title: Input rep3

first: David

middle: R

last: Kelley

state: MA

address: 7 Divinity Ave.

institute: Harvard University

data_processing:
CASAVA v1.8.3 used to called bases.
Tophat 2.0.9 with default parameters used to align fRIP-Seq reads to hg19 and GENCODE v18 reference annotation.
Cuffdiff 2.1.1 used to estimate gene abundances and perform statistical comparisons between the RIP and input alignments.
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff gene_exp.diff

growth_protocol: K562 cells (ATCC cat #CCL-243) were grown in RPMI 1640 (Invitrogen, cat #22400105) with 10% FBS and 1% Antiboiotic-Antimycotic 100X (Invitrogen, cat #15240062).

extract_protocol:
We re-suspended frozen pellets in 1 mL of RIPA lysis buffer (50mM Tris (pH 8), 150 mM KCl, 0.1% SDS, 1% Triton-X, 5 mM EDTA, 0.5% sodium deoxycholate, 0.5 mM DTT (add fresh) + protease inhibitor cocktail (Thermo Scientific, PI-87785) + 100 U/ml RNaseOUTTM  (Life Technologies , 10777-019)). We incubated cells at 4°C for 10 minutes before lysing on a Branson® digital sonifier using 10% amplitude for 0.7 seconds on and 1.3 seconds off at 30 second intervals for a total of 90 seconds. We used chilled tube holders and swapped them out between shearing runs to reduce temperature elevation. After lysis, we spun the lysate at 4°C max speed for 10 minutes.  We collected supernatant and diluted by adding equal volume of fRIP binding/wash buffer (150 mM KCl, 25 mM Tris (pH 7.5), 5 mM EDTA, 0.5% NP-40, 0.5 mM DTT (add fresh), 1X PIC (add fresh), 100 U/mL RNaseOUT  (add fresh)). At this point, we removed 50 μl of lysate for input sample and stored at -20°C for later RNA purification and library construction. After dilution, we clarified the lysate by passage through a 0.45 μM syringe filter. We then “pre-cleared” filtered lysate by incubating with Dynabeads® Protein G (Life Technologies cat#10004D) at a concentration of 25 μl of beads per 5 million cells for 30 minutes at 4°C with slow rotation. We flash froze pre-cleared lysate in 1 mL aliquots of ~5 million cells and stored it at -80 °C. For fRIP, we thawed lysate on ice and added 6 μg of HuR antibody (Santa Cruz, sc-5483). After addition of antibody, we rotated lysate at 4°C for 2 hours before adding 50 μl of Dynabeads® Protein G. We rotated beads and lysate at 4°C for 1 hour before washing 2X with 1 mL of fRIP binding/washing buffer + 1X PIC and 100 U/mL RNaseOUT. After the final wash, we removed the supernatant and froze and stored the beads at -20°C.
We re-suspended the frozen beads in 56 μl of RNase-free water and added 33uL of 3X reverse-crosslinking buffer (3X PBS (without Mg or Ca), 6% N-Lauroyl Sarcosine, 30 mM EDTA, 15 mM DTT (add fresh)), 10 μl of Proteinase K (Life Technologies, cat #AM9516), and 1 μl of RNaseOUT to both the re-suspended beads and input sample. We performed protein degradation and reverse-crosslinking for 1 hour at 42°C, then another 1 hour at 55°C. We added beads and reaction buffer to 1 mL of TriZol (Life Technologies, 15596-026). After agitation, we added 200 μl of chloroform followed by ~15 seconds of vigorous agitation and a 20 minute microcentrifuge spin at 4°C max speed. We collected the aqueous layer, added it to 750 μl of ethanol + 1 μl GlycoBlue™, and ran it over a Qiagen RNeasy® min-elute column (Qiagen, cat #74204). We extracted RNA using the buffer RWT/3X isopropanol modification detailed in “Appendix B: Optional On-Column DNAse Digestion…” of the Qiagen miRNeasy® Mini Handbook. We eluted RNA in 15μl of RNase-free water. To remove ribosomal RNA, we fed ≥ 70 ng of input and fRIP RNA into the Ribo-Zero™ Magnetic Gold Kit (Epicentre, cat #MRZG12324) followed by a cleanup using Agencourt RNAClean XP beads (Beckman Coulter, cat #A63987) and elution with 19.5 uL of Elute, Prime, Fragment mix from the TruSeq RNA Sample Preparation Kit (Illumina, cat #RS-122-2001). We performed library construction per the vendor’s instructions, starting with the “Incubate RFP” step. We pooled the resulting cDNA libraries and subjected them to paired-end sequencing on an Illumina HiSeq 2500 at a depth of 31 base pairs per read.

treatment_protocol: We collected cells with a gentle 5 minute spin 500g and washed with room temperature PBS. We re-suspended at 5e6 cells per ml in room temperature RPMI media sans FBS or Antibiotic-Antimycotic and added formaldehyde to a final concentration of 0.1%. We cross-linked at room temperature for 10 minutes and then halted it by quenching for 5 minutes at room temperature after adding glycine to a final concentration of 125 mM at a medium pace. We spun cells for 5 minutes 500g and washed 2X in 4°C PBS. We flash froze pellets of 10e6 cells and stored them at -80 °C.

tag: antibody


title: Heart

status: Public on Sep 10 2014

type: SRA

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

library_source: genomic

data_processing:
Library strategy: HELP-tagging
HELP pipeline is described in Suzuki et al. Genome Biol 2010 (PMID: 20359321).
Genome_build: mm9
Supplementary_files_format_and_content: ID_REF: ID for reference, chr: chromosome, pos: position of HpaII site, angle: degree of DNA hypomethylation, conf: degree of confidence, higher values have higher confidency.

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J mouse, adult 26-week

growth_protocol: DB3 ES cells were cultured on gelatin-coated feeder-free plates in complete ES medium, GMEM (Sigma), 10% FBS (MBL), 1000 U/ml leukemia inhibitory factor (LIF) (ESGRO, Chemicon), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids (NEAA), 2 mM GlutaMAX, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin (50 U/50 µg/ml). Medium was changed daily and cells were split every 2 to 3 days routinely.

extract_protocol:
Genomic DNA was extracted from individual cell populations separately. Cells were lysed in sodium dodecyl sulfate (SDS)-containing DNA extraction buffer (100 mM Tris-HCl, pH 8.0, 200 mM NaCl, 50 mM EDTA) and treated with proteinase K for 3 h at 55°C. The residual RNA was digested by incubation in the presence of RNase A for 1 h in 37°C. Lysates were subjected to three rounds of phenol–chloroform–isoamylalcohol (PCI; Invitrogen) extraction and the genomic DNA was precipitated by ethanol, washed with 70% ethanol, dried, and then dissolved in TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). The quality of purified genomic DNA was checked by gel and Nanodrop (260/280=1.7-1.9, 260/230>2).
The HELP tagging assay was performed on purified genomic DNAs. The protocol was modified for NEBNext Multiplex Oligos for Illumina (NEB) from the original protocol (http://wasp.einstein.yu.edu/index.php/Protocol:HELP_tagging). Briefly, genomic DNA was digested by HpaII or MspI, the former only cutting at CCGG sequences where the central CG dinucleotide is unmethylated. AS and AE adapters were prepared by annealing two oligo DNAs separately. The first Illumina AE adapter was ligated to the compatible cohesive end created, juxtaposing an EcoP15I site beside the HpaII/MspI digestion site and allowing EcoP15I to digest within the flanking genomic DNA sequence. An A-overhang was created, allowing the ligation of the second Illumina AS adapter. This created both AE-insert-AS products and AS-insert-AS molecules. By performing a T7 polymerase-mediated in vitro transcription from a promoter sequence located on the AE adapter, we selectively enriched for the AE-insert-AS product as single-strand RNA. After cDNA synthesis by specific primers, PCR amplification was performed corresponding primer set. The quantification was performed by KAPA quantification kit.

treatment_protocol: The ES cells were cultured and harvested at the 80% confluent. The dispersed cells were collected, snap-frozen and stored in -80 C. The cardiomyocytes were all dissociated by trypsin and collagenase and separated by Ficoll gradient or size selection. To isolate the cardiac fibroblasts, dissociated cells were expanded on a culture dish and checked the absence of cardiomyocytes by TMRM (Nat Methods 2009 Hattori). Tissues and cells were isolated from animals, snap-frozen and stored in -80 C.

tag: cell type

value: freshely disseted heart tissue

tag: restriction enzyme

value: HpaII

tag: strain

tag: developmental stage

value: adult 26-week


title: HuR fRIP rep3

city: Cambridge

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: HuR


title: Input rep2


title: Liver

source_name: C57BL/6J mouse, adult 8-week

value: freshely disseted liver tissue

value: adult 8-week


title: Input rep1


title: P1CM MspI

description: used for nomalizing the HpaII representation

source_name: C57BL/6J mouse, postnatal day 1

value: isolated cardiomyocytes

value: MspI

value: postnatal day 1


title: W8CF

value: isolated cardiac fibroblasts


title: Hutt60_LCL

city: Chicago

first: Irene

last: Gallego Romero

state: IL

address: 920 E 58th St, CLSC 317

department: Human Genetics

institute: University of Chicago

description: Sample 28

data_processing:
Mapping with TopHat2/Bowtie2
Removal of reads that do not map to highly orthologous regions between human and chimpanzee with featureCounts
Loess normalization on log2 CPM using voom
RPKM calculation
Genome_build: hg19
Supplementary_files_format_and_content: Processed data .txt file reports RPKMs

molecule: polyA RNA

source_name: LCL

growth_protocol: Standard iPSC and precursor cell line conditions as described in text

extract_protocol:
Qiagen Rneasy
TruSeq

tag: cell type (precursor used to generate ipscs)

value: LCL

tag: passage

tag: gender

value: Female


title: W8CM


title: P1CM


title: HuR fRIP rep2


title: E9CM

source_name: C57BL6/J mouse, embryonic day 9

value: embryonic day 9


title: P1CF


title: HuR fRIP rep1


title: C40280_iPSC

description: Sample 7

data_processing:
Mapping with TopHat2/Bowtie2
Removal of reads that do not map to highly orthologous regions between human and chimpanzee with featureCounts
Loess normalization on log2 CPM using voom
RPKM calculation
Genome_build: PanTro3
Supplementary_files_format_and_content: Processed data .txt file reports RPKMs

organism: Pan troglodytes

source_name: induced pluripotent stem cell line

value: induced pluripotent stem cell line


title: C40210_FB

description: Sample 20

source_name: dermal fibroblast

value: dermal fibroblast


title: Hutt45_LCL

description: Sample 27

value: Male


title: GFPES

source_name: EB3 embryonic stem cell line

value: cultured ES cells


title: C3647_FB

description: Sample 15


title: C3651_iPSC

description: Sample 3


title: HCT116 RNA polymerase II ChIP-seq rep1

city: Los Angeles

first: Peggy

middle: J

last: Farnham

state: CA

address: 1450 Biggy Street NRT 6503

department: GMCB

institute: University of Southern California Graduate Student

data_processing:
All ChIP-seq data was mapped to hg19 using BWA (default parameters) and peaks were called using Sole-search with the following parameters: Permutation:5; Fragment:250; AlphaValue: 0.00010 = 1.0E-4; FDR: 0.00010 = 1.0E-4; PeakMergeDistance:0; HistoneBlurLength:1200 for H3K4me3 and H3K27ac).
Whole genome bisulfite sequence: Raw reads were mapped using Bowtie2 and percent methyl-C/C was calculated for every CpG dinucleotide in the human genome by Bis-SNP package.
RNA-seq: Raw reads were mapped to hg19 (Ensembl 72) using Tophat2, and Partek Flow version 3.0.14.0321 was used tocarry out read quantification gene expression signal and gene-specific differential expression analyses.
Genome_build: hg19
Supplementary_files_format_and_content: CpG methylation value in Bed format (type=bedDetail)
Supplementary_files_format_and_content: ChIP-seq peak files in gff format
Supplementary_files_format_and_content: Signal density in bigwig format

source_name: HCT116 RNA polymerase II ChIP-seq

growth_protocol: The human cell lines HCT116 (ATCC #CCL-247) and DKO1 were grown in McCoy's 5A Medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin and were harvested for downstream experiments at 80% confluence.

