title: β-actin knockout Mouse Embryonic Fibroblast_input2

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Raw reads were quality assessed using FastQC v0.11.5 and then quality trimmed using Trimmomatic
Surviving paired reads were then aligned against the mouse reference genome mm10 using bwa-mem
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
RPKM normalized bamCoverage files were produced using deeptools2
RPKM normalized bamCoverage files for two replicates of each condition were averaged and blacklisted regions were removed using deeptools2
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: bigwig files containing RPKM normalized ChIP-Seq signal for each sample and bigwig files of averaged replicates of each condition

source_name: Mouse Embronic Fibroblast

extract_protocol:
Mouse Embryonic fibroblasts were crosslinked using 1% formaldehyde (Sigma cat. No. F8775) for 10 minutes. Quenching was carried out using 0.125 M Glycine for 5 minutes and cells were then lysed using lysis buffer 1 -LB1-(50 mM Hepes KOH pH 7.5, 10 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP–40, 0.25% Triton X-100). Nuclei were pelleted, collected and washed using lysis buffer 2 -LB2- (10 mM Tris HCl pH 8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA). This was followed by lysis using lysis buffer 3 LB3 (10 mM Tris HCl pH 8; 100 mM NaCl, 1mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate, 0.5% N-laurylsarcosine). Chromatin was sheared using Qsonica Sonicator (4 cycles of 3 minutes at 70 % Amplitude), and then checked on 0.8% agarose gel. 100 μg of fragmented chromatin was mixed with antibody. The protein-antibody immunocomplexes were recovered by the Pierce Protein A/G Magnetic Beads (Thermo-Scientific). Beads and attached immunocomplexes were washed twice using Low salt wash buffer (LS) (0.1% SDS; 2mM EDTA, 1% Triton X-100, 20 mM Tris HCl pH8, 150 mM NaCl), and High Salt (HS) wash buffer (0.1% SDS, 2mM EDTA, 1% Triton X-100, 20 mM Tris HCl pH8, 500 mM NaCl) respectively. The beads were re- suspended in elution buffer (50 mM Tris HCl pH8, 10 mM EDTA, 1% SDS). De-crosslinking was achieved by adding 8µl 5 M NaCl and incubating at 65°C overnight. RNase A (1 µl 10 mg/ml) was added for a 30 min incubation at 37°C. Then, 4 µl 0.5 M EDTA, 8 µl 1 M Tris-HCl, and 1 µl 20 mg/ml proteinase K (0.2 mg/ml) were added for a 2 hours incubation at 42°C to digest the chromatin. DNA was purified by QIAquick PCR purification kit (Qiagen, Germantown, MD, USA) for qPCR analysis and sequencing.
ChIP-seq library preparation was done using the TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA, USA) and then sequenced with the NextSeq550 sequencing platform (performed at the NYUAD Sequencing Center).

value: fibroblast

value: BALB/c

tag: developmental stage

value: 10.5 day old embryos

tag: genotype

value: Beta actin KO

tag: chip antibody

value: none (input)


title: BWS, CID0031

status: Public on May 01 2021

type: genomic

city: Cambridge

first: Eguzkine

last: Ochoa

address: Addenbrookes Hospital

department: Medical Genetics

country: United Kingdom

institute: University of Cambidge

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChips using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood using Gentra Puregene Blood Kit (Qiagen)

tag: gender

value: F

tag: age

tag: disorder

value: CID

tag: disorder type

value: BWS

tag: tissue

value: blood


title: rna_iWATneg

type: SRA

city: NEW ORLEANS

first: Zhi

last: Liu

state: United States

address: 2734 CALHOUN

country: USA

institute: Tulane

library_source: transcriptomic

data_processing:
[scRNA-seq]  Sequencing data were processed on CellRanger v.3.1.0 pipeline with default parameters, including demultiplexing, conversion to FASTQs using bcl2fastq2 v.2.27.1 software, alignment to the mm10 mouse reference genome, filtering, and unique molecular identified (UMI) counting.
[scATAC-seq]  Peak matrixes and metadata were generated by Cell Ranger ATAC v.1.1.0 pipeline with default parameters and aligned to the mm10 mouse reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: [scRNA-seq]  Matrix table with raw gene counts for every gene and every cell
[scATAC-seq]  Matrix table with raw chromatin accessibility counts for every barcode and every cell

molecule: total RNA

organism: Mus musculus

source_name: Inguinal white adipose tissues

growth_protocol: Isolated adipose SVF cells were seeded into plates at the density of 4 x 10e3 cells/cm2 in MesenCultTM Expansion medium (STEMCELL, 05513), and treated with MesenCultTM Adipogenic Differentiation cocktail (STEMCELL, 05507) with 90% cell confluence. Cells were cultured for 7 days after pro-adipogenic induction prior to being harvested for following sequencing experiments.

extract_protocol:
For isolation of adipose SVF cells, fat tissues were dissected into ice-cold PBS and minced with scissors in a sterile 5 ml tube containing 4 ml of either iBAT digestion buffer (1X HBSS, 3.5% BSA, and 2 mg/ml collagenase type II) and incubated at 37°C for 1 hr under agitation or WAT digestion buffer (1X DPBS, 1% BSA, 2.5 mg/ml dispase and 4 mg/ml collagenase D) for 40 min. The digestion mixture was passed through a 100 μm cell strainer into a 50 ml tube. Digestion was stopped by adding 15 ml PBS containing 2% fetal bovine serum (FBS; Gibco, 10270106) and centrifuged at 500 g for 5 min at room temperature. The supernatant was aspirated, and red blood cells were lysed by incubating the SVF pellet with 2 ml RBC lysis buffer (Invitrogen, 00433357). The number and viability of cells in the suspension were determined using Trypan Blue stain according to the manufacturer’s recommendations.
Following separation by FACS,cells were loaded using Chromium Single Cell 3’ v2 Reagent Kit, and libraries were run on the Illumina NextSeq 550 Sequencing System as 150-bp paired-end reads. To isolate nuclei for scATAC-seq assay, cells were lysed for 4 min on ice according to 10x genomics protocol (CG000169 Rev D). ScATAC-seq libraries were prepared using the 10x Genomics platform with the Chromium Single Cell ATAC Library & Gel Bead Kit as recommended by the manufacturer and sequenced on the Illumina NextSeq 550 Sequencing System as 150-bp paired-end reads.

value: Inguinal white adipose tissue

tag: cell type

value: Cultured Wnt- adipocytes

tag: strain

value: C57/B6 or B6/CD1 mixed background

value: 7-8 weeks old

tag: number and sex

value: 10 males and 10 females


title: Sample_NEUFAM07-04 BS panel sequencing

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description:
BS panel Sequencing from BS_Sample_NEUFAM07-04
NEUFAM07_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM07_myDiff_results_sex.age_as_covariates.xls

library_source: genomic

data_processing:
MeDIP: Basecalling using bcl2fastq v2.20.0.422
MeDIP: Quality Check with FASTQC 0.11.5
MeDIP: Trimming adapters and low quality with trimmomatic
MeDIP: Mapping to hg19 human reference with BWA-MEM v0.7.15
MeDIP: Deduplication with Picard Tools
MeDIP: Methylated Regions identified with MACS2
MeDIP: Merging regions with Bedtools
MeDIP: Differential Methyaltion Analysis with edgeR
Supplementary_files_format_and_content: MeDIP: peaks.bed.gz of Methylated regions identified with MACS2 and gzipped
BiSulfite: Basecalling using bcl2fastq v2.20.0.422
BiSulfite: Quality Check with FASTQC 0.11.5
BiSulfite: Trimming adapters and low quality with trimmomatic
BiSulfite: Alignment to hg19 human reference with Bsmap
BiSulfite: Deduplication with Picard Tools
BiSulfite: Filtering for properly paired reads and clipping overlapping regions in pairs
BiSulfite: Methylation analysis with methratio.py (supplied with Bsmap)
BiSulfite: Differential Methyaltion Analysis with methylKit
Genome_build: hg19
Supplementary_files_format_and_content: BiSulfite: Excel files with results coming from methylKit R package including interval region, pvalue, qvalue and methylation difference

source_name: whole blood

extract_protocol:
Whole blood was collected in EDTA tubes and genomic DNA (gDNA) extraction was performed with phenol–chloroform standard method or with the Maxwell 16 blood DNA purification kit (Promega) according to manufacturer’s protocol. Quantity and quality of gDNA were determined by Qubit BR dsDNA assay (ThermoFisher) and 1.5% agarose gel, respectively
MeDIP: One μg of each gDNA sample was mechanically fragmented on a focused ultrasonicator Covaris E220 (Covaris). Sequencing libraries were prepared with NextFlex Methylseq 1 kit (Bioo Scientific) according to the manufacturer’s protocol
MeDIP: The ligated libraries were pooled and immunoprecipitated in the same reaction using MagMeDIP kit (Diagenode), followed by purification with IPure v2 kit (Diagenode) and PCR amplification. Paired-end sequencing was performed on the Illumina HiSeq 2500 platform with read length of 100 bp.
BiSulfite: A SeqCap Epi custom panel (Roche) was designed by NimbleDesign software (Roche).   Sequencing libraries were prepared with KAPA Hyper Prep kit (Kapa Biosystems) according to the manufacturer’s protocol, starting from 1 μg of gDNA mechanically fragmented on a focused ultrasonicator Covaris E220 (Covaris). After ligation, bisulfite conversion was performed by EZ DNA Methylation-Lighting kit (Zymo Research), followed by enrichment of the regions of interest with custom probes using SeqCap Epi enrichment kit (Roche).

value: whole blood

tag: condition

value: healthy

tag: Sex

value: female

tag: family


title: Sample_NEUFAM41-01 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM41-01
NEUFAM41_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM41_myDiff_results_sex.age_as_covariates.xls


title: BWS, CID0027


title: β-actin knockout Mouse Embryonic Fibroblast_input1

value: fibroblast


title: Sample_NEUFAM07-03 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM07-03
NEUFAM07_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM07_myDiff_results_sex.age_as_covariates.xls

value: MS


title: BWS, CID0030

value: M


title: Sample_NEUFAM07-02 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM07-02
NEUFAM07_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM07_myDiff_results_sex.age_as_covariates.xls


title: Wild Type Mouse Embryonic Fibroblast_input2

value: BALB/c

value: 10.5 day old embryos

value: WT


title: Sample_NEUFAM07-01 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM07-01
NEUFAM07_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM07_myDiff_results_sex.age_as_covariates.xls


title: BWS, CID0024

value: F

value: CID


title: BWS, CID0025

value: BWS

value: blood


title: β-actin knockout Mouse Embryonic Fibroblast_IP2

value: Beta actin KO

value: anti-REST


title: BWS, CID0026


title: Sample_NEUFAM05-14 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM05-14
NEUFAM05_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM05_myDiff_results_sex.age_as_covariates.xls


title: BWS, CID0021


title: β-actin knockout Mouse Embryonic Fibroblast_IP1


title: BWS, CID0023


title: Sample_NEUFAM05-13 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM05-13
NEUFAM05_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM05_myDiff_results_sex.age_as_covariates.xls


title: Sample_NEUFAM05-06 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM05-06
NEUFAM05_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM05_myDiff_results_sex.age_as_covariates.xls


title: Wild Type Mouse Embryonic Fibroblast_IP1


title: BWS, CID0020


title: Sample_NEUFAM05-05 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM05-05
NEUFAM05_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM05_myDiff_results_sex.age_as_covariates.xls

value: male


title: BWS, CID0058


title: Wild Type Mouse Embryonic Fibroblast_IP2


title: Sample_NEUFAM05-04 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM05-04
NEUFAM05_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM05_myDiff_results_sex.age_as_covariates.xls


