title: ND_thyroid-mouse-KO-H3K4me3-IP

description: mouse_thyroid-H3K4me3.ChIP_unified_peaks.bed.gz

value: H3K4me3, Abcam, ab8580


title: Placenta, Chlorpyrifos, CPF6-569

description: MGI Tech

value: Placenta

value: Gestational day 17


title: Fetal Brain, Deltamethrin, DM-2-506

description: MGI Tech

value: Deltamethrin


title: LID_thyroid-mouse-WT-hmod-input

description: input for H3K4me3 and H3K27me3 ChIPs

value: WT

value: Low Iodine Diet (LID, TD.95125, Harlan)


title: Fetal Brain, Control, CTL-3-562

description: MGI Tech


title: 5246

description: Normal self-esteem monocyte DNA


title: 6095

description: Normal self-esteem monocyte DNA


title: LID_thyroid-mouse-WT-H3K4me3-IP


title: Fetal Brain, Control, CTL11-557

description: MGI Tech


title: LID_thyroid-mouse-WT-H3K27me3-IP


title: LID_thyroid-mouse-KO-hmod-input

description: input for H3K4me3 and H3K27me3 ChIPs


title: 5245

description: Normal self-esteem monocyte DNA


title: 5229

description: Normal self-esteem monocyte DNA


title: Fetal Brain, Control, CTL-4-561

description: MGI Tech


title: Fetal Brain, Chlorpyrifos, CPF10-548

description: MGI Tech

value: Chlorpyrifos


title: Placenta, Chlorpyrifos, CPF7-567

description: MGI Tech


title: ND_thyroid-mouse-WT-H3K4me3-IP


title: Fetal Brain, Control, CTL-8-560

description: MGI Tech


title: Placenta, Chlorpyrifos, CPF10-572

description: MGI Tech


title: ND_thyroid-mouse-KO-H3K27me3-IP


title: 5227

description: Normal self-esteem monocyte DNA


title: Fetal Brain, Control, CTL-9-593

description: MGI Tech


title: 5223

description: Low self-esteem monocyte DNA

value: Low


title: Fetal Brain, Deltamethrin, DM-6-514

description: MGI Tech


title: ND_thyroid-mouse-WT-RNA-rep3

data_processing:
Reads were filtered to require on a mean base quality score >20 for both ends in the pair.
Read pairs were mapped against the hg19 reference genome by STAR (version 2.5) with the following parameters: -- outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical.
Mapped read counts per gene were collected by Subread featureCounts (version 1.5.0-p1) with paramters -s0 -Sfr -p.
Coverage tracks were generated via STAR (version 2.5) inputAlignmentsFromBAM function with parameters --outWigStrand Unstranded --outWigNorm RPM, then converted to bigWig format by UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: coverage tracks in bigWig format
Supplementary files format and content: raw counts per gene in tab-delimited text format

growth_protocol: Mice were weaned at 3 weeks and fed Normal diet (NIH31) or Low iodine diet (Harlan TD.95125).

extract_protocol:
Ambion RNAqueous-Micro kit was used for RNA extraction.
RNA libraries were prepared using TruSeq RNA library preparation kit from Illumina following manufacturer’s protocol.

value: NIH-31, normal diet (ND)


title: Placenta, Deltamethrin, DM-6-533

description: MGI Tech


title: 6107

description: Low self-esteem monocyte DNA


title: 5215

description: Low self-esteem monocyte DNA


title: Fetal Brain, Control, CTL13-555

description: MGI Tech

value: Fetal Brain


title: 5197

description: Normal self-esteem monocyte DNA


title: ND_thyroid-mouse-WT-RNA-rep1

value: thyroid


title: ND_thyroid-mouse-WT-RNA-rep2

value: 1 month


title: Placenta, Control, CTL-2-516

description: MGI Tech


title: ND_thyroid-mouse-KO-RNA-rep3


title: ND_thyroid-mouse-KO-RNA-rep4


title: 5134

description: Normal self-esteem monocyte DNA


title: Placenta, Control, CTL-4-515

description: MGI Tech


title: Fetal Brain, Control, CTL-5-503

description: MGI Tech


title: 5121

description: Normal self-esteem monocyte DNA


title: ND_thyroid-mouse-KO-RNA-rep2


title: Placenta, Control, CTL1-582

description: MGI Tech


title: ND_thyroid-mouse-KO-RNA-rep1


title: 5226

description: Normal self-esteem monocyte DNA


title: Uro_P_16_BiolRep3

city: Los Angeles

first: Karen

last: Sears

address: 612 Charles E Young Drive

institute: UCLA

data_processing:
RNA-Seq analysis was conducted on the UIUC Web-based Galaxy platform (galaxy.illinois.edu) using Tuxedo protocol
Reads were mapped to the Miniopterus natalensis genome, Mnat.v1

organism: Pteronotus quadridens

source_name: uropatagium

extract_protocol:
EZNA Total RNA kit (Omega BioTek)
Illumina TruSeq Stranded mRNA kit

value: uropatagium


title: LID_thyroid-mouse-KO-H3K27me3-IP


title: 6096

description: Normal self-esteem monocyte DNA


title: Placenta, Deltamethrin, DM-3-539

description: MGI Tech


title: 5218

description: Normal self-esteem monocyte DNA


title: ND_thyroid-mouse-WT-RNA-rep4


title: Uro_P_16_BiolRep2


title: LID_thyroid-mouse-WT-RNA-rep4


title: Fetal Brain, Control, CTL12-553

description: MGI Tech

value: Control


title: LID_thyroid-mouse-WT-RNA-rep3


title: Placenta, Control, CTL11-577

description: MGI Tech


title: Uro_P_14_BiolRep3


title: Placenta, Control, CTL12-583

description: MGI Tech


title: LID_thyroid-mouse-WT-RNA-rep2


title: 5192

description: Normal self-esteem monocyte DNA

value: Normal


title: Uro_P_16_BiolRep1


title: Fetal Brain, Chlorpyrifos, CPF14-544

description: MGI Tech


title: Uro_P_14_BiolRep2


title: Uro_P_14_BiolRep1


title: LID_thyroid-mouse-WT-RNA-rep1


title: LID_thyroid-mouse-KO-RNA-rep3


title: Placenta, Chlorpyrifos, CPF5-562

description: MGI Tech


title: Plagio_P_16_BiolRep3

source_name: plagiopatagium

value: plagiopatagium


title: Fetal Brain, Chlorpyrifos, CPF9-543

description: MGI Tech


title: LID_thyroid-mouse-KO-RNA-rep4


title: Placenta, Chlorpyrifos, CPF8-568

description: MGI Tech


title: Plagio_P_16_BiolRep1


title: LID_thyroid-mouse-KO-H3K4me3-IP


title: Placenta, Deltamethrin, DM-2-526

description: MGI Tech


title: LID_thyroid-mouse-KO-RNA-rep2


title: plagio_P_14_BiolRep3


title: LID_thyroid-mouse-KO-RNA-rep1


title: Plagio_P_16_BiolRep2


title: Placenta, Chlorpyrifos, CPF14-559

description: MGI Tech


title: plagio_P_14_BiolRep2


title: BMDM_IL4_IL13_TNFa_rep_6

city: Biberach

first: karim

last: el kasmi

address: Birkendorferstr 65

department: Immunology & Respiratory

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & CO. KG

description:
859_088
mRNA

data_processing:
Basecalling has been done with bcl2fastq v2.20.0.422.
Alignment has been performed with STAR v2.5.2 using mm10/GRCm38 genome reference.
Read counts has been obtained with featureCounts v1.5.1.
Demultiplexing was performed using bcl2fastq v2.20.0.422 from Illumina (https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html).
Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in (Schlager et al., 2020)): filtered reads were mapped against the Mus musculus (mouse) genome mm10/GRCm38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner (Dobin et al., 2013) allowing for soft clipping of adapter sequences.
For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE M11 for mouse. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (Li and Dewey, 2011) and featureCounts (v1.5.1) (Liao, Smyth and Shi, 2014). Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) (Sayols, Scherzinger and Klein, 2016) at the respective steps.
Genome_build: ENSEMBL mm10
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: murine bone marrow derived macrophages (BMDMs)

growth_protocol: Mouse BMDMs were generated from male C57BL/6 mice (Charles River Laboratories).

extract_protocol:
RNA was isolated using MagMax (biosystems #AM1830) following the manufacturer's procedure. Final elution 50uL. Total RNA was quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 48-channel Fragment Analyzer (Agilent), respectively.
RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). At total RNA input of 250ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 upstream and the NEXNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). The only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification, instead of the recommended SPRIselect Beads. Final sequencing libraries were quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). mRNA libraries were also assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 48-channel Fragment Analyzer (Agilent). All sequencing libraries were then normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina).

treatment_protocol: Mouse bone marrow were differentiated into BMDMs over 7 days with rhM-CSF (50 ng/mL). For the experiment, BMDMs were stimulated for 24 hours with rhM-CSF (10 ng/mL) in combination with the treatment group, rmIL-4 (10 ng/mL; catalogue number 404-ML/CF from R&D Systems), rmIL-13 (10 ng/mL; catalogue number 413-ML/CF from R&D Systems), rmTNFα (10 ng/mL; catalogue number 410-MT/CF from R&D Systems).

