title: Human_fetal_da_cell_1_RNASeq

source_name: Immortalized fetal DA cell rep 2


title: F1_Control4_SGM7

status: Public on Apr 14 2020

type: SRA

city: Toronto

first: Stephen

last: Matthews

state: Ontario

address: 1 King's College Circle

country: Canada

institute: University of Toronto

library_source: transcriptomic

data_processing:
Sequenced reads were aligned to cavPor3 genome assembly using TOPHAT2 and default settings
Gene read counts were generated using Genomic Alignemnts (version 1.6.3) and outliers removed using Cook's distance with default cutoffs.
Count data were normalized by residuals using RUVSeq (version 3.12.1)
Differential gene expression was assessed using EdgeR's (version 3.12.1) genral linear model likelihood ratio test and FDR-corrected p< 0.05 was considered significant.
Bisulfite treated DNA Seq reads were trimmed using Trimmomatic-0.32, then aligned to the guinea pig genome (cavPor3) using bsmap-2.74 v0.12.5. Picard-tools-1.93 was used to remove duplicates. Methylation levels were determined for individual CpG sites using bsmap-2.74 with a minimal coverage of 10 reads.
Changes in methylation for 100bp windows (50bp apart) and individual CpGs were detected using the calculateDiffMeth() function from MethylKit (v.1.4.0) in R (version 3.2.3). Data were annotated using Homer v4.6 with the annotatePeaks script and CavPor3 genome.
Genome_build: cavPor3
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample- EdgeR output, Methylkit output 100bp methylatio output and single nucleotide resolution (SNR) methylation output

molecule: total RNA

organism: Cavia porcellus

source_name: Hippocampus

extract_protocol:
Brains were removed, and hippocampus was surgically extracted and flash frozen on dry ice. RNA was harvested using AllPrep RNA/DNA/microRNA Universal Extraction Kit (Qiagen Cat#80224).TruSeq RNA Library Preparation Kit V2 (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; Bisulfite DNA libraries were prepared from purified DNA, using the KAPA Library Prep Kit Illumina (Roche) according SeqCap Epi Enrichment System User’s guide

tag: generation

tag: treatment

value: Control

tag: age

value: post natal day 40

tag: Sex

value: Female


title: Las_WL3

city: Yangling

first: yongjun

last: wu

address: No. 22 Xinong Road, Yangling Demonstration Zone

country: China

institute: Northwest A&F University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps. Prior to assembly, the low quality reads (1,reads containing sequencing adaptors; 2,reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed .software CutAdapter, parameters -o 5 -p 100
Read alignment software, software HISAT, version 2.0, parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts. Software StringTie, version 1.3.0, parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: *_expression.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Lactuca sativa

source_name: leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 5 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 60±2 μmol·m–2·s–1 (Las_WL group. low light intensity), 175±2 μmol·m–2·s–1 (Las_ML group, medium light intensity) or 340±2 μmol·m–2·s–1 (Las_SL group, high light intensity).

tag: strain

value: The Hong Kong Glass lettuce

tag: tissue

value: leaf

value: low light intensity

value: 24 days after emergence


title: F1_Control6_SGM9


title: adh1_Ca_coculture_rep4

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

country: USA

institute: The Jackson Laboratory

data_processing:
Basecalls - Illumina native app
Trimming - Illumina native app to trim adapter sequences
Quality Control CLC Genomics Workbench: quality score = 0.05, ambiguous bases = 2, auto adapter trim = NO, trim bases 5' and 3', filter length above =  NO,  filter length below = NO
Alingment to Pseudomonas aeruginosa strain PA14  genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
Extraction of unmapped reads - CLC Workbench
Allignment to Ca SC5314  genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
Reporting - CLC Workbench export raw counts, TPM, CPM and RPKM
Genome_build: UCBPP-PA14 (www.pseudomonas.com)  and SC5314 (www.candidagenome.org , Assembly22)
Supplementary_files_format_and_content: csv including TPM

organism:
Pseudomonas aeruginosa
Candida albicans

source_name: dual species colony biofilm

growth_protocol: C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µ of P. aeruginosa overnight culture from LB was spotted on top. Co-culture colony biofilms were incubated at 30℃ for 16 hours before cells were collected.

extract_protocol:
Cell pellets were dissolved in Trizol and cells were lysed by bead beating. Lysate was phase separated by centrifugation and from the aqueous phase RNA was precipitated by linear acrylimide. Centrifugation collected the RNA into a pellet that was, after supernatent removal, washed with ethanol and resuspended into deionized, nuclease-free water.
RNA was treated with Dnase using the Rneasy MinElute protocol and ribo-depletion using RiboZero (bacteria). Library prep was done as the Illumina TrueSeq Stranded RNAseq.

treatment_protocol: P. aerguinosa was grown on WT and adh1∆/∆ C. albicans. P. aeruginosa and C. albicans were also grown alone.

value: PA14 and CAF2

tag: taxonomy id


title: F1_Control3_SGM5


title: adh1_Ca_coculture_rep3


title: Human_fetal_da_cell_3_RNASeq

city: Nashville

first: Dhivya

last: Sudhan

state: TN

address: 777 Preston Research Building

department: Hematology/Oncology Division

institute: Vanderbilt University

data_processing:
Quality control on raw reads was performed using FastQC.
STAR v2.5.3a used for reads mapping.
FeatureCounts v1.15.2 was used to count the number of mapped reads to each gene.
BiomaRt package was used to map mouse genes to human genes, and only uniquely mapped genes between human and mouse were kept.
Significantly differentially expressed genes with FDR-adjusted p-value≤0.01 and absolute fold-change≥2.0 were detected by DESeq2 (v1.18.1).
Genome Ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package.
Gene set enrichment analysis was performed using the GSEA package.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

organism: Homo sapiens

source_name: Immortalized fetal DA cell rep 1

growth_protocol: Primary human and mouse myometrial cells, as well as PHM1 cells were cultured in DMEM (Corning MT17205CV) supplemented with 10% fetal bovine serum (FBS), 2mM L-Glutamine, 100 U/ml penicillin-streptomycin. hTERT-HM cells were cultured in DMEM-F12 (Gibco 11-039-021) supplemented with 10% FBS and 100 U/ml penicillin-streptomycin. Primary adult aorta cells were cultured in  vascular cell basal medium (ATCC® PCS-100-030™). Fetal aorta and DA cells were cultured in DMEM (Gibco 11965-092) supplemented with 10% FBS and 100 U/ml penicillin-streptomycin.

extract_protocol:
Flash frozen tissues stored in -80oC were homogenized in TRIzolTM reagent (Invitrogen) using a bead homogenizer (Fisherbrand™ Bead Mill 24) for two 20sec cycles at 5000 rpm. Near-confluent cells were lysed using 1mL TRIzolTM reagent. Total RNA was isolated per the Trizol’s manufacturer instructions,  DNase-treated (DNA-free kit, Ambion) and then sent to the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core for quality control and cDNA library preparation. The RNA was analyzed with an Agilent Bioanalyzer 2100, which showed that all samples had an RIN>8.
The coding RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and paired end libraries were generated using the NEBNext Ultra II Directional RNA Library Kit for Illumina (7760).

tag: passage

tag: cell type

value: Immortalized fetal DA cell


title: adh1_Ca_coculture_rep2


title: F1_Control2_SGM4


title: Human_fetal_aorta_cell_1_RNASeq

source_name: Primary fetal aorta cell rep 2

value: Primary fetal aorta cell


title: Las_WL1


title: Las_WL2


title: adh1_Ca_coculture_rep1


title: PAO1_1

city: Atlanta

first: Joanna

middle: B

last: Goldberg

state: Georgia

address: O. Wayne Rollins Research Center, Room 3009 1510 Clifton Road NE

institute: Emory University

data_processing:
RNAseq reads were trimmed using cutadapt v2.3 with a minimum length cutoff of 18bp. The reads were then mapped to PAO1 refseq genome NC_002516.2 using bowtie2 v2.3.5 with end-to-end alignment.  The number of reads mapped to each genomic feature was calculated using HTSeq v11.1 and features with less than 10 mapped reads were discarded
Genome_build: PAO1 refseq genome NC_002516.2
Supplementary_files_format_and_content: .count.txt files contain the number of reads mapped to each genomic feature calculated using HTSeq

organism: Pseudomonas aeruginosa

growth_protocol: Overnight cultures of the P. aeruginosa strains were grown in 3ml MOPS-succinate, cultures were back diluted to an OD600 of 0.01 in 20 ml MOPS-succinate and allowed to grow to exponential phase, shaking at 200 rpm.

extract_protocol:
Cells were lysed by bead beating and RNA was precipitated using chloroform and isopropanol. Pellets were washed with ethanol and quantified using NanoDrop.
mRNA was enriched using Ambion MICROBExpress kit. Enriched mRNA was fragmented using NEBNext Fragmentation Module kit and libraries were prepared using NEBNext Multiplex Small RNA Library Prep kit.

treatment_protocol: 2 ml aliquots from each culture were added directly to 10ml of RNAlater, stored at 4°C for 24 hours, and then transferred to -80°C until samples were processed.

tag: genotype

value: Wild Type

tag: group

value: non-mucoid


title: Con_2

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Control

data_processing:
Each sample produced more than 20M clean reads, that were mapped to the mm9 reference genome using STAR.
Then, Cufflinks was used to generate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) table.
Genome_build: mm9
Supplementary_files_format_and_content: A csv file including FPKM values for all samples.

