title: HCT116 H3K4me1 ChIP Seq


title: SW480 H3K4me1 ChIP Seq

status: Public on Feb 08 2017

type: SRA

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

country: USA

institute: Case Western Reserve University

library_source: genomic

data_processing:
Adapter and quality trimming of both ChIP-Seq and RNA-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded
ChIP-seq reads were aligned to hg19 with Bowtie2 version 2.0.6, using default parameters. RNA-Seq reads were aligned to hg19 using TopHat v1.3.2
Potential PCR duplicates were removed from aligned ChIP Seq reads files
ChIP-Seq peaks were called using MACS v1.4. Cufflinks v1.3.0, run with genomic bias correction, was used to calculate transcript abundancies in the RNA-Seq data.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq WIG tracks were generated with MACS v.14. The WIG signal was divided by mean WIG signal for each sample, and the WIGs were converted to bigWIGs

molecule: genomic DNA

organism: Homo sapiens

source_name: CRC cell line

growth_protocol: CRC cell lines were grown in MEM media supplemented as previously described, except for COLO205 cells which were grown in RPMI-1640 supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin/streptomycin.

extract_protocol:
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For DNase Hypersensitivity, nuclei were isolated and treated with DNase I. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer’s protocol.
ChIP-Seq libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of ~250 bp were band isolated from an agarose gel. DNase Hypersensitivity libraries were prepared as previously described.  Briefly, DNase I treated DNA was blunt-ended. DNA fragments were ligated to biotinylated linkers and digested with MmeI, producing 2 bp overhangs for ligation with a second linker or Illumina adapters. DNA was then PCR amplified and library fragments of ~86 bp were band isolated from a gel. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For RNA-Seq samples, CRC cells at ~0.5×10^6 cells/well in 6-well plates were treated with 500nM JQ1 for 0.5, 1, 6, or 24 hours, or 0 hours as a control

tag: tissue

value: colorectal cancer cell line

tag: cell line

tag: chip antibody

value: rabbit anti-H3K4me1 (Abcam #8895)


title: L1

city: Pisa

first: Tommaso

last: Giordani

address: via del Borghetto 80

department: Department of Agricolture, Food and Enviroment

country: Italy

institute: University of Pisa

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed using trimmomatic version 0.33 with the following parameters: CROP 115, HEADCROP 15,MINLEN 100
Ribosomal RNA sequences from public database NCBI were used to remove rRNA from libraries using CLC Genomic workbench (v. 8.0.3) mapping strategy.
Reads were mapped using CLC-Genomic Workbench 8.0.3 onto a Ovis aries transcriptome (Oar v. 4.0)
Gene expression level was calculated and expressed as mreads per kilobase per million reads mapped (RPKM) as described in Mortazavi et al. (2008)
Genome_build: Reference transcriptome: GCF_000298735.2_Oar_v4.0_rna.fna
Supplementary_files_format_and_content: Tab-delimited text file including RPKM values for each sample

molecule: total RNA

organism: Ovis aries

source_name: milk somatic cells

growth_protocol: Three Comisana 90 days of lactation sheep were used. Starting in February 2015, each sheep was fed grass hay and a commercial concentrate for three weeks. Diet was formulated according to a nutrient requirements of an ewe weighing 65 kg and producing 1 kh of milk at 6,5% fat. Animal health was constantly monitored.

extract_protocol:
MSC were pelletted from 250 ml of fresh milk at 1100g for 10 min at 4°C. The cell pellet was washed twice in PBS, pH 7.2 with 0.5 mM EDTA and resuspended in 3 ml of Trizol Reagent (Life Technologies). RNA extraction continued following the Trizol protocol, performing all centrifugation steps at 4°C and isopropanol precipitation at -80°C for 30 min. A DNAse I (Roche) treatment was performed according to the manufacturer’s instructions, to completely remove genomic DNA contamination. Finally RNA was purified by phenol/chloroform extraction and precipitated following standard procedures.
RNA-Seq library was generated using the TruSeq RNA-Seq Sample Prep kit, according to the manufacturer protocol (Illumina Inc., San Diego, CA, USA)

treatment_protocol: The same  sheep were fed grass, hay and a concentrate containing 20 % of extruded linseed on dry matter basis for three weeks. Milk from each sheep was collected at the beginning and at the end of  the experiment.

tag: breed

value: Comisana

tag: sheep id

value: milk somatic cells


title: COLO205 H3K4me1 ChIP Seq


title: C37 H3K4me1 ChIP Seq

source_name: Colon Crypt

value: normal colon crypt


title: C3


title: C1


title: C28 H3K4me1 ChIP Seq


title: H1-KI+Cre HE GFP+ rep2

city: Guangzhou

first: Hao

last: Sun

address: Kaiyuan avenue 190

country: China

institute: GIBH

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 mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: ES derived Hemogenic endothelium

extract_protocol:
RNA was harvested using Trizol reagent. 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

tag: cell type

tag: genotype

value: GATA2/eGFP knockin


title: H1-KI+Cre HE GFP- rep1

value: eGFP-CD34+CD31+CD43- endothelial cells


title: Young_1_7_2

city: Seoul

first: Hang-Rae

last: Kim

address: 103 Daehak-ro, Jongno-gu

department: Anatomy and Cell Biology

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
Sequences were sorted using their unique barcode, and low-quality reads (average quality score < 25 or read length < 300 bp) were removed.
Primer sequences were trimmed by pairwise alignment and the hmm-search program of the HMMER 3.0 package
Trimmed sequences were clustered to correct for sequencing error, and representative sequences were assigned to operational taxonomic units (OTUs; 97% identity)
Taxonomic identification was performed using the EzTaxon-e database (http://eztaxon-e.ezbiocloud.net/) by the highest pairwise similarity among the top five BLASTN results
Possible chimera sequences were removed using the UCHIME software. The read numbers in each sample were normalized by random subsampling, and the diversity indices were calculated using the Mothur software. A Unifrac clustering, heatmap and principal coordinate analysis were performed using CLcommunity (ChunLab). We also performed LEfSe analysis on the website http://huttenhowe.sph.harvard.edu/galaxy.
Genome_build: EzTaxon-e database (http://eztaxon-e.ezbiocloud.net)
Supplementary_files_format_and_content: tab-delimited text files include ‘microbial phylotypes classification’ for each sample; sum (number): each bacteria species sequence read number,    sum (ratio): (each bacteria species sequence read number/total bacteria species read number)*100 as a percentage from total read read number.

organism: Mus musculus

source_name: gut microbiota (ceca contents)

extract_protocol:
DNA was extracted using the FastDNA SPIN extraction kit (MP Biomedicals, Santa Ana, CA, USA).
PCR amplification of the V1-V3 region of bacterial 16S rRNA gene was performed using universal primers incorporating the FLX Titanium adapters and a sample barcode sequence. The forward primer (27F, bold type) was 5¢-CCT-ATC-CCC-TGT-GTG-CCT-TGG-CAG-TCT-CAG-Linker-AGA-GTT-TGA-TCC-TGG-CTC-AG-3¢, in which the sequence of the 454 adapter2 is shown underlined and the 454 key in italics. The reverse primer (536R, bold type) was 5¢-CCA-TCT-CAT-CCC-TGC-GTG-TCT-CCG-ACT-CAG-Barcode-Linker-TTA-CCC-GCG-GCT-GCT-GGC-AC-3¢, in which the 454 adapter 1 sequence is underlined and the 454 key is shown in italics. The amplified PCR products were purified, quantified and subjected to emulsion PCR using protocols developed by Roche Life Sciences (Roche, Branford, CT, USA).
Pyrosequencing was performed by ChunLab Inc. (Seoul, Korea) using a 454b GS FLX Titanium Sequencing System according to the method

treatment_protocol: To compare the overall structural changes in the gut microbiota, young and old mice were treated with vehicle, syringaresinol (SYR, 10 mg/kg or 50 mg/kg), or caloric restriction (CR).

tag: strain

tag: age

value: 6 weeks

tag: invervention

value: free


title: H1-KI+Cre HE GFP+ rep1


title: H1-KI+Cre HE GFP- rep2


title: CRC_6A H3K27ac ChIP Seq

source_name: primary CRC tumor tissue

value: primary colorectal cancer tumor

value: rabbit anti-H3K27ac (Abcam #4729)


title: CRC_23A H3K27ac ChIP Seq


title: C29 H3K4me1 ChIP Seq


title: V1024 H3K4me1 ChIP Seq


title: C28 H3K27me3 ChIP Seq

value: mouse anti-H3K27me3 (Abcam #6002)


title: CRC_7A H3K27ac ChIP Seq


title: CRC_17A H3K27ac ChIP Seq


title: P20_3

city: Urbana

first: Daniel

middle: J

last: Urban

state: Illinois

address: 515 Morrill Hall, 505 S. Goodwin Ave

department: Animal Biology

institute: University of Illinois at Urbana-Champaign

data_processing:
Initial RNA-Seq analysis was conducted on the UIUC web-based Galaxy platform (galaxy.illinois.edu), using the Tuxedo protocol.
Sequence files were uploaded, along with an opossum reference genome (monDom5) from ensemble.org.
The basic sequence follows: Edit sequences trims ends, TopHat aligns reads to the genome, Cufflinks assembles the reads into transcripts, Cuffmerge blends multiple samples from the same stage, and Cuffdiff reports genes and transcripts that are differentially expressed between stages
Genome_build: monDom5
Supplementary_files_format_and_content: xlsx file with separate tabs for all genes expressed and genes with significant differential expression. The Sample 1 and Sample 2 columns in the processed data file are stating which stages are being compared for each line (q1 = P16, q2 = P18, and q3 = P20).

organism: Monodelphis domestica

source_name: Meckel's cartilage and anterior malleus

extract_protocol:
Samples were cryosectioned to collect tissue for RNASeq. N = 3 specimens were collected for each stage (16, 18 and 20 day) and an Arcturus Veritas Microdissection Instrument was used to laser capture microdissect (LCM) the MC and malleus (with minimal surrounding perichondrium) focusing on their connection area. RNA isolation was completed using an Arcturus PicoPure RNA Isolation Kit, and the Clontech SMARTer Ultra Low Input RNA Kit for RNA amplification.
RNA-Seq Libraries were constructed using a Nextera XT DNA Sample Preparation Kit, along with a Nextera XT Index Kit and TruSeq Dual Index Sequencing Primers.