extract_protocol:
Whole Genome Bisulfite Sequencing (WGBS): Genomic DNA was collected from HCT116 and DKO1 cells using a Qiagen QIAeasy DNA mini kit. ChIP-seq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA-seq: RNA was collected from cells using Trizol (Life Technologies Catalog#15596018).
Whole Genome Bisulfite Sequencing (WGBS): Genomic DNA (2 μg) was sonicated using a Covaris to an average molecular weight of 150 bp.  Achievement of the desired size range was verified by Bioanalyzer (Agilent) analysis. Fragmented DNA was repaired to generate blunt ends using the END-It kit (Epicentre Biotechnologies, Madison, WI) according to manufacturer’s instructions.  Following incubation, the treated DNA was purified using AmpureX beads from Agencourt.  In general, magnetic beads were employed for all nucleic acid purifications in the following protocol.  Following end repair, A-tailing was performed using the NEB dA-tailing module according to manufacturer’s instructions (New England Biolabs, Ipswich, MA). Adapters with a 3’ ‘T’ overhang were then ligated to the end-modified DNA.  For whole genome bisulfite sequencing, modified Illumina paired-end (PE) adapters were used in which cytosine bases in the adapter are replaced with 5-methylcytosine bases.   Depending on the specific application, we utilized either Early Access Methylation Adapter Oligos that do not contain barcodes, or the adapters present in later versions of the Illumina DNA Sample Preparation kits, which contain both indices and methylated cytosines.  Ligation was carried out using ultrapure, rapid T4 ligase (Enzymatics, Beverly, MA) according to manufacturer’s instructions.  The final product was then purified with magnetic beads to yield an adapter-ligation mix. Prior to bisulfite conversion, bacteriophage lambda DNA that had been through the same library preparation protocol described above to generate adapter-ligation mixes was combined with the genomic sample adapter ligation mix at 0.5% w/w.  Adapter-ligation mixes were then bisulfite converted using the Zymo DNA Methylation Gold kit (Zymo Research, Orange, CA) according to the manufacturer’s recommendations. Final modified product was purified by magnetic beads and eluted in a final volume of 20 ul. Amplification of one-half the adapter-ligated library was performed using Kapa HiFi-U Ready Mix for the following protocol: 98° 2’; then six cycles of  98° 30”, 65° 15” , 72° 60”; with a final 72° 10’ extension, in a 50 ul total volume reaction. The final library product was examined on the Agilent Bioanalyzer, then quantified using the Kapa Biosystems Library Quantification kit according to manufacturer’s instructions.   Optimal concentrations to get the right cluster density were determined empirically but tended to be higher than for non-bisulfite libraries.  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1.  Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5.
RNA-seq was performed for HCT116 and DKO1 in replicate. RNA was collected from cells using Trizol (Life Technologies Catalog#15596018) and  paired-end libraries were prepared using the Illumina TruSeqV2 Sample Prep Kit (Catalog #15596-026), starting with 1 ug total RNA. Libraries were sequenced on an Illumina Hi-Seq 2000. ChIP-seq: protocol was described in Comparison of sample preparation methods for ChIP-chip assays. O'geen H et.al Biotech 2006, 41:577–580.

value: human colorectal cancer cell line

tag: genotype/variation

value: wild type

tag: chip antibody

value: RNA polymerase II

tag: chip antibody vendor

value: Covance

tag: chip antibody cat.#

tag: chip antibody lot #


title: H19114_LCL

description: Sample 26


title: Heart MspI

value: freshely disseted heart tissue

value: adult 26-week


title: H19101_LCL

description: Sample 25


title: H28834_FB

description: Sample 23


title: H18489_LCL

description: Sample 24


title: DKO1 RNA polymerase II ChIP-seq rep2

source_name: DKO1 RNA polymerase II ChIP-seq

value: mutations in DNA methyltransferases (double knockout)


title: DKO1 RNA polymerase II ChIP-seq rep1


title: DKO1 H3K4me3 replicate 2 ChIP-seq

source_name: DKO1 H3K4me3 ChIP-seq

value: CST

value: lot# 4


title: H20961_FB

description: Sample 22


title: Hutt60_iPSC

description: Sample 14


title: DKO1 H3K4me3 replicate 1 ChIP-seq


title: Hutt45_iPSC

description: Sample 13


title: DKO1 H3K27ac replicate 2 ChIP-seq

source_name: DKO1 H3K27ac ChIP-seq

value: Active Motif


title: H28834_iPSC

description: Sample 12


title: H20961_iPSC

description: Sample 11


title: DKO1 RNA-seq replicate 2

description: DKO1 RNAseq rep2

source_name: DKO1 RNA-seq


title: DKO1 H3K27ac replicate 1 ChIP-seq


title: H18489_iPSC

description: Sample 8


title: H19114_iPSC

description: Sample 10


title: ORGL1

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

data_processing:
Post processing was done using Illumina Casava 1.82
Reads were aligned to the Drosophila melanogaster reference genome release 5.45 using Bowtie 2.1.
Count tables were generated in R  using UCSC Refseq Genes
Transcripts with a combined count less than 27 in the 9 samples were filtered out.
Count data was normalized and converted to Count Per Million (cpm) using the Voom package.
RPKM values were calculated for each transcript and averages of different isoforms were taken for each gene for downstream analysis.
Genome_build: Dm3 R5.45
Supplementary_files_format_and_content: Text files with gene RPKM values

organism: Drosophila melanogaster

source_name: Whole gut from adult female

extract_protocol:
Guts were dissected and put in Trizol on ice. RNA was harvested using Trizol reagent.
Illumina TruSeq Stranded mRNA LT kit (cat# RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: diet

value: 10% glucose

tag: repeat

value: Oregon R

tag: tissue

value: gut


title: DKO1 RNA-seq replicate 1

description: DKO1 RNAseq rep1


title: HCT116 whole genome bisulfite sequence

description: HCT116 WGBS

source_name: HCT116 whole genome bisulfite sequence


title: H19101_iPSC

description: Sample 9

value: induced pluripotent stem cell line


title: DKO1 whole genome bisulfite sequence

description: DKO1 WGBS

source_name: DKO1 whole genome bisulfite sequence


title: ORAG3

value: Agar


title: 22Rv1_ARFL-/ARVs-

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bedGraph file

source_name: prostate cancer cell

growth_protocol: Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).

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 Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: 22Rv1 cell were transfected with non-target siRNA (designated as ARFL+/ARVs+), siRNA targeting AR exon7 to knockdown AR-FL (designated as ARFL-/ARVs+), and siRNA targeting AR exon1 to knockdown all AR isoforms (designated as ARFL-/ARVs-), then cultured with charcoal-stripped serum (CSS) medium for 72 hours.

value: prostate cancer

tag: chip antibodies

value: Androgen Receptor (Santa Cruz, N-20)


title: 22Rv1_input

tag: cell type


title: ORAG2


title: 22Rv1_ARFL-/ARVs+


title: ORAG1


title: 22Rv1_ARFL+/ARVs+


title: siMEF2A2

status: Public on Sep 09 2014

city: Toronto

first: John

middle: C

last: McDermott

state: ON

address: 4700 Keele Street

country: Canada

institute: York University

data_processing:
Base calls are made using the Illumina CASAVA pipeline. Base quality is encoded in phred 33.
Reads are trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters are removed from the reads, and all reads are required to have a length of at least 32 b.p. Trimming and clipping are done with the Trimmomatic software.
The filtered reads are aligned to a reference genome. the genome used in the analysis is mm10 The alignment is done with the combination of tophat/bowtie software. It generates a Binary Alignment Map file (.bam).
The Cufflinks program is used to assemble aligned RNA-Seq reads into transcripts and to estimate their abundances (FPKM)
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

growth_protocol: C2C12 were grown on gelatin coated plates in Dulbecco’s Modified Eagle Medium (DMEM) with High Glucose and L-Glutamine (Hyclone) supplemented with 10% fetal bovine serum (HyClone) and 1% Penicillin/Streptomycin (Invitrogen)

extract_protocol:
RNA was extracted using the Qiagen Rneasy Purification Kit.
Illumina TruSeq RNA Sample Prep Kit (firststrand TruSeq RNA). RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: C2C12 were transfected with 30 nM siRNA using Lipofectamine. C2C12 were induced to differentiate in differentiation medium (DM) containing DMEM/High Glucose/L-Glutamine supplemented with 2% Horse Serum (Hyclone) and 1% Penicillin/Streptomycin for 48 hr.

value: Myoblast

tag: transfected with


title: siMEF2A1


title: scr2

value: scrambled


title: scr1

value: scrambled siRNA


title: MEF2A_ChIP-exo [mouse]

data_processing:
library strategy: ChIP-exo
Basecalls performed using  CASAVA 1.7.0
ChIP-exo reads were aligned to the mm10 or rn5 genome using BWA 0.5.9
Data were filtered using the following specifications: Picard (no duplicates) and samtools q37
peaks were called using MACS 1.4.2 (--nomodel --shiftsize=20 --to-large)
Genome_build: mm10 or rn5
Supplementary_files_format_and_content: BED files were generated using MACS and contain chrom, chromstart, chromend, peak name and score (-10*log10pvalue of peak region) columns

source_name: Myoblast

extract_protocol:
Lysates were clarified from sonicated nuclei and MEF2A-DNA complexes were isolated with antibody.
Libraries were prepared according to Rhee and Pugh (2011). Briefly, after ChIP, P2 adapters were ligated to DNA fragments using T4 ligase. Lambda exonuclease was added to digest unbound DNA. Samples were eluted and sequences were extended with phi29 polymerase. P2 adapters, specific to the 5' end were added. Samples were purified, run on a gel, and samples between 120-160 bp were selcted for sequencing. Libraries were sequenced on the Illumina sequencer following the manufacturer's protocol.

treatment_protocol: C2C12 were induced to differentiate in differentiation medium (DM) containing DMEM/High Glucose/L-Glutamine supplemented with 2% Horse Serum (Hyclone) and 1% Penicillin/Streptomycin for 48 hr.