value: bone marrow derived macrophage (BMDM)

value: Male

tag: treatment 1

value: IL4 (dose 10ng/ml, treatment start timepoint 0h, treatment end timepoint 24h)

tag: treatment 2

value: IL13 (dose 10ng/ml, treatment start timepoint 0h, treatment end timepoint 24h)

tag: treatment 3

value: TNFa (dose 10ng/ml, treatment start timepoint 0h, treatment end timepoint 24h)


title: BMDM_Control_rep_6

description:
859_086
mRNA

value: untreated


title: BMDM_IL4_IL13_rep_6

description:
859_087
mRNA


title: Placenta, Control, CTL-8-517

description: MGI Tech

value: Placenta

value: Gestational day 17


title: Fetal Brain, Chlorpyrifos, CPF12-542

description: MGI Tech

value: Chlorpyrifos


title: Heart_P_16_BiolRep3

source_name: heart

value: heart


title: BMDM_IL4_IL13_TNFa_rep_5

description:
859_071
mRNA


title: Placenta, Deltamethrin, DM-1-536

description: MGI Tech

value: Deltamethrin


title: BMDM_IL4_IL13_rep_5

description:
859_070
mRNA


title: Heart_P_16_BiolRep2


title: Fetal Brain, Control, CTL-1-502

description: MGI Tech

value: Fetal Brain


title: Heart_P_16_BiolRep1


title: Placenta, Control, CTL-7-523

description: MGI Tech


title: BMDM_Control_rep_5

description:
859_069
mRNA


title: Heart_P_14_BiolRep3


title: Fetal Brain, Control, CTL-6-563

description: MGI Tech


title: Placenta, Chlorpyrifos, CPF2-564

description: MGI Tech


title: BMDM_IL4_IL13_TNFa_rep_4

description:
859_054
mRNA


title: BMDM_Control_rep_4

description:
859_052
mRNA


title: Heart_P_14_BiolRep1


title: Heart_P_14_BiolRep2


title: Placenta, Control, CTL-9-524

description: MGI Tech


title: FL_P_16_BiolRep3

source_name: forelimb

value: forelimb


title: BMDM_IL4_IL13_rep_4

description:
859_053
mRNA


title: Fetal Brain, Chlorpyrifos, CPF11-545

description: MGI Tech


title: BMDM_IL4_IL13_TNFa_rep_3

description:
859_037
mRNA


title: BMDM_IL4_IL13_rep_3

description:
859_036
mRNA


title: plagio_P_14_BiolRep1


title: BMDM_Control_rep_3

description:
859_035
mRNA


title: FL_P_16_BiolRep1


title: FL_P_16_BiolRep2


title: Placenta, Control, CTL15-576

description: MGI Tech


title: Placenta, Control, CTL18-580

description: MGI Tech


title: Fetal Brain, Control, CTL-10-501

description: MGI Tech


title: FL_P_14_BiolRep3


title: BMDM_IL4_IL13_TNFa_rep_2

description:
859_020
mRNA


title: BMDM_IL4_IL13_rep_2

description:
859_019
mRNA


title: LCS7846_GV_WT3_M_CleanData

first: Vincenzo

middle: A

last: Gennarino

state: NY

address: 701 W 168th Street, Room 1402 HHSC

institute: Columbia University Medical Center

data_processing: Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston), to remove adapter dimers, junk, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats. Subsequently, unique sequences of 18–26 nucleotides in length were mapped to specific species precursors in miRBase 22.0 (http://www.mirbase.org/) by BLAST search to identify known miRNAs and novel 3p- and 5p-derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species of mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpins opposite the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The last two were also defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicted from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12), (2) number of base pairs in the stem region of the predicted hairpin (≥16), (3) cutoff of free energy (kCal/mol ≤-15), (4) length of hairpin (up and down stems + terminal loop ≥50), (5) length of hairpin loop (≤20), (6) number of nucleotides in one bulge in mature region (≤8), (7) number of biased errors in one bulge in mature region (≤4), (8) number of biased bulges in mature region (≤2), (9) number of errors in mature region (≤7), (10) number of base pairs in the mature region of the predicted hairpin (≥12), (11) percent of mature region in stem (≥80).

organism: Mus

source_name: Cerebellum

extract_protocol:
RNA extraction with qiagen miRNeasy kit
Library preparation and microRNA sequencing was performed by LC Sciences according to the following criteria. Total RNA was extracted from cerebellum of WT and Pum1-/- male and female at 10 weeks of age using the miRNeasy kit (QIAGEN, # 217004) according to the manufacturer’s instructions. The total RNA quality and quantity were assessed with Bioanalyzer 2100 (Agilent Technologies, Santa Clara) with RIN number > 7.0. Approximately 1 µg of total RNA were used to prepare the small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego). Then the single-end sequencing 50bp was performed on an Illumina Hiseq 2500 at LC Sciences (Hangzhou, China) following the vendor’s recommended protocol.

value: Cerebellum

tag: cell line

value: 10 weeks

value: WT


title: FL_P_14_BiolRep2

tag: tissue


title: LCS7846_GV_WT3_F_CleanData

value: Female


title: BMDM_Control_rep_2

description:
859_018
mRNA

value: bone marrow derived macrophage (BMDM)

tag: strain


title: FL_P_14_BiolRep1


title: LCS7846_GV_WT2_M_CleanData

value: Male


title: BMDM_IL4_IL13_TNFa_rep_1

description:
859_003
mRNA

value: IL4 (dose 10ng/ml, treatment start timepoint 0h, treatment end timepoint 24h)


title: LCS7846_GV_WT2_F_CleanData


title: BMDM_IL4_IL13_rep_1

description:
859_002
mRNA

value: IL13 (dose 10ng/ml, treatment start timepoint 0h, treatment end timepoint 24h)


title: ctrl-2

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

country: China

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 2.19
Reads were mapped to Treeshrew genome using tophat2 (version 2.0.8) with default parameters.
For RNA-seq, fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks version 2.1.1; Differentialy expressed genes were determined using cuffdiff (version 2.1.1).
Assembly: TS_3.0 from Treeshrew database (http://www.treeshrewdb.org/)
Supplementary files format and content: tab-delimited text files include FPKM values for each RNA-seq Sample

organism: Tupaia chinensis

source_name: cell line

growth_protocol: Tree shrew spermatogonial stem cells  were routinely maintained on inactivated tree shrew sertoli cells in the culture medium:StemPro-34 SFM supplemented with StemPro supplement, 10% FBS, 1 mM penicillin, 2 mM L-Glutamine, 0.1 mM β-mercaptoethanol, 1 mM sodium pyruvate, 1 mM NEAA (nonessential amino acid), 60 μM putrescine, 40 ng/mL human GDNF (recombinant human glial cell  line-derived neurotrophic factor), 10 ng/mL human EGF (epidermal growth factor), 1 000 U mouse LIF (leukemia inhibitory factor), 2 ng/mL human bFGF (basic  fibroblast growth factor). To harvest tree shrew SSCs, cells were cultured on gelatin-coated dishes about 3-5 hours to avoid contamination of somatic cells.

extract_protocol:
Total RNA  were extracted  using standard Trizol procedure.
RNA libraries were constructed by Novogene Corporation (Beijing, China). RNA-seq libraries were constructed using Illumina NEBNext® UltraTM RNA Library Prep Kit.

treatment_protocol: 100 uM nicotinamide ribose was added to medium.

value: cell line

value: home made

value: spermatogonial stem cells

value: wild type

tag: passage number


title: LCS7846_GV_WT1_M_CleanData

tag: treatment


title: BMDM_Control_rep_1

description:
859_001
mRNA

tag: cell type

value: untreated


title: ctrl-1

tag: genotype


title: NR-2

value: 100 uM nicotinamide ribose


title: NR-1


title: BMSC_RNAseq_3D_rep3

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR (for RNA-seq) and Bowtie2 (for ATAC-seq).
For RNA-seq, aligned reads with high quality were quantified by HTSeq. For ATAC-seq, we eliminated the reads mapped to mitochondrial DNA, duplicated and unkown by Sambamba and only unique reads were analysed.
For RNA-seq, reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids. For ATAC-seq, we performed peak calling using MACS2, summarized the read counts by FeatureCounts and obtained the differential peaks by DESeq2.
For RNA-seq, Unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts by determined by UMI number to get rmdup.count file. For ATAC-seq, enriched motifs in differential peaks between different samples using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq, there were tab-delimited text files including raw count values for each sample. For ATAC-seq, there were tab-delimited text files including different peaks and binary files including all peaks.

source_name: mouse bone marrow stromal cells

growth_protocol: 2D culture BMSCs were cultured with  medium of α-MEM (Gibco) supplemented with 20% FBS (Gibco), 1% P/S (Thermo Fisher Scientific), 1% sodium pyruvate (Gibco) and 10 μM Y-27632 (Selleck Chemicals). 3D culture BMSCs were mixed with 5% GelMA and radiated with UVA for 60 seconds. Then add the same culture medium. 3D cocultured HSCs were co-cultured with BMSCs in 5% GelMA,

extract_protocol:
5,000 freshly sorted mouse BMSCs (CD45-Ter119-Tie2-GFP+DsRed+) were derived from ScfGFP;Cxcl12DsRed mice bone marrow and lysed in Trizol. 5,000 2D-cultured BMSCs and 3D-cultured BMSCs were lysed in trizol. Total RNA was extracted, digested with DNase I and purified using RNAclean Kit. Mouse primary young HSCs were acquired directly from 8-12 weeks old mice and primary old HSCs were from 12-13 month old mice. Young and old 3D cultured HSCs were 3D-cultured from primary young and old HSCs. Total RNA was extracted following the manufacturer’s instruction and purified by micro RNA purification kit (Tiangen).For ATAC-seq, 20,000 freshly isolated, 2D-cultured and 3D-cultured BMSCs were derived from ScfGFP;Cxcl12DsRed mice.
RNA-seq libraries were constructed through a modified Smartseq2 method, and sequenced on a HiSeq X Ten system (Illumina) or Novaseq 6000 (Illumina) as paired-end 150-bp reads. ATAC-seq libraries were prepared according to TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502-01), and sequenced on a HiSeq X Ten system (Illumina) as paired-end 150-bp reads.