organism: Mus musculus

source_name: Control

growth_protocol: Normal rearing condition

extract_protocol:
Total liver RNA was extracted using Trizol. mRNA was enriched through Oligo dT Selection.
Library was constructed at BGI following their standard protocol (Library construction + Sequencing (20M reads, BGISeq 50SE)); DNA nanoball synthesis and sequencing on BGISEQ platform

treatment_protocol: Normal rearing condition

value: Liver

value: 8 weeks


title: Las_ML3

value: medium light intensity


title: F1_Beta5_SGM32

value: Beta


title: WT_Ca_coculture_rep5


title: Las_ML2


title: Human_fetal_aorta_cell_2_RNASeq

source_name: Primary fetal aorta cell rep 1


title: F1_Control1_SGM1


title: WT_Ca_coculture_rep4


title: F1_Beta4_SGM35


title: Tsc1_1

description: Liver-specific Tsc1 knockout

source_name: Liver-specific Tsc1 knockout


title: F1_Beta3_SGM6


title: Human_adult_aorta_cell_1_RNASeq

source_name: Primary adult aorta cell rep 3

value: Primary adult aorta cell


title: WT_Ca_coculture_rep3


title: Human_adult_aorta_cell_2_RNASeq

source_name: Primary adult aorta cell rep 2


title: WT_Ca_coculture_rep2


title: Las_SL2

value: high light intensity


title: F1_Beta2_SGM3

value: post natal day 40


title: WT_Ca_coculture_rep1


title: Human_adult_aorta_cell_3_RNASeq

source_name: Primary adult aorta cell rep 1


title: Las_SL1


title: Human_adult_aorta_cell_4_RNASeq

source_name: Primary adult aorta cell rep 4


title: input DNA

status: Public on Apr 13 2020

city: GuangZhou

first: Zhang

middle: Can

last: Feng

address: Graduate school, building 493, 135 xingang west road

institute: Sun Yat-sen University

description: nuclear RNA

data_processing:
Adaptor sequences were trimmed off by Cutadapt (version 2.8).
reads of each sample were aligned to the hg19 reference genomes by using Hisat2 (version 2.2.0) with default parameters
Reads with mapping quality less than 20nt and duplicated reads were removed by Samtools
The remaining reads were converted to normalized BigWig files for genomic visualization using Deeptools (version 3.4.1), with reads coverage for each window of 100 bp was normalized by CPM (Counts Per Million mapped reads).
Peaks called between IP and input samples using MACS2 (version 2.2.4) (Marinov et al., 2014) with the parameters '--nomodel –nolambda'
Genome_build: hg19
Supplementary_files_format_and_content: bed files include call peak against input for each Sample

extract_protocol:
Fragmentary DC1 associated nascent RNA were isolated with Flag beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human Embryonic Kidney

tag: antibody


title: DMSO 2

description: nuclear RNA

value: Flag-beads


title: zeocin 1

description: nuclear RNA

value: zeocin


title: DMSO 1

description: nuclear RNA


title: Las_ML1

value: The Hong Kong Glass lettuce

value: leaf


title: 26PA

city: Taizhou City

first: Dongguo

last: Wang

state: Zhejiang Province

address: 381 Dong Zhongshan Rd of Jiaojiang district

department: Clinical lab medicine

institute: Taizhou Municipal Hospital

data_processing:
The FASTQ sequence data were obtained from the RNA-seq data using Base Calling V 0.11.4.
The low quality reads, including adaptor sequences, sequences with a quality score < 20, and sequences with an N base rate of raw reads > 10% were removed by using Cutadapt V 1.9.1 with TopHat and Ensemble gene annotation.
The expression of mRNAs and lncRNAs were determined and outputted using Cuffquant V 2.2.1.
Genome_build: The clean reads were aligned with the human reference genome, Ensemble GRCh38.p7.

source_name: adjacent normal tissue of rectal adenocarcinoma

extract_protocol:
RNA isolation was conducted by using a Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: rectal adenocarcinoma patient

tag: tissue type


title: 31CA

source_name: rectal adenocarcinoma tissue

value: rectal adenocarcinoma tissue


title: 23PA

value: adjacent normal tissue of rectal adenocarcinoma


title: zeocin 2

description: nuclear RNA


title: 26CA


title: Las_SL3

value: 24 days after emergence


title: adh1_Ca_coculture_rep5

value: PA14 and CAF2


title: RiboSeq_SH2

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description:
ribosome protected RNA
Ribosome Sequencing SH

data_processing:
For all RiboSeq and RNASeq samples, reads were mapped, using default parameters, with HISAT2 [2] to GRCh38, using Ensembl release 84 gtf for transcript definitions . Only primary alignments were retained and reads were removed if they mapped to rRNA, tRNA and pseudogenes according to hg38 RepeatMasker definitions from UCSC.
A full set of transcript and CDS sequences for Ensembl release 84 was then established. Only canonical transcripts (defined as those with the longest CDS for each gene) were retained with their corresponding CDS. Reads were then mapped to the canonical transcriptome with bowtie2 [3], using default parameters.
For RiboSeq, the P-site position of each read was predicted by riboWaltz and confirmed by inspection (reads were shifted 13 bases from the 5’ end). Counts were made by aggregating P-sites overlapping with the CDS and PPKMs (P-sites Per Kilobase Million) were then generated through normalising by CDS length and total counts for the sample. Differential expression was performed between controls and FKBP10 SH duplicates using edgeR [5] on default settings. Transcripts were only kept in the analysis if they had a CPM>1 in both duplicates for either control or FKBP10 SH or both.
For RNASeq, Counts were made by aggregating any reads overlapping with the CDS and RPKMs were then generated through normalising by CDS length and total counts for the sample. Differential expression was performed as with the RiboSeq.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data for RiboSeq samples shows the P-site counts for each CDS which is then normalised to PPKMs (P-sites Per Kilobase Million). For RNASeq, counts and RPKMs are given.

source_name: Lung adeocarcinoma cells control

growth_protocol: Cells were grown to reach 80% confluence, total extracts were treated with RNAse I (Epicentre) 1.65U (0.005U/1ug of RNA), and monosomes were isolated after separation on a sucrose gradient. Gradient 10-50% sucrose was loaded with 80 µg of total RNA or 700-800 µg of total protein.

extract_protocol: Libraries were constructed using standard Illumina protocols

value: A549 pulmonary adenocarcinomic human alveolar basal epithelial cells


title: RiboSeq_SH1


title: RNASeq_Ctrl2

description:
total RNA
RNA Sequencing Control


title: RNASeq_SH1

description:
total RNA
RNA Sequencing SH


title: input DNA, zeocin

description: nuclear RNA


title: RiboSeq_Ctrl2

description:
ribosome protected RNA
Ribosome Sequencing Control


title: RNASeq_Ctrl1

description:
total RNA
RNA Sequencing Control


title: RNASeq_SH2

description:
total RNA
RNA Sequencing SH


title: F1_Beta1_SGM2

value: Female


title: Zika_control_CH223191_nanoliposomes3

city: Boston

first: Francisco

middle: Javier

last: Quintana

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
DGE libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
Reads were first demulitplex using Picard (v.2.17.11) IlluminaBaseCallsToSam; with well indices CCGGCA (F4), CGCACC (F7), CGGACG (F10), CGTCCG (G1), GACGCC (G4), and GCCCAG (G7).
Reads were aligned using GRCm38 Mouse genome with STAR (v2.4.2a) with default parameters
Duplicate reads are marked with Picard UmiAwareMarkDuplicatesWithMateCigar to identify duplicate reads based on UMI sequence and alignment start site.
Gene are then quantified using RSEM v1.2.21 with paired-end option and accessed for quality using RNA-SeQC.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format with gene ID, symbol, and RPKM

source_name: Pups' CNS from ZIKV-infected mothers treated with CH223191-nanoliposomes

extract_protocol:
RNA from pups' CNS was obtained using TRIZOL
Libraries were prepared by the Broad Institute according to the 3' DGE protocol as described (Soumillon et al., bioRxiv 2014)

treatment_protocol: 8-10 weeks old pregnant female SJL mice were intra-peritoneally infected with 10^6 PFUs of Zika BR (BeH815744) on E14 and followed daily. Nanoliposomes were given daily from E13 until birth at 5 mg/kg bodyweight (total volume: 100 µl) also by i.p. route

value: SJL

value: Day of birth

value: CNS


title: Zika_control_CH223191_nanoliposomes2


title: RiboSeq_Ctrl1


title: Zika_control_nanoliposomes4

source_name: Pups' CNS from ZIKV-infected mothers treated with control nanoliposomes


title: Zika_control_nanoliposomes2


title: Zika_control_nanoliposomes3


title: 31PA


title: Zika_control_nanoliposomes1


title: Zika_control_CH223191_nanoliposomes1


title: 23CA


title: LKR10 shMLL4-1-rep1

city: Waltham

first: Ming

last: Tang

state: Massachusetts

address: 21 Hickory Drive, 1

department: Computational biology

institute: Immunitas Therapeutics

data_processing:
raw fastqs were mapped to mm10 using STAR
raw counts were obtained using FeatureCount
bigwig files were generated using deeptools and normalized to RPKM
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (signal track)

source_name: mouse lung cancer cell line

extract_protocol:
Total RNA was prepared from shControl (shLuc) and MLL4-knockdown (shMLL4-1 and shMLL4-3) LKR-10 cells using Trizol reagent (Life Technologies). Briefly, to isolate total RNA from shLUC, shMLL4-1 and shMLL4-3 infected LKR-10 cells, first the cells were selected in 1ug/ml puromycin containing medium and were harvested at 70-80% of confluency. Total RNA was isolated using Trizol reagent (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse lung cancer cell line

tag: cell line


title: LKR10 Control-rep1


title: LKR10 shMLL4-3-rep1


title: LKR10 Control-rep2


title: LKR10 shMLL4-3-rep2


title: P22 nuclear RNA-seq Chd4 cKO 4

city: St. Louis

first: Jared

middle: V

last: Goodman

state: MO

address: 4523 Clayton Ave

institute: Washington University in St. Louis School of Medicine

data_processing: Nuclear RNA-seq sequences were adapter-trimmed using Cutadapt and subjected to quality control using PRINSEQ (v0.20.4) (Schmieder and Edwards, 2011) and aligned to mouse genome GRCm38/mm10 using STAR (v2.5.3a) (Dobin et al., 2013). Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction, known junction saturation, and reads distribution over known gene models with Picard Tools (v2.19.0) (http://broadinstitute.github.io/picard/) , qualimap (v2.2.1) (García-Alcalde et al., 2012), RSeQC (2.6.2) (Wang et al., 2012). RNA-seq reads in features were counted using HTseq (v0.6.1) (Anders et al., 2015). Reads in exons were used to quantify gene abundance in mRNA-seq data. Enhancer RNAs (eRNAs) were identified using bidirectional windows originating from DnaseI-seq peak centers that overlapped with H3K27ac- and H3K4me1-marked enhancers and spanning 2 kb upstream on the Crick (−) strand or 2 kb downstream on the Watson (+) strand. Windows overlapping with known coding regions and lncRNAs (with 1 kb extension from both transcription start site and transcription end site) were excluded from analysis. DESeq2 (v1.26.0) (Love et al., 2014) was used to estimate the change in feature expression between conditions. Features with fewer than ten counts were removed from all analyses.

molecule: nuclear RNA

source_name: Cerebellum

extract_protocol: Total RNA was extracted from nuclei. rRNA was then depleted.

