title: DDX3 WT iCLIP rep2

description:
Protein enriched RNA
DDX3_WT_iCLIP.bw

data_processing:
library strategy: iCLIP-seq
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg19) genome using bowtie2
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing unique RT stops from the high confidence intersection of biological replicates of DDX3 iCLIP

growth_protocol: HEK293 cells were grown under standard serum conditions and FLAG-tagged DDX3 variant expression (FLAG-DDX3 WT or R534H) was induced with doxycycline

extract_protocol:
Lysates were clarified from sonicated HEK293 and DDX3-RNA complexes were isolated first with anti-FLAG (Sigma, A2220) then anti-DDX3 (Abcam, ab37160) antibody.
Libraries were prepared according to the FAST-iCLIP protocol (PMID: 25411354)

treatment_protocol: Cells were UV crosslinked at 254nm for 0.3J/cm^2 to in vivo fix RNA-RBP interactions

tag: flag-tagged protein

tag: rip antibody

value: anti-FLAG (Sigma, catalog# F1804, lot# SLBF6631) then anti-DDX3 (Abcam, catalog# ab37160, lot# GR57731-4 ) antibody


title: MM16_shLuc_RNAseq_rp3

status: Public on Apr 21 2016

type: SRA

city: Milano

first: Luisa

last: Lanfrancone

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each interference condition (shLuc and shKMT2D) for each MM patient.
processed data files format and content: tab delimited text file containing differential expression fold changes (FC) for genes expressed at least in one sample (>1RPKM), between normalized baseMean intensities of shKMT2D/shLuc conditions, for each patient (3 replicas were used for each condition for each patient)
Genome_build: hg19

molecule: polyA RNA

organism: Homo sapiens

source_name: metastasis of cutaneous melanoma

growth_protocol: Cells isolated from secondary PDXs were infected with lentiviral vectors expressing luciferase and KMT2D shRNAs, selected in purumycin and then harvested for further analysis

extract_protocol:
total RNA was extracted with qiagen RNeasy mini kit (cat# 74106) according to manufacturer protocol
libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 1µg of total RNA

tag: cell type

value: patient derived xenograft cells

tag: passage

tag: melanoma mutation

tag: infected shrna

value: shLuc


title: MM27_shKMT2D_RNAseq_rp1


title: ESC_E14_1 [RRBS-seq]

city: Montpellier

first: Tristan

last: Bouschet

address: 141 rue de la cardonille

department: CNRS 5203, INSERM U661

country: France

institute: Institut de Génomique Fonctionnelle

library_source: genomic

data_processing:
Image analyses and base calling were performed using the Illumina HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.17). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
Trim Galore was used to perform adapter trimming and quality control in two subsequent steps. The 2 additional bases that contain a cytosine which was artificially introduced at the end-repair step during the library preparation (--rrbs option) were  removed.
Three genomes were prepared for Bismark using bismark_genome_preparation script: mm9 mouse reference (C57BL/6), JF1 and 129P2 references based on mm9 mouse reference; Novoutil IUPAC (option –g) was used to replace the BL/6 base with the JF1 or 129P2 base at each SNP position. Bismark software (version 0.14.3) from the Babraham Institute was used to align trimmed RRBS reads to the appropriate mouse genome.
For allele-specific methylation, two separate alignments against the C57BL/6 and JF1 genomes prepared with Bismark were performed using the Bismark option "--non_bs_mm" to also report the number of non-bisulfite mismatches per read.
Then, a script provided by Felix Krueger from the Babraham Institute (combine_Bismark_BAM_allele_specifically_SE.pl) post-processed the two resulting BAM files to decide whether the read was specific for one or the other allele or whether the read was unassignable because the number of non-BS mismatches was the same, i.e. did not cover a SNP position.
Then, bismark_methylation_extractor script extracted the methylation call for every single C analysed.
JF1 SNP positions were filtered out by a custom script (Filtre_positions_SNP-JF1_pour_CpG_report.pl) from the Montpellier GenomiX facility.
Genome_build: mm9 ; JF1 and 129P2 (based on mm9)
Supplementary_files_format_and_content: . cov files produced by Bismark : tab-delimited files with columns chromosome, start, end, methylation percentage, count methylated, count non-methylated

molecule: genomic DNA

organism: Mus musculus

growth_protocol: E14atg2 ESCs were maintained on gelatin-coated dishes in DMEM (Life Technologies) supplemented with 15% ES-certified FBS (Life Technologies), 0.1mM non-essential amino acids (Life Technologies), 1mM sodium pyruvate (Life Technologies), 0.1mM beta-mercaptoethanol (Sigma), 50U/ml penicillin/streptomycin and 10³U/ml LIF (ESGRO, Millipore) as previously described (Gaspard et al., Nature. 2008 Sep 18;455(7211):351-7. doi: 10.1038/nature07287).  Hybrid ESCs were derived from blastocysts obtained by crossing a C57BL/6J female (Oct4-GFP transgenic) with a JF1 male, and reciprocally, and maintained on gelatin-coated dishes in ESGRO-complete-plus medium containing GSK3β-inhibitor, LIF and BMP4 (Millipore, SF001-500P) (Kota et al. Dev Cell. 2014;31(1):19-33).

extract_protocol:
Genomic DNA was prepared using PureLink genomic DNA kit (Life Technologies)
RRBS was performed on 200 ng of genomic DNA that was digested with MspI (Thermo Scientific) for 5 h, followed by end-repair, A-tailing (with Klenow fragment, Thermo Scientific) and ligation to methylated indexed Illumina adapters using T4 DNA ligase (Thermo Scientific) in Tango 1X buffer (Auclair et al. Genome Biol. 2014;15(12):545). Fragments were purified using AMPure XP magnetic beads (Agilent; Boyle et al. Genome Biol. 2012, 3;13(10):R92). Two rounds of bisulfite conversion were then performed using the EpiTect kit (Qiagen). Final RRBS libraries were PCR amplified with PfUTurbo Cx hotstart DNA polymerase (Agilent), purified with AMPure magnetic beads, quantified with a Qubit fluorometer (Life Technologies), and verified by Fragment analyzer (Advanced Analytical) and qPCR (Kapabiosystems).
Directional RRBS libraries were sequenced on an Illumina HiSeq 2000 as 100 bp reads using the Sequence By Synthesis technique at the Montpellier GenomiX facility.

treatment_protocol: To generate cortical cells in vitro, E14 and hybrid ESCs were plated onto gelatin-coated or matrigel (hESC qualified matrix, BD)-coated dishes, respectively. Next day, ESC media was changed for DDM as described (Gaspard et al., Nature. 2008 Sep 18;455(7211):351-7. doi: 10.1038/nature07287.), except that DDM was supplemented with B27 (without vitamin A) to improve hybrid cells survival. DDM was supplemented with cyclopamine (1 uM) from days 2 to 10 to enhance dorsalization of telencephalic progenitors (Gaspard et al., 2009). Differentiation was stopped at days 12 (d12) and 21 (d21) of culture.

tag: strain

tag: cell/tissue type

value: ESCs at d0


title: ESC_E14_2 [RRBS-seq]


title: ESC_JB6_1 [RRBS-seq]

value: JF1 x C57BL/6J hybrid


title: MM27_shKMT2D_RNAseq_rp3


title: DDX3 WT iCLIP rep1

city: Stanford

first: Sekyung

last: Oh

state: CA

address: 1201 Welch Road, MSLS P224

department: Neurology and Neurological Sciences

country: USA

institute: Stanford University School of Medicine

description:
Protein enriched RNA
DDX3_WT_iCLIP.bw

molecule: total RNA

value: Embryonic kidney

tag: cell line

tag: gender

value: female

tag: treatment

value: control

value: DDX3 WT


title: Rluc control ribosome profiling rep1

description:
Ribosome-protected mRNA fragments
Ribosome profiling

data_processing:
library strategy: Ribo-seq
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg19) genome using bowtie2
Gene assignment, and peak calling was performed as in ribosome profling (PMID: 19213877)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing unique ribosome-protected mRNA fragments for each replicate

growth_protocol: HEK293 cells were grown under standard serum conditions and FLAG-tagged Renilla luciferease (Rluc) control, DDX3 WT, or DDX3 R534H expression was induced by doxycycline addition.

extract_protocol:
Lysates were treated with RNase I, ribosomes were collected, ribosomal RNAs were depleted with Ribo-Zero kit (EpiCentre), and ribosome-protected mRNA fragments were enriched.
Libraries were prepared according to the ribosome profiling protocol (PMID: 19213877) and ARTseqTM Ribosome Profiling Kit protocol (EpiCentre).

treatment_protocol: Cells were treated with or without 0.5 mM sodium arsenite for 45 minutes.

tag: expressed protein

value: Rluc control


title: DDX3 WT Ars iCLIP rep2

description:
Protein enriched RNA
DDX3_WT_Ars_iCLIP.bw

value: sodium arsenite


title: MM16_shLuc_RNAseq_rp2


title: ESC_BJ1_1 [RRBS-seq]

value: C57BL/6J x JF1 hybrid


title: MM16_shLuc_RNAseq_rp1


title: DDX3 WT Ars iCLIP rep1


title: DDX3 R534H iCLIP rep2

description:
Protein enriched RNA
DDX3_R534_iCLIP.bw

value: DDX3 R534H


title: MM16_shKMT2D_RNAseq_rp3


title: Rbfox2_soluble_brain

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description: iCLIP with anti-Rbfox2 antibodies on a soluble nucleoplasm fraction purified from nuclei of mouse brain.

data_processing:
library strategy: iCLIP-seq
PCR duplicates were removed by comparing random portions of the sequenced barcodes. Unique reads were mapped to the mouse genome (mm9/NCBI37) using Bowtie, allowing up to two nucleotide mismatches. Mapped reads were further mapped to the Known Gene table .
iClip data analyses were performed following the published paper (Konig J*, Zarnack K*, Curk T, Gregor R, Kayikci M, Zupan,B, Luscombe NM, Ule J (2010))
Genome_build: mm9
Supplementary_files_format_and_content: The significant crosslinksites were selected based on the FDR <=0.01

extract_protocol:
Nuclei from UV-irradiated tissue were purified as described (Grabowski PJ, Methods. 2005 37:323-330). HMW nuclear fraction and soluble  nucleoplasm were obtained as described (Damainov et all 2015, submitted)
iCLIP protocol (König J et al, Nat Struct Mol Biol. 2010 17(7): 909–915) with few modifications (Damianov et al 2015, submitted).

treatment_protocol: Brain tissue was triturated as described (Ule J et al, Methods. 2005 37:376-386) and UV-irradiated at 600 mJ/cm2

tag: age

value: 6 week

value: male

tag: tissue

value: Brain

tag: fraction

tag: antibody

value: anti-Rbfox2 antibodies (RBM9, A300-864A, Bethyl)


title: Rbfox3_soluble_brain

description: iCLIP with anti-Rbfox3 antibodies on a soluble nucleoplasm fraction purified from nuclei of mouse brain.

value: anti-Rbfox3 antibodies (NeuN, MAB377, Millipore)


title: MM16_shKMT2D_RNAseq_rp2

value: patient derived xenograft cells


title: DDX3 R534H iCLIP rep1

description:
Protein enriched RNA
DDX3_R534_iCLIP.bw

value: anti-FLAG (Sigma, catalog# F1804, lot# SLBF6631) then anti-DDX3 (Abcam, catalog# ab37160, lot# GR57731-4 ) antibody


title: DDX3 R534H ribosome profiling rep1


title: MM13_shLuc_RNAseq_rp3

value: shLuc


title: Rbfox1_soluble_brain

description: iCLIP with anti-Rbfox1 antibodies on a soluble nucleoplasm fraction purified from nuclei of mouse brain.

value: anti-Rbfox1 antibodies (1D10, (Gehman et al., Nat. Genet. 43, 706-711)


title: DDX3 R534H Ars iCLIP rep2

description:
Protein enriched RNA
DDX3_R534_Ars_iCLIP.bw

value: Embryonic kidney


title: MM16_shKMT2D_RNAseq_rp1


title: DDX3 R534H Ars iCLIP rep1

value: female


title: Rbfox1_soluble_hindbrain

description: iCLIP with anti-Rbfox1 antibodies on a soluble nucleoplasm fraction purified from nuclei of mouse hindbrain.

