title: H9 ESCs TFIIIC ChIP-seq (TFIIIC-110) rep2

city: Birmingham

first: keith

middle: e

last: giles

state: AL

address: 1825 University Blvd/ SHEL 706

department: Biochemistry & Molecular Genetics/ Stem Cell Institute

institute: University of Alabama at Birmingham

description: TFIIICMeta.tsv

data_processing:
Basecalls were performed by Hudson Alpha Institute for Bioinformatics
FASTQ files wer quality filtered using fastx (-q 20, -p 80)
filtered FASTQ files were then collapsed to remove potential PCR duplicates
fasta file was aligned to hg19 using bowtie2 default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Pol3CountTable.csv : csv.  Served as count table for DESeq2. Files were created using BEDTools coverage bed with -counts option for each tRNA gene
Supplementary_files_format_and_content: Pol3Meta.tsv : tab separated values that represent a meta-analysis of Pol 3 at all tDNA within 1kb of the TSS for hESCs and ACTA treatment.
Supplementary_files_format_and_content: Pol3UpMeta.tsv : tab separated values that represent a meta-analysis of Pol 3 at upregulated tDNA within 1kb of the TSS for hESCs and ACTA treatment.
Supplementary_files_format_and_content: Pol3DownMeta.tsv : tab separated values that represent a meta-analysis of Pol 3 at downregulated tDNA within 1kb of the TSS for hESCs and ACTA treatment.
Supplementary_files_format_and_content: TFIIIBMeta.tsv : tab separated values that represent a meta-analysis of TFIIIB at All tDNA within 1kb of the TSS for hESCs and ACTA treatment.
Supplementary_files_format_and_content: TFIIIBUpMeta.tsv : tab separated values that represent a meta-analysis of TFIIIB at upregulated tDNA within 1kb of the TSS for hESCs and ACTA treatment.
Supplementary_files_format_and_content: TFIIIBDownMeta.tsv : tab separated values that represent a meta-analysis of TFIIIB at downregulated tDNA within 1kb of the TSS for hESCs and ACTA treatment.
Supplementary_files_format_and_content: TFIIICMeta.tsv : tab separated values that represent a meta-analysis of TFIIIC at All, Up-, and  Downregulated tDNA within 1kb of the TSS for hESCs and ACTA treatment.
Supplementary_files_format_and_content: SMADMeta.tsv : tab separated values that represent a meta-analysis of both SMAD2/3 and SMAD4 at  All tDNA within 1kb of the TSS for hESCs and endoderm.
Supplementary_files_format_and_content: SMADMetaDown.tsv : tab separated values that represent a meta-analysis of both SMAD2/3 and SMAD4 at  upregulated tDNA within 1kb of the TSS for hESCs and endoderm.
Supplementary_files_format_and_content: SMADMetaUp.tsv : tab separated values that represent a meta-analysis of both SMAD2/3 and SMAD4 at  downregulated tDNA within 1kb of the TSS for hESCs and endoderm.
Supplementary_files_format_and_content: InputMeta.tsv : tab separated values that represent a meta-analysis of Input signal at  All, up-, and downregulated tDNA within 1kb of the TSS for hESCs and endoderm.
Supplementary_files_format_and_content: H3K4me3Meta.tsv : tab separated values that represent a meta-analysis of H3K4me3 for All, up-, and downregulated tDNA within 1kb of the TSS for hESC and endoderm
Supplementary_files_format_and_content: H3K27me3Meta.tsv : tab separated values that represent a meta-analysis of H3K27me3 for All, up-, and downregulated tDNA within 1kb of the TSS for hESC and endoderm
Supplementary_files_format_and_content: IsoacceptorCountTable.tsv  : tab seaparated values that contain the count table for DESeq2 quantitation of isoacceptor levels by RNAseq for shControl, shRad21, and shCtcf; taken from GSE67516
Supplementary_files_format_and_content: ESCrep1_peaks.tsv : tab separated values containing MACs peaks output
Supplementary_files_format_and_content: ESCrep2_peaks.tsv : tab separated valuescontaining MACs peaks output
Supplementary_files_format_and_content: ESCrep3_peaks.tsv : tab separated values containing MACs peaks output
Supplementary_files_format_and_content: GROseqisoACountTable.tsv : tab separated values that contain count tables for DESeq2 analysis of tRNA isoacceptor levels from GRO-seq
Supplementary_files_format_and_content: 48hoursSCFdown.tsv : tab separated values that contain the SCFdown for each transcript given the change in tRNA levels at 48 hours

source_name: H9 ESCs

growth_protocol: H9 ESCs were cultured on Matrigel coated plates (corning #354277) in mTeSR 1 media (STEMCELL Technologies # 05857), washed with DMEM/F12 (GE Healthcare # SH3002302) and passaged with accutase (MP Biomedicals # 091000449) and ROCK Inhibitor Y-27632 (BD # 562822)

extract_protocol:
ChIP was performed using 1% formaldehyde cross-linking for 10 minutes at room temperature.  Cells were lysed with 1X PBS in RIPA buffer and sonicated for 30 minutes in a biorupter on high with 50s "on" cycles followed by 10s "off".  Chromatin lysate was cleared with a 1 minue high speed spin and incubated with antibody overnight at 4o.
Libraries for high-throughput sequencing on Illumina Hi-seq were generated using TruSeq library preparation protocol.

treatment_protocol: For ACTIVIN A treatment, cells were grown to about 75–80% confluency. The cells were washed with PBS and 10 ml of RPMI-1640 (GE Healthcare # SH30027.01) was added with 1X B-27 supplement (Life Technologies # 17504–044) along with ACTIVIN A (Sigma # SRP3003) to a final concentration of 50 ng/ml

value: TFIIIC Santa Cruz sc-81406


title: Activin A TFIIIC ChIP-seq (TFIIIC-110) rep1

status: Public on Feb 02 2020

type: SRA

country: USA

description: TFIIICMeta.tsv

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: antibody


title: KO-5

city: Clayton

first: Ian

last: Smyth

state: Victoria

address: Wellington Rd

department: Department of Biochemistry & Molecular Biology, Department of Anatomy & Developmental Biology

country: Australia

institute: Monash University

library_source: transcriptomic

data_processing:
RNA sequencing data was processed with Skewer adaptor trimmer
Reads were mapped with HiSat2
The resulting ordered Bam files were analysed in Seqmonk v1.43
Library duplication and QC metrics were assessed.
Differentially expressed genes between groups were determined using the count based DeSeq2 method with a multiple testing corrected p-value cut off of p<0.05 and independent filtering applied.
This list was further filtered following count/total sequences log2 transformation selecting for fold change ratios greater or equal to 1.5.
Genome_build: Mus musculus GRCm38_v90 genome assembly
Supplementary_files_format_and_content: excel file contains fold change ratios for all detected entities before statistical and fold change filtering on one tab, and filtered list on another.

molecule: total RNA

organism: Mus musculus

source_name: Islets

growth_protocol: In vivo animal tissue

extract_protocol:
Whole islets were isolated and total RNA purified using the RNAqueous Kit (Ambion).  Samples were further DNAse treated with the TURBO DNA-free kit (Ambion) as per the manufacturer’s instructions.  RNA integrity and concentration was determined by Bioanalyszer and Qubit.
PolyA based cDNA libraries were prepared from 8 week islet RNA samples using NEB Next Ultra Directional RNA Library Prep Kit for IlluminaRNA sequencing (E7420S)

treatment_protocol: Genetic Abca12 deletion (or not for Cre controls)

tag: strain

tag: age

value: 8 weeks old

tag: tissue

value: pancreas

tag: genotype

value: KO (Abca12 tm1d)


title: NALM1

status: Public on Feb 03 2020

type: genomic

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

description: FFPE

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research.  After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification.  The amplified DNA is then enzymatically fragmented using end-point fragmentation.  The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer.  The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization.  The DNA hybridizes with the array overnight in an oven at 48⁰C.  After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

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

data_processing: minfi- R package was used to analyze the data. Data was preprocessed, quantile normalized and poor samples and probes were removed based on mean detection Pvalues per sample. 'dmpFinder' was used to identify the differenitally methylated probes between MPNSTs and DMs. qvalue < 0.01 are considered significant.

label: Cy5 and Cy3

source_name: Skin melanoma

label_protocol: Standard Illumina Protocol

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit

tag: cancer type

value: NALM

value: Skin melanoma


title: Activin A TFIIIB ChIP-seq (BRF1) rep2

description:
TFIIIBMeta.tsv
TFIIIBUpMeta.tsv
TFIIIBDownMeta.tsv

value: TFIIIB Bethyl #A301-228A


title: KO-4


title: H9 ESCs TFIIIC ChIP-seq (TFIIIC-110) rep1

description: TFIIICMeta.tsv


title: KO-3


title: KO-2


title: Sample_30-2L

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George street

department: Internal Medicine

institute: Yale University

description: mRNA

data_processing:
After sequencing, reads were filtered based on qc and the Illumina adapter was removed.
Alignment against total human genome (GRCh38, GTF= GENECODE v 27) was performed using STAR with params=' --runThreadN 12  --outFilterMismatchNmax 4  --quantMode GeneCounts  '
Total number of reads for each individual human mRNA were counted by STAR software.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.ReadsPerGene.tab: Tab-delimited files containing: column 1 – gene ID; column 2 – counts for unstranded RNA-seq; column 3 – counts for the 1st read strand aligned with RNA; column 4 – counts for the 2nd read strand aligned with RNA.

source_name: HUVEC

growth_protocol: HUVEC cells were grown in EGM Bullet Kit medium in culture. PDMS matrix with a 3 or 30 kPa module were made, and 4 dishes for each condition were coated overnight with 1% fibronectin.

extract_protocol:
Cells were lysated using TRIzol follow the company protocols.
Total RNA were used to prepare Illumina libraries using the Lexogen SPLIT kit.

treatment_protocol: No cell treatment.

tag: cell type

value: Human umbilical vein endothelial cell (HUVEC)

tag: growth condition

value: 30 kPa


title: Activin A TFIIIC ChIP-seq (TFIIIC-110) rep2

description: TFIIICMeta.tsv


title: H9 ESCs TFIIIB ChIP-seq (BRF1) rep1


title: NALM4

description: FFPE


title: MALM7

description: FFPE

value: MALM


title: KO-1


title: Activin A Pol III ChIP-seq (RPC32) rep2

description:
Pol3CountTable.csv
Pol3Meta.tsv
Pol3UpMeta.tsv
Pol3DownMeta.tsv

value: Pol III Santa Cruz #sc-21754


title: H9 ESCs Pol III ChIP-seq (RPC32) rep3


title: MALM8

description: FFPE


title: Sample_30-2S

description: microRNA

data_processing:
After sequencing, reads were filtered based on qc and the Illumina adapter was removed.
Alignment against total human genome (GRCh38, GTF= GENECODE v 27) was performed using STAR with params=' --runThreadN 16  --outFilterMismatchNmax 1  --outFilterMultimapScoreRange 0  --quantMode TranscriptomeSAM GeneCounts  --outReadsUnmapped Fastx  --outSAMtype BAM SortedByCoordinate  --outFilterMultimapNmax 10  --outSAMunmapped Within  --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0  --outFilterMatchNmin 16  --alignSJDBoverhangMin 1000  --alignIntronMax 1  --outWigType wiggle  --outWigStrand Stranded  --outWigNorm RPM
Total number of reads for each individual human microRNA were counted by STAR software.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.ReadsPerGene.tab: Tab-delimited files containing: column 1 – gene ID; column 2 – counts for unstranded RNA-seq; column 3 – counts for the 1st read strand aligned with RNA; column 4 – counts for the 2nd read strand aligned with RNA.