tag: developmental stage


title: P18_3


title: P18_1


title: P20_2


title: V9P H3K27ac ChIP Seq


title: P18_2


title: C2


title: V429 H3K4me1 ChIP Seq


title: V940 H3K27ac ChIP Seq


title: P16_1


title: P16_3


title: V866 H3K27ac ChIP Seq


title: B6spo11ko_H3K36me3_ChIPseq_Rep2

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

country: France

institute: CNRS

description:
processed data file:
CHIP_H3K36me3_B6_spo11_coverage.bw

data_processing:
Base-calling was performed  using CASAVA
ChIPseq reads were aligned to the mm9 genome using Bowtie (H3K4me3), Bowtie2 (PRDM9, H3K36me3) or BWA and its modified algorithm proposed in Khil et al., 2012  (DMC1)
Reads that were unmapped, multi-mapped, unpaired, duplicated were filtered out in each experiment, unpaired reads were removed for paired-end experiments, and reads that  mapped with more than 1 mismatch were removed in all but DMC1 ChIPseq experiments.
Peaks were called using MACS1.3.7 (H3K4me3) or MACS2 (PRDM9, DMC1, H3K36me3)
IDR method was used to deal with replicates for PRDM9 and DMC1 peaks
Genome_build: mm9
Supplementary_files_format_and_content: bedfiles represent peaks called from MACS1.3.7 or MACS2 for all but H3K36me3 ChIPseq experiments ; bigwig were built from merged replicates after alignment step for H3K36me3 ChIPseq experiment

extract_protocol:
Cell suspension was prepared by filtering homogenized tissue, then lysed.Lysates were sonicated and chromatin complexes were isolated with appropriate antibody.
Standard library construction was performed with the Illumina Trueseq protocol (Illumina, IP-202-9001DOC). For DMC1 ChIP an additional step of kinetic enrichment was performed as described in Khil et al. 2012.
ChIP-seq for all but DMC1 CHIPseq experiment ; SSDS method described in Khil et al. 2012 for DMC1 ChIPseq

treatment_protocol: Antibodies against PRDM9 were homemade (anti-PRDM9 BdM). They were raised by immunizing two rabbits with recombinant full-length PRDM9Cst protein fused to 6x HIS at the N-terminus. PRDM9 polyclonal serum was then affinity-purified by incubation with PRDM9Dom2 recombinant protein immobilized on a nitrocellulose membrane.

tag: tissue/cells

value: whole-testis

value: 13 days post-partum

value: anti-H3K36me3 (Diagenode, Premium, C15410192)


title: B6spo11ko_H3K36me3_Input_Rep1


title: B6spo11ko_H3K36me3_ChIPseq_Rep1


title: P20_1


title: RJ2_H3K36me3_Input_Rep1

description:
processed data file:
CHIP_H3K36me3_RJ2_coverage.bw


title: RJ2_H3K36me3_ChIPseq_Rep1


title: V855 H3K27ac ChIP Seq


title: V784 H3K27ac ChIP Seq


title: B6_H3K36me3_Input_Rep2

description:
processed data file:
CHIP_H3K36me3_B6_coverage.bw


title: RJ2_H3K36me3_ChIPseq_Rep2


title: V968 H3K27ac ChIP Seq


title: B6_H3K36me3_Input_Rep1


title: B6_H3K36me3_ChIPseq_Rep1


title: RJ2_DMC1_ChIPseq_Rep2

description:
processed data file:
CHIP_DMC1_RJ2_peaks.bed

value: 5 weeks post-partum

value: anti-DMC1 (Santa Cruz, C-20)


title: V481 H3K27ac ChIP Seq

value: colorectal cancer cell line


title: V5 H3K27ac ChIP Seq


title: RJ2_DMC1_ChIPseq_Rep1


title: P16_2


title: B6_DMC1_ChIPseq_Rep2

description:
processed data file:
CHIP_DMC1_B6_peaks.bed


title: B6spo11ko_PRDM9_Input_Rep2

description:
processed data file:
CHIP_PRDM9_B6_spo11_peaks.bed

value: anti-PRDM9 (BdM)


title: B6_DMC1_ChIPseq_Rep1


title: V432 H3K27ac ChIP Seq


title: V429 H3K27ac ChIP Seq


title: B6spo11ko_PRDM9_Input_Rep1


title: V456 H3K27ac ChIP Seq


title: B6prdm9ko_PRDM9_ChIPseq_Rep1

description:
processed data file:
CHIP_PRDM9_B6_prdm9KO_peaks.bed


title: B6spo11ko_PRDM9_ChIPseq_Rep1


title: RJ2_PRDM9_ChIPseq_Rep2

description:
processed data file:
CHIP_PRDM9_RJ2_peaks.bed


title: B6_H3K36me3_ChIPseq_Rep2


title: V703 H3K27ac ChIP Seq


title: RJ2_PRDM9_Input_Rep1


title: V457 H3K27ac ChIP Seq


title: V411 H3K27ac ChIP Seq


title: V206 H3K27ac ChIP Seq


title: RJ2_PRDM9_ChIPseq_Rep1


title: V1106 H3K27ac ChIP Seq


title: B6prdm9ko_PRDM9_Input_Rep1


title: B6_PRDM9_Input_Rep2

description:
processed data file:
CHIP_PRDM9_B6_peaks.bed


title: B6_PRDM9_ChIPseq_Rep2


title: V1074 H3K27ac ChIP Seq


title: RJ2_PRDM9_Input_Rep2


title: B6_PRDM9_ChIPseq_Rep1


title: V1058 H3K27ac ChIP Seq


title: susc-reexp1hr_28d_Input_s3

city: New York

first: Ian

middle: S

last: Maze

state: NY

address: 1470 Madison Avenue, 9-109

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: Susceptible + acute stress (Input)

data_processing:
Raw sequencing reads were aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0). Only uniquely mapped reads were retained.
Alignments were subsequently filtered using the SAMtools package (v0.1.19) to remove duplicate reads.
Differential region analysis between conditions was performed using diffReps (v1.55.4) with with parameter settings "--pval 0.001 --frag 250 --window 250" as an initial run. Detected differential events were then further filtered with additional stringent cutoffs of pvalue < 0.0001 and absolute fold change > 3.
Annotation of called peaks and differential regions to their genomic features (promoters, gene bodies, intergenic, etc.) was performed using the RegionAnalysis program of diffReps (v1.55.4)
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel files containing lists of differential regions identified from i) Control vs. acute, and ii) control vs. susceptible + acute comparisons.

source_name: nucleus accumbens

extract_protocol:
H3.3 crosslinking ChIP assays on NAc tissues (bilateral NAc from 5 animals was pooled/N) were performed exactly as previously described (PMID: 26139371). All experiments were analyzed in biological triplicates.
Illumina TruSeq ChIP Kit (Manufacturer protocols were followed exactly)

treatment_protocol: For ChIP-seq experiments, control and susceptible mice (determined in SI test 48 h post-defeat) were killed 28 d following the final defeat episode. Mice were either taken directly from their home-cage (baseline) or following a stress re-exposure (5 min acute aggression, followed by 55 min housed adjacent to aggressor; i.e., stress-primed).


title: V1009 H3K27ac ChIP Seq


title: B6spo11ko_PRDM9_ChIPseq_Rep2


title: V1024 H3K27ac ChIP Seq


title: susc-reexp1hr_28d_Input_s2

description: Susceptible + acute stress (Input)


title: V1051 H3K27ac ChIP Seq


title: susc-reexp1hr_28d_H33IP_s3

description: Susceptible + acute stress (H3.3 ChIP)


title: HCT116 H3K27ac ChIP Seq


title: SW480 H3K27ac ChIP Seq


title: B6_PRDM9_Input_Rep1


title: Crypt5 H3K27ac ChIP Seq


title: C28 H3K27ac ChIP Seq


title: ctrl_28d_Input_s2

description: Control (Input)


title: ctrl_28d_Input_s3

description: Control (Input)


title: ctrl_28d_Input_s1

description: Control (Input)


title: COLO205 H3K27ac ChIP Seq


title: susc-reexp1hr_28d_H33IP_s1

description: Susceptible + acute stress (H3.3 ChIP)


title: susc-reexp1hr_28d_Input_s1

description: Susceptible + acute stress (Input)


title: susc-reexp1hr_28d_H33IP_s2

description: Susceptible + acute stress (H3.3 ChIP)


title: V576 Dnase I Hypersensitiviy


title: ctrl_28d_H33IP_s3

description: Control (H3.3 ChIP)


title: V410 Dnase I Hypersensitiviy


title: ctrl_28d_H33IP_s2

description: Control (H3.3 ChIP)


title: ctrl_28d_H33IP_s1

description: Control (H3.3 ChIP)


title: C37 H3K27ac ChIP Seq


title: ctrl-acuteexp1hr_28d_Input_s3

description: Acute Stress (Input)


title: C36 Dnase I Hypersensitiviy


title: ctrl-acuteexp1hr_28d_Input_s2

description: Acute Stress (Input)


title: ctrl-acuteexp1hr_28d_Input_s1

description: Acute Stress (Input)


title: V389 Dnase I Hypersensitiviy


title: NBE_1011225_DREAM

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description: Adjacent normal breast tissue was isolated from patients with breast cancer, then epithelial cells were isolated and grown in culture for a few passages before DNA isolation

data_processing:
Library strategy: DREAM
Illumina HiSeq2500 paired end sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to hg19 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*Xma/(c*Xma+Sma)), where c=2.342 was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), MethReads (observed number of reads corresponding to methylated CpG, Xma), UnmethReads (observed number of reads corresponding to unmethylated CpG, Sma), RawMethylation (unadjusted methylation value), AdjMethylation (methylation value adjusted based on the spiked in standards).