value: Forebrain


title: MM13_shLuc_RNAseq_rp1


title: Rbfox1_soluble_forebrain

description: iCLIP with anti-Rbfox1 antibodies on a soluble nucleoplasm fraction purified from nuclei of mouse forebrain.


title: Rbfox3_HMW_hindbrain

description: iCLIP with anti-Rbfox3 antibodies on a high molecular weight (HMW) nuclear fraction purified from nuclei of mouse hindbrain.

value: Hindbrain


title: MM13_shLuc_RNAseq_rp2


title: Rbfox3_HMW_forebrain

description: iCLIP with anti-Rbfox3 antibodies on a high molecular weight (HMW) nuclear fraction purified from nuclei of mouse forebrain.


title: Rbfox2_HMW_hindbrain

description: iCLIP with anti-Rbfox2 antibodies on a high molecular weight (HMW) nuclear fraction purified from nuclei of mouse hindbrain.


title: MM13_shKMT2D_RNAseq_rp2


title: ESC_BJ1_2 [RRBS-seq]

value: ESCs at d0


title: SZ3_3

city: New York

first: Kristen

last: Brennand

state: NY

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: 1835#1 Neurons#3

data_processing:
The Illumina TruSeq RNA kit was used for 100nt/paired end reads, 4 samples were run per lane using the standard Truseq indices.  Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at both the geneic and exonic levels for UCSC and ensemble annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the read count for each gene

source_name: hiPSC forebrain Neurons

growth_protocol: hiPSC forebrain neurons were derived as described previously (Brennand et al., 2011). For neural differentiations, NPCs were dissociated with Accutase and plated in neural differentiation media (DMEM/F12-Glutamax, 1XN2, 1X B27-RA, 20 ng/ml BDNF, 20 ng/ml GDNF (Peprotech), 1 mm dibutyrl-cyclicAMP (Sigma), 200 nm ascorbic acid (Sigma) onto PORN/Laminin-coated plates. 200,000 cells/well of a 6-well plate. hiPSC derived-neurons were differentiated for 6 weeks.

extract_protocol:
Cells were lysed in RNA BEE (Tel-test, Inc). RNA was chloroform extracted, pelleted with isopropanol, washed with 70% ethanol and resuspended in water. RNA was treated with RQ1 RNAse-free DNAse (Promega) for 30 minutes at 37C and then the reaction was inactivated by incubation with EGTA Stop buffer at 65C for 10 minutes.
RNA libraries were prepared for sequencing using standard Illumina protocols
Hi-Seq, 100nt, Paired-End Read, 4 samples per lane

tag: diagnosis

value: Schizophrenia

tag: repository source fibroblast id

value: GM01835 (Coriell)


title: Rbfox2_HMW_forebrain

description: iCLIP with anti-Rbfox2 antibodies on a high molecular weight (HMW) nuclear fraction purified from nuclei of mouse forebrain.


title: SZ3_5

description: 1835#1 5


title: SZ2

description: 1792#1 Neurons#A

value: GM01792 (Coriell)


title: SZ1_B

description: 2038#1 Neurons#B

value: GM02038 (Coriell)


title: MM13_shKMT2D_RNAseq_rp1


title: SZ1_A

description: 2038#1 Neurons#A

value: male


title: ChIPSeq_MM27_shLuc_aKMT2D

data_processing:
Basecalls were performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.6.2 with the default parameters
Low-quality and multiple-mapping reads were removed using Samtools with option ‘‘-q 1’
Peaks for KMT2D, H3K4m3and H3K27ac were called using MACS 1.4.1 with default setting
Peaks for H3K4m1 were called using both MACS 1.4.1 (default setting) and SICER V1.1 with the following parameters: hg19 1  200  200 0.84 200 100; the union of these two lists was used as final set of peaks.
bigwig files were obtained with a combination of bedtools (v2.16.1) sub-commands: aligned reads (bam) were converted in bed with bamToBed and extended to approximately 200 bp with slopbed; then genomeCoverageBed were used to generate the wig file, which in turn is transformed to bigwig with the UCSC Genome Browser utility wigToBigWig.
Genome_build: hg19

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP 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 for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody

value: KMT2D (Sigma, HPA035977)


title: Rbfox1_HMW_hindbrain

description: iCLIP with anti-Rbfox1 antibodies on a high molecular weight (HMW) nuclear fraction purified from nuclei of mouse hindbrain.

value: 6 week


title: C6

description: 9429#3 Neurons#A

value: Control

value: AG09429 (Coriell)


title: Rbfox1_HMW_forebrain

description: iCLIP with anti-Rbfox1 antibodies on a high molecular weight (HMW) nuclear fraction purified from nuclei of mouse forebrain.


title: ChIPSeq_MM27_shLuc_aH3K4m3

tag: cell type

value: patient derived xenograft cells

value: H3K4me3 (Active Motif, 39159)


title: C5

description: 9319#2 Neurons#A

value: AG09319 (Coriell)


title: ChIPSeq_MM27_shLuc_aH3K4m1

tag: passage

value: shLuc

value: H3K4me1 (Abcam, ab8895)


title: C4

description: 4506#B Neurons#A

value: female

value: GM04506 (Coriell)


title: C3

description: 3651#A Neurons #A

value: GM03651 (Coriell)


title: ChIPSeq_MM27_shLuc_aH3K27ac

tag: melanoma mutation

value: H3K27ac (Abcam, ab4729)


title: in vivo P0 Ctx JB6_rep3

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using CASAVA 1.8.2 (Illumina).
A hybrid genome was generated using Novoutil IUPAC (Novocraft), consisting of the C57BL/6 genome (mm9) where the nucleotides at the known JF1 SNPs (Takada et al. Genome Res. 2013 23: 1329-1338.) were replaced with the IUPAC ambiguous codes for B6 and JF1 bases.
For samples of the 129P2 strain, a 129P2 genome was generated using Novoutil IUPAC (Novocraft) with option –g , consisting of the C57BL/6 genome (mm9) where the nucleotides at the known 129P2 SNPs (Sanger Institute, ftp ://ftp-mouse.sanger.ac.uk/REL-1111-SNPs/) were replaced with 129P2 bases.
The reference sequence set for RNA-seq was generated from the hybrid genome using MakeTranscriptome (USeq 8.6.6, Huntsman Cancer Institute shared resources) that takes a UCSC refFlat table of transcripts (refFlat.txt.gz; 2012-01-15) and generates two multi fasta files of transcripts and splices (known and theoretical). 11 mitochondrial genes (retrieved from UCSC knowGene table) were manually added. Novoindex (V3.01.01; Novocraft), which allows up to two IUB ambiguous codes per k-mer, was used to build the k-mer index of these reference transcriptomic sequences (with k = 13 and step size s = 1 bp). The reads were mapped to this hybrid transcriptome using Novoalign (Novocraft), with the following options: -l 25, -t 90, -a, -r All, -o SAM. The transcriptomic coordinates were converted to genomic coordinates using SamTranscriptomeParser (USeq 8.6.6) and redundant alignments (when reads mapped to more than one genomic location) were discarded (Script post back to genome coordinates v1.pl, MGX).
The counting was performed with HTSeq count (union mode). As the sequencing was strand-specific, the reads had to map to the opposite strand of the gene.
Data were normalized using RLE normalization factors (edgeR).
Genome_build: Derived from mm9 (see « data processing step »)
Supplementary_files_format_and_content: Excel file with 2 columns for gene description. The next columns correspond to the normalized abundance measurements (RLE normalization using edgeR statistical package) for each sample.

source_name: in vivo P0 Ctx JB6_rep3

growth_protocol: E14atg2 ESC were maintained on gelatin-coated dishes in DMEM (Life Technologies) supplemented with 15% ES-certified FBS (Life Technologies), 0.1mM non-essential amino acids (Life Technologies), 1mM sodium pyruvate (Life Technologies), 0.1mM beta-mercaptoethanol (Sigma), 50U/ml penicillin/streptomycin and 10³U/ml LIF (ESGRO, Millipore) as previously described (Gaspard et al., Nature. 2008 Sep 18;455(7211):351-7. doi: 10.1038/nature07287.).  Hybrid ESCs were derived from blastocysts obtained by crossing a C57BL/6J female (Oct4-GFP transgenic) with a JF1 male, and reciprocally, and maintained on gelatin-coated dishes in ESGRO-complete-plus medium containing GSK3β-inhibitor, LIF and BMP4 (Millipore, SF001-500P) (Kota et al., submitted).

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions.
RNA-Seq libraries were prepared using the 'TruSeq Stranded mRNA Sample Preparation kit' (Illumina) according to the manufacturer's instructions.

treatment_protocol: To generate cortical cells in vitro, E14 and hybrid ESC were plated onto gelatin-coated or matrigel (hESC qualified matrix, BD)-coated dishes, respectively. Next day, ESC media was changed for DDM as described (Gaspard et al., Nature. 2008 Sep 18;455(7211):351-7. doi: 10.1038/nature07287.), except that DDM was supplemented with B27 (without vitamin A) to improve hybrid cells survival. DDM was supplemented with cyclopamine (1 M) from days 2 to 10 to enhance dorsalization of telencephalic progenitors (Gaspard et al., 2009). At day 12 of corticogenesis, cells were eventually splitted on poly-L-lysine/Laminin and allowed to differentiate for 2 or 9 additional days (12+2 and 12+9 respectively) in order to facilitate the counting of the proportion of cells in immunofluorescence experiments (Gaspard et al.,Nat Protoc. 2009;4(10):1454-63. doi: 10.1038/nprot.2009.157; Gaspard et al., 2008). Differentiation was stopped at days 12 and 21 of culture.

value: JF1 x C57BL/6 hybrid

tag: Sex

value: Female


title: in vivo P0 Ctx JB6_rep2

source_name: in vivo P0 Ctx JB6_rep2

tag: strain


title: in vivo P0 Ctx JB6_rep1

source_name: in vivo P0 Ctx JB6_rep1


title: MM13_shKMT2D_RNAseq_rp3

tag: infected shrna


title: ChIPSeq_MM27_shKMT2D_aH3K4m3


title: in vivo P0 Ctx BJ1_rep4

source_name: in vivo P0 Ctx BJ1_rep4

value: C57BL/6 x JF1 hybrid


title: C1

description: BJ#2 Neurons#A

value: male

value: BJ


title: ChIPSeq_MM27_shKMT2D_aH3K4m1


title: in vivo P0 Ctx BJ1_rep3

source_name: in vivo P0 Ctx BJ1_rep3


title: ChIPSeq_MM27_shKMT2D_aH3K27ac


title: Control 96h replicate 2

city: Bethesda

first: Leonardo

last: Mariño-Ramírez

state: MD

address: 8600 Rockville Pike

department: CBB

institute: NCBI/NLM/NIH

data_processing:
Base-calling performed with CASAVA version 1.8.2
Trimmomatic version 0.32 was used to remove sequence adapters and bases of low quality using a sliding window of length 4, cutting when the average Phred quality score fell below 20
Trimmed paired-end reads were mapped using HISAT2 version 2.0.0-beta with option --no-unal and other parameters default
Raw-counts for feature gene were obtained using HTSeq version 0.6.0 with default parameters
Genome_build: ASM31385v1
Supplementary_files_format_and_content: Single matrix in tab-separated values format with raw-counts of mapped reads. Rows are genes, columns are samples.