extract_protocol:
Cells were lysated using TRIzol follow the company protocols. Total RNA were run in a 15% denaturizing gel with 7 M urea (0.8 ml 10x TBE, 1.4 ml water, 3.8 g urea, 3 ml acrylamide, 64 ul 10% APS, 4 ul TEMED). The region between 15 and 31 nt was cut and small RNA fraction was extracted from the gel using 0.3 M NaCl-TE overnight and purified using isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: Control-2

value: Control


title: BATF3_sh2_dup2

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
RNA-seq datasets of control samples, knockdown samples for BATF3 were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 4 control vs 4 knockdown samples (2 sh knockdown with 2 replicates).
Genome_build: hg19
Supplementary_files_format_and_content: txt file for differentially expressed genes (*DEG.txt) and featureCount read count for all sample

source_name: TL-Om1 cells

growth_protocol: TL-Om1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the BGISeq500 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

treatment_protocol: TL-Om1 cells were infected with the various shRNA-expressing lentiviruses. At 36 hours post infection, puromycin selection was carried out for 36 hours, after which total RNA were harvested.

tag: cell line

tag: knockdown

value: BATF3 knockdown


title: H9 ESCs Pol III ChIP-seq (RPC32) rep2


title: BATF3_sh2_dup1


title: H9 ESCs TFIIIB ChIP-seq (BRF1) rep2


title: RMCH1LV

city: La Jolla

first: Paul

middle: A

last: Insel

state: CA

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

data_processing:
FASTQC to inspect quality of sequencing.
Kallisto v0.43.1 on rat reference transcriptome, ensembl release 79, with bias correction, yielding transcript-level TPM and counts estimates.
Transcript-level expression was converted to gene-level expression using tximport.
Differential expression analysis was performed using gene-level counts estimates as input for edgeR
Sets of differentially expressed genes were subsequently analyzed via tools such as Enrichr, GSEA and STRING
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: excel files with gene expression in TPM and estimated counts, obtained from tximport

organism: Rattus norvegicus

source_name: Left Ventricle

extract_protocol:
Snap-frozen ventricular tissue was homogenized in RLT Lysis buffer (Qiagen). RNA from this lysate was extracted using the RNeasy mini kit (Qiagen) with on-column DNase-1 digestion.
Libraries were constructed at the UCSD IGM core using the Illumina Truseq stranded mRNA protocol, using ~0.5-1 ug of total RNA as input.
RNA-sequencing on a Hiseq-4000, 12 samples multiplexed on a single lane (~25-30 million single reads per sample)

treatment_protocol: Adult rats were kept in either normoxia or hypoxia (10% O2) for 2 weeks before euthanizing and collecting cardiac tissue.

value: Sprague-Dawley

value: 3-4 months

value: Left Ventricle


title: Activin A Pol III ChIP-seq (RPC32) rep1


title: BATF3_sh1_dup2


title: MALM10

description: FFPE


title: MALM3

description: FFPE


title: H9 ESCs Pol III ChIP-seq (RPC32) rep1


title: flower-smg7-1_rep1

city: Nankang

first: Ho-Ming

last: Chen

state: Taipei

address: No. 128, Sec. 2, Academia Road

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
Adaptor sequences were trimmed using fastx_clipper of the FASTX-Toolkit (with -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCA -c).
Trimmed reads were quality-filtered using fastq_quality_filter of the FASTX-Toolkit (with -q 30 -p 90)
Trimmed reads of 20-21nt were selected and raw abundance was counted using custom Perl scripts.
Supplementary_files_format_and_content: Tab-delimited text files contain trimmed sequences of 20-21 nt and raw abundance.

organism: Arabidopsis thaliana

source_name: flower

growth_protocol: Arabidopsis seedlings was grown on 0.8% Bacto-agar plates containing half-strength Murashige and Skoog (MS) medium (pH 5.7) and 1% sucrose under a 16/8-h light/dark cycle at 22°C.  For smg7-1 and the WT control, the soil-grown plants were first grown at 22°C then transferred to 28°C.

extract_protocol:
Total RNA was extracted from the powder of frozen plant tissues by PureLink Plant RNA Reagent (Thermo Fisher).
PARE libraries were constructed from 80 μg total RNA following the protocol described previously ( Zhai J, Arikit S, Simon SA, Kingham BF, Meyers BC: Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods 2014, 67:84-90).

value: flower

tag: ecotype

tag: growth medium

value: soil

value: smg7-1 mutant

tag: treatment


title: flower-smg7-1_rep2


title: MALM5

description: FFPE


title: control_GFP_sh2_dup2

value: control


title: MALM2

description: FFPE


title: control_GFP_sh2_dup1


title: flower-WT_rep1

value: wild-type


title: KO 5wk-B130

extract_protocol:
Whole islets were isolated and total RNA purified using the RNAqueous Kit (Ambion).  Samples were further DNAse treated with the TURBO DNA-free kit (Ambion) as per the manufacturer’s instructions.  RNA integrity and concentration was determined by Bioanalyszer and Qubit.
PolyA based cDNA libraries were prepared from 5 week islet RNA samples using the services of Australian Genome Research Facility (AGRF).

value: 5 weeks old

value: pancreas

value: KO


title: 12d-CHX_rep2

data_processing:
Library strategy: PARE
Adaptor sequences were trimmed using fastx_clipper of the FASTX-Toolkit (with -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCA -c).
Trimmed reads were quality-filtered using fastq_quality_filter of the FASTX-Toolkit (with -q 30 -p 90).
Trimmed reads of 20-21nt were selected and raw abundance was counted using the custom Perl scripts.
Supplementary_files_format_and_content: Tab-delimited text files contain trimmed sequences of 20-21 nt and raw abundance.

source_name: seedlings

value: seedlings

value: 1/2 MS + 1% sucrose + 0.8% agar

value: Treatment of 10 µg/ml cyclohexmine for 6 hours


title: control_GFP_sh1_dup2


title: 12d-CHX_rep1


title: control_GFP_sh1_dup1


title: 12d-Mock_rep2

value: Mock for cyclohexmine treatment


title: flower-WT_rep2


title: AN3

description: FFPE

value: AN

value: Skin melanoma


title: 12d-Mock_rep1


title: HET 5wk-B126

value: HET


title: 10d-fry1-6_rep2

value: fry1-6 mutant


title: p65_sh2_dup2

data_processing:
RNA-seq datasets of control samples, knockdown samples for IRF4 and knockdown samples for p65 were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 4 control vs 4 knockdown samples (2 sh knockdown with 2 technical replicates).
Genome_build: hg19
Supplementary_files_format_and_content: count

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the Illumina Hiseq4000 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

value: ATL

value: p65 knockdown


title: HET 5wk-B127


title: MALM1

description: FFPE

value: MALM


title: KO 5wk-B125


title: 10d-xrn4-6_rep2

value: xrn4-6 mutant


title: p65_sh2_dup1


title: 10d-xrn4-6_rep1


title: 10d-WT_rep2


title: AN2

description: FFPE


title: KO 5wk-B114


title: AN1

description: FFPE


title: 10d-fry1-6_rep1


title: HET 5wk-B123


title: RNA-seq_LG-mESCs

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka

department: Department of Toxicology, Faculty of Veterinary Medicine

country: Japan

institute: Okayama University of Science

data_processing:
In this study, all of data processing for ChIP-seq was performed by using Galaxy platform (https://usegalaxy.org/).
Same fastq files were concatenated by using program “Concatenate datasets tail-to-head (Galaxy Version 1.0.0)”
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie (version 1.1.2).
Peaks were called using MACS (ver 1.0.1) with the following setting: Tag size (100), Band width (125), Pvalue cutoff for peak detection (1e-5).
In RNA-seq analysis, all of data processing (mapping and calculation of RPKM) was performed CLC Genomic workbench 7.0 (CLC bio).
Genome_build: mm9
Supplementary_files_format_and_content: wig files and bed files were generated using MACS (ver1.0.1) with the following setting: Extend tag from its middle point to a wigextend size fragment (-1), Resolution for saving wiggle files (10). The Reads Per Kilobase per Million mapped reads (RPKM) in each sample and fold change were calculated using CLC Genomic workbench 7.0 (CLC bio) with the default parameters (csv file).

growth_protocol: mESCs line J1, derived from 129S4/SvJae mouse embryos, were maintained the stemness on the gelatin-coated dish in D-MEM (Wako, 042-32255) supplemented 20% fetal bovine serum, 2 mM L-glutamine (Wako, 073-05391), 1 mM Na-pyruvate (Wako, 190-14881), Non-essential amino acid (Wako, 139-15651), 0.1 mM 2-Mercaptoethanol (Wako, 198-15781), Penicillin-Streptomycin (Wako, 168-23191) and 1,500 U/mL LIF (ESGRO; Millipore, ESG1107). Glucose concentration was adjusted using 2.5 M glucose solution (Sigma-Aldrich, G8769-100ML) to 1 or 25 mM.

extract_protocol:
ChIP-enriched DNA was obtaind by using ChIP-IT Express Enzymatic (Active Motif, 53009) and S40Gc specific antibody (20B2). Total RNA was isolated from cells using Direct-zol RNA Kit (Zymo Research, R2052) according to the manufacturer’s instructions.
The ends of 50 ng of ChIP-enriched DNA and Input DNA were repaired using T4 DNA polymerase (New England Biolabs, M0203) and phosphorylated with T4 polynucleotide kinase (New England Biolabs, M0201). A single adenine base was added to the 3 prime-end with Klenow fragments (New England Biolabs, M2012). TruSeq DNA adapters (Illumina, FC-121-2001/-2002) were ligated to the fragments with T4 DNA ligase (New England Biolabs, M2200). Ligation products between 200 and 600 bp were purified on AMpure XP beads (Beckman Coulter, A63880) to remove unligated adapters and subjected to 14 cycles of PCR amplification by KAPA Library Amplification Kit (KAPA BIOSYSTEMS, KK2611). RNA-seq libraries were constructed using TruSeq Strand mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Completed libraries were quantified using an Agilent 2000 BioAnalyzer system.

treatment_protocol: mESCs were cultured in ES medium containing 25 mM (control, HG-mESCs) or 1 mM glucose (LG-mESCs) for 96 hrs.