source_name: normal breast epithelial cells

growth_protocol: MCF7 cell line was cultured in DMEM medium with 10% fetal bovine serum, normal breast epithelial cells were grown in 1:1 DMEM/F12 medium with 2.4 g/L sodium bicarbonate, 5% chelated horse serum, 20 ng/ml EGF (BD Biosciences), 100 ng/ml cholera toxin (Sigma-Aldrich), 10 mg/L insulin (Sigma-Aldrich), 0.5 mg/L hydrocortisone (Sigma-Aldrich), and 0.04 mM calcium chloride (Sigma-Aldrich)

extract_protocol:
phenol-chloroform
Five micrograms of genomic DNA spiked with 500 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: tissue of origin

value: breast

tag: disease

value: adjacent normal tissue from 49 year old patient with infiltrating ductal carcinoma

tag: gender

value: female


title: C34 Dnase I Hypersensitiviy

value: normal colon crypt


title: MCF7_DREAM

source_name: MCF7 breast cancer cell line

value: breast cancer cell line

value: mammary gland, breast; derived from metastatic site:pleural effusion; ER positive


title: ctrl-acuteexp1hr_28d_H33IP_s3

description: Acute Stress (H3.3 ChIP)


title: V389 input DNA


title: C29 H3K27ac ChIP Seq


title: V410 H3K4me1 ChIP Seq

value: rabbit anti-H3K4me1 (Abcam #8895)


title: ctrl-acuteexp1hr_28d_H33IP_s2

description: Acute Stress (H3.3 ChIP)


title: NBE_1013140_DREAM

value: adjacent normal tissue from 69 year old patient with lobular carcinoma in situ


title: ctrl-acuteexp1hr_28d_H33IP_s1

description: Acute Stress (H3.3 ChIP)


title: V852 input DNA


title: V410 input DNA


title: V576 H3K27ac ChIP Seq

value: rabbit anti-H3K27ac (Abcam #4729)


title: V852 H3K27ac ChIP Seq


title: V576 H3K4me1 ChIP Seq


title: TMD8 DMSO Phospho-H3Y41

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

data_processing:
ChIP-Seq Analysis
Calculation Method: To analyze the H3Y41-P ChIP-Seq data, redundant tags were discarded and only only unique tags within each given experiment (DMSO or AZD1480) were used to perform peak calling. 36 bp sequence tags were aligned to human genome build 36 (hg18) with Bowtie software. A maximum of two mismatches was allowed for each read. To perform "peak calling", the genome was divided into "bins" of 25 bp. Each sequencing tag was associated with the bin of its start site and an additional extension of 7 bins (for a total of 200bp) along the direction of its read to match the average library size. For a given experiment, the number of "hits" in a bin was defined as the number of extended tags associated with that bin. Peaks were defined by merging consecutive significant bins. The height of the peak was defined as the largest number of hits in any of the bins forming the peak. The "apex" of the peak was defined as the bin that had this largest number of hits. In the case of ties, the earliest such peak was chosen as the apex. A threshold of apex >10 tags/bin was used to define high-stringency H3Y41-P binding peaks. To compare the results of two experiments (DMSO vs AZD1480), ChIP-Seq data were normalized by total tags count. A binomial p-value was calculated for the degree to which the ratio between the tag counts of the two experiments in a given bin differs from the ratio of the total number of tags in the two experiments. Bins for which this resulted in a (one-sided) p-value less than 0.01 were deemed significant. The p-value of the peak was set to be the most significant binomial p-value for the bins that made-up that peak.
Genome_build: hg18
Supplementary_files_format_and_content: bed file

source_name: TMD8 DMSO Phospho-H3Y41

extract_protocol:
Phospho-H3Y41 Antibody Extraction
Other: For treated samples, 20 Million cells were collected by centrifugation, resuspended in room temperature RPMI without FBS (2 Mln cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Chromatin shearing was performed with a Bioruptor sonicating bath (Diagenode). Chromatin immunoprecipitation was performed with a phospho-H3Y41 antibody (Abcam #ab26310).
ChIP-enriched DNA samples were used to create adapter-ligated libraries for massively parallel sequencing with the ChIP-Seq DNA Sample Prep Kit (Illumina).

treatment_protocol:
Treatment type: compound
Agent: DMSO (Dimethyl sulfoxide)
Treatment time: 16 hours
In-vitro treatment: Cells were treated with DMSO.

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)


title: TMD8 AZD1480 IgG Control

source_name: TMD8 AZD1480 IgG Control

extract_protocol:
IgG Negative Control Extraction
Other: For treated samples, 20 million cells were collected by centrifugation, resuspended in room temperature RPMI without FBS (2 Mln cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Chromatin shearing was performed with a Bioruptor sonicating bath (Diagenode). Chromatin immunoprecipitation was performed with normal rabbit IgG (Santa Cruz #sc-2027) as a negative control.
ChIP-enriched DNA samples were used to create adapter-ligated libraries for massively parallel sequencing with the ChIP-Seq DNA Sample Prep Kit (Illumina).

treatment_protocol:
Treatment type: compound
Agent: AZD1480
Treatment time: 16 hours
Treatment dose: 2 uM


title: TMD8 DMSO IgG Control

source_name: TMD8 DMSO IgG Control


title: V576 input DNA


title: V410 H3K27ac ChIP Seq


title: V457 H3K4me1 ChIP Seq


title: Crypt5 H3K4me1 ChIP Seq


title: V389 H3K27ac ChIP Seq


title: V410 H3K27me3 ChIP Seq

value: mouse anti-H3K27me3 (Abcam #6002)


title: C31 Dnase I Hypersensitiviy


title: phr_XR-seq_exp2

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

data_processing:
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: NC_000913.2

organism: Escherichia coli

growth_protocol: Nonselective LB medium at 37o.

extract_protocol:
HIRT lysis procedure.
Hu et al. 2015 Genes Dev 29(9):948-960 procedure.

treatment_protocol: Irradiation at an OD600 of 0.8 with 120 J/m2 UVC at room temperature. Chilled after 5 minutes.

tag: genotype/variation

value: phr -


title: phr_XR-seq_exp1


title: mfd_XR-seq_exp2

value: mfd -


title: TMD8 AZD1480 Phospho-H3Y41

source_name: TMD8 AZD1480 Phospho-H3Y41


title: M3I1_M3

city: Hangzhou

first: Yicun

last: Chen

state: Zhejiang

address: Fuchun Street

department: Institute of Subtropical Forestry

institute: Chinese Academy of Forestry

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 assembly use Trinity
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Trinity assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ;Trinity assembly result

organism: Vernicia montana

source_name: V. montana_F. oxysporum_late stage_root

growth_protocol: V. fordii and V. montana plantlets with two or three leaves and approximately 30 cm in height were used. All plantlet were kept under growth chamber conditions at 26℃ with 16-h light/8-h dark photoperiod.

extract_protocol:
Total RNA was extracted from the plant roots and root-stem transition region using the EASYspin plant RNA mini kit (Aidlab, Beijing, China) QIAGEN RNeasy plant mini kit (QIAGEN, Valencia, CA). RNA integrity was confirmed using the UV-Vis Spectrophotometer Q5000 (Quawell, USA). All RNA samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) ≥8.0. mRNA was purified from 30 µg of total RNA using Sera-mag Magnetic Oligo(dT) Beads (Illumina) and fragmented into small pieces using divalent cations under elevated temperature.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Before inoculation, the plantlet was sterilized in a solution containing 75% ethanol for 1 min, and 0.5% sodium hypochlorite for 3 min, and then 90% ethanol for 30 sec, and followed by rinsing three times in sterile water. For inoculation, a spore concentration of 1×10^6 spores per mL, diluted with sterile distilled water, was used to inoculate the plants. Before inoculations, the plants were carefully removed from the soil, and the roots were rinsed with sterile water and then dipped for 30 min into the fungal inoculum. The plants were sampled at 2-15 dpi (days post inoculation). The root, peel and leaves were cut and immediately frozen in liquid nitrogen and stored at -80℃ until retrieved for RNA preparation.

tag: tissue

value: seedling; root

tag: infected with

value: Fusarium oxysporum

tag: pathogen infection stage

value: 3; late stage


title: uvrD_XR-seq_exp2

value: uvrD -


title: WT_XR-seq_exp2

value: Wild-type


title: M3L_M3


title: M3H_M3


title: M2I1_M2

source_name: V. montana_F. oxysporum_middle stage_root

value: 2; middle stage


title: V389 H3K4me1 ChIP Seq

value: colorectal cancer cell line

tag: cell line

tag: chip antibody


title: Tj-w1118_Rep1

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were mapped to Drosophila melanogaster genome BDGP release 5/dm3 using STAR (STAR_2.3.0e_r291)
Gene level FPKM was estimated using cufflinks (v2.1.1) with GTF file from Ensemble release 74
Genome_build: D. melanogaster BDGP release 5/dm3
Supplementary_files_format_and_content: tab-delimited text files include gene level FPKM valuse for each Sample

organism: Drosophila melanogaster

source_name: Whole ovary

growth_protocol: Drosophila animals were grown on cornmeal agar in 27 degrees Celsius.

extract_protocol:
GeneJET RNA purification kit (Thermo Scientific, K0732)
RNA libraries were prepared for sequencing using Illumina TruSeq RNA v2 protocols

value: ovarian tissues


title: M1L_M1

source_name: V. montana_F. oxysporum_early stage_root

value: 1; early stage


title: Tj-Kay_Rep2


title: WT_ovary_Rep3


title: M1I1_M1


title: WT_ovary_Rep2


title: piwi_ovary_Rep2


title: M0L_M0

source_name: V. montana_no pathogen infection_root

value: 0; no pathogen infection


title: uvrD_XR-seq_exp1


title: M2H_M2


title: mfd_XR-seq_exp1


title: Tj-Kay_Rep1


title: Biological Replicate 2 of caper mutant embryos

status: Public on Feb 07 2017

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

data_processing:
Quality trim to a minimum of Q15
Map to the mm10 genome using GSNAP version 2014-12-17 using the commandline /vol2/home/analysiscore/bin/gsnap_20120720_250/gsnap -d Drosophila_melanogaster.BDGP5 -v Drosophila_melanogaster.dbSNP --use-splicing=Drosophila_melanogaster.BDGP5.78.splice_sites --max-mismatches=0.06 -i2 -n1 -Q --gunzip --nofails -B5 -t12 --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $file $file_R2 > ./Illumina_data/$j.sam
sort and index using SAMTOOLS
Call relative expression using JunctionSeq
Genome_build: BDGP5
Supplementary_files_format_and_content: Excel file containing FPKM values

source_name: whole embryo lysate

growth_protocol: Embryos were collected on apple juice plates with yeast.