organism: Musa acuminata

source_name: pool from root, pseudostems and leaves

growth_protocol: sample harvested after 96h

extract_protocol:
Total RNA was extracted from banana roots, pseudostems and leaves using the QIAGEN RNeasy plant mini kit (QIAGEN, Valencia, CA). mRNA was purified from 30 μg of total RNA using Sera-mag Magnetic Oligo (dT) Beads (Illumina). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not inoculated

tag: cultivar

value: Williams

tag: innoculation

tag: time point

value: after 96h


title: Control 96h replicate 1


title: ChIPSeq_MM16_shLuc_aKMT2D

value: KMT2D (Sigma, HPA035977)


title: Control 96h replicate 3


title: C2

description: 3440#5 Neurons#A

value: Control

tag: gender

value: GM03440 (Coriell)


title: in vivo E13.5 DT JB6_rep3

source_name: in vivo E13.5 DT JB6_rep3


title: ChIPSeq_MM16_shLuc_aH3K4m1

value: patient derived xenograft cells


title: in vivo P0 Ctx BJ1_rep2

source_name: in vivo P0 Ctx BJ1_rep2

value: Male


title: in vivo P0 Ctx BJ1_rep1

source_name: in vivo P0 Ctx BJ1_rep1


title: ChIPSeq_MM16_shLuc_aH3K4m3

value: shLuc

value: H3K4me3 (Active Motif, 39159)


title: Control 48h replicate 2

growth_protocol: sample harvested after 48h

value: after 48h


title: in vivo E13.5 DT JB6_rep1

source_name: in vivo E13.5 DT JB6_rep1


title: ChIPSeq_MM16_shLuc_aH3K27ac


title: ChIPSeq_MM16_shKMT2D_aKMT2D


title: Control 48h replicate 3


title: Control 48h replicate 1


title: Control 1h replicate 3

growth_protocol: sample harvested after 1h

value: after 1h


title: ChIPSeq_MM16_shKMT2D_aH3K4m3


title: Control 1h replicate 2


title: in vivo E13.5 DT BJ1_rep1

source_name: in vivo E13.5 DT BJ1_rep1


title: in vivo E13.5 DT BJ1_rep2

source_name: in vivo E13.5 DT BJ1_rep2


title: ChIPSeq_MM16_shKMT2D_aH3K4m1

value: H3K4me1 (Abcam, ab8895)


title: Control 1h replicate 1


title: ChIPSeq_MM13_shLuc_aKMT2D


title: in vivo E13.5 DT JB6_rep2

source_name: in vivo E13.5 DT JB6_rep2

value: JF1 x C57BL/6 hybrid


title: in vitro Ctx d21 E14_rep3

source_name: in vitro Ctx d21 E14_rep3


title: Bacillus 96h replicate 2

growth_protocol: sample harvested 96h post inoculation

treatment_protocol: Inoculated with Bacillus amyloliquefaciens

value: Bacillus amyloliquefaciens

value: 96h post inoculation


title: ChIPSeq_MM13_shLuc_aH3K4m3


title: Bacillus 96h replicate 1


title: in vitro Ctx d21 E14_rep1

source_name: in vitro Ctx d21 E14_rep1


title: in vitro Ctx d12 E14_rep3

source_name: in vitro Ctx d12 E14_rep3


title: in vitro Ctx d12 E14_rep2

source_name: in vitro Ctx d12 E14_rep2


title: ChIPSeq_MM13_shKMT2D_aH3K4m3

source_name: metastasis of cutaneous melanoma


title: ChIPSeq_MM13_shLuc_aH3K27ac

value: H3K27ac (Abcam, ab4729)


title: Bacillus 48h replicate 1

growth_protocol: sample harvested 48h post inoculation

value: 48h post inoculation


title: Bacillus 48h replicate 2

value: Williams


title: in vitro Ctx d12 E14_rep1

source_name: in vitro Ctx d12 E14_rep1


title: ChIPSeq_MM13_shKMT2D_aH3K27ac


title: Bacillus 48h replicate 3


title: in vivo E13.5 DT BJ1_rep3

source_name: in vivo E13.5 DT BJ1_rep3

value: C57BL/6 x JF1 hybrid

value: Female


title: in vitro Ctx d21 JB6_rep2

source_name: in vitro Ctx d21 JB6_rep2


title: ChIPSeq_MM16_shKMT2D_aH3K27ac


title: in vitro Ctx d21 E14_rep2

source_name: in vitro Ctx d21 E14_rep2


title: Bacillus 1h replicate 2

source_name: pool from root, pseudostems and leaves

growth_protocol: sample harvested 1h post inoculation

value: 1h post inoculation


title: Bacillus 1h replicate 1


title: Diseased Gall Bladder 1

city: Framingham

first: Andrew

middle: Danner

last: Johnson

state: MASSACHUSETTS

address: The Framingham Heart Study

department: Cardiovascular Epidemiology and Human Genomics Branch

institute: National Heart, Lung and Blood Institute

description:
Sample name: CR559860
Same patient as CR562345.

data_processing:
Sequencing data were demultiplexed and converted to FASTQ format.
Paired-end reads were aligned to RefSeq (hg19) using TopHat (v2.0.9) with the parameter setting: -g 1 -N 2 -r 200.
RNA reads-per-kilobase-per million mapped (RPKM) was calculated with RSeQC v2.3.6.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files. RPKM and raw read counts were calculated with RSeQC v2.3.6.

source_name: Gall bladder, adult, diseased

extract_protocol:
Total RNA was received from OriGene (CR559860, CR562345) or BioChain (A509245, A509248, A607331).
RNA-seq libraries were prepared using Ovation RNAseq v2 (NuGEN Technologies, Inc.) following guidelines for the Ovation SP Ultralow DR Multiplex System (NuGEN Technologies, Inc.). Library quality was verified for each sample using MiSeq (Illumina, Inc.) sequencing with 75bp paired-end reads.

value: gall bladder

value: female

tag: age (years)

tag: disease state

value: chronic gallstones


title: in vitro Ctx d12 JB6_rep2

source_name: in vitro Ctx d12 JB6_rep2

value: Male


title: Bacillus 96h replicate 3


title: ChIPSeq_MM13_shLuc_aH3K4m1

value: patient derived xenograft cells

value: shLuc


title: Pseudomonas 96h replicate 3

treatment_protocol: Inoculated with Pseudomonas fluorescens

value: Pseudomonas fluorescens


title: Non-disease Gall Bladder 3

description: Sample name: A607331

source_name: Gall bladder, adult, non-diseased

tag: tissue

value: healthy


title: Pseudomonas 96h replicate 2


title: Non-disease Gall Bladder 2

description: Sample name: A509248


title: ChIPSeq_MM13_shKMT2D_aH3K4m1

value: H3K4me1 (Abcam, ab8895)


title: ESCs JB6_rep2

source_name: ESCs JB6_rep2

value: JF1 x C57BL/6 hybrid


title: ESCs JB6_rep1

source_name: ESCs JB6_rep1


title: Pseudomonas 96h replicate 1

value: 96h post inoculation


title: in vitro Ctx d21 BJ1_rep2

source_name: in vitro Ctx d21 BJ1_rep2


title: Bacillus 1h replicate 3

value: Bacillus amyloliquefaciens


title: Pseudomonas 48h replicate 1

value: 48h post inoculation


title: in vitro Ctx d21 JB6_rep1

source_name: in vitro Ctx d21 JB6_rep1


title: Pseudomonas 48h replicate 2

value: Williams


title: in vitro Ctx d12 BJ1_rep1

source_name: in vitro Ctx d12 BJ1_rep1

value: C57BL/6 x JF1 hybrid


title: Pseudomonas 1h replicate 3


title: in vitro Ctx d21 BJ1_rep1

source_name: in vitro Ctx d21 BJ1_rep1


title: in vitro Ctx d12 BJ1_rep2

source_name: in vitro Ctx d12 BJ1_rep2


title: Diseased Liver 1

description:
Sample name: CR562345
Same patient as CR559860.

source_name: Liver, adult, diseased

value: liver


title: Pseudomonas 1h replicate 2

value: 1h post inoculation


title: ESCs BJ1_rep2

source_name: ESCs BJ1_rep2


title: in vitro Ctx d12 JB6_rep1

source_name: in vitro Ctx d12 JB6_rep1


title: HSPC_MLV

status: Public on Apr 20 2016

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

data_processing:
Library strategy: Retroviral scanning (MLV)
Data analysis performed as previously described (Cattoglio et al. 2010b).
Genome_build: Hg19

source_name: Hematopoietic stem/progenitor cells (HSPC)

growth_protocol: Committed erythroid and myeloid progenitors/precursors (EPP and MPP) were isolated as pools of CD34lowCD36high and CD34-CD13+ populations, after induction for five days in culture in the presence of SCF, IL3 and either Epo or G-CSF, respectively

extract_protocol: Genomic DNA was extracted and digested with MseI. 3’ LTR vector-genome junctions were amplified by linker-mediated PCR (LM-PCR), adapted to the GS-FLX Genome Sequencer (Roche/454 Life Sciences, Branford, CT) pyrosequencing platform.

value: Human CD34+ stem/progenitor cells

value: Human umbilical cord blood


title: Pseudomonas 1h replicate 1


title: ESCs BJ1_rep1

source_name: ESCs BJ1_rep1


title: MPP_MLV

source_name: Myeloid progenitors/precursors (MPP)

value: CD34+-derived human myeloid progenitors/precursors


title: ChIP-seq_HSPC_H3K4me1

description: ChIP DNA

data_processing:
Reads from each sample were mapped in three consecutive steps taking into account from 0 to a maximum of 2 mismatches. After each mapping step the unmapped reads were filtered out and remapped by increasing of one. The results of each mapping step were then pooled together into a single bam file.
We performed ChIP-seq peak calling using SICER default parameters (Zang et al. 2009) and using each INPUT data to model the background noise.
Genome_build: hg19
Supplementary_files_format_and_content: peak bed file

extract_protocol:
Chromatin was prepared after cross-linking for 10’ at RT with 1% formaldehyde-containing medium, using truChIP™ High Cell Chromatin Shearing Kit with SDS Shearing Buffer (Covaris). Nuclear extracts were sonicated to obtain DNA fragments averaging 200 bp in length and  immunoprecipitated the equivalent of 107 cells overnight with 10 μg of rabbit antibodies against H3K4me1, H3K4me3 and H3K27ac, as previously described (Cattoglio et al., 2010b; Cui et al., 2009).
Libraries were prepared according to Illumina's instructions accompanying  the standard protocol of Illumina ChIP-seq DNA sample preparation kit (IP-102-1001, Illumina Inc.).

tag: antibody


title: ChIP-seq_HSPC_H3K4me3

description: ChIP DNA


title: ChIP-seq_MPP_H3K4me3

description: ChIP DNA

value: H3K4me3 (ab8580, Abcam)


title: ChIP-seq_MPP_H3K4me1

description: ChIP DNA

value: H3K4me1 (ab8895, Abcam)


title: ChIP-seq_EPP_H3K27ac

description: ChIP DNA

source_name: Erythroid progenitors/precursors (EPP)

value: CD34+-derived human erythroid progenitors/precursors

value: H3K27ac (ab4729, Abcam)


title: ChIP-seq_EPP_H3K4me1

description: ChIP DNA


title: Pseudomonas 48h replicate 3

source_name: pool from root, pseudostems and leaves

value: Pseudomonas fluorescens


title: ChIP-seq_MPP_input

description: Input DNA

value: none (nuclear extracts sonicated but non-immunoprecipitated)


title: ChIP-seq_EPP_H3K4me3

description: ChIP DNA


title: CAGE_MPP

description: CAGE promoters

data_processing:
DNAFORM at RIKEN GeNAS performed CAGE data analysis. Briefly, tags were extracted and mapped to human genome version hg19 (NCBI build 37), with a minimum match length of 21 bases and a maximum of one error; tags mapping the human ribosomal DNA sequence were eliminated. For CAGE tags mapping to multiple genome locations, a weighting strategy, based on the number of CAGE tags within a 200bp neighbourhood around each candidate mapping location, was applied. Equal weights were used if no unique tags were found within the 200 bp region for all candidate mapping locations (Faulkner et al. 2008).
We defined level‐1 promoters ("transcription start sites") by summing the weighted number of CAGE tags at each genome position. Then we clustered level-1 promoters into level-2 promoters ("promoters") if they were within 20 bp of each other on the same chromosomal strand. We calculated the expression level for each level-1 and level-2 promoter by dividing the number of CAGE tags of each promoter in each experimental condition by the total number of mapped CAGE tags in that condition, and multiplying by 1,000,000 (tags-per-million, TPM). The expression of each level-2 promoter of at least 10 TPM in at least one experimental condition was imposed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM (tags-per-million) values of CAGE promoters for each Sample

extract_protocol:
RNA was extracted from multipotent and lineage-committed progenitors using RNeasy Plus Mini kit (QIAGEN).
CAGE library preparation was performed by DNAFORM Inc. at RIKEN Omics Science Center.