title: β-actin knockout Mouse Embryonic Fibroblast_2

data_processing:
Raw reads were quality assessed using FastQC v0.11.5 and then quality trimmed using Trimmomatic
Reads were aligned to the mm10 genome using bowtie2
mm10 repeat annotation was downloaded from repeatmasker.org and Simple_repeats and Low_complexity repeats were removed
Repenrich2 was run using default settings with the filtered repeat annotation to generate counts
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: counts

extract_protocol: TruSeq Ribo-Zero


title: Sample_NEUFAM05-03 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM05-03
NEUFAM05_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM05_myDiff_results_sex.age_as_covariates.xls


title: β-actin knockout Mouse Embryonic Fibroblast_3


title: β-actin knockout Mouse Embryonic Fibroblast_1


title: BWS, CID0019


title: BWS, CID0016


title: Sample_NEUFAM05-02 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM05-02
NEUFAM05_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM05_myDiff_results_sex.age_as_covariates.xls


title: Sample_NEUFAM05-01 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM05-01
NEUFAM05_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM05_myDiff_results_sex.age_as_covariates.xls


title: BWS, CID0015


title: Wild Type Mouse Embryonic Fibroblast_3


title: Sample_MSFAM02-07 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_MSFAM02-07
MSFAM02_myDiff_results_CpGs_sex.age_as_covariates.xls
MSFAM02_myDiff_results_sex.age_as_covariates.xls


title: Wild Type Mouse Embryonic Fibroblast_1


title: BWS, CID0014


title: BWS, CID0018


title: Sample_MSFAM02-06 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_MSFAM02-06
MSFAM02_myDiff_results_CpGs_sex.age_as_covariates.xls
MSFAM02_myDiff_results_sex.age_as_covariates.xls


title: E4BP4 TG - E4BP4_2

city: Ube

first: Akihiko

last: Taguchi

state: Yamaguchi

address: 1-1-1 minamikogushi

country: Japan

institute: Yamaguchi University

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the mm10 reference genome and displayed using UCSC annotated genes using bowtie2 version 2.2.6 with default parameters.
Visualization in the Integrative Genomics Viewer (IGV): Alingment files were transformed into "Tag Directory" using Homer  version 4.11.1  “makeTagDirectory", then bedgraph files were created using Homer "makeUCSCfile" and specifying "-norm 1e7" for normalization to 10 million reads.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files were generated using HOMER.

source_name: E4BP4 TG - E4BP4

extract_protocol:
After cervical dislocation, mouse liver was perfused with a buffer containing Hanks' balanced salt solution, and cross-inked for 30 minutes with 2mM DSG and for 10 minutes with 1% formaldehyde by perfusion, followed by frozen at -80C. Then, Liver was homogenated by gentleMACS Dissociators. Nuclei were isolated in buffer containing 1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0, and protease inhibitors and sonicated using a Diagenode Bioruptor to shear chromatin to 200-1000bp fragments. Protein-DNA complexes were incubated with antibodies against two kinds of E4BP4 (sc-28203, Santa Cruz Biotechnology)and immunoprecipitated with IgG paramagnetic beads (Invitrogen). Eluted chromatin was isolated using MinElute PCR purification columns (Qiagen).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and NEBNext Library Quant Kit for Illumina (New England Biolabs).

value: 8 week old

tag: genotype/variation

value: liver-specific E4BP4 transgenic

value: liver


title: Sample_NEUFAM41-05 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM41-05
NEUFAM41_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM41_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: female


title: BWS, CID0012


title: BWS, CID0017


title: BWS, CID0013


title: yeast strain ΔYGP1, rep2

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

description:
DYGP_2
BGL-6Kl; ΔYGP1

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Sequenced reads for adaptor sequence, and low-quality sequence were trimmed and removed using Fastp.
Saccharomyces_cerevisiae Ensembl_29 was used as reference genome for alignments.
Genome_build: Saccharomyces_cerevisiae Ensembl_29
Supplementary_files_format_and_content: normalized_abundance_measurements_DYGP_VS_BGL6Kl.txt: Tab-delimited text file includes normalized abundance measurements.

organism: Saccharomyces cerevisiae

source_name: yeast strain

growth_protocol: Yeast strains were grown in YPD medium at 30°C, 200 rpm for 48 h.

extract_protocol:
The total RNA was extracted using TRIzol Reagent (Life Technologies Invitrogen, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment.

value: BGL-6Kl; <delta>YGP1


title: E4BP4 TG - E4BP4_1

value: E4BP4 (sc-28203, Santa Cruz Biotechnology)


title: yeast strain ΔYGP1, rep1

description:
DYGP_1
BGL-6Kl; ΔYGP1


title: E4BP4 TG - input DNA_2

source_name: E4BP4 TG - input DNA

value: input


title: yeast strain BGL-6Kl, rep2


title: Sample_NEUFAM07-05 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM07-05
NEUFAM07_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM07_myDiff_results_sex.age_as_covariates.xls

value: healthy


title: Sample_MSFAM02-03 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_MSFAM02-03
MSFAM02_myDiff_results_CpGs_sex.age_as_covariates.xls
MSFAM02_myDiff_results_sex.age_as_covariates.xls

value: MS


title: E4BP4 TG - input DNA_1


title: Sample_MSFAM02-02 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_MSFAM02-02
MSFAM02_myDiff_results_CpGs_sex.age_as_covariates.xls
MSFAM02_myDiff_results_sex.age_as_covariates.xls


title: BWS, CID0009

value: F


title: Sample_MSFAM02-04 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_MSFAM02-04
MSFAM02_myDiff_results_CpGs_sex.age_as_covariates.xls
MSFAM02_myDiff_results_sex.age_as_covariates.xls


title: Sample_MSFAM02-01 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_MSFAM02-01
MSFAM02_myDiff_results_CpGs_sex.age_as_covariates.xls
MSFAM02_myDiff_results_sex.age_as_covariates.xls


title: yeast strain BGL-6Kl, rep1


title: Transgenic ZT12-3 [TG12-3]

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the mm10 reference genome and displayed using UCSC annotated genes using STAR version 2.7.3awith default parameters.
Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory", then differantial expression alaysis (DeSeq2) was perfomed using Homer　“getDiffExpression.pl"
TPM files were created using Homer "analyzeRepeats.pl" and specifying "-count exons -tpm" .
Genome_build: mm10
Supplementary_files_format_and_content: DeSeq2 analysis were performed using HOMER.
Supplementary_files_format_and_content: TPM files were generated using HOMER.

source_name: Transgenic ZT12

growth_protocol: Chow: normal diet and randomly fed, temprature: 22℃±1℃, Light-dark cycle: 12-hour light and 12-hour dark (lights on at AM8 and lights off at PM8)

extract_protocol:
Gastrocnemius muscle was removed, and total RNA was isolated using RNeasy mini kit (Invitrogen). Polyadenylated mRNA was separated from 100 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were generated using NEBNext Ultra RNA LibraryPrep kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and NEBNext Library Quant Kit for Illumina (New England Biolabs).

tag: strain background

value: transgenic mice with liver specific E4BP4 overexpression

value: Gastrocnemius muscle


title: BWS, CID0010

value: CID

value: BWS

value: blood


title: Transgenic ZT12-2 [TG12-2]


title: BWS, CID0007

value: M


title: Transgenic ZT12-1 [TG12-1]


title: BWS, CID0008


title: Sample 15_input_Ikzf3_WT_thymus

city: Bunkyo

first: Motoi

last: Yamashita

state: Tokyo

address: 1-5-45, Yushima

institute: Tokyo Medical and Dental University

data_processing:
Basecalls were performed using Illumina offline basecaller (OLB) version 1.9.4
RNA-seq sequences were aligned on mm10 using Hisat2 (version 2.1.0) with default parameters, and read counts were calculated using Htseq (version 0.12.4) using RefGenes as the reference.
ChIP-seq sequences were aligned on mm9 using BWA (Burrows-Wheeler Aligner, version 0.7.17)  with default parameters.
Peaks were called using MACS2 (version 2.1.1) with default parameters.
Genome_build: mm10 for RNA-seq and mm9 for ChIP-seq
Supplementary_files_format_and_content: tab-delimited text file include raw read count for each RNA-seq sample. BED6+3 format file for each ChIP-seq sample.

extract_protocol:
Sample 1-6: Bone marrow B220+ cells were purified using anti-CD45R coated MACS beads (Miltenyi Biotec) following manufacturer’s instruction. Pre-pro B cell (B220+AA4.1+IgM-CD43+CD24-) and pre-B cell (B220+AA4.1+IgM-CD43-CD24+) were isolated by flow cytometry. Total RNA was extracted by TRIzol reagent (Thermo Fisher Scientific), followed by DNA digestion by RNA Clean & Concentrator-5 (ZYMO RESEARCH), and mRNA was obtained by poly (A) selection with mRNA DIRECT kit (Thermo Fisher Scientific). RNA-seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocol.
Sample7-16: Lysates were purified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Sample 1-6: Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)
Sample7-16: Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs)

value: thymus

value: thymocytes


title: Sample 2_Ikzf3_WT_pre-B_rep2

source_name: Ikzf3+/+_pre-B cell

value: bone marrow

value: pre-B cell


title: Sample 3_Ikzf3_WT_pre-B_rep3


title: Wild Type ZT12-2 [W12-2]

source_name: Wild Type ZT12

value: wild type


title: Sample 1_Ikzf3_WT_pre-B_rep1


title: BWS, CID0005


title: Wild Type ZT12-1 [W12-1]


title: BWS, CID0003


title: BWS, CID0006


title: Sample_NEUFAM41-08 BS panel sequencing

description:
BS panel Sequencing from BS_Sample_NEUFAM41-08
NEUFAM41_myDiff_results_CpGs_sex.age_as_covariates.xls
NEUFAM41_myDiff_results_sex.age_as_covariates.xls

value: whole blood

value: female


title: tumor endothelial cells - Rat IgG treated -2

city: Aurora

first: Yi

last: Sun

state: CO

department: Surgery

institute: UC Denver

description:
C2
Control Sample 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR software (Galaxy Ver. 2.7.5b).
Gene expression differential analysis was performed by DESeq2 (Ver.1.28.1) software.
The volcano plot and GO biological pathways analysis were generated using GraphPad Prism 7.0 software and RStudio 1.3.1073 (with GO.db 3.11.4).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: final_counts.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: normalized_counts.txt: Tab-delimited text file includes normalized counts.

source_name: endothelial cells

growth_protocol: KPC cells (4x10^5) were subcutaneously injected into the right flank of C57BL/6 mice.

extract_protocol:
Tumor tissues were minced and digested with 25ug/ml Liberase to obtain the single cell suspension. Tumor endothelial cells were isolated using FACS sorting (CD31+CD45- population). Total RNA was extracted and purified using QIAGEN RNeasy Mini Kit (Cat.74104) from tumor endothelial cells.
The mRNA libraries were constructed using Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Cat. 634411).
150bp paired-end RNA sequencing was performed on Illumina NovaSEQ 6000 platform and the RNA-seq data were generated by the Genomics and Microarray Shared Resource at UCCC.

treatment_protocol: After tumor became palpable, mice were randomized into different treatment groups. Antibody treatment was given by IP 48 hours before the EC extraction.

