title: HMGD1 ChIP-seq replicate 3

city: La Jolla

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute

data_processing:
HMGD1 SOLiD output files were converted to fastq using custom script
Mapped HMGD1 reads to the Drosophila genome using BWA v0.6.1
Estimated the mean HMGD1 fragment length of each replicate by computing the offset that gave the highest covariation of read depth between the forward and reverse strands
Estimated HMGD1 nucleosome midpoint locations as the read start plus the offset (or minus the offset for those that mapped to the reverse strand.
Aligned the MNase-seq and H1 paired-end reads to the genome using the standard SOLiD pipeline and discarded those where only one side of pair mapped
Estimated the distribution of H1 and MNase-seq fragment sizes from separation of read pairs, and discarded read pairs outside of the central 95% of distribution (101-191bp)
Estimated H1 and MNase-seq nucleosome midpoints as the midpoint between read pairs
Genome_build: dm3
Supplementary_files_format_and_content: wig files containing counts of mapped fragment midpoints at each genomic position

source_name: late embryonic stage cells

growth_protocol: D. Melanogaster S2-DRSC cells (obtained from the Drosophila Genomics Resource Center) were cultured in Schneider's Drosophila medium (Invitrogen) supplemented with 10% FCS (Hyclone).

extract_protocol:
MNase digested nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Applied Biosystems protocol for SOLiD fragment paired-end sequencing. Briefly, DNA was end-repaired and 5’-phosphorylated by incubation in DNATerminator end-repair kits, as recommended by the manufacturer (Lucigen Corp., Middleton, WI). SOLiD adapters were ligated and the DNA molecules PCR amplified (very low cycle number) and sequenced by using the Applied Biosystems protocol for SOLiD fragment paired-end sequencing. After adapter ligation DNA was PCR amplified with SoLiD primers for less than 12 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 a SoLid flow cell for cluster generation.

value: late embryonic cells

tag: passages

tag: antibody

value: customized antibody


title: HMGD1 ChIP-seq replicate 2

status: Public on Dec 01 2013

type: SRA

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

tag: cell type

tag: strain


title: HMGD1 ChIP-seq replicate 1


title: HMGD1 ChIP-seq replicate 4


title: Adult Human Islet T2D WFU005

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
adapter trimming: 3' Solexa or Illumina adapter sequence was trimmed from reads allowing up to 1 mismatch per 4 bases.
alignment: Trimmed reads were aligned to mature miRNAs, RefSeqs, and human genome using ELAND and allowing up to 2 mismatches
family grouping: mature miRNAs that shared reads with lengths between 19 and 25bp were put into ad hoc groups for reporting read counts
read taillying: reads were tallied for groups of miRNAs then normalized to reads per million
differential expression: reads per million where quantile normalized then evaluated for statistical significance using SAMR (T2D v Control only)
Genome_build: mirBase 20

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human islets and relevant donor information including age, gender, diabetes status, hemoglobin A1c and BMI were obtained from the Islet Cell Resource Center of the University of Pennsylvania, the NIDDK-supported Integrated Islet Distribution Program (iidp.coh.org) and the National Disease Research Interchange. The donorÕs diabetes status was defined by the patientÕs medical record, and, when available, the hemoglobin A1c.

extract_protocol:
Small RNA was isolated from the islets by using the mirVana miRNA Isolation Kit (Ambion Cat# AM1560).
The glucose experiment and sorted alpha/beta cells were processed with the Illumina truSeq small RNA kit, whereas the whole islet T2D v CTL experiments were processed with the older v1 pre-truSeq kit from Illumina using the long multi-day protocol. Briefly Illumina's 3' adapter then 5' adapter were ligated to small RNA, then amplified using RT-PCR. RT was done with Illumina's RT primer, then PCR with the Primer 1 and Primer 2. Finally libraries were size selected using a gel and aiming for products which correspond to inserts of 22 to 30nt. Consequently, prior to alignment either the truSeq adapter sequence that begins TGGAATTCTCGGGTGCCAAGG or the v1 adapter sequence that begins with TCGTATGCCGTCTTCTGCTTGT need to be trimmed from the reads.