extract_protocol:
Drosophila OreR and caperCC01391 embryos were collected and RNA was extracted using TRIzol Reagent (Invitrogen).After DNase I (Roche) treatment, RNA was purified with a phenol:chloroform extraction and resuspended in RNAse-free water.
RNA libraries were prepared and sequenced by the University of Colorado Genomics and Microarray core using the Illumina TruSeq Stranded RNA library preparation kit.
RNA-Seq: Paired-end 2x125bp sequencing was performed in a single lane using an Illumina HiSEQ 2500.

value: whole embryo lysate


title: Biological Replicate 3 of caper mutant embryos


title: M0I1_M0


title: piwi_ovary_Rep1


title: Tj-Kay_Rep3


title: Tj-w1118_Rep3


title: Biological Replicate 2 of OreR embryos

value: OreR


title: Biological Replicate 1 of OreR embryos


title: M0H_M0


title: Biological Replicate 3 of OreR embryos


title: Biological Replicate 1 of caper mutant embryos


title: Tj-w1118_Rep2


title: M2L_M2


title: GCCAAT-WT3

city: Portland

first: Jay

last: Mellies

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

description: enriched for mRNA

data_processing:
For the whole-transcriptome analysis, sequencing was verified using FASTQC (version 0.11.2) to confirm base-call quality in each indexed file.
Indices corresponding to the same sample were merged, and then uploaded to a cloud-based variant of Galaxy named RNA23 Rocket
Using Bowtie2 (version 2.0.2), sequenced reads were mapped to an EPEC O127:H6 reference genome (EMBL/GenBank accession codes FM180568, FM180569, and FM180570).
Mapped reads were quality checked with SAMstat (version 1.08), and transcripts were assembled in Cufflinks (version 2.0.2)
Differential gene expression (DGE) was then performed on fragments per kilobase mapped (FPKM) values in Cufflinks’ Cuffdiff package (version 0.0.7).
DGE analysis used a false-discovery rate (FDR) of 0.10.
Subsequent data visualizations were performed in R (version 3.1.2) using the cummeRbund package (version 3.0)
Genome_build: FM180568
Genome_build: FM180569
Genome_build: FM180570
Supplementary_files_format_and_content: bedgraph: Data presented in a 4 column BED format, of which the first column is the chromosome, the second column is the start position of the chromosome, the third column is the end position, and the fourth column is the fragments per kilobase mapped (FPKM) for that sample. Chromosome positions are specified as 0-relative. The first chromosome position is 0. The last position in a chromosome of length N would be N - 1. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data are in numerical order.
Supplementary_files_format_and_content: tabular: Tabular data that informs the excel spreadsheet. The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Data contain gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant.
Supplementary_files_format_and_content: xls: The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Excel spreadsheet containing gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant.

organism: Escherichia coli O127:H6 str. E2348/69

source_name: Whole bacterial cell RNA transcriptome

growth_protocol: LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5).

extract_protocol:
Samples were diluted 1:1 in RNA Protect (Qiagen, Carlsbad, CA) to inhibit RNase activity and then centrifuged (5000 x g, 10 min). Pellets were resuspended in TE/lysozyme (10 mg/ml lysozyme, 0.5% SDS, pH 8.0) with added proteinase K (1.5 mg/ml). RNA was isolated using Qiagen’s RNeasy kit according to manufacturer instructions with slight modification. Before centrifugation, β-mercaptoethanol was added to RNeasy kit buffer RLT (10% v/v). Additionally, during the wash step RNase-free DNase (Qiagen, Carlsbad, CA) was diluted in RNeasy kit buffer RDD (310 Kunitz units/mL), added to the purification column, and incubated for 15 minutes at room temperature (RT). After isolation, spectrophotometric NanoDrop (NanoDrop 1000 v3.8.1; Thermo Fisher) curves were obtained for each total RNA sample and verified for purity, as defined by absorbance ratios at 260/280 nm and 260/230 nm. Total RNA samples were sent to Oregon State University’s Center for Genome Research and Biocomputing. RNA integrity (RIN) measurements were taken using an Agilent Bioanalyzer, resulting in RIN scores of 10, out of a possible 10, for each sample. Ribosomal RNA was depleted using the RiboZero rRNA removal kit (Life Technologies, Eugene, OR).
Resulting mRNA was reverse-transcribed to cDNA libraries via SuperScript III First Strand reverse transcription kit (Invitrogen, Carlsbad, CA, 18080051) as per the manufacturer’s instructions. The cDNA libraries were multiplexed to distinguish replicates from one another, barcoded for sequencing, and then amplified with random hexamers for 15 PCR cycles. Transcripts were sequenced for 50 bases in single-end fashion within one lane of an Illumina Hiseq 2000 flow cell. This yielded roughly 30 million reads per sample.

treatment_protocol: Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600).

value: WT typical EPEC

tag: source

value: Levine et al., 1985


title: TGACCA-WT1

description: enriched for mRNA


title: WT_ovary_Rep1


title: M1H_M1


title: BMMC.DNMT3A-KO

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads quality filtered according to the Illumina pipeline and sequencing adaptors were removed using by Trimmomatic (PMID:24695404).
Reads were mapped to the UCSC mm10 reference genome using Bowtie2 with "--very-sensitive" parameter (PMID: 22388286). Only reads that uniquely mapped to the genome were used in subsequent analysis. Reads that did not align to the nuclear genome or aligned to the mitochondrial genome or marked as duplicate reads were removed. Then read positions were corrected for transposon insertion offset as described in (PMID:24097267).
ATAC-seq peaks in each sample were identified using MACS2 with the following settings: " -g mm --nomodel --extsize 100 -q 0.01"
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

source_name: Primary bone marrow-derived mast cells (BMMCs)

growth_protocol: Primary murine mast cells were differentiated from the bone marrow of DNMT3A-KO mice and WT littermates as previously described (PMID: 20827536) and cultured in the presence of IL-3 as survival factor. Briefly, bone marrow cells were isolated from femurs and tibias of 3-4 weeks old mice and differentiated in IMDM complete medium until they were homogeneously mast cells (>95% Kit+ FcεRIα+ at surface staining) (IMDM complete medium: Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.1 mM nonessential amino acids, and 50 mM beta-mercaptoethanol, recombinant murine IL-3).

extract_protocol: Nuclei were isolated using 0.1% Igepal containing buffer and subsequently transposed with adapter-loaded hyperactive Tn5 transposase (home-made). Tagmented DNA was purified and PCR-amplified to obtain a barcoded DNA library. Libraries were sequenced on an Illumina HiSeq 2000 at 10M reads depth (50 base pair Single Read).

tag: cell type

value: BMMC

tag: sample preparation

value: Cells were differentiated for 4 weeks in vitro in the presence of IL-3

tag: growth protocol

value: IL-3 was used as a survival and growth factor


title: WAT RNA Day 0

city: Wenzhou

first: Chunming

last: Ding

address: Wenzhou Medical University, University Town, Chashan, Wenzhou, Zhejiang, P.R China

institute: Wenzhou Medical University

data_processing:
Reads were aligned to mm9, using Tophat (version tophat-2.0.11) and genes were quantified using Cufflinks (Version 2.1.1)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM of the genes

source_name: Cultured white pre-adipocytes

extract_protocol:
Qiagen miRNeasy Mini Kit
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: Cultured white pre-adipocytes


title: WAT RNA Day 6

source_name: Cultured white adipocytes

value: Cultured white adipocytes


title: BMMC.WT

value: wild type


title: BAT RNA Day 6

source_name: Cultured brown adipocytes

value: Cultured brown adipocytes


title: BAT RNA Day 4


title: maternal KO + MO seq-48-rep

city: Chicago

first: Boxuan

middle: Simen

last: Zhao

state: IL

address: 929 E. 57th. Street

department: Chemistry

institute: University of Chicago

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column AA

data_processing:
Data analysis for each experiment: (1) for m6A-seq, reads were aligned to the reference genome (danRer10) using Tophat (v2.0.14, ref) with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c). (2) for m6A-CLIP-seq, after removing the adapter sequence, the reads were mapped to the reference genome (danRer10) using bowtie2. Peak calling method was similar to previous study (chen kai's Angew 2015). Briefly, mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER (homer ref here) to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. (3) for mRNA-Seq, Reads were mapped with Tophat and Cufflink (v2.2.1) was used to calculate the FPKM of each gene to represent their mRNA expression level.
Genome_build: danRer10
Supplementary_files_format_and_content: FPKM

organism: Danio rerio

source_name: whole zebrafish embryo

growth_protocol: growth protocol_embryos were collected and cultured in medium at 28.5 °C, and then harvested at each time point into TRIzol.

extract_protocol:
extract protocol_total RNA was extracted using Direct-zol (Zymo) from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003).
library construction protocol_Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: treatment protocol _

tag: development time (h.p.f.)