value: subcutaneous KPC tumor

value: endothelial cells

tag: treatment

value: control Rat IgG


title: Wild Type Mouse Embryonic Fibroblast_2

value: fibroblast

value: BALB/c

tag: developmental stage

value: 10.5 day old embryos

value: WT


title: tumor endothelial cells - anti-CD93 treated -1

description:
T1
Treated Sample 1

value: anti-CD93 antibody


title: Transgenic ZT0-1 [TG0-1]

source_name: Transgenic ZT0

value: transgenic mice with liver specific E4BP4 overexpression

value: Gastrocnemius muscle


title: tumor endothelial cells - anti-CD93 treated -2

description:
T2
Treated Sample 2


title: tumor endothelial cells - Rat IgG treated -1

description:
C1
Control Sample 1


title: Warming F10L2 WGBS-seq

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

country: China

institute: Yangzhou University

description: Warming line 2

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing low-quality reads, N bases, reads below the 36 bases long, and unpaired reads.
Bismark software (version 0.16.1; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to A. thaliana genome (TAIR10) with the default parameters. The Arabidopsis genome (TAIR10) was firstly transformed to bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012). Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner.
Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence, and the methylation state of all cytosine positions in the read is inferred.
The bisulfite non-coversion rate was calculated as the percentage of cytosines sequenced at cytosine reference positions in the lambda genome. Accodingly, the bisulfite coversion rate (one minus non-coversion rate) for each sample was obtained.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files (CX_report.txt) include chromosome, position, strand, methylated_reads, unmethylated_reads, context, and tri-nucleotide. Tab-delimited text file (Sample_convertion rate.txt) include the convertion rate of each context (C, CHG, CHH) for each sample.

organism: Arabidopsis thaliana

source_name: Warming leaf

growth_protocol: Wild-type Columbia (Col-0) strain of A. thaliana was used to conduct mutation accumulation (MA) experiments. The Arabidopsis plants was planted in soil and grown in a growth chamber under a 16-h light/8-h dark photoperiod and 150 μmol m-2s-1 of photosynthetically active radiation (PAR) provided by fluorescent tubes (Philips Electronics Trading & Services, Shanghai, China), at different temperatures and 50/80% relative humidity (RH).

extract_protocol:
Genomic DNA was extracted and purified from each plant using a MiniBEST Plant Genomic DNA Extraction Kit (TaKaRa, Dalian, China).
Genomic DNA was fragmented to 200–300 bp with a Covaris sonicator, followed by end repair and adenylation. The purified DNA fragments were bisulfite converted using the EZ DNA Methylation-GoldTM Kit (Zymo Research). Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.

treatment_protocol: Three temperature treatments for MA lines in growth chambers: 23/18°C (light/dark) for Control treatment (five lines; Control line 1~Control line 5), 28/23°C for Warming treatment (five lines; Warming line 1~Warming line 5), and 32/27°C for Heat treatment (five lines; Heat line 1~Heat line 5).

tag: ecotype

value: Columbia

value: leaf

tag: development stage

value: Bolting stage (inflorescence emergence)

value: Warming treatment

tag: generation

value: Generation 10


title: Warming F10L3 WGBS-seq

description: Warming line 3


title: Warming F10L4 WGBS-seq

description: Warming line 4


title: BWS, CID0004

tag: gender

value: F

tag: age

value: CID

value: BWS

value: blood


title: Warming F10L5 WGBS-seq

description: Warming line 5


title: Mature CD24- Vγ1+ γδ T-cells, Adult 2

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

department: Immunology

country: Canada

institute: University of Toronto

data_processing:
RNA sequencing was performed using Illumina NovaSeq 6000.
Raw data were aligned to GRCm38 using HISAT2 version 2.1.
Raw read counts were obtained using HTSeq version 0.1.
Genome_build: GRCm38.
Supplementary_files_format_and_content: Tab-delimited text files with read counts.

source_name: Mature CD24- Vγ1+ γδ T-cells

growth_protocol: For isolation of fetal samples, mature CD24- Vγ1+ γδ T-cells were sorted from newform RBPJ Control thymi using BD FACSAria Fusion. For isolation of adult samples, mature CD24- Vγ1+ γδ T-cells were sorted from 9 week old adult RBPJ Inducible thymi that were treated with doxycycline from 6-9 weeks of age using BD FACSAria Fusion.

extract_protocol:
Total RNA was extracted using TRIzol.
Library construction was done using Takara SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian.

value: Adult Thymus

value: Mature CD24- Vgamma1+ gammadelta T-cells

tag: genotype

value: RBPJ Inducible


title: Wild Type ZT0-3 [W0-3]

source_name: Wild Type ZT0

value: wild type

tag: tissue


title: Mature CD24- Vγ1+ γδ T-cells, Adult 1

tag: cell type


title: Warming F10L1 WGBS-seq

description: Warming line 1


title: Transgenic ZT0-2 [TG0-2]


title: Heat E10L4 WGBS-seq

description: Heat line 4

source_name: Heat leaf

value: Heat treatment


title: Heat E10L5 WGBS-seq

description: Heat line 5


title: Wild Type ZT0-1 [W0-1]


title: Wild Type ZT0-2 [W0-2]


title: Mature CD24- Vγ1+ γδ T-cells, Fetal 2

value: Newborn Thymus

value: RBPJ Control


title: β-actin heterozygous Mouse Embryonic Fibroblast (ChIP-seq)

source_name: Mouse Embryonic Fibroblast

extract_protocol:
Mouse Embryonic fibroblasts were crosslinked using 1% formaldehyde (Sigma cat. No. F8775) for 10 minutes. Quenching was carried out using 0.125 M Glycine for 5 minutes and cells were then lysed using lysis buffer 1 -LB1-(50 mM Hepes KOH pH 7.5, 10 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP–40, 0.25% Triton X-100). Nuclei were pelleted, collected and washed using lysis buffer 2 -LB2- (10 mM Tris HCl pH 8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA). This was followed by lysis using lysis buffer 3 LB3 (10 mM Tris HCl pH 8; 100 mM NaCl, 1mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate, 0.5% N-laurylsarcosine). Chromatin was sheared using Qsonica Sonicator (4 cycles of 3 minutes at 70 % Amplitude), and then checked on 0.8% agarose gel. 100 μg of fragmented chromatin was mixed with 5μg of (Ezh2 (D2C9) XP Rabbit mAb antibody-Cell signaling). The protein-antibody immunocomplexes were recovered by the Pierce Protein A/G Magnetic Beads (Thermo-Scientific). Beads and attached immunocomplexes were washed twice using Low salt wash buffer (LS) (0.1% SDS; 2mM EDTA, 1% Triton X-100, 20 mM Tris HCl pH8, 150 mM NaCl), and High Salt (HS) wash buffer (0.1% SDS, 2mM EDTA, 1% Triton X-100, 20 mM Tris HCl pH8, 500 mM NaCl) respectively. The beads were re- suspended in elution buffer (50 mM Tris HCl pH8, 10 mM EDTA, 1% SDS). De-crosslinking was achieved by adding 8µl 5 M NaCl and incubating at 65°C overnight. RNase A (1 µl 10 mg/ml) was added for a 30 min incubation at 37°C. Then, 4 µl 0.5 M EDTA, 8 µl 1 M Tris-HCl, and 1 µl 20 mg/ml proteinase K (0.2 mg/ml) were added for a 2 hours incubation at 42°C to digest the chromatin. DNA was purified by QIAquick PCR purification kit (Qiagen, Germantown, MD, USA) for qPCR analysis and sequencing.
ChIP-seq library preparation was done using the TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA, USA) and then sequenced with the NextSeq550 sequencing platform (performed at the NYUAD Sequencing Center).

tag: strain

value: BALB/c

value: 10.5 day old embryos

value: Embryonic Fibroblast

value: beta-actin heterozygous

tag: chip antibody


title: Heat E10L2 WGBS-seq

description: Heat line 2

value: Columbia

value: leaf

value: Bolting stage (inflorescence emergence)


title: Heat E10L3 WGBS-seq

description: Heat line 3

value: Generation 10


title: β-actin knockout Mouse Embryonic Fibroblast (ChIP-seq)

value: beta-actin knockout


title: Wild Type Mouse Embryonic Fibroblast (ChIP-seq)

value: Wild Type


title: Wild Type ZT12-3 [W12-3]

value: Gastrocnemius muscle


title: Heat E10L1 WGBS-seq

description: Heat line 1


title: β-actin heterozygous Mouse Embryonic Fibroblast rep2 (ChIP-seq)

value: Ezh2 (D2C9) XP Rabbit mAb antibody-Cell signaling


title: β-actin heterozygous Mouse Embryonic Fibroblast rep1 (ChIP-seq)


title: Control D10L5 WGBS-seq

description: Control line 5

source_name: Control leaf

value: Control


title: Control D10L4 WGBS-seq

description: Control line 4


title: DD+-

data_processing:
RNA sequencing was performed using Illumina NovaSeq 6000.
Raw data were aligned to GRCm38 using Cell Ranger 5.0.
Raw read counts were obtained using Cell Ranger 5.0.
Genome_build: GRCm38.
Supplementary_files_format_and_content: .tsv and .mtx files.

source_name: CD3+Vγ4+ KN6 γδ T-cells

growth_protocol: For isolation of BD and DD samples, KN6 cells were sorted from 8-10 week old adult KN6 Transgenic mice. For isolation of BD++, BD+-, DD++, and DD+- samples, KN6 cells were sorted from 8-10 week old adult RBPJ Inducible; KN6 Transgenic mice that were initially treated with doxycycline for 8 days, followed by 4 days of continued doxycycline treatment (++ samples) or 4 days of discontinued doxycycline treatment (+- samples).

extract_protocol:
CD3+Vγ4+ KN6 cells were sorted from thymi using BD FACSAria Fusion.
Library construction was done using 10x Genomics Chromium Controller v3.

tag: tissue origin

value: Adult Thymus

value: RBPJ Inducible; KN6 Transgenic


title: BD+-


title: BD++


title: Control D10L2 WGBS-seq

description: Control line 2


title: DD++


title: Control D10L3 WGBS-seq

description: Control line 3


title: BD

value: KN6 Transgenic


title: DD


title: BTN_D7_3

city: Dallas

first: Chase

middle: Arthur

last: Pagani

state: Texas

address: 6000 Harry Hines Blvd

institute: The University of Texas Southwestern

data_processing:
Cell Ranger Single Cell Software Suite 1.3 was used to perform sample de-multiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core
Genome_build: mm10

molecule: polyA RNA

source_name: Day 7 post Burn/Tenotomy with neurectomy injury site

extract_protocol:
Tenotomy injury site, consisting of tissue from the Achilles’ tendon insertion at the gastrocnemius to the distal tendon enthesis at the calcaneus and surrounding tissue, excluding bone and skin, was harvested 7 days after injury. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40μm sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines.
3' Samples:  3' V3.1 Chemistry with NextGEM Chip G  NovaSeq 6000 S4 flowcell 300 cycle kit - this was loaded to target 250M reads/sample (5000 cells, 50K reads/cell), at 300pM (these were shared flowcells)  Read lengths: 150 x 8 x 150

treatment_protocol: C57B6 mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. A 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon. The Achilles tendon was separated from surrounding tissue and dissected at it’s midsection. For the sciatic neurectomy, blunt dissection was performed through the biceps femoris to expose the sciatic nerve. The sciatic nerve was transected with reflection and suturing of the proximal nerve stump to the nearby semitendinosus muscle to prevent re-innervation.  As a control, sham nerve injuries consisted of surgical exposure of the sciatic nerve without transection. Incisions were sutured closed with 5-0 Vicryl suture.

value: tendon

tag: location

value: tendon injury site


title: Time after treatment 27 h, rep3

city: Daegu

first: Kitae

last: Song

state: jung-gu

address: DGIST, 333, Techno jungang-daero,, Hyeonpung-myeon

country: South Korea

institute: Institute for Basic Science

data_processing:
Raw reads were checked quality and trimmed using FastQC (Andrews, 2010)
the trimmed reads were mapped to the Arabidopsis thaliana genome (TAIR10) using STAR (Dobin et al., 2013)
 After alignment, the gene-level raw count data files were generated using HTSeq (Anders et al., 2015)
Genome_build: Arabidopsis thaliana genome (TAIR10)
Supplementary_files_format_and_content: HTSeq count file (TXT)

source_name: Excised leaf

extract_protocol:
Total mRNA was extracted from leaves using WelPrep.
Library construction and sequencing were performed using Illumina Hiseq 2500 platform.