tag: protocol

value: 1 mM glucose

value: Undifferentiated embryonic stem cells


title: p65_sh1_dup1


title: p65_sh1_dup2


title: RNAseq_HG-mESCs

value: 25 mM glucose


title: IRF4_sh2_dup1

value: IRF4 knockdown


title: Ogt_HG-mESCs_ChIP-seq

tag: chip-antibody

value: α-Ogt (Rabbit polyclonal antibody, Abcam, ab50273)


title: IRF4_sh1_dup2


title: gH2AX_HG-mESCs_ChIP-seq

value: α-γH2AX (Rabbit polyclonal antibody, Abcam, ab2893)


title: MALM4

description: FFPE


title: 10d-WT_rep1

value: seedlings

value: 1/2 MS + 1% sucrose + 0.8% agar

value: wild-type


title: IRF4_sh1_dup1


title: Activin A TFIIIB ChIP-seq (BRF1) rep1

value: TFIIIB Bethyl #A301-228A


title: HUH7-2

city: Nanning

first: Manya

last: Wu

address: No.22, Shuangyong Road

country: China

institute: Guangxi Medical University

data_processing:
The original image data of the sequencing result was subjected to image base recognition (Base Calling) using the software Bcl2fastq (v2.17.1.14)
The original sequencing data (Pass Filter Data) was obtained, and the result was stored in the FASTQ file format.
The quality of the sequencing data was analyzed using the software FastQC (v0.10.1).
The second-generation sequencing data quality statistical software Cutadapt (v1.3) was used to remove the linker and low-quality sequence from the raw data (Pass Filter Data) to obtain clean data for subsequent information analysis.
Genome_build: The clean data was compared to the reference genome sequence using HISAT2 (v2.0.1) alignment software, and the results were compared.
Supplementary_files_format_and_content: All the alignments for transcript assembly were passed to the software Stringtie (v1.0.4).

source_name: liver cancer cells

growth_protocol: Huh-7 cultures were maintained in RPMI-1640 while HepG2 was cultured in Eagle’s Minimum Essential Medium supplemented with 10 % fetal bovine serum (FBS) (Gibco, USA) at 37 ˚C in a humidified incubator containing 5 % CO2.

extract_protocol:
Total RNA was isolated with TRIzolTM reagent (Invitrogen, USA)/RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). RNA purity was assessed using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity was checked using the RNA Nano 6000 Assay Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1 % agrose gel. Only samples (1μg total RNA) with an RNA integrity number (RIN) of ≥ 7 were subjected to deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols(NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®).

treatment_protocol: Cells were treated with 1.5 μM sorafenib (Selleck Chemicals, Houston, TX, USA) after plating into a 6 cm cell culture dish (1×105 cells per dish) for 24 hours. The viable cells still attached to the dish respectively were treated with various concentrations (1.5, 3.0, 4.5, 6.0, 7.5 and 9.0 μM) and maintained for 15-21 days. To the end of the fifth month, the cells were becoming stable resistant to sorafenib and re-named Huh-7-S and HepG2-S cells.

tag: passage

value: sorafenib-sensitive


title: Sample_30-1S

description: microRNA

value: Human umbilical vein endothelial cell (HUVEC)

value: 30 kPa


title: HUH7-S-3

value: sorafenib-resistant


title: HUH7-S-2


title: HUH7-3


title: HUH7-S-1


title: GFP_sh2_dup2

value: ATL

value: control


title: H2AX_HG-mESCs_ChIPseq

value: α-H2AX (Rabbit polyclonal antibody, Abcam, ab11175)


title: IRF4_sh2_dup2


title: Input_LG-mESCs_ChIPseq

value: 1 mM glucose


title: HUH7-1


title: Mutant2 OS3-H3F3A_K27M

type: RNA

city: Gifu

first: Hiroyuki

last: Tomita

address: 1-1 Yanagido

institute: Gifu University

description: cultured for 2days and then extracted RNA

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray 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 (G2505B) using one color scan setting for 1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cells with K27M mutation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug 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: All the cells cultured in minimum essential medium α (MEM-α) with GlutaMAX supplemented with 10% fetal bovine serum(FBS), 5μg/ml bovine insulin, 0.2% D-glucose and 0.1% penicillin-streptomycin solution at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using a RNeasy kit (Qiagen, TX, USA) according to the manufacturer’s protocol. cDNAs were synthesized using a SuperScript III First-Strand Synthesis Kit (Life Technologies, Inc., MD, USA).

treatment_protocol: For 2days, OS3 glial cells with K27M mutation (Mutant) and OS3 glial cells with only empty vector (control)  cultured in minimum essential medium α (MEM-α) with GlutaMAX supplemented with 10% fetal bovine serum(FBS), 5μg/ml bovine insulin, 0.2% D-glucose and 0.1% penicillin-streptomycin solution at 37°C and 5% CO2.

tag: gender

value: male

value: brain

value: glial cell

value: H3.3-K27M mutation


title: MALM6

description: FFPE

value: MALM

value: Skin melanoma


title: Control2 OS3-vector

source_name: cells with empty vector


title: Mutant3 OS3-H3F3A_K27M


title: HEPG2-S-3


title: Mutant1 OS3-H3F3A_K27M


title: GFP_sh2_dup1


title: Control1 OS3-vector


title: HEPG2-S-2


title: BATF3_sh1_dup1

value: BATF3 knockdown


title: Input_HG-mESCs_ChIPseq

value: 25 mM glucose

value: Undifferentiated embryonic stem cells


title: HEPG2-S-1


title: GFP_sh1_dup2


title: HEPG2-3

value: sorafenib-sensitive


title: S40Gc_LG-mESCs_ChIPseq

value: 20B2 (mouse monoclonal antibody, prepared in-house)


title: HEPG2-2


title: Control-1

value: 8 weeks old

value: pancreas

value: Control


title: DE2-5

city: Beijing

first: Qiang

last: Tu

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
sequencing reads processing and filtering, customized data processing pipeline (python)
genome mapping, STAR(v2.5.2a) using default parameters, and customized data processing pipeline (python)
quantification based on barcode counts,  customized data processing pipeline (python)
Genome_build: ENSEMBL human GRCh38, mouse GRCm38, and medaka ASM223467v1
Supplementary_files_format_and_content: plain text，quantification count matrix  based on barcode counts, raws are genes and columns  are samples (sample name_barcode_sample)

organism: Oryzias latipes

source_name: gonadal fragments

extract_protocol:
RNA extraction using Both TRIzol and Qiagen RNeasy Micro Kit
Decode-seq: Reverse transcription and template switching using SuperScript II Reverse Transcriptase, library preparation using Illumina Nextera XT DNA Library Prep Kit

value: offspring of d-rR-Tg(olvas-GFP) and Qurt

value: gonadal fragments,(include gonads, intestines, and body trunks)

tag: developmental stage

value: stage 39

value: in 28 ◦C fresh water, 14 h light and 10 h dark


title: HEPG2-1


title: DE2-4

tag: strain


title: DE3-4

organism:
Homo sapiens
Mus musculus

source_name: HEK293T cells, Mouse MEF cells

value: C57BL/6 x DBA/2

value: cells

value: DMEM,2 mM L-glutamine,100 units/ml Penicillin-Streptomycin,10\% FBS(HEK293T), 15\% FBS(Mouse MEF)


title: GFP_sh1_dup1

value: ATL

value: control


title: ChIP_Input

data_processing:
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is q-value < 0.01, keep-dup=1
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files of p65 called with MACS2

extract_protocol:
Library construction from the p65 ChIP-seq samples and sequencing of paired-end 49-bp-long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Paired-end ChIP-Seq sequencing

treatment_protocol: TL-Om1 cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and p65-DNA complexes were isolated with antibody.  A sample of whole cell extract (Input) was sequenced and used as the background to determine enrichment.

tag: chip antibody


title: DE8-12-1

data_processing:
sequencing reads processing and filtering, customized data processing pipeline (python)
genome mapping, STAR (v2.5.2a) using default parameters, and customized data processing pipeline (python)
quantification based on barcode counts, customized data processing pipeline (python)
Genome_build: ENSEMBL human GRCh38, mouse GRCm38, and medaka ASM223467v1
Supplementary_files_format_and_content: plain text，quantification count matrix based on barcode counts, raws are genes and columns are samples (sample name_barcode_sample)

tag: human cell line

tag: mouse strain

tag: mouse cell type

value: MEF

value: DMEM, 2 mM L-glutamine, 100 units/ml Penicillin-Streptomycin, 10% FBS (HEK293T), 10% FBS (Mouse MEF)


title: DE8-12-2


title: DE3-3

tag: tissue


title: DE8-6


title: DE1-3


title: DE2-3


title: DE1-1


title: DE1-2


title: DE2-2


title: IRF4_ChIP-Seq

data_processing:
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is P-value < 1E-9
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files of IRF4 called with MACS2 1E-9

source_name: TL-OM1 cells

extract_protocol:
Library construction from the IRF4 ChIP-seq samples and sequencing of paired-end 49-bp-long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single-end ChIP-Seq sequencing

treatment_protocol: TL-Om1 cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and IRF4-DNA complexes were isolated with antibody.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.

value: TL-OM1 cells

tag: cell type

value: adult T-cell leukemia/lymphoma cell line

value: IRF-4 Antibody (M-17):sc-6059


title: p65_ChIP-Seq

tag: cell line


title: S40Gc_HG-mESCs_ChIPseq

value: 25 mM glucose

value: Undifferentiated embryonic stem cells

value: 20B2 (mouse monoclonal antibody, prepared in-house)


title: Tle1/3/4-deficient HSCs rep2 [Tle134b]

status: Public on Feb 01 2020

city: Xi'an

first: Xiaoke

last: Ma

state: Shaanxi

address: No.2 South TaiBai Road

institute: Xidian University

data_processing:
reads are mapped using the Tophat software using default parameters
only the unique mapped reads are obtained for downstream analysis using samtool
use the cufflink to obtain the expression level of genes (Reads Per Kilobase of exon per Megabase of library size (RPKM) )
use the EdgeR software to obtain the differentially expressed genes
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Tle1/3/4-deficient HSCs

extract_protocol:
Lin-cKit+Sca1+ CD150+CD48– HSCs  were sort-purified from the bone marrow and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

tag: strain background

tag: genotype/variation

value: bone marrow

value: hematopoietic stem cells (HSCs)

tag: phenotype

value: Lin-cKit+Sca1+ CD150+CD48-


title: Control HSCs rep3 [VavC3]

source_name: Control HSCs


title: Tle1/3/4-deficient HSCs rep1 [Tle134a]


title: Control HSCs rep2 [VavC2]


title: Tle3 ChIPSeq

data_processing:
Reads were mapped using bowtie version 2
peaks were called using MACS version 1.4
Genome_build: mm9
Supplementary_files_format_and_content: bed files

source_name: Lin–cKit+ T cells_Tle3 ChIPSeq

extract_protocol:
Lin–cKit+ T cells were purified from WT C57BL/6 mice. The cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with an anti-Tle3 antibody or normal IgG, which were then properly washed and immunoprecipitated DNA extracted.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

tag: age

value: 8-10 weeks

value: wild type

value: hematopoietic progenitors

value: Lineage negative, cKit positive

value: anti-Tle3 antibody (Proteintech Group Cat. No. 11372-1-AP)


title: IgG ChIPSeq

source_name: Lin–cKit+ T cells_input

value: normal IgG


title: Control HSCs rep1 [VavC1]

value: control


title: input DNA


title: Control3 OS3-vector

value: male

value: brain

value: glial cell

tag: genotype


title: SAMPLE3: miR-210-3p _1

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

description: Total RNA extracted form SAS cell, and 100 ng of RNA for analysis

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent)

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: miR-210-3p transfected SAS cells

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: SAS cells were obtained from the Japanese Collection of Research Bioresources Cell Bank. SAS cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Invitrogen, CA, USA) supplemented with 10% heat-inactivated FBS, 1% AA and 10mg/mL Puromicine at 37 °C in 5% CO2.

extract_protocol: Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: SAS cells were transfected with microRNA and cultured for 48 hours. After 48 hours, total RNA of SAS cells was extracted.