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: KO73 H3K4me3

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis

data_processing:
Reeads were aligned to mm9 mouse genome with Bowtie (Langmead et al., 2009)
We used HOMER (Heinz et al., 2010) to call peaks using default settings
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated using HOMER.

source_name: H3f3b null testis tissue

extract_protocol:
Chromatin Preparation: Testes were initially isolated and stored at -80C. Tissue was tehn chopped and placed in a 15ml conical with DMEM. 37% formaldehyde was added toa final concentration of 1% and rocked for 12 minutes. 1.25 ml of glycine was added, rocked for 2 minutes then centrifuged. Tissue was then washed three times with 10ml sterile PBS. 1 ml cell lysis buffer(5 mM PIPES pH8, 85 mM KCl. Add igepal fresh each time to give a final concentration of 1% (10 μl/ml) plus protease inhibitors (Roche – 11 836 170 001)) was added and incubated for 15 min. Cells were then dounced 23 times, transferred to 1.5 ml tube and spun for 5 min at 2500G. Cells were then re-suspended in 200ul nuclear lysis buffer (50 mM Tris-HCl pH8, 10 mM EDTA, and 1% (w/v) SDS plus protease inhibitor) and incubated on ice for 30 minutes. Pellet was flash frozen in LN2, thawed slightly and sonicated (15 minutes, 30 seconds on, 1 minute off). PCR was used to check fragment size.  Chromatin was diluted with IP dilution buffer (50 mM Tris-HCl pH7.4, 150 mM NaCl, 1% (v/v) igepal, 0.25% (w/v) deoxycholic acid, 1 mM EDTA pH8 plus protease inhibitors).
Aliquots of each sample were taken and incubated with one of the following antibodies overnight at 4 degrees C: 3ul of anti trimethyl histone H3 Lys 4 (H3K4me3, Millipore # 04-745). 15ul of each sample was also saved for input. Samples were incubated with antibody overnight at 4 degrees C. 15 ul magnetic Protein G beads (Cell Signaling 9006S) were added to each sample and incubated for 2 hours at 4. Beads were magnetized and washed 2x in IP dilution buffer, 1x in IP wash buffer 2 (100 mM Tris-HCl pH 9, 500 mM LiCl, 1% (v/v) igepal, 1% (w/v) deoxycholic acid), 2x in IP wash buffer 3 (100 mM Tris-HCl pH 9, 500 mM LiCl, 150 mM NaCl, 1% (v/v) igepal, 1% (w/v) deoxycholic acid).  Chromatin was eluted with 100ul elution buffer (50 mM NaHCO3, 1% (w/v) SDS) and vortexed at RT for 50 min. Beads were magnetized, supernatant (including input) was incubated at 67 degrees C O/N to reverse crosslinks. Qiagen's QiaQuick PCR purification Kit (Qiagen 28104) was used to purify DNA, and RT-PCR and qPCR was used to determine specificty of chromatin.
Libraries were prepared according to directions stated O'geen et al. 2011 (PMID: 21913086)

value: Adult Mouse Testis tissue

tag: strain

value: H3f3b null

value: H3K4me3 (Millipre #04-745)


title: KO67 input


title: WT66 input

source_name: H3f3b WT/WT testis tissue

value: H3f3b WT/WT


title: A107

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

data_processing:
Raw paired-end sequenced reads (as fastq format) underwent quality control (FASTQC) in Galaxy.
Low quality reads were filtered with the FASTX toolkit in Galaxy ("filter by quality"), with a quality cutoff of 20 and a minimun percentage of 90.
High-quality reads were aligned to the mouse genome (mm10) in Galaxy using Tophat v1.4.0 (with custom settings –p 8 –r 175).
Genome-aligned sequenced reads for each sample were examined using Cufflinks in Galaxy, using RefSeq gene identification from the UCSC table browser. For each sample, gene/transcript expression levels were determined by computing the fragments per kilobase of exon per million mapped reads (FPKM). All values were quartile-normalized to improve expression estimates of low-abundance transcripts.
Gene expression differences between groups (i.e., scrambled vs H2a.Z knockdown) were calculated in CuffDiff using all replicates for each group and per-condition dispersion modeling. Significance testing was conducted on genes with a minimum of 100 aligned reads in a locus, and statistical significance was assessed using Student's t-tests and an false-discovery rate of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with FPKM values for each sample (Columns) and each gene (rows). The first row contains column identifiers. The first column contains Refseq gene names.

source_name: H2A.Z shRNA_contextual fear conditioning

extract_protocol:
Total RNA from area CA1 of the hippocampus was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.9) and library construction for polyA+ RNA sequencing.
Directional poly-A+ RNA llibraries were contructed at HudsonAlpha Genomic Services Lab using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes). RNA libraries were quantified (Kapa Library Quant Kit, Kapa Biosystems), and underwent sequencing (25M total 50bp paired-end reads) on an Illumina sequencing platform (HiSeq2000).

tag: age

value: 9-12 weeks

tag: animal condition

value: trained in contextual fear conditioning

tag: infected with

value: AAV expressing an shRNA against H2A.Z

value: CA1 of hippocampus


title: KO73 input


title: WT74 H3K4me3


title: WT74 input


title: KO67 H3K4me3


title: S110

source_name: scrambled shRNA control

value: AAV expressing a scrambled shRNA control


title: A101

source_name: H2A.Z shRNA_naive

value: naïve


title: A104


title: S109


title: RNAPII_cycl_rep2

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description: RNAPII occupancy examined cycling non starved wt Hela Cells

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
alignment (ChIPseq, RNAseq and GROseq)) bowtie 2.1.0 (end-to-end , sensitive))
tag density files RSeQC package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using RSeqQC package and the wigtobigWig script provided by UCSC. BedGraph were generated using the Bedtools package

source_name: HeLa

growth_protocol: Wild-type Hela cells were cultivated in DMEM 10% FBS, starvation was performed for 48h in 0.5% FBS before EGF treatment

extract_protocol: ChIP-Seq DNA Sample Prep Kit (Illumina, inc.)

treatment_protocol: Inducible cell clones were trated with doxycycline 1microgr/ml 72h before collection. EGF stimulation was performed for 20 minutes with 100ng/ml of recombinant EGF. RNA were extracted using QIAGEN Rneasy columns with on column DNAse treatment.

tag: cell line

value: HeLa

tag: treatment

tag: antibody

tag: source

value: IP with Ab  RNAPII rabbit polyclonal N20 (Santa Cruz, sc-899)

tag: sample type

value: ChIP-seq


title: INTS11_cycl_rep1

description: INTS11 occupancy examined cycling non starved wt Hela Cells

value: IP with Ab  anti-INTS11 rabbit polyclonal (Bethyl, A301-274A)


title: INTS11_cycl_rep2

value: INTS11 occupancy examined cycling non starved wt Hela Cells

value: anti-INTS11 rabbit polyclonal (Bethyl, A301-274A)


title: RNAPII_cycl_rep1

value: RNAPII occupancy examined cycling non starved wt Hela Cells

value: RNAPII rabbit polyclonal N20 (Santa Cruz, sc-899)


title: RNA_cycl

description: total RNA was sequenced in cycling wt Hela Cells

value: Hela wt cells

value: RNA-seq


title: RNAPII_DOX_EGF_rep2

description: RNAPII occupancy examined after EGF stimulation in a  doxocycline inducible knock-down cell line for INTS11


title: A102


title: RNAPII_CTRL_EGF_rep2

value: RNAPII occupancy examined after EGF stimulation in a  doxocycline inducible knock-down cell line for INTS11


title: IgG_cycl

description: IgG ChIP control in wt Hela cells

value: IgG ChIP control in wt Hela cells

value: rabbit IgG (Santa Cruz, sc-2027)

value: IP with Ab   rabbit IgG (Santa Cruz, sc-2027)


title: RNAPII_CTRL_EGF_rep1


title: WT66 H3K4me3

value: Adult Mouse Testis tissue

tag: genotype/variation

value: H3f3b WT/WT

tag: chip antibody

value: H3K4me3 (Millipre #04-745)


title: RNAPII_20min_rep2

description: RNAPII occupancy examined before and after EGF stimulation in starved wild-type Hela Cells

value: HeLa


title: RNAPII_DOX_EGF_rep1

value: IP with Ab  RNAPII rabbit polyclonal N20 (Santa Cruz, sc-899)


title: RNAPII_0min_rep2

value: RNAPII occupancy examined before and after EGF stimulation in starved wild-type Hela Cells

value: ChIP-seq


title: A100

value: 9-12 weeks

value: naïve

value: AAV expressing an shRNA against H2A.Z

value: CA1 of hippocampus


title: GRO_DOX_EGF_rep2

description: Nascent RNA was profiled after EGF stimulation in a doxocycline inducible knock-down cell line for INTS11

molecule: nuclear RNA

extract_protocol: GRO-seq

value: HeLa Tet-inducible INTS11 shRNA cell clone

value: GRO-seq


title: RNAPII_0min_rep1

value: RNAPII rabbit polyclonal N20 (Santa Cruz, sc-899)


title: GRO_CTRL_EGF_rep2

value: Nascent RNA was profiled after EGF stimulation in a doxocycline inducible knock-down cell line for INTS11


title: A106

value: trained in contextual fear conditioning


title: GRO_DOX_EGF_rep1


title: INTS11_0min_rep2

description: INTS11 occupancy examined before and after EGF stimulation in starved wild-type Hela Cells

value: IP with Ab  anti-INTS11 rabbit polyclonal (Bethyl, A301-274A)


title: S108

value: AAV expressing a scrambled shRNA control


title: INTS11_20min_rep2

value: INTS11 occupancy examined before and after EGF stimulation in starved wild-type Hela Cells

value: anti-INTS11 rabbit polyclonal (Bethyl, A301-274A)


title: INTS11_0min_rep1

value: HeLa


title: INTS11_20min_rep1


title: DOX_RNA_rep2

description: total RNA was sequenced in a Hela cell clone upon EGF stimulation and depletion of INTS11

value: RNA-seq


title: DOX_EGF_RNA_rep2

value: total RNA was sequenced in a Hela cell clone upon EGF stimulation and depletion of INTS11


title: IgG_ChIP-exo [mouse]

value: Myoblast

value: Normal Rabbit IgG

tag: chip antibody vendor

value: Millipore


title: RNAPII_20min_rep1

value: RNAPII occupancy examined before and after EGF stimulation in starved wild-type Hela Cells

value: IP with Ab  RNAPII rabbit polyclonal N20 (Santa Cruz, sc-899)

value: ChIP-seq


title: ELL2_CTRL_EGF_rep2

description: ELL2 was profiled in a Hela cell clone upon EGF stimulation and depletion of INTS11

value: IP with non-commercial rabbit anti-ELL2 Ref PMID 20159561


title: CTRL_RNA_rep1

value: HeLa Tet-inducible INTS11 shRNA cell clone


title: ELL2_CTRL_rep2

value: ELL2 was profiled in a Hela cell clone upon EGF stimulation and depletion of INTS11

value: non-commercial rabbit anti-ELL2 Ref PMID 20159561


title: GRO_CTRL_EGF_rep1

value: Nascent RNA was profiled after EGF stimulation in a doxocycline inducible knock-down cell line for INTS11

value: GRO-seq


title: CTRL_RNA_rep2


title: ELL2_DOX_EGF_rep1


title: CTRL_EGF_RNA_rep2


title: DOX_RNA_rep1


title: CTRL_EGF_RNA_rep1


title: ELL2_DOX_rep2


title: ELL2_DOX_EGF_rep2


title: ELL2_DOX_rep1


title: DOX_EGF_RNA_rep1


title: AFF4_DOX_EGF_rep2

description: AFF4 was profiled in a Hela cell clone upon EGF stimulation and depletion of INTS11

value: IP with non-commercial rabbit anti-AFF4 Ref PMID 20159561


title: AFF4_CTRL_EGF_rep2

value: AFF4 was profiled in a Hela cell clone upon EGF stimulation and depletion of INTS11

value: non-commercial rabbit anti-AFF4 Ref PMID 20159561


title: AFF4_DOX_rep1

value: HeLa


title: ELL2_CTRL_rep1


title: AFF4_CTRL_EGF_rep1


title: IgG_ChIP-exo [rat]

organism: Rattus norvegicus

source_name: Primary cardiomyocytes

growth_protocol: Primary neonatal cardiomyocytes were prepared from 1 to 3 day old rats using the Neonatal Cardiomyocyte Isolation System (Worthington Biochemical Corp)

value: Primary rat cardiomyocytes


title: AFF4_DOX_EGF_rep1


title: ELL2_CTRL_EGF_rep1


title: AFF4_DOX_rep2


title: AFF4_CTRL_rep1


title: MEF2A_ChIP-exo 1 [rat]

value: Santa Cruz Biotechnology


title: Δfur with Fe 2 (RNA-seq)