value: Bone Marrow

tag: condition

value: 3D culture

tag: age

value: 8~12 weeks


title: BMSC_RNAseq_3D_rep2


title: LCS7846_GV_KO3_M_CleanData

value: Cerebellum


title: LCS7846_GV_KO3_F_CleanData

value: 10 weeks


title: LCS7846_GV_KO4_F_CleanData


title: p53-1


title: LCS7846_GV_KO1_M_CleanData


title: BMSC_RNAseq_2D_rep3

value: 2D culture


title: p41-1


title: LCS7846_GV_KO2_M_CleanData


title: p41-2


title: Uro_E_16_BiolRep3

organism: Erophylla sezekorni

value: uropatagium


title: LCS7846_GV_KO1_F_CleanData

value: Female


title: BMSC_RNAseq_2D_rep2


title: p26-1


title: BMSC_RNAseq_2D_rep1


title: p26-2


title: Uro_E_16_BiolRep2


title: p17-2


title: BMSC_RNAseq_Pri_rep1

value: Primary


title: p53-2


title: p17-1


title: HSC_RNAseq_3D_Old_rep3

source_name: mouse hematopoietic stem cells

value: 3D coculture

value: 12~13 months


title: BMSC_RNAseq_Pri_rep2


title: Uro_E_16_BiolRep1


title: Uro_E_14_BiolRep2


title: BMSC_RNAseq_3D_rep1


title: Uro_E_14_BiolRep3


title: HSC_RNAseq_3D_Old_rep2


title: HSC_RNAseq_3D_Old_rep1


title: WT : 4 : 1216 [PLS_Ali_MSp]

type: RNA

city: RIVERSIDE

first: Declan

last: McCole

address: 3401 Watkins Drive

department: Biomedical Sciences

institute: University of California Riverside

description: 50ug of total RNA was used for each sample. WT samples were used as reference samples for comparison in analysis.

hyb_protocol: 50 ng of total RNA was used in the hybridization from each sample following manufacturer's guidelines (18 hours at 65°C). Samples were loaded into a AutoImmune Profiling Nanostring panel with the addition of 30 custom targets screening for markers of host-bacteria interaction, autophagy, immune response and iron transport (PLS_Ali_MSp).

scan_protocol: Scanning of the panels was performed by nCounter SPRINT Profiler and data analysis by nSolver Analysis Software 4.0.

data_processing: Results from each panel were normalized in nSolver software 4.0. using the advanced analysis 2.0 function which relies on the gNorm algorithm. nSolver-generated principal component analysis and heat maps were used to evaluate specific sample clustering and to identify covariants. Principal component analysis identified that at least of set of littermates (co-housing) clustered together, hence data analysis was normalized taking into account littermate effect as a covariate. The same analysis was performed to identify sex differences but none was found. Then, the normalized data from each intestinal segment was consolidated using the MultiRLF function and used for differential expression between genotypes to identify specific targets that exhibit significantly increased or decreased gene expression. p-value was set at 0.05. Benjamini-Yekutieli test was used to calculate the false discovery rate for multiple comparisons analysis. Q-value was set at 0.1.

label: codeset probes

source_name: Isolated Ileal IECs

label_protocol: Samples were labelled with panel-specific codesets, or barcodes, probes designed by Nanostring.

extract_protocol: Distal ileum sections were cut opened longitudinally and immersed in 500uL of Cell Recovery Solution (Corning, Cat. No. 354253) for two hours on ice, and then shaken with forceps to release the intestinal crypts/villi into the solution. Samples were centrifuged at 1.5xG for 10 minutes at 4°C. The supernatant was aspirated and IECs washed with ice-cold PBS (x2). Samples were stored in RNA later and frozen at -80°C until day of experiment. RNA later was removed and cells lysed with syringe and needle (22G). Total RNA was isolated using QIAGEN RNeasy mini kit. RNA estimation was done using Qubit 2.0. Sample purity was assessed by NanoDrop absorbance 260/280 ratio.

value: WT

tag: littermate group

tag: mouse number

tag: Sex


title: HSC_RNAseq_3D_Young_rep3


title: HSC_RNAseq_3D_Young_rep2


title: KO : 4 : 1218 [PLS_Ali_MSp]

value: KO


title: Uro_E_14_BiolRep1


title: HET : 4 : 1215 [PLS_Ali_MSp]

value: HET


title: plagio_E_16_BiolRep2

value: plagiopatagium


title: BMSC_RNAseq_Pri_rep3


title: HSC_RNAseq_3D_Young_rep1


title: HET : 3 : 1245 [PLS_Ali_MSp]


title: plagio_E_16_BiolRep1


title: plagio_E_14_BiolRep3


title: plagio_E_14_BiolRep2


title: KO : 3 : 1243 [PLS_Ali_MSp]


title: HSC_RNAseq_Pri_Old_rep3


title: HSC_RNAseq_Pri_Old_rep2


title: plagio_E_14_BiolRep1


title: Heart_E_16_BiolRep3

value: heart


title: WT : 2 : 957 [PLS_Ali_MSp]

value: Male


title: KO : 2 : 954 [PLS_Ali_MSp]


title: Heart_E_16_BiolRep2


title: HSC_RNAseq_Pri_Young_rep2

value: Bone Marrow


title: plagio_E_16_BiolRep3


title: HSC_RNAseq_Pri_Young_rep3


title: HSC_RNAseq_Pri_Young_rep1


title: KO : 4 : 1214 [PLS_Ali_MSp]


title: Heart_E_16_BiolRep1


title: BMSC_ATACseq_3D_rep3

value: 3D culture


title: JCe0059b

city: Lausanne

first: David

last: Gfeller

address: Rue du Bugnon 25A

department: Department of Oncology UNIL CHUV; Ludwig Institute for Cancer Research Lausanne

institute: University of Lausanne

description: TCR beta sequencing

data_processing:
library strategy: TCR-seq
Deep sequencing of the TCR alpha and beta chain was performed on Illumina instrument
fastq reads were demultiplexed, assembled and aligned to databases of TCRa and TCRb with MIGEC (v1.2.9)
Assembly: IMGT human TCR genes
Supplementary files format and content: Tab delimited .txt file including V and J genes, CDR3 sequences, counts…

extract_protocol:
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction
Libraries were prepared using targeted TCR amplification (Bobisse et al, Nat Commun. 2018 Mar 15;9(1):1092)

tag: multimer

tag: donor


title: BMSC_ATACseq_3D_rep2

value: 8~12 weeks


title: JCe0059a

description: TCR alpha sequencing


title: JCe0058b

description: TCR beta sequencing


title: BMSC_ATACseq_3D_rep1


title: BMSC_ATACseq_2D_rep3


title: KO : 1 : 809 [PLS_Ali_MSp]


title: Heart_E_14_BiolRep1


title: HET : 2 : 950 [PLS_Ali_MSp]


title: BMSC_ATACseq_2D_rep2


title: FL_E_16_BiolRep1

value: forelimb


title: FL_E_16_BiolRep3


title: FL_E_16_BiolRep2


title: BMSC_ATACseq_Pri_rep3


title: JCe0050b

description: TCR beta sequencing


title: JCe0050a

description: TCR alpha sequencing


title: JCe0049b

description: TCR beta sequencing


title: HSC_RNAseq_Pri_Old_rep1


title: BMSC_ATACseq_2D_rep1


title: Heart_E_14_BiolRep3


title: FL_E_14_BiolRep2


title: FL_E_14_BiolRep3


title: Heart_E_14_BiolRep2


title: WT : 1 : 810 [PLS_Ali_MSp]


title: FL_E_14_BiolRep1


title: BMSC_ATACseq_Pri_rep2


title: JCe0049a

description: TCR alpha sequencing


title: JCe0058a

description: TCR alpha sequencing


title: HET : 1 : 811 [PLS_Ali_MSp]


title: Human PBMC 44

status: Public on Apr 05 2023

city: Chicago

first: Anthony

last: Reder

state: IL

address: 5841 S Maryland Ave

department: Neurology

institute: University of Chicago Medicine

hyb_protocol: Samples were randomized and hybridized to highly sensitive comprehensive  Clariom D microarrays (ThermoFisher Scientific)

data_processing:
RMA expression value derived from Expression Console software; core-exon analysis
Raw CEL files from arrays were imported, log2-transformed,  and normalized; gene expression was analyzed as described  previously (Feng et al, 2019a). Transcriptome Analysis  Console (TAC) version 4.02 (ThermoFisher) identified differentially expressed genes (DEGs).

label: biotin

source_name: MS Patient

growth_protocol: PBMC were isolated by density gradient centrifugation (Lympholyte, Cedarlane Laboratories, Burlington, NC) within 1–4 h of phlebotomy. Cell lysates were stored at -80!C  in ‘‘buffer RLT plus’’ (Qiagen) for <12 months.

extract_protocol: Total RNA was purified using RNeasy (Qiagen).