value: SAS

value: squamous cancer

tag: miRNA


title: SAMPLE1: miR-629-3p _1

source_name: miR-629-3p transfected SAS cells


title: SAMPLE8: miR-Negative Control _2

source_name: miR-Negative Control transfected SAS cells


title: SAMPLE5: miR-874-3p _1

source_name: miR-874-3p transfected SAS cells


title: het_NC14_72_17111404

city: Evanston

first: Shelby

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

data_processing:
Sequenced reads were barcode-split and adapters were removed using Trim Galore
Trimmed reads were mapped to the Drosophila melanogaster genome (dm6) using Bowtie2
Alignments were converted to .bam format, duplicates were marked using Picard MarkDuplicates, and reads were filtered for quality score (>=10), cuplication, and were required to be mapped, properly paired, and non secondary alignments. Single-end reads were not filtered for proper pairing.
For ATAC, paired end read fragments <= 100 bp were considered to have originated from 'open' chromatin. Replicates were pooled and average coverage over open regions was calculated over 10 bp discrete windows. For experiment 2 (opa mutant ATAC), pooled reads were randomly sampled from the wild-type and heterozygous samples to match the read depth of the pooled opa mutant sample.
For ChIP, reads were pooled and coverage was calculated over 10 bp windows.
Peaks were called with MACS2 on pooled reads for ATAC-seq
Peaks were called with MACS2 on individual replicates for ChIP-seq, and reproducible peaks were determined using the Irreproducible Discovery Rate approach (Encode).
Nucleosomes within 2500 bp regions flanking the maximum open position as determined by MACS2 on ATAC data were called using NucleoATAC. Both smoothed nucleosome profiles and dyad position/occupancy scores are provided in the processed data file deposit.
Genome_build: dm6
Supplementary_files_format_and_content: Coverage is proveded as .wig formatted files. Peaks are provided as tab-delimited text with additional logical indexers that indicate categories of peaks as determined by analysis. Predicted nucleosome positions are provided in two formats: smoothed nucleosome profiles from NucleoATAC are provided in bedgraph format, and dyad positions with estimated occupancy are provided in .bed format.

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
ATAC samples were processed as described previously (Blythe and Wieschaus, eLife 2016 Nov 23;5. pii: e20148. doi: 10.7554/eLife.20148.). ChIP samples were processed as described previously (Blythe and Wieschaus, Cell 2015 Mar 12;160(6):1169-81. doi: 10.1016/j.cell.2015.01.050)
ATAC libraries were made using the Nextera Tn5 transposase as described in the cited protocol. ChIP libraries were made using the NEBNext Ultra II Library prep kit.

value: w; opa[IIP32]/His2Av-GFP

tag: timepoint

tag: Sex

value: F

tag: experiment


title: het_NC14_72_17111406


title: het_NC14_72_17111507


title: opa_NC14_72_17111506

value: M


title: het_NC14_72_17111503


title: wt_NC14_72_17111501


title: SAMPLE6: miR-874-3p _2


title: wt_NC14_72_17111505


title: SAMPLE7: miR-Negative Control _1


title: het_NC14_72_17111405


title: SAMPLE4: miR-210-3p _2


title: wt_NC14_72_17111502


title: SAMPLE2: miR-629-3p _2


title: wt_NC14_72_17111401


title: het_NC14_72_17111402


title: het_NC14_72_17111403


title: het_NC14_72_17111105


title: het_NC14_72_17111107


title: het_NC14_72_17111407


title: het_NC14_72_17111104


title: Adult T5

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

institute: Michigan State University

data_processing:
After investigating the quality of the raw data (the quality was judged based on Illumina’s Q score, which represents the error rate at
each base, built on a log10 score), sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor
quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference ovine genome available on ENSEMBL
(Oaries_v3.1.90) using the STAR aligner v.2.5.2b. The STAR aligner uses a splice aligner that detects splice junctions and
incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts
Genome_build: Ovine genome (Oaries_v3.1.90)
Supplementary_files_format_and_content: DEGs of fetal and adult with raw values in csv file

organism: Ovis aries

source_name: Ovary

extract_protocol:
Total RNA was extracted from fresh frozen whole ovary samples using Qiagen RNeasy Plus Universal mini kit. The samples were sequenced using a 2x150bp Paired End (PE) configuration. The total number of reads/sample were 45-50 million. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq wereas converted into fastq files and de-multiplexed using Illumina'’s bcl2fastq 2.17 software.
RNA sequencing libraries were prepared using 500 ng RNA, and the NEBNext Ultra RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: Prenatal T-treated sheep were generated by intramuscular administration of 100 mg of 1.2 mg/kg T propionate (Sigma-Aldrich Corp.) suspended in cottonseed oil to pregnant Suffolk sheep twice weekly from Days 30 to 90 of gestation

tag: treatment

value: testosterone

tag: breed

value: Suffolk sheep

value: Ovary

value: Year 2


title: Adult T4

value: wild type


title: Adult T6


title: Adult T7


title: wt_NC14_72_17111102


title: Fetal T2

value: Day 90


title: Adult C4


title: Adult C5


title: Adult C7


title: opa_NC14_72_17111106


title: Fetal C3


title: Fetal C2


title: Adult C6


title: opa_NC14_72_17111101


title: Fetal T1


title: boctRM9_NC14_72_17091305

value: w; His2Av-GFP bcd osk cic e tsl Tl[RM9]/+ bcd osk cic e tsl Tl[RM9]


title: boctRM9_NC14_72_17091102


title: boctRM9_NC14_12_17091202


title: boctRM9_NC14_72_17091201


title: boctRM9_NC14_12_17091203


title: wt_NC14_72_17091501

value: w; His2Av-GFP

value: WT


title: Fetal C1

value: control


title: iXist-ChrX_XistDelA_2C2_input

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Library strategy: m6A-seq
For conventional m6A-seq data, first we removed the rRNA reads computationally by mapping the single-end reads to the mouse rRNA build with Bowtie2 (Langmead and Salzberg, 2012). The remaining unmapped reads were then aligned to mm10 genome by STAR (v2.4.2a) (Dobin et al., 2013) with “--single-end” mode. BigWig files were generated by Bedtools (Quinlan and Hall, 2010) and normalized to 10 million mapped reads (Generate_BigWig_from_RNA_seq_Bam_mm10.sh), then visualized in IGV or UCSC.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS + 10% DMSO.

extract_protocol: Total RNAs were isolated by Trizol, and were used for m6A-seq.

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1.5μg/mL) to the culture medium for 24 hours.

tag: gender

value: female

value: mouse embryonic stem cells

value: Dox

tag: antibody


title: wt_NC14_72_17091302


title: Fetal T3


title: iXist-ChrX_XistDelA_C1_input


title: boctRM9_NC14_12_17091103


title: het_NC14_72_17111103


title: wt_NC14_12_17091304


title: wt_NC14_72_17091301


title: wt_NC14_12_17091306


title: iXist-ChrX_XistDelA_2C2_m6AIP

value: anti-m6A antibody (Synaptic Systems, 202 003)


title: iXist-ChrX_WT_input

source_name: iXist-ChrX(mESC)


title: iXist-ChrX_XistDelA_C1_m6AIP


title: iXist-ChrX_WT_m6AIP


title: RNA-Seq_101bp_PE_Male_Gut_yw_7d_Rep2new

city: Bethesda

first: Alexei

last: Arnaoutov

state: MD

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

data_processing:
We used Illumina Casava1.8.2 for basecalling
Shortreads from RNA-Seq were mapped onto Drosophila Reference Genome 6 (PMID: 25589440) using TopHat 2.1.1 (PMID: 23618408) with -g 1 and -G parameters with FlyBase gene annotation model 6.12.
We used HTSeq 0.6.1p1 (PMID: 25260700) to measure gene-level read counts with the “-s reverse” option.  We provide Cufflinks 2.2.1-generated (PMID: 23222703) FPKM values (Fragments Per Kilobase of transcript per Million mapped reads) in this GEO submission that we prepared.  We used the -G, -u, and -b parameters.
Genome_build: Drosophila Reference Genome Release 6 (Berkeley Drosophila Genome Project)
Supplementary_files_format_and_content: Gene-level expression measurements from HTSeq (read count) and Cufflinks (FPKM values) are provided in a tab-limited text format

molecule: polyA RNA

source_name: midgut

growth_protocol: We cultured flies using Jazz-Mix food (Thrermo Fisher Scientific, Waltham, MA) for the samples that we performed 50bp single-end RNA-Seq.  For samples with 76bp single-end RNA-Seq, we cultured files as appeared in Broderick et al 2014 (PMID: 24865556) with minor modifications.

extract_protocol:
We extracted total RNA using 1 ml of Trizol (Thrermo Fisher Scientific, Waltham, MA) as in manufacturer’s guideline.
We prepared stranded RNA libraries using Illumina TruSeq mRNA kit (Illumina, San Diego, CA).

treatment_protocol: We treated 30 flies with 100 ul of autoclaved yeast paste with or without 400 uM deoxyadenosine, deoxyguanosine, or 40mM hydroxyurea.

tag: developmental stage

value: adult

value: 7  day

tag: growth condition

value: normal

value: Female

value: deltaIRBIT

tag: replicate number

value: Replicate 2 new

tag: ercc spikein


title: RNA-Seq_101bp_PE_Male_Gut_yw_7d_Rep1new

value: Replicate 1 new


title: wt_NC14_12_17091303

value: F


title: iXist-ChrX_XistDelm6A/T1_11C_Dox1

data_processing:
The RNA-seq data mapping pipeline was similar to our previous study (Pintacuda et al., 2017). Briefly, the raw fastq files of read pairs were first mapped to an rRNA build by bowtie2 (v2.3.2) (Langmead and Salzberg, 2012) and rRNA-mapped reads discarded. The remaining unmapped reads were aligned to the ‘N-masked’ genome (from mm10 coordinates) with STAR (v2.4.2a) using parameters “--outFilterMultimapNmax 1 --outFilterMismatchNmax 4 --alignEndsType EndToEnd” for all the sequencing libraries (Dobin et al., 2013). Unique alignments were retained for further analysis. We made use of 23,005,850 SNPs between Cast and 129S genomes and employed SNPsplit to split the alignment into distinct alleles (Cast and 129S) using the parameter “--paired”. The (allelic) read numbers were counted by the program featureCounts (-t transcript -g gene_id -s 2) (Liao et al., 2014) and the alignments were sorted by Samtools (Li et al., 2009). Bigwig files were generated by Bedtools (Quinlan and Hall, 2010) and visualized by IGV (Robinson et al., 2011) or UCSC Genome Browser. For biallelic analysis, counts were normalized to 1 million mapped read pairs (as CPM) by the edgeR R package. Genes with at least 10 SNP-covering reads across all the samples were further taken to calculate the allelic ratio of where Xi and Xa indicate inactive and active allele, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: text

growth_protocol: ES cells were grown in DMEM media supplemented with 10% fetal calf serum (Seralab), 2 mM L-glutamine, 1X non-essential amino acids, 50 µM β-mercaptoethanol, 1X penicillin / streptomycin (all from Life Technologies) and 1000 U/mL LIF (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2. Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 to 1.5 µg/mL of doxycycline for 24 hours.