tag: developmental stage

tag: genotype/variation

value: Chd4 cKO

value: Cerebellum


title: P22 nuclear RNA-seq Chd4 cKO 3


title: P22 nuclear RNA-seq Chd4 cKO 2


title: P22 nuclear RNA-seq Ctrl 3

value: control


title: P22 nuclear RNA-seq Chd4 cKO 1


title: P22 nuclear RNA-seq Ctrl 1


title: P22 nuclear RNA-seq Ctrl 2


title: P60 H3K27ac Chd4 cKO 1

library_source: genomic

data_processing: DNaseI-seq and ChIP-seq reads were aligned to mm10 using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012). Conversion of sam to bam files was performed using Samtools (v1.3) (Li et al., 2009). DNaseI-seq reads per kilobase per million (rpkm) was quantified using Deeptools (v2.4.2) bamCoverage with no extension (Ramírez et al., 2016). ChIP-seq rpkm was quantified using Deeptools bamCompare assuming a 300bp fragment size (-e 300) with reads centered (--centerReads) and input subtracted. Signal was then divided by the binsize to generate DNaseI- or ChIP-seq reads per million (rpm). To generate genomic tracks for viewing on the UCSC genome browser, DNaseI-seq biological replicates were concatenated using Samtools then quantified as described above (James Kent et al., 2002). ChIP-seq reads were concatenated using Samtools, then rpkm was quantified using Deeptools bamCoverage assuming a 300bp fragment size (-e 300) with reads centered (--centerReads). Signal was then divided by the binsize to generate DNaseI- or ChIP-seq rpm. DNaseI-seq peaks were called using MACS2 (v2.1.1.20160309) at a q-value of less than 0.01 (-q 0.01) without model building (--nomodel), an extension of 200bp (--extsize 200), and a shift of -100bp (--shift -100) (Zhang et al., 2008). Peaks from control and Chd4 cKO were then merged and called as significantly different using Diffbind (v2.6.6) running DESeq2 (v1.20.0) (Love et al., 2014; Ross-innes et al., 2012). Chd4 ChIP-seq peaks were called using MACS2 (v2.1.1.20160309) using the broad settings (--broad) at a q-value of less than 0.05 (-q 0.05 –-broad-cutoff 0.05) without model building (--nomodel) and an extension of 300bp (--extsize 300). DNaseI- and ChIP-seq signal at DHS was quantified as the average signal among biological replicates in the 1kb around the TSS or center of the DRE.

molecule: genomic DNA

extract_protocol: Protein-DNA complexes were isolated from sonicated lysates.

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: P22 H3K4me1 Chd4 cKO 2

value: H3K4me1 (Active Motif 39297)


title: P60 H3K27ac Ctrl 1


title: P22 H3K4me1 Ctrl 2


title: P22 H3K4me1 Ctrl 1


title: P22 H3K4me1 Chd4 cKO 1


title: P60 H3K27ac Chd4 cKO 2


title: LKR10 shMLL4-1-rep2


title: P60 Input Chd4 cKO

value: none (input)


title: P60 H3K27ac Ctrl 2


title: P60 Input Ctrl


title: Ctcf ChIP-seq Chd4 cKO2

data_processing:
DNaseI-seq and ChIP-seq reads were aligned to mm10 using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012). Conversion of sam to bam files was performed using Samtools (v1.3) (Li et al., 2009). DNaseI-seq reads per kilobase per million (rpkm) was quantified using Deeptools (v2.4.2) bamCoverage with no extension (Ramírez et al., 2016). ChIP-seq rpkm was quantified using Deeptools bamCompare assuming a 300bp fragment size (-e 300) with reads centered (--centerReads) and input subtracted. Signal was then divided by the binsize to generate DNaseI- or ChIP-seq reads per million (rpm). To generate genomic tracks for viewing on the UCSC genome browser, DNaseI-seq biological replicates were concatenated using Samtools then quantified as described above (James Kent et al., 2002). ChIP-seq reads were concatenated using Samtools, then rpkm was quantified using Deeptools bamCoverage assuming a 300bp fragment size (-e 300) with reads centered (--centerReads). Signal was then divided by the binsize to generate DNaseI- or ChIP-seq rpm. DNaseI-seq peaks were called using MACS2 (v2.1.1.20160309) at a q-value of less than 0.01 (-q 0.01) without model building (--nomodel), an extension of 200bp (--extsize 200), and a shift of -100bp (--shift -100) (Zhang et al., 2008). Peaks from control and Chd4 cKO were then merged and called as significantly different using Diffbind (v2.6.6) running DESeq2 (v1.20.0) (Love et al., 2014; Ross-innes et al., 2012). Chd4 ChIP-seq peaks were called using MACS2 (v2.1.1.20160309) using the broad settings (--broad) at a q-value of less than 0.05 (-q 0.05 –-broad-cutoff 0.05) without model building (--nomodel) and an extension of 300bp (--extsize 300). DNaseI- and ChIP-seq signal at DHS was quantified as the average signal among biological replicates in the 1kb around the TSS or center of the DRE.
Genome_build: mm10
Supplementary_files_format_and_content: Txt files represent the output from Diffbind. Bed files represent the MACS2-called DHS sites at or outside of transcription start sites. Bedpe files represent the Hi-C domains and loops called by Arrowhead and HiCCUPS, respectively. Hic files represent the binarized Hi-C matrices from individual replicates or the pooled sum of all replicates.

source_name: Ctcf ChIP-seq Chd4 cKO

value: Ctcf (Millipore 07-729)


title: Ctcf ChIP-seq Chd4 cKO1


title: Ctcf ChIP-seq Ctrl2

source_name: Ctcf ChIP-seq Ctrl


title: Hi-C Chd4 cKO2

data_processing:
HiC-Pro (v2.10.0) was used to generate contact matrices using the mm10 mouse genome as reference (Servant et al., 2015). Valid pairs determined by HiC-Pro was used as input to generate Hi-C contact matrices at 1, 5, 10, 20, 40, 150, 500 kb and 1 million base pair resolutions. addNorm function from Juicer (v1.5.6) was used to perform genome-wide normalization (Durand et al., 2016). Observed over expected (O/E) and Knight-Ruiz (KR)-normalized Hi-C contacts from genomic bins were extracted using juicer-tools (v1.8.9) dump. For visualization of contact matrices in figures S3A and S3E, KR-normalized Hi-C contacts were extracted from genomic bins using juicer-tools (v1.8.9) straw then scaled to the same sequencing depth (Figures S3A, S3E); otherwise, KR-normalized, Observed/Expected Hi-C contacts were extracted from genomic bins using juicer-tools (v1.8.9) dump. Visualization of the Pearson’s matrix was performed using Juicebox (v1.9.8) at 40kb resolution (Durand et al., 2016). The similarity of biological replicates was compared using unnormalized contacts across all chromosomes at 1Mb resolution.
Genome_build: mm10
Supplementary_files_format_and_content: Txt files represent the output from Diffbind. Bed files represent the MACS2-called DHS sites at or outside of transcription start sites. Bedpe files represent the Hi-C domains and loops called by Arrowhead and HiCCUPS, respectively. Hic files represent the binarized Hi-C matrices from individual replicates or the pooled sum of all replicates.

source_name: Hi-C Chd4 cKO

extract_protocol: Nuclei were digested and blunt-end ligated in the presence of a biotinylated nucleotide. Ligation complexes were then isolated from sonicated DNA by streptavidin pull-down.


title: Hi-C Chd4 cKO3


title: Ctcf ChIP-seq Ctrl1


title: Hi-C Ctrl3

source_name: Hi-C Ctrl


title: Hi-C Chd4 cKO1

description: Bonni_181114chd4komboi_NEBNext_Index_19_GTGAAACGAT_S3


title: Hi-C Ctrl1


title: Hi-C Ctrl2


title: Erythroid differentiation S3 Tiled-C replicate 2

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Tiled-C product (DNA)
Enriched 3C library
S3-2
S3_comb_downsampled_2000_iced.matrix
S3_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

data_processing:
CCseqBasic pipeline (https://github.com/Hughes-Genome-Group/CCseqBasicF/releases)
Custom scripts (https://github.com/oudelaar/TiledC)
ICE normalization (Imakaev et al. Nature Methods 2012)
Genome_build: mm9
Supplementary_files_format_and_content: Sparse matrix format (bin1 \t bin2 \t ICE normalized interaction count \n) and bed file for bin number annotation. Processed data files have been down-sampled to be comparable between conditions as decribed in the Methods section of the paper.

source_name: Primary haematopoietic/erythroid progenitor cells

extract_protocol:
Cells were grown, treated and processed as described in the Methods section of the paper.
Tiled-C combines 3C library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

value: Primary erythroid progenitor cells isolated from fetal liver

tag: immunophenotype

value: Lin- CD71:high Ter119:high

tag: regions analyzed

value: alpha-globin


title: Erythroid differentiation S2 Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
S2-2
S2_comb_downsampled_2000_iced.matrix
S2_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

growth_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.

value: Primary haematopoietic/erythroid progenitor cells

value: Lin- CD71:high Ter119:med


title: Erythroid differentiation S3 Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
S3-1
S3_comb_downsampled_2000_iced.matrix
S3_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

treatment_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.


title: Erythroid differentiation S1 Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
S1-2
S1_comb_downsampled_2000_iced.matrix
S1_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

value: Lin- CD71:high Ter119-


title: Erythroid differentiation S2 Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
S2-1
S2_comb_downsampled_2000_iced.matrix
S2_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed


title: Erythroid differentiation S0-medium Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
S0M-2
S0M_comb_downsampled_2000_iced.matrix
S0M_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

value: Lin- CD71:med Ter119-


title: DKO_2

description: Liver-specific Tsc1/Depdc5 DKO

source_name: Liver-specific Tsc1/Depdc5 DKO

value: Liver

tag: age

value: 8 weeks


title: Erythroid differentiation S0-low Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
S0L-2
S0L_comb_downsampled_2000_iced.matrix
S0L_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

tag: strain

value: Lin- CD71- Ter119-


title: Erythroid differentiation S0-low Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
S0L-1
S0L_comb_downsampled_2000_iced.matrix
S0L_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

tag: tissue


title: Erythroid differentiation MPP2 Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
MPP2-2
MPP2_comb_downsampled_2000_iced.matrix
MPP2_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

value: Primary haematopoietic progenitor cells isolated from bone marrow

value: LSK Flt3- CD48+ CD150+


title: Erythroid differentiation MPP2 Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
MPP2-1
MPP2_comb_downsampled_2000_iced.matrix
MPP2_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed


title: Erythroid differentiation MPP3 Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
MPP3-2
MPP3_comb_downsampled_2000_iced.matrix
MPP3_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

value: LSK Flt3- CD48+ CD150-


title: Erythroid differentiation MPP3 Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
MPP3-1
MPP3_comb_downsampled_2000_iced.matrix
MPP3_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed


title: Erythroid differentiation LMPP Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
LMPP-2
LMPP_comb_downsampled_2000_iced.matrix
LMPP_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

value: LSK Flt3+


title: Erythroid differentiation HSPC Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
HSPC-2
HSC_comb_downsampled_2000_iced.matrix
HSC_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

value: LSK Flt3- CD48- CD150+


title: CT1_Control FT

type: RNA

first: Sunita

middle: R

last: Setlur

address: 221 Longwood Avenue

description: Nanostring miRNA V1.5 Assay

hyb_protocol: Following this, the ligated targets were hybridized with capture and reporter probes at 65°C for 18 hours.