value: Excised leaf

value: 21-day-old plant

value: dark and cold


title: Wild Type Mouse Embryonic Fibroblast rep2 (ChIP-seq)

value: BALB/c

value: 10.5 day old embryos

value: Embryonic Fibroblast


title: Control D10L1 WGBS-seq

description: Control line 1

value: Columbia

value: leaf

value: Bolting stage (inflorescence emergence)

value: Generation 10


title: Wild Type Mouse Embryonic Fibroblast rep1 (ChIP-seq)

value: Wild Type

value: Ezh2 (D2C9) XP Rabbit mAb antibody-Cell signaling


title: BTN_D7_2


title: Transgenic ZT0-3 [TG0-3]

value: transgenic mice with liver specific E4BP4 overexpression

value: Gastrocnemius muscle


title: Time after treatment 26.5 h, rep3


title: Untransfected control_bind

city: Kyoto

first: Kaoru

middle: R

last: Komatsu

address: 53 Kawahara-cho, Shogoin Sakyo-ku

institute: Kyoto University

description:
RelativeFrequency_4mer.csv
RelativeFrequency_5mer.csv
RelativeFrequency_6mer.csv

data_processing:
Library strategy: RNA Bind-n-seq
Base calling: Illumina RTA 1.18.54
The adapter sequences of the reads were trimmed by cutadapt 1.10 with parameter -e set to 0.2.
Low-quality reads (averaged quality score of <30) were filtered with a custom script written in Julia 1.1.
20-mer sequences were used for k-mer analysis
Supplementary_files_format_and_content: CSV files include relative frequency and enrichment score for k-mer.

molecule: other

organism: synthetic RNA

source_name: in vitro random RNA library

extract_protocol:
The interacted RNA was isolated by phenol-chloroform extraction and ethanol precipitation. The RNA pellet was suspended in 24 µl of nuclease-free water and subjected to RT with SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific, #18090010). Prior to reverse transcription, 20 µL of purified RNA library was mixed with 1 µL of 10 µM reverse primer (5'-GCGTCCATGGTCGACCTGAGGTCC-3'), 1 µL of 10 mM dNTPs, and 4 µL of nuclease water, and then denatured at 65°C for 5 minutes. The mixture was combined with a premix of 8 µL of 5X SSIV Buffer, 2 µL of 100 mM DTT, 2 µL of RNase OUT (Thermo Fisher Scientific, #10777019), and 2 µL of SuperScript IV Reverse Transcriptase.
To prepare an input random RNA library, 0.5 pmol of input random RNA library was reverse transcribed. After digestion of RNA with 2 µl of RNaseH for 20 min at 37°C, the cDNA preparation was amplified by PCR in a reaction mixture containing 1× Platinum SuperFi PCR Master Mix, 5 µM forward primer (5'-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGACGTGACACGACGTGC-3'), 5 µM reverse primer (5'-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGCGTCCATGGTCGACCTGAGGTCCGACG-3'), 1× SuperFi GC Enhancer, and 2 µl of cDNA and adjusted to 25 µl with nuclease-free water. The incubation protocol included an initial denaturation at 98°C for 30 s, 20 cycles of denaturation at 98°C for 10 s and extension at 72°C for 10 s, and a final extension at 72°C for 5 min. Single-stranded DNA was digested with Illustra ExoProStar exonuclease I (GE Healthcare Life Sciences, #US78211), and the PCR products were purified with the use of a MinElute PCR Purification Kit (Qiagen, #28006) before the addition of Illumina sequencing barcodes by 10 cycles of PCR with index primers from a Nextera XT Index Kit (Illumina, #FC-131-1001). The reaction mixture contained 1× Platinum SuperFi PCR Master Mix, 5 µl of Index 1 (i7) primer, 5 µl of Index 2 (i5) primer, 1× SuperFi GC Enhancer, and at most 5 µl of the PCR products, and the volume was adjusted to 50 µl with nuclease-free water. The incubation protocol included an initial denaturation at 98°C for 30 s; 10 cycles of denaturation at 98°C for 10 s, annealing at 55°C for 10 s, and extension at 72°C for 20 s; and a final extension at 72°C for 5 min. The resulting sequencing library was quantified with the use of a KAPA Library Quantification Kit (Illumina) Universal qPCR Mix (Kapa Biosystems, #07960140001). The library was sequenced for 150 cycles on the Illumina MiSeq platform and with a MiSeq Reagent Kit v3 (Illumina, #MS-102-3001).

tag: expression

value: Control


title: BTN_D7_1

value: tendon


title: Time after treatment 26 h, rep3


title: Time after treatment 25.5 h, rep3


title: Bicc1 O/E_bind


title: β-actin knockout Mouse Embryonic Fibroblast rep2 (ChIP-seq)

value: beta-actin knockout


title: Time after treatment 25 h, rep3

value: Excised leaf


title: BTS_D7_3

source_name: Day 7 post Burn/Tenotomy with sham neurectomy injury site

value: tendon injury site


title: RS+IS_21D_rep3

city: shijiazhuang

first: Pengxiang

last: Tian

state: hebei

address: 215 heping west road

institute: The second hospital of hebei medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads generated by RNA-seq were processed by removing the Illumina adapters with Trimmomatic and then low-quality regions at the 5' and 3' ends were deleted.
The reads (stored in fastq format) were then aligned to the rat (RGSC/rn6) reference genome Rnor_6.0, downloaded from Ensembl (ftp://ftp.bl.org/pub/relee-a-/rattus_norvegicus/), using HISAT2
Sorted bam files were quantified for gene expression using the HTseq-count tool , and a counts file was generated
Counculat TPM with Internal scripting
Genome_build: RGSC/rn6
Supplementary_files_format_and_content: tab-delimited text files include counts and TPM values for each Sample

organism: Rattus norvegicus

source_name: rat testis

extract_protocol:
testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Ribosomal RNA was removed using the Epicentre Ribo-Zero™ Gold kit (Rat) (Epicentre, an Illumina company, Madison, WI, USA). These libraries were constructed based on the recommendations of the NEBNext®Ultra™ Directed RNA Library Preparation Kit. RNA fragments and short-stranded RNA were carried using NEBNext First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using a random hexamer primer and M-MuLV reverse transcriptase. Subsequently, second strand cDNA was synthesized using DNA polymerase I and RNase h, the purified second strand cDNA ends were repaired, and then poly(A) and A adapters were added. A fragment of approximately 300 base pairs (bp) was selected using the UNG enzyme.

value: SD

value: testis

value: 8 weeks

tag: experimental desgin


title: β-actin knockout Mouse Embryonic Fibroblast rep1 (ChIP-seq)

data_processing:
Raw reads were quality assessed using FastQC v0.11.5 and then quality trimmed using Trimmomatic
Surviving paired reads were then aligned against the mouse reference genome mm10 using bwa-mem
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
RPKM normalized bamCoverage files were produced using deeptools2
RPKM normalized bamCoverage files for two replicates of each condition were averaged and blacklisted regions were removed using deeptools2
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: bigwig files containing RPKM normalized ChIP-Seq signal for each sample and bigwig files of averaged replicates of each condition

value: BALB/c

value: 10.5 day old embryos

value: Embryonic Fibroblast


title: RS+IS_21D_rep1


title: RS+IS_21D_rep2


title: Time after treatment 24 h, rep3

value: 21-day-old plant

value: dark and cold


title: RS+IS_14D_rep3


title: BTS_D7_1


title: Time after treatment 23.5 h, rep3


title: RS+IS_14D_rep2


title: MKO_Tac_BL-HiC_Rep3

city: Beijing

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

institute: School of Basic Medicine, Peking Union Medical College

description:
BL-Hi-C of myod ko differentiating myocytes at 12h treated with Tacedinaline
MKO_Tac.hic
MKO_Tac_5k.h5
MKO_Tac_loops.bedpe

data_processing:
RNA-seq reads were aligned to the mm9 genome with TopHat (v2.1.0) using default settings. Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq, followed by FPKM transformation by normalizing gene exon length and sequencing depth.
ChIP-Seq reads were mapped to mm9  genome with Bowtie2. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIA-PET2 was used to trim the bridge linkers of BL-Hi-C data and HiC-Pro to align reads, filter artifact fragments, and remove duplicates; Juicer was applied to the resulting uniquely mapped contacts to generate individual or merged Hi-C files that could be deposited as contact matrices with multiple resolutions.
Loops were called by HiCCUPS at 3kb, 5 kb and 10 kb resolutions with modified parameters for pooled Hi-C matrices of each  condition.
Genome_build: mm9
Supplementary_files_format_and_content: .hic files were genrated by Juicer which compress Hi-C matrix under mutiscale resolutions;.h5 files were generated by HiCExplorer which can be visualized by  pyGenomeTracks;.bedpe files were loops called by HiCCUPS;.bigwig files were generated using MACS2;.excel  file includes gene count for each sample

source_name: Differentiating myocytes for 12h

extract_protocol:
Primary myoblasts were isolated from the hindlimb skeletal muscle of WT and KO mice at 2~3 weeks, minced and digested in a mixture of type II collagenase and Dispase B (Roche Applied Science). Cells were filtered from debris, centrifuged and cultured in growth medium (F-10 Ham’s medium supplemented with 20% FBS, 10 ng/ml basic fibroblast growth factor, 1% penicillin– streptomycin and 1% glutamine) on collagen-coated cell culture plates at 37 °C in 5% CO2. At 60-70% confluence, cells can be switched to differentiation medium (DMEM with 2% horse serum).
Hi-C were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). Briefly, cells were cross-linked with formaldehyde and nucleuses were isolated by lysis buffers. The chromain was then randomly fragmented by 4-bp enzymes (HaeIII) and then two proximal fragments were connected by 20 bp biotinylated bridge linker in nucleus. A whole genome chromatin was extracted and sheared into 400 bp. Then the biotinylated junctions were captured by M-280 streptavidin magnetic beads. After amplification, the DNA were ready for library construction. RNA for NRA-seq was harvested using Trizol reagent. For ChIP-seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with related antibody.
Hi-C libaries were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645)

tag: passage

value: skeletal muscle

value: myod KO


title: MKO_Tac_BL-HiC_Rep1


title: MKO_Tac_BL-HiC_Rep2


title: Time after treatment 23 h, rep3

tag: treatment


title: Mature CD24- Vγ1+ γδ T-cells, Fetal 1

value: Newborn Thymus

value: Mature CD24- Vgamma1+ gammadelta T-cells

value: RBPJ Control


title: RS+IS_14D_rep1


title: MKO_DMSO_BL-HiC_Rep3

description:
BL-Hi-C of myod ko differentiating myocytes at 12h treated with DMSO
MKO_DMSO.hic
MKO_DMSO_5k.h5
MKO_DMSO_loops.bedpe


title: RS+IS_3D_rep2


title: Time after treatment 24.5 h, rep3


title: Time after treatment 21 h, rep3


title: Time after treatment 21.5 h, rep3


title: Time after treatment 22 h, rep3


title: MKO_DMSO_BL-HiC_Rep1


title: RS+IS_3D_rep1


title: WT_c646_BL-HiC_Rep4

description:
BL-Hi-C of wildtype differentiating myocytes at 27h treated with c646
WT_c646.hic
WT_c646_5k.h5
WT_c646_loops.bedpe

source_name: Differentiating myocytes for 27h

value: wild type


title: Time after treatment 20 h, rep3


title: Control_rep1

value: Control


title: WT_c646_BL-HiC_Rep2


title: WT_c646_BL-HiC_Rep3


title: Time after treatment 20.5 h, rep3

value: Excised leaf


title: BTS_D7_2

value: tendon

value: tendon injury site


title: WT_c646_BL-HiC_Rep1


title: Time after treatment 22.5 h, rep3


title: RS+IS_3D_rep3

value: SD

value: testis


title: MKO_DMSO_BL-HiC_Rep2


title: WT_DMSO_BL-HiC_Rep5

description:
BL-Hi-C of wildtype differentiating myocytes at 27h treated with DMSO
WT_DMSO.hic
WT_DMSO_5k.h5
WT_DMSO_loops.bedpe


title: Control_rep3

value: 8 weeks


title: WT_DMSO_BL-HiC_Rep4


title: Time after treatment 26 h, rep2


title: WT_DMSO_BL-HiC_Rep3


title: WT_DMSO_BL-HiC_Rep2


title: Time after treatment 25 h, rep2


title: Control_rep2


title: WT_DMSO_BL-HiC_Rep1


title: Time after treatment 25.5 h, rep2


title: Time after treatment 27 h, rep2


title: MKO_DM_BL-HiC_Rep8

description:
BL-Hi-C of myod ko differentiating myocytes at 24h
MKO_DM.hic
MKO_DM_5k.h5
MKO_DM_loops.bedpe

source_name: Differentiating myocytes for 24h


title: SKOV-1_72hr_vehicle_rep3

type: RNA

city: Suzhou

first: Ping

last: Wang

address: No.199 Ren ai Road

department: School of public health

institute: Soochow University

description: Gene expression in human ovarian cancer SKOV-3 cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human lncRNA Microrray V5 (4*180K,Design ID:076500)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: SKOV-3 cells were treated with vehicle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: SKOV-13 cells were cultured with  RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: SKOV-3 cells were treated with 1α,25(OH)2D3 (100 nmol/L) or vehicle (the same concentration of ethanol) for 72 hours.