extract_protocol:
Chromatin RNA was extracted from one confluent 15 cm dish of mESCs. Briefly, cells were trypsinised and washed in PBS. Cells were lysed on ice in RLB (10 mM Tris pH 7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40), and nuclei were purified by centrifugation through a sucrose cushion (24% sucrose in RLB). The nuclei pellet was resuspended in NUN1 (20 mM Tris pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol), then lysed with NUN2 (20 mM Hepes pH 7.9, 300 mM, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea). Samples were incubated for 15 minutes on ice then centrifuged at 2800 g to isolate the insoluble chromatin fraction. The chromatin pellet was resuspended in TRIzol by passing multiple times through a 23 gauge needle. Finally chromatin-associated RNA was purified through standard TRIzol/chloroform extraction followed by isopropanol precipitation. Samples were then treated with Turbo DNAse, and 500ng – 1µg of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by qPCR with KAPA Library Quantification DNA standards (KAPA Biosystems). The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq500.
TruSeq RNAseq

tag: strain background

value: 129S X Cast

tag: tissue

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

tag: agent

tag: time course

tag: medium

value: ES medium

tag: molecule subtype

value: Chromatin-Associated RNA


title: iXist-ChrX_XistDelA_C11_Dox

tag: genotype/variation


title: iXist-ChrX_XistDelA_C11_NoDox


title: iXist-ChrX_XistDelA_2C2_Dox


title: iXist-ChrX_XistDelA_2C2_NoDox


title: iXist-ChrX_XistDelm6A/T1_11C_NoDox2


title: RNA-Seq_76bp_SE_Male_Gut_yw_HU_40d_Rep1_ERCC78A

value: midgut

tag: age

value: 40 day

tag: Sex

value: Male

value: Hydroxyurea

tag: genotype

value: yw


title: iXist-ChrX_XistDelm6A/T1_11C_Dox2

value: mouse embryonic stem cells

value: Dox


title: RNA-Seq_76bp_SE_Male_Gut_yw_HU_axenic_40d_Rep3_ERCC78B

value: adult

value: axenic

tag: treatment


title: RNA-Seq_76bp_SE_Male_Gut_yw_HU_axenic_40d_Rep2_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_yw_HU_40d_Rep3_ERCC78A

value: normal


title: RNA-Seq_76bp_SE_Male_Gut_yw_HU_axenic_40d_Rep1_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_yw_HU_40d_Rep2_ERCC78A


title: iXist-ChrX_XistDelA_C1_Dox

tag: gender

value: Female


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_axenic_40d_Rep2_ERCC78B

value: dGuo


title: iXist-ChrX_XistDelA_C1_NoDox


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_axenic_40d_Rep1_ERCC78B


title: iXist-ChrX_WT_NoDox


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_7d_Rep2_ERCC78B

value: 7 day


title: iXist-ChrX_XistDelm6A/T1_11C_NoDox1

value: 129S X Cast


title: SWngfRPF4

city: Richardson

first: Theodore

middle: J

last: Price

state: TX

address: 800 W Campbell Rd.

institute: University of Texas at Dallas

description: all_sample.prot_cod.polyA_rmd.str_spc.xlsx

data_processing:
Basecalling by Illumina Basespace onsite
Quality check with FastQC 0.11.5, to determine trimming parameters
Trimmed for low-quality (3bp from 5’ end, 7bp from 3’ end, >= 5bp poly-A tail, and adapter contamination with in-lab un-published customized tool written in C language.
Trimmed reads are mapped to gencode.vM10 (mm10) library with Tophat 2.1.1
Post-mapping filtering for strand-specific reads
FPKM values per gene is quantified by Cufflinks 2.2.1, with gencode.vM10 (mm10) library
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet with TPM of protein coding genes for each sample

source_name: DRG neuronal culture

growth_protocol: Cells were distributed evenly in 3 poly-D-lysine-coated culture dishes (100 mm diameter) (BD Falcon) and  incubated at 37 °C in a humidified 95% air/5% CO2 incubator for 6 days. Culture media was changed every other day.

extract_protocol:
Ribosome bound RNA fragments and corresponding sets for total RNA were isolated as described in Ingolia et al., 2012 and Hornstein et al., 2016 with minor adjustments in the composition of the polysome lysis buffer (20 mM Tris-HCl, pH 7.5, 250 mM NaCl, 15 mM MgCl2, 1 mM DTT, 0.5% (vol/vol) Triton X-100, 2.5 U/ml DNase I, 40U/mL RNasin and 50ug/mL emetine). MicroSpin S-400 columns (GE Healthcare) were used to isolate ribosome bound RNAs. After rRNA was removed using RiboCop rRNA depletion kit (Lexogen), footprints were dephosphorylated then size selected (28-34nt) by PAGE on 15% TBE-Urea gels (Bio-Rad).
Footprints and total RNA libraries were generated by SMARTer smRNA-Seq kit for Illumina (Clonetech) and Quantseq 3ʹ mRNA-Seq library kit (Lexogen) respectively.

treatment_protocol: Cells were treated with NGF (20ng/mL) and IL-6 (50ng/mL) for 20 minutes followed by addition of emetine (50mg/mL) for 1 minute

tag: strain

value: Swiss Webster

value: 4 weeks

value: WT

tag: library prep

value: ribosome profiling

value: Taconic


title: SWngfRPF3


title: SWngfRPF2


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_axenic_40d_Rep3_ERCC78B

value: midgut

tag: developmental stage

value: 40 day

tag: growth condition

value: Male


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_7d_Rep1_ERCC78B

value: yw

tag: replicate number

tag: ercc spikein


title: SWngfRPF1


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_40d_Rep3_ERCC78A

tag: tissue


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_40d_Rep2_ERCC78A


title: SWngfQT4

value: quant-seq protocol


title: RNA-Seq_76bp_SE_Male_Gut_yw_dAdo_axenic_7d_Rep3_ERCC78A

value: adult

value: dAdo


title: RNA-Seq_76bp_SE_Male_Gut_yw_dAdo_axenic_7d_Rep2_ERCC78A

value: axenic


title: SWngfQT2


title: SWnegRPF2

value: naive


title: SWngfQT1


title: RNA-Seq_76bp_SE_Male_Gut_yw_dAdo_axenic_7d_Rep1_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_yw_dAdo_7d_Rep3_ERCC78B

value: normal


title: SWnegRPF1


title: RNA-Seq_76bp_SE_Male_Gut_yw_dAdo_7d_Rep2_ERCC78B

value: 7 day


title: RNA-Seq_76bp_SE_Male_Gut_yw_dAdo_7d_Rep1_ERCC78B


title: iXist-ChrX_WT_Dox

tag: strain background

value: 129S X Cast

value: Female

value: mouse embryonic stem cells

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

tag: agent

value: Dox

value: ES medium

value: Chromatin-Associated RNA


title: RNA-Seq_76bp_SE_Male_Gut_yw_axenic_7d_Rep3_ERCC78B

value: midgut


title: B6negRPF2

value: 4 weeks

value: WT

value: ribosome profiling

value: UT Dallas


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_7d_Rep3_ERCC78B

value: adult

value: Male

value: dGuo

value: yw


title: B6negRPF1

value: naive


title: SWnegQT2

value: Swiss Webster

value: quant-seq protocol

value: Taconic


title: RNA-Seq_76bp_SE_Male_Gut_yw_axenic_7d_Rep2_ERCC78B

value: 7 day

value: axenic


title: SWnegQT1


title: RNA-Seq_76bp_SE_Male_Gut_yw_axenic_7d_Rep1_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_yw_axenic_40d_Rep3_ERCC78A

value: 40 day


title: RNA-Seq_76bp_SE_Male_Gut_yw_dGuo_40d_Rep1_ERCC78A

value: normal


title: SWngfQT3


title: B6negQT1


title: RNA-Seq_76bp_SE_Male_Gut_yw_axenic_40d_Rep2_ERCC78A

value: midgut


title: CKO_rep3

city: Sendai

first: Masayuki

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

data_processing:
Illumina bcl2fastq software used for basecalling.
Reads mapped against mouse (mm9) genome using the TopHat v2.0.9  with option of -g 1 -p 4 --library-type=fr-firststrand.
Differential gene analaysis performed using Cuffdiff v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genotype were generated using Cuffdiff.

source_name: mouse pulmonary primary endothelial cells

growth_protocol: Individual lungs of 7-10 days pups were collected in isolation medium  containing DMEM, 10% FBS  and antibiotics  and digested with Collagenase/Dispase. the singlle cell suspension was first purifed with beads conjugated PECAM antibody in 0.1% BSA/PBS , cultured for 5 days in endothelial growth medium (Vasculife) containing 10 mM L-glutamine, 50 μg/mL ascorbic acid, 1 μg/mL hydrocortisone hemisuccinate, 0.75 units/mL heparin sulfate, 5% FBS, 5 ng/mL rhEGF, 0.2% EnGS and 1% penicillin-streptomycin, After 5 days of culture, cells were harvested purified again with purified anti ICAM-1  beads conjuagated antibody and cultured again for 5 days in the same culture media.

extract_protocol:
Total RNA was prepared by using RNeasy Mini Kit (QIAGEN) and 1.5 μg of total RNA was used for further steps. Isolation of poly(A)-tailed RNA and library construction were performed using SureSelect Strand Specific RNA Sample Prep Kit (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nrf2 induction was assessed at basal level in both SCD::Keap1F/F and SCD::Keap1F/F::Tie1-Cre  endothelial cells

value: Mixed background

tag: source

value: lungs

value: Post natal day 7-10


title: RNA-Seq_76bp_SE_Male_Gut_yw_axenic_40d_Rep1_ERCC78A


title: Control_rep3


title: CKO_rep1


title: RNA-Seq_76bp_SE_Male_Gut_yw_7d_Rep2_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_yw_7d_Rep1_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_yw_40d_Rep3_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_yw_7d_Rep3_ERCC78A


title: 4sU_3_4OHT_FP_pulse.bam

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description:
4sU-labeled RNA
4sU-seq

data_processing:
Fastq files were generated using Illuminas base calling software GenerateFASTQ v1.1.0.64 and overall sequencing quality was analyzed using the FastQC script.
For 4sU-seq, reads were mapped to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters –g 1 –no-coverage-search.
Reads mapping to ribosomal rRNA (defined by UCSCs RepeatMasked table filtered for rRNA) were removed and all samples were normalized to the sample with the smallest number of mapped reads.
Bedgraph files were generated with "bedtools genomecov" function (Quinlan et al., 2010) after removal of reads falling in exons.
Genome_build: hg19
Supplementary_files_format_and_content: Sequencing-depth normalized .bedgraph files as defined by UCSC: http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1.8

source_name: U2OS MYC-ER cells

growth_protocol: U2OS cells were cultured in DMEM (Thermo Scientific) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich). U2OS MYC-ER were cultured as previously described (Liu L et al). All cell lines were routinely tested for mycoplasma contamination.

extract_protocol:
RNA was extracted, 4sU-RNA was enriched as previously described (Baluapuri et al., 2019).
Libraries were then prepared as previously described (Baluapuri et al., 2019).
RNA was extracted, 4sU-RNA was enriched as previously described (Baluapuri et al., 2019).
Libraries were then prepared as previously described (Baluapuri et al., 2019).
4sU-seq

treatment_protocol: BAY-880 was designed and synthesized by Bayer as a NUAK1 tool inhibitor, pladienolide B (PlaB) was purchased from Santa Cruz and flavopiridol (FP) and 4-hydroxytamoxifen (4-OHT) were purchased from Sigma. For RNA-seq, U2OS MYC-ER cells were treated for 4h with 10µM BAY-880 or DMSO as control and MYC-ER was activated for 20h with 100µM 4-OHT or ethanol as control. For 4sU-seq, U2OS cells were treated for 2h with 10µM BAY-880, 1 µM pladienolide B or DMSO, then added 200µM 4sU for 15min (pulse), then washed with PBS and treated in 4sU-free medium for additional 2h (chase). Both RNA-seq and 4sU-seq treatments were stopped by adding Qiazol (Qiagen). For ChIP-seq, U2OS cells were treated for 4h with 10µM BAY-880, 50 nM flavopiridol or DMSO. Treatment was stopped by adding formaldehyde.