scan_protocol: The next day, the hybridized probes were purified on nCounter Prep Station and counted on nCounter Digital Analyzer.

data_processing: The data was analyzed using nSolver. Briefly, miRNA normalization was carried out using the top 100 expressed miRNAs (i.e. top 10% of miRNAs expressed above background) for tissue samples without any background subtraction. A similar strategy was used to normalize the data from plasma samples. The metastatic tumor sample M5 failed the normalization QC and was excluded from further analysis. Similarly, the control plasma sample CS1 was excluded from the analysis.

label: Biotin

source_name: Control tube

label_protocol: Plasma and tissue extracted miRNAs were subjected to nCounter miRNA sample preparation according to the manufacturer’s instructions. Briefly, 100ng and 10ng miRNA from tissue and plasma samples respectively, were ligated with unique oligonucleotide tags (miR-tag).  The label used is a digital molecular barcode in this platform

growth_protocol: Samples were frozen in -80°C freezer prior to extraction

extract_protocol: Norgen’s Animal Tissue RNA Purification Kit and Plasma/Serum RNA Purification Kits, respectively as per manufacturer’s instructions. The samples were subjected to an on-column Dnase digestion step during extraction

treatment_protocol: Tissue samples were placed on dry ice and the tissue was excised for RNA extraction

value: Fallopian tube


title: Erythroid differentiation HSPC Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
HSPC-1
HSC_comb_downsampled_2000_iced.matrix
HSC_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed


title: Double-stranded oligo enrichment, 100K Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
ds-100K-2
ds_100K_5000_iced.matrix
alpha_5000_coordinates.bed

source_name: Primary erythroid cells

value: Primary erythroid cells isolated from phenylhydrazine treated spleen

value: Primary erythroid cells


title: Erythroid differentiation LMPP Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
LMPP-1
LMPP_comb_downsampled_2000_iced.matrix
LMPP_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed


title: Erythroid differentiation S1 Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
S1-1
S1_comb_downsampled_2000_iced.matrix
S1_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

value: Primary erythroid progenitor cells isolated from fetal liver


title: Double-stranded oligo enrichment, 10K Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
ds-10K-3
ds_10K_5000_iced.matrix
alpha_5000_coordinates.bed

value: alpha-globin


title: Double-stranded oligo enrichment, 10K Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
ds-10K-2
ds_10K_5000_iced.matrix
alpha_5000_coordinates.bed


title: Low input 2K Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
2K-1
2K-1_fs_5000_iced.matrix
2K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Low input 2K Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
2K-2
2K-2_fs_5000_iced.matrix
2K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Double-stranded oligo enrichment, 10K Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
ds-10K-1
ds_10K_5000_iced.matrix
alpha_5000_coordinates.bed


title: Double-stranded oligo enrichment, 100K Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
ds-100K-3
ds_100K_5000_iced.matrix
alpha_5000_coordinates.bed


title: Low input 5K Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
5K-3
5K-3_fs_5000_iced.matrix
5K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Low input 2K Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
2K-3
2K-3_fs_5000_iced.matrix
2K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Erythroid differentiation S0-medium Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
S0M-1
S0M_comb_downsampled_2000_iced.matrix
S0M_comb_downsampled_5000_iced.matrix
alpha_2000_coordinates.bed
alpha_5000_coordinates.bed

value: Primary haematopoietic/erythroid progenitor cells


title: Low input 5K Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
5K-1
5K-1_fs_5000_iced.matrix
5K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Low input 5K Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
5K-2
5K-2_fs_5000_iced.matrix
5K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Low input 10K Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
10K-3
10K-3_fs_5000_iced.matrix
10K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Dabo1_37_rep1

city: Hudidnge

first: Wenbo

last: Dong

state: Sweden

address: Hälsovägen 7C   Neohuset

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description:
Processed data files:
Dabo1_37_signal_normalized.bar
Dabo1_37_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the forward and reverse (R) strands of pombe genome (Sanger 2007)

hyb_protocol: Samples were prepared and hybridized to GeneChip S.pombe Tiling 1.0FR Array according to Affymetrix specifications

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing:
The signal raw data files were normalized through Affymetrix Tiling analysis Software (TAS)
The replicate result was first normalized and merged into one file. The normalized microarray data were mapped to S. pombe genome (Sanger 2007).
Results files are provided as .bar and .bar.txt files.

label: biotin

organism: Schizosaccharomyces pombe

source_name: abo1∆ strain (Hu2318) with induction at 37°C for 4 hours

growth_protocol: Standard YES medium was used for cell culture. Standard fission yeast genetic techniques and media were used according to Moreno et al (1991). Yeast cells were grown to mid-logarithmic phase.

extract_protocol: Cells were then harvested by centrifugation at 3000 rpm and lysed by incubation with TES buffer (10mM Tris-HCl, pH 7.5, 10mM EDTA and 0.5% SDS). RNA was extracted by using hot acid-phenol method

treatment_protocol: Wild type (Hu2185) and abo1∆ strain (Hu2318) were cultured to mid-log exponential phase and continuously induced at 25°C, 30°C and 37°C for 4 hours.

tag: treatment

value: Induction at 37 degrees C for 4 hours

value: abo1 delta

tag: growth phase

value: mid-log exponential phase


title: Dabo1_37_rep2

description:
Processed data files:
Dabo1_37_signal_normalized.bar
Dabo1_37_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the reverse strans of pombe genome (Sanger 2007)

label_protocol: Samples were prepared and hybridized to GeneChip S.pombe Tiling 1.0FR Array according to Affymetrix specifications


title: Dabo1_25_rep2

description:
Processed data files:
Dabo1_25_signal_mormalized.bar
Dabo1_25_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the reverse strans of pombe genome (Sanger 2007)

source_name: abo1∆ strain (Hu2318) withnduction at 25°C for 4 hours

value: Induction at 25 degrees C for 4 hours


title: Low input 20K Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
20K-2
20K-2_fs_5000_iced.matrix
20K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed

tag: cell type


title: Low input 20K Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
20K-3
20K-3_fs_5000_iced.matrix
20K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Dabo1_25_rep1

description:
Processed data files:
Dabo1_25_signal_mormalized.bar
Dabo1_25_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the forward and reverse (R) strands of pombe genome (Sanger 2007)

tag: genotype


title: WT_37_rep2

description:
Processed data files:
WT_37_signal_normalized.bar
WT_37_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the reverse strans of pombe genome (Sanger 2007)

source_name: wild type (Hu2185) with induction at 37°C for 4 hours

value: wildtype


title: Low input 10K Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
10K-2
10K-2_fs_5000_iced.matrix
10K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Low input 20K Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
20K-1
20K-1_fs_5000_iced.matrix
20K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Dabo1_30_rep2

description:
Processed data files:
Dabo1_30_signal_normalized.bar
Dabo1_30_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the reverse strans of pombe genome (Sanger 2007)

source_name: abo1∆ strain (Hu2318) with induction at 30°C for 4 hours

value: Induction at 30 degrees C for 4 hours


title: Double-stranded oligo enrichment, 100K Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
ds-100K-1
ds_100K_5000_iced.matrix
alpha_5000_coordinates.bed


title: WT_37_rep1

description:
Processed data files:
WT_37_signal_normalized.bar
WT_37_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the forward and reverse (R) strands of pombe genome (Sanger 2007)


title: Low input 100K Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
100K-3
100K-3_fs_5000_iced.matrix
100K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: WT_30_rep2

description:
Processed data files:
WT_30_signal_normalized.bar
WT_30_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the reverse strans of pombe genome (Sanger 2007)

source_name: wild type (Hu2185) with innduction at 30°C for 4 hours


title: WT_25_rep2

description:
Processed data files:
WT_25_signal_normalized.bar
WT_25_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the reverse strans of pombe genome (Sanger 2007)

source_name: wild type (Hu2185) withnduction at 25°C for 4 hours


title: WT_25_rep1

description:
Processed data files:
WT_25_signal_normalized.bar
WT_25_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the forward and reverse (R) strands of pombe genome (Sanger 2007)


title: Low input 100K Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
100K-2
100K-2_fs_5000_iced.matrix
100K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Low input 100K Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
100K-1
100K-1_fs_5000_iced.matrix
100K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed


title: Mouse embryonic stem cells, sox2 and tal1, Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
ES_loci-3
sox2_ES_all_downsampled_5000_iced.matrix
tal1_ES_all_downsampled_5000_iced.matrix
sox2_5000_coordinates.bed
tal1_5000_coordinates.bed

source_name: E14 embryonic stem cell line

value: E14 embryonic stem cell line

value: Embryonic stem cells

value: sox2, tal1


title: Mouse embryonic stem cells, sox2 and tal1, Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
ES_loci-2
sox2_ES_all_downsampled_5000_iced.matrix
tal1_ES_all_downsampled_5000_iced.matrix
sox2_5000_coordinates.bed
tal1_5000_coordinates.bed

source_name: A9 embryonic stem cell line

value: A9 embryonic stem cell line


title: P22 nuclear RNA-seq Ctrl 4

source_name: Cerebellum

value: control

value: Cerebellum


title: Dabo1_30_rep1

description:
Processed data files:
Dabo1_30_signal_normalized.bar
Dabo1_30_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the forward and reverse (R) strands of pombe genome (Sanger 2007)


title: Low input 10K Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
10K-1
10K-1_fs_5000_iced.matrix
10K-ALL_5000_iced.matrix
alpha_5000_coordinates.bed

value: Primary erythroid cells isolated from phenylhydrazine treated spleen


title: Mouse erythroid cells, sox2 and tal1, Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
Ery_loci-3
sox2_Ery_all_downsampled_5000_iced.matrix
tal1_Ery_all_downsampled_5000_iced.matrix
sox2_5000_coordinates.bed
tal1_5000_coordinates.bed

value: Primary erythroid cells


title: Mouse erythroid cells, sox2 and tal1, Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
Ery_loci-2
sox2_Ery_all_downsampled_5000_iced.matrix
tal1_Ery_all_downsampled_5000_iced.matrix
sox2_5000_coordinates.bed
tal1_5000_coordinates.bed


title: UP#3-24_hour.162281

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina)
A base call trimming step was applied to remove low-confidence base calls from read ends
FASTQs were aligned using STAR v.2.4.2a
Gene counts were generated using htseq-count
QC and metrics was performed using the Picard family of tools (v1.134)
Genome_build: NCBI build37.1
Supplementary_files_format_and_content: counts_raw_gs.txt

extract_protocol:
A 6-mm punch skin biopsy was collected from unexposed skin, and from skin 6hr and 24hr after UV exposure. Tissue was stored in RNA later and samples from PA shipped to UW. Following RNA isolation at UW, the RNA yield was 2-3 ug RNA (all samples had RIN >9.5).
cDNA libraries were prepared from 1 μg of total RNA using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA) and the Sciclone NGSx Workstation (Perkin Elmer, Waltham, MA).