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
Genome_build: ASM584v2
Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Total RNA isolated from E. coli

growth_protocol: E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

value: Δfur

tag: agent

value: Fe


title: Δfur with DPD 2 (RNA-seq)

value: DPD


title: MN_Scerevisiae_rpd3_S-phase

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: Mononucleosomal DNA

data_processing:
Alignment: bowtie 0.12.7
The smoothed signal generated by using the multilevel 1-D biorthogonal wavelet decomposition/reconstruction tool implemented in the Python pywavelets library, is used to calculate the average spacing between boundary peaks for individual nucleosomes.
The resulting combined profile was wavelet-smoothed to generate the final nucleosome positioning profile.
We used the R64-1-1 assembly of the S. cerevisiae genome, available at: http://www.ncbi.nlm.nih.gov/assembly/285498/ , for the alignment.
genome build: R64-1-1

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cultures were grown in YP medium (1% yeast extract, 2% bacto peptone) supplemented with 2% glucose (YPD) at 23ºC to a final concentration of 0.7× 107 cells/ml. Cells were synchronized in G1 phase by adding 5 μg/ml α factor (αF) for one generation time and released into fresh medium in the presence of 0.2M hydroxyurea for one hour.

extract_protocol:
200 ml cultures at 1x107 cells/ml were collected in G1 and at 60 minutes in S-phase in the presence of 0.2 M HU for preparation of mononucleosomal DNA. Cells were treated with 10 mg of Zymolyase  20T during 10 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 600 or 450 units/ml (WT and rpd3 strains respectively) of micrococcal nuclease (MNAse) at 37 ºC during 10 minutes. The amount of MNase was optimized experimentally for each strain to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina Genome Analyzer IIx using the single-end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture type

value: S-phase in the presence of 0.2M HU

tag: time

value: 60 minutes


title: AFF4_CTRL_rep2

value: ChIP-seq


title: WT with Fe 1 (RNA-seq)

value: WT


title: RpoB with DPD and rifampicin 2 (ChIP-exo)

data_processing:
library strategy: ChIP-exo
ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
Genome_build: ASM584v2
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

source_name: Immunoprecipitated DNA

growth_protocol: E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.

extract_protocol: ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: anti-RpoB (Neoclone, WP002)

value: DPD and rifampicin


title: RpoB with DPD 2 (ChIP-exo)


title: WT with Fe 2 (RNA-seq)


title: MN_Scerevisiae_WT_G1

description: Mononucleosomal DNA

value: G1 arrest


title: Δfur with Fe 1 (RNA-seq)


title: MN_Scerevisiae_WT_S-phase

description: Mononucleosomal DNA


title: MN_Scerevisiae_rpd3_G1

description: Mononucleosomal DNA


title: WT with DPD 1 (RNA-seq)


title: Δfur with DPD 1 (RNA-seq)


title: WT with DPD 2 (RNA-seq)


title: Fur with Fe 1 (ChIP-exo)

value: anti-myc (Santa Cruz Biotech, sc-28207)


title: Fur with DPD 2 (ChIP-exo)


title: RpoB with Fe 1 (ChIP-exo)


title: RpoB with DPD and rifampicin 1 (ChIP-exo)


title: Fur with DPD 1 (ChIP-exo)


title: RpoB with Fe 2 (ChIP-exo)


title: 2079-JTG-4-2

status: Public on Sep 08 2014

city: Nashville

first: Sataree

last: Khuansuwan

state: TN

address: 465 21st Avenue South

department: Biological Sciences

institute: Vanderbilt University

description:
Sample name:  8
Sample 7 and sample 8 are technical replicates

data_processing:
Raw sequencing reads were processed through CASAVA-1.8.2 for FASTQ conversion and demultiplexing.
Raw 51 or 101 bp single-end reads generated from the Illumina HiSeq 2000 were first assessed for sequence quality using the FastQC software version 0.10.0 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Reads were trimmed to 40 or 80 bp using trimmomatic software version 0.32.
Each sequencing data set was independently mapped to the zebrafish genome with a bowtie2 index generated from Danio_rerio.Zv9.70 (Ensembl) downloaded from Illumina’s iGenomes collection (https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn) using the TopHat2 program (Kim et al., 2013) with novel splice discovery disabled.
HiSeq 2000 libraries were aligned with the following options: “-p 2 -G genes.gft --no-novel-juncs” where genes.gft contains the Ensembl coding transcripts in GTF format downloaded from Illumina’s iGenomes collection.
Differentially expressed genes between control and tbx2b morphant pineal cell samples were identified by using Cuffdiff 2 program (Trapnell et al., 2013) with the following options: “-b genome.fa -p 2 -u -c 5 genes.gtf” where genome.fa is a multifasta file downloaded from Illumina’s iGenomes collection. We used a 1.8-fold change in expression and an FDR adjusted p value (q value) of ≤ 0.05 as cut offs.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include fold-change between two conditions (NIC versus tbx2b morpholino injected)

organism: Danio rerio

source_name: FAC sorted pineal complex cells

growth_protocol: Zebrafish were raised at 28.5°C on a 14/10 light/dark cycle. Embryos obtained from natural mating were staged according to hours post-fertilization (hpf).

extract_protocol:
All equipment used for RNA isolation was pretreated with RNAse Away (Molecular BioProducts). When required, the ratio of the Trizol-LS volume to the sample volume were brought up to 3:1 with addition of nuclease-free water. Cells were lysed by pipetting the mixture several times. RNA was extracted using Trizol-LS similar to the manufacturer’s protocol, with one modification: we used Phase Lock Gel-Heavy tubes (PLG, Fisher) during the phase separation step. Each PLG tube was prepared for use by centrifugation at 14,000 rpm (18,000 g; Beckman Coulter Microfuge 18 centrifuge) for 2 minutes at room temperature. 800 µL of cell lysate (in Trizol-LS) was added to a pre-spun PLG tube and incubated for 5 minutes at room temperature to allow for complete dissociation of nucleoprotein complexes. Chloroform was added to the PLG tube at a ratio of 200 µL per 1mL of Trizol-LS plus sample mixture initially used. The tube was then shaken vigorously by hand (without vortexing) for 15 seconds. Phase separation was achieved via centrifugation at 13,200 rpm (16,100 g; Eppendorf 5415D centrifuge) for 15 minutes at 4°C. The clear, aqueous top phase containing RNA, atop the PLG, was then transferred to a fresh tube via decanting or by using a pipette. Ice-cold isopropanol was added to the aqueous phase at a ratio of 500 µL per 1 mL Trizol-LS plus sample initially used, along with 3 µL of 20mg/mL mussel glycogen (Roche, used as a carrier for the precipitation of nucleic acids). Samples were mixed by repeated inversion and incubated at room temperature for 10 minutes. To allow for precipitation of RNA, samples were incubated at -20°C for at least 1 hour (up to 16 hours). RNA was pelleted via centrifugation at 13,200 rpm (16,100 g; Eppendorf 5415D centrifuge) for 15 minutes at 4°C, resulting in a visible RNA pellet. The supernatant was discarded and the pellet was washed twice with 1 mL of ice-cold 75% ethanol. The location of the pellet was marked and the pellet was allowed to air-dry at room temperature; after drying the pellet became translucent. The pellet was resuspended with 20 µL of nuclease-free water plus 1 µL of RNase inhibitor (40U/µL RNasin, Promega) at 55°C for 10 minutes. The sample was then gently pipetted to ensure complete resuspension of RNA. Because the subsequent RNA-seq includes a poly-A selection, there was no need to treat samples with DNase. RNA was stored at -80°C until needed. RNA quantity was determined using the RNA assay program on a Qubit fluorometer (Life Technologies). Each FAC-sorted Kaede-positive cell yields an average of 3.5 pg of RNA, ranging from 1.3-5.8 pg of RNA/cell (n=11). These values are similar to yields obtained from neuronal cells in another study (Saxena et al., 2012). RNA quality and integrity were analyzed by capillary electrophoresis using the RNA Pico chip on an Agilent 2100 Bioanalyzer. Our protocol typically yielded total RNA with RIN integrity values ranging from 6.0-8.5, with an average of 7.2 (n=14) (Fig. 3). We observed improved RNA integrity values when we spent less time completing the RNA extraction process (Fig. 3, Supp. Fig. 3). In our hands, the use of a commercially available column (Purelink RNA Micro Kit, Invitrogen) led to a significant loss of total RNA (Supp. Fig. 3), despite following the manufacturer’s protocol precisely.
cDNA sequencing libraries preparation and sequencing was performed by the Genome Sciences Resource at Vanderbilt University Medical Center (Nashville, TN) using the Illumina TruSeq RNA Sample Preparation Kit as previously described (Elmore et al., 2012; Venkateswaran et al., 2013). High-throughput RNA-seq was performed on four libraries (two control groups and two tbx2b knockdown groups) twice. Using the multiplexing strategy of the TruSeq protocol, each technical replicate, consisting of four libraries, was performed on one lane of the Illumina HiSeq 2000 utilizing version 3 chemistry. On average, 40 million 51-101 bp single-end reads were generated for each group, which should be sufficient to detect differentially expressed genes. A study performed in human and mouse tissues has shown that sequencing beyond the depth of 3 million reads does not increase transcript detection (Ramsköld et al., 2009). Others have concluded that cDNA sequencing with 30-40 million 25 bp reads is sufficient to detect major splice isoforms for abundant and moderately abundant transcripts in mouse and that 1X coverage of the transcriptome can be achieved with 40 million 25 bp reads (Mortazavi et al., 2008).