title: Non-disease Gall Bladder 1

description: Sample name: A509245

value: gall bladder

value: female

value: healthy


title: CAGE_EPP

description: CAGE promoters


title: CAGE_HSPC

description: CAGE promoters


title: ChIP-seq_MPP_H3K27ac

description: ChIP DNA


title: EPP_MLV


title: ChIP-seq mouse 3T3 shLuc Input

first: Keji

last: Zhao

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

description:
3T3 shRNA (Luc control) Input
GA8174

data_processing:
[ChIP-seq] Basecalls performed using RTA 1.7 or Illumina Casava1.7
[ChIP-seq] ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed for further analysis in each library.
[ChIP-seq] We identified Enriched-ChIP iregions using MACS.
[RNA-seq] Basecalls performed using RTA 1.7 or Illumina Casava1.7
[RNA-seq] RNA-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 for further analysis in each library.
[RNA-seq] We computed the rpkm value for each gene.
[bPPI-seq] Basecalls performed using RTA 1.7 or Illumina Casava1.7
[bPPI-seq] bPPI-seq reads were mapped to the mouse genome (mm9) using tophat, and the parameter multihits =15.
[bPPI-seq] We computed the rpkm value for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: [ChIP-seq] Bed: plain text file. Each line is a peak region. The six columns are chrom, start position, end position, peak name, and -10log10(p-value).
Supplementary_files_format_and_content: [RNA-seq] rpkm: plain text file. Each row is a gene.The three columns are gene, rpkm value, and readcount.
Supplementary_files_format_and_content: [bPPI-seq] rpkm: plain text file. First few rows include the information of the rpkm calculations. Then the four columns are gene, accession number, rpkm value, and readcount.

source_name: NIH/3T3 tet-on 3G cells

extract_protocol:
[ChIP-seq SELEX] 300ng of the resultant library mouse genomic DNA was run again with the new empty sepharose beads and GST-Osr1 beads, and the process was repeated four times.Eluted DNA was purified by MinElute Reaction Cleanup Kit (Qiagen). The DNA ends were repaired and generated a protruding 3’ A as described above. Following ligation of a pair of Solexa adaptors to the repaired ends, 150 to 400bp fragments were recovered from agarose gel. Then DNA was amplified using the index primers for 18 cycles and the 150-400bp fragments were isolated from agarose gel again.
[ChIP-seq SELEX] The libraries enriched at rounds two, three, and four were sequenced using Illumina high throughput sequencing
[RNA-seq] For mRNA-seq library prep:  a random primer (invitrogen cat# 48190-011) was used to prime the purified PolyA tailed-RNA and the cDNA synthesis was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen cat# 11917-010)  according to the users manual. The ds cDNA was subject to sonication in Diagenode's Bioruptor (level M, total of 30 minutes of 20 seconds ON and 20 seconds OFF)  to a size range of 100-400bp. Indexed library was prepared using Illumina's multiplexing sample prep oligonucleotide kit (Ref# 1005709) with Epicentre's End-It DNA End-repair Kit (Epcentre, cat# ER81050) according to the user's manual and Illumina's multiplexing sample preparation guide.
[RNA-seq] The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10”; 68°C, 30”; 72°C, 30” for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq2000.
[bPPI-seq] Total RNAs of sorted cells were extracted using QIAzol (Qiagen) and purified with miRNeasy micro kit (Qiagen) and DNase set (Qiagen). Purified RNAs were reverse transcribed using PrimeScript Reverse Transcriptase (Takara) with an oligo dT primer. The cDNAs were amplified by VNC-specific and T7 primers and fragmented to 200 to 500bp by sonication. The DNA ends were repaired using End-It DNA End-repair Kit (Epicentre), followed by treatment with Klenow Fragment exo- (New England Biolabs) to generate a protruding 3’A base used for adaptor ligation. Following ligation of a pair of top-Phops-oligo-17bp/T7MmeI-18bp adaptors, the fragments between 250-650bp were isolated from agarose gel. Then the DNA was amplified by MmeI-SD1/2/3 and T7 primers to add an MmeI recognition site at both ends, followed by digestion with MmeI (New England Biolabs).
[bPPI-seq] After treatment with Klenow Enzyme (New England Biolabs), indexed libraries were prepared with a Multiplexing Sample Preparation Oligonucleotide Kit (Illumina) according to the user's manual. The fragments between 250-500bp were isolated for sequencing on an Illumina next generation sequencing platform.
[ChIP-seq] Cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
[ChIP-seq] Libraries were prepared according to Illumina's instructions. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3′ A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. Libraries were sequenced on the Hi-seq following the manufacturer's protocols. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).

tag: protocol

value: shRNA (Luc control)


title: ChIP-seq mouse 3T3 shOSR1 Input

description:
3T3 shRNA (Osr1 knockdown) Input
GA8176

value: shRNA (Osr1 knockdown)


title: ChIP-seq mouse 3T3 shH2A.Z Input

description:
3T3 shRNA (H2A.Z knockdown) Input
GA8175

value: shRNA (H2A.Z knockdown)


title: RNA-Seq mouse 3T3 shH2A.Z(2)

description:
3T3 shRNA (H2A.Z knockdown)
GA8177


title: RNA-Seq mouse 3T3 shOsr1(1)

description:
3T3 shRNA (Osr1 knockdown)
GA8178


title: ChIP-seq_EPP_input

description: Input DNA


title: RNA-Seq mouse 3T3 shOsr1(2)

description:
3T3 shRNA (Osr1 knockdown)
GA8179


title: RNA-Seq mouse 3T3 shLuc(1)

description:
3T3 shRNA (Luc control)
GA7878


title: RNA-Seq mouse 3T3 shLuc(2)

description:
3T3 shRNA (Luc control)
GA7879


title: ChIP-seq mouse 3T3 shOSR1 OSR1(1)

description:
3T3 shRNA (Osr1 knockdown), Osr1ChIP antibody (Santa Cruz, catalog#  sc68392)
GA8172


title: RNA-Seq mouse 3T3 shH2A.Z(1)

description:
3T3 shRNA (H2A.Z knockdown)
GA7880


title: ChIP-seq mouse 3T3 shOSR1 H2A.Z(1)

description:
3T3 shRNA (Osr1 knockdown), H2A.Z ChIP antibody (Abcam, catalog# ab4174)
GA8170


title: ChIP-seq mouse 3T3 shH2A.Z OSR1(2)

description:
3T3 shRNA (H2A.Z knockdown), Osr1ChIP antibody (Santa Cruz, catalog#  sc68392)
GA8169


title: ChIP-seq mouse 3T3 shOSR1 OSR1(2)

description:
3T3 shRNA (Osr1 knockdown), Osr1ChIP antibody (Santa Cruz, catalog#  sc68392)
GA8173


title: ChIP-seq mouse 3T3 shOSR1 H2A.Z(2)

description:
3T3 shRNA (Osr1 knockdown), H2A.Z ChIP antibody (Abcam, catalog# ab4174)
GA8171


title: ChIP-seq mouse 3T3 shH2A.Z OSR1(1)

description:
3T3 shRNA (H2A.Z knockdown), Osr1ChIP antibody (Santa Cruz, catalog#  sc68392)
GA8168


title: ChIP-seq mouse 3T3 shH2A.Z H2A.Z(2)

description:
3T3 shRNA (H2A.Z knockdown), H2A.Z ChIP antibody (Abcam, catalog# ab4174)
GA8167


title: ChIP-seq mouse 3T3 shLuc H2A.Z(2)

description:
3T3 shRNA (Luc control), H2A.Z ChIP antibody (Abcam, catalog# ab4174)
GA8163


title: ChIP-seq mouse 3T3 shLuc H2A.Z(1)

description:
3T3 shRNA (Luc control), H2A.Z ChIP antibody (Abcam, catalog# ab4174)
GA8162


title: ChIP-seq mouse 3T3 shLuc OSR1(1)

description:
3T3 shRNA (Luc control), Osr1ChIP antibody (Santa Cruz, catalog#  sc68392)
GA8164


title: ChIP-seq mouse 3T3 shLuc OSR1(2)

description:
3T3 shRNA (Luc control), Osr1ChIP antibody (Santa Cruz, catalog#  sc68392)
GA8165


title: ChIP-seq mouse 3T3 shH2A.Z H2A.Z(1)

description:
3T3 shRNA (H2A.Z knockdown), H2A.Z ChIP antibody (Abcam, catalog# ab4174)
GA8166


title: Pv neurons from WT mice brain: Pv17-Pv32

city: Woodbury

first: Megan

last: Crow

state: New York

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

description:
flowcell: BC49TLACXX
lane 1

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads from read2 were mapped to mm9 whole genome using bowtie v0.12.7 with parameters -p 7 -o
random unique tags from read1 were matched to mapped reads from read2
duplicate tags for each matched mapped reads were discarded
mapped reads with unique tags retained and aggregated
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include absolute unique tag count values for each single cell

source_name: frontal cortex

growth_protocol: mouse housed in 12hr day light cycle, fed ad libitum

extract_protocol:
fresh intact brain sliced in ACSF, dissected, triturated to isolate single RFP neurons
2 round linear amplification with MessageAmp-II aRNA kit followed by cDNA lib preparation with Illumina TrueSeq smallRNA kit
polyA based library preparation with each aRNA containing unique random tag

treatment_protocol: no experimental treatment; Nkx2.1-CreER mouse induced at E17.5 w/ 150ul 20mg/ml Tamoxifen to express RFP

value: brain

tag: strain/genotype

value: Pv-ires-Cre; Ai14

tag: animal

tag: age

value: postnatal day 29

tag: library batch


title: Pv neurons from WT mice brain: Pv49-Pv64

description:
flowcell: BC49TLACXX
lane 2

value: postnatal day 35


title: ChC neurons from WT mice brain: ChC49-ChC64

description:
flowcell: AC3L7GACXX
lane 2

value: Nkx2.1-CreER; Ai14

value: postnatal day 32


title: Pv neurons from WT mice brain: Pv33-Pv48

description:
flowcell: BC49TLACXX
lane 2


title: Pv neurons from WT mice brain: Pv1-Pv16

description:
flowcell: BC49TLACXX
lane 1


title: ChC neurons from WT mice brain: ChC33-ChC48

description:
flowcell: AC3L7GACXX
lane 2


title: ChC neurons from WT mice brain: ChC17-ChC32

description:
flowcell: AC3L7GACXX
lane 1

value: postnatal day 31


title: ChIP-Seq mouse SELEX Osr1

description:
GA6640
Library strategy: SELEX

source_name: brain

tag: selection method

value: GST-Osr1 beads


title: 20150415_3780: H3K27ac WIBR3 (ΔE/G-T) hES-derived neurons

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: WIBR3-Clone  #24092 (Intron-4 enhancer genotype: ;ΔE/G-T) H3K27ac ChIP-Seq