value: skin tissue biopsy

value: baseline

tag: uv timepoint (hours)


title: Mouse embryonic stem cells, sox2 and tal1, Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
ES_loci-1
sox2_ES_all_downsampled_5000_iced.matrix
tal1_ES_all_downsampled_5000_iced.matrix
sox2_5000_coordinates.bed
tal1_5000_coordinates.bed


title: Mouse erythroid cells, sox2 and tal1, Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
Ery_loci-1
sox2_Ery_all_downsampled_5000_iced.matrix
tal1_Ery_all_downsampled_5000_iced.matrix
sox2_5000_coordinates.bed
tal1_5000_coordinates.bed


title: UW03-24_hour.162273


title: UP#3-0_hour.162280


title: UW05-6_hour.162278


title: Mouse embryonic stem cells, alpha-globin, Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
ES_alpha-3
alpha_ES_all_downsampled_2000_iced.matrix
alpha_2000_coordinates.bed

value: alpha-globin


title: Mouse embryonic stem cells, alpha-globin, Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
ES_alpha-2
alpha_ES_all_downsampled_2000_iced.matrix
alpha_2000_coordinates.bed


title: UW03-6_hour.162272


title: UW02-24_hour.162270


title: UW03-0_hour.162271


title: WT_30_rep1

description:
Processed data files:
WT_30_signal_normalized.bar
WT_30_R_signal_normalized.bar
Result file is normalized from the two replicates and mapped to the forward and reverse (R) strands of pombe genome (Sanger 2007)

source_name: wild type (Hu2185) with induction at 30°C for 4 hours


title: Mouse embryonic stem cells, sox2 and tal1, Tiled-C replicate 4

description:
Tiled-C product (DNA)
Enriched 3C library
ES_loci-4
sox2_ES_all_downsampled_5000_iced.matrix
tal1_ES_all_downsampled_5000_iced.matrix
sox2_5000_coordinates.bed
tal1_5000_coordinates.bed


title: Mouse embryonic stem cells, alpha-globin, Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
ES_alpha-1
alpha_ES_all_downsampled_2000_iced.matrix
alpha_2000_coordinates.bed


title: Input_Dabo1_2

data_processing:
Basecalls performed using Illumina bcl2fastq-1.8.4
ChIP-seq reads were aligned to the ASM294v2 genome assembly using STAR version 3.2 with configurations --alignIntronMax 1 --bamRemoveDuplicatesType UniqueIdenticalNotMulti
Genome_build: Schizosaccharomyces_pombe.ASM294v2
Supplementary_files_format_and_content: bedGraph files

source_name: abo1∆ strain (Hu2318)

growth_protocol: Standard YES medium was used for cell culture. Standard fission yeast genetic techniques and media were used according to Moreno et al (1991). Yeast cells were grown to mid-logarithmic phase (5x10^6 cell/ml). Harvest 200x10^6 cells.

extract_protocol:
For each IP,  30ul of sheard chromatin and 1ug of H3K9me2 antibody were prepared, and 10ul of protein A/G coated magnetic beads was used. After incubation and washing steps, final ChIP DNA was extracted through Qiagen PCR purification kit.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext® Ultra™ II DNA Library Prep Kit

treatment_protocol: Use final 1% formaldehyde to crosslink at room temperature for 30min and quench the fixation by adding glycine.The spinned down cell pellet was resuspended in ice code Lysis buffer(150mM NaCl, 50mM Hepes-KOH pH7.5, 0.1%SDS, 1%Triton X-100, 0.1% sodium deoxycholate, 1mM EDTA) with proteinase inhibitor (PI).Lyse cell in Fastprep machine 7 times during 30sec at max speed. Spin down the debris of  yeast cells and keep the supernatant. The supernatant was then sent for sonication by Bioruptor Pico Sonicator (11 cycles of 30 sec on 30 sec off) to get the sheard chromatin. Spin down the debris again.

tag: cell growth phase


title: Mouse erythroid cells, sox2 and tal1, Tiled-C replicate 4

description:
Tiled-C product (DNA)
Enriched 3C library
Ery_loci-4
sox2_Ery_all_downsampled_5000_iced.matrix
tal1_Ery_all_downsampled_5000_iced.matrix
sox2_5000_coordinates.bed
tal1_5000_coordinates.bed


title: Mouse erythroid cells, alpha-globin, Tiled-C replicate 2

description:
Tiled-C product (DNA)
Enriched 3C library
Ery_alpha-2
alpha_Ery_all_downsampled_2000_iced.matrix
alpha_2000_coordinates.bed


title: Mouse erythroid cells, alpha-globin, Tiled-C replicate 3

description:
Tiled-C product (DNA)
Enriched 3C library
Ery_alpha-3
alpha_Ery_all_downsampled_2000_iced.matrix
alpha_2000_coordinates.bed


title: UW02-0_hour.162269


title: UW05-24_hour.162279


title: UW01-24_hour.162268


title: Mouse erythroid cells, alpha-globin, Tiled-C replicate 1

description:
Tiled-C product (DNA)
Enriched 3C library
Ery_alpha-1
alpha_Ery_all_downsampled_2000_iced.matrix
alpha_2000_coordinates.bed


title: Input_Dabo1_1


title: Input_wt_2

source_name: Wild type (Hu2185)

value: wild type


title: Con_MEF_RNAseq_3

first: Amy

last: Royall

state: Oxfordshire

address: Radcliffe Observatory Quarter

department: Zoology

data_processing:
Raw reads generated using FeatureCounts software
Genome_build: mm10
Supplementary_files_format_and_content: Raw reads for all geneIDs for each replicate of all 3 experimental conditions gathered from default FeatureCount output

molecule: polyA RNA

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Primary MEFs were cultured in DMEM containing 10% Feotal Bovine Serum and 1% Penstrep on plasticware coated in 0.001% poly-L-Lysine

extract_protocol:
Cells were placed under chemical selection (puromycin) for 5 days, following selection they were allowed to recover for 48 hours in rich DMEM media. Total RNA was extracted using Qiagen micro Rneasy kit.
Libraries were made using TruSeq illumina poly-A selection kit and sequences on one NextSeq500 chip

treatment_protocol: Cells were electroporated using NEPA21 electroporation system using constructs with a co-expressed puromycin-resistance gene

value: MEF

tag: passage

value: Control (just puromycin) - v5 tagged [ectopically expressed gene]


title: UW05-0_hour.162277


title: Con_MEF_RNAseq_2


title: Input_wt_1

value: mid-log exponential phase


title: ChIP_Dabo1_2

value: abo1 delta

value: H3K9me2 (ab1223, Abcam)


title: human UND1 iPSCs-derived BME-like cell

city: Daejeon

first: Na Geum

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

description:
Gene expression of BME-like cells derived from human UND iPSC
UND1 BME-like cell

data_processing:
Illumina Highseq 2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using Tophat (version 2.0.11)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited xlsx files include FPKM values for each Sample

source_name: Brain microvascular endothelial-like cell

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq® Stranded mRNA Library Prep Sample Kit (Cat# 20020595) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions accompanying TruSeq® Stranded mRNA Library Prep Sample Kit (Cat# 20020595).  One 1 ug of total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM), followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library. Finally, quality and band size of libraries were assessed using Agilent 2100 bioanalyzer (Agilent). Libraries were quantified by qPCR using CFX96 Real Time System (Biorad). After normalization, sequencing of the prepared library was conducted on the Highseq 2500 (Illumina) with 100 bp paired-end reads.

value: Human induced pluripotent stem cell-derived-brain microvascular endothelial-like cell

tag: passages


title: human SPD1-2 iPSCs-derived BME-like cell

description:
Gene expression of BME-like cells derived from human SPD iPSC
SPD1-2 BME-like cell


title: human FAD2 iPSCs-derived BME-like cell

description:
Gene expression of BME-like cells derived from human FAD iPSC
FAD2 BME-like cell


title: euthCrx_MEF_RNAseq_3

value: human Crx - v5 tagged [ectopically expressed gene]


title: ChIP_wt_2

value: H3K9me2 (ab1221, Abcam)


title: Con_MEF_RNAseq_1


description:
Gene expression of human primary brain microvascular endothelial cells derived from human brain cortex tissue
pBMEC

source_name: brain microvascular endothelial cell

value: Human brain cortex tissue-derived brain microvascular endothelial cell


title: euthCrx_MEF_RNAseq_2


title: ChIP_wt_1

value: H3K9me2 (ab1220, Abcam)


title: euthCrx_MEF_RNAseq_1


title: metaCrx_MEF_RNAseq_3

value: metatherian (opossum) Crx -v5 tagged [ectopically expressed gene]


title: metaCrx_MEF_RNAseq_2


title: RNAi-2

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

description: The lateral buds from the same node of WT and transgenic cucumber plants were collected for RNA-seq analysis.

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the cucumber genome sequence (ftp://cucurbitgenomics.org/pub/cucurbit/genome/cucumber/Chinese_long/) using HISAT. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 CPM (counts per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include CPM(counts per Million) values for 4 Samples .

organism: Cucumis sativus

source_name: axillary bud

growth_protocol: The cucumber seeds were germinated at 28°C in dark and then grown in a growth chamber at 16h day (25°C) and 8h night (18°C) until two true-leaf stage. Seedlings were then transferred to the greenhouse of China Agricultural University in Beijing.

extract_protocol:
The lateral buds from the same node of WT and transgenic cucumber plants were collected for RNA-seq analysis,and RNA was isolated with Transzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A 585-bp specific fragment of the CsBRC1 coding sequence was used for generating the CsBRC1-RNAi construct and the empty PFGC-1008 vector was used as transformation control. The recombinant construct was introduced into Agrobacterium strain GV3101 and transformed into cucumber inbred line R1461.

value: two-month old plant

value: lateral bud


title: RNAi-1


title: UW01-6_hour.162267

value: skin tissue biopsy


title: WT-2


title: WT-1


title: metaCrx_MEF_RNAseq_1


title: Flox.B.6wk.M.SpNo3

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

country: Denmark

institute: National Genome Center

data_processing:
Raw data was processed according to the cufflinks program, and normalized gene expression was obtained using the cuffquant function. All parameters were set at default values.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab separated txt file countaining cuffquant normalized gene expression values, one column for each sample, one row for each gene.