treatment_protocol: 15 patients infused with Ocrelizumab for 0.5 and 6 months, missing one timepoint.

value: M

tag: treatment duration (month)

tag: ms-type

value: RRMS-s

value: PBMC


title: Human PBMC 42

scan_protocol: Samples were randomized and hybridized to highly sensitive comprehensive  Clariom D microarrays (ThermoFisher Scientific)

value: F


title: Human PBMC 40

label_protocol: Samples were randomized and hybridized to highly sensitive comprehensive  Clariom D microarrays (ThermoFisher Scientific)


title: Human PBMC 43


title: Human PBMC 39

value: SPMS-a


title: Human PBMC 38


title: Human PBMC 32


title: Human PBMC 29


title: Human PBMC 37


title: Human PBMC 23


title: Human PBMC 27


title: Human PBMC 24


title: Human PBMC 36


title: Human PBMC 22


title: Human PBMC 33


title: Human PBMC 35

value: SPMS-s


title: Human PBMC 31

value: RRMS-a


title: Human PBMC 30


title: Human PBMC 28


title: Human PBMC 34


title: Human PBMC 19


title: Human PBMC 25


title: Human PBMC 21


title: Human PBMC 20


title: Human PBMC 17


title: Human PBMC 41


title: Human PBMC 18


title: BMSC_ATACseq_Pri_rep1

value: Primary


title: Human PBMC 26


title: Human PBMC 15


title: Human PBMC 13


title: Human PBMC 14


title: Human PBMC 12


title: Human PBMC 10


title: Human PBMC 4


title: Human PBMC 7


title: Human PBMC 6


title: Human PBMC 8


title: Human PBMC 9


title: Human PBMC 2


title: Human PBMC 5


title: Human PBMC 1


title: CN+ONX0914 rep2

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

data_processing:
Short-read trimming (Trimmomatic v.0.39)
Short-read alignment to reference genome (STAR 2.7.3a, genome version GRCm39.104)
Short-read counting (featureCounts v2.00)
Assembly: GRCm39.104
Supplementary files format and content: featureCounts output files, first column is an Ensembl gene id, and second – number of reads assigned to exonic regions of specific gene.

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using the Extract RNA reagent (Evrogen).
The concentration of RNA was measured with a Qubit Fluorometer (Invitrogen). The quality of RNA was determined with an Agilent BioAnalyzer 2100 using an RNA 600 nano kit. The RNA Integrity Number (RIN) of all RNA samples was not less than 8. Libraries for RNA-seq were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s guidelines. One hundred bp single-end sequencing was conducted on an Illumina NextSeq 2000 platform.

treatment_protocol: Male aged-matched CD1 strain mice were receiving 10mg/kg of ONX-0914 (Apexbio, USA) intraperitoneally twice a week during 2 month period

value: Hippocampus


title: CN+ONX0914 rep1


title: CN rep3

value: NO


title: CN+DMSO rep2

value: DMSO


title: CN+DMSO rep3


title: CN rep1


title: HCC1954_Pa1

city: DALLAS

first: Srinivas

last: Malladi

state: Texas

address: NB7218, DEPARTMENT OF PATHOLOGY, UT SOUTHWESTERN MEDICAL CENTER

department: PATHOLOGY

institute: UT Southwestern Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
The trimmed reads were a whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: Normalized count table as a tab delimited text file

source_name: HCC1954 Pa cells

growth_protocol: Culutured in R3F

extract_protocol:
Total RNA was extracted using RNeasy Kit (Qiagen). Libraries were prepared with either TruSeq RNA Sample Prep Kit v2 (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 million cells were cultured in 1ml R3F for overnight

value: Parental cells


title: HCC1954_Pa3


title: H, Liver tissue, HBV infected, AST>40, biol rep5

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

data_processing:
Illumina HiSeq platform used for basecalling.
Raw image Data files obtained by Illumina HiSeq are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences, and the results are stored in FASTQ (.fq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with read counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNAs were extracted from liver tissue using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
The liver tissue which AST<40 were obtained from liver surgery(L)
The liver tissue which AST>40 were obtained from liver transplantation patients(H)

value: Liver

tag: infection

value: HBV

tag: tissue source

value: liver transplantation

tag: ast


title: H, Liver tissue, HBV infected, AST>40, biol rep4

tag: tissue


title: H, Liver tissue, HBV infected, AST>40, biol rep6


title: Human PBMC 16


title: CN rep2

tag: strain


title: HCC1954_Pa2

tag: cell line


title: Human PBMC 11


title: H, Liver tissue, HBV infected, AST>40, biol rep3


title: Human PBMC 3


title: P4

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Liver tissue from 22-month-old (Old) animal treated with PDX.

data_processing:
STAR (version 2.6.0c) was used to align sequence reads to mouse genome build mm10.
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
Variance-stabilizing-transformed (VST) expression values were computed using the DESeq2 R package (version 1.23.10).
Assembly: mm10
Supplementary files format and content: counts.txt: 55450 x 15 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 55450 x 15 matrix of variance-stabilizing-transformed (VST) expression values

source_name: liver tissue

growth_protocol: C57BL/6 mice were obtained from the National Institute on Aging (NIA) and group-housed in a pathogen-free facility at 20–23 °C under a 12-h light to dark cycle with food (Chow diet, Prolab® IsoPro® RMH 3000) and water ad libitum.

extract_protocol:
Total RNA was isolated using miRNeasy® Mini Kit (Qiagen) according to the manufacturer's protocol. Briefly, 50-60 mg of crushed frozen liver from female mice were homogenized in QIAzol lysis reagent (RNeasy Plus Mini Kit, Qiagen) and then transferred to a RNeasy® Mini column to be further processed with a genomic DNA elimination step by following the manufacturer’s RNA isolation protocol. Total isolated RNA was tested to fit high quality and integrity standards, as determined by the 28S/18S rRNA peak and area ratios (ranges 1.8-2.1 and 1.9-2.5, respectively) and the RNA integrity number (RIN, range 8.2-8.7) using RNA 6000 Pico Assay RNA chips run in Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
200 ng total RNA was used for mRNAseq library preparation using the NEBNext Poly(A) Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: The therapeutic treatment consisted of 9 weeks of daily oral gavage with either corn oil (120 μL, Mazola® 100% pure, cholesterol free) as vehicle (Old, n=18-19 and Adult n=15) or PDX in corn oil (30 ng/g of BW; Cayman Chemical Company, n=12-16). Gavaging occurred from 8-11 AM and animals were gavaged in an alternating group and sex order.

value: liver tissue

value: 22 months (Old)

tag: treatment

value: PDX

tag: delta body_weight,_%

tag: walking speed,_rpm

tag: grip force_test,_g

tag: treadmill distance,_m

tag: voluntary running_wheel,_km/d

tag: frailty index_(fi)_score

tag: sum of_positive_frailty_criteria

tag: frailty status

value: Frail


title: H, Liver tissue, HBV infected, AST>40, biol rep2


title: P5

tag: age


title: L, Liver tissue, HBV infected, AST<40, biol rep4

value: liver surgery


title: H, Liver tissue, HBV infected, AST>40, biol rep1


title: L, Liver tissue, HBV infected, AST<40, biol rep3


title: L, Liver tissue, HBV infected, AST<40, biol rep2


title: L, Liver tissue, HBV infected, AST<40, biol rep1


title: P3

value: Prefrail


title: O5

description: Liver tissue from 22-month-old (Old) animal treated with vehicle.

value: vehicle


title: P1

value: Robust


title: O3


title: P2


title: O1


title: O2


title: GM21 fibroblasts, RAS overexpression, day 8 post-transduction rep2

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

data_processing:
fastq files were quality checked with multiqc
fastq files were trimmed with trimmomatic te moreve adapters and aligned using bowtie 2 with the local option in paired-end mode
alignment files were cleaned of optical and PCR duplicates with PicardTools and samtools and blacklisted against artifact regions of the hg19 human genome build.
Enriched regions were identified using macs v.2.2.7.1 (macs2 callpeak --nomodel --shiftsize --shift-control--gsize hs -p 1e-3). The identified peaks were subsequently processed using the irreproducibility discovery rate (IDR) pipeline, generating time point-specific reproducible peak sets at each time point. Reproducible peaks were collapsed into master peaksets per histone modification analyzed.
Signal visualization tracks were generated with deeptools using the RPGC approach to obtain 1X coverage after merging time point replicates into a single bam file.
Assembly: hg19
Supplementary files format and content: BigWig and narrowPeak

growth_protocol: Human somatic GM21 foreskin fibroblasts (Coriell Institute, Camden, NJ) and WI-38 human fetal lung fibroblasts (European Collection of Authenticated Cell Cultures, Porton Down, UK) were cultured in a DMEM medium containing 10% fetal bovine serum (FBS) and 1× penicillin/streptomycin (Corning) at 37 °C in a 2% oxygen atmosphere

extract_protocol:
DNA was extracted using a Qiagen MinElute kit.
Libraries were produced by PCR amplification (12 cycles) of tagmented DNA using an NEB Next High-Fidelity 2× PCR Master Mix. Library quality was assessed using an Agilent Bioanalyzer 2100.

treatment_protocol: Nuclei were extracted by incubating cells in nuclear extraction buffer (containing 10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuging at 500 × g at 4 °C for 5 min. The supernatant was carefully removed by pipetting, and the transposition was performed by resuspending nuclei in 50 µl of Transposition Mix containing 1× TD Buffer (Illumina, San Diego, CA) and 2.5 µl Tn5 (Illumina) for 30 min at 37 °C.