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: hES-derived neurons WIBR3-Clone  #24092 (Intron-4 enhancer genotype: ΔE/G-T)

growth_protocol: HiPSCs and hESC line WIBR3 (Whitehead Institute Center for Human Stem Cell Research, Cambridge, MA) and BGO1 (NIH Code: BG01; BresaGen, Inc., Athens, GA) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15% fetal bovine serum (FBS) (Hyclone), 5% KnockOut Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). Targeted hESC WIBR3 clones #23169, #23236, #23275, #24092,  were generated in a sub-clone of WIBR3 with a targeted in-frame insertion of EGFP into the Nurr1 locus.  Differentiation into neural precursor cells (NPCs) and terminal differentiated neurons was performed according to previously established protocols. HESC colonies were harvested using 1.5 mg/ml collagenase type IV (Invitrogen), separated from the MEF feeder cells by gravity, gently triturated and cultured for 8 days in non-adherent suspension culture dishes (Corning) in EB medium [DMEM (Invitrogen) supplemented with 20% KnockOutTM Serum Replacement (Invitrogen), 0.5 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma)] supplemented with 50 ng/mL human recombinant Noggin (Peprotech) and 1000 nM dorsomorphin (Stemgent). Subsequently human EBs were plated onto poly-L-ornithine (15 μg/ml, Sigma), laminin (1 µg/ml Sigma), fibronectin (2 µg/ml Sigma)-coated tissue culture dishes in N2 medium supplemented with 50 ng/mL human recombinant Noggin (Peprotech), 1000 nM dorsomorphin (Stemgent) and FGF2 (20 ng/ml, R&D systems). After 8 days, neural rosette-bearing EBs were cut out by microdissection, dissociated using 0.05% trypsin/EDTA solution (Invitrogen) and subsequently expanded on poly-L-ornithine, laminin and fibronectin coated cell culture dishes a density of 5 x 105 cells/cm2 in N2 medium supplemented with FGF2 (20 ng/ml, R&D systems). Proliferating NPCs were passaged 2 to 4 times before induction of terminal differentiation into neurons by growth factor withdrawal in N2 medium supplemented with ascorbic acid (Sigma). Differentiated neurons were used for Chip-seq analysis 31 days after growth factor withdrawal.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

tag: cell type

value: Neuron

tag: chip antibody

tag: antibody manu.

value: Abcam

tag: antibody catalog


title: 20150415_3779: H3K27ac WIBR (ΔE/A-C) hES-derived neurons

description: WIBR3-Clone  #23275 (Intron-4 enhancer genotype: ;ΔE/A-C) H3K27ac ChIP-Seq

source_name: hES-derived neurons WIBR3-Clone  #23275 (Intron-4 enhancer genotype: ΔE/A-C)


title: 20140922_3085: H3K4me1 BGO1 WT hES-derived neuron

description: BG01 H3K4me1 Chip-seq

source_name: BGO1 WT hES-derived neuron


title: 20150415_3784: Input WIBR3 (ΔE/G-T) hES-derived neurons

description: WIBR3-Clone  #24092 (Intron-4 enhancer genotype: ;ΔE/G-T) Input


title: 20150415_3783: Input  WIBR3 (ΔE/A-C) hES-derived neurons

description: WIBR3-Clone  #23275 (Intron-4 enhancer genotype: ;ΔE/A-C) Input


title: 20150415_3775: H3K27ac WIBR3 WT hES-derived neurons

description: WIBR3 p23 (Intron-4 enhancer genotype: G-T; A-T) H3K27ac ChIP-Seq

source_name: WIBR3 WT hES-derived neurons (Intron-4 enhancer genotype: G-T/A-T)


title: 20150415_3777: H3K27ac WIBR3 (ΔE/A-T) hES-derived neurons

description: WIBR3-Clone  #23169 (Intron-4 enhancer genotype: ;ΔE/A-T) H3K27ac ChIP-Seq

source_name: hES-derived neurons WIBR3-Clone  #23169 (Intron-4 enhancer genotype: ΔE/A-T)


title: ChIP-seq_HSPC_input

description: Input DNA

value: Human CD34+ stem/progenitor cells


title: 20150415_3776: Input WIBR3 WT hES-derived neurons

description: WIBR3 p23 (Intron-4 enhancer genotype: G-T; A-T) Input


title: 20150415_3781: Input WIBR3 (ΔE/A-T) hES-derived neurons

description: WIBR3-Clone  #23169 (Intron-4 enhancer genotype: ;ΔE/A-T) Input


title: Wildtype MNase-Seq 20 minute digest replicate 1

city: Athens

first: Zachary

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

institute: University of Georgia

data_processing:
BWA version 0.7.10
samtools v1.2
igvtools2.3.14
Homer v4.7.2
processed data files format and content: tdf file constructed using IGVtools. Read counts were determined for 25 base pair windows
genome build: GCF_000182925.2

organism: Neurospora crassa

source_name: mycelium

growth_protocol: Conidia were grown for 5 hours in 50mL of Vogel's minimal medium

extract_protocol:
Cells were treated with 1% formaldahyde and resuspended in NPS buffer. Chromatin was release by treatment with Micrococcal nuclease. DNA was then run on a gel and band corresponding to mononuclesomes were extracted and used to make libraries.
Libraries were constructed using the Illuina TruSeq ChIP-seq libarary according to manufacturer instructions except that only 4 cycles of PRC were performed to limit bias against A:T sequences

treatment_protocol: All treatments are wildtype versus mutant

tag: genotype

value: wildtype

value: mycelium


title: hH1 RNA-seq Rep3

description: processed data file: RNA_Seq_isoforms.fpkm_table.txt

data_processing:
Tophat 2.0.14
cufflinks2.2.1
igvtools2.3.14
processed data files format and content: Cuffnorm_Isomform_FPKM_Tracking
genome build: GCF_000182925.2

extract_protocol:
Cells were collected by centrifugation and acid-phenol:chloroform extraction was performed to isolate RNA
Ribosomal RNA was removed using epicenter Ribo-zero kit for yeast and stranded RNA libraries were constructed using the Illumina stranded RNA-seq kit


title: ChIP-seq_HSPC_H3K27ac

description: ChIP DNA


title: hH1 RNA-seq Rep1


title: hH1 RNA-seq Rep2


title: Wildtype Negative control ChIP rep2

extract_protocol:
Cells were treated with 1% formaldahyde and resuspended in ChIP lysis buffer. Cells were disrupted by sonication and immunoprecipitation was performed with the indicated antibody.
Libraries were constructed using the Illuina TruSeq ChIP-seq libarary according to manufacturer instructions except that only 4 cycles of PRC were performed to limit bias against A:T sequences


title: Wildtype RNA-seq Rep1


title: H1-FLAG ChIP rep1

value: anti-FLAG antibodies (cat # F1804; Sigma-Aldrich)


title: H1-FLAG ChIP rep2


title: Wildtype RNA-Seq Rep2


title: Wildtype Mnase-Seq single-end


title: hH1 Mnase-seq single-end


title: S1 (mat a) rep3

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

data_processing:
Data were mapped to the Neurospora crassa (version 12) reference genome
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: Neurospora crassa (version 12)
Supplementary_files_format_and_content: tab delimited text file, see metafile for column headers

source_name: genomic DNA

growth_protocol: Grown in liquid VMM for 48 hours at 32 degrees C.

extract_protocol: Genomic DNA (gDNA) was isolated using standard methods for Neurospora (Pomraning et al. 2009; Methods). MethylC-seq libraries were constructed according to Urich et al. MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols (2015).

tag: strain

value: S1 (mat a)


title: Wildtype Negative control ChIP rep1


title: ChC neurons from WT mice brain: ChC1-ChC16

description:
flowcell: AC3L7GACXX
lane 1

tag: Sex

value: female


title: 20150415_3778: H3K27ac WIBR3 (ΔE/G-C) hES-derived neurons

description: WIBR3-Clone  #23236 (Intron-4 enhancer genotype: ;ΔE/G-C) H3K27ac ChIP-Seq

source_name: hES-derived neurons WIBR3-Clone  #23236 (Intron-4 enhancer genotype: ΔE/G-C)


title: 20150415_3782: Input WIBR3 (ΔE/G-C) hES-derived neurons

description: WIBR3-Clone  #23236 (Intron-4 enhancer genotype: ;ΔE/G-C) Input


title: hH1 MNase-Seq 60 minute digest replicate 2


title: S1 (mat a) rep2


title: S1 (mat a) rep1


title: hH1 MNase-Seq 60 minute digest replicate 1


title: H1 RIP rep2

value: H1 RIP


title: H1 RIP rep1


title: Wildtype MNase-Seq 60 minute digest replicate 1


title: hH1 MNase-Seq 20 minute digest replicate 1


title: H1 delta rep1

value: H1 delta


title: Wildtype MNase-Seq 20 minute digest replicate 2


title: Wildtype RNA pol II ChIP rep2

value: anti-unphosphorylated C-terminal repeat of RNA polymerase II (8WG16; cat# MMS-126R; Covance)


title: hH1 MNase-Seq 20 minute digest replicate 2


title: Wildtype RNA pol II ChIP rep1


title: late prediv M2G ribosome profiling

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

description: Ribosome footprints (mRNA)

data_processing:
Reads were subtracted of rRNA/tRNA using bowtie 0.12.8, then unmapped reads were mapped to the Caulobacter NA1000 genome (CP001340) using bowtie 0.12.8.
Ribosome profiling: The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)][Li et al,. Nature 484, 538 (2012)].
RNAseq: The position of each alignment is distributed into to the 5' most base
Abundance measurements were done using R.P.K.M. by calculating the reads per kb per million mapped reads in each sample.
Genome_build: NA1000: CP001340
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Each line in the processed file has three columns: Col 1: Genomic coordinate based on CP001340, Col 2: Strand, Col 3: Total read weight assigned to the coordinate, Only genomic coordinates with non-zero read weight are included in the text file, Reads aligning to rRNA, tRNA and non-coding RNA are not included.

organism: Caulobacter vibrioides NA1000

source_name: Whole cell lystate

growth_protocol: Caulobacter crescentus NA1000 were innoculated at OD600 0.05 and grown to OD600 0.5 at 28C at 200RPM.  Cells were then synchronized using the ludox method (Evinger and Agabian J. Bact 1977), and the resusltant swarmer cells were resuspended in M2G and aliquots were taken every 30 minutes until cell division.

extract_protocol:
Cells were lysed by mixer mill using 6 cycles of 3 min at 15Hz.  In between cycles, the chamber was resuspended in liquid nitrogen to keep frozen.  For ribosome profiling: Ribosome protected mRNA fragments were size selected via gel purification. For RNA-seq:  frozen lysate were phenol chloroform extracted at 65C, ethanol precipitated, and sheared by base hydrolysis at 95C.  Resulting mRNA fragments were size selected via gel purification.
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].

treatment_protocol: Cells were incubated with 100ug/mL Chloramphenicol for 2 min and rapidly collected by centrifugation.  Cells were resuspended in lysis buffer and dripped into liquid nitrogen.

value: late prediv M2G


title: H3K27ac_ChIP-seq_rep1

city: Macclesfield

first: Muhammad

middle: Ahmad

last: Maqbool

address: Alderley Park

department: Cancer Research UK Manchester Institut

country: United Kingdom

institute: University of Manchester

data_processing:
All samples were aligned to mouse genome (mm9, build 37) using Bowtie aligner (allowing 2 mismatches, keeping uniquely aligned reads only). Piles of tags with same coordinates, due to artifacts of PCR or unannotated regions of the genome were removed according to a thresholding method.
Uniquely aligned tags were further elongated after estimating optimal elongation size in silico and enabling to use the original fragment length for further processing.
All samples were input subtracted and signals were scaled so that the same number of units appeared in each experiment after merging of the replicates.
Genome_build: mm9
Supplementary_files_format_and_content: wig, contains score of binding

source_name: Rag KO Primary Thymocytes

extract_protocol:
Nuclear lysates from cross-linked cells were sonicated to fragment chromatin and histone-DNA complexes were immuno-precipitated with anti-H3K27ac antibody.
At least 1ng of ChIP DNA was used for library preparation according to the Illumina ChIP-seq protocol. Briefly, after end-repair and adapter ligation, fragments were size-selected (cut) on an agarose gel prior to pre-amplification and clustering. The size-selected and pre-amplified fragments were verified on a 2100 Bioanalyzer (Agilent, USA) before sequencing on a Genome Analyzer II (Illumina, USA) according to manufacturer’s instructions.