treatment_protocol:
FACS sorting on dispersed human islets was performed as described in Bramswig, N. C. et al. Epigenomic plasticity enables human pancreatic alpha to beta cell reprogramming. The Journal of clinical investigation 123, 1275-1284,  doi:10.1172/JCI66514 (2013).
15,000 IEQ of human islets obtained from three donors were incubated in 5.56mM glucose for 6 hours. Islets were washed twice in 1x PBS and then divided and re-plated in media containing 1mM, 5.56mM or 16.7mM glucose for 16 hours

tag: condition

tag: tissue

value: whole islet


title: ChIP-seq_C/EBPα_GMP_replicate

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaloes vej 5

department: BRIC/Finsen Laboratory

country: Denmark

institute: University of Copenhagen/Rigshospitalet

data_processing:
All data was mapped with bowtie v. 0.12.7, using standard parameters
All data was converted into BigWig format and vizualized in the UCSC genome browser
Genome_build: mm9
Supplementary_files_format_and_content: Raw data files in fastq and processed files as bigwig

organism: Mus musculus

extract_protocol:
Chromatin 500.000 FACS sorted LSKs or GMPs was incubated with antibodies recognizing C/EBPa. For histone modification 100.000 FACS sorted cells were used for ChIP. The antibody-bound chromatin was captured with Protein-A sepharose beads, washed, de-cross-linked and precipitated. DNA was extracted using standard phenol-chloroform extraction
Precipitated DNA were mixed with 2 ng E. Coli DNA and amplified using NEB Next ChIP-seq sample prep reagent set 1 (New England Biolabs) according to manufacturers protocol.

value: Haematopoietic progenitor cells

value: C57BL/6 cebpa flox/flox

tag: gender

value: male

value: Cebpa:Santa Cruz 14-AA


title: Het_DG

city: New York

first: Shifra

middle: Liba

last: Klein

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Alignment: Fragments were mapped to the mosue genome using TopHat version 2.0.2 (http://tophat.cbcb.umd.edu) with bowtie version 1.0.0 against mm9 and annotated with NCBIM37 coding transcripts
Assembly and differential analysis: Transcripts were assembled and quantitated using Cufflinks 2.0.2 (http://cufflinks.cbcb.umd.edu) against the NCBIM37 reference transcriptome
Genome_build: NCBIM37
Supplementary_files_format_and_content: Cuffdiff expression tracking

molecule: polyA RNA

source_name: Dentate Gyrus

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dentate gyrus

tag: genotype

value: WT from TNF alpha +/- mothers


title: WT_CA1

value: WT from WT mothers


title: Nes_nPTB_WT

city: Los Angeles

first: Areum

last: Han

address: 6577 MacDonald Research Lab. 675 Charles E. Young Dr. South

institute: UCLA

description: Not strand specific library

data_processing:
Illumina Casava software used for basecalling.
Nestin sequenced reads were mapped to mm9 whole genome and transcriptome using tophat with parameters-m 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --num-threads 4 --max-multihits 5 --solexa1.3-quals --library-type fr-unstranded --segment-mismatches 2
Emx sequenced reads were mapped to mm9 whole genome and transcriptome using tophat with parameters -m 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --num-threads 3 --max-multihits 5 --solexa1.3-quals --library-type fr-firststrand --segment-mismatches 2  --no-novel-juncs
Gene expression values, FPKM, were calculated using a cufflinks program.
Exon inclusion ratios were calculated using a splicetrap program.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM and exon inclusion level values for each Sample

source_name: E18 Mouse Brain

growth_protocol: Animals were housed in a 12-h light/dark cycle with food and water available ad libitum.

extract_protocol:
Trizol after tissue homogenization.
Illumina TruSeq. The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000 platform).