tag: condition

value: 6ng tbx2b splice MO injected (tbx2b knockdown)

tag: cell type

value: Kaede positive positive heads of Tg(flhBAC:kaede)vu376

tag: developmental stage

value: 24-26 hpf embryo


title: 2079-JTG-1-1

description:
Sample name:  5
Sample 5 and sample 6 are technical replicates

value: Non-injected controls (wild-type)


title: 2079-JTG-1-2

description:
Sample name:  6
Sample 5 and sample 6 are technical replicates


title: 2064-JTG-2-2

description:
Sample name:  4
Sample 3 and sample 4 are technical replicates

value: 5ng tbx2b splice MO injected (tbx2b knockdown)


title: 2079-JTG-4-1

description:
Sample name:  7
Sample 7 and sample 8 are technical replicates


title: RpoB with DPD 1 (ChIP-exo)


title: RpoB with Fe and rifampicin 1 (ChIP-exo)

value: Fe and rifampicin


title: RpoB with Fe and rifampicin 2 (ChIP-exo)


title: Fur with Fe 2 (ChIP-exo)


title: 2064-JTG-2-1

description:
Sample name:  3
Sample 3 and sample 4 are technical replicates


title: MIT2.K79me1

city: New York

first: Scott

last: Armstrong

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
Sequence reads were aligned to genome assembly mm9 using BWA with default parameters.
Wiggle (wig) files were generated using a using a custom pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: The wiggle file contains average read density over the whole genome. (http://genome.ucsc.edu/goldenPath/help/wiggle.html)

source_name: Leukemic bone marrow

growth_protocol: leukemic BM cells cultured in DMEM 15%FBS + pen/strep and 10ng/ml IL6, 20ng/ml SCF, 6ng/ml IL3

extract_protocol: Standard Illumina TruSeq DNA sample preparation protocol for the library prep

treatment_protocol: Standard formaldehyde fixation (1%)

tag: background strain

tag: tissue

value: bone marrow

tag: diagnosis

value: leukemia

value: Ab3261 Abcam


title: MIT4.K79me2

value: Ab3594 Abcam


title: MIT2.K79me2


title: MIT5.K79me2


title: MIT6.K79me3

value: Ab2621 Abcam


title: MIT4.K27me3

value: 07-449 Millipore


title: MIT5.K27me3


title: 2064-JTG-1-2

description:
Sample name:  2
Sample 1 and sample 2 are technical replicates


title: MIT5.K79me3


title: MIT4.K79me1


title: MIT3.K79me1


title: MIT6.K27me3


title: MIT3.K79me2


title: LSK1.K79me3


title: LSK1.K79me1


title: MIT1.K79me2


title: 2064-JTG-1-1

description:
Sample name:  1
Sample 1 and sample 2 are technical replicates


title: LSK3.K79me3


title: MIT5.K79me1


title: MIT1.K79me1


title: GMP1.K79me1


title: GMP1.K79me3


title: LSK3.K79me1


title: CRE6.K79me3


title: M.marinum RNA-seq rep1

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Illumina Casava1.8 software used for basecalling.
Read mapping using bowtie
Genome_build: M.bovis: NC_002945.3; M.marinum: NC_010612.1
Supplementary_files_format_and_content: Unnormalized read coverages in wig format (*_forward.wig = plus strand; *_reverse.wig= minus strand)

organism: Mycobacterium marinum

source_name: M.marinum RNA-seq

extract_protocol: RNA-seq: 5 ug of total RNA from each condition was rRNA depleted. Zinc-mediated fragmentation was carried out. cDNA was generated where the second strand was marked with dUTP. Standard Illumina library manipulation was carried out and and Illumina-compatible adapters with in-line indexing were used. Prior to limited amplification, the 2nd uracil marked strand was digested utilising Uracil-DNA Glycosylase enzyme. Sequenced libraries were strand-specific.

tag: growth phase

value: log phase

tag: genotype

value: wild type


title: M.marinum TSS-seq rep2

description: SRA098318 (SRX347162)

data_processing:
Library strategy: TSS-Seq
Illumina Casava1.8 software used for basecalling.
Read mapping using bowtie
Genome_build: M.bovis: NC_002945.3; M.marinum: NC_010612.1
Supplementary_files_format_and_content: Unnormalized read coverages in wig format (*_forward.wig = plus strand; *_reverse.wig= minus strand)

source_name: M.marinum TSS-seq

extract_protocol: TSS-seq: The RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C) and then treated with T4 polynucleotide kinase (PNK). The RNA species which carry a 5' mono-phosphate were degraded using Terminator exonuclease (Epicentre). The exonuclease resistant mRNA (primary transcripts with 5'PPP) were poly(A)-tailed using poly(A) polymerase. The samples were then split into two parts. One half (5'PP+ samples) was treated with RNA 5' polyphosphatase (Epicentre) to degrade 5'PPP ends to 5'P, while the other half (5'PP- samples) was left untreated. Afterwards, a RNA adapter was ligated to the 5'-phosphate of the RNA fragments. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 20-30 ng/μ l using a high fidelity DNA polymerase.The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.


title: M.marinum RNA-seq rep2


title: M.marinum TSS-seq rep1

description: SRA098318 (SRX347162)


title: GMP2.K79me3


title: CRE4.K27me3


title: CRE3.K79me1


title: CRE6.K27me3


title: CRE1.K79me2


title: CRE5.K79me2


title: CRE5.K27me3


title: CRE5.K79me3


title: CRE1.K79me1


title: CRE2.K79me1


title: CRE4.K79me1


title: CRE4.K79me2


title: CRE2.K79me2


title: GMP2.K79me1


title: CRE5.K79me1


title: CRE3.K79me2


title: M.Bovis RNA-seq rep2

organism: Mycobacterium tuberculosis variant bovis

source_name: M.Bovis RNA-seq


title: M.Bovis RNA-seq rep1


title: HB9_2

city: Philadelphia

first: Matthew

middle: E R

last: Butchbach

state: PA

address: 1020 Locust St

institute: Thomas Jefferson University

data_processing:
quality control check with FastQC v.0.10.1
removal of adapter sequences and poly-A tails with CutAdapt
mapped to reference mouse genome (NCBI m37) with TopHat v.2.04
transcript assembly and abundance measurements with Cufflinks
differential expression with Cuffdiff
data visualization with CummeRbund
Genome_build: NCBI m37
Supplementary_files_format_and_content: abundances for each identified transcript for Hb9 control as compared to A2 SMA mESC-derived MNs. Values are measured in fragments per kilobase of exon per million fragments mapped (FPKM).

growth_protocol: mESCs were first induced to form embryoid bodies and then treated with 1 microM retinoic acid and 1 microM Smoothened agonist for 5 days

extract_protocol:
GFP-positive motor neurons were isolated from dissociated, differentiated neurospheres by FACS; RNA was isolated using QIAGEN Rneasy kit
cDNA libraries were generated from total RNAs using the TruSeq RNA Sample Prep Kit (Illumina) according to manufacturer's directions

value: motor neurons derived from Hb9 normal mESCs

tag: strain/background

value: FVB/N

value: wildtype


title: SMA-A2_1

value: motor neurons derived from A2 SMA mESCs


title: HB9_3


title: SMA-A2_2


title: M.Bovis TSS-seq rep2

description: SRA098318 (SRX347163)

source_name: M.Bovis TSS-seq


title: SMA-A2_3


title: s29HC

city: BETHESDA

last: Canna

state: MD

department: MIIB

institute: NIAMS

description: Sample 24

data_processing:
CASAVA software v1.8.2 was used for basecalling
Sequenced reads were mapped to NCBI Build 37.2 whole genome using TopHat software v2.0.8 with "no-coverage-search" option
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek GS version 6.6
Genome_build: NCBI 37.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: healthy pediatric controls

extract_protocol:
Total RNA was extracted from human blood samples collected in PaxGene tubes (Qiagen, Valencia, CA). RNA integrity was analyzed with Agilent 2100 Bioanalyzer.
mRNA purification and fragmentation, complementary DNA synthesis and target amplification were performed using the Illumina® TruSeq RNA Sample Preparation Kit (Illumina). Pooled cDNA libraries were sequenced using HiSeq 2000 Illumina® platform (Illumina).

value: Healthy

value: Peripheral blood


title: s30HC

description: Sample 25


title: s28HC

description: Sample 23


title: M.Bovis TSS-seq rep1

description: SRA098318 (SRX347163)


title: s31HC

description: Sample 26


title: s58

description: Sample 22


title: s36

description: Sample 19

source_name: NOMID patients with inactive disease after anakinra treatment

value: Neonatal-Onset Multisystem Inflammatory Disease (NOMID)

tag: disease/health status

value: inactive

tag: treatment status

value: Post anakinra treatment


title: S26

description: Sample 9

source_name: NOMID patients with active disease prior to anakinra treatment

value: active

value: Prior to anakinra treatment


title: s35

description: Sample 18


title: S25

description: Sample 8


title: s32

description: Sample 15


title: S30

description: Sample 13


title: S40

description: Sample 7

source_name: patient with NLRC4-MAS

value: NLRC4-Macrophage Activation Syndrome (MAS)

value: well

tag: timepoint


title: s34

description: Sample 17


title: HB9_1


title: s31

description: Sample 14


title: s37

description: Sample 20


title: s38

description: Sample 21


title: S29

description: Sample 12


title: s33

description: Sample 16


title: S05

description: Sample 5


title: S06

description: Sample 6


title: S04

description: Sample 4


title: S03

description: Sample 3

value: flare


title: S02

description: Sample 2


title: S27

description: Sample 10


title: Flower bud

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.3 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3. The filtered reads were pre-processed using modified perl script provided in the miRTools software.
After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were screened stepwise against annotated non-coding RNA sequences, including plant snoRNA, tRNA and rRNA. The remaining  reads were screened against repeat sequences from RepBase and chickpea chloroplast sequence.
Genome_build: CGAP v1.0 (http://nipgr.res.in/CGAP/home.php)
Supplementary_files_format_and_content: Processed data files are in fasta format containing collapsed unique reads after QC along with read count

organism: Cicer arietinum

source_name: Mature plant

growth_protocol: Seedlings were grown in a culture room and mature plants were grown in field

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using Small RNA Sample Preparation Kit (Illumina) according to the manufacture’s protocol

tag: germplasm line

value: flower bud


title: Stem

value: stem


title: Mature leaf

value: mature leaf


title: S28

description: Sample 11


title: Mature flower

value: mature flower


title: Root

source_name: Seedling

value: root


title: Young pod

value: young pod


title: Shoot

value: shoot


title: C0LSeL2_P

city: Newark

first: Shawn

last: Thatcher

state: DE

address: 15 Innovation Way

institute: University of Delaware

description: Parallel Analysis of RNA Ends (PARE) library

data_processing:
Illumina Casava software used for basecalling.
Adapter trimming was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome matching was performed using Bowtie, with 0 mismatches allowed
Genome_build: Arabidopsis TAIR10 genome
Supplementary_files_format_and_content: tag count file

organism: Arabidopsis thaliana

source_name: late senescence leaf biorep 2

growth_protocol: Plants were grown in short days (8 hours) for two weeks on 1/2 x MS 0.8% agar plates. Seedlings were transferred to artificial soil in 7x7x8 cm containers and grown with a light/dark cycle of 16/8 hours (long days).