value: Primary Thymocytes

tag: background strain

value: H3K27ac (abcam, ab4729)


title: control

city: Cincinnati

first: Vladimir

last: Kalinichenko

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
Dissected Mouse Lungs
FoxF1.fl.fl.Lung

data_processing:
Base calling, alignment, filtering as well as quality control were performed by the CCHMC DNA Sequencing and Genotyping Core.
Data values were given as expressed FKPM for each transcript with appropriate gene ID.
Differentially expressed genes were analyzed using DESeq and p-value was calculated using chi squared likelihood-ratio test in Agilent Genespring GX Suite. Gene with expressed altered by a factor of 1.5 in endFoxf1 knockout lungs were selected for gene set enrichment analysis using ToppGene Suite.  Statistical significance of each bioprocess was calculated using negative log2 transformation of p-value.
genome build: mm9
Supplementary_files_format_and_content: text files with FPKM values

source_name: Mouse Lung

extract_protocol:
mRNA was isolated using Qiagen RNeasy Mini Kit
Libraries were prepared and quality controlled by the Cincinnati Children's Hosptial Medical Center DNA Sequencing and Genotyping Core Facilities and Staff

value: Foxf1 fl/fl

value: Lung


title: early stalk M2G ribosome profiling

description: Ribosome footprints (mRNA)

value: early stalk M2G


title: post division M2G ribosome profiling

description: Ribosome footprints (mRNA)

value: post division M2G


title: late stalk M2G ribosome profiling

description: Ribosome footprints (mRNA)

value: late stalk M2G


title: H3K27ac_ChIP-seq_rep2


title: swarmer M2G ribosome profiling

description: Ribosome footprints (mRNA)

value: swarmer M2G


title: post division M2G RNA-seq

description: rRNA depleted RNA


title: early prediv M2G ribosome profiling

description: Ribosome footprints (mRNA)

value: early prediv M2G


title: late prediv M2G RNA-seq

description: rRNA depleted RNA


title: Wildtype MNase-Seq 60 minute digest replicate 2

value: wildtype

value: mycelium


title: early prediv M2G RNA-seq

description: rRNA depleted RNA


title: H1 delta rep2


title: siSNRNP40-1

first: Alexander

last: Nguyen

address: 1230 York Ave

institute: Rockefeller University

data_processing:
For RNA-seq data analysis, the reads were trimmed to remove matches to linkers and low-quality bases (cutadapt v1.2.1).
Tophat (v. 2.0.8)39 was then used to map the reads to the human transcriptome (build hg19).
Cufflinks and cuffmerge (v.2.0.2) were then used to calculate reads per kilo base per million (RPKM) and consolidated results across the samples.
Finally, cuffdiff (v.2.0.2) was used to calculate log-fold changes and the associated statistics.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include transcript abundances in samples as quantified by cuffdiff. Biological replicates were averaged.

source_name: cell line

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep.

extract_protocol:
Cells were extracted 48 hours later using total RNA isolation kit (Norgen Biotek) with DNAse I treatment followed by Ribo-Zero Gold rRNA removal (Epicentre).
Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on HiSeq 2500.

treatment_protocol: 10,000 cells were seeded and were transfected the next day with siRNAs via Lipofectaime 2000 (Invitrogen).

tag: type

value: siSNRNP40 #1 GGAAUAGACAAUGAUAUC

tag: replicate

tag: cell line

value: LV-M100 (sublcone of MDA-MB-231)


title: siSNRNP40-2

value: siSNRNP40 #2 GGAUUUGACCGACUGAUA


title: MHC

first: Todd

last: Evans

address: 1300 York Avenue, Box282

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Raw Reads QC: FastQC v0.11.2
Alignment: STAR Aligner 2.3.0e_r291
Counting Reads: bedtools v2.17.0
Count normalization: DESeq2_1.2.10
Genome_build: mm10
Supplementary_files_format_and_content: All_gene_normalized.counts.txt

source_name: sorted aMHC:mCherry positive cells

extract_protocol:
RNA was prepared from sorted cells with Absolutely RNA Nanoprep kit. The cDNA libraries were generated using TruSeq RNA Sample Preparation (Illumina). Each library was sequenced using 50 bp single-reads in the HiSeq2500 format (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Contactin2:eGFP transduced with Lenti-viral aMHC:mCherry ESC line

tag: protocol

value: Day 4 of differentiated cells were treated with Sodium Nitroprusside(SN)

tag: sorted, sn-induced cell population

value: αMhc:mCherry+ (MHC)


title: GFP

source_name: sorted Cntn2:eGFP+/aMHC:mCherry-dim double  positive cells

value: Cntn2:eGFP+/dim αMhc:mCherry+(GFP)


title: NEG

source_name: sorted Cntn2:eGFP/aMHC:mCherry double negative cells

value: negative


title: siControl-2

value: Control siRNA -BLOCK-iT Fluorescent Oligo (Life Technologies)


title: siControl-1

value: Control siRNA - NC1 (IDT)


title: swarmer M2G RNA-seq

description: rRNA depleted RNA


title: Wildtype RNA-Seq Rep3

tag: tissue


title: CD5hi_rep3

status: Public on Apr 19 2016

city: Aurora

first: Ross

middle: M.

last: Kedl

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Sequence reads of 30 or more nt were mapped to the mm10 (GRCm38) assembly of the mouse genome with the STAR RNA-Seq aligner version 2.4.1d using gene annotation data from Ensembl version 78
For each gene in the Ensembl 78 annotation, reads were counted using the HTSeq software version 0.6.0
Statistical comparisons of the gene expression between the cell types were performed with the DESeq2 package version 1.8.1 for the R statistical software version 3.2.0.
Genome_build: mm10

source_name: Splenocytes

extract_protocol:
RNA was extracted using the Qiagen RNeasy plus kit (Cat# 74134) in accordance with the supplied manual.
A modified Kapa Biosystems (Wilmington, MA, USA) KAPA Stranded mRNA-Seq kit for whole transcriptome libraries was used to primarily target all polyA RNA. Briefly, library construction proceeded from isolation of total RNA species, followed by mRNA (poly-A) isolation, 1st and 2nd strand cDNA synthesis, Life Technologies Ion adaptor ligation, amplification, and bead templating.

tag: cell phenotype

value: CD8+; CD44lo/CD49dlo; 20% highest expressers of CD5


title: CD5-VM_rep2

value: CD8+; CD44hi/CD49dlo


title: CD5-VM_rep3


title: CD5lo_rep3

value: CD8+; CD44lo/CD49dlo; 20% lowest expressers of CD5


title: KO

description:
Dissected Mouse Lungs
PdgficreER.FoxF1.fl.fl.Lung

value: Pdgfb-iCreER / FoxF1 fl/fl

value: Lung


title: CD5lo_rep2


title: CD5hi_rep2


title: CD5-VM_rep1


title: Oct4 ChIP-Seq at G1

city: Seoul

first: Jihoon

last: Shin

address: Biomedical Science Building, 103 Daehakro, Jongro-gu

country: South Korea

institute: Seoul National University College of Medicine

description: nocodazole treated for 10 hours

data_processing:
Reads after sequencing were mapped against to the mouse genome using Bowtie 2 version 2.2.6.
The outputs were sorted by Picard tools and reliable reads based on mapping score were used in subsequent processes.
We used MACS v.1.4.2 tool to select binding sites of Oct4 with default setting.
TDF files were generated by using the igvtools package.
Genome_build: mm9
Supplementary_files_format_and_content: tdf

source_name: mouse embryonic stem cells (E14)

extract_protocol:
Cells were cross-linked with 1% (v/v) formaldehyde for 5 minutes at 37℃ and lysed. Then, nuclear pellets were sheared with Focused-ultrasonicator (Covaris) and immunoprecipitated. The immune complexes were eluted by adding 250ul of elution buffer containing 1% (w/v) SDS and 0.1M NaHCO3 two times. Cross-linking was reversed by adding of 20ul of 5M NaCl and incubated overnight at 65C. DNA was precipitated with ethanol and kept in -20℃ for the further use.
The immunoprecipitated (20ng/μL) samples were used for library preparation for Illumina sequencing using the TruSeq ChIP kit (Illumina, San Diego, CA) following the manufacturer's protocol. Briefly, 20 ng of immunoprecipitated DNA samples was end repaired-ligated to Illumina adaptors and selected for a fragment size of approximately 300 bp by gel extraction. Multiplex Illumina primers were used to amplify gel-extracted products.

value: Oct4 (Santa Cruz, sc-5279)

tag: phase


title: Oct4 ChIP-Seq at G2/M

description: 1 hour release of nocodazole treated cells


title: CD5hi_rep1


title: WT_H3K27me3 ChIP-seq

city: Syracuse

first: Golam

last: Mohi

address: 766 Irving Avenue

department: Pharmacology

institute: SUNY Upstate Medical University

data_processing:
Base calling performed using Illumina Real Time Analysis (RTA) v2. The RTA software is part of the NextSeq Control Software (NCS).
Reads were aligned to the mouse genome sequences (mm10) using Partek Flow, Version 3.0 (Partek Incorporated). Bowtie2 method was used in Partek Flow.
Peaks detection was performed using Strand NGS, Version 2.0 (Strand Genomics). MACS (Model-based Analysis for ChIP-Seq) method was selected for peak detection in Strand NGS software.
Genes had peaks within 5kb upstream to 0.5kb downstream of the transcription start sites (TSS) and p value less than 10-5 were determined as genes with significant H3K27me3 enrichment in Strand NGS.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using MACS in Galaxy. Peaks with p value less than 10-5 were selected.

source_name: LSK (Lin-Sca-1+c-kit+) cells sorted from WT mouse bone marrow, 12 weeks after pI-pC injections

growth_protocol: Control, MxCre Jak2VF/+ and MxCre Jak2VF/+ EZH2-/- mice were injected with five doses of pI-pC (300μg/dose) at 4 weeks after birth. BM cells were harvested at 12 weeks after pI-pC injections.

extract_protocol:
ChIP experiment was performed with EpiTect ChIP OneDay Kit (Qiagen) according to the manufacturer’s protocol and H3K27me3 antibody (07-449, Millipore)
Libraries were prepared using Illumina TruSeq ChIP Sample Prep Kit (Illumina) with immune-precipitated DNA for each sample. The sizes of the libraries were validated utilizing the DNA 1000 chip on the Agilent 2100 Bioanalyzer. The quantification of the libraries was done using the KAPA Library Quantification Kit.

treatment_protocol: Harvested bone marrow cells were stained with antibodies against cell surface markers and LSK (Lin-Sca-1+c-kit+) cells were sorted with FACS AriaII (BD)

tag: genotype/variation

value: WT

value: bone marrow

value: LSK (Lin-Sca-1+c-kit+) cell


title: IgG control

value: mouse IgG (Santa Cruz, sc-2025)


title: CREBKO

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

country: China

institute: Tsinghua university

data_processing:
Basecalls performed using bcl2fastq Conversion Software v1.8.4
RNA-seq reads were aligned to the mm10 genome using SOAP2.
Genome_build: mm10
Supplementary_files_format_and_content: read counts files were generated using Htseq-Count.

source_name: in vitro-generated Th17 cells

growth_protocol: The isolated naïve T cells were cultured under Th17 (IL6+TGFb+IL1b+IL23) for 6 days

extract_protocol:
Total cellular RNA was extracted by using TRIZOL reagent (Invitrogen). The mRNA was enriched by using the Dynabeads® mRNA DIRECT™ Micro Kit (Thermos Fisher Scientific, catalog NO. 61021).
The RNAseq library was prepared and amplified using NEXTflex™ RNA-Seq Kit (Bioo Scientific, catalog NO. 5129-02).