treatment_protocol: Standard Dissection

tag: genotype/variation

value: WT

tag: age

value: Embryonic Day 18

value: Mixed C56Bl/6:129S2 background


title: Emx_nPTB_WT

description: Strand Specific Library

source_name: P1 Mouse Cortex

value: Postnatal Day 1


title: ChIP-seq_C/EBPα_LSK_replicate


title: ptbp1kd

description: Sample 2

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome and transcriptome using tophat with parameters --coverage-search --microexon-search --library-type=fr-firststrand --min-isoform-fraction=0.
Gene expression values, FPKM, were calculated using a cufflinks program.
Exon inclusion ratios were calculated using a splicetrap program.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM
*genes.fpkm_tracking.txt: fpkm for gene,
*isoforms.fpkm_tracking.txt: fpkm for isoform,
*transcripts.gtf: gene description
and exon inclusion level values for each Sample (splicetrap*.txt)

growth_protocol: Mouse neuroblastoma (N2A) cells were cultured in DMEM with 10% FBS and 2mM L-glutamine.

extract_protocol:
Total RNA was collected using Trizol (Invitrogen) according to the manufacturer's instructions. The RNA was further treated with DNase I to avoid DNA contamination.
RNA-seq libraries were constructed following standard protocols (Illumina TruSeq RNA Sample Prep Kit). To make strand-specific libraries, we added two extra steps to the protocol. After first strand cDNA synthesis, remaining dNTPs were removed by a size selection using beads (AMPure XP). Second-strand cDNA was synthesized with dNTP mix with dUTP instead of dTTP. After sequencing adaptors were ligated, USER (Uracil-Specific Excision Reagent enzyme;NEB) was added to reactions to degrade the second strand cDNA with uracil. The samples were incubated for 15min at 37°C and the reaction were inactivated at 94°C for 5min. The samples were put in ice and preceded to next PCR amplification step.
The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000 platform).

treatment_protocol: At 70 to 80% confluency, cells were trypsinized and suspended in the growth medium. DNA–Lipofectamine 2k (Invitrogen) complexes were prepared and mixed with cells in a tube according to manufacturer’s instructions. Tubes were incubated for 5 h with mixing in every half hour. Then cells were centrifuged and cultured in plates for 3 d. Proteins and RNA was extracted from collected cells.

value: neuroblastoma cell (N2a)

tag: transfected with

value: single knock down of ptbp1


title: ChIP-seq_C/EBPα_GMP


title: Nes_nPTB_KO

description: Not strand specific library

value: PTBP2 Nestin-KO


title: control

description: Sample 1

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome and transcriptome using tophat with parameters --coverage-search --microexon-search --library-type=fr-firststrand --min-isoform-fraction=0.
Gene expression values, FPKM, were calculated using a cufflinks program.
Exon inclusion ratios were calculated using a splicetrap program.
Genome_build: mm9
Supplementary_files_format_and_content:
tab-delimited text files include FPKM
*genes.fpkm_tracking.txt: fpkm for gene,
*isoforms.fpkm_tracking.txt: fpkm for isoform,
*transcripts.gtf: gene description
and exon inclusion level values for each Sample (splicetrap*.txt)

value: shControl

value: shRNA transfection control


title: Jmjd2b_KD_Nanog_replicate_2

city: Shanghai

first: Zhen

last: Shao

address: 320 Yueyang Road

country: China

institute: Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

description: Jmjd2b shRNA KD in mESCs

data_processing:
Basecalls performed using Solexa pipeline for data generated by HiSeq 2000 or Helicos pipeline for data generated by Helicos Heliscope.
Sequencing reads were aligned to mouse genome assembly mm9 using Illumina software pipeline (data generated by HiSeq 2000) or Helisphere (data generated by Helicos).
Only ChIP-seq reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: Mapped read bed file (reporting the coordinates of aligned reads) which were converted from BAM files by using BAMtools; wig file which contain the read densities normalized by sequencing depth; and peak bed file which were outputed by MACs (reporting the coordinates of peaks called by MACS).