tag: cell type

value: skin fibroblast

value: H-RAS-G12-V overexpression


title: GM21 fibroblasts, RAS overexpression, day 8 post-transduction rep1


title: GM21 fibroblasts, RAS overexpression, day 45 post-transduction rep2


title: GM21 fibroblasts, RAS overexpression, day 56 post-transduction rep1


title: GM21 fibroblasts, RAS overexpression, day 8 post-transduction rep3


title: GM21 fibroblasts, RAS overexpression, day 56 post-transduction rep2


title: A2

description: Liver tissue from 6-month-old (Adult) animal treated with vehicle.

value: 6 months (Adult)


title: A3


title: A4


title: A5


title: GM21 fibroblasts, RAS overexpression, day 45 post-transduction rep1


title: A1


title: GM21 fibroblasts, RAS overexpression, day 32 post-transduction rep1


title: GM21 fibroblasts, RAS overexpression, day 32 post-transduction rep2


title: O4


title: VFAT-SCID-Sham-4

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Reads were trimmed using Trimmomatic v 0.38 to remove adapter content and low-confidence base calls
Trimmed reads were aligned to the bovine reference using HISAT2 v 2.1.0
Raw read counts were generated using the R/Bioconductor package Genomic Alignments v 1.16.0
Normalized counts, FPKM values, and log2 fold changes were computed using DESeq2 v 1.20.0
Assembly: GRCm38
Supplementary files format and content: raw_counts.csv contains raw read counts per gene per sample, as calculated by the GenomicAlignments R/Bioconductor package, in comma-separated value format
Supplementary files format and content: normalized_counts.csv contains read counts per gene per sample, normalized by sample using DESeq2 v 1.20.0 with default settings, in comma-separated value format
Supplementary files format and content: fpkm.csv  contains FPKM values as computed by DESeq2 v 1.20.1, in comma-separated value format

source_name: Visceral adipose tissue

extract_protocol:
The tissues were removed, flash frozen ij liquid nitrogen, and RNA was extracted using Qiagen RNeasy Plus Universal Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Visceral adipose tissue

value: Male Fox Chase SCID Mouse- CB17/Icr-Prkdcscid/IcrlcoCrl

tag: surgery

value: Sham

tag: transplantation


title: GM21 fibroblasts, RAS overexpression, day 23 post-transduction rep4


title: VFAT-SCID-Sham-5


title: GM21 fibroblasts, RAS overexpression, day 23 post-transduction rep3


title: GM21 fibroblasts, RAS overexpression, day 23 post-transduction rep2


title: VFAT-SCID-Sham-2


title: VFAT-SCID-Scrambled-NaKtideCells-PNx-4

value: Partial Nephrectomy

value: Lenti-adipo-scrambled


title: GM21 fibroblasts, RAS overexpression, day 23 post-transduction rep1


title: VFAT-SCID-Scrambled-NaKtideCells-PNx-3-2nd


title: VFAT-SCID-Scrambled-NaKtideCells-PNx-3


title: VFAT-SCID-Sham-3


title: GM21 fibroblasts, RAS overexpression, day 18 post-transduction rep2


title: VFAT-SCID-PNx-5


title: VFAT-SCID-PNx-4


title: GM21 fibroblasts, RAS overexpression, day 14 post-transduction rep1


title: GM21 fibroblasts, empty vector, day 8 post-transduction rep2

value: Empty vector control


title: VFAT-SCID-PNx-2


title: GM21 fibroblasts, RAS overexpression, day 14 post-transduction rep2


title: GM21 fibroblasts, empty vector, day 56 post-transduction rep2


title: VFAT-SCID-Scrambled-NaKtideCells-PNx-1


title: GM21 fibroblasts, empty vector, day 8 post-transduction rep4


title: VFAT-SCID-PNx-3


title: GM21 fibroblasts, empty vector, day 8 post-transduction rep1


title: GM21 fibroblasts, RAS overexpression, day 18 post-transduction rep1


title: VFAT-SCID-PNx-1


title: GM21 fibroblasts, empty vector, day 56 post-transduction rep1


title: GM21 fibroblasts, empty vector, day 32 post-transduction rep2


title: VFAT-SCID-Sham-1


title: GM21 fibroblasts, empty vector, day 32 post-transduction rep1


title: VFAT-SCID-Lenti-NaKtideCells-PNx-4

value: Lenti-adipo-NaKtide


title: VFAT-SCID-Scrambled-NaKtideCells-PNx-2


title: VFAT-SCID-Lenti-NaKtideCells-PNx-3


title: GM21 fibroblasts, empty vector, day 8 post-transduction rep3


title: VFAT-SCID-ControlCells-PNx-5

value: Control Cells


title: VFAT-SCID-Lenti-NaKtideCells-PNx-1


title: VFAT-SCID-ControlCells-PNx-3


title: GM21, Day 32, Rep 1, input

data_processing:
fastq files were quality checked with multiqc
fastq files were trimmed with trimmomatic te moreve adapters and aligned using bowtie 2 with the local option
alignment files were cleaned of optical and PCR duplicates with PicardTools and samtools and blacklisted against artifact regions of the hg19 human genome build.
Enriched regions were identified using macs v.2.2.7.1 (macs2 callpeak --nomodel --shiftsize --shift-control--gsize hs -p 1e-3). The identified peaks were subsequently processed using the irreproducibility discovery rate (IDR) pipeline, generating time point-specific reproducible peak sets at each time point. Reproducible peaks were collapsed into master peaksets per histone modification analyzed.
Signal visualization tracks were generated with deeptools using the RPGC approach to obtain 1X coverage after merging time point replicates into a single bam file.
Assembly: hg19
Supplementary files format and content: BigWig and narrowPeak (except input)

extract_protocol:
Immunoprecipitation was performed overnight at 4 °C with rotation using 1 × 106 cell equivalents per immunoprecipitation using antibodies (5 µg) against H3K4me1 (Active Motif, Carlsbad, MA; Cat no. 39297) and H3K27ac (Active Motif, Carlsbad, MA; Cat no. 39133). Subsequently, 30 µl of Ultralink Resin (Thermo Fisher Scientific, Waltham, MA) was added and allowed to tumble for 4 h at 4 °C. The resin was pelleted by centrifugation and washed three times in low-salt buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 20 mM EDTA, 20 mM Tris-HCl pH 8.0), one time in high-salt buffer (500 mM NaCl, 0.1% SDS, 1% Triton X-100, 20 mM EDTA, 20 mM Tris-HCl pH 8.0), two times in lithium chloride buffer (250 mM LiCl, 1% IGEPAL CA-630, 15 sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0) and two times in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Washed beads were resuspended in elution buffer (10 mM Tris-Cl pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS) treated with RNAse H (30 min, 37 °C) and Proteinase K (2 h, 37 °C), 1 µl glycogen (20 mg/ml; Ambion, Austin, TX) was added and decrosslinked overnight at 65 °C. For histone modifications, DNA was recovered by mixing the decrosslinked supernatant with 2.2× SPRI beads followed by 4 min of incubation at room temperature. The SPRI beads were washed twice in 80% ethanol, allowed to dry, and DNA was eluted in 35 µl of 10 mM Tris-Cl pH 8.0.
Libraries were constructed using an Accel-NGS 2S Plus DNA Library kit (21024; Swift Biosciences, Ann Arbor, MI) and amplified for 9 cycles. Libraries were then resuspended in 20 µl of low EDTA–TE buffer. Libraries were quality controlled in an Agilent Technologies 2100 Bioanalyzer (Applied Biosystems, Santa Clara, CA) and quantified using an Invitrogen Qubit DS DNA HS Assay kit (Q32854) (Thermo Fischer Scientific, Waltham, MA).

treatment_protocol: Chromatin was collected from GM21 fibroblasts retrovirally transduced with an empty vector (referred to as day 0) or H-RASG12V at days 10, 18, 22, and 32 after transduction. A total of 0.8-1 × 107 cells (per time point, from 10 pooled biological replicates) were fixed in 1% formaldehyde for 15 min, quenched in 2 M glycine for an additional 5 min, and pelleted by centrifugation at 2,000 r.p.m., 4 °C for 4 min. Nuclei were extracted in extraction buffer 2 (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100 and proteinase inhibitor cocktail) on ice for 10 min, followed by centrifugation at 3,000 × g at 4 °C for 10 min. The supernatant was removed, and nuclei were resuspended in nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, and proteinase inhibitor cocktail). Sonication was performed using a Branson sonicator until the desired average fragment size (100–300 bp) was obtained. Soluble chromatin was obtained by centrifugation at 12,000 r.p.m. for 15 min at 4 °C, and chromatin was diluted tenfold.