treatment_protocol: The cells were stimulated with plated bound CD3 for 4 hrs before TRIZOL extraction

tag: cell type

value: CREB KO


title: CREBWT

value: wildtype


title: Group 11. FFPE of group 3

city: Rotterdam

first: Elena

last: Martens-Uzunova

address: Wytemaweg 80

department: Urology

country: Netherlands

institute: Erasmus MC

description: carcinoma of the prostate

data_processing:
CLC-Bio Genomics Workbench (v. 4.9)
Data Import using Illumina Genome Analyzer Single Read importer. Parameters: Quality score = Illumina Pipeline 1.3 and 1.4 Discard sequence names = Yes  Discard quality scores = No
“Small RNA Analysis” workflow
Read-summarizing and adapter-removal parameters from the “Extract and Count” tool: Minimum sampling count:  4; Minimum and maximum number of nucleotides in reads: 15 and 35 nt, respectively; no 3’- or 5’- terminal nucleotide removal
Each read was screened with “no fixed adapter length” for the (partial) presence of Illumina small RNA adapter: CAAGCAGAAGACGGCATACGA on the minus strand with alignment mismatches and gaps allowance at a mismatch cost of 3, and a gap cost of 5, minimum score: ns, minimum score end: 3. If adapter was not found reads were discarded from further analysis
Filtered sequence reads were mapped to sncRNAdb with a maximum of 2 mismatches allowed using the “Annotate and Merge” tool
Boundaries of sdRNAs, tRFs and other sncRNA-derived RNAs (sncdRNAs) and specific location on the precursor sequence were done using Fragment Location Annotation and Identification Mapper (Hoogstrate Y et al., Bioinformatics. 2015; 31:665-673)
Genome_build: Custom sncRNAdb based on hg 19 (Hoogstrate Y et al., Bioinformatics. 2015; 31:665-673)
Supplementary_files_format_and_content: tab-delimited text file including raw and RPM values for each small RNA-derived RNA in each sample

source_name: prostate

growth_protocol: Samples obtained by radical prostatectomy

extract_protocol:
RNA Bee total RNA extraction
Illumina Small RNA Sample Preparation Guide, Part #1004239

tag: organ

value: prostate

tag: status

value: tumor

tag: source

value: primary tumor

tag: storage

value: FFPE


title: suvh2suvh9_RNAseq

first: Yongqiang

last: Li

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

description:
RNAseq_suvh2suvh9
Processed data file(s): col_suvh2suvh9_gene_exp.diff

data_processing:
RNAseq: Sequenced clean reads were mapped to Arabidopsis thaliana (tair10) whole genome using tophat v2.0.6 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10. Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.1) with the provision of a GTF annotation file (tair10).  Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Supplementary_files_format_and_content: tab-delimited files include FPKM values for each Sample.  Column 5 represents wild type and column 6 represents mutant.

organism: Arabidopsis thaliana

extract_protocol:
RNAseq: Seeding materials was ground into powder in liquid nitrogen; total RNA was harvested using TRIzol® Reagent (Invitrogen); then total RNA samples were treated with DNase I and the mRNA is enriched by using the oligo(dT) magnetic beads.
RNAseq: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: suvh2suvh9 mutant

value: seedling


title: Input - Chromatin sample 1

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

data_processing:
Resulting reads were aligned to mouse genome (mm9) using ELAND (Illumina)
sequence aligns (35 bases) were then 3’ extended in silico to a length of 110 bp and assigned to 32bp bins along the genome
peaks were called using the MACS algorithm (Model-based Analysis of ChIP-Seq) (Zhang et al., 2008) with default parameters, except that the genome length was specified with the ‘-g mm’ option for mouse (1.87e9)
Mapping genome features were performed with bedtools (Quinlan and Hall, 2010) using mm9 annotation from UCSC genome browser
Genome_build: mm9
Supplementary_files_format_and_content: BAR fragment density

source_name: THY1+ spermatogonia

growth_protocol: DBA/2 mice from Jackson Laboratories (Bar Harbor, ME) were bred to produce pup male mice. Testes from 6-8 day-old pups were used to produce testis cell suspensions that are subsequently enriched for SSCs, and cultured on mitomycin-C treated SNL76/7 feeders in a defined serum-free medium supplemented with glial cell line-derived neurotrophic factor (GDNF, 20ng/ml) and fibroblast growth factor 2 (FGF2, 1 ng/ml), as described [Supplemental Fig. 1; (Ogawa et al., 1997;Kanatsu-Shinohara et al., 2003;Nagano et al., 2003;Kanatsu-Shinohara et al., 2003;Oatley and Brinster, 2006;Benavides-Garcia et al., 2015)].

extract_protocol:
Chromatin from three independent biological preparations of THY1+ spermatogonia at passages 9-11 were used for ChIP essentially as described previously (Hermann et al., 2008;Hermann and Heckert, 2005). Briefly, cells were fixed by addition of 1% v/v formaldehyde to the culture media at RT°C for 15 min and fixation was quenched with addition of excess glycine (to 125mM). Cells were scraped, pelleted and washed twice with DPBS + 0.5% IGEPAL. Cell pellets were subjected to one freeze-thaw cycle, suspended in lysis buffer (10mM EDTA, 50mM Tris pH 8.1, 1% SDS and 1X protease inhibitor cocktail) and cells were disrupted with a dounce homogenizer. Chromatin was sheared to an average length of 300-500 bp via sonication and quantified by spectrophotometry. An aliquot of chromatin (Input) was treated with RNase, proteinase K and heated to reverse the crosslinks, and then isolated with ethanol precipitation. Aliquots of chromatin (30 µg) were precleared with protein-A or protein-G agarose beads (Invitrogen) and then incubated with 5ug of primary antibodies for PLZF (goat anti-PLZF IgG, sc-11146, Santa Cruz Biotechnology), RNA polymerase II phospho-CTD-Ser2 (mouse anti-POLII-pSer2-CTD, 61083, Active Motif) and SALL4 (rabbit anti-SALL4 IgG, ab29112, Abcam) at 4°C overnight. Protein-A or Protein-G agarose beads were then used to isolate immune complexes from SALL4 and PLZF/POLII IPs, respectively, and then washed, eluted with SDS buffer, and treated with both RNase A and proteinase K. Following overnight incubation at 65°C to reverse crosslinks, ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. To confirm chromatin quality prior to next-generation sequencing, ChIP qPCR was performed for RNA polymerase II pCTD-Ser2 in triplicate reactions with primers against intronic regions of the Actb (+1831) and Gapdh (+2089) genes using SYBR Green Supermix (Bio-Rad; Supplemental Fig. 2A). Quantitative PCR signals were normalized to those obtained from input DNA and calculated as copies of DNA detected per 1000 genome equivalents of input DNA (1000 cells). A genomic region located in a gene desert on Chromosome-6 (Untr6) served as a negative control as described (Franco et al., 2012).
For next-generation sequencing, ChIP and input samples were prepared for amplification by converting overhangs into phosphorylated blunt ends, 3’ adenylation, ligation of Illumina adaptors and library size selection (175-225 bp) on an agarose gel. Adaptor-ligated libraries were then amplified for 18 cycles and resulting DNAs were purified, quantified, and tested by qPCR to assess quality of amplification reactions. Amplified DNA libraries subjected to Illumina sequencing with Genome Analyzer II or HiSeq2000 instruments.

tag: strain

value: THY1+ spermatogonia

tag: chip antibody

value: Input


title: morc6_RNAseq

description:
RNAseq_morc6
Processed data file(s): col_morc6_gene_exp.diff

value: morc6 mutant


title: Group 8. LN-PCa

description: metastatic lesion

source_name: lymph node

value: lymph node

value: metastatic lesion

value: fresh-frozen


title: SALL4 ChIP - Chromatin sample 2


title: Input - Chromatin sample 2


title: early stalk M2G RNA-seq

description: rRNA depleted RNA

value: early stalk M2G


title: Group 10. PCa 6 TMPRSS2-ERG fusion

description: carcinoma of the prostate


title: PLZF ChIP - Chromatin sample 2

value: PLZF


title: Group 7. PCa TURP hormone refractory disease

description: carcinoma of the prostate


title: MxCre Jak2VF/+_H3K27me3 ChIP-seq

source_name: LSK (Lin-Sca-1+c-kit+) cells sorted from MxCre Jak2VF/+ mouse bone marrow, 12 weeks after pI-pC injections

value: MxCre Jak2VF/+

value: bone marrow

value: LSK (Lin-Sca-1+c-kit+) cell


title: Col-0_RNAseq

description:
RNAseq_col
Processed data file(s): col_morc6_gene_exp.diff, col_suvh2suvh9_gene_exp.diff

source_name: col

value: wild type


title: Group 4. PCa 6 recurrent

description: carcinoma of the prostate

value: prostate

value: tumor


title: SALL4 ChIP - Chromatin sample 1


title: PLZF ChIP - Chromatin sample 1


title: Group 6. PCa 8 recurrent

description: carcinoma of the prostate

value: primary tumor


title: MxCre Jak2VF/+ EZH2-/-_H3K27me3 ChIP-seq

source_name: LSK (Lin-Sca-1+c-kit+) cells sorted from MxCre Jak2VF/+ EZH2-/- mouse bone marrow, 12 weeks after pI-pC injections

value: MxCre Jak2VF/+ EZH2-/-


title: Group 5. PCa 7 recurrent

description: carcinoma of the prostate


title: CD5lo_rep1

value: CD8+; CD44lo/CD49dlo; 20% lowest expressers of CD5


title: Group 9. PCa 6 recurrent no chromosomal alterations

description: carcinoma of the prostate


title: Group 1 NAP

description: Normal tissue adjasent ot tumor

value: normal


title: Group 3. PCa 6 cured

description: carcinoma of the prostate


title: Group 2. BPH

description: Benign prostate hyperplasia


title: hESC_D16

city: Shanghai

first: Naihe

last: Jing

state: Shanghai

address: 320 Yueyang road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Day 16 differentiated cells

data_processing:
Aligns RNA-Seq reads to the genome using TopHat version 2.0.4
Assembles transcripts using Cufflinks version 2.0.2
Merges transcript assemblies using Cuffmerge
Finds differentially expressed genes and transcripts, detects differential splicing using Cuffdiff version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: Txt file includes FPKM values for each Sample

source_name: Day 16 differentiated cells

growth_protocol: Human ES cell–derived neural cells were generated according to the Dr. Zhang Shunchun's report (Stem Cells, 2007)

extract_protocol:
Total RNA was extracted with Trizol reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Day 16 differentiated cells (NPCs)


title: hESC_D20

description: Day 20 differentiated cells

source_name: Day 20 differentiated cells

value: Day 20 differentiated cells (NPCs)


title: hESC_D18

description: Day 18 differentiated cells

source_name: Day 18 differentiated cells

value: Day 18 differentiated cells (NPCs)


title: hESC_D22

description: Day 22 differentiated cells

source_name: Day 22 differentiated cells

value: Day 22 differentiated cells (NPCs)


title: hESC_D14

description: Day 14 differentiated cells

source_name: Day 14 differentiated cells

value: Day 14 differentiated cells (NPCs)


title: hESC_D10

description: Day 10 differentiated cells

source_name: Day 10 differentiated cells

value: Day 10 differentiated cells (NPCs)


title: hESC_D12

description: Day 12 differentiated cells

source_name: Day 12 differentiated cells

value: Day 12 differentiated cells (NPCs)


title: hESC_D8

description: Day 8 differentiated cells

source_name: Day 8 differentiated cells

value: Day 8 differentiated cells (NPCs)


title: hESC_D6

description: Day 6 differentiated cells

source_name: Day 6 differentiated cells

value: Day 6 differentiated cells (NPCs)


title: hESC_D4

description: Day 4 differentiated cells

source_name: Day 4 differentiated cells

value: Day 4 differentiated cells (NPCs)


title: hESC_D2

description: Day 2 differentiated cells

source_name: Day 2 differentiated cells

value: Day 2 differentiated cells (NPCs)


title: late stalk M2G RNA-seq

description: rRNA depleted RNA

source_name: Whole cell lystate

value: late stalk M2G


title: hESC_D0

description: undifferentiated hESCs

source_name: undifferentiated hESCs

value: undifferentiated hESCs


title: Input

description: Day 12 differentiated cells

data_processing:
Mapping to the Genome using bowtie version 0.12.8
Creation Tag directories using HOMER, makeTagDirectory
UCSC visualization using makeUCSCfile
Finding enriched peaks using findPeaks which is a program contains in HOMER
Genome_build: hg19
Supplementary_files_format_and_content: text files with peak coordinates generated by HOMER; text files with GO terms and counts; bedgraph files

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with AF9 or TET2 antibodies.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.