source_name: Spleen

extract_protocol:
Total RNA was extracted following the Immunoligcal Genome Consortium standard protocol (https://www.immgen.org/). One thousand cells (≥ 99% purity) were double-sorted directly into 96-well plates containing TCL buffer (Qiagen) and 1% beta-mercaptoethanol and frozen.
Broad Technology Labs for SmartSeq2 library preparation and NextSeq500 sequencing

value: 6 weeks

tag: Sex

value: Male

value: Klf12 flox/flox beta-actin Cre-

tag: cell population

value: B220+IgM+IgD+ B cells


title: Flox.B.6wk.M.SpNo2


title: ChIP_Dabo1_1

value: H3K9me2 (ab1222, Abcam)


title: Flox.B.6wk.M.SpNo1


title: WT.B.6wk.M.SpNo3

value: Klf12 +/+ beta-actin Cre-


title: WT.B.6wk.M.SpNo2


title: Hepatocytes_DE_p20

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

institute: Korea National Institute of Health

data_processing:
sequenced reads were aligned to human reference genome (GRCh38, hg38) using STAR 2.5.2b aligner with two-pass approach.
The read counts were normalized via regularized log transformation using the DESeq2 package.
Genome_build: GRCh38, hg38
Supplementary_files_format_and_content: comma-separated values file include normalized count values for each samples.

source_name: human induced pluripotent stem cell

extract_protocol:
RNA samples were prepared from collected cell pellets using an Rneasy plus mini kit (QIAGEN).
Illumina TruSeq Sample preparation kit (Illumina) was used to construct sequencing libraries.

value: iPSC-derived definitive endoderm


title: Hepatocytes_HE_p20

value: iPSC-derived hepatic endoderm


title: Hepatocytes_HLC_p37

value: iPSC-derived hepatocyte like cell


title: Cardiomyocytes_stage3_p47

value: iPSC-derived cardiomyocyte progenitor cells


title: Hepatocytes_HLC_p20


title: Hepatocytes_iPS_p37

source_name: cord blood

value: human induced pluripotent stem cell


title: Hepatocytes_HE_p37


title: Hepatocytes_iPS_p20


title: Hepatocytes_DE_p37


title: WT.B.6wk.M.SpNo1


title: Cardiomyocytes_stage2_p47


title: Cardiomyocytes_stage1_p47


title: Flox.T8.6wk.M.SpNo2

value: CD8+TCR beta+CD25- T cells


title: Cardiomyocytes_stage3_p25


title: Flox.T8.6wk.M.SpNo1


title: Flox.T8.6wk.M.SpNo3


title: vector CON335-infected HFL-1 fibroblasts, biological rep3

city: Beijing

first: Dong

last: Leng

address: No.8 Gongti South Road

institute: Beijing Chao-Yang Hospital, Capital Medical University

description: Gene expression data from fibroblast

hyb_protocol: The fragmented biotin-labeled RNA was hybridized to the Affymetrix chip GeneChip® Prime ViewTM Human Gene Expression Array.

scan_protocol: Chips were measured with Gene Chip Scanner 3000.

data_processing: Data saved in .CEL files were analyzed by Affymetrix Power Tools using default analysis settings and RMA normalization method.

source_name: Fetal lung fibroblasts HFL-1

label_protocol: In vitro transcription (IVT) was  performed to obtain fragmented biotin-labeled RNA according to the manufacturer’s instructions (Gene Chip 3’-IVT Express Kit).

growth_protocol: Human fetal lung fibroblast HFL-1 cells in F-12K medium supplemented with 10% (v/v) fetal bovine serum were cultured at 37C in a 5% CO2 humidified incubator. The cell culture medium was replaced every 2 days and the cells were passaged at a 1:2 ratio every 3 days.

extract_protocol: Total RNA was extracted from cells using the Total RNA Isolation Reagent Trizol.

treatment_protocol: The lentivirus Hyal1 and the control CON 335 were transfected into 40% confluent HFL-1 fibroblasts in the presence of 5μg/ml polybrene and cell culture medium was replaced 16 h after infection.

tag: cell line

value: Fetal lung fibroblasts

value: control


title: vector CON335-infected HFL-1 fibroblasts, biological rep1

description: Gene expression data from fibroblast


title: HYAL1 overexpressed HFL-1 fibroblast, biological rep2

description: Gene expression data from fibroblast

value: HYAL1 overexpression


title: vector CON335-infected HFL-1 fibroblasts, biological rep2

description: Gene expression data from fibroblast


title: Testosterone replicate 5

city: Athens

first: Kristen

middle: Jean

last: Navara

state: GA

address: 203 Poultry Science Building

department: Poultry Science

institute: The University of Georgia

description:
TEST5
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

data_processing:
Read mapping was performed using TopHat v2.0.14.
Raw count extraction was performed using HTSEQ v0.6.1p1.
Genome_build: Ensembl: ftp://ftp.ensembl.org/pub/release-93/fasta/gallus_gallus/dna/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Ggal_RNA_Seq_raw_count_matrix.txt: Tab-delimited text file, raw count matrix.

organism: Gallus gallus

source_name: 8 pooled ovarian germinal discs

extract_protocol:
RNA isolation protocol: The RNA from the samples was extracted using the Norgen’s Single Cell RNA Purification Kit (catalog no. 51800, Norgen Biotek Corp.). A Nanodrop© spectrophotometer (ND-1000 Nanodrop Technologies, Wilmington, DE, USA) was used to assess the initial RNA purity and concentration of each sample. To ensure adequate RNA quantity for analysis, we pooled nine GD region samples (8μl from each) per replicate. We created 5 pooled replicates per treatment group, for a total of 15 replicates. The RNA integrity of each replicate was assessed on an Agilent 2100 Bioanalyzer instrument (Model 62939B, Agilent Technologies, Santa Clara, CA, USA) at the Georgia Genomics and Bioinformatics Core (GGBC) at the University of Georgia (Athens, GA).
RNA-Seq for the Illumina' TruSeq strand-specific kit.

treatment_protocol: Treatment & tissue collection protocol: White leghorn laying hens (Gallus gallus) were injected with either corticosterone (1.5mg dissolved in 0.5ml peanut oil), testosterone (1.5mg dissolved in 0.5ml peanut oil), or a control injection (0.5ml peanut oil) at 5h prior to predicted ovulation based on previous laying patterns. All hens were killed via lethal injection approximately 1.5h post-injection (which is 3.5h before ovulation), when the sex chromosomes should be segregating, and the F1 follicles were collected. The GD region was removed from the F1 follicle and briefly washed in Krebs buffer to remove any yolk material. It was placed in 0.5mL reaction tube filled with 100μl of Buffer RL (Norgen Biotek Corp.). Then 100μl of 70% ethanol was added to the sample and it was vortexed thoroughly until the GD material was completely broken down. The samples were placed in -80°C for future use.

tag: breed

value: White Leghorn

value: Female

value: ovarian germinal discs

tag: drug treatment

value: Testosterone (1.5mg in 0.5ml peanut oil)

tag: time collected before ovulation

value: 3.5 hours

tag: replicate


title: Cardiomyocytes_iPS_p25


title: Cardiomyocytes_iPS_p47


title: WT.T8.6wk.M.SpNo3

tag: strain

tag: age

value: 6 weeks

value: Male


title: Cardiomyocytes_stage1_p25


title: Testosterone replicate 4

description:
TEST4
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

tag: tissue


title: Corticosterone replicate 5

description:
CORT5
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

value: Corticosterone (1.5mg in 0.5ml peanut oil)


title: HYAL1 overexpressed HFL-1 fibroblast, biological rep1

description: Gene expression data from fibroblast


title: HYAL1 overexpressed HFL-1 fibroblast, biological rep3

description: Gene expression data from fibroblast


title: Testosterone replicate 3

description:
TEST3
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt


title: Corticosterone replicate 4

description:
CORT4
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt


title: Neuronal_cells_p40

value: iPSC-derived neuron like cells


title: Flox.T4.6wk.M.SpNo2

value: Klf12 flox/flox beta-actin Cre-

value: CD4+TCR beta+CD25- T cells


title: HuH-7, SLMP53-2, 42uM, replicate N2

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description: Gene expression of HuH-7 cells, treated with 3x IC50 SLMP53-2 (48 µM), for 24 hours

hyb_protocol: 1.65 mg of Cy3-labeled cRNA (specific activity: 13.7 ±2.01 pmol Cy3 per mg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Fragmentation Buffer and 2x GE (Gene Expression) Blocking Agent (Gene Expression Hybridization Kit, p/n 5188-5242, Agilent Technologies) following manufacturer’s instructions. On completion of the fragmentation reaction, 55 ml of 2x Hi-RPM Hybridization Buffer were added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K V2 Microarray kit (G4846A, Agilent Technologies) for 17 hours at 65°C in a rotating hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C, Agilent Technologies) using the AgilentHD_GX_1Color Profile (Scan Area: 61x21.6 mm; Scan resolution: 5 mm, dye channel set to 100% Green PMT) of Agilent ScanControl software 8.1.3 (Agilent Technologies).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09).
Background signal has been correct using Edwards method as implemented inlimma package. Normalization between samples has been performed using quantile method as implemented in limma package.

source_name: HuH-7, SLMP53-2, 42uM, replicate N2

label_protocol: Agilent-014850 4x44K  Whole Human Genome Microarrays were used  following the manufacturer’s protocol. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (p/n 5190-2331, Agilent Technologies)  synthesis, cRNA synthesis, amplification and purification

growth_protocol: Huh-7 cells were cultures in RPMI 1640 (Thermo Fisher Scientific, Waltham, MA, USA) in 6-well plates, seeding 2.1*10^4 cells/cm2

extract_protocol: 24 hours after the treatments cells were harvested and total RNA was extracted (Illustra RNAspin Mini, GE Healthcare, Chicago, IL, USA). Four biological replicates per treatment type were prepared. RNA purity and concentrations were measured by Nanodrop. An and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), using samples with RIN (RNA integrity number) >8.