extract_protocol:
Leaves and siliques were collected and frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  low molecular weight RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012).  PARE libraries were constructed from 50 micrograms of total RNA using previously described methods (German et al. 2009)

value: leaf

tag: Stage

value: late senescence


title: C0LSeE2_P

source_name: early senescence leaf biorep 2

value: early senescence


title: C0LSeL1_P

source_name: late senescence leaf biorep 1


title: C0LM_P

source_name: mature leaf

value: mature


title: C0LSeE1_P

source_name: early senescence leaf biorep 1


title: C0SSeL

source_name: late senescence silique

value: silique


title: C0SSeE

source_name: early senescence silique


title: C0LY_P

source_name: young leaf

value: young


title: C0SM

source_name: mature silique


title: C0LSeE

source_name: early senescence leaf


title: C0SY

source_name: young silique


title: C0LY


title: C0LSeL

source_name: late senescence leaf


title: S01

description: Sample 1

value: Prior to anakinra treatment

value: Peripheral blood


title: C0LM


title: control piwi rep2

first: Jean-Yves

last: Roignant

address: genopode building

institute: University of Lausanne

description: transcript RNA

data_processing:
Basecalling was performed with Casava 1.8.2 for samples 1-4 and with Casava 1.8 for samples 5-8
reads were sorted according to barcode (front barcode)
barcodes were trimmed
RNA-seq analysis  reads were aligned to BDP5 (dm3) using Tophat 2.0.9, as transcript reference the Ensemble release 73 was used (Drosophila_melanogaster.BDGP5.73.gtf)
reads were counted using HT-Seq count version 0.5.3p9
Differentially expressed transcripts were detected using DESeq
Genome_build: BDGP5 (dm3)
Supplementary_files_format_and_content: tab separated file containing read counts per gene/transposon

source_name: ovaries

extract_protocol:
Ovaries were dissected, flash frozen in liquid nitrogen, and RNAs were harvested using Trizol reagent. Ribosomal RNAs were depleted using two rounds of Epicentre Ribo-Zero magnetic beads. 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 a custom strand specific RNA-seq protocol

value: ovaries

tag: age

value: 4-6 days


title: control RnpS1 KD rep1

description: transcript RNA

value: tj-GAL4; nos-GAL4-VP16


title: control piwi rep1

description: transcript RNA


title: RnpS1 KD rep2

description: transcript RNA


title: piwi mutant rep1

description: transcript RNA


title: RnpS1 KD rep1

description: transcript RNA


title: Biological sample #6, KCl stimulated, infected with control shRNA, Input DNA

status: Public on Sep 07 2014

city: Boston

first: Athar

middle: N.

last: Malik

address: 200 Longwood Avenue, Goldenson 405

institute: Harvard Medical School

data_processing:
Data filtering was performed to remove adaptor sequences, contamination and low-quality reads from raw reads
ChIP-Seq sequencing reads were aligned to the July 2007 assembly of the mouse genome (NCBI 37, mm9) using the Burrows-Wheeler Aligner (BWA) with default settings.
The resulting bwa files were then converted to sam files and uniquely mapped reads were extracted from the sam files. Sam files of the uniquely mapped reads were then converted to bam files.
Bam files were then used for peak calling using Model-based Analysis of ChIP-Seq (MACS) with the following parameters: -f BAM -g mm --nomodel --shiftsize=150.
To visualize ChIP-Seq data on the UCSC genome browser, ChIP-Seq bam files were converted to bigwig track format to display the number of input normalized ChIP-Seq reads, normalized to 20 million total reads.
Genome_build: mm9
Supplementary_files_format_and_content: bed, and bigwig files were generated using standard methods

source_name: DIV7 mCTX neurons

growth_protocol: Embryonic day 16.5 cortices from C57BL/6 mice were dissected, dissociated, plated at 40M cells on 15 cm cell culture dishes. Neurons were subsequently grown in vitro in a cell culture incubator that maintained a temperature of 37 degrees C and a CO2 concentration of 5%.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared by BGI (Beijing Genomics Institute) according to standard Illumina protocols.

treatment_protocol: On day in vitro 6, neurons were silenced overnight with 1 μM TTX and 100 µM DL-AP5.  The next morning, neurons were left silenced (unstimulated condition) or stimulated for 2 hours with KCl (KCl condition).

value: mouse cortical neurons

tag: days in vitro

tag: strain

tag: chip antibody


title: control RnpS1 KD rep2

description: transcript RNA


title: Biological sample #6, KCl stimulated, infected with c-Fos shRNA, Input DNA

tag: cell type


title: Biological sample #6, KCl stimulated, infected with control shRNA, CFOS ChIP-Seq using sc52 antibody


title: Biological sample #6, KCl stimulated, infected with control shRNA, FOSB ChIP-Seq using sc48 antibody


title: Biological sample #6, KCl stimulated, infected with FosB shRNA, FOSB ChIP-Seq using sc48 antibody


title: Biological sample #6, KCl stimulated, infected with c-Fos shRNA, CFOS ChIP-Seq using sc52 antibody


title: Biological sample #6, KCl stimulated, infected with FosB shRNA, Input DNA


title: Biological sample #5, KCl stimulated, infected with FosB shRNA, FOSB ChIP-Seq using sc48 antibody


title: Biological sample #5, KCl stimulated, infected with c-Fos shRNA, Input DNA


title: Biological sample #5, KCl stimulated, infected with control shRNA, Input DNA


title: Biological sample #4, KCl stimulated, FOSB ChIP-Seq using sc48 antibody


title: Biological sample #4, KCl stimulated, JUNB ChIP-Seq using sc46 antibody


title: Biological sample #5, KCl stimulated, infected with control shRNA, FOSB ChIP-Seq using sc48 antibody


title: Biological sample #5, KCl stimulated, infected with control shRNA, CFOS ChIP-Seq using sc52 antibody


title: Biological sample #5, KCl stimulated, infected with c-Fos shRNA, CFOS ChIP-Seq using sc52 antibody


title: piwi mutant rep2

description: transcript RNA


title: Biological sample #4, KCl stimulated, CFOS ChIP-Seq using sc52 antibody


title: Biological sample #4, KCl stimulated, input DNA


title: Biological sample #4, unstimulated, CFOS ChIP-Seq using sc7202 antibody


title: Biological sample #4, unstimulated, JUNB ChIP-Seq using sc46 antibody


title: Biological sample #4, unstimulated, FOSB ChIP-Seq using sc48 antibody


title: Biological sample #4, unstimulated, input DNA


title: Biological sample #5, KCl stimulated, infected with FosB shRNA, Input DNA


title: Biological sample #4, unstimulated, CFOS ChIP-Seq using sc52 antibody


title: Biological sample #3, KCl stimulated, CFOS ChIP-Seq using sc7202 antibody


title: Biological sample #3, KCl stimulated, CFOS ChIP-Seq using sc52 antibody


title: Biological sample #3, KCl stimulated, input DNA


title: Biological sample #3, unstimulated, FOSB ChIP-Seq using sc48 antibody


title: Biological sample #3, unstimulated, CFOS ChIP-Seq using sc7202 antibody


title: Biological sample #1, KCl stimulated, H3K27ac ChIP-Seq

description:
03_05_B1B2merged_KCl_H3K27ac_ab4729_p1e-5_peaks_distal.bed
03_05_B1B2merged_KCl_H3K27Ac_ab4729_E300_track.bw
03_05_B1B2merged_KCl_H3K27ac_ab4729_p1e-5_peaks_genomewide.bed
03_B1_KCl_H3K27ac_ab4729_E300_track.bw
40_IncH3K27ac_at_distal_CBP+H3K4Me1.bed
41_ConH3K27ac_at_distal_CBP+H3K4Me1.bed
42_DecH3K27ac_at_distal_CBP+H3K4Me1.bed
43_NoH3K27ac_at_distal_CBP+H3K4Me1.bed


title: Biological sample #3, unstimulated, CFOS ChIP-Seq using sc52 antibody


title: Biological sample #1, unstimulated, H3K27ac ChIP-Seq

description:
01_04_B1B2merged_un_H3K27ac_ab4729_p1e-5_peaks_distal.bed
01_04_B1B2merged_un_H3K27Ac_ab4729_E300_track.bw
01_04_B1B2merged_un_H3K27ac_ab4729_p1e-5_peaks_genomewide.bed
01_B1_un_H3K27ac_ab4729_E300_track.bw
40_IncH3K27ac_at_distal_CBP+H3K4Me1.bed
41_ConH3K27ac_at_distal_CBP+H3K4Me1.bed
42_DecH3K27ac_at_distal_CBP+H3K4Me1.bed
43_NoH3K27ac_at_distal_CBP+H3K4Me1.bed


title: Biological sample #2, unstimulated, H3K27ac ChIP-Seq

description:
01_04_B1B2merged_un_H3K27ac_ab4729_p1e-5_peaks_distal.bed
01_04_B1B2merged_un_H3K27Ac_ab4729_E300_track.bw
01_04_B1B2merged_un_H3K27ac_ab4729_p1e-5_peaks_genomewide.bed
04_B2_un_H3K27ac_ab4729_E300_track.bw
40_IncH3K27ac_at_distal_CBP+H3K4Me1.bed
41_ConH3K27ac_at_distal_CBP+H3K4Me1.bed
42_DecH3K27ac_at_distal_CBP+H3K4Me1.bed
43_NoH3K27ac_at_distal_CBP+H3K4Me1.bed


title: Biological sample #3, unstimulated, input DNA


title: Biological sample #1, KCl stimulated, input DNA


title: Biological sample #4, KCl stimulated, CFOS ChIP-Seq using sc7202 antibody


title: Biological sample #1, unstimulated, input DNA


title: Input_DNA_control_TS3.5

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

description: Whole cell genomic DNA Seq

data_processing:
Basecalls performed using CASAVA from Illumina
ChIP-seq and Input DNA reads were aligned to the mm9 genome assembly using BOWTIE2 version 2.1.0 with the default configuration.
Aligned unique genomic location reads (sam file) transfer to bed file
Peaks (or domains) were called (vs. Input DNA), or compared (vs. ESC1 H2A.X ChIP, from GSE42306) using R-seg (0.4.8) following -mode 2 (or -mode 3) and default setting.
The  differentially enriched/devoid (vs. ESC1 ChIP)  domains whose size are more than 250Kb or less than 5Kb are filtered out. And then, for TSCdevoided regions, defined as the intersection part from ESC specific enriched domains.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated from R-seg (mode 2 or mode 3).   The "scores" mean  HMM domain scores; The input DNA samples files  only contain the Bowtie alighment results.