tag: cell line

value: Ovarian cancer cellls

value: vehicle


title: SKOV-1_72hr_vehicle_rep2


title: Sorghum_Compatible_72 hai_Rep 3

city: Urbana

first: Tiffany

last: Jamann

state: IL

address: 1102 S Goodwin Ave, Turner Hall

department: Crop Sciences

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina). Adaptors were trimmed from the 3'-end of the reads.
The maize and sorghum reads were aligned to their respective genomes using the splice-aware aligner STAR v2.7
The read counts per gene were then quantified from the alignments using ‘featureCounts’ in the subread package. Multi-mapping reads and reads with ambiguous assignments were removed.
The Bioconductor package “edgeR” was used for quality control and normalization. The count per million (CPM) was calculated using the package "edgeR".
The genes with less than one count per million (CPM) in more than three samples were filtered out. The trimmed mean of M-values (TMM) normalization factors were calculated to correct for different library sizes and composition bias and to obtain normalized log2CPM values with a prior count of three.
The package “limma”  was used to calculate differentially expressed genes (DEGs).
Genome_build: GCF_000005005.2_B73_RefGen_v4 from NCBI
Genome_build: Sbicolor_454v3 from Phytozome
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and for every sample.
Supplementary_files_format_and_content: summary files include a summary statistic table for each gene.
Supplementary_files_format_and_content: csv files include log normalized count data for every gene and for every sample.

organism: Sorghum bicolor

source_name: leaf

growth_protocol: S. turcica strains (Et28A and 15st008) were cultured inlactose-caesin hydrolysate agar (LCA) media for 2 weeks under 12hr/12hr light/dark environment at room temperature. Maize (B73) and sorghum (BTx623) were grown in the greenhouse at the Plant Care Facility at the University of Illinois at Urbana-Champaign.

extract_protocol:
RNA was extracted using a combination of TriZol (ThermoFisher Scientific, Waltham, MA) and an RNAeasy miniElute cleanup kit (QIAGEN, Germantown, MD).
The libraries were prepared using a TruSeq Stranded mRNAseq Sample Prep kit (Illumina, San Diego, California) and quantified using qRT-PCR.

treatment_protocol: Each maize and sorghum plant was treated with either mock, maize-specific S. turcica (Et28A) or sorghum-specific S. turcica (15st008) when plants were approximately V3 stage. Fungal concentrations were 4^10^3 spores/ml.

value: leaf

tag: cultivar

value: BTx 623

tag: timepoint

value: 72 hours after inoculation

tag: replication

tag: group

value: Compatible interaction


title: Time after treatment 24 h, rep2

tag: age

value: 21-day-old plant

value: dark and cold


title: SKOV-1_72hr_vehicle_rep1


title: Sorghum_Compatible_72 hai_Rep 2

institute: University of Illinois at Urbana-Champaign


title: MKO_DM_BL-HiC_Rep7

value: skeletal muscle

tag: genotype

value: myod KO


title: Sorghum_Compatible_72 hai_Rep 1

tag: tissue


title: MKO_DM_BL-HiC_Rep6


title: Time after treatment 23 h, rep2


title: Sorghum_Compatible_24 hai_Rep 3

value: 24 hours after inoculation


title: SKOV-1_72hr_VD_rep2

description: Gene expression by 1,25(OH)2D3 in human ovarian cancer SKOV-3 cells

source_name: SKOV-3 cells were treated with 1,25(OH)2D3 (100 nmol/L)

tag: cell type


title: Time after treatment 19.5 h, rep3

value: Excised leaf


title: Time after treatment 22.5 h, rep2


title: Time after treatment 24.5 h, rep2


title: MKO_DM_BL-HiC_Rep4


title: Time after treatment 22 h, rep2


title: MKO_DM_BL-HiC_Rep3


title: Sorghum_Compatible_24 hai_Rep 1

tag: strain


title: Time after treatment 23.5 h, rep2


title: MKO_DM_BL-HiC_Rep5


title: Sorghum_Incompatible_72 hai_Rep 3

value: Incompatible interaction


title: MKO_DM_BL-HiC_Rep2


title: Time after treatment 21.5 h, rep2


title: Time after treatment 21 h, rep2


title: SKOV-1_72hr_VD_rep3


title: WT_c646_BL-HiC_Rep5

value: wild type


title: Sorghum_Incompatible_72 hai_Rep 2


title: Time after treatment 20.5 h, rep2


title: MKO_DM_BL-HiC_Rep1


title: MKO_GM_BL-HiC_Rep6

description:
BL-Hi-C of myod ko proliferating myoblasts
MKO_GM.hic
MKO_GM_5k.h5
MKO_GM_loops.bedpe

source_name: Proliferating myoblasts


title: Time after treatment 20 h, rep2


title: Sorghum_Incompatible_72 hai_Rep 1


title: Time after treatment 19.5 h, rep2


title: RKO d190-3

city: Baltimore

first: Alyssa

last: Kallman

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University, School of Medicine

description: Dropseq scRNAseq

data_processing:
Fastq files were processed and filtered according to the Dropseq cookbook version 1.0.1
processed reads were aligned to GRCh38 using the STAR RNA aligner
exons were tagged using the Homo_sapiens.GRCh38.88.gtf annotations file
Genome_build: GRCh38
Supplementary_files_format_and_content: raw UMI count matrices with genes as rows and cells as columns

source_name: stem cell derived retinal organoids

growth_protocol: EP1 stem cells were grown in mTeSR1 (Stem cell tech 05850) on matrigel (BD Biosciences 354230) coated plates and maintained by passaging with accutase (Sigma A6964-100ml).  After passaging cells were plated in mTesr with blebbistatin (Sigma B0560-1mg).  Organoids were differentiated according to Wahlin et al 2017.  Stem cells were dissociated to single cells then plated at 3000 cells per well in 96 well U-bottom plates in mTesr with 5 uM blebbistatin.  On day 1 organoids were fed BE6.2 media (10 mL E6 stock [100 mL water, 97 mg insulin (Roche 11376497001), 53.5 mg holo-transferrin (Sigma T0665-500MG), 320 mg L-ascorbic acid (Sigma  A8960-5G), 5 uL of 14 mg/mL sodium selenite (Sigma S5261-10G)], 5 mL B27 without vitamin A (Gibco 12587010), 2.5 mL Glutamax (Gibco 16140071), 2.5 mL MEM NEAA (Gibco 11140-050), 2.5 mL sodium pyruvate (Gibco 11360-070), 1 mL 219 g/L NaCl, DMEM (Gibco to 250 mL) plus 2% v/v matrigel and 3 uM Wnt inhibitor (EMD Millipore 681669).  On days 2-3 organoids were fed with BE6.2 plus 1% v/v matrigel and 3uM Wnt inhibitor, then 50% media exchange with BE6.2 plus 1% v/v and 3 uM Wnt inhibitor on days 4-7.  50% exchange was continued on days 8-9 with only BE6.2.  On day 10 organoids were transferred to 10 cm dishes and fed with BE6.2 plus 100 nM SAG (EMD Millipore 364590-63-6) until day 12.  Optic vesicles were manually excised from organoids using tungsten needles from days 10-14.  Organoids were fed with LTR medium (125 mL F12 (Gibco 11765), 50 mL FBS (Gibco 16140071), 10 mL B27 (Gibco 17504044), 5 ml Glutamax, 5 mL MEM NEAA, 5 ml sodium pyruvate, 500 uL 1M taurine (Sigma T-8691), and DMEM up to 500 mL) plus 100 nM SAG until day 18.  Organoids were fed with only LTR medium on days 18-19.  From days 20-27, organoids were fed with LTR plus 500 nM retinoic acid (Sigma R2625-50mg), and days 28-42 with LTR plus 500 nM retinoic acid and 10 uM DAPT (Calbiochem 565770).  Organoids were fed with LTR plus 500 nM retinoic acid until day 120, then fed with only LTR.

extract_protocol:
Organoids were dissociated to single cells with papain (Worthington) to 1 mg ml-1 and 5 μL DNase (Roche) per mL, using 200 μL papain mix per organoid.  After 1-2 hours when organoids appeared fully dissociated the reaction was quenched with media containing 10% FBS (Gibco).  Single cells were resuspended in HBSS (Gibco) and 0.1 mg mL-1 BSA at 120,000 cells per mL
Illumina nextera XT multiplexed with N70X indices according to the Dropseq protocol

value: RPGRIP1 KO

tag: replicate


title: MKO_GM_BL-HiC_Rep5


title: RKO d225-2

description: Dropseq scRNAseq


title: RKO d190-2

description: Dropseq scRNAseq


title: MKO_GM_BL-HiC_Rep4


title: SKOV-1_72hr_VD_rep1


title: RKO d225-1

description: Dropseq scRNAseq


title: Sorghum_Incompatible_24 hai_Rep 2


title: Time after treatment 27 h, rep1


title: Wild Type Mouse Embryonic Fibroblast_input1

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

address: Saadiyat Campus, Abu Dhabi

institute: New York University Abu Dhabi

source_name: Mouse Embronic Fibroblast

extract_protocol:
Mouse Embryonic fibroblasts were crosslinked using 1% formaldehyde (Sigma cat. No. F8775) for 10 minutes. Quenching was carried out using 0.125 M Glycine for 5 minutes and cells were then lysed using lysis buffer 1 -LB1-(50 mM Hepes KOH pH 7.5, 10 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP–40, 0.25% Triton X-100). Nuclei were pelleted, collected and washed using lysis buffer 2 -LB2- (10 mM Tris HCl pH 8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA). This was followed by lysis using lysis buffer 3 LB3 (10 mM Tris HCl pH 8; 100 mM NaCl, 1mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate, 0.5% N-laurylsarcosine). Chromatin was sheared using Qsonica Sonicator (4 cycles of 3 minutes at 70 % Amplitude), and then checked on 0.8% agarose gel. 100 μg of fragmented chromatin was mixed with antibody. The protein-antibody immunocomplexes were recovered by the Pierce Protein A/G Magnetic Beads (Thermo-Scientific). Beads and attached immunocomplexes were washed twice using Low salt wash buffer (LS) (0.1% SDS; 2mM EDTA, 1% Triton X-100, 20 mM Tris HCl pH8, 150 mM NaCl), and High Salt (HS) wash buffer (0.1% SDS, 2mM EDTA, 1% Triton X-100, 20 mM Tris HCl pH8, 500 mM NaCl) respectively. The beads were re- suspended in elution buffer (50 mM Tris HCl pH8, 10 mM EDTA, 1% SDS). De-crosslinking was achieved by adding 8µl 5 M NaCl and incubating at 65°C overnight. RNase A (1 µl 10 mg/ml) was added for a 30 min incubation at 37°C. Then, 4 µl 0.5 M EDTA, 8 µl 1 M Tris-HCl, and 1 µl 20 mg/ml proteinase K (0.2 mg/ml) were added for a 2 hours incubation at 42°C to digest the chromatin. DNA was purified by QIAquick PCR purification kit (Qiagen, Germantown, MD, USA) for qPCR analysis and sequencing.
ChIP-seq library preparation was done using the TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA, USA) and then sequenced with the NextSeq550 sequencing platform (performed at the NYUAD Sequencing Center).