source_name: Jmjd2b KD mESCs

growth_protocol: mESCs were grown in standard mouse ES cells media with LIF

extract_protocol:
[Illumina] Purified ChIP DNA was measured in Qubit (Invitrogen). 2-10ng of purified ChIP DNA was used to prepare sequencing libraries, using NEB next generation ChIP sequencing Kit and Illumina ChIP seq kit according to the manufacturer's instructions.
[Helicos] ChIP DNA was processed for 3' polyA tailing, followed by 3'ddATP-blocking. Processing samples by ligation, amplification and size selection are not required by Helicos sequencing.

treatment_protocol: mESCs were crosslinked with 1% formaldehyde, reaction was quenched by 0.125M glycine, trypsinized, sonicated in SDS Chip buffer, followed by incubation with 5µg of antibodies overnight. Protein A or G beads were added to ChIP reactions to immunoprecipitate chromatin. Beads were washed several times, de-crosslinked at 65ºC overnight, followed by RNase and Proteinase K treatment to collect ChIP-ed DNA, which was ready for library preparation. For bioChIP reactions, streptavidin beads (Dynabeads MyOne Streptavidin T1- Invitrogen) were used for the precipitation of chromatin, and 2% SDS was applied for first washing step. All other steps were same as conventional ChIP protocol.

tag: phenotype

value: agouti

value: ESC

value: Jmjd2b shRNA KD

tag: chip antibody

value: Nanog (A300-397A), Bethyl Laboratories


title: MNase-seq replicate 1

value: late embryonic cells


title: PD12_POL2

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

data_processing:
DNA libraries were sent to Illumina Sequencing Services for sequencing on a Illumina HiSeq 2000. Sequences (50 bases) were aligned to the mouse genome (NCBI Build 37, July 2007) using BWA algorithm. Aligns were extended in silico at their 3’-ends  to a length of 150 bp and assigned to 32-nt bins along the genome. The resulting histograms were stored in BAR (Binary Analysis Results) files. Peak locations were determined by applying a threshold of 18 (5 consecutive bins containing .18 aligns) and storing the resulting intervals in BED files (Affymetrix TAS software). These files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals).
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: NCBI Build 37, July 2007
Supplementary_files_format_and_content: Peak locations were determined by applying a threshold of 18 (five consecutive bins containing 18 aligns) and storing the resulting intervals in Browser Extensible Data (BED) files.

source_name: postnatal day 12 female mouse uterus

extract_protocol:
Uterine tissue samples (~ 100 mg) were submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes.  Fixation was stopped by the addition of 0.125 M glycine.  The tissue pieces were then treated with a TissueTearer and finally spun down and washed twice in PBS.  Chromatin was isolated by disrupting the cells with a Dounce homogenizer.  Lysates were sonicated using a Misonix Sonicator 3000 (Vernon Hills, IL, USA) equipped with a microtip in order to shear the DNA to an average length of 300-500 bp.  Lysates were cleared by centrifugation and stored at -80 C.  Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by phenol/chloroform extraction and ethanol precipitation.  Purified DNA was quantified on a NanoDrop spectrophotometer.  Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.  For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen, Carlsbad, CA, USA).  Immunoprecipitation was performed using 4 µg of goat anti-FOXA2 polyclonal IgG (Catalog number sc-6554 from Santa Cruz Biotechnology, Santa Cruz, CA, USA) or 2 µg of rabbit anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) polyclonal antibody (Catalog number ab5095 from Abcam, Cambridge, MA, USA).  Following overnight incubation at 4oC, Protein A agarose was added and incubation at 4oC continued for another 3 h.  Immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. Immune complexes were eluted from the beads with SDS buffer, and subjected to RNase treatment and proteinase K treatment.  Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit. Briefly, DNA ends were polished and 5-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. After addition of 3’-adenine to blunt ends using Klenow (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size fractionated to 200-250 base pairs (bp) on a 2% agarose gel.  After a PCR amplification [30 sec at 98°C; (10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C) for 18 cycles followed by 5 min at 72°C] with Phusion High-Fidelity DNA Polymerase (New England Biolabs, Ipswich, MA, USA), the resulting DNA libraries were tested by RT-qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

value: whole uterus

value: postnatal day 12


title: DOPP2.5+3.5_FOXA2

source_name: day of pseudopregnancy 2.5 and 3.5 female mouse uterus

value: day of pseudopregnancy 2.5+3.5


title: DOPP2.5+3.5_POL2


title: CREB with Proteasome Inhibitor

city: Houston

first: Andre

last: Catic

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: CREB with Proteasome Inhibitor