tag: treatment (4-oht or etoh)

tag: treatment (bay880, plab, fp or dmso)

value: FP

tag: antibody

value: non


title: Control_rep2

tag: age


title: CKO_rep2

tag: genotype


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_HU_axenic_7d_Rep3_ERCC78B

value: adult

tag: Sex

value: Male

tag: treatment

value: Hydroxyurea

value: deltaIRBIT


title: 4sU_3_4OHT_BAY880_pulse.bam

description:
4sU-labeled RNA
4sU-seq


title: 4sU_3_4OHT_DMSO_pulse.bam

description:
4sU-labeled RNA
4sU-seq

value: DMSO


title: RNA-Seq_76bp_SE_Male_Gut_yw_40d_Rep1_ERCC78B

value: yw


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_HU_axenic_7d_Rep2_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_yw_40d_Rep2_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_HU_7d_Rep3_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_HU_7d_Rep2_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_HU_axenic_7d_Rep1_ERCC78B


title: ChIPRxseq_phosphoPNUTS_input_spike.normalized.bam

data_processing:
For ChIP-Rxseq, readsFor ChIP-Rx-seq, reads were mapped independently to the human hg19 and murine mm10 (spike-in) genome with bowtie v1.2 (Langmead et al., 2009) and default settings and a spike-in normalization factor was calculated by dividing the number of mapped reads of the spike-in of the smallest sample by the number of mapped reads of the spike-in for each sample. For each sample, this factor was multiplied by the number of reads that map to the human genome and all bam files were adjusted to this read count.  Input samples for all biological conditions were sequenced to a lower depth and combined after mapping.
Bedgraph files were generated with "bedtools genomecov" function (Quinlan et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Spike-in normalized .bedgraph files as defined by UCSC: http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1.8

extract_protocol:
ChIP-Rxseq sample preparation was performed as previously described (Herold et al., 2019). Samples were spiked with 10% NIH3T3 cells.
Libraries were prepared as previously described (Herold et al., 2019).

value: pPNUTS (see Methods)


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_HU_7d_Rep1_ERCC78A

value: 7 day


title: 4sU_3_EtOH_FP_pulse.bam

description:
4sU-labeled RNA
4sU-seq

value: EtOH


title: 4sU_3_EtOH_BAY880_pulse.bam

description:
4sU-labeled RNA
4sU-seq


title: 4sU_3_EtOH_DMSO_pulse.bam

description:
4sU-labeled RNA
4sU-seq


title: Control_rep1

tag: strain


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_axenic_7d_Rep3_ERCC78A

value: axenic

value: deltaIRBIT+gene


title: 4sU_2_4OHT_DMSO_rep3.bam

description: 4sU-labeled RNA

data_processing:
Library strategy: 4sU-seq
For ChIP-Rxseq, readsFor ChIP-Rx-seq, reads were mapped independently to the human hg19 and murine mm10 (spike-in) genome with bowtie v1.2 (Langmead et al., 2009) and default settings and a spike-in normalization factor was calculated by dividing the number of mapped reads of the spike-in of the smallest sample by the number of mapped reads of the spike-in for each sample. For each sample, this factor was multiplied by the number of reads that map to the human genome and all bam files were adjusted to this read count.  Input samples for all biological conditions were sequenced to a lower depth and combined after mapping.
Bedgraph files were generated with "bedtools genomecov" function (Quinlan et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Spike-in normalized .bedgraph files as defined by UCSC: http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1.8

extract_protocol:
RNA was extracted, 4sU-RNA was enriched as previously described (Baluapuri et al., 2019).
Libraries were then prepared as previously described (Baluapuri et al., 2019).


title: ChIPRxseq_phosphoPNUTS.spike.normalized.bam


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_axenic_40d_Rep2_ERCC78A

value: midgut

value: 40 day


title: 4sU_2_4OHT_DMSO_rep1.bam

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_axenic_7d_Rep1_ERCC78A


title: 4sU_2_4OHT_DMSO_pulse.bam

description: 4sU-labeled RNA


title: 4sU_3_4OHT_NVP2_pulse.bam

description:
4sU-labeled RNA
4sU-seq


title: 4sU_2_EtOH_DMSO_rep3.bam

description: 4sU-labeled RNA


title: 4sU_2_EtOH_DMSO_rep2.bam

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_7d_Rep3_ERCC78A

value: normal


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_7d_Rep1_ERCC78A


title: 4sU_2_EtOH_DMSO_rep1.bam

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_40d_Rep3_ERCC78B


title: 4sU_2_EtOH_DMSO_pulse.bam

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_40d_Rep2_ERCC78B


title: 4sU_2_4OHT_BAY880_rep2.bam

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_axenic_7d_Rep2_ERCC78A


title: 4sU_2_4OHT_BAY880_rep3.bam

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_axenic_7d_Rep3_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_axenic_7d_Rep2_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_40d_Rep1_ERCC78B


title: 4sU_2_4OHT_BAY880_rep1.bam

description: 4sU-labeled RNA


title: 4sU_2_4OHT_BAY880_pulse.bam

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_axenic_40d_Rep1_ERCC78A


title: 4sU_2_4OHT_DMSO_rep2.bam

description: 4sU-labeled RNA


title: 4sU_2_EtOH_BAY880_rep3.bam

description: 4sU-labeled RNA


title: 4sU_2_EtOH_BAY880_rep2.bam

description: 4sU-labeled RNA


title: 4sU_2_EtOH_BAY880_rep1.bam

description: 4sU-labeled RNA


title: ChIPRxseq_RNAPII_4OHT_DMSO

description: ChIP-Rxseq

value: RNAPII (A10,Santa Cruz, sc-17798)


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_7d_Rep2_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_axenic_40d_Rep1_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_7d_Rep3_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_axenic_40d_Rep2_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_axenic_7d_Rep1_ERCC78A


title: ChIPRxseq_RNAPII_4OHT_BAY880

description: ChIP-Rxseq


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_7d_Rep1_ERCC78B


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_40d_Rep3_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_40d_Rep1_ERCC78A


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_gene_7d_Rep2_ERCC78A


title: RNA-Seq_76bp_SE_Female_Gut_yw_HU_axenic_40d_Rep1_ERCC78B

value: Female


title: RNA-Seq_76bp_SE_Female_Gut_yw_HU_40d_Rep3_ERCC78A


title: 4sU_2_EtOH_BAY880_pulse.bam

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Female_Gut_yw_HU_40d_Rep1_ERCC78A


title: RNA-Seq_76bp_SE_Female_Gut_yw_HU_40d_Rep2_ERCC78A


title: 9C

city: Manhattan

first: Aliza

last: Rubenstein

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Basecalling performed using Illumina RTA v2.
bcl2fastq used to convert BCL files to fastq files
Quality control using FastQC v0.11.05
Quality control using Picard 2.7.1 RNASeqMetrics STRAND_SPECIFICITY=NONE
Reads were aligned using STAR v2.5.2b
Gene counts were quantified using featureCounts v1.5.0 with the following settings: -M --fraction -g gene_id
Genome_build: hg38
Supplementary_files_format_and_content: space-delimited matrix of counts per transcript per sample (rows represent transcripts, columns represent samples).  First six columns are transcript information (geneid, chromosome, start, end, strand, length).

source_name: vastus lateralis muscle

extract_protocol:
TriZol extraction (TRI Reagent, Molecular Research Center, Cincinnati, OH)
The SMARTer® Ultra® Low Input RNA kit (Takara, Mountain View, CA) was used to generate cDNA from 9 ng of total RNA. Using the ThruPLEX® DNA-seq kit (Takara), 1-2 ng of double-stranded cDNA was end-repaired and A-tailed to prepare for adaptor ligation. Indexed adaptors were ligated to sample DNA, and the adaptor-ligated DNA library quality was assessed by measuring nanomolar concentration and the fragment size in base pairs. Sequencing was performed on the NextSeq 500 unit (Illumina, San Diego, CA)

tag: fiber-type

value: Type IIa

value: old

value: untrained

tag: subjectid

value: basal


title: 8A

value: Type I


title: 9A


title: 8C


title: 7A


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_axenic_40d_Rep1_ERCC78B

tag: developmental stage

value: adult

tag: growth condition

value: dGuo


title: tub-opa_NC13_12_19081201

value: w; tub>opa/+;His2Av-GFP/+

tag: timepoint

value: F

tag: experiment


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_axenic_40d_Rep3_ERCC78B

tag: tissue

value: yw

tag: replicate number

tag: ercc spikein


title: ChIPRxseq_RNAPII_EtOH_DMSO

description: ChIP-Rxseq

tag: treatment (4-oht or etoh)

value: EtOH

value: DMSO


title: OE7-2

city: Shanghai

first: zhenjun

last: li

address: Beidi rd 2901

institute: Shanghai academy of agricultural sciences

data_processing:
The raw reads were first processed through in-house Perl scripts, which removed reads containing the sequencing adapters, reads with over 10% ambiguous ‘N’ nucleotides, and reads with over 50% of bases with a quality score lower than 5.
Gene function was annotated using NCBI BLAST 2.2.28+ with an E-value threshold of 10-5 for the NCBI non-redundant protein (Nr) database, the NCBI non-redundant nucleotide sequences database (Nt), the Swiss-Prot protein database, and the Clusters of Orthologous Groups of proteins database (COG), and the Kyoto Encyclopedia of Genes and Genomes database (KEGG).
The FPKM method (Fragments Per kb per Million fragments) was used to calculate the transcript expression levels
MARS (MA-plot-based method with Random Sampling model) from DEGseq package was used for identifying differentially expressed genes (Wang et al., 2010)
The method of Audic and Claverie was applied to determine the P-value, which corresponds to the differential transcript expression. P-value ≤0.001 and the absolute value of log2Ratio ≥1 were used as the threshold to judge the significance of differential gene expression.
Supplementary_files_format_and_content: Excel files include FPKM values and annotations for each gene and differentially expressed genes between two samples

organism: Solanum lycopersicum

source_name: Aerial part

growth_protocol: All seedlings were grown on soil/vermiculite (3:1, v/v) at 28 °C in an environment controlled chamber at a light intensity of 150 μmol photons m−2 s−1 and a 16/8 h light/dark photoperiod.