value: fibroblast

value: BALB/c

tag: developmental stage

value: 10.5 day old embryos

value: WT

tag: chip antibody

value: none (input)


title: Time after treatment 26.5 h, rep1


title: RKO d190-1

description: Dropseq scRNAseq


title: Time after treatment 26 h, rep1


title: RKO d150-3

description: Dropseq scRNAseq


title: MKO_GM_BL-HiC_Rep2


title: RKO d150-2

description: Dropseq scRNAseq


title: Sorghum_Mock_72 hai_Rep 2

value: leaf

value: BTx 623

value: mock

value: No interaction


title: Time after treatment 26.5 h, rep2

value: 21-day-old plant

value: dark and cold


title: Sorghum_Incompatible_24 hai_Rep 3


title: RKO d190-4

description: Dropseq scRNAseq


title: Time after treatment 25.5 h, rep1


title: Sorghum_Mock_72 hai_Rep 1

value: 72 hours after inoculation


title: WT_DM_BL-HiC_Rep8

description:
BL-Hi-C of wildtype differentiating myocytes at 24h
WT_DM.hic
WT_DM_5k.h5
WT_DM_loops.bedpe

value: skeletal muscle


title: Time after treatment 25 h, rep1

value: Excised leaf


title: RKO d150-1

description: Dropseq scRNAseq


title: WT_DM_BL-HiC_Rep7


title: Sorghum_Mock_24 hai_Rep 3

value: 24 hours after inoculation


title: Sorghum_Mock_72 hai_Rep 3


title: Sorghum_Mock_24 hai_Rep 2


title: RKO d120-2

description: Dropseq scRNAseq


title: MKO_GM_BL-HiC_Rep3

value: myod KO


title: Time after treatment 24.5 h, rep1


title: RKO d120-1

description: Dropseq scRNAseq

value: RPGRIP1 KO


title: Sorghum_Mock_24 hai_Rep 1


title: WT_DM_BL-HiC_Rep6

value: wild type


title: Sorghum_Incompatible_24 hai_Rep 1

value: Incompatible interaction


title: WT_DM_BL-HiC_Rep4


title: MKO_GM_BL-HiC_Rep1


title: Time after treatment 23 h, rep1


title: RKO d90-2

description: Dropseq scRNAseq


title: Time after treatment 23.5 h, rep1


title: Time after treatment 24 h, rep1


title: WT_DM_BL-HiC_Rep3


title: Time after treatment 22.5 h, rep1


title: RKO d90-1

description: Dropseq scRNAseq


title: C397H_6

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

description: DNA was isolated from 3-week old leaf tissue, bisulfite converted, library prepped, and sequenced

data_processing:
1x50 bp bisulfite reads were aligned to the TAIR10 genome using the BSMAP program (Xi Y, Li W,. BMC Bioinformatics. 2009) using a QC trim score >= 33, -n 0 mapping type  and filtering for less than 5 n using 8% or less overall read mismatch. Aligned reads were converted to bisulfite methylation values via methratio.py (from BSMAP).  Methylation ratios at each cytosine were converted to bedGraph files using awk and to bigWig files using the UCSC executable script "bedGraphToBigWig". Methylation ratios were also used to call differentially methylated cytosines (DMCs) via the R package MethylKit (https://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html) and methdiff.py (from BSMAP). DMCs called by both MethylKit and methdiff.py were used for subsequent analysis and were identified by using BEDtools overlap function between the two sets of DMCs.
Genome_build: TAIR10
Supplementary_files_format_and_content: Methratio output files  were converted to bedGraph via custom awk scripts and bedGraph files were converted to BigWig files via the UCSC "bedGraphToBigWig" executable script.

source_name: 3-week old leaf tissue

growth_protocol: Plants were grown on 1/2X MS agar (0.7%) + 50mg/mL hygromycein for 10 days under long day conditions (16hrs light/8hrs dark) and then transferred to soil under long day conditions. After three weeks of growth from seedlings, leaf tissue was harvested and frozen in liquid nitrogen for DNA extraction for sequencing.

extract_protocol:
DNA extracted using  Qiagen DNeasy Plant Mini Kit (catalog # 69104)
Bisulfite-seq were prepared as Pignatta, D. et al Bio-Protocols 2015.

treatment_protocol: (See Growth)

value: drm1-2 drm2-2 cmt3-1 mutations and C397H-FLAG transgene

tag: ecotype


title: RKO d120-3

description: Dropseq scRNAseq


title: Sorghum_Compatible_24 hai_Rep 2

value: Compatible interaction


title: Time after treatment 22 h, rep1


title: RKO d70-3

description: Dropseq scRNAseq


title: WT_GM_BL-HiC_Rep6

description:
BL-Hi-C of wildtype proliferating myoblasts
WT_GM.hic
WT_GM_5k.h5
WT_GM_loops.bedpe


title: WT_DM_BL-HiC_Rep1


title: Time after treatment 21.5 h, rep1


title: RKO d90-4

description: Dropseq scRNAseq


title: C397A_4

value: drm1-2 drm2-2 cmt3-1 mutations and C397A-FLAG transgene


title: Time after treatment 21 h, rep1


title: WT_GM_BL-HiC_Rep5


title: WT_GM_BL-HiC_Rep3


title: Time after treatment 20 h, rep1


title: C13 d225-2

description: Dropseq scRNAseq

value: CRB1 KO


title: WT_DRM2

value: drm1-2 drm2-2 cmt3-1 mutations and DRM2-FLAG transgene


title: KRASG12D+Cerulein (n=3)

city: Woluwe Saint-Lambert

first: Mohamad

last: Assi

state: Brussels

address: 75 Hippocrate Avenue

country: Belgium

institute: de Duve Institute

description: Total RNA (rRNA depleted)

data_processing:
Illumina HiSeq 2x150bp
Raw data of FASTQ format were firstly processed through fastp to generate clean data. Q20, G30 and GC content were then calculated
Paired-ends were there mapped to the reference genome using HISAT2 software
Featurecounts was used to count the read numbers mapped of each gene
DESeq2 R package was used to determine differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: Text file contains FPKM values for each sample

source_name: Pancreatic acinar cells

growth_protocol: CD1-enriched (adult mice)

extract_protocol:
RNAqueous Kit (AM1912, Ambion)
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol:
Pancreas digestion and FACS sorting
Cerulein (125 g/Kg); 7 injections/day, every other day, for 3 days followed by 1 day of recovery

value: FACS-sorted acinar cells


title: WT_GM_BL-HiC_Rep2


title: C397R_9

value: drm1-2 drm2-2 cmt3-1 mutations and C397R-FLAG transgene


title: WT_GM_BL-HiC_Rep4


title: C13 d190-3

description: Dropseq scRNAseq


title: RKO d70-1

description: Dropseq scRNAseq


title: KRASG12D+Cerulein (n=2)

description: Total RNA (rRNA depleted)


title: WT_DM_BL-HiC_Rep2


title: Time after treatment 19.5 h, rep1

value: 21-day-old plant


title: C13 d190-2

description: Dropseq scRNAseq


title: C13 d190-1

description: Dropseq scRNAseq


title: KRASG12D+Cerulein (n=1)

description: Total RNA (rRNA depleted)


title: WT_GM_BL-HiC_Rep1


title: β-actin knockout Mouse Embryonic Fibroblasts expressing GFP rep2 (Hi-C)

data_processing:
Raw fastq files were aligned and filtered using the HiCUP pipleline (Wingett, Steven et al. F1000Research vol. 4 1310. 20 Nov. 2015) with parameters specific to the arima protocol
Processed and filtered bam files were converted to HOMER tag directories followed by PCA analysis using HOMER command runHiCpca.pl (Heinz S, Benner C, Spann N, Bertolino E et al. Mol Cell 2010 May 28;38(4):576-589)
Reads were mapped as single end for HiC analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files with PC-1 values for 500kb bins

source_name: Mouse Embryonic Fibroblast

extract_protocol:
Samples with 1 million cells per condition were fixed with 2% formaldehyde for 10 mins. The cell pellets were washed twice by 1X PBS and then stored at -80 deg. The frozen pellets were shipped on dry ice to Genome Technology Center at NYU Langone Health, NY. All subsequent processing was performed by Genome Technology Center at NYU Langone Health using standard DNA extraction and library preparation protocols.
Hi-C was performed at Genome Technology Center at NYU Langone Health, NY from 1 million cells cross-linked with 2% formaldehyde in RT for 10 minutes. Experiments were performed in duplicates following the instructions from Arima Hi-C kit (Arima Genomics, San Diego, CA). Subsequently, Illumina-compatible sequencing libraries were prepared by using a modified version of KAPA HyperPrep library kit (KAPA BioSystems, Willmington, MA). Quality check steps were performed to assess the fraction of proximally ligated DNA labeled with biotin, and the optimal number of PCR reactions needed to make libraries. The libraries were loaded into an Illumina flowcell (Illumina, San Diego, CA) on a NovaSeq instrument for paired-end 50 reads.

value: BALB/c

value: 10.5 day old embryos

value: Embryonic Fibroblast

value: beta-actin knockout

tag: expressing

value: GFP


title: Sample 16_input_Ikzf3_G158Rhomo_thymus

data_processing:
Basecalls were performed using Illumina offline basecaller (OLB) version 1.9.4
RNA-seq sequences were aligned on mm10 using Hisat2 (version 2.1.0) with default parameters, and read counts were calculated using Htseq (version 0.12.4) using RefGenes as the reference.
ChIP-seq sequences were aligned on mm9 using BWA (Burrows-Wheeler Aligner, version 0.7.17)  with default parameters.
Peaks were called using MACS2 (version 2.1.1) with default parameters.
Genome_build: mm10 for RNA-seq and mm9 for ChIP-seq
Supplementary_files_format_and_content: tab-delimited text file include raw read count for each RNA-seq sample. BED6+3 format file for each ChIP-seq sample.