tag: genotype

value: maternal ythdf2 KO

tag: treatment

value: ythdf2 MO


title: piwi_ovary_Rep3

tag: strain


title: maternal KO + MO seq-36-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column Y


title: BWAT RRBS D6

data_processing:
paired-end reads were filtered based on qseq score
reads were aligned to the bisulfite-converted mouse genome (UCSC Build mm9, NCBI37, July 2007) using Bowtie
Genome_build: mm9
Supplementary_files_format_and_content: Methylation percentage of the CpG sites

source_name: Cultured brown induced white adipocytes

extract_protocol:
none provided by submitter
Modified Illumina RRBS Sample Preparation Protocol
Illumina's RRBS for Methylation Analysis

tag: cell types

value: Cultured brown induced white adipocytes


title: BAT RNA Day 0

source_name: Cultured brown pre-adipocytes

value: Cultured brown pre-adipocytes


title: maternal KO + MO seq-24-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column W


title: WT MO seq-48-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column Z

value: WT

value: control MO


title: WT MO seq-24-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column V


title: WAT RRBS Day 6


title: WT seq-14-17 somite stage-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column T


title: WAT RNA Day 4


title: maternal-zygotic KO seq-14-17 somite stage-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column U

value: maternal-zygotic ythdf2 KO


title: BAT RRBS Day 6 NE 4 HR


title: WT MO seq-36-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column X


title: maternal-zygotic KO seq-24-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column S


title: WAT RRBS Day 0


title: BAT RRBS Day 4


title: BAT RRBS Day 0


title: BAT RRBS Day 6


title: maternal-zygotic KO seq-8-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column Q


title: maternal-zygotic KO seq-12-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column R


title: maternal-zygotic KO seq-6-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column P


title: WT seq-12-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column N


title: WT seq-8-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column M


title: maternal KO seq-6-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column J


title: WT seq-6-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column L


title: maternal KO seq-4-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column I


title: HCC1954sh3plus

city: Boston

first: Brenton

last: Paolella

state: Massachusetts

address: 450 Brookline Ave. Smith 1010

institute: Dana-Farber Cancer Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, FASTQ files were aligned using TOPHAT v1.4 with parameters "--mate-inner- dist 300 --mate-std-dev 500 --no-sort-bam --no-convert-bam -p 4" and aligned to hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using RNASeqMetrics 44
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample in .gct file format

source_name: breast cancer cell line

growth_protocol: RPMI 10% FBS

extract_protocol:
Qiangen RNA easy extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: for doxycycline samples, treated with 100 ng/mL for 4 days to induce SF3B1 suppression

tag: cell line name

tag: doxycycline added

value: plus dox

tag: gene target of shrna


title: maternal WT seq-6-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column E


title: ACAGTG-WT2

description: enriched for mRNA

tag: genotype/variation

value: WT typical EPEC


title: BWAT RRBS D4


title: C51singledeltash4minus

value: Cal51 CRISPR copy loss

value: minus dox


title: maternal KO seq-2-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column H


title: maternal KO seq-0-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column G


title: C51singledeltash4plus


title: maternal WT seq-8-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column F


title: maternal KO seq-8-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column K


title: HCC1954sh4plus


title: maternal WT seq-2-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column C


title: C51sh4plus


title: WAT RRBS Day 4


title: maternal WT seq-4-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column D


title: maternal WT seq-0-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column B


title: C51sh4minus


title: WT MO seq-48

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 1  column AO


title: maternal KO + MO seq-48

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 1  column AY


title: maternal KO + MO seq-36

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 1  column AW


title: C51doubledeltash4plus

value: Cal51 CRISPR copy neutral


title: maternal KO + MO seq-24

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 1  column AU


title: WT seq-24-rep

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 2 column O


title: HCC1954sh4minus


title: WT MO seq-36

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 1  column AX


title: C51sh3plus


title: WT seq-14-17 somite stage

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 1 column AR


title: BT5sh4plus


title: WT MO seq-24

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 1  column AT


title: Hs5sh4plus


title: C51doubledeltash4minus


title: BT5sh4minus


title: maternal-zygotic KO seq-8

description: mzKO Y2-/- 8h

data_processing:
Data analysis for each experiment: (1) for m6A-seq, reads were aligned to the reference genome (danRer10) using Tophat (v2.0.14, ref) with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c). (2) for m6A-CLIP-seq, after removing the adapter sequence, the reads were mapped to the reference genome (danRer10) using bowtie2. Peak calling method was similar to previous study (chen kai's Angew 2015). Briefly, mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER (homer ref here) to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. (3) for mRNA-Seq, Reads were mapped with Tophat and Cufflink (v2.2.1) was used to calculate the FPKM of each gene to represent their mRNA expression level.
Genome_build: danRer10
Supplementary_files_format_and_content: bed file, contains peaks locations

growth_protocol: embryos were collected and cultured in medium at 28.5 °C, and then harvested at each time point into TRIzol.

extract_protocol:
total RNA was extracted using Direct-zol (Zymo) from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).


title: GRO-TTX_2_hr_2

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

description: nascent RNA

data_processing:
Library strategy: GRO-Seq
The sequencing reads were mapped to the mm10 UCSC annotation using TOPHAT (Trapnell, et al., 2009) with the parameters (-a 8 -m 0 -I 500000 -p 8 -g 20 --library-type fr-firststrand --no-novel-indels  --segment-mismatches 2) for RNA-Seq.
For GRO-Seq, the raw fastq reads were trimmed using cutadapt with parameters -a AAAAAAAAAAAAAAAAAAAA -z -e 0.10 -f fastq -m 32 (Chae et al., 2015).
RPKM calculations were done using the HOMER package by normalizing to 10 million reads
Tracks for visualization on UCSC browser are generated using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Strand specific bigWig files for visualizing expression levels on a genome browser.

source_name: Cortical neurons

growth_protocol: Primary cortical neurons from E16/18 mice were cultured in Neurobasal media with B-27 and Glutamax until DIV12

extract_protocol:
RNA was extracted using Trizol reagent.
Libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions

treatment_protocol: Neurons were treated with 1 uM TTX or 50 uM Bicuculline for 30 m, 2 h, 4h, or 6 h

value: Cortical neurons

tag: developmental stage

value: TTX

tag: time


title: maternal-zygotic KO seq-14-17 somite stage

description:
processed data file: processed data FPKM.xlsx
data column in the file:
panel 1 column AS


title: GRO-TTX_4_hr_2

description: nascent RNA


title: maternal-zygotic KO seq-6

description: mzKO Y2-/- 6h


title: maternal-zygotic KO seq-24

description: mzKO Y2-/- 24h


title: WT seq-12

description: wild-type 12h


title: GRO-Untreated_2

description: nascent RNA

value: Untreated


title: Hs5sh4minus


title: GRO-TTX_4_hr_1

description: nascent RNA


title: C51shLucplus

value: Luciferase


title: GRO-TTX_30_min_2

description: nascent RNA


title: HCC1954shLucplus


title: WT seq-8

description: wild-type 8h


title: WT seq-6

description: wild-type 6h


title: GRO-TTX_30_min_1

description: nascent RNA


title: GRO-TTX_2_hr-1

description: nascent RNA


title: ythdf2-MO seq rep2

data_processing: Data analysis for each experiment: (1) for m6A-seq, reads were aligned to the reference genome (danRer10) using Tophat (v2.0.14, ref) with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c). (2) for m6A-CLIP-seq, after removing the adapter sequence, the reads were mapped to the reference genome (danRer10) using bowtie2. Peak calling method was similar to previous study (chen kai's Angew 2015). Briefly, mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER (homer ref here) to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. (3) for mRNA-Seq, Reads were mapped with Tophat and Cufflink (v2.2.1) was used to calculate the FPKM of each gene to represent their mRNA expression level.


title: ythdf2-MO seq rep1


title: GRO-Untreated_1

description: nascent RNA


title: control-MO seq rep2


title: control-MO seq rep1


title: Bic-6h-2

data_processing:
The sequencing reads were mapped to the mm10 UCSC annotation using TOPHAT (Trapnell, et al., 2009) with the parameters (-a 8 -m 0 -I 500000 -p 8 -g 20 --library-type fr-firststrand --no-novel-indels  --segment-mismatches 2) for RNA-Seq.
For GRO-Seq, the raw fastq reads were trimmed using cutadapt with parameters -a AAAAAAAAAAAAAAAAAAAA -z -e 0.10 -f fastq -m 32 (Chae et al., 2015).
RPKM calculations were done using the HOMER package by normalizing to 10 million reads
Tracks for visualization on UCSC browser are generated using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Strand specific bigWig files for visualizing expression levels on a genome browser.

molecule: polyA RNA

value: Bic


title: UN-2


title: WT seq-24

description: wild-type 24h


title: TTX-2h-2


title: maternal KO seq-8

value: maternal ythdf2 null


title: Bic-2h-2


title: maternal KO seq-6


title: TTX-6h-1


title: maternal KO seq-4


title: maternal KO seq-2


title: Bic-6h-1


title: maternal WT seq-8


title: TTX-2h-1


title: Bic-2h-1


title: maternal-zygotic KO seq-12

description: mzKO Y2-/- 12h


title: maternal WT seq-2


title: TTX-6h-2


title: m6A-CLIP-8


title: maternal WT seq-0


title: WAT-derived mouse macrophages, high fat diet 22 weeks, WT mouse

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
high fat diet, 22 weeks
M1_WT_M1_CKO.csv

data_processing:
Pair-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500 at the depth of ~75 million reads per sample. Basecal was performed using CASAVA 1.8. Read quality was evaluated using FASTQC.
50-bp paired reads were mapped to annotated mouse genome (mm10, build 38.75, 41,128 genes and 87,108 transcripts) with CLC Bio Genomic Workbench 7.5 software (Qiagen). Duplicated reads with more than 5 copies were discarded
For BMMΦ, differential expression was analyzed using CLC implementation of EDGE algorithm with the unique exon read (uer) count as a proxy of gene expression levels. Genes with a Benjamini-Hochberg false discovery rate (FDR)-corrected p-value < 0.01 and log2(uer)>1 were considered to be differentially expressed, and shown as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
For WAT-derived MΦ per gene RPKMs were used as a measure of expression. Following filtering, all genes with RPKM>1 in at least one genotype (10,126 feature IDs) were sorted by fold change relative to the expression level in the WT CD11c+ inflammatory MΦ
Genome_build: mm10, build 38.75
Supplementary_files_format_and_content: comma separated values, containing the expression values (unique exon reads, RPKM and EDGE_R FDR corrected p values), for in vitro differentiated macrophages treated with IL4 and untreated control  and white adipose tissue derived macrophages

source_name: WAT-derived mouse macrophages

growth_protocol: C57BL/6 mice (NCI, Charles River Laboratories) and their transgenic derivatives below were maintained in the Hospital for Special Surgery Animal Facility in full compliance with institutional guidelines approved by the HSS Animal Care and Use Committee.  The Mx1-Cre+/+; GRIP1fl/fl (GRIP1 cKO) and matching Mx1-Cre-/-; GRIP1fl/fl (WT) strains and their handling were previously described

extract_protocol:
Total RNA was isolated using QIAgen RNAeasy kit from BMMΦ incubated for 18 h with or without 20 ng/ml of IL4 (3 biological replicates), or from WAT-derived CD45+F4/80+CD11b+CD11c+CD206- MΦ from HFD-fed WT and cKO mice
For BMMΦ, RNA was polyA-enriched and converted into Illumina-compatible sequencing library with TrueSeq mRNA-Seq sample preparation kit (Illumina). For WAT-derived MΦ, SMART-Seq v3 Ultra Low Input RNA Kit (Clontech) followed by Nextera library prep kit were used to prepare Illumina-compatible sequencing libraries. Quality control of RNA and library was performed using BioAnalyser 2100 (Agilent).