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen Life Technologies, USA) following the manufacturer’s instructions and was treated with RNase-free DNase I (Takara, Japan) to avoid genomic DNA contamination. For each sample, RNA was extracted from 10 randomly selected seedlings (as one biological replicate). Two replicates were conducted for RNA extraction for each genotype.
The poly (A) mRNA was isolated from the total RNA samples using oligo (dT) attached magnetic beads (Invitrogen) and was fragmented into short pieces using divalent cations under elevated temperature. First- and second-strand cDNA was generated using mRNA-Seq sample preparation (Illumina Inc., San Diego, CA, USA) and random hexamer primers. The double-stranded cDNA fragments were subjected to end repair, and sequencing adapters were ligated to both ends. The final cDNA library was selectively enriched by PCR and purified using the AMPure XP system (Beckman Coulter, Beverly, USA).

value: One-week-old seedlings

tag: number of plants

value: 10 seedlings

tag: SlMYB14-overexpressing line


title: tub-opa_NC13_12_19081205


title: 6C

tag: age


title: tub-opa_NC13_12_19081204


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_axenic_40d_Rep2_ERCC78B

value: midgut

value: 40 day

value: axenic

tag: genotype


title: OE7-1


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_7d_Rep2_ERCC78B

value: 7 day

value: normal

tag: Sex

value: Female


title: tub-opa_NC13_12_19081202


title: ChIPRxseq_input

description: ChIP-Rxseq

tag: treatment (bay880, plab, fp or dmso)

tag: antibody


title: ChIPRxseq_RNAPII_EtOH_BAY880

description: ChIP-Rxseq

value: RNAPII (A10,Santa Cruz, sc-17798)


title: OE5-2


title: 5C

tag: fiber-type

value: Type IIa

value: old

value: untrained

value: basal


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_7d_Rep1_ERCC78B

value: adult

tag: treatment

value: dGuo


title: 7C

tag: subjectid


title: OE5-1

tag: developmental stage


title: tub-opa_NC13_12_19081104

value: w; tub>opa/+;His2Av-GFP/+

tag: timepoint

value: M


title: 6A

value: Type I


title: ZS4-2

value: One-week-old seedlings

value: 10 seedlings

tag: wild-type


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_40d_Rep3_ERCC78A

tag: tissue

value: midgut

value: 40 day

tag: growth condition

value: yw


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_7d_Rep3_ERCC78B

value: 7 day

value: normal

tag: replicate number

tag: ercc spikein


title: WT_NC13_12_19081208

value: w; His2Av-GFP

value: F

tag: experiment


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_40d_Rep2_ERCC78A

value: Female


title: WT_NC13_12_19081207


title: 3C

value: Type IIa

value: old

value: untrained


title: RNA-Seq_76bp_SE_Female_Gut_yw_dAdo_axenic_7d_Rep3_ERCC78A

value: adult

value: axenic

value: dAdo


title: WT_NC13_12_19081103

value: M


title: 3A

value: Type I

value: basal


title: 4C


title: 4A


title: RNA-Seq_76bp_SE_Female_Gut_yw_dGuo_40d_Rep1_ERCC78A

value: midgut

value: dGuo


title: 5A


title: WT_NC13_12_19081102


title: RNA-Seq_76bp_SE_Female_Gut_yw_dAdo_axenic_7d_Rep2_ERCC78A

value: yw


title: RNA-Seq_76bp_SE_Female_Gut_yw_dAdo_axenic_7d_Rep1_ERCC78A

value: 7 day


title: WT_NC13_12_19081101


title: 2C


title: WT_NC13_12_19081206


title: 2A


title: RNA-Seq_76bp_SE_Female_Gut_yw_dAdo_7d_Rep3_ERCC78B

value: normal


title: RNA-Seq_76bp_SE_Female_Gut_yw_dAdo_7d_Rep2_ERCC78B


title: 1C


title: het_NC14_72_17111504

value: w; opa[IIP32]/His2Av-GFP


title: 1A


title: ZS4-1

value: One-week-old seedlings

tag: number of plants

value: 10 seedlings


title: RNAseq_4OHT_BY880_rep3

description: processed data file: RNAseq_log2CPM.txt

data_processing:
Fastq files were generated using Illumina's base calling software GenerateFASTQ v1.1.0.64 and overall sequencing quality was analyzed using the FastQC script.
4sU-seq:
Reads were mapped to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters –g 1 –no-coverage-search.
Reads mapping to ribosomal rRNA (defined by UCSCs RepeatMasked table filtered for rRNA) were removed and all samples were normalized to the sample with the smallest number of mapped reads.
Bedgraph files were generated with "bedtools genomecov" function (Quinlan et al., 2010) after removal of reads falling in exons.
ChIP-seq:
Reads were mapped to the human genome (hg19) with bowtie v1.2 (Langmead et al., 2009) and default settings. Input samples for all biological conditions (DMSO, BAY-880, FP) were sequenced to a lower depth and combined after mapping.
Duplicates were removed using "samtools rmdup" tool (Li et al., 2009) and samples were normalized to the sample with the smallest number of reads by randomly picking reads.
Bedgraph files were generated with "bedtools genomecov" function (Quinlan et al., 2010).
RNA-seq:
Reads were aligned to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters –g 1 –n 1 --library-type fr-firststrand –no-coverage-search and samples were normalized to the number of mapped reads in the smallest sample.
For gene expression analysis, reads per gene (Ensembl gene database) were counted with the “summarizeOverlaps” function from the R package “GenomicAlignments” using the “union”-mode and non- or weakly expressed genes were removed (mean read count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: *.bedgraph: Sequencing-depth normalized .bedgraph files as defined by UCSC: http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1.8
Supplementary_files_format_and_content: RNAseq_log2CPM.txt: Sequencing-depth normalized and log2-transformed count matrix (CPM=counts per million mapped reads) containing all samples.

extract_protocol:
RNA extraction was performed with the miRNeasy Mini kit (Qiagen) according to manufacturer’s instruction and using in-column DNase digestion.
RNA quality was assessed employing a Fragment Analyzer (Agilent) and directional libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions.

tag: cell line

value: U2OS MYC-ER

tag: treatment (4-oht or etoh)


title: RNAseq_4OHT_BY880_rep2

description: processed data file: RNAseq_log2CPM.txt


title: tub-opa_NC13_12_19081105

value: w; tub>opa/+;His2Av-GFP/+

tag: Sex


title: RNAseq_4OHT_BY880_rep1

description: processed data file: RNAseq_log2CPM.txt

tag: treatment (bay880, plab, fp or dmso)


title: RNA-Seq_76bp_SE_Female_Gut_yw_axenic_7d_Rep1_ERCC78B

tag: age

value: Female

tag: genotype


title: RNA-Seq_76bp_SE_Female_Gut_yw_axenic_7d_Rep2_ERCC78B

value: adult

tag: treatment


title: RNAseq_EtOH_BY880_rep3

description: processed data file: RNAseq_log2CPM.txt

value: EtOH


title: RNA-Seq_76bp_SE_Female_Gut_yw_axenic_50d_Rep2_ERCC78A

value: 50 day

value: axenic


title: RNA-Seq_76bp_SE_Female_Gut_yw_axenic_50d_Rep1_ERCC78A


title: RNA-Seq_76bp_SE_Female_Gut_yw_axenic_40d_Rep1_ERCC78A

value: 40 day


title: Opa_ChIP_R3

value: w; opa-3xmyc

value: blastoderms


title: RNA-Seq_76bp_SE_Female_Gut_yw_axenic_40d_Rep2_ERCC78A

value: midgut


title: RNA-Seq_76bp_SE_Female_Gut_yw_dAdo_7d_Rep1_ERCC78B

value: dAdo

value: yw


title: Opa_ChIP_R2


title: Opa_ChIP_R1


title: RNAseq_EtOH_BY880_rep1

description: processed data file: RNAseq_log2CPM.txt


title: RNA-Seq_76bp_SE_Female_Gut_yw_axenic_7d_Rep3_ERCC78B

value: 7 day


title: RNAseq_EtOH_BY880_rep2

description: processed data file: RNAseq_log2CPM.txt


title: RNAseq_EtOH_DMSO_rep3

description: processed data file: RNAseq_log2CPM.txt

value: DMSO


title: RNAseq_4OHT_DMSO_rep1

description: processed data file: RNAseq_log2CPM.txt


title: RNA-Seq_76bp_SE_Female_Gut_yw_7d_Rep3_ERCC78A

value: normal


title: RNA-Seq_76bp_SE_Female_Gut_yw_7d_Rep2_ERCC78A


title: w_ChIP_R3

value: w


title: RNAseq_EtOH_DMSO_rep2

description: processed data file: RNAseq_log2CPM.txt

value: U2OS MYC-ER


title: RNAseq_4OHT_DMSO_rep2

description: processed data file: RNAseq_log2CPM.txt


title: RNA-Seq_76bp_SE_Female_Gut_yw_7d_Rep1_ERCC78A


title: w_ChIP_R2


title: ChIPseq_PNUTS_BAY880

source_name: U2OS cells

extract_protocol:
ChIP-Seq sample preparation was performed as previously described (Herold et al., 2019).
Libraries were prepared as previously described (Herold et al., 2019).

tag: chip antibody

value: PNUTS (Bethyl, A300-439A-T)


title: RNA-Seq_76bp_SE_Female_Gut_yw_40d_Rep3_ERCC78B

tag: developmental stage

value: Female


title: RNA-Seq_76bp_SE_Male_Gut_IRBIT_40d_Rep2_ERCC78A

value: adult

value: Male

value: deltaIRBIT


title: w_ChIP_R1

tag: timepoint


title: RNA-Seq_76bp_SE_Female_Gut_yw_40d_Rep1_ERCC78B


title: RNA-Seq_76bp_SE_Female_Gut_yw_40d_Rep2_ERCC78B


title: Putamen, MSA10-2

city: Copenhagen NW

first: Rasmus

last: Rydbirk

state: Please Select

address: Nielsine Nielsens Vej 6B, stair 11B, 2nd Floor

department: Department of Neurology

country: Denmark

institute: Bispebjerg-Frederiksberg Hospital

data_processing:
Data were trimmed using Trimmomatic v. 0.38 in paired-end mode (PE) including clipping Illumina adapter sequences (ILLUMINACLIP) using the following specifications: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed data were aligned to GRCh38 release 94, thereby creating BAM files, using STAR v. 2.5.3a with genome index created using --sjdbOverhang 100
A count table was produced for aligned data using summarizeOverlaps from GenomicAlignments in R v. 3.5.0 using the following specifications: mode="Union", singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE
Genome_build: GRCh38 rel. 94
Supplementary_files_format_and_content: A tab-delimited text file containing raw gene counts per sample.

source_name: Putamen

extract_protocol:
Whole brains were slabbed and frozen at -80 °C. RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen; #80224).
300 ng RNA per sample was used as inpt for library preparation using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold rRNA Removal Kit (Illumina; #RS-122-2303).