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genome using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/), version 1.4
Genome_build: mm9
Supplementary_files_format_and_content: The bigwigs were created with the following steps: Reads were aligned to the reference genome using bowtie with at most 2 mismatches. The SAM file with those alignments was converted to BAM format and then sorted using samtools, and then the sorted alignments were converted to wig format using a custom python script. Finally, the wigs were converted to bigWigs using wigToBigWig (which can be downloaded from http://hgdownload.cse.ucsc.edu/admin/exe/).

source_name: 3T3-L1 cells (ATCC #CL-173)

growth_protocol: 3T3-L1 cells were obtained by ATCC and cultured at undifferentiated state (as fibroblasts) following standard recommendations. 15 Mio cells were processed for an average ChIP-seq run.

extract_protocol:
After fixation in PBS/1% para-Formaldehyde (37ºC, 10 min), nuclei were isolated by lysis in Triton-X100 buffer and sonicated to ca. 200 bp length. DNA was co-immunoprecipitated with the respective antibodies over night.
Libraries were prepared according to Illumina's instructions (New England Biolabs, Cat. No. E6200). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Treatment was performed with 25 microM lactacystin or 0.1% DMSO (mock) for three hours.

tag: epitope

value: a.a. 5-24 of human CREB

value: 17-600 (Millipore)

tag: molecule

value: CREB

tag: treatment

value: lactacystin


title: PSMB1

value: M2 (Sigma Aldrich)