tag: antibody

value: input chromatin

tag: time

value: Day 32


title: GM21, Day 32, Rep 2, K4me1, ActiveMotif

value: H3K4me1 (Active Motif, Cat no. 39297)


title: VFAT-SCID-ControlCells-PNx-2

tag: tissue

tag: strain


title: VFAT-SCID-ControlCells-PNx-1


title: Kidney-SCID-Sham-5

source_name: Kidney tissue

value: Kidney tissue


title: GM21, Day 22, Rep 2, input

tag: cell line

value: Day 22

tag: treatment


title: GM21, Day 32, Rep 1, K27ac, ActiveMotif

value: H3K27ac (Active Motif, Cat no. 39133)


title: GM21, Day 32, Rep 2, K27ac, ActiveMotif

value: skin fibroblast


title: GM21, Day 22, Rep 1, input

value: H-RAS-G12-V overexpression


title: GM21, Day 32, Rep 1, K4me1, ActiveMotif


title: Kidney-SCID-Sham-4


title: GM21, Day 22, Rep 2, K27ac, ActiveMotif


title: Kidney-SCID-Sham-3-2nd


title: GM21, Day 22, Rep 2, K4me1, ActiveMotif


title: GM21, Day 22, Rep 1, K27ac, ActiveMotif


title: VFAT-SCID-Lenti-NaKtideCells-PNx-5


title: Kidney-SCID-Sham-3


title: GM21, Day 32, Rep 2, input


title: GM21, Day 18, Rep 2, input

value: Day 18


title: Kidney-SCID-Sham-2


title: Kidney-SCID-Sham-1


title: GM21, Day 18, Rep 1, input


title: VFAT-SCID-Lenti-NaKtideCells-PNx-2

value: Visceral adipose tissue


title: Kidney-SCID-Scrambled-NaKtideCells-PNx-5

value: Male Fox Chase SCID Mouse- CB17/Icr-Prkdcscid/IcrlcoCrl


title: VFAT-SCID-ControlCells-PNx-4


title: GM21, Day 18, Rep 2, K4me1, ActiveMotif


title: GM21, Day 22, Rep 1, K4me1, ActiveMotif


title: GM21, Day 18, Rep 1, K4me1, ActiveMotif


title: GM21, Day 18, Rep 2, K27ac, ActiveMotif


title: Kidney-SCID-Scrambled-NaKtideCells-PNx-2


title: Kidney-SCID-Scrambled-NaKtideCells-PNx-1


title: GM21, Day 10, Rep 2, input

value: Day 10


title: Kidney-SCID-PNx-5

value: Partial Nephrectomy


title: GM21, Day 18, Rep 1, K27ac, ActiveMotif


title: Kidney-SCID-PNx-4


title: Kidney-SCID-PNx-1


title: Kidney-SCID-PNx-2


title: GM21, Day 10, Rep 1, input


title: Kidney-SCID-PNx-3


title: GM21, Day 10, Rep 2, K4me1, ActiveMotif


title: GM21, Day 10, Rep 1, K4me1, ActiveMotif


title: Kidney-SCID-Lenti-NaKtideCells-PNx-5


title: GM21, Day 10, Rep 1, K27ac, ActiveMotif


title: GM21, Day 10, Rep 2, K27ac, ActiveMotif


title: GM21, Day 0, Rep 2, input

value: Day 0


title: Kidney-SCID-Lenti-NaKtideCells-PNx-4


title: Kidney-SCID-Lenti-NaKtideCells-PNx-3


title: GM21, Day 0, Rep 1, input


title: GM21, Day 0, Rep 2, K4me1, ActiveMotif


title: Kidney-SCID-Lenti-NaKtideCells-PNx-2


title: GM21, Day 0, Rep 1, K4me1, ActiveMotif


title: Kidney-SCID-Lenti-NaKtideCells-PNx-1


title: GM21, Day 0, Rep 1, K27ac, ActiveMotif


title: GM21, Day 0, Rep 2, K27ac, ActiveMotif


title: Kidney-SCID-Scrambled-NaKtideCells-PNx-4

value: Lenti-adipo-scrambled


title: Kidney-SCID-Scrambled-NaKtideCells-PNx-3


title: Kidney-SCID-ControlCells-PNx-5


title: Kidney-SCID-ControlCells-PNx-2


title: Kidney-SCID-ControlCells-PNx-1


title: Kidney-SCID-ControlCells-PNx-3


title: Heart-SCID-Sham-5

source_name: Heart tissue

value: Heart tissue

value: Sham


title: Heart-SCID-Sham-4


title: MOLM13_RNAseq_single_14

first: Oana

last: Ursu

address: 415 Main Street

institute: Broad Institute

data_processing:
demultiplex: cellranger mkfastq. Cellranger 6.1.2
alignment and counts: cellranger count. Cellranger 6.1.2. This results in the deposited files (genes.tsv, cells.tsv, matrix.mtx and protospacer_calls.csv), quantifying the number of UMIs/gene/cell, and assigning each cell to the perturbation(s) it received.
Assembly: "single" and "combo" experiments: human transcriptome version GRCh38. SHARE-seq: hg19
Supplementary files format and content: Perturb-seq experiments: Processed expression matrices (matrix.mtx files) containing raw UMI counts are provided in mtx (Market Exchange) format, as produced by the cellranger software. Each line represents the counts (third column) for a given gene (second column) in a given cell (first column). The cells and genes are represented as their indices in the files (cells.tsv and genes.tsv, respectively).   NOTE: this expression matrix includes the number of UMIs recorded for each perturbation in each cell, in addition to the number of UMIs for each gene's expression. It is recommended to remove these perturbation UMI counts from the expression matrix before normalization of expression data, and treat them as a separate entity.    The assignments of cells to specific perturbations are provided in the protospacer_calls.csv files. The first column provides the name of the cell, the second specifies how many distinct perturbations were found in that cell, the third column specifies the names of the perturbations found in the cell, separated by “|” and the fourth column notes the number of UMIs supporting the presence of each perturbation in the cell, in the order provided in the third column, again separated by “|”.    SHARE-seq experiment: For SHARE-seq, the expression data are provided as described for the Perturb-seq experiments, in mtx format, consisting of the files (MOLM13_SHAREseq_RNA.cells.tsv, MOLM13_SHAREseq_RNA.genes.tsv and MOLM13_SHAREseq_RNA.matrix.mtx). In addition, for the ATAC-seq measurements in SHARE-seq, we identify peaks of chromatin accessibility and provide the counts recorded for each peak in each cell in mtx format in the files MOLM13_SHAREseq_ATAC.cells.tsv, MOLM13_SHAREseq_ATAC.peaks.tsv.

source_name: MOLM13 AML cell line

growth_protocol: MOLM-13 cells were grown in RMPI 1640 medium (no glutamine) supplemented with 10% FBS (Omega), 1% Penicillin-Streptomycin (Gibco), and 1% GlutaMax (Gibco).  Cells were maintained in an incubator at 37 degrees Celsius with 5% Carbon Dioxide.

extract_protocol:
We used 6000 cells per channel, for 15 channels for the "single" experiment, and 3 channels for the "combo" experiment.
The “single” and “combo” experiments were profiled with 15 and 3 channels, respectively, and were sequenced paired-end on an Illumina Hi-Seq instrument at a ratio of 3 channels of 10x to 1 lane of sequencing (5 for the “single” experiment, and 1 for the “combo” experiment), using paired end reads as follows.     For the “single” experiment, read 1 is 28 bases long (16 for cell barcode, 12 for UMI), read 2 is 91 bases long and sample index read is 8 bases long.     For the “combo” experiment, read 1 is 28 bases long (16 for cell barcode, 12 for UMI), read 2 is 91 bases long and sample index read is 8 bases long.     Perturbations were assigned to cells using dial-out PCR. Dial-out PCR products were sequenced on an Illumina Mi-seq, paired-end (for all experiments, read 1 is 28 bases and read 2 is 60 bases long), with read 1 having the same structure as in the high-throughput sequencing of the libraries described above. Each experiment required only one Mi-Seq run to process the dial-out libraries.

treatment_protocol: 1. Perturb-seq experiments: We performed Perturb-seq on MOLM13 cells, following either individual perturbation of subunits (“single” experiment) or combinatorial perturbation of selected subunit combinations (“combo” experiment).     2. SHARE-seq experiment: We performed SHARE-seq on MOLM13 cells following CRISPR-mediated knockout of specific mSWI/SNF subunits, obtaining both RNA-seq and ATAC-seq readouts in the same single cell. We performed SHARE-seq for 5 conditions: control guide, ARID1A, SMARCD2, SMARCA4 and BRD9, each with 2 replicate wells in an arrayed format.

tag: experiment type

value: single perturbation

tag: readout

value: 3' sc-RNAseq


title: MOLM13_RNAseq_combo_2

value: combinatorial perturbation


title: MOLM13_RNAseq_combo_1


title: Heart-SCID-Sham-3


title: Heart-SCID-Sham-1


title: MOLM13_RNAseq_single_15


title: MOLM13_RNAseq_single_11


title: MOLM13_RNAseq_single_13


title: MOLM13_RNAseq_single_12


title: Heart-SCID-Sham-2


title: MOLM13_RNAseq_single_10


title: Heart-SCID-Scrambled-NaKtideCells-PNx-5


title: Heart-SCID-Scrambled-NaKtideCells-PNx-3


title: Heart-SCID-Scrambled-NaKtideCells-PNx-2


title: MOLM13_RNAseq_single_9


title: MOLM13_RNAseq_single_8


title: Kidney-SCID-ControlCells-PNx-4

value: Kidney tissue

value: Control Cells


title: Heart-SCID-PNx-5


title: MOLM13_RNAseq_combo_3


title: Heart-SCID-Scrambled-NaKtideCells-PNx-1


title: MOLM13_RNAseq_single_6


title: MOLM13_RNAseq_single_4


title: MOLM13_RNAseq_single_7


title: MOLM13_RNAseq_single_5


title: MOLM13_RNAseq_single_3


title: Heart-SCID-PNx-4


title: Heart-SCID-PNx-2


title: Heart-SCID-PNx-3


title: MOLM13_RNAseq_single_1


title: Heart-SCID-Lenti-NaKtideCells-PNx-5

value: Lenti-adipo-NaKtide


title: MOLM13_RNAseq_single_2


title: Heart-SCID-PNx-1


title: Heart-SCID-Scrambled-NaKtideCells-PNx-4


title: Tempus Blood  (P05BW4)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Tempus Blood  (P05BW4)