title: AF9 ChIP

description: Day 12 differentiated cells

value: anti-AF9 (NOVUS, NB100-1566)


title: D0INPUT

description: undifferentiated hESCs

data_processing:
Mapping to the Genome using bowtie version 0.12.8
Creation Tag directories using HOMER, makeTagDirectory
UCSC visualization using makeUCSCfile
Finding enriched peaks using MACS
Genome_build: hg19
Supplementary_files_format_and_content: text files with peak coordinates generated by MACS; bedgraph files

extract_protocol:
Genomic DNA were extracted and 5mC or 5hmC modified DNA fragments were enriched.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.


title: D12AMC

description: Day 12 differentiated cells

tag: dip antibody

value: anti-5mC (Active motif, Cat.#39649)


title: IU8567_RNA-seq rep 2

first: Malcolm

middle: E

last: Winkler

address: 1001 E. Third Street

data_processing:
Bases were called using bcl2fasta v2.16.0.10
Reads were quality and adapter trimmed using Trimmomatic v0.33 using default parameters, Illumina adapters, and a minimum read length of 35bps
Mapping was accomplished with bowtie2 version 2.1.0 by mapping to chromosome NC_008533 and the plasmid NC_005022
Genome_build: NC_008533.1
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest including genes and intergenic regions for each fastq file; intergenic regions are identified as follows Inter.<molecule>.<strand>.<basepair_begin>.<basepair_end>

organism: Streptococcus pneumoniae

source_name: Exponentially grown cells

growth_protocol: Cultures of strains IU6741 (∆pbp1a), IU8553 (∆pbp1a mltG(∆488bp)), IU8567 (∆pbp1a mltG(∆488bp) ∆pbp2b) and IU1824 (pbp1a+ mltG+ pbp2b+ parent) grown exponentially in BHI media at 37ºC to OD620 ≈0.15 to 0.2. Starter cultures were used to inoculate 30 mL cultures of BHI broth in 50 mL conical tubes.

extract_protocol:
RNA was prepared from cultures of strains IU6741 (∆pbp1a), IU8553 (∆pbp1a mltG(∆488bp)), IU8567 (∆pbp1a mltG(∆488bp) ∆pbp2b) and IU1824 (pbp1a+ mltG+ pbp2b+ parent). RNA was extracted from 23 ml of exponentially growing culture (OD620 ≈ 0.15) using a FastRNA Pro Blue Kit (MP Bio) according to the manufacturer's guidelines. Briefly, cells were collected by centrifugation at 14, 500 xg for 5 min at 4°C. Cells were resuspended in 1 mL RNApro (MP Bio) and processed twice in a Fast-Prep 24 homogenizer (MP Bio) for 40 s at setting 6.0. Chloroform and 100% ethanol were used to extract and precipitate the RNA from the resulting lysate, and the miRNeasy minikit (Qiagen) with on-column DNase I treatments was used to purify RNA.
cDNA libraries were prepared from total RNA by the Center for Genomics and Bioinformatics at Indiana University in Bloomington, Indiana. The mRNA was enriched from 1 μg of total RNA using RiboZero™ rRNA Removal Kit (Bacteria) (EpiCentre, Inc.). rRNA-depleted mRNA samples were purified using RNeasy Minelute Cleanup Kit (Qiagen). Double-stranded cDNA synthesis was performed following ScriptSeq™ Complete Kit (Bacteria) Preparation guide (EpiCentre, Inc.) in accordance with the manufacturer's standard protocol. Entire resultant mRNA sample was fragmented using divalent cations via incubation for 5 min at 85°C. The first strand of cDNA was synthesized by reverse transcription using random-sequence primers containing a tagging sequence at their 5′ ends. Di-tagged cDNA was synthesized by random annealing of a terminal-Tagging Oligo to the 3′ end of the cDNA for extension of the cDNA by DNA polymerase. Di-tagged cDNA was purified using Agencourt AMPure® XP beads (Beckman Coulter) followed by PCR amplification for 15 cycles using Failsafe™ PCR enzyme and ScriptSeq™ Index PCR Primer set (EpiCentre, Inc.). This step generated the second strand of cDNA and completed the addition of Illumina adapter sequences incorporating a user-defined barcode. The amplified libraries were purified using Agencourt AMPure® XP beads. Quality and quantity were assessed using D1000 TapeStation (Agilent Technologies) and Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies), respectively. Sequencing was performed at the Greehey Children’s Cancer Research Institute Genome Sequencing Facility at the University of Texas Health Science Center at San Antonio, Texas. Cluster generation was performed using TruSeq PE Cluster Kit v3-cBot-HS (Illumina).
Single-end, 50 bp sequencing was performed using TruSeq SBS Kit v3-HS (Illumina) on a HiSeq 2000 sequencer (Illumina). Image analysis, base calling, sequencing reads de-multiplexing were followed by default Illumina procedure.

tag: mutation


title: IU8567_RNA-seq rep 3


title: D12A5HMC

description: Day 12 differentiated cells

value: anti-5hmC (Millipore, Cat.#MABE317, Lot. Q2063315)


title: TET2 ChIP

description: Day 12 differentiated cells

value: anti-TET2 (Abiocode, R-1086)


title: IU8553_RNA-seq rep 3

value: ∆pbp1a mltG(∆488bp) ∆pbp2b


title: D0A5HMC

description: undifferentiated hESCs


title: suvh9_rep1_BS-sesq

data_processing:
Bisulfite-Seq: Bisulfite sequencing reads were mapped to the TAIR10 reference genome by using Bismark(v0.10.0) allowing two mismatches(Krueger and Andrews, 2011). Only reference genome cytosines covered with at least 5 reads were considered for analysis.
Supplementary_files_format_and_content: The bigwig files give methylation level for all Cs (three contexts) with depth >= 5. The methylation level of each cytosine site was represented by the percentage of the number of reads reporting a C relative to the total number of reads reporting a C or T.

extract_protocol:
BSseq: Genomic DNA was extracted from 2-week-old seedlings by CTAB and purified with phenol:chloroform (1:1).
Bsseq:  Bisulfite sequencing libraries were prepared using standard Illumina protocols

value: suvh9 mutant

value: seedling


title: IU8553_RNA-seq rep 2


title: suvh2suvh9_rep2_BS-sesq

value: suvh2suvh9 mutant


title: suvh9_rep2_BS-sesq


title: D0AMC

description: undifferentiated hESCs


title: IU8553_RNA-seq rep 1


title: IU6741_RNA-seq rep 3

value: ∆pbp1a mltG(∆488bp)


title: IU6741_RNA-seq rep 2


title: morc6suvh9_rep2_BS-sesq

value: morc6suvh9 mutant


title: suvh2suvh9_rep1_BS-sesq


title: morc6suvh9_rep1_BS-sesq


title: IU1824_RNA-seq rep 2


title: morc6_rep1_BS-sesq

value: morc6 mutant


title: IU1824_RNA-seq rep 1


title: IU6741_RNA-seq rep 1


title: Col-0_rep2_BS-sesq

value: wild type


title: IU1824_RNA-seq rep 3


title: morc6_rep2_BS-sesq


title: D12INPUT

description: Day 12 differentiated cells

value: Day 12 differentiated cells (NPCs)


title: Col-0_rep1_BS-seq


title: Input - Chromatin sample 3

source_name: THY1+ spermatogonia

value: THY1+ spermatogonia

value: Input


title: SRSF2-KO liver

first: Ning

last: Wei

address: 320 Yueyang RD.

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include number of reads and FPKM values for each Sample.

source_name: liver from mice at Day 11 after born

extract_protocol:
liver at Day11 after birth were collected and frozened in Liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: Day 11 after birth

value: liver

tag: genotype


title: SALL4 ChIP - Chromatin sample 3


title: IU8567_RNA-seq rep 1


title: WT liver

value: WT


title: PLZF ChIP - Chromatin sample 3

value: PLZF


title: Zebrafish 28-30hpf embryo mBAC4 Bio-CAP

status: Public on Apr 18 2016

city: Oxford

first: Hannah

middle: Katherine

last: Long

state: Oxfordshire

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

data_processing:
Library strategy: Bio-CAP
Tc1 and Tc0 mouse Bio-CAP reads were aligned to the appropriate reference genome using Bowtie version 1.0.0 allowing a maximum of two mismatches in the entire read, and retaining only uniquely mapping reads.
PCR duplicates were removed uisng Picard-Tools MarkDuplicates version 1.105(1632).
Peaks were called using MACS version 14 against an input file, with tag size 50, bandwidth 300, mfold 10,30 and pvalue cutoff of 1e-5.
Peaks closer than 200bp apart were merged.
Peaks from biological replicates were merged and only peaks found in both replicated were retained
Peaks overlapping a deleted region or breakpoint on human chromosome 21 in the Tc1 mouse were removed from further analysis.
To identify differentially hypomethylated loci, total normalised read count was compared for human and Tc1 mouse at all peaks identified in the two species, peaks with over a 2-fold changes in read density were determined to be differentially methylated between human and mouse. Peaks found at a duplicated region in Tc1 mouse were compensated for during the differential peak-calling.
Zebrafish embryo Bio-CAP reads were aligned to the zebrafish and mouse genome using  version 2.1.0 bowtie2 default settings.
Genome_build: Genome_build: Tc1 (composite mm9 chromosomes and hg19 chr21), mm9, hg19 and danRer7.

organism: Danio rerio

source_name: 28-30hpf embryo

extract_protocol:
Samples were obtained either as fresh-frozen samples or were dissected in-house and fresh-frozen. Samples were subjected to manual homogenisation followed by DNA purification by phenol chloroform extraction or using the QIAGEN 100/G genomic tip kit. For each individual Bio-CAP experiment, 25 μl of NeutrAvidin Agarose Resin (Thermo Scientific, 29200) was washed with BC100 buffer and then incubated with 50 μl of 0.5 μg/μl biotinylated hKDM2b-CxxC protein diluted in BC100 buffer for 1 hour at 4°C. The conjugated resin/CxxC protein was then washed with CAP100 buffer (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 100 mM NaCl). Genomic DNA was sonicated to an average size of 150-250 bp using a Diagenode Bioruptor. Sonicated DNA was then diluted in CAP100 buffer to a concentration of 16 μg/ml and a 100 μl Input sample was retained. For each Bio-CAP experiment, 500 μl of diluted sonicated DNA, corresponding to approximately 8 μg of DNA, was added to the conjugated CxxC resin. The DNA and resin were incubated at 4°C for 1 hour with gentle mixing. The resin was then collected by centrifugation at 1500 x g for 3 minutes at 4°C, and the unbound flowthrough (FT) material was removed. The resin and any associated DNA was washed twice with 1 ml of CAP100 buffer, before the first elution was performed by adding 50 μl of CAP300 (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 300 mM NaCl) to the resin and incubating at room temperature for 10 minutes. Following centrifugation a 50 μl elution fraction was carefully collected. The elution process was repeated using another 50 μl of CAP300 and the 300 mM elution fractions were pooled (giving a total volume of 100 μl). Subsequent elutions were performed in the same way using buffers with 500 mM, 700 mM and 1 M NaCl sequentially. Each 100 μl elution fraction, together with 100 μl of both the Input and FT samples, was purified using a PCR purification column (Qiagen) and DNA was eluted in a volume of 50 μl. The 700 mM and 1 M fractions were pooled for sequencing.
Bio-CAP material was quantified using the High Sensitivity Qubit system (Invitrogen) and the fragmentation profile was assessed using a DNA HS Agilent 2200 TapeStation chip or a DNA HS Agilent 2100 Bioanalyzer chip. Bio-CAP material was then prepared for Solexa sequencing using the NEBNextTM DNA Sample Prep Master Mix Set 1, according to manufacturer's specifications.   Next generation sequencing was performed using two Illumina sequencing platforms: HiSeq and NextSeq Systems yielding 51bp and 80bp single-end reads respectively. Sequencing was carried out according to the manufacturer’s instructions.

tag: developmental stage

value: 28-30hpf embryo


title: Zebrafish 28-30hpf embryo mBAC1 Bio-CAP


title: Zebrafish 28-30hpf embryo mBAC2 Bio-CAP


title: Zebrafish 28-30hpf embryo mBAC3 Bio-CAP