extract_protocol:
Sample 1-6: Bone marrow B220+ cells were purified using anti-CD45R coated MACS beads (Miltenyi Biotec) following manufacturer’s instruction. Pre-pro B cell (B220+AA4.1+IgM-CD43+CD24-) and pre-B cell (B220+AA4.1+IgM-CD43-CD24+) were isolated by flow cytometry. Total RNA was extracted by TRIzol reagent (Thermo Fisher Scientific), followed by DNA digestion by RNA Clean & Concentrator-5 (ZYMO RESEARCH), and mRNA was obtained by poly (A) selection with mRNA DIRECT kit (Thermo Fisher Scientific). RNA-seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocol.
Sample7-16: Lysates were purified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Sample 1-6: Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)
Sample7-16: Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs)

value: thymus

value: thymocytes


title: KRASG12D (n=3)

description: Total RNA (rRNA depleted)


title: C13 d150-4

description: Dropseq scRNAseq


title: β-actin knockout Mouse Embryonic Fibroblasts expressing NLS-tagged human β-actin rep2 (Hi-C)

value: NLS-tagged human β-actin


title: C13 d150-2

description: Dropseq scRNAseq


title: β-actin knockout Mouse Embryonic Fibroblasts expressing NLS-tagged human β-actin rep1 (Hi-C)


title: KRASG12D (n=1)

description: Total RNA (rRNA depleted)


title: β-actin knockout Mouse Embryonic Fibroblasts expressing NLS-tagged mouse β-actin rep2 (Hi-C)

value: NLS-tagged mouse β-actin


title: C13 d150-1

description: Dropseq scRNAseq


title: KRASG12D (n=2)

description: Total RNA (rRNA depleted)


title: SAMPLE 9_MDAPCa2a

city: Knoxville

first: Rebeca

last: SanMartin

state: TN

address: 1311 Cumberland Avenue

institute: University of Tennessee Knoxville

description: Gene expression data from cells grown under normal condtions

data_processing: Carried out by Thermo Fisher Scientific Microarray Analysis Services: Summarization SST-RMA algorithm1 was carried out in Transcriptome Analysis Console (TAC) Software

label: biotin

source_name: MDAPCa2a cell line, grown under normal conditions

growth_protocol:
LNCaP: ATCC RPMI, 10%FBS, 100 ug/ml penicillin-streptomycin.
22RV1: ATCC RPMI, 10%FBS, 100 ug/ml penicillin-streptomycin.
DU145: DMEM, 10%FBS, 100 ug/ml penicillin-streptomycin.
PC3: ATCC RPMI, 10%FBS, 100 ug/ml penicillin-streptomycin.
VCaP: DMEM-F12 Ham 1:1, 10%FBS, 100 ug/ml penicillin-streptomycin.
MDAPCa2a: HPC1 Media, 10%FBS, 100 ug/ml penicillin-streptomycin. FNC coating Mix (Athena Enzyme Systems)
MDAPCa2b: HPC1 Media, 10%FBS, 100 ug/ml penicillin-streptomycin. FNC coating Mix (Athena Enzyme Systems)

extract_protocol: Qiagen RNeasy with DNAse was used on 4 million cell pellets, followed by tratement with RNeasy MinElute Cleanup Kit with DNAse treatment  as per the manufacturer's instructions.

tag: passage number

value: Prostate epithelium

tag: Stage

value: Bone Metastatic

tag: racial background

value: African American


title: WT+Cerulein (n=3)

description:
Total RNA (rRNA depleted)
Transgenic mice


title: SAMPLE 10_MDAPCa2b

hyb_protocol: Carried out by Thermo Fisher Scientific Microarray Analysis Services

source_name: MDAPCa2b cell line, grown under normal conditions

tag: cell line


title: SAMPLE 8_MDAPCa2a

scan_protocol: Carried out by Thermo Fisher Scientific Microarray Analysis Services


title: SAMPLE 4_DU145

source_name: DU145 cell line, grown under normal conditions

label_protocol: Carried out by Thermo Fisher Scientific Microarray Analysis Services

value: Brain metastasis

value: Caucasian


title: SAMPLE 5_PC3

source_name: PC3 cell line, grown under normal conditions

value: Bone Metastatic:Osteoclastic


title: C13 d120-3

description: Dropseq scRNAseq

value: CRB1 KO


title: β-actin knockout Mouse Embryonic Fibroblasts expressing NLS-tagged mouse β-actin rep1 (Hi-C)


title: SAMPLE 7_VCaP

source_name: VCaP cell line, grown under normal conditions

value: VCaP

value: Bone Metastatic:Osteoblastic


title: SAMPLE 6_VCaP


title: C13 d120-2

description: Dropseq scRNAseq


title: SAMPLE 11_MDAPCa2b


title: β-actin heterozygous Mouse Embryonic Fibroblast rep2 (Hi-C)

value: BALB/c

value: 10.5 day old embryos

value: beta-actin heterozygous


title: WT+Cerulein (n=1)

value: FACS-sorted acinar cells


title: C13 d225-3

description: Dropseq scRNAseq


title: C13 d120-1

description: Dropseq scRNAseq


title: SAMPLE 3_DU145


title: β-actin heterozygous Mouse Embryonic Fibroblast rep1 (Hi-C)

value: Embryonic Fibroblast


title: C13 d225-1

description: Dropseq scRNAseq


title: C13 d91-6

description: Dropseq scRNAseq


title: WT (n=3)


title: β-actin knockout Mouse Embryonic Fibroblast rep2 (Hi-C)

value: beta-actin knockout


title: WT (n=2)


title: C13 d91-4

description: Dropseq scRNAseq


title: SAMPLE 1_LNCaP

source_name: LNCaP cell line, grown under normal conditions

value: LNCaP

value: Lymph node metastasis


title: WT+Cerulein (n=2)


title: SAMPLE 2_22RV1

source_name: 22RV1 cell line, grown under normal conditions

value: Prostate epithelium

value: Adenocarcinoma. Metastatic to mouse bone


title: C13 d91-1

description: Dropseq scRNAseq


title: β-actin knockout Mouse Embryonic Fibroblast rep1 (Hi-C)


title: mimic sample 3

city: Nottingham

first: Dimitra

last: Makri

state: Nottinghamshire

address: Room E/D 1615, D Floor, East Block Division of Child Health, Obstetrics and Gynaecology Queen's Medical Centre

department: Obstetrics and Gynaecology

institute: University of Nottingham

description: human endometrial stromal cells transfected with 30nM of miR-371a-3p mimic and further cultured for 72 h

scan_protocol: Washing and staining steps were performed by a GeneChip Fluidics station 450 and scanning was done using ™ Scanner 3000 7G System (ThermoFisher Scientific/Affymetrix, UK) according to manufacturer’s instructions at the Nottingham Arabidopsis Stock Centre (NASC), School of Biosciences, University of Nottingham.

data_processing: The raw CEL files were normalized using RMA background correction with quantile normalization, log base 2 transformation with adjustment for GC content. Differentially expressed genes were considered significant when p-value was <0.05, false discovery rate, FDR ≤ 0.05 with Benjamini-Hochberg correction, and fold-change of >1.5 or < -1.5.

source_name: endometrial cells transfected with miR-371a-3p mimic

label_protocol: The quality and integrity of the total RNA were evaluated on the Agilent-2100 Bioanalyzer system. Only samples surpassing the minimal quality threshold (RIN > 8.0) were used in the subsequent transcriptomic assessment. CDNA was prepared from 50 ng/µl of total RNA as per the GeneChip™ WT-PLUS Reagents (ThermoFisher Scientific/Affymetrix, UK) and followed by in vitro transcription to produce cRNA, end-labelled and hybridized for 16 h at 45oC to Clariom™ S Human Arrays (ThermoFisher Scientific/Affymetrix, UK).

growth_protocol: Human endometrial stromal cells (hESCs) were cultivated in T-75 flasks according to manufacturer’s instructions (ATCC, USA). All medium components were purchased from Sigma-Aldrich (USA), unless otherwise stated. The cells were cultured in complete growth medium comprising a 1:1 mixture of Dulbecco’s modified Eagle’s medium and Ham’s F-12 medium with 3.1 g/L glucose and 1 mM sodium pyruvate without phenol red supplemented with 1.5 g/L sodium bicarbonate, 1% ITS + Premix, 500 ng/ml puromycin, 90%; charcoal/dextran treated fetal bovine serum, 10%. The cells were cultured at 37oC, 5% CO2, the medium was renewed every 2-3 days, and sub-culturing was carried out every 5-6 days at a ratio of 1:6. Transfection was carried out after 8 consecutive passages.

extract_protocol: Culture medium was removed from the wells and a mix of 1% β-mercaptoethanol in RLT buffer was added in each well (200 µl) and left for 1 min. The cells were mechanically disrupted and the RLT mix containing the cells was stored at -80oC until extraction. RNA extraction was carried out using the RNeasy Mini Kit according to the protocol provided (Qiagen, USA) with a minor modification at the final step where 20 µl of H2O were used for elution. An extra procedure for RNA clean-up using ethanol precipitation was carried out due to the high guanidine salts: RNA concentration ratio which interferes with the amplification steps of the microarray.

treatment_protocol: The Lipofectamine RNAiMAX Transfection Reagent (ThermoFisher, UK) was used for delivery of the mirVana hsa-miR-371a-3p mimic (Invitrogen, UK). The supplied protocol was followed for preparation of the miRNA-lipid complexes in Opti-MEM reduced serum medium (ThermoFisher, UK). The complexes were added in 24-well culture plates containing endometrial cells at a confluency of 25-30% at 30nM concentration per well. The cells were further cultured for 72 h at 37oC. The mirVana miR-1 positive control, Cy3™ Dye-Labeled Pre-miR negative control, BLOCK-iT™ Fluorescent Oligo Alexa Fluor Red and FITC controls (Invitrogen, UK) were used to monitor  transfection efficiency. Negative control wells containing only growth medium or with equivalent volume of Opti-MEM were also run in parallel. Transfections were carried out in 4 consecutive repetitions in triplicate plates. Every 24 h the wells were examined under the microscope to assess cell survival and proliferation.

value: human endometrial stromal cells

tag: treatment

value: transfected with miR-371a-3p mimic


title: RKO d225-3

description: Dropseq scRNAseq

value: RPGRIP1 KO


title: Cit-K-Pos (#1659)

description:
CRISPR-Edited mice
Cit-K-Pos_-Neg_FPKM.txt

growth_protocol: B6D2F2 (adult mice)

treatment_protocol: Pancreas digestion and FACS sorting

tag: sorted cells

value: KRAS-Pos


title: C13 d70-4

description: Dropseq scRNAseq

value: CRB1 KO


title: Wild Type Mouse Embryonic Fibroblast rep2 (Hi-C)

state: Abu Dhabi

value: Wild Type


title: mimic sample 2

hyb_protocol: CDNA was prepared from 50 ng/µl of total RNA as per the GeneChip™ WT-PLUS Reagents (ThermoFisher Scientific/Affymetrix, UK) and followed by in vitro transcription to produce cRNA, end-labelled and hybridized for 16 h at 45oC to Clariom™ S Human Arrays (ThermoFisher Scientific/Affymetrix, UK).


title: WT (n=1)


title: Wild Type Mouse Embryonic Fibroblast rep1 (Hi-C)


title: C13 d70-3

description: Dropseq scRNAseq


title: Cit-K-Pos (#1551)


title: C13 d70-1

description: Dropseq scRNAseq


title: control sample 3 (C3)

description: human endometrial stromal cells grown in culture conditions recommended by the manufacturer without the addition of transfection reagents or miRNA mimic and run in parallel with the treatment samples

source_name: endometrial cells cultured in control conditions

value: control


title: WT d225-2

description: Dropseq scRNAseq

value: WT


title: Cit-K-Neg/Low (#1659)

value: KRAS-Neg/Low


title: Cit-K-Pos (#1577)


title: Cit-K-Neg/Low (#1577)


title: Cit-K-Neg/Low (#1551)


title: WT d225-1

description: Dropseq scRNAseq


title: 2296-3_quad_ex_MMVVg

first: Mark

middle: E

last: Anderson

state: MD

address: Rangos 471, 855 N. Wolfe Street

department: Department of Medicine

institute: Johns Hopkins School of Medicine

description: Mutant knockin mice whose CaMKIIγ M281/M282 were replaced by V281/V282

data_processing:
#Quality check: fastqc
#Trimming: (tests were done to decide that  trimming was not necessary.)
Reads alignment was done with Tophat using  mm10_refseq_nopseudo transcriptome index
ClassifyReads: #counts of how many reads are exonic, intronic, intergenic and overlaping a splice junction
Stringtie: assembly the reads into transcripts
Stringtie --merge :  # merging transcripts form all samples in one nonredundant file. Automatically filters a number of transfrags that are probably artfifacts. A reference annotation file  was used in order to merge novel isoforms and known isoforms and maximize overall assembly quality.  # This will be used further on, in the analysis (cuffdiff);
Cuffdiff  v2.2.1: # used to find significant changes in transcript expression.
Samtools: samtools index file.bam
IGV: # vizualize  alignments and assemblies
Genome_build: Genome version : mm10
Supplementary_files_format_and_content: .xlsx file of FPKM values. One biological sample per column.