treatment_protocol: 8-wk old mice were placed on HFD (BioServ, F6379) or regular chow (LabDiet, 5001) for 20 wks and weighted weekly. Following 20 wks, animals were sacrificed, livers and eWAT dissected and weighted.

tag: breed

value: C67BL/6, Mx1-Cre-/-; GRIP1fl/fl

tag: age

value: 28 weeks

tag: Sex

value: male

tag: tissue

value: Whtie adipose tissue


title: Primary macrophages, IL4-18h, replicate 3

description:
chow
M0_M2_IL4.csv

source_name: Bone-Marrow Derived

value: 8 weeks

value: Bone Marrow derived macrophages


title: WAT-derived mouse macrophages, high fat diet 22 weeks, GRIP1(Ncoa2) conditional knockout  mouse

value: C67BL/6, Mx1-Cre+/+; GRIP1fl/fl


title: m6A-CLIP-6

value: WT


title: Primary macrophages, IL4-18h, replicate 2

description:
chow
M0_M2_IL4.csv


title: Primary macrophages, IL4-18h, replicate 1

description:
chow
M0_M2_IL4.csv


title: Primary macrophages, untreated, replicate 3

description:
chow
M0_M2_IL4.csv


title: m6A-CLIP-4


title: Primary macrophages, untreated, replicate 2

description:
chow
M0_M2_IL4.csv


title: m6A-CLIP-2


title: Primary macrophages, untreated, replicate 1

description:
chow
M0_M2_IL4.csv


title: m6A-CLIP-0


title: maternal KO seq-0


title: input-CLIP-8


title: input-CLIP-6


title: input-CLIP-4


title: input-CLIP-0


title: maternal WT seq-4


title: input-CLIP-2


title: Q-KO3-RNA-seq

first: Lijun

last: Liu

address: 450 brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
Basecall was performed using CASAVA
Reads were aligned to mm9
FPKM was calculated for RNA-seq.
Illumina Bcl2fastq v2.16
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output and normalized FRPKM counts were generated using cufflinks
Supplementary_files_format_and_content: FPKMs

source_name: Q-KO

growth_protocol: ES cells were cultured in in Knockout DMEM (Invitrogen) with  MEK inhibitor PD184352 (Cayman Chemical, 1 mM), GSK3 inhibitor CHIR99021 (Cayman Chemical, 3 mM) and 100 U/ml LIF.

extract_protocol:
For regular RNA-seq protocol, total RNA is extracted through Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Embryonic stem cells

value: without any G1 cyclin


title: Q-KO2-RNA-seq


title: Q-KO1-RNA-seq


title: UN-1

tag: cell type


title: Ctrl3-RNA-seq

source_name: Ctrl

value: wild type


title: Ctrl2-RNA-seq


title: Ctrl1-RNA-seq


title: m6A-IP-8

tag: development time (h.p.f.)


title: maternal WT seq-6

tag: genotype


title: input-8

tag: treatment


title: m6A-IP-4


title: m6A-IP-2


title: input-6


title: m6A-IP-0


title: input-4


title: CA16-96h

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

data_processing:
ﬁltering of low-quality sequences, namely, those with undetermined nucleotides (Ns), a quality score (Q-score) less than 10, or reads shorter than 18 nt
removal of the adapter sequences
elimination of noncoding RNAs (e.g., rRNA, tRNA, snoRNA, or snRNA) and repetitive RNAs by mapping clean reads of small RNAs (sRNAs) using Rfam (http://rfam.janelia.org/) and piRNA (http://pirnabank.ibab.ac.in/).

source_name: Human Umbilical Vein Endothelial

growth_protocol: HUVECs purchased from Jennino Biological Technology were cultured in Dulbecco’s modiﬁed eagle medium (DMEM) (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, USA), 1% L-glutamine (Gibco, USA), and 1% penicillin/streptomycin (Sigma, USA) in a humidified atmosphere containing 95% air and 5% CO2 at 37°C.

extract_protocol:
Samples from the previously mentioned groups were sent to the National Engineering Center for Biochips in Shanghai. miRNA was isolated from each group using a mirVanamiRNA Isolation Kit (Ambion, USA) in accordance with the manufacturer’s guidelines. RNA purification was carried out after RNA isolation using a miRNeasy Mini kit (Qiagen, Germany) following the manufacturer’s instructions. The quality and integrity of the purified RNA were determined by capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA); only samples with an RNA integrity number (RIN) value greater than 7 were retained for miRNA profile analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For in vitro virus infection, approximately 1×106HUVECs per well were plated in 6-well plates and incubated overnight at 37°C under 5% CO2. When HUVECs were 80% confluence in the 6-well plates, they were infected with EV71 (subgenotype C4, GenBank EU812515.1) or the CA16-G20 strain (subgenotype B, GenBank JN590244.1), which had been isolated from an epidemic in Fuyang, China, in 2008 and from an HFMD patient in Guangxi, China, in 2010, respectively, at a multiplicity of infection (MOI) of 1. The cells were collected at 0, 72, and 96 hours post infection (hpi), resuspended in Trizol (TIANGEN, China) and stored at -80°C until used. Cells infected with EV71 and CA16 for 0 hpi were used as controls. Simultaneously, we defined the following experimental groups: EV71-0h, EV71-72h, EV71-96h, CA16-0h, CA16-72h, and CA16-96h.

tag: time point

value: HUVECs

tag: infection


title: H2A.Z_DP

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
For the Genome Analyzer II System, basecalls were performed using manufacturer’s instructions via CASAVA.
ChIP-seq reads were aligned to the mm10genome assembly using Bowtie 2 to sorted BAM via stdoutput using --very-sensitive-local | samtools view -S - -b | samtools sort -
Tag shift (macs14)
Wig coverage track generation (macs14)
Peak detection (macs14)
Genome_build: mm9
Supplementary_files_format_and_content: Variable step 10bp wig files depicting ChIP-Seq coverage

source_name: primary CD4+ CD8+ DP thymocytes

growth_protocol: Thymuses were extracted from 5-6-week-old C57BL/6 wild type mice and stored in RPMI medium. Cohorts of litter mates were used as biological replicates. To recover thymocytes, thymuses were subsequently passed twice through a 70µm Falcon cell strainer and stored in PBS. Cells were crosslinked 10 min in 10% formaldehyde followed by 5 min quenching in 250 mM glycine. DP cells were subsequently sorted via AutoMACS using, in turn, α-CD8-PE antibody conjugated to α-PE beads, and α-CD4 beads (Miltenyi).

extract_protocol:
For ChIP-Seq, thymocytes were aliquoted in crosslinked pellets of 5 107 cells and lysed by rotation for 10 min at 4°C in 2x 1.25ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA, pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100). Following centrifugation at 1,350g for 5 minutes at 4°C, nuclei were subsequently treated with 2x1.25ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was resuspended in 1.5ml LB3 (1mM EDTA pH8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM, NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) in 15ml polypropylene falcon tubes and then sonicated for 10 cycles (30 seconds on, 30 seconds off) at 40W using a VCX130 sonicator (VibraCell) down to an average size of about 250bp. 50µl aliquots were collected as Input controls. All buffers contained final concentrations of 1X protease inhibitors (Roche, France) as well as 0.2mM PMSF and 1μg /ml pepstatin. ChIPs were conducted protein-G DynaBeads (Invitrogen).Antibody and bead mixes were washed three times with 1ml BSA blocking buffer (0.5% BSA in 1x DPBS), incubated and rotated overnight at 4°C, and subsequently washed another three times with 1ml BSA blocking buffer. Immunoprecipitation was carried out overnight in 750µl LB3 at 4°C on a rotating wheel. Samples were then washed 8 times in 1ml RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in 1ml TE buffer with 50mM NaCL. Two 15-min and 10-min subsequent elutions were carried out in a waterbath at 65°C, vortexing every other minute, for a final volume of 100µl. 100µl 1X elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) was added to eluates which were reverse-crosslinked overnight in a 65°C waterbath. Equal volumes of TE buffer (100µl) were added to samples as well as 0.2μg/ml RNAse A and placed at 37°C for 2 hours, followed by proteinase K treatment at 0.2μg/ml at 55°C. DNA purification was carried out via phenol-chloroform extraction followed by elution using QiaQuick PCR purification kits. (QiaGen) Samples were pooled per replicate then SpeedVac-ed down to 30µl. DNA quantification of eluates was obtained using Bioanalyzer High Sensitivity chips (Agilent).
Library preparation was carried out as per manufacturer’s instructions (Illumina) using 2.4ng material. Samples were subsequently size-selected via gel migration and extraction, with average cut sizes at about 300 bp including adapters. The quality of the libraries was checked with the BioAnalyzer DNA High sensitivity and by Q-PCR. Sequencing was performed using a Genome Analyzer II (Illumina) at the CNAG, Barcelona, Spain.