source_name: TS cell

growth_protocol: ES and TS cells are cultured with standard protocol

extract_protocol:
ChIP DNA samples were obtained with Native ChIP protocol; briefly, chromatin were fractionated and then  subject to Mnase digestion to generate mononucleosomes. Then the mononucleosome fraction was extracted with high salt buffer and H2A.X-containing nucleosomes were isolated and enriched with anti-H2A.X (custom-made) antibodies.
Libraries were prepared according to Illumina's standard protocol, with instructions accompanying the DNA Sample Kit

treatment_protocol: No treatment

tag: strain background

value: mixed

value: Trophoblast stem (TS) cells

tag: passages

value: passage 25-40


title: H2AX_TSC_wt_GFP_TS3.5

description: H2A.X ChIP-Seq


title: iPSC OSK9

description: ChIP-Seq

data_processing:
Basecalls performed using CASAVA from Illumina
ChIP-seq DNA reads were aligned to the "mm9" mouse genome assembly using BOWTIE version 2.1.0 with the default configurations.
Aligned unique genomic location reads (sam file) transfer to bed file
Enriched  or devoid domains were called (vs. ESC4 control line H2A.X ChIP) using RSEG (0.4.8) following " -mode 3" and default setting.
The  differentially enriched/devoid  domains whose size are more than 200Kb or less than 5Kb are filtered out.
Genome_build: mm9
Supplementary_files_format_and_content: BED files were generated from RSEG (mode 3).   The "scores" mean  HMM domain scores; The control line samples file only contain the alighment BED results.

source_name: reprogramming from MEF cell

growth_protocol: ES and iPS cells are cultured with standard protocol

extract_protocol:
ChIP DNA samples were obtained with Native ChIP protocol; briefly, chromatin were fractionated and then  subject to Mnase digestion to generate mononucleosomes. Then the mononucleosome fraction was extracted with high salt buffer and H2A.X-containing nucleosomes were isolated and enriched with anti-H2A.X antibodies.
Libraries were prepared according to Illumina's standard protocol, with instructions accompanying the DNA Sample Kit

tag: cell line

value: iPSC OSK9

tag: passage

tag: reprogramming factors

value: Oct4, Sox2, Klf4

tag: antibody

value: H2A.X (Xiao lab)


title: iPSC OSK2

description: ChIP-Seq

value: iPSC OSK2


title: iPSC OSKM8

value: iPSC OSKM8

value: Oct4, Sox2, Klf4 and Myc


title: iPSC OSKM5

value: iPSC OSKM5


title: iPSC SNEL3

value: iPSC SNEL3

value: Sall4, Nanog, Esrrb and Lin28


title: Biological sample #3, KCl stimulated, FOSB ChIP-Seq using sc48 antibody


title: iPSC SNEL1

value: iPSC SNEL1


title: ESC control line (ESC4)

source_name: embryo

value: ESC control line (ESC4)


title: ESC test line

value: ESC test line


title: Biological sample #2, KCl stimulated, H3K27ac ChIP-Seq

description:
03_05_B1B2merged_KCl_H3K27ac_ab4729_p1e-5_peaks_distal.bed
03_05_B1B2merged_KCl_H3K27Ac_ab4729_E300_track.bw
03_05_B1B2merged_KCl_H3K27ac_ab4729_p1e-5_peaks_genomewide.bed
05_B2_KCl_H3K27ac_ab4729_E300_track.bw
40_IncH3K27ac_at_distal_CBP+H3K4Me1.bed
41_ConH3K27ac_at_distal_CBP+H3K4Me1.bed
42_DecH3K27ac_at_distal_CBP+H3K4Me1.bed
43_NoH3K27ac_at_distal_CBP+H3K4Me1.bed


title: H2AX_Flox_Flox_ESC_mRNA-seq

description: Processed data file: ESC_KO_vs_WT.txt

data_processing:
Basecalls performed using CASAVA from Illumina.
Alignment reads to mouse genome mm9 plus splicing library with tophat2.
FPKM calculated with Cufflink2 (and cuffdiff2 compare two samples genes differential expression).
Genome_build: MGSCv37
Supplementary_files_format_and_content: cuffdiff2 result file.

source_name: H2A.X Flox Flox ESC

growth_protocol: Mouse iPSC and ESC culture on feeder with standard media and standard protocol (LIF 1000U).

extract_protocol:
Standard Invitrogen total RNA Trizol protocol.
Illumina "TruSeq" mRNA-Seq.

treatment_protocol: Just before extracting RNA, split cells to gelatin-coated plates to get feeder-free cells.

tag: strain/background

value: ESC

tag: parental cells

value: embryo


title: iPSC OSK4

description: ChIP-Seq

value: iPSC OSK4


title: H2AX_Cre_KO_ESC_mRNA-seq

description: Processed data file: ESC_KO_vs_WT.txt

source_name: H2A.X Cre KO ESC

tag: genotype/variation

value: H2A.X KO


title: H2AX_iPSC_4N_positive_PF1_mRNA-seq

description: Processed data file: iPS_PF1_vs_PF2.txt

source_name: H2A.X iPSC 4N+ PF1

value: 129Sv/C57 mix

value: iPSC

value: peritoneal fibroblasts


title: H2AX_iPSC_4N_negative_TTF2_mRNA-seq

description: Processed data file: iPS_TTF1_vs_TTF2.txt

source_name: H2A.X iPSC 4N- TTF2

value: tail tip fibroblasts


title: H2AX_iPSC_4N_positive_TTF1_mRNA-seq

source_name: H2A.X iPSC 4N+ TTF1


title: H2AX_iPSC_4N_negative_PF2_mRNA-seq

description: Processed data file: iPS_PF1_vs_PF2.txt

source_name: H2A.X iPSC 4N- PF2


title: Input_DNA_ESC1_wt_control_129andC57

description: Whole cell genomic DNA Seq

data_processing:
Basecalls performed using CASAVA from Illumina
ChIP-seq and Input DNA reads were aligned to the mm9 genome assembly using BOWTIE version 0.12.5 with the following configurations: -v 1 -m 1 --best -S
Aligned unique genomic location reads (sam file) transfer to bed file
Peaks (or blocks) were called (vs. Input DNA), or compared (vs. ESC1 H2A.X ChIP) using R-seg following -mode 2 (or -mode 3) and default setting, except that bin size is set to 5Kb.
The  differentially enriched/devoid (vs. ESC1 ChIP)  domains whose size are more than 100Kb or less than 10Kb are filtered out.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated from R-seg (mode 2 or mode 3).   The "scores" mean  HMM domain scores

source_name: ES cell

growth_protocol: ES, iPS and MEF cells are cultured with standard protocol

extract_protocol:
ChIP DNA samples were obtained with Native ChIP protocol; briefly, chromatin were fractionated and then  subject to Mnase digestion to generate mononucleosomes. Then the mononucleosome fraction was extracted with high salt buffer and H2A.X-containing nucleosomes were isolated and enriched with anti-H2A.X or Flag-tag antibodies.
Libraries were prepared according to Illumina's standard protocol, with instructions accompanying the DNA Sample Kit

value: mouse ES cell

value: 129Sv/C57 mixed background


title: Input_DNA_ESC2_wt_ES_C57

description: Whole cell genomic DNA Seq

value: pure C57 background


title: Input_DNA_WT_MEFs_2

description: Whole cell genomic DNA Seq

source_name: MEF cell

value: mouse primary embryonic fibroblasts cell

value: 129/c57 mixed background


title: Input_DNA_iPSC_4N_negative_Bcell5

description: Whole cell genomic DNA Seq

source_name: iPS cell from B cell

value: mouse secondary system derived iPS cell


title: Input_DNA_iPSC_4N_negative_Bcell4

description: Whole cell genomic DNA Seq


title: Input_DNA_iPSC_4N_negative_Bcell2

description: Whole cell genomic DNA Seq


title: Input_DNA_iPSC_4N_negative_PF2

description: Whole cell genomic DNA Seq

source_name: iPS cell from PF cell


title: Input_DNA_iPSC_4N_negative_TTF2

description: Whole cell genomic DNA Seq

source_name: iPS cell from TTF cell


title: Input_DNA_iPSC_4N_positive_Bcell1

description: Whole cell genomic DNA Seq


title: H2AX_iPSC_4N_negative_Bcell5

description: H2A.X ChIP-Seq

tag: antibody vendor

value: Abcam

tag: antibody cat#


title: H2AX_ESC3_wt_ES_129andC57

description: H2A.X ChIP-Seq


title: H2AX_WT_MEFs_1

description: H2A.X ChIP-Seq


title: H2AX_ESC2_wt_ES_C57

description: H2A.X ChIP-Seq


title: H2AX_iPSC_4N_negative_Bcell3

description: H2A.X ChIP-Seq


title: H2AX_iPSC_4N_negative_Bcell2

description: H2A.X ChIP-Seq


title: H2AX_ESC1_wt_control_129andC57

description: H2A.X ChIP-Seq


title: Input_DNA_WT_MEFs_1

description: Whole cell genomic DNA Seq


title: H2AX_iPSC_4N_negative_TTF2

description: H2A.X ChIP-Seq


title: H2AX_iPSC_4N_negative_PF2

description: H2A.X ChIP-Seq


title: iPSC OSKM_test

value: iPSC OSKM_test

value: Oct4, Sox2, Klf4 and Myc

value: H2A.X (Xiao lab)


title: Input_DNA_WT_Flag_MEFs_rep2

description: Whole cell genomic DNA Seq

source_name: Reconstitute Flag tag MEF cell

value: mouse embryonic fibroblasts cell (reconsitute with H2A.X-Flag)


title: Input_DNA_iPSC_4N_positive_TTF1

description: Whole cell genomic DNA Seq


title: H2AX_iPSC_4N_positive_Bcell1

description: H2A.X ChIP-Seq


title: H2AX_iPSC_4N_positive_TTF1

description: H2A.X ChIP-Seq


title: IgG_control

description: No-Antibody IgG control sample Seq

value: No-Antibody IgG control sample Seq


title: H2AX_WT_Flag_MEFs_rep2

description: Flag-Tag ChIP-Seq

value: Flag-Tag ChIP-Seq


title: H2AX_WT_Flag_MEFs_rep3

description: Flag-Tag ChIP-Seq


title: H2AX_WT_Flag_MEFs_rep1

description: Flag-Tag ChIP-Seq


title: Input_DNA_iPSC_4N_positive_PF1

description: Whole cell genomic DNA Seq


title: Input_DNA_ESC3_wt_ES_129andC57

description: Whole cell genomic DNA Seq


title: Input_DNA_WT_Flag_MEFs_rep1

description: Whole cell genomic DNA Seq


title: H2AX_WT_MEFs_2

description: H2A.X ChIP-Seq


title: miR-17-5p-transfected_P10-5_RISC

status: Public on Sep 06 2014

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description:
Ago2-IP-RNA (RISC RNA)
10-day-old rat, biological replicate 9

data_processing:
Illumina Casava1.8 software was used for basecalling; all reads are 50 nt with phred33 quality scores
Sequence reads were mapped to the transcriptome, defined by the UCSC genes.gtf, for the rn5 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10 .
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the UCSC rn5 genes.gtf.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each gene

source_name: islets of control 10-day-old rat

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions, but allowing 30 min room temperature isopropanol precipitation to enhance miRNA extraction.  Alternatively, Ago2 was immunoprecipitated from transfected islet cells using Wako Pure anti-Ago2 monoclonal antibody and protein G-Dynabeads (Invitrogen), followed by RNA extraction with Trizol as performed for total RNA.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31. Ago2-IP RNA (RISC RNA) was chemically fragmented and non-strand-specific, single-end RNA-Seq libraries prepared, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.