tag: disease state

value: multiple system atrophy

value: brain (putamen)

tag: pmi

tag: rin


title: Putamen, MSA9-2

tag: tissue


title: Putamen, MSA10-1


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_HU_axenic_7d_Rep2_ERCC78B

tag: growth condition

value: axenic

value: Hydroxyurea

tag: replicate number

tag: ercc spikein


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_HU_axenic_7d_Rep3_ERCC78B

value: midgut


title: 4sU_PlaB_rep3

description: 4sU-labeled RNA

data_processing:
Library strategy: 4sU-seq
Fastq files were generated using Illumina's base calling software GenerateFASTQ v1.1.0.64 and overall sequencing quality was analyzed using the FastQC script.
4sU-seq:
Reads were mapped to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters –g 1 –no-coverage-search.
Reads mapping to ribosomal rRNA (defined by UCSCs RepeatMasked table filtered for rRNA) were removed and all samples were normalized to the sample with the smallest number of mapped reads.
Bedgraph files were generated with "bedtools genomecov" function (Quinlan et al., 2010) after removal of reads falling in exons.
ChIP-seq:
Reads were mapped to the human genome (hg19) with bowtie v1.2 (Langmead et al., 2009) and default settings. Input samples for all biological conditions (DMSO, BAY-880, FP) were sequenced to a lower depth and combined after mapping.
Duplicates were removed using "samtools rmdup" tool (Li et al., 2009) and samples were normalized to the sample with the smallest number of reads by randomly picking reads.
Bedgraph files were generated with "bedtools genomecov" function (Quinlan et al., 2010).
RNA-seq:
Reads were aligned to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters –g 1 –n 1 --library-type fr-firststrand –no-coverage-search and samples were normalized to the number of mapped reads in the smallest sample.
For gene expression analysis, reads per gene (Ensembl gene database) were counted with the “summarizeOverlaps” function from the R package “GenomicAlignments” using the “union”-mode and non- or weakly expressed genes were removed (mean read count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: *.bedgraph: Sequencing-depth normalized .bedgraph files as defined by UCSC: http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1.8
Supplementary_files_format_and_content: RNAseq_log2CPM.txt: Sequencing-depth normalized and log2-transformed count matrix (CPM=counts per million mapped reads) containing all samples.

tag: cell line

value: PlaB


title: Putamen, MSA9-1


title: 4sU_PlaB_rep1

description: 4sU-labeled RNA

tag: treatment (4-oht or etoh)


title: 4sU_PlaB_rep2

description: 4sU-labeled RNA


title: ChIPseq_PNUTS_FP

value: FP


title: 4sU_BAY880_rep3

description: 4sU-labeled RNA


title: Putamen, MSA8-1

tag: Sex


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_HU_7d_Rep3_ERCC78A

value: 7 day


title: Putamen, MSA8-2


title: ChIPseq_PNUTS_DMSO

tag: treatment (bay880, plab, fp or dmso)

value: DMSO


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_HU_7d_Rep2_ERCC78A

tag: age

value: normal


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_HU_axenic_7d_Rep1_ERCC78B

tag: genotype


title: Putamen, MSA7-2


title: 4sU_BAY880_rep2

description: 4sU-labeled RNA


title: 4sU_BAY880_rep1

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_HU_7d_Rep1_ERCC78A

tag: treatment


title: ChIPseq_input

value: BAY880, FP, DMSO

tag: chip antibody


title: Putamen, MSA7-1


title: 4sU_DMSO_pulse

description: 4sU-labeled RNA


title: J

city: guangzhou

first: yuling

last: huang

address: No. 250, Changgang East Road, Haizhu District, Guangzhou

institute: Center for Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University

description: 30 sperm specimens, to help pregnant patients donate;

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner. Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: In order to avoid technical variability and evaluate methylation differences between samples, the log2-ratio getting from raw data value should be normalized. We perform Median-centering, quantile normalization and linear smoothing in this analysis process by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample, it can be used to further peak-finding analysis. so, 'the normalized log2-ratio data' correspond to 'MeDIP/input' log2-ratio data.

source_name: sperm

label_protocol:
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
The immunoprecipitated DNA was eluted and purified by phenol chloroform extraction and ethanol precipitation. The total input and immunoprecipitated DNA were labeled with Cy3- and Cy5-labeled random 9-mers, respectively, and hybridized to NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Microarray, which is a multiplex slide with 3 identical arrays per slide, and each array includes 27,728 CpG Islands regions (from about - 2440bp to +610bp of the TSSs) totally covered by ~720,000 probes.

extract_protocol:
Oocyte collection and DNA extraction   Oocyte of patients and ovulation volunteers who assisted in pregnancy treatment in hospitals of Guangyi Hospital from January 2010 to December 2015 were collected. All the volunteers age ranged from 22-40 years.    Under a stereomicroscope, individual eggs were placed in Tyrode's solution (Sage) using a stripping egg (about 140 μm in diameter, Cook). After the disappearance of the zona pellucida observed under a stereomicroscope, (About 0.1 mL / drop), the oocytes were placed in a buffer containing 2 μL of lysis buffer A (10 mM Tris-HCl, 1 mM EDTA, 10% SDS, 1% proteinase K, pH 8.0). After the cells were completely lysed, the cells were placed in a water bath at 37 ° C for about 1 hour to fully lyse the cells. Then the cell were centrifuged at 10,000 rpm for 2 minutes and stored at -80 ° C until use. 2 μl of the last wash droplet were took for PCR reaction blank control.    Sperm collection and DNA extraction   Sperm of patients who accepted IVF treatment in Guangzhou Medical Third Affiliated Hospital from January 2010 to December 2015 were collected. The patient's husband age ranged from 22-40 years, secondary to infertility without any male factor in patients with her husband's semen. Density gradient centrifugation and upstream separation were applied for collection of sperm. The differential lysis method [89] was used, and DNA was extracted by the kit procedure in combination with reagents using Genomic DNA urification Kit (Promega).    2PN and 4 cell embryos collected and DNA extraction    Methods of ICSI: ICSI fertilization was performed on oocytes and spermatozoa from the above sources, and the mature egg was selected to remove the egg droplet to the center of the field of view. Hold the egg with the Holding needle, oocyte was transfer to the clearest state under microinjection needle, the polar body is located at 6,7 o'clock or 11,12 o'clock position, so that the injection of quasi-oocyte was in the middle 3 o'clock position.   The sperm were pushed to the tip of the injection needle, injection needle was placed in the oocyte 3 o'clock vertically through the zona pellucida until sperm was pushed within the cytoplasm of the middle of the egg. After the eggs were injected one by one, they were repeatedly rinsed in a pre-prepared G1.5 Plus Petri dish and placed in 37 ° C, 5% CO2, 5% O2, 90% N2 incubators and cultured in G1.5 Plus droplets separately.   For IVF fertilization, GIVF-plus which has been equilibrated overnight was used to prepare fertilized droplets according to the standard of 0.1 ml per microtube droplet per 3 eggs. Then this fertilized droplets were stored in incubator (37 ° C, 6% CO2) with coverage of mineral oil. Moderate amount of sperm was added to prepared fertilized dish under a microscope. And concentration was adjusted to 1.0 × 10 6 / ml. this sperm droplets were stored in incubator (37 ° C, 6% CO2) to wait for fertilization.  After 3-4 hour’s pre-incubation, eggs were transferred to the fertilized dish. 2-3 eggs were added to one semen drop and this fertilized drop was returned to the embryo box for overnight cultivation.  2PN Collection: Prokaryotic cells were observed at 16-20 hours after ICSI or IVF under inverted microscope and fertilization information was recorded. Two circular structures with nucleolar precursors in the cytoplasm were the male and female pronuclei (2PN). Two polar bodies (2PB) can be seen in the perivitelline space when normal fertilization occured. 12 prokaryotic and ICSI-derived prokaryotes from 2PN-derived IVF will be collected to extract DNA. DNA extraction method was identical to oocyte genomic DNA extraction method.  2 prokaryotic embryos were cotinue to culture to D2 at 16-20 hours after ICSI or IVF. And 5 cells which had 4 cells, uniform blastomere size and lower fragments rate (less than 5%) were used in present study. DNA extraction method was identical to oocyte genomic DNA extraction method.     D3 embryo collection and DNA extraction  After two years of successful transplant, donated embryos were stored via vitrified cryopreservation method. After thawing, there were 7-9 available embryos which had uniform size and lower cell debris rate (less than 20%). And 5 of them were used in present study. DNA extraction method was identical to oocyte genomic DNA extraction method.    morulae collection and DNA extraction  The thawed D3 embryos were continue to cultured in 37 °C, 5% CO2, 5% O2, 90% N2 incubators. After overnight culturing, 6 mulberry embryos which were completely fused and with less than 20% fragmentation were used in present study. DNA extraction method was identical to oocyte genomic DNA extraction method.    Collection of blastocyst ICM and TE and their DNA extraction  The above thawed D3 embryos were cultured to D5 embryos, and high quality blastocysts were screened for this study. Screening of D5 high-quality blastocysts was based on Garden's grading standards: stage of inner cell mass and trophoblast were A or B blastocysts. Separation of ICM and trophoblast blastocyst was performed via mechanical methods, the capillary pipette segregate ICM and trophoblast blastocyst under stereomicroscope bluntly. The isolated ICM and TE were washed for several times in PBS and then these isolated ICM and TE were extracted with reference to the DNA extraction method of the oocyte.
Genomic DNA were extracted according to the manufacturer’s instructions and sonicated to random fragments in size about 200-1000 bp. Immunoprecipitation of methylated DNA was performed using Biomag TM magnetic beads coupled mouse monoclonal antibody against 5-methylcytidine.

tag: fraction

value: immunoprecipitated DNA

tag: cell type

value: sperm

value: input DNA


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_axenic_7d_Rep3_ERCC78A

tag: developmental stage

value: adult

value: Female

value: deltaIRBIT+gene


title: Putamen, MSA6-2

description: Over 20% alignment to mm10

tag: disease state

value: multiple system atrophy

value: Male

tag: pmi


title: Putamen, MSA6-1

description: Over 20% alignment to mm10

tag: tissue

value: brain (putamen)

tag: rin


title: 4sU_DMSO_rep3

description: 4sU-labeled RNA


title: 4sU_DMSO_rep2

description: 4sU-labeled RNA


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_axenic_7d_Rep2_ERCC78A

tag: growth condition

value: axenic

tag: replicate number


title: Putamen, MSA5-2


title: 4sU_DMSO_rep1

description: 4sU-labeled RNA

tag: cell line


title: Putamen, MSA5-1


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_axenic_40d_Rep2_ERCC78A

value: midgut

value: 40 day

tag: ercc spikein


title: C4-2b enz resistant 3

city: Seoul

first: Kyoung-Hwa

last: Lee

address: 101 Daehak ro

department: Urology

country: South Korea

institute: Seoul National University Hospital

description: prostatic carcinoma

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include EdgeR-normalized values for each sample.

source_name: enzalutamide resistant C4-2b

growth_protocol: Parental and enzalutamide resistant C4-2b cells were cultured in RPMI-1640 medium at 37 °C in 5% CO2, which was supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: parental cell line

value: bone-metastatic LNCaP-derivative


title: Putamen, MSA4-1

tag: Sex


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_axenic_40d_Rep1_ERCC78A

tag: age


title: C4-2b enz resistant 2

description: prostatic carcinoma


title: Putamen, MSA4-2


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_axenic_7d_Rep1_ERCC78A

value: 7 day

tag: genotype


title: H

description: The pregnant D3 embryos were given up for more than two years after the pregnancy was promoted. After thawing, the seeds were further cultured to 5 D5 or D6 high quality blastocysts, and TE cells were isolated by mechanical method.

source_name: Blastocyst trophoblast

growth_protocol: Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice

value: Blastocyst trophoblast


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_7d_Rep3_ERCC78A

value: normal

tag: treatment


title: C

description: 8 cell cleavage stage embryos: Patients who underwent ART, gave birth to a successful D3 embryo for more than two years, and signed an informed consent form for scientific research, 4 pieces.

source_name: 8 cell cleavage stage embryo

growth_protocol: After two years of successful transplant, donated embryos were stored via vitrified cryopreservation method. After thawing, there were 7-9 available embryos which had uniform size and lower cell debris rate (less than 20%). And 5 of them were used in present study. DNA extraction method was identical to oocyte genomic DNA extraction method.

value: 8 cell cleavage stage embryo