tag: strain

value: 5-6 weeks

tag: cells used

tag: antibody

value: Abcam Ab4174


title: CA16-72h


title: CA16-0h


title: EV71-96h


title: EV71-72h


title: input-2


title: m6A-IP-6


title: input-0


title: EV71-0h


title: TTAGGC-D3

description: enriched for mRNA

tag: genotype/variation

value: {delta}perC::kanR, coisogenic to WT

tag: source

value: Bustamante et al., 2011


title: AcCC Sample 1

city: Stanford

first: Xue

last: Gong

state: CA

institute: Stanford University

description: RNA-Seq data for AcCC Sample 1

data_processing:
Mapping by Bowtie v1.1.2 using default parameters for the AcCC FFPE samples
Gene fusion by ChimeraScan v0.4.5 using default parameters for the AcCC FFPE samples
Mapping by Tophat v2.0.0 using default parameters for the Rat cells (DNAnexus proprietary)
Quantilifcation by Cufflinks v2.0.2 using default parameters; Rat cells (DNAnexus proprietary)
Genome_build: hg19
Supplementary_files_format_and_content: ChimeraScan output for AcCC FFPE samples, and Tab-delimited text files include RPKM values for Rat cells

source_name: Acinic cell carcinoma

growth_protocol: FFPE specimens cored

extract_protocol:
Total RNA by Qiagen Allprep FFPE
Barcoded cDNA libraries prepared from total RNA by rRNA depletion and TruSeq RNA Sample Preparation Kit v2
Paired-end 75-bp reads sequencing  on an Illumina HiSeq 2000 instrument (Genomic Health)

tag: tumor type

value: Acinic cell carcinoma

value: Salivary gland


title: AcCC Sample 3

description: RNA-Seq data for AcCC Sample 3

extract_protocol:
Total RNA by Qiagen FFPE
Barcoded cDNA libraries prepared from total RNA by rRNA depletion and TruSeq RNA Sample Preparation Kit v2
Paired-end 75-bp reads sequencing  on an Illumina HiSeq 2000 instrument (Genomic Health)


title: CGATGT-D2

description: enriched for mRNA

source_name: Whole bacterial cell RNA transcriptome


title: A367_1

city: wuhan

first: songsong

last: wu

state: Hubei

address: No. 1  Shizishan Street

department: College of Plant Science and Technology,

institute: Huazhong Agricultural University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sclerotinia sclerotiorum whole genome using bowtie v0.12.2
Genome_build: Sclerotinia sclerotiorum
Supplementary_files_format_and_content: excel file include reads count for each Sample

organism: Sclerotinia sclerotiorum

source_name: mycelia

growth_protocol: PDA medium, 20℃, 3 days

extract_protocol:
mycelia  were collected for total RNA, extraction using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: virus infection

value: SsMYRV4 free

tag: developmental stage

value: 3 days-old


title: ATCACG-D1

description: enriched for mRNA


title: AcCC Sample 2

description: RNA-Seq data for AcCC Sample 2


title: REO_3

value: SsMYRV4 infection


title: SMGC6-MSANTD3

description: RNA-Seq data for SMGC6-MSANTD3

organism: Rattus norvegicus

growth_protocol: SMGC6 cells grown as published

extract_protocol:
Total RNA by Qiagen RNeasy
Barcoded cDNA libraries prepared from total RNA by TruSeq mRNA Sample Preparation Kit
Paired-end 101bp reads sequencing  on an Illumina HiSeq 2000 instrument (Stanford Center for Genomics and Personalized Medicine)

treatment_protocol: Transduced with MSANTD3

tag: cell line


title: SMGC6-empty vector

description: RNA-Seq data for SMGC6-empty vector

source_name: SMGC6-empty vector

treatment_protocol: Transduced with empty vector

tag: tissue


title: SAEC + cytokine + HTS rep3

status: Public on Feb 06 2017

description:
Cyto_HTS_3
Barcode: CTTGTA

data_processing:
Quality trim to a minimum of Q15
Map to the hg19 genome using GSNAP version 2012-07-20 using the commandline gsnap -d hg19_total -v snp135_strict --use-splicing=hg19_total.ucscRefGeneSpliceSites --max-mismatches=0.06 -i2 -n1 -Q --gunzip --nofails -B5 -t12 --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $file > ./Illumina_data/$j.sam
sort and index using SAMTOOLS
call FPKM using CUFFLINKS
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing FPKM values

source_name: SAEC + cytokine + HTS

growth_protocol: Primary human small airway epithelial cells (SAECS, Lonza Bioproducts, Allendale NJ) in P2 were grown to 80% confluence in Ti 75 flasks in a humidified chamber with 5% CO2 and re-seeded into 6, 12, or 24 well plates depending on the experimental requirement.

extract_protocol:
Total RNA was extracted with Qiagen Rneasy Mini Kit
Illumina directional mRNA prep

treatment_protocol: The following 4 conditions were tested using 3 replicates each: control (untreated), cytokine-treated [cytomix; TNF-α 10n/mL, IL-1β 10ng/mL (Sigma Aldrich, St Louis, Mo) and IFN-γ 10ng/mL (R&D Biosystems, Minneapolis, MN)], HTS (400mOsm hypertonic saline) and HTS+cytokines.

value: SAEC-Small Airway Epithelial Cells (Lonza CC-2547)

tag: agent

value: cytokine + HTS


title: SAEC + HTS rep1

description:
HTS_1
Barcode: CAGATC

source_name: SAEC + HTS

tag: cell type

value: HTS


title: SAEC + HTS rep3

description:
HTS_3
Barcode: GATCAG


title: SAEC + HTS rep2

description:
HTS_2
Barcode: ACTTGA


title: H3K4me2 [9590]

city: Vienna

first: Maria

last: Fischer

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

data_processing:
Peaks were determined by using the MACS program version 1.3.6.1 (16) with default parameters, a cutoff of a P value of < 10-10 and a genome size of 2,654,911,517 bp (mm9). The identified peaks were then assigned to target genes as described (12). For comparisons of ChIPseq data, we down-sampled all reads before peak calling to the ChIP-seq experiment with the lowest number of aligned reads.
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (19) with the overlap resolution mode set to ‘union’. The datasets were grouped according to cell type and organism and analyzed using the R package DESeq2 version 1.4.1 (20). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. In detail, the following DESeq2 analyses were performed: all mouse pro B cell samples were analyzed together considering the genotype effects (model design formula: “~ genotype”). Mouse tumor cells and mouse wild-type large pre-B cells were also grouped and analyzed in the same manner, as were human tumor cells and human wild-type pre-B cells.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs; text tab delim = TPM values in ASCII text format tab delimited

source_name: pro-B

extract_protocol:
phenol-chloroform extraction
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) as described (Parkhomchuk et al. 2009) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000/2500 system with a read length of 50 nucleotides (single-read) or 100/125 nucleotides (paired-end) according to the manufacturer’s guidelines.

tag: cell preparation

value: pro-B culture

tag: cell sorting strategy

value: CD19+ MACS-sorted

tag: chip antibody

value: H3K4me2 Ab (Upstate 07-030)


title: SAEC + cytokine + HTS rep1

description:
Cyto_HTS_1
Barcode: TAGCTT


title: H3K27me3 [9219]

tag: genotype

value: H3K27me3 Ab (T.Jenuwein)


title: H3K9ac [9589]

value: H3K9ac Ab (Upstate 07-352)


title: SAEC rep2

description:
Con_2
Barcode: CGATGT

source_name: SAEC

value: control


title: SAEC rep1

description:
Con_1
Barcode: ATCACG


title: SAEC + cytokine + HTS rep2

description:
Cyto_HTS_2
Barcode: GGCTAC


title: SAEC + cytokine rep2

description:
Cyto_2
Barcode: ACAGTG

source_name: SAEC + cytokine

value: cytokine


title: H3K4me3 [9591]

value: H3K4me3 Ab (Abcam ab8580-100)


title: SAEC rep3

description:
Con_3
Barcode: TTAGGC


title: Ik1 wild-type 48h DOX rep2

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences, then mapped to hg19 reference genome using tophat2 (Kim et al., 2013 PMID: 23618408) with parameters  -p 16 --no-coverage-search, also -G parameter was used in conjunction with the Gencode annotation gtf file (gencode.v23.annotation.gtf)
Uniquely mapped reads were counted using Htseq-counts version v0.6.0 with the parameters -m union -r pos -i gene_name -a 10 --stranded=yes
Genome_build: hg19
Supplementary_files_format_and_content: matrix of normalized HTSeq-counts

source_name: PDX2 Ik6 pre-B ALL + TET-Ik1

growth_protocol: Single cell suspensions were prepared from in vitro cell cultured cells.

extract_protocol:
RNA was isolated using TRI Reagent (Molecular Research Center, Inc.) followed by purification with an RNeasy kit (Qiagen), or direct isolation by RNA-isolation kit (Qiagen and Macherey-Nagel), with on-column RNase-free DNase I treatment. 1 ug of total RNA was depleted of rRNA using RiboErase (KAPA Biosystems).
RNA libraries were prepared for sequencing using the Kapa Biosystems Kapa Stranded RNA-seq library kit

treatment_protocol: Cell suspensions were either untreated or treated with doxycycline (DOX) for the indicated time, prior to sorting cells based on GFP signal

tag: cell-line

value: pre-B ALL xenograft

tag: induction time

value: 48 hour

tag: treatment


title: Ik1 wild-type 24h DOX rep1&2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences, then mapped to hg19 reference genome using bowtie 2.2.2, duplicate fragments for each sample were discarded, as well as reads mapping to chrM. Bedgraph files from pooled duplicates are provided as supplementary files.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files from pooled duplicates are provided as supplementary files.

extract_protocol:
Nuclei were prepared from 50,000 sorted cells prior to transposition. Following transposition, DNA was extracted and 10 cycles of PCR was performed.
According to the ATAC-seq protocol (Buenrostro JD, PMID: 24097267)

treatment_protocol: Cell suspensions were either treated with doxycycline (DOX) for 24h, prior to sorting 50,000 cells based on GFP signal.