value: Sprague-Dawley

tag: tissue

value: islets

tag: age (weeks)

value: anti-Ago2 (Wako Pure monoclonal)


title: miR-17-5p-transfected_P10-2_RISC


title: miR-17-5p-transfected_P10-4_RISC


title: H2AX_iPSC_4N_positive_PF1

description: H2A.X ChIP-Seq


title: miR-17-5p-transfected_P10-6_RISC


title: control-transfected_P10-3_RISC


title: miR-17-5p-transfected_P10-6_mRNA

description:
polyA-RNA
10-day-old rat, biological replicate 9


title: control-transfected_P10-1_RISC


title: control-transfected_P10-2_RISC


title: miR-17-5p-transfected_P10-5_mRNA

description:
polyA-RNA
10-day-old rat, biological replicate 8


title: miR-17-5p-transfected_P10-4_mRNA

description:
polyA-RNA
10-day-old rat, biological replicate 7


title: H2AX_iPSC_4N_negative_Bcell4

description: H2A.X ChIP-Seq


title: sertoli wt rep3

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using TOPHAT
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated and isoforms were assembled by using a protocol from Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

source_name: testis

growth_protocol: Normal growth

extract_protocol:
P4 Testes were removed, frozen in RNA shield (Zymo), and RNA was harvested using Trizol reagent.mRNAs purified from  2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: testis

tag: age

value: post natal day 4

tag: genotype

value: wild type


title: miR-17-5p-transfected_P10-1_mRNA

description:
polyA-RNA
10-day-old rat, biological replicate 5

tag: strain


title: miR-17-5p-transfected_P10-2_mRNA

description:
polyA-RNA
10-day-old rat, biological replicate 6


title: sertoli wt rep2


title: control-transfected_P10-3_mRNA

description:
polyA-RNA
10-day-old rat, biological replicate 4


title: sertoli wt rep1


title: 3-month-old male rat, biological replicate 6_miRNAseq

description: base calling quality score: phred33

data_processing:
Illumina Casava1.8 software was used for basecalling; all reads are 50 nt and use phred33 quality scores
Indexes have been removed from the supplied raw data files. However, raw reads still contain Illumina sequencing adapters 3' to the termination of small RNAs. Thus, pre-processing of raw reads needs to involve sequence removal including, and 3' to, the Illumina adapter sequence.
The E-miR software package (Buermans et al 2010, see below) was used to map trimmed sequencing reads to the rat genome (rn5) and quantitate mapped reads.  Rat noncoding RNA and miR-3p/5p annotation was current as of June 2014.
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, t Hoen PA. New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 2010;11:716. PubMed PMID: 21171994; PubMed Central PMCID: PMC3022920.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include microRNA names, Ensembl transcript information, chromosomal location, and counts.

source_name: islets of control 3-month male rat

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions, but allowing 30 min room temperature isopropanol precipitation to enhance miRNA extraction.
Illumina TruSeq small RNA preparation kits (version C) were used for all library construction.  3' and 5' adapters capable of recognizing non-mRNA species were sequentially ligated to 1 microgram of total islet RNA, followed by reverse transcription, limited PCR amplification to add indexes, and size-selection.

tag: Sex

value: M


title: sertoli upf2 rep3

value: Upf2 KO


title: control-transfected_P10-1_mRNA

description:
polyA-RNA
10-day-old rat, biological replicate 1


title: sertoli upf2 rep2


title: 3-month-old male rat, biological replicate 3_miRNAseq

description: base calling quality score: phred33


title: 3-month-old male rat, biological replicate 1_miRNAseq

description: base calling quality score: phred33


title: 10-day-old rat, biological replicate 6_miRNAseq

description: base calling quality score: phred33


title: 3-month-old male rat, biological replicate 5_miRNAseq

description: base calling quality score: phred33


title: 3-month-old male rat, biological replicate 2_miRNAseq

description: base calling quality score: phred33


title: control-transfected_P10-2_mRNA

description:
polyA-RNA
10-day-old rat, biological replicate 3


title: sertoli upf2 rep1


title: 10-day-old rat, biological replicate 4_miRNAseq

description: base calling quality score: phred33


title: 10-day-old rat, biological replicate 1_miRNAseq

description: base calling quality score: phred33


title: 3-month-old male rat, biological replicate 4_miRNAseq

description: base calling quality score: phred33


title: 10-day-old rat, biological replicate 3_miRNAseq

description: base calling quality score: phred33


title: 10-day-old rat, biological replicate 5_miRNAseq

description: base calling quality score: phred33


title: 10-day-old rat, biological replicate 4_mRNA

description: base-calling quality score = phred33

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions, but allowing 30 min room temperature isopropanol precipitation to enhance miRNA extraction.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.


title: 3-month-old male rat, biological replicate 3_mRNA

description: base-calling quality score = phred33


title: Patient 66

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

data_processing:
Basecalls were using 1.7.0
RNA-seq reads were aligned with RUM 2.0.4 to the hg19 genome
RPKM were called using RUM
Junctions were called using RUM
Mutations were called using bcftools, annotated with SnpEFF 3.1, and intersected against dbSNP v137, 1000 Genomes, and HapMap v3.3
Genome_build: hg19
Supplementary_files_format_and_content: RPKM files were generated with RUM.
Supplementary_files_format_and_content: tab-delimited junctions file in BED format

source_name: Frozen metastatic cells from bone marrow biopsy

extract_protocol:
Trizol followed by RNeasy cleanup
Libraries were prepared by using 50ng of total RNA into NuGEN's Ovation RNA-Seq cDNA amplification kit, followed by paired-end library construction using NEBNext. All steps were prepared according to manufacturer's protocols

treatment_protocol: Frozen bone marrow biopsy samples

tag: metastatic site

value: bone marrow

tag: fragmentsize


title: 3-month-old male rat, biological replicate 1_mRNA

description: base-calling quality score = phred33


title: 3-month-old male rat, biological replicate 2_mRNA

description: base-calling quality score = phred33


title: 10-day-old rat, biological replicate 1_mRNA

description: base-calling quality score = phred33


title: Patient 74


title: Patient 49


title: Patient 71


title: Patient 55


title: Patient 39


title: Patient 24


title: Patient 28


title: Sox17-ESC_dox_Day6_RNA-seq

status: Public on Sep 05 2014

city: Toronto

first: Angela

last: McDonald

state: Ontario

address: 686 Bay Street

institute: The Hospital for Sick Children

description:
Sox17-ESC + dox Day 6
4J_D6_SORT

data_processing:
Reads were aligned to the mouse genome using TopHat v 2.0.11.
Aligned reads were assembled using Cufflinks v 2.1.2.
Assemblies were merged using Cuffmerge.
Downstream analyses of differentially expressed genes was performed using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file was obtained following cuffdiff analysis which includes FPKM values of transcripts for each sample

source_name: Sox17-ESC RNA-seq

growth_protocol: ESCs and XEN cells were cultured according to standard protocols (ESCs on mouse embryonic fibroblasts in serum and LIF and XEN cells in serum and mouse embryonic fibroblast conditioned media).

extract_protocol:
Tizol was used to extract total RNA according to the manufacturer's instuctions.
RNA-seq libraries were constructed using TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Sox17-ESCs were grown in standard ESC conditions with the addition of 100ng/ml doxycycline

tag: cell type

value: embryonic stem cells (ESCs)

value: Sox17 overexpression

tag: length of dox treatment

value: 6 days


title: 10-day-old rat, biological replicate 3_mRNA

description: base-calling quality score = phred33


title: Sox17-ESC_dox_7hrs_RNA-seq

description:
Sox17-ESC + dox 7 hours
4J_dox_7hrs

value: 7 hours


title: Sox17-ESC_dox_21hrs_RNA-seq

description:
Sox17-ESC + dox 21 hours
4J_dox_21hrs

value: 21 hours


title: Sox17-ESC_nodox_RNA-seq

description:
Sox17-ESC no dox
4J_no_dox

value: 0 hours


title: fly_Htt_rep1

city: Houston

first: hao

last: zhao

address: 1 Baylor Plaza

institute: BAYLOR COLLEGE OF MEDICINE

data_processing: The raw reads were mapped using Tophat (version 1.12) and Cufflinks. The following parameter settings were used: inner distance (-r) was set to be 150, minimum intron size (-i) to be 40 and maximum intron size (-I) to be 20000. Other parameters were set to be default values. If a read was mapped to multiple locations, only one randomly selected alignment of this read was kept. Reference genomes used were dm3 and mm9.

source_name: fly

extract_protocol:
Total RNA was extracted  using Trizol  reagent from invitrogen and RNA was cleaned using Qiagen RNA clean up columns, after total RNA was extracted and clean mRNA was isolated using Dynabeds oligo (dT) 25 kit from invitrogen, when mRNA was isolated and clean double stranded cDNA was synthetized using Superscript double stranded cDNA synthesis Kit from invitrogen. Heads of 1000 animals were used per genotype.
The Sequencing Library was constructed by using 50ng of RNA and the NuGEN Ovation RNA-Seq kit. The double-stranded amplified library was fragmented on a Covaris S2 with end repair, and paired-end adaptor ligation using reagents from New England Biolabs (NEBNextR DNA Sample Prep Master Mix Set 1) for the Illumina platform.
Insert size 300 bp, standard variation 35 of the paired-end data.

value: fly


title: Sox17-ESC_dox_35hrs_RNA-seq

description:
Sox17-ESC + dox 35 hours
4J_dox_35hrs

value: 35 hours


title: XEN_RNA_seq

description:
IM8AR XEN cells
IM8AR_XEN

value: extraembryonic endoderm (ExEn) stem (XEN) cells

value: wild-type


title: ESC_RNA-seq

description:
R1 ESCs
R1


title: fly_modifier_rep1


title: CT26LacZ-control-rep1

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation.
Reads were aligned to the mm9 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://biowhat.ucsd.edu/homer/
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression values (raw tags, RPKM, log2 fold change, P-value) and UCSC Bedgraphs are provided.

source_name: murine colorectal carcinoma

growth_protocol: The cell culture and infections were carried out on approximately 80% confluent cultures in 10 cm dishes with 7 ml of fresh low glucose DMEM (Sigma) supplemented with 10% FCS, L-glutamine and Penicillin/Streptomycin under humified atmosphere in 5% CO2.

extract_protocol:
RNA was purified using RNeasy Mini Kit and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit.
The RNA was base-hydrolyzed, dephosphorylated with PNK and fragments of 50-400 nts were gel extracted from 10% polyacrylamide TBE-urea gel. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 8-10 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000 according to the manufacturer's instructions.

treatment_protocol: CT-26 cells were infected with MOI=0.01 and collected 12h post infection. The success of infection 12h p.i. was monitored with fluorescence microscope and by measuring the virus titer from the cell supernatants.

tag: transgene

value: LacZ transgene

value: CT26LacZ tumor

tag: infection

value: control


title: CT26LacZ-SFV-infected-rep1

value: SFV


title: CT26LacZ-control-rep2


title: CT26WT-SFV-infected-rep1

tag: passage

value: CT26WT tumor


title: CT26WT-SFV-infected-rep2


title: Sox17-ESC_dox_49hrs_RNA-seq

description:
Sox17-ESC + dox 49 hours
4J_dox_49hrs

value: 49 hours


title: CT26WT-control-rep1


title: CT26WT-control-rep2