treatment_protocol: Cells were treated at ~60% confluence by SLMP53-2 at 28uM or 42uM. DMSO was used as control

value: cell line derived from hepatocellular carcinoma

value: p53mutant Y220C

tag: treatment

value: 3x IC50 SLMP53-2 (48 µM), for 24 hours


title: HuH-7, SLMP53-2, 42uM, replicate N4

source_name: HuH-7, SLMP53-2, 42uM, replicate N4

tag: cell type


title: WT.T8.6wk.M.SpNo2

tag: genotype

value: Klf12 +/+ beta-actin Cre-

value: CD8+TCR beta+CD25- T cells


title: Testosterone replicate 2

description:
TEST2
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt


title: Testosterone replicate 1

description:
TEST1
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt


title: HuH-7, SLMP53-2, 42uM, replicate N1

source_name: HuH-7, SLMP53-2, 42uM, replicate N1


title: HuH-7, SLMP53-2, 28uM, replicate N3

description: Gene expression of HuH-7 cells, treated with 2x IC50 SLMP53-2 (28 µM), for 24 hours

source_name: HuH-7, SLMP53-2, 28uM, replicate N3

value: 2x IC50 SLMP53-2 (28 µM), for 24 hours


title: Flox.T4.6wk.M.SpNo3


title: Flox.T4.6wk.M.SpNo1


title: HuH-7, SLMP53-2, 28uM, replicate N2

source_name: HuH-7, SLMP53-2, 28uM, replicate N2


title: HuH-7, SLMP53-2, 42uM, replicate N3

source_name: HuH-7, SLMP53-2, 42uM, replicate N3


title: Corticosterone replicate 2

description:
CORT2
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

value: White Leghorn


title: Neuron_rosettes_p40

value: iPSC-derived rosettes


title: Neuron_rosettes_p20


title: Neuron_iPS_p20

value: human induced pluripotent stem cell


title: WT.T8.6wk.M.SpNo1


title: Corticosterone replicate 3

description:
CORT3
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

value: Female

value: ovarian germinal discs


title: Neuronal_cells_p20


title: WT.T4.6wk.M.SpNo3

value: 6 weeks


title: Corticosterone replicate 1

description:
CORT1
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

value: 3.5 hours


title: WT.T4.6wk.M.SpNo2

value: Male


title: Control replicate 3

description:
CNTL3
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

value: Control (peanut oil)


title: Flox.NK.6w.M.SpNo2

value: Klf12 flox/flox beta-actin Cre-

value: CD3-NK1.1+ NK cells


title: Control replicate 2

description:
CNTL2
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt


title: WT.T4.6wk.M.SpNo1

value: CD4+TCR beta+CD25- T cells


title: Neuron_iPS_p40


title: Control replicate 1

description:
CNTL1
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt


title: HCC1569_siAP2C_rep3

city: St Louis

first: Tiandao

last: Li

address: 4444 Forest Park Ave

institute: Washington University

description:
transient knockdown
HCC1569_siNT_vs_siAP2C.txt

data_processing:
Sample processing was done by the University of Nebraska
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cuffdiff was used for FPKM quantification and differential expression
Genome_build: Human Feb.2009 (GRCh37/hg19) (hg19)
Supplementary_files_format_and_content: Cuffdiff results in txt format

source_name: human breast carcinoma

growth_protocol: Cell lines HCC1954, HCC1569 and SKBR3 were purchased from the American Type Culture Collection (ATCC; Manassas, VA, USA) and propagated in the appropriate medium as recommended by manufacturer. Additionally, all media were supplemented with 10% FBS (LS26140079, Gibco, USA), 1% 100X Pen/Strep antibiotics (10378016, Gibco, USA), and 0.2% Plasmocin (Cat# ant-mpp, InvivoGen, USA). The cell lines were cultured in a standard humidified incubator at 37° C and 5% CO2 (16). The cells were not tested and authenticated by the authors. Only early passages of cell lines (less than 10) were used for experiments.

extract_protocol:
mRNA from cell lysates were obtained from cell lines using the Rneasy Mini Kit (Qiagen, Valencia, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected using small interfering RNA (siRNA) directed towards non-targeting #2 (NT Thermo Fisher Scientific ID:4390843), TFAP2C (TFS ID:10.7041) with lipofectamine RNAiMAX reagent (Cat# 13778150, Thermo Fisher Scientific, USA), accordingly a manufacturer’s instruction. After 72 to 96 hours of incubation, cell were immediately analyzed or used in consequent experiments. Cell clones of HCC1954 lines with stable knockdown of TFAP2C (Cat#TRCN0000019745, Sigma, USA) and negative control (Cat#SHC002, Sigma, USA) were generated using lentivirus-mediated shRNA cassette.

value: between 5 and 10

tag: transfection reagent

value: Lipofectamine RNAi_Max

tag: sirna/shrna

value: TFAP2C siRNA ID:107041


title: SKBR-3 TFAP2C (2nd ChIP-Seq sample)

description: SKBR-3 TFAP2C

data_processing:
Raw sequences generated from Illumina/Solexa sequencer were aligned using NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 250 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format.
Genome_build: hg18
Supplementary_files_format_and_content: fastq and wig

source_name: human breast carcinoma cell line

growth_protocol: Cell lines were cultured and propagated according ATCC recommendations. SKBR-3: https://www.atcc.org/products/all/HTB-30.aspx#culturemethod and HCC1954: https://www.atcc.org/products/all/CRL-2338.aspx#culturemethod

extract_protocol:
Lysates were clarified from sonicated nuclei and TFAP2C-DNA complexes were isolated with antibody.
One hundred million cells were cross-linked for 10 min at 37°C using 0.7% formaldehyde, 0.125 M glycine. Cells were washed twice with PBS, re-suspended in lysis buffer and incubated for 5 minutes. Cells were collected by centrifugation and cell pellets were frozen in liquid nitrogen and stored at minus 80°C. Cell pellets were thawed in lysis buffer, collected by centrifugation and cell nuclei were re-suspended in RIPA buffer. Chromatin was sonicated using conditions determined empirically for MCF-7 cells to achieve an optimal fragment length between 100 to 400 bp. After sonication, samples were centrifuged at 20,000 × g for 10 min at 4°C. The supernatant containing cross-linked DNA/histones was diluted with IP dilution buffer to 2 mg/ml. Half the sample was immunoprecipitated with 10 μg of TFAP2C monoclonal antibody SC-12762 (Santa Cruz Biotechnology, Santa Cruz, CA), which was previously shown to be specific for TFAP2C without cross reactivity to TFAP2A, and half with control nonspecific IgG (Upstate, Waltham, MA) with the addition of Dynal sheep anti-mouse Dynabeads and allowed to recognize their antigens overnight at 4°C with rotation. Protein/antibody/DNA complexes were collected magnetically followed by washing and elution. Protein/DNA cross-links were reversed using 200 mmol/L NaCl at 65°C overnight. DNA was treated with Proteinase K and RNase A and was recovered with QIAquick PCR Kit (Qiagen) according to manufacturer's suggested protocol. Purified DNA was quantified by using a NanoDrop ND-1000 (NanoDrop, Wilmington, DE).

tag: antibody

value: TFAP2C monoclonal antibody (Santa Cruz, sc-12762)


title: Flox.NK.6w.M.SpNo3


title: HCC1569_siAP2C_rep2

tag: passage


title: BT474 CSC

city: Nanjing

first: Yongmei

last: Yin

address: No.300 Guangzhou Rd

institute: Nanjing Medical University

data_processing:
Basecalls performed using Solexa CHASTITY
The trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch.
Sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin.
When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs (Based on ALL_Isoform value).
Genome_build: miRBase v21. The sequences of the novel miRNAs are available in the file "novel_miRNAs_predicted_by_miRDeep2.xls" on the series record.
Supplementary_files_format_and_content: Excel file with raw and normalized read counts

source_name: breast cancer stem cell

growth_protocol: BT474 were cultured in RPMI-1640 medium (Gibco)；MDA-MB-468 were cultured in DMEM medium (Gibco);  supplemented with 10% (v/v) fetal bovine serum (Gibco), 100 U/ml penicillin (Gibco), and 100 U/ml streptomycin (Gibco) at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol:
Total RNA was isolated from non-TNBC stem cells (BT474) and TNBC stem cells (MDA-MB-468) using Trizol reagent (Ambion, Carlsbad, CA), and then assessed by an Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA).
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina HiSeq per the manufacturer's instructions.

treatment_protocol: Breast cancer stem-enriched subpopulations were sorted from MDA-MB-468 (ER-, PR-, HER2-) and BT474 (ER+) with CD24 and CD44 cell-surface markers by flow cytometric analysis

value: breast cancer derived stem cell

tag: cell markers

value: CD24 and CD44


title: HCC1569_siNT_rep3

value: Negative control siRNA#2


title: HCC1954 TFAP2C

description: HCC1954 TFAP2C

tag: passages


title: m6A_M3KO_rep3

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

data_processing:
Due to the addition of 3 nucleotides on 5’end of the second sequencing read (R2)   from the Pico v2 SMART Adapter, paired-end reads were trimmed using   Trim Galore v0.4.4 with the options: --three_prime_clip_R1 3 --clip_R2 3
Reads were aligned onto the mouse ribosomal sequence (GenBank: BK000964.3) using Bowtie v1.2 allowing at most 3 mismatches. Previously unmapped reads were aligned onto the mouse reference genome (mm10) using STAR v2.6.0c reporting randomly one position, allowing 4% of mismatches (--outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04).
PCR duplicates were removed using STAR with the option --bamRemoveDuplicatesType UniqueIdenticalNotMulti. Bigwig files were produced with deepTools v2.5.3 using the option –normalizeUsingRPKM.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files

source_name: Embryonic Stem Cell

growth_protocol: ES Cells were either cultured in serum-free 'LIF +2i' medium

extract_protocol:
m6A IP was carried out using Magna MeRIP m6A Kit (Millipore) according to the manufacturer’s instructions. total RNA was extracted using Trizol, DNaseI-treated and RNA was chemically fragmented into 100-nucleotide-long fragments and 350µg of total RNA were subjected to each immunoprecipitation (IP) with affinity purified anti-m6A antibody.
RNA was purified using RNeazy Kit (Qiagen) and processed for library generation using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa). Sequencing was performed in 100pb paired-end reads using using Novaseq 6000.