value: 24 hour


title: Ik1 wild-type uninduced rep1

value: uninduced


title: GFP control 12h DOX rep2

source_name: PDX2 Ik6 pre-B ALL + TET-empty vector

value: 12 hour

value: empty vector


title: Ik1 wild-type uninduced rep2


title: GFP control 48h DOX rep1


title: Ik1 wild-type 12h DOX rep2


title: GFP control 12h DOX rep1


title: Ik1 wild-type 12h DOX rep1


title: GFP control uninduced rep1


title: SAEC + cytokine rep3

description:
Cyto_3
Barcode: GCCAAT

value: SAEC-Small Airway Epithelial Cells (Lonza CC-2547)


title: SAEC + cytokine rep1

description:
Cyto_1
Barcode: TGACCA


title: Ik1_input

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences, then mapped to hg19 reference genome using bowtie2. Peaks were called against input using MACS2. Processed bed files are provided as supplementary files. Bigwig files were generated with bamtools and are also provided as supplementary files.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files for significant peaks for each replicate called against input are provided as supplementary files.

source_name: Ik6 pre-B ALL + TET-Ik1

growth_protocol: Single cell suspensions were prepared from in vitro cell cultured cells. On the day before DOX treatment, (Day -1), cells were seeded at 1x10e6 cell/ml.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
According to the NEBNext ChIP-seq protocol, with 12-15 cycles of PCR.

treatment_protocol: Cell suspensions were treated with doxycycline (DOX) for the indicated time, prior to sorting (based on GFP+) and fixation with 1% formaldehyde for 10 minutes. Following quenching with 0.125M glycine for 5 minutes, cell pellets were washed with PBS and snap frozen. Cells were lysed and nuclear extracts were sonicated.

value: in vitro growing pre-B ALL xenograft-derived cells

tag: antibody


title: control_H3K27ac_rep2

source_name: Ik6 pre-B ALL + TET-empty vector

tag: genotype/variation


title: control_input


title: Ik1 wild-type 48h DOX rep1


title: GFP control 24h DOX rep1&2


title: Ik1_H3K4me3_rep2


title: Ik1_H3K27ac_rep2


title: Ik1_H3K27ac_rep1


title: control_H3K4me3_rep1


title: GFP control 48h DOX rep2


title: control_H3K27ac_rep1


title: control_H3K4me3_rep2


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 32

first: John

middle: N

last: Campbell

address: Center for Life Science, room 7-717

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
Base calls performed with bcl2fastq2.15.0.4
Alignment by TopHat v2.0.14. [Using “-M”, “--no-coverage-search”, “--segment-length 10”]
Removal of duplicates and low quality reads, indexing, and sorting: Picard 2.5.0 and samtools 0.1.19.
Assigned reads to features: featureCounts-1.4.6. [Using recommended setting and a custom meta-annotation that merges overlapping isoforms.]

Genome_build: Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CSV file containing expression values by sample (columns) and gene ID (rows)

source_name: Arcuate Nucleus/Median Eminence

extract_protocol:
GFP+ cells were manually isolated from a cell suspension prepared by triturating and washing papain-digested Arc-ME
Single cells were frozen at -80degC and then processed into RNA-seq libraries using Smart-Seq2 (Picelli et al., 2015) and Nextera XT

tag: strain

value: (C57BL/6 x DBA)F2

value: Arcuate-Median Eminence

tag: Sex

value: M

tag: average age

value: 63 days

tag: number of mice pooled


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 43


title: GFP control uninduced rep2


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 34


title: IKZF1_ICN1_C

city: San Francisco

first: Hilde

last: Schjerven

address: 513 Parnassus Ave

department: Laboratory Medicine

institute: UCSF

description: barcode: GCCAAT

data_processing:
Sequenced at the University of Southern California Epigenome Data Production Facility
Aligned to hg19 by the University of Southern California Epigenome Data Production Facility
Bedgraph visualization files created with BEDtools (Quinland and Hall, 2010) either using command-line in Mac Terminal and/or Galaxy.
Peaks called with SoleSearch (Blahnik, K.R. et al. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 38, e13 (2010))
Merged peak lists (union) found by TSS (transcriptional start site) mode and wgm (within gene mode) in SoleSearch were compared across all 6 datasets, listing total number of peaks called/annotated to each gene (across all 6 datasets), and total peaks for that gene within each ChIP-Seq sample. Number of datasets (of total 6) that contain peaks annotated for each gene was also listed (tab delimited txt file from excel).
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph visualization files created with BEDtools (Quinland and Hall, 2010) either using command-line in Mac Terminal and/or Galaxy.
Supplementary_files_format_and_content: Merged peak lists (union) found by TSS (transcriptional start site) mode and wgm (within gene mode) in SoleSearch were compared across all 6 datasets, listing total number of peaks called/annotated to each gene (across all 6 datasets), and total peaks for that gene within each ChIP-Seq sample. Number of datasets (of total 6) that contain peaks annotated for each gene was also listed (tab delimited txt file from excel).

growth_protocol: Cells were grown on irradiated OP9 feeder cells, in Alpha Minimum Essential medium (MEM-Alpha, Gibco) supplemented with 20% fetal bovine serum (FBS), GlutaMax, 100 IU/ml penicillin and 100 μg/ml streptomycin (Gibco)

extract_protocol:
Cells were fixed in 1% formaldehyde at room temperature for 10 min and Ikaros ChIP were performed with two different Ikaros Antibodies using protocol essentially as descrbed in O'Geen, H., Frietze, S. & Farnham, P.J. Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol. Biol. 649, 437–455 (2010)
Single-end multiplexed libraries were created essentially as described in O'Geen, H., Frietze, S. & Farnham, P.J. Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol. Biol. 649, 437–455 (2010)

value: Xenograft-derived BCR-ABL1+ (Ph+) human pre-B ALL

tag: chip-ab

value: Ikaros C-terminal (Source:Smale lab, Reference:Hahm et al., 1998)

tag: replicate

value: ICN1 (Ik-C Ab)


title: IKZF1_ICN1_H_r2

description: barcode: CAGATC

value: anti-Ikaros, clone H-100 (Santa Cruz, cat # sc-13039 X)

value: ICN1-replicate2 (H-100 Ab)


title: input-ICN1

description: barcode: ACAGTG


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 31

tag: tissue


title: IKZF1_LAX2_C

description: barcode: CTTGTA

tag: cell type

value: LAX2 (Ik-C Ab)


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 29


title: IKZF1_ICN1_H_r1

description: barcode: CGATGT

value: ICN1-replicate1 (H-100 Ab)


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 27


title: IKZF1_LAX2_H_r1

description: barcode: TGACCA

value: LAX2-replicate1 (H-100 Ab)


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 25


title: input-LAX2

description: barcode: TGACCA


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 26


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 24


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 13


title: Ik1_H3K4me3_rep1

value: 48 hour


title: IKZF1_LAX2_H_r2

description: barcode: CGATGT

value: LAX2-replicate2 (H-100 Ab)


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 12


title: transected spinal cord b

city: Durham

first: Mayssa

last: Mokalled

state: NC

address: 307 Research Dr.

department: Cell Biology

institute: Duke University Medical Center

description: Ekkwil

data_processing:
Quality QC using Fastx
Trimming of adapters and short sequences using Fastx
Mapping using Bowtie2
Assembly using Cufflinks
Quantification using Cuffdiff
Genome_build: zebrafish Zv9 genome
Supplementary_files_format_and_content: gene_exp.diff file includes gene expression data of injured spinal cord tissue relative to sham-injured control tissue

source_name: spinal cord, transected, 2 weeks post-injury

growth_protocol: Adult, 6 months old wild-type zebrafish were used for this study

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
TruSeq libraries were constructed according to manufacturer's instructions

treatment_protocol: Animals underwent complete cervical spinal cord transection, and spinal cord tissue was collected 2 weeks post-injury.  Control animals were sham injured and spinal cord was collected at 2 weeks post-sham.

tag: age

value: 6 months

value: spinal cord

tag: tratment

value: 2 weeks after transection-injury


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 15

value: (C57BL/6 x DBA)F2


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 11

value: Arcuate-Median Eminence


title: sham spinal cord b

description: Ekkwil

source_name: spinal cord, sham control, 2 weeks post-sham

value: 2 weeks after sham-injury


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 14

value: M

value: 63 days


title: transected spinal cord a

description: Ekkwil


title: sham spinal cord a

description: Ekkwil


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 9


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 8


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 4


title: lin-45 500 mM 1

city: Cambridge

first: Nicholas

last: Burton

state: MA

address: 77 Massachusetts Ave.

institute: MIT

data_processing:
For QC purposes, BEDTools (version 2.25.0) was used to count the reads falling into genes, coding regions, intronic regions, 5' or 3' UTRs, flanking 3-kb genic regions and intergenic regions.
The reads were first cleaned up by removing reads aligned to rRNAs (BWA 0.6.1 and BEDTools 2.25.0 were used).
RSEM (version 1.2.15) was used to estimate gene levels based on ce10 ensembl annotations downloaded from UCSC genome table browser.
The gene expression count table was then imported into Deseq (version 1.10.1) for differential gene expression test.
Genome_build: ce WS206
Supplementary_files_format_and_content: Excel file containing gene information, raw read counts computed by RSEM, gene expression FPKM values, log2 FPKM values, average of log2FPKMs and variance of log2 FPKMs

organism: Caenorhabditis elegans

source_name: embryos

extract_protocol:
Embryos were lysed using a BeadBug and 0.5mm zirconium beads. Total RNA was collected using RNAeasy kit from Qiagen and DNAse treated with DNAseI from NEB
RNA integrity and concentration were checked on a Fragment analyzer (Advanced Analytical). The mRNA was purified by polyA-tail enrichment, fragmented, reverse transcribed into cDAN (Illumina TruSeq). cDNA samples were then end repaired and adaptor liged using the SPRI-works fragment library system I (Beckman Coulter Genomics) and indexed during amplification. Libraries were quantified using the fragment analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq.

tag: timepoint

value: Embryos 3 hours post egg prep

tag: mutant

tag: parents growth condtions

value: 50 mM NaCl

tag: embryos growth condtions

value: 500 mM NaCl


title: N2 500 mM 2


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 5


title: lin-45 500 mM 2


title: N2 500 mM 1


title: N2 300-500 mM 1

value: 300 mM NaCl


title: N2 300-500 mM 2


title: lin-45 50 mM 2


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 2


title: lin-45 50 mM 1


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 1


title: N2 50 mM 1


title: RIP-Cre::AAV-loxSTOPlox-GFP+ Arc-ME Cell 17