value: DMSO


title: Ubiquitin with alpha-Amanitin and Proteasome Inhibitor

value: lactacystin and alpha-Amanitin


title: cJun


title: CREB

description: CREB


title: WT_DG

value: Dentate gyrus

value: WT from WT mothers


title: Het_CA1

value: WT from TNF alpha +/- mothers


title: Emx_nPTB_KO

description: Strand Specific Library

value: PTBP2 Emx-KO

value: Postnatal Day 1

value: Mixed C56Bl/6:129S2 background


title: PPAR-gamma


title: Jmjd2c_KD_RNA Pol II 8WG16

description: Jmjd2c shRNA KD in mESCs

source_name: Jmjd2c KD mESCs

value: agouti

value: male

value: ESC

value: Jmjd2c shRNA KD

value: RNA Pol II 8WG16 (MMS-126R), Covance


title: PD12_FOXA2

value: whole uterus

value: postnatal day 12


title: Jmjd2c_KD_Spt5

description: Jmjd2c shRNA KD in mESCs

value: Spt5 (H-300) (sc-28678),  Santa Cruz Biotechnology


title: Jmjd2c_KD_RNA Pol II_Ser2p

description: Jmjd2c shRNA KD in mESCs

value: RNA Pol II Ser2p, clone 3E10 (04-1571), Millipore


title: Jmjd2c_KD_RNA Pol II_Ser5p

description: Jmjd2c shRNA KD in mESCs

value: RNA Pol II Ser5p, CTD4H8 (MMS-128P), Covance


title: Jmjd2c_KD_Oct4

description: Jmjd2c shRNA KD in mESCs

value: Oct4(N-19)(sc-8628), Santa Cruz Biotechnology


title: Jmjd2c_KD_H3K4me3

description: Jmjd2c shRNA KD in mESCs

value: H3K4me3 (ab1012), Abcam


title: Jmjd2c_KD_Nanog

description: Jmjd2c shRNA KD in mESCs

value: Nanog (A300-397A), Bethyl Laboratories


title: Jmjd2c_KD_H3K9me3

description: Jmjd2c shRNA KD in mESCs

value: H3K9me3 (ab8898), Abcam


title: Jmjd2c_KD_H3K36me3

description: Jmjd2c shRNA KD in mESCs

value: H3K36me3 (ab9050), Abcam


title: Jmjd2c_KD_Ezh2

description: Jmjd2c shRNA KD in mESCs

value: ChIPAb+ Ezh2, clone AC22 (17-662), Millipore


title: Jmjd2c_KD_H3K27me3

description: Jmjd2c shRNA KD in mESCs

value: H3K27me3 (ab6002), Abcam


title: Jmjd2c_KD_Ctr9

description: Jmjd2c shRNA KD in mESCs

value: agouti

value: Ctr9 (A301-395A), Bethyl Laboratories


title: Jmjd2b_KD_Nanog

description: Jmjd2b shRNA KD in mESCs

value: male

value: ESC

value: Jmjd2b shRNA KD


title: PSMB1 with Proteasome Inhibitor

description: PSMB1 with Proteasome Inhibitor

value: M2 (Sigma Aldrich)

value: lactacystin


title: Jmjd2b_KD_Oct4

description: Jmjd2b shRNA KD in mESCs


title: Jmjd2b_KD_H3K36me3

description: Jmjd2b shRNA KD in mESCs


title: Jmjd2b_KD_cMyc

description: Jmjd2b shRNA KD in mESCs

value: cMyc (9402), Cell signaling


title: Jmjd2b_KD_H3K9me3

description: Jmjd2b shRNA KD in mESCs


title: AntiGFP_KD_RNA Pol II 8WG16

description: Anti-GFP shRNA KD in mESCs

source_name: Anti-GFP KD mESCs

value: Anti-GFP shRNA KD

value: RNA Pol II 8WG16 (MMS-126R), Covance


title: Jmjd2b_KD_H3K4me3

description: Jmjd2b shRNA KD in mESCs


title: AntiGFP_KD_Oct4

description: Anti-GFP shRNA KD in mESCs

value: Oct4(N-19)(sc-8628), Santa Cruz Biotechnology


title: Jmjd2b_KD_H3K27me3

description: Jmjd2b shRNA KD in mESCs


title: Jmjd2b_KD_H3K27ac

description: Jmjd2b shRNA KD in mESCs

value: H3K27ac (ab4729), Abcam


title: AntiGFP_KD_RNA Pol II_Ser5p

description: Anti-GFP shRNA KD in mESCs

value: RNA Pol II Ser5p, CTD4H8 (MMS-128P), Covance


title: AntiGFP_KD_H3K9me3

description: Anti-GFP shRNA KD in mESCs

value: H3K9me3 (ab8898), Abcam


title: AntiGFP_KD_H3K36me3

description: Anti-GFP shRNA KD in mESCs

value: H3K36me3 (ab9050), Abcam


title: AntiGFP_KD_H3K4me3

description: Anti-GFP shRNA KD in mESCs

value: H3K4me3 (ab1012), Abcam


title: AntiGFP_KD_Ctr9

description: Anti-GFP shRNA KD in mESCs


title: mESC_K4me3_solexa

description: wild type mouse ES cells

source_name: Mouse ES cells

value: wild type


title: AntiGFP_KD_RNA Pol II_Ser2p

description: Anti-GFP shRNA KD in mESCs

value: agouti

value: RNA Pol II Ser2p, clone 3E10 (04-1571), Millipore


title: AntiGFP_KD_Ezh2

description: Anti-GFP shRNA KD in mESCs

value: male

value: ChIPAb+ Ezh2, clone AC22 (17-662), Millipore


title: mESC_BioJmjd2b_solexa

description: Biotinylated Jmjd2b mouse ES cells, with BirA ligase

value: ESC

value: Biotinylated protein ChIP-ed with Streptavidin beads


title: Cebpa ChIP-seq

data_processing:
Alignment to Mus genome Using bowtie v. 0.12.8 with standard parameters
Processing for coverage calculation: Bedtools version 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files containing read coverage
Supplementary_files_format_and_content: Bed file for cebpa, containing called peaks, using MACS v 1.4.2