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26..
We use quantile method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: RSEM expected counts

source_name: Tempus Blood

extract_protocol:
Liver Biopsy: RNA samples from cryopreserved liver biopsies were prepared by TRIzol extraction (Thermo Fisher), and the quantity, purity, and integrity of the samples were measured with Nanodrop (Thermo Scientific) and Bioanalyzer (Agilent).PBMC: Whole blood from patient was collected in Tempus Blood RNA tubes (Applied Biosystems) and stored in -80oC. RNA was extracted using the Tempusä Spin RNA Isolation Kit (Invitrogen). In short, stabilised blood was transferred to a 50 ml tube, and diluted with PBS. After vortexing, the tube was then centrifuged and the pellet resuspended. Resuspended RNA was transferred into purification filter, then purified and eluted using a microcentrifuge.
RNA libraries were prepared and amplified using TruSeq Stranded mRNA sample preparation with the corresponding kit (Illumina Inc, USA). Paired-end 101 bp sequencing were done reaching approximately a total of 50 milions of reads by sample.

tag: time point

value: at four weeks


title: Tempus Blood  (P04BW4)

description: Tempus Blood  (P04BW4)


title: Tempus Blood  (P02BW4)

description: Tempus Blood  (P02BW4)


title: Tempus Blood  (P06BW4)

description: Tempus Blood  (P06BW4)


title: Heart-SCID-Lenti-NaKtideCells-PNx-3


title: Tempus Blood  (P03BW4)

description: Tempus Blood  (P03BW4)


title: Heart-SCID-Lenti-NaKtideCells-PNx-4


title: Heart-SCID-Lenti-NaKtideCells-PNx-2


title: Heart-SCID-Lenti-NaKtideCells-PNx-1


title: Tempus Blood  (P01BW4)

description: Tempus Blood  (P01BW4)


title: Heart-SCID-ControlCells-PNx-3


title: Heart-SCID-ControlCells-PNx-4


title: Tempus Blood  (P04BBSN)

description: Tempus Blood  (P04BBSN)

value: Baseline


title: Tempus Blood  (P05BBSN)

description: Tempus Blood  (P05BBSN)


title: Heart-SCID-ControlCells-PNx-5


title: Heart-SCID-ControlCells-PNx-1


title: Heart-SCID-ControlCells-PNx-2


title: Tempus Blood  (P02BBSN)

description: Tempus Blood  (P02BBSN)


title: Tempus Blood  (P03BBSN)

description: Tempus Blood  (P03BBSN)


title: Tempus Blood  (P01BBSN)

description: Tempus Blood  (P01BBSN)


title: Liver Biopsy (P06W4)

description: Liver Biopsy (P06W4)

source_name: Liver Biopsy


title: Liver Biopsy (P05W4)

description: Liver Biopsy (P05W4)


title: Liver Biopsy (P04W4)

description: Liver Biopsy (P04W4)


title: Liver Biopsy (P03W4)

description: Liver Biopsy (P03W4)


title: Tempus Blood  (P06BBSN)

description: Tempus Blood  (P06BBSN)


title: Liver Biopsy (P06SN)

description: Liver Biopsy (P06SN)


title: Liver Biopsy (P01W4)

description: Liver Biopsy (P01W4)


title: Liver Biopsy (P03SN)

description: Liver Biopsy (P03SN)


title: Liver Biopsy (P05SN)

description: Liver Biopsy (P05SN)


title: Liver Biopsy (P01SN)

description: Liver Biopsy (P01SN)


title: Liver Biopsy (P02SN)

description: Liver Biopsy (P02SN)


title: Liver Biopsy (P02W4)

description: Liver Biopsy (P02W4)


title: mPFC, oxt_f1

city: St. Louis

first: Arvind

last: Palanisamy

state: MO

address: 660 S Euclid Ave

department: Anesthesiology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined, aligned, and quantitated with Illumina's DRAGEN Bio-IT system version 3.9.3-8
Assembly: Ensembl Release 101 Rnor_6.0.101
Supplementary files format and content: Gene counts with TPM in tab-delimitted text format

source_name: medial prefrontal cortex

extract_protocol:
Total RNA was extracted from bilateral mPFC using RNAeasy kit (Qiagen). Only RNA with RIN > 8.0 were used for RNA-seq.
oligo-dT

tag: Sex

value: Female

value: Sprague Dawley

value: medial prefrontal cortex

value: Oxytocin


title: mPFC, oxt_f3


title: Tregs from NOD.Drak2-/- mouse, biological rep2

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

description: Gene expression data from regulatory T cells obtained from lymph nodes of a NOD.Drak2-/- mouse.

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45 degrees celsius while rotating at 60 rpm.

scan_protocol: The cartridges were stained and washed on the Gene Chip FS450 fluidics station and then scanned on the Gene Chip Scanner 3000 7G.

data_processing: Cel files were analyzed using the oligo package in R, with background subtraction, quantile normalization, and summarization via median polish accomplished with the rma function.

source_name: Regulatory T cells (CD4+ CD8- CD25+ CD45RBlo) sorted from lymph nodes

label_protocol: The concentration was determined by nanodrop and then 125 ng of intact high-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit resulting in fragmented labeled cDNA.

extract_protocol: RNA was extracted with the Qiagen Rneasy micro kit.

treatment_protocol: Regulatory T cells were purified from lymph nodes of mice by FAC sorting with antibodies specific for CD4 (RM4-5), CD8 (53-6.7), and CD45RB (C363-16A).

value: lymph nodes

tag: genotype

value: 4-8 weeks

value: female


title: Tregs from NOD mouse, biological rep5

description: Gene expression data from regulatory T cells obtained from lymph nodes of a NOD mouse.

value: NOD


title: Tregs from NOD.Drak2-/- mouse, biological rep3


title: mPFC, oxt_f2


title: Tregs from NOD.Drak2-/- mouse, biological rep1


title: mPFC, oxt_f4


title: Tregs from NOD.Drak2-/- mouse, biological rep4


title: Tregs from NOD mouse, biological rep6


title: mPFC, oxt_f5


title: Tregs from NOD mouse, biological rep3


title: GM21 fibroblasts, RAS, biol rep 3, day 8

description: Gene expression profiling of the entry and exit from RAS-induced senescence in GM21 fibroblasts

hyb_protocol: Hybridization cocktail of fragmented and labeled ss-cDNA were incubated 16hr, 60rpm at 45°C on Human Transcriptome Arrays 2.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing:
Raw Affymetrix HTA 2.0 array intensity data were analyzed using open-source Bioconductor packages on R. All the data were normalized all together using the robust multi-array average normalization approach implemented in the oligo package (Carvalho and Irizarry, 2010). Internal control probe sets were removed and average expression deciles over all treatment and time points. Probes whose average expression was lower than the 4th expression decile were removed for subsequent analyses.
To remove sources of experimental variation and consider batch effects, data were finally corrected with the sva package. Principal component analysis and bi-clustering based on Pearson’s correlation and Ward’s aggregation criterion were used to confirm consistency between biological replicates and experimental conditions at each step of the pre-processing.

source_name: GM21 fibroblasts at day 8 post-transduction with H-RAS-G12V

label_protocol: Fragmented and labeled DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol from 100 ng total RNA starting material and 5.5 µg single strand cDNA.

extract_protocol: Macherey-Nagel RNA XS columns. At least 200 ng RNA with RIN number 9 were used for library construction.

treatment_protocol: GM21-RASV12 fibroblasts and their empty vector counterparts were generated by retroviral transduction. GM21 fibroblasts constitutively expressing non-targeting and POU2F2-targeting shRNAs (pLKO.1-Neo-CMV-tGFP, pLKO.1-Neo-CMV-tGFP-TRCN0000245324 and pLKO.1-Neo-CMV-tGFP-TRCN0000245325) (Millipore-Sigma, Saint Louis, MO) were generated by lentiviral transduction and selected with 400 µg/ml neomycin for seven days. Cells were subsequently retrovirally transduced with RASV12

value: skin fibroblast


title: Liver Biopsy (P04SN)

description: Liver Biopsy (P04SN)


title: GM21 fibroblasts, RAS, biol rep 3, day 56

source_name: GM21 fibroblasts at day 56 post-transduction with H-RAS-G12V


title: Tregs from NOD.Drak2-/- mouse, biological rep7


title: mPFC, oxt_m1

value: Male


title: Tregs from NOD mouse, biological rep4


title: GM21 fibroblasts, RAS, biol rep 3, day 32

source_name: GM21 fibroblasts at day 32 post-transduction with H-RAS-G12V


title: mPFC, oxt_m2


title: mPFC, oxt_f6


title: Tregs from NOD.Drak2-/- mouse, biological rep5


title: Tregs from NOD mouse, biological rep1


title: Tregs from NOD mouse, biological rep2


title: mPFC, oxt_m4


title: mPFC, oxt_m5


title: mPFC, oxt_m6


title: mPFC, oxt_m3


title: GM21 fibroblasts, RAS, biol rep 3, day 22

source_name: GM21 fibroblasts at day 22 post-transduction with H-RAS-G12V


title: mPFC, sal_f2

value: Saline


title: mPFC, sal_f4


title: mPFC, sal_f3


title: GM21 fibroblasts, empty vector, biol rep 3, day 56

description: Gene expression profiling of time alone in GM21 fibroblasts

source_name: GM21 fibroblasts empty vector time-alone control at day 56 post-transduction