tag: development stage

tag: medium

tag: genotype/variation

value: Mettl3 KO


title: HCC1569_siAP2C_rep1

tag: cell line


title: HuH-7, DMSO, replicate N4

description: Gene expression of HuH-7 cells, treated with DMSO for 24 hours

source_name: HuH-7, DMSO, replicate N4

value: cell line derived from hepatocellular carcinoma

value: p53mutant Y220C

value: DMSO for 24 hours


title: HuH-7, SLMP53-2, 28uM, replicate N4

source_name: HuH-7, SLMP53-2, 28uM, replicate N4

value: 2x IC50 SLMP53-2 (28 µM), for 24 hours


title: HuH-7, DMSO, replicate N1

source_name: HuH-7, DMSO, replicate N1


title: HuH-7, DMSO, replicate N2

source_name: HuH-7, DMSO, replicate N2


title: Control replicate 5

description:
CNTL5
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

tag: breed

value: White Leghorn

tag: Sex

value: Female

value: ovarian germinal discs

tag: drug treatment

tag: time collected before ovulation

value: 3.5 hours

tag: replicate


title: HCC1569_siNT_rep2


title: HuH-7, SLMP53-2, 28uM, replicate N1

source_name: HuH-7, SLMP53-2, 28uM, replicate N1

tag: cell type

tag: treatment


title: HuH-7, DMSO, replicate N3

source_name: HuH-7, DMSO, replicate N3

tag: genotype


title: Flox.NK.6w.M.SpNo1

source_name: Spleen

tag: strain

tag: age

value: 6 weeks

value: Male

value: Klf12 flox/flox beta-actin Cre-

tag: cell population

value: CD3-NK1.1+ NK cells


title: WT.NK.6wk.M.SpNo2

value: Klf12 +/+ beta-actin Cre-


title: WT.NK.6wk.M.SpNo3


title: Control replicate 4

description:
CNTL4
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt

source_name: 8 pooled ovarian germinal discs

tag: tissue

value: Control (peanut oil)


title: m6A_M3KO_rep1

tag: antibody


title: m6A_M3KO_rep2

tag: development stage


title: MDA-MB-468 CSC

value: breast cancer derived stem cell

tag: cell markers

value: CD24 and CD44


title: HCC1569_siNT_rep1

tag: passage

value: between 5 and 10

tag: transfection reagent

value: Lipofectamine RNAi_Max

tag: sirna/shrna

value: Negative control siRNA#2


title: m6A_WT_rep3

tag: medium

tag: genotype/variation

value: Wild-type


title: USOS-CSA-KO-CPD-Xrseq Rep1

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

description: Excised oligomer released in Nucleotide Excision Repair (XR-seq)

data_processing:
Library strategy: XR-seq
Base calling using Casava v1.8.2. Demultiplexing performed allowing 1 mismtach in the index
Flanking adapter sequences were removed from the reads using trimmomatic (Bolger et al. 2014).
Reads were aligned to the hg38 human genome using bowtie (Langmead et al. 2009) with the command options  -q --nomaqround --phred33-quals -m 4 -n 2 -e 70 -l 20 --best –S
PCR duplicates were removed using PicardCommandLine Mark Duplicates (http://broadinstitute.github.io/ picard/)
Per base read counts were calculated using bedtools genomecov and normalized per million mapped reads per chromosome and split to plus and minus strands. Read counts were calculated in 25nt windows to create repair signal maps in bigwig file format.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files of the data normalized to mapped read counts and separated by strands.

growth_protocol: Cell lines  were cultured at 37°C in an atmosphere of 5% CO2 in DMEM  supplemented with penicillin/streptomycin and 10% Fetal bovine serum

extract_protocol: XR-seq was performed as previously described (Hu. et al Genes and Dev. 2016, Adar S. et al PNAS 2016). Briefly, cells were harvested 3h after treatment with 20J/m2 UVC (254nm). Primary excision products were pulled down by TFIIH coimmunoprecipitation with anti-p62 and anti-p89 antibodies (Santa Cruz Biotechnology sc25329 and sc271500), and ligated to both 5′ and 3′ adaptors. Ligation products containing CPD were purified by immunoprecipitation with the anti-CPD antibody (Cosmo Bio NM-DND-001) and repaired in-vitro by Drosophila melanogaster CPD photolyase. Repaired DNA were PCR-amplified with Index primers and purified by 10% native polyacrylamide gels.

treatment_protocol: For UV irradiation cells were grown to ~70% confluence. Culture medium was removed, and then cells were placed under a 254 nm germicidal lamp for a total dose of 20J/m2 . Following irradiation, fresh culture medium was added to the cells, which were further incubated for the indicated time. Cells were washed with ice-cold PBS, harvested with a cell scraper in PBS and collected by centrifugation at 2500rpm for 4min.

value: CSA KO

value: osteosarcoma

tag: uv treatment

tag: time after irradiation


title: WT.NK.6wk.M.SpNo1

tag: Sex


title: m6A_WT_rep2


title: USOS-UVSSA-KO-CPD-Xrseq Rep1

value: UVSSA KO

tag: cell type


title: AA14

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
D2CKO_AA14

data_processing:
Single cells were identified using UMI Tools
Reads corresponding to individual cells aligned to reference genome using STAR
R1 contains barcode (bp 1-16) and UMI (bp 17-26)
R2 contains the cDNA
Uniquely mapped reads were assigned to genes using featureCounts
UMI Tools was used to generate final raw count table
Raw counts were processed using Seurat for clustering and differentially expressed gene analysis
Genome_build: MM10/GRCm38p6
Supplementary_files_format_and_content: gzipped tab-delimited text file with rows as cells, columns as genes. Additional columns for meta data are also added prior to genes.

source_name: striatum

extract_protocol:
Mice (P9) were sacrificed by rapid decapitation and brains were quickly removed and placed in ACSF (126mM NaCl, 20mM NaHCO3, 20mM D-Glucose, 3mM KCl, 1.25mM NaH2PO4, 2mM of CaCl2 and MgCL2 freshly added) bubbled with 95%O2 and 5%CO2. Coronal slices at 500um were made using a VF-200 Compresstome in ACSF and transferred to a recovery chamber at room temperature in ACSF with 50uM AP5, 20uM DNQX, and 100nM TTX (ACSF+cb){Tasic:2016jp}. Striatal punches were taken from these slices and incubated in 1mg/ml of pronase in ACSF+cb for 5min. Punches were washed with ACSF+ 0.04% BSA twice and gently dissociated into single-cell suspension using polished Pasteur pipettes with 600um, 300um, and 150um opening diameters, sequentially. Cells were centrifuged and washed twice, filtered through Flowmi Tip 40uM strainers, and resuspended with ACSF+ 0.04% BSA. Cell viability was quantified using the trypan blue exclusion method and cell concentration was adjusted for targeted sequencing of 5,000 cells/sample using the 10X Genomics Single Cell 3’ Reagent Kits v2 protocol to prepare libraries (Zheng et al., 2017).  Libraries were sequenced using the McDermott Sequencing Core at UT Southwestern.
Followed 10X Genomics kit manufacturer guidelines

value: striatum

value: F

value: post-natal day 9

tag: genotype

value: D2-Cre tg/+; Foxp1flox/flox


title: AA16

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
D1CKO_AA16

tag: strain

value: M

value: D1-Cretg/+; Foxp1flox/flox


title: AA13

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
D1CKO_AA13

tag: age


title: Input_KO

value: Mettl3 KO


title: Input_WT


title: m6A_WT_rep1


title: USOS-UVSSA-KO-CPD-Xrseq Rep2


title: AA12

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
DDCKO_AA12

value: D1-Cre tg/+; D2-Cre tg/+; Foxp1flox/flox


title: AA11

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
DDCKO_AA11


title: USOS-CPD-Xrseq Rep2

value: wild type


title: AA15

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
D1CKO_AA15


title: USOS-CPD-Xrseq Rep1


title: AA9

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
D2CKO_AA9


title: HCC1954_shAP2C_rep1

description: stable knockdown

data_processing:
Sample processing was done by the University of Nebraska
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cuffdiff was used for FPKM quantification and differential expression
Genome_build: Human Feb.2009 (GRCh37/hg19) (hg19)

growth_protocol: Cell lines HCC1954 and SKBR3 were purchased from the American Type Culture Collection (ATCC; Manassas, VA, USA) and propagated in the appropriate medium as recommended by manufacturer. Additionally, all media were supplemented with 10% FBS (LS26140079, Gibco, USA), 1% 100X Pen/Strep antibiotics (10378016, Gibco, USA), and 0.2% Plasmocin (Cat# ant-mpp, InvivoGen, USA). The cell lines were cultured in a standard humidified incubator at 37° C and 5% CO2 (16). The cells were not tested and authenticated by the authors. Only early passages of cell lines (less than 10) were used for experiments.

tag: cell line

value: Lentiviral particles

value: Cat#TRCN0000019745, Sigma, USA


title: HCC1954_shAP2C_rep3

description: stable knockdown

value: between 5 and 10


title: HCC1954_shAP2C_rep2

description: stable knockdown


title: HCC1954_shNT_rep2

description: stable knockdown

value: Cat#SHC002, Sigma, USA


title: Zc3h13 KO ESC_Rep 2

data_processing:
Adapters were trimmed using Atropos v1.1.16.
The paired-end reads alignment was performed onto the Mouse reference genome (mm10) with STAR v2.7.0a reporting randomly one position, allowing 6% of mismatches (--outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06).
Repeats annotation was downloaded from repeatmaskerull-length LTR copies, we used the same strategy as done previously using the perl tool “One code to find them all”.
Reconstructed transposons annotation and basic genes annotation from GENCODE v18 were merged and used as input for quantification with featureCounts v1.5.1. Differential expression analysis was performed using edgeR’s normalisation combined with voom transformation from limma R package. P-values were computed using limma and adjusted with the Benjamini-Hochberg correction. Genes and transposon families were declared as differentially expressed if FDR<5% and log2 Fold-change > 0.75
Genome_build: mm10
Supplementary_files_format_and_content: text file and Table count for gene and transposon family expression

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies), then DNase-treated and column purified (Qiagen RNeasy Kit).
RNA-seq libraries were prepared from 500ng of DNase-treated RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Sequencing was performed in 100pb paired-end reads using using Novaseq 6000.

value: Zc3h13 KO


title: AA8

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
CTL_AA8

tag: tissue


title: hFXRWat2

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

hyb_protocol: Hybridisation of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45C in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual.

scan_protocol: Washing and staining of the arrays was done on a Affymetrix 450 fluidics stations using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual. Arrays where then scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual.

data_processing: The data where normalized using VSN normalisation strategies using the MADMAX analysis pipeline pmid:21778530

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 500ng of total RNA without rRNA reduction

extract_protocol: Total RNA was prepared form WAT and BAT adipose tissue of 10wk old mice fed a chow diet.

tag: strain background

value: adipose-specific human FXR overexpressors

tag: gender

value: male

tag: diet

value: chow

value: White Adipose Tissue (WAT)


title: hFXRWat4


title: WTAP KO ESC_Rep 1

tag: development stage

value: Wtap KO


title: hFXRWat3


title: Mettl14 KO ESC_Rep 2

value: Mettl14 KO


title: hFXRWat1


title: ControlWat4

value: wild type (control)


title: Zc3h13 KO ESC_Rep 1


title: HCC1954_shNT_rep1

description: stable knockdown

tag: passage

tag: transfection reagent


title: ControlWat3


title: Mettl14 KO ESC_Rep 1

tag: medium


title: AA10

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
D1CKO_AA10

value: striatum

value: F

value: post-natal day 9


title: WTAP KO ESC_Rep 2

tag: genotype/variation


title: HCC1954_shNT_rep3

description: stable knockdown

tag: sirna/shrna


title: hFXRBat4

description: SAMPLE 9

value: Brown Adipose Tissue (BAT)


title: HCC1954_siAP2C_rep3

description: transient knockdown

value: Lipofectamine RNAi_Max

value: TFAP2C siRNA ID:107041


title: ControlWat2


title: hFXRBat5


title: ControlWat1


title: Mettl3 KO ESC_Rep 2

value: Mettl3 KO


title: Mettl3 KO ESC_Rep 1


title: AA6

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
D2CKO_AA6

value: D2-Cre tg/+; Foxp1flox/flox