source_name: Hematopoietic Stem Cells

growth_protocol: In vivo

extract_protocol:
FACS sorting on hematopoietic stem cell markers (Lin- Sca-1+ Kit+)
Kit: NEBNEXT ChIP-seq prep set1 (E6200S)

value: Hematopoietic Stem Cells

tag: compartment

value: LSK (Lin- Sca-1+ Kit+)

value: Cebpa, Santa Cruz 14-AA

value: C57BL/6 cebpa flox/flox;Mx1Cre


title: IgG-mock ChIP-seq

data_processing:
Alignment to Mus genome Using bowtie v. 0.12.8 with standard parameters
Processing for coverage calculation: Bedtools version 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files containing read coverage

value: IgG, Sigma, I8140


title: AntiGFP_KD_cMyc

description: Anti-GFP shRNA KD in mESCs

value: Anti-GFP shRNA KD

value: cMyc (9402), Cell signaling


title: AntiGFP_KD_Nanog

description: Anti-GFP shRNA KD in mESCs

value: Nanog (A300-397A), Bethyl Laboratories


title: Jmjd2c_KD_cMyc

description: Jmjd2c shRNA KD in mESCs

value: Jmjd2c shRNA KD


title: input

description: control input sample


title: AntiGFP_KD_H3K27me3

description: Anti-GFP shRNA KD in mESCs

value: H3K27me3 (ab6002), Abcam


title: mESC_K27me3_solexa

description: wild type mouse ES cells

value: wild type


title: AntiGFP_KD_Spt5

description: Anti-GFP shRNA KD in mESCs

value: agouti

value: Spt5 (H-300) (sc-28678),  Santa Cruz Biotechnology


title: mESC_BioJmjd2c_solexa

description: Biotinylated Jmjd2c mouse ES cells, with BirA ligase

value: male


title: mESC_Input_solexa

description: wild type mouse ES cells


title: lincFoxf1a_E14-5_Lung_15KO

status: Public on Nov 30 2013

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
reads were aligned to the mouse (mm9) reference genome assemblies using Tophat2 using default options.
Mapped reads were assembled into transcripts with Cufflinks v2.0.2
Aligned reads were used as input for Cuffdiff2 to determine expression levels (FPKM) and differential expression between conditions using the default options.
CummeRbund v2.1 (http://compbio.mit.edu/cummeRbund/) was used to process, index, and visualize the output of the Cuffdiff2 analyses.
Genome_build: mm9
Supplementary_files_format_and_content: CummeRbund diffTable output. Contains log ratios and differential significance test results.

source_name: E14.5 Embryonic Lung

growth_protocol: Mice were housed under controlled pathogen-free conditions (Harvard University’s Biological Research Infrastructure) and experiments were approved by the Harvard University Committee on the Use of Animals in Research and Teaching.

extract_protocol:
Tissue was harvested and homogenized in Trizol. Total RNA was extracted using the Qiagen Rneasy kit via the Qiacube.
500ng total RNA was used as input for the TruSeq RNA-Seq kit (Illumina) for each of the samples described. Libraries were quality-controlled and determined to be free of adapter dimers by running on a DNA 7500 chip for the Bioanalyzer (Agilent)

value: Lung


title: CebpaKO H3K27Me3 ChIP-seq 1

value: H3K27Me3,Cell Signaling, C36B11

value: knock out


title: Ubiq_Lacta_rep1

description: Ubiquitin with Proteasome Inhibitor

value: lactacystin

value: M2 (Sigma Aldrich)