title: GM21 fibroblasts, RAS, biol rep 3, day 25

source_name: GM21 fibroblasts at day 25 post-transduction with H-RAS-G12V


title: mPFC, sal_f5


title: GM21 fibroblasts, empty vector, biol rep 3, day 8


title: GM21 fibroblasts, RAS, biol rep 3, day 45

source_name: GM21 fibroblasts at day 45 post-transduction with H-RAS-G12V


title: GM21 fibroblasts, empty vector, biol rep 3, day 32

source_name: GM21 fibroblasts empty vector time-alone control at day 32 post-transduction


title: GM21 fibroblasts, RAS, biol rep 2, day 32


title: GM21 fibroblasts, RAS, biol rep 2, day 45


title: GM21 fibroblasts, RAS, biol rep 2, day 56


title: mPFC, sal_f6


title: GM21 fibroblasts, RAS, biol rep 2, day 25


title: mPFC, sal_m2


title: mPFC, sal_f1


title: mPFC, sal_m3


title: GM21 fibroblasts, RAS, biol rep 2, day 22


title: GM21 fibroblasts, RAS, biol rep 2, day 14

source_name: GM21 fibroblasts at day 14 post-transduction with H-RAS-G12V


title: GM21 fibroblasts, RAS, biol rep 2, day 19

source_name: GM21 fibroblasts at day 19 post-transduction with H-RAS-G12V


title: GM21 fibroblasts, empty vector, biol rep 2, day 8


title: GM21 fibroblasts, RAS, biol rep 2, day 8


title: mPFC, sal_m1


title: mPFC, sal_m6


title: mPFC, sal_m4


title: GM21 fibroblasts, RAS, biol rep 2, day 21

source_name: GM21 fibroblasts at day 21 post-transduction with H-RAS-G12V


title: Patient HP05 normal

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

description:
RNA-seq_countmatrix.csv
HP05_N

data_processing:
Illumina RTA v2.4.11 software was used for basecalling and bcl2fastq v2.17.14 was used for generating fastq files.
RNA-seq reads were trimmed for adaptor sequence and low quality, then mapped to GRCh38 whole genome using STAR v2.6.1a with parameters with default settings. Reads mapped to annotated genes were counted and aggregated using HTSeq_count v0.6.1.
miRNA-seq reads were mapped and counted using the primary analysis procedure of Qiagen online miRNA-seq analysis software (https://geneglobe.qiagen.com/sg/analyze).
Single cell data was mapped and counted using Cellranger (v5.0.1) and the filtered feature matrix was used in Seurat analysis (v3.0).
Differential gene expression was analyzed using R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw gene count values for each gene.

source_name: Pancreas

extract_protocol:
Total RNA was extracted with Qiagen AllPrep DNA/RNA/miRNA Universal kit.
RNA-seq libraries were prepared for sequencing using Tecan Universal NuQuant Kit, miRNA-seq libraries were prepared using QIAseq miRNA kit, and single cell RNA-seq library was constructed using 10x Genomics 5' GXE kit.

value: Duodenum Tissue

value: not collected


title: Patient HP03 PDAC

description:
RNA-seq_countmatrix.csv
HP03_T

value: Pancreatic tumor


title: Patient HP04 normal

description:
RNA-seq_countmatrix.csv
HP04_N


title: Patient HP04 PDAC

description:
RNA-seq_countmatrix.csv
HP04_T


title: Patient HP03 normal

description:
RNA-seq_countmatrix.csv
HP03_N

value: Pancreatic benign tissue


title: GM21 fibroblasts, RAS, biol rep 1, day 8


title: mPFC, sal_m5


title: GM21 fibroblasts, RAS, biol rep 1, day 50

source_name: GM21 fibroblasts at day 50 post-transduction with H-RAS-G12V


title: GM21 fibroblasts, RAS, biol rep 1, day 46

source_name: GM21 fibroblasts at day 46 post-transduction with H-RAS-G12V


title: GM21 fibroblasts, RAS, biol rep 1, day 56


title: GM21 fibroblasts, RAS, biol rep 1, day 21


title: GM21 fibroblasts, empty vector, biol rep 2, day 56


title: GM21 fibroblasts, empty vector, biol rep 2, day 32


title: GM21 fibroblasts, RAS, biol rep 1, day 32


title: Patient HP05 PDAC

description:
RNA-seq_countmatrix.csv
HP05_T


title: Patient HP02 PDAC

description:
RNA-seq_countmatrix.csv
HP02_T

value: male


title: Patient HP02 normal

description:
RNA-seq_countmatrix.csv
HP02_N


title: GM21 fibroblasts, RAS, biol rep 1, day 18

source_name: GM21 fibroblasts at day 18 post-transduction with H-RAS-G12V


title: Patient HP01 PDAC

description:
RNA-seq_countmatrix.csv
HP01_T


title: GM21 fibroblasts, RAS, biol rep 1, day 13

source_name: GM21 fibroblasts at day 13 post-transduction with H-RAS-G12V


title: m658

city: San Francisco

first: Qing

last: Dong

institute: UCSF

data_processing:
Paired-end reads were mapped to mouse reference genome (mm10) by Hisat2 (v2.0.5).
Quantification of gene expression was analyzed by featureCounts (version 1.5.0-p3).
Differential gene expression levels in mutant and WT tissues were compared using the DESeq2 R package (version 1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: cortex

growth_protocol: All experimental animals were singly housed on a LD 12:12 cycle and given ad libitum access to food and water.

extract_protocol: Paried-end RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cortex

value: 8 month


title: m660


title: GM21 fibroblasts, empty vector, biol rep 1, day 8


title: RNA-seq Prrx1Cre conditional knockout  replicate 4

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

description: PxCre; Hic1 f/f 4

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using Tophat 2 with Bowtie 2.
FPKM values were generated using Cufflinks.
Assembly: Ingenuity Pathway Analysis was run using a differential expression list generated by Cufflinks filtered for p < 0.05.
Supplementary files format and content: mm10
Supplementary files format and content: xlsx files include FPKM gene values for each Sample

source_name: embryonic forelimb

growth_protocol: Mice were bred and raised using standard approved animal care committee methodology.

extract_protocol:
N/A
Forelimbs were homogenized in RNAzol lysis reagent and further processed as per manufacturer's instructions to obtain RNA for library preparation and subsequent NGS.
tru seq stranded mRNA

treatment_protocol: Adult dams >7 weeks of age were paired in timed matings and subsequently sacrificed at embryonic day thirteen and a half at which point forelimbs were dissected and RNA was isolated for interrogation.

value: embryonic forelimb

value: KO

tag: developmental stage


title: RNA-seq Prrx1Cre conditional knockout  replicate 5

description: PxCre; Hic1 f/f 5


title: RNA-seq Prrx1Cre conditional knockout  replicate 6

description: PxCre; Hic1 f/f 6


title: RNA-seq Prrx1Cre conditional knockout  replicate 7

description: PxCre; Hic1 f/f 7


title: m659


title: RNA-seq Prrx1Cre conditional knockout  replicate 1

description: PxCre; Hic1 f/f 1


title: RNA-seq Prrx1Cre conditional knockout  replicate 2

description: PxCre; Hic1 f/f 2


title: RNA-seq Prrx1Cre conditional knockout  replicate 3

description: PxCre; Hic1 f/f 3


title: RNA-seq Prrx1Cre conditional heterozygous  replicate 3

description: PxCre; Hic1 f/+ 3

value: HET


title: m665


title: m671


title: RNA-seq Prrx1Cre conditional heterozygous  replicate 1

description: PxCre; Hic1 f/+ 1


title: p20 Irx5KO 4

city: Irvine

first: Jefferson

middle: K

last: Chen

address: UC Irvine

institute: UC Irvine

description: p20 Irx5KO

data_processing:
Deseq2 was used to identify differentially expressed genes. Gene ontology was conducted using Metascape
Assembly: mm10
Supplementary files format and content: TSV files containing Kallisto abundances

source_name: hair follicle stem cell

extract_protocol:
P18 and P20 back skin was dissected and incubated in 0.25% trypsin (Invitrogen 1505-065) for 2hrs at 34C. The epidermal side was mechanically separated and resuspended in 2% FBS PBS. Debris was removed with 40uM and 70uM mesh filters. Whole epidermis samples were processed for bulk RNA-seq. For HFSC bulk RNAseq, cells were labeled with CD45f (eBioscience 12-0495), Ly-6A/E (eBioscience 45-5981-82), CD34 (eBioscience 50-0341-82), and DAPI.  Ly-6A/E- CD34+ CD45f+ HFSC were isolated for bulk RNAseq
RNA quality was determined with Aglient Bioanalyzer; only samples with RNA Integrity Number > 8 were used. Library preparation with Illumina TrueSeq library preparation kit
Single end Illumina HiSeq 2500 sequencing was performed at the University of California, Irvine High Throughput Genomics Facility. Read alignment was preformed using Kallisto/0.46.2

value: hair follicle stem cell


title: Patient HP01 normal

description:
RNA-seq_countmatrix.csv
HP01_N


title: m661


title: GM21 fibroblasts, RAS, biol rep 3, day 13


title: RNA-seq Prrx1Cre conditional wildtype  replicate 4

description: Hic1 f/+ 4

value: WT