extract_protocol:
To extract high quality total RNA, the quadriceps muscles were processed first in the Trizol reagent (ThermoFisher Scientific, Catalog # 15596018) and then purified by RNeasy mini columns (Qiagen, catalog # 74104) as follows. To avoid sampling bias, the entire quadriceps muscle were homogenized in Trizol reagent at the weight (mg) to volume (µL) ratio of 1:15. One mL of homogenate was processed following the manufacture’s protocol until the step of phase separation. Then, 0.5 mL of the aqueous phase was mixed with an equal volume of 70% ethanol for subsequent RNA purification by RNeasy mini kit (Qiagen, catalog # 74104) with on-column DNAse (RNase-Free DNase Set, Qiagen catalog # 79254) treatment. The concentration of the RNA was determined by Qubit fluorometric quantitation (Qubit RNA BR Assay Kit, ThermoFisher Scientific, catalog # Q10210). The integrity of the total RNA was determined by a Fragment Analyzer (Advanced Analytical Technologies, Inc) to be greater than 9.0.
1 µg of total RNA from each sample was used for RNA sequencing library preparation with the TruSeq® Stranded mRNA Library Prep kit (Illumina, catalog # 20020594). The libraries were barcoded by TruSeq® RNA Unique Dual Indexes (Illumina, catalog # 20022371) and quantified by qPCR on a Bio-Rad CFX Connect Real-Time PCR detection system with the NEBNext Library Quant Kit for Illumina (New England Biolabs, catalog # E7630L). The libraries were normalized to 10 nM, pooled and sequenced.
RNA sequencing was carried out at Johns Hopkins School of Medicine Genetic Resources Core Facility on a NovaSeq 6000 sequencing system (Illumina) with a S1 flow cell for 200 cycles, generating 100 bp paired-end reads.

treatment_protocol: Male mice between 13 and 15 weeks of age were used for the RNA sequencing experiments. The mice were first acclimated to the treadmill (Exer 3/6, Columbus Instrument, Columbus, OH) for 10 minutes on three consecutive days. The treadmill inclined at 10° and the speed was 0, 5 m×min-1, and 10 m×min-1for day 1, 2 and 3 respectively. To minimize the effects of training on the skeletal muscles, the mice rested for 7 days before sample collection. On the day of sample collection, food was withdrawn from the mice at 9:00 AM to minimize the effects of food intake on signalling and gene transcription in the muscles. At 12:00 PM, the mice ran on a treadmill set to 10° of inclination. The treadmill speed was set at 10 m×min-1 for 2 minutes to allow the mice to warm up. The speed was then increased to 15 m/min and then continuously ramped up from 15 m×min-1 to 23 m×min-1 at a rate of acceleration of 0.6 m×min-2.  When the running protocol ended, the mice had run 350 meters, which was lower than the average running capacity of CaMK2gVV/CaMK2gVV mice tested by the same treadmill protocol. Any mice that did not finish the protocol were excluded from subsequent sample collection. After exercise, the mice were allowed to rest for 3 hours with access to water but not food. Then they were euthanized by cervical dislocation after being anesthetized by isoflurane. The quadriceps muscles were quickly excised, frozen, and stored in liquid nitrogen.

tag: strain background

tag: genotype/variation

tag: gender

value: male

value: exercised

value: quadriceps muscle


title: 2161-7_quad_ex_MMVVg

tag: tissue


title: 2296-2_quad_ex_MMVVg


title: 2161-5_quad_ex_MMVVg


title: WT d190-3

description: Dropseq scRNAseq

tag: genotype

tag: age


title: GCEPB-_Replicate3

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

description:
gender: Female-Male
fpkm_RNAseq and counts_RNAseq

data_processing:
The reads were quality-trimmed to remove ambigious bases at read ends and adapter sequences using cutadapt and only uniquely mapped concordant mate pairs were used in the downstream analysis. The trimmed reads were aligned to the mouse reference genome sequence (mm10) using Tophat v2.1. Transcripts were assembled using Cufflinks, and the expression level estimation for each gene was calculated. These values are reported in fragments per kilobase of transcript per million fragments mapped (FPKM). Total read counts for each gene were calculated using HTseq.
genome build: mm10
processed data files format and content: fpkm_RNAseq.xls and counts_RNAseq.xls contain the gene expression levels in 15 samples.

source_name: Ventricular-Subventricular Zone

extract_protocol:
Cell populations were directly FACS-sorted into PicoPure RNA isolation kit (Arcturus) and immediately frozen on dry ice to increase RNA yield. All RNA preparations were treated with DNAse(Qiagen).
Whole transcriptome amplification was performed using the SMARTer Ultra Low Input RNA Sequencing-HV Kit (Clontech), which utilizes modified oligo(dT) primers. cDNA libraries were generated with Nextera transposase (Illumina) according to the manufacturer’s protocol. The samples were analyzed on an Agilent Bioanalyzer. High quality libraries were sequenced as paired-end 100bp reads on a HiSeq2000/2500 (Illumina) at Columbia Genome Center.

value: pooled male and female

tag: strain


title: 2296-5_quad_sed_MMVVg

value: sedentary


title: 2126-4_quad_sed_MMVVg


title: mimic sample 1


title: WT d150-2

description: Dropseq scRNAseq

tag: replicate


title: control sample 1 (C1)


title: 2074-5_quad_sed_MMVVg


title: DU145-CR_riba

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description:
DU145-CR_R
Gene expression data from DU145-CR cells  treated with riba after trasfected with siControl

hyb_protocol: The samples were hybridized to Human Clariom S-arrays or D-arrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

source_name: prostate cancer

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: DU145, LNCaP, DU145-CR, PC3-CR, and 22Rv1 cells were cultured in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: LNCaP and 22Rv1 cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or dihydrotestosterone (DHT) (10 nM) for 24 h. DU145, DU145-CR, and PC3-CR cells were treated with siRNA for 72 h before RNA extraction. DU145 and DU145-CR cells were treated with vehicle or riba 10 μM for 48 h.

tag: cell type

value: AR-negative Castration-resistant prostate cancer (CRPC) cell line

tag: sirna

value: siControl

tag: ligand/treatment

value: riba 10 μM


title: DU145-CR_siOCT4

description:
DU145-CR_siOCT4
Gene expression data from DU145-CR cells  treated with vehicle (water) after trasfected with siOCT4

value: vehicle


title: WT d150-1

description: Dropseq scRNAseq


title: control sample 2 (C2)

value: human endometrial stromal cells


title: DU145-CR_siNRF1

description:
DU145-CR_siNRF1
Gene expression data from DU145-CR cells  treated with vehicle (water) after trasfected with siNRF1


title: 2074-2_quad_sed_MMVVg


title: DU145-CR_Control

description:
DU145-CR_Control
Gene expression data from DU145-CR cells  treated with vehicle (water) after trasfected with siControl

value: Vehicle


title: GPB+_Replicate3


title: WT d190-1

description: Dropseq scRNAseq


title: PC3-CR_siCont

description:
PC3-CR_siCont
Gene expression data from PC3-CR cells trasfected with siControl


title: CTX-RNAseq-Replicate3

source_name: Cortex


title: 2297-3_quad_ex_WT_of_MMVVg

description: Wildtype littermate  of the CaMK2gVV/CaMK2gVV mutant mice

source_name: Wildtype_exercised_quadriceps muscle

value: Wildtype


title: GCEPB+_Replicate3


title: 2246-4_quad_ex_WT_of_MMVVg


title: WT d122-2

description: Dropseq scRNAseq

source_name: stem cell derived retinal organoids


title: WT d122-1

description: Dropseq scRNAseq


title: PC3-CR_siNRF1

description:
PC3-CR_siNRF1
Gene expression data from PC3-CR cells trasfected with siOCT4


title: PC3-CR_siOCT4

description:
PC3-CR_siOCT4
Gene expression data from PC3-CR cells trasfected with siNRF1


title: WT d120-2

description: Dropseq scRNAseq


title: GCPB+_Replicate3


title: 22Rv1_siOCT4_DHT

description:
siOCT4_DHT_Rv
Gene expression data from 22Rv1 cells  treated with DHT 10 nM after trasfected with siOCT4

value: DHT 10 nM


title: WT d120-1

description: Dropseq scRNAseq


title: WT_3

city: Nanjing

first: You-Qiang

last: Su

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.8b)
Reads aligned to genes are counted by cufflinks (v2.1.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Oocyte

extract_protocol:
Reverse transcription was carried out directly on the whole oocyte lysate using the SMARTer Ultra Low Input RNA for Illumina Sequencing - HV kits (Takara Bio Inc., Kusatsu, Japan) according to the manufacturer’s instructions. The resulting first strand cDNA was purified and then amplified for 17 cycles by PCR. After amplification, the cDNA was purified and subjected to library construction for deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 22-day old mice were primed with PMSG at the dose of 5 IU/mouse, and 48 hours later, they were injected with hCG at the dose of 5 IU/mouse. The mice were euthanized 14 hour later and the ovulated oocytes were collected from the oviduct. 3 sets of samples were collected for each genotype with each sample containing 5 ovulated oocytes in less than 3 μl of lysis buffer.

tag: cell

value: Oocyte

value: post natal day 24

value: wild type


title: WT_2


title: WT_1


title: 2161-4_quad_ex_WT_of_MMVVg


title: β-actin knockout Mouse Embryonic Fibroblasts expressing GFP rep1 (Hi-C)

value: BALB/c

tag: developmental stage

value: 10.5 day old embryos

value: Embryonic Fibroblast

value: beta-actin knockout

tag: expressing

value: GFP


title: 2161-9_quad_ex_WT_of_MMVVg

value: male

value: exercised

value: quadriceps muscle


title: WT d91

description: Dropseq scRNAseq

value: WT


title: 22Rv1_siOCT4_Veh

description:
siOCT4_veh_Rv
Gene expression data from 22Rv1 cells treated with vehicle (ethanol) after trasfected with siOCT4

tag: cell line

value: AR-negative Castration-resistant prostate cancer (CRPC) cell line


title: CKO_3

value: CKO


title: 2127-3_quad_sed_WT_of_MMVVg

source_name: Wildtype_sedentary_quadriceps muscle

tag: treatment

value: sedentary


title: 22Rv1_siControl_DHT

description:
Control_DHT_Rv
Gene expression data from 22Rv1 cells treated with DHT 10 nM after transfected with siControl

value: siControl


title: WT d90-1

description: Dropseq scRNAseq


title: 2127-1_quad_sed_WT_of_MMVVg

value: Wildtype


title: 2074-1_quad_sed_WT_of_MMVVg


title: CKO_2

value: Oocyte


title: WT d70-1

description: Dropseq scRNAseq


title: WT d70-2

description: Dropseq scRNAseq


title: 22Rv1_siControl_Veh

description:
Control_veh_Rv
Gene expression data from 22Rv1 cells treated with vehicle (ethanol) after transfected with siControl

value: Vehicle


title: LNCaP_siOCT4_Veh

description:
siOCT4_veh_LN
Gene expression data from LNCaP cells treated with vehicle (ethanol) after trasfected with siOCT4

value: LNCaP


title: RKO d70-2

description: Dropseq scRNAseq

value: RPGRIP1 KO


title: 2032-3_quad_sed_WT_of_MMVVg


title: WT_DM_BL-HiC_Rep5

description:
BL-Hi-C of wildtype differentiating myocytes at 24h
WT_DM.hic
WT_DM_5k.h5
WT_DM_loops.bedpe

source_name: Differentiating myocytes for 24h

tag: passage

value: skeletal muscle

value: wild type