title: Ubiq_Lacta_rep2

description: Ubiquitin with Proteasome Inhibitor


title: Ubiq_DMSO_rep2

description: Steady state ubiquitin

value: DMSO


title: lincSox2_E18-5_Brain_31KO

source_name: E18.5 Embryonic Brain

value: Brain


title: lincBrn1b_P7_Brain_2KO

source_name: P7 Whole Brain


title: lincSox2_E18-5_Brain_46WT


title: lincSox2_E18-5_Brain_48WT


title: Ubiq_DMSO_rep1

description: Steady state ubiquitin


title: AntiGFP_KD_H3K27ac

description: Anti-GFP shRNA KD in mESCs

value: ESC

value: H3K27ac (ab4729), Abcam


title: lincBrn1b_P7_Brain_1KO


title: lincBrn1b_E15-5_Tel_4KO

source_name: E15.5 Embryonic Telencephalon

value: Telencephalon


title: lincBrn1b_E15-5_Tel_3WT


title: lincBrn1b_P7_Brain_2WT


title: lincBrn1b_P7_Brain_1WT


title: lincBrn1b_E15-5_Tel_2KO


title: mESC_BirA_solexa

description: Mouse ES cells with BirA ligase, without any biotinylated protein (Control)

source_name: Mouse ES cells with BirA ligase

value: ChIP-ed with Streptavidin beads


title: lincBrn1b_E13-5_Tel_1KO

source_name: E13.5 Embryonic Telencephalon


title: RIPThoc2

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description: Sample 2

data_processing:
library strategy: RIP-seq
Basecalls were performed by MiSeq reporter software
Reads were aligned to index of RefSeq transcripts, derived from UCSC table browser 01/29/2013, using bowtie 0.12.8, employing parameters -v2 -m10 -k10 --best --strata
Transcript coordinates were translated to mm9 genomic coordinates, and duplicate alignments resulting from overlapping transcripts were removed using custom scripts
Read coverage tracks were generated using bedtools 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, read coverage

growth_protocol: mouse embryonic stem cells J1 was cultured in ESGRO medium

extract_protocol:
RNA IP was performed using RNA IP kit from Millipore according to manufacturer's protocol
library was generated by use of RNA Truseq kit from Illumina

tag: cell line

value: embryonic stem cells

tag: rip antibody


title: lincFoxf1a_E14-5_Lung_13KO


title: lincBrn1b_E13-5_Tel_2WT


title: lincBrn1b_E13-5_Tel_1WT


title: lincBrn1b_E13-5_Tel_2KO


title: lincFoxf1a_E14-5_Lung_11WT


title: MeDIP-seq_3T3-L1_Day0

status: Public on Nov 29 2013

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

data_processing:
Basecalls performed using CASAVA version 1.8
MeDIP-seq reads were aligned to the mm9 genome assembly using CASAVA 1.8
After duplicate removing using Picard tools (http://picard.sourceforge.net), the MeDIP-seq data were processed using MEDIPS (Chavez L et al., Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage, Genome Res, 20, 1441-1450). A linear regression issued from this analysis was obtained and used to compute the relative DNA methylation score (rms) corresponding to the rpm (reads per million) signal normalized to local CpG densities.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MEDIPS. Scores represent rms (relative DNA methylation score).

source_name: 3T3-L1 cells

growth_protocol: 3T3-L1 cells were cultured as in Mikkelsen TS et al. (Mikkelsen TS et al., Comparative epigenomics analysis of murine and human adipognesis. Cell, 143, 156-169. 3T3-L1 were grown until confluency and harvested two days post-confluency

extract_protocol:
Genomic DNA was prepared using a DNA extraction kit (Dneasy Blood and Tissue kit, Qiagen) with a supplementary step of RNAse digestion. Genomic DNA was then sonicated to produce fragments ranging from 200 bp to 500 bp. Methylated DNA were then immunoprecipitated using antibody directed against 5-methylcytosine
Libraries were prepared according to Illumina's instructions

tag: cell type

value: Fibroblast

tag: passage

tag: medip antibody

value: Antibody directed against 5-methylcytosine (Diagenode, Mab-081-100)


title: lincSox2_E18-5_Brain_28KO

tag: tissue


title: lincBrn1b_E15-5_Tel_5WT


title: lincBrn1b_E15-5_Tel_6KO


title: Input

description: Sample 1


title: mRNA lifetime-SiControl-TI-3h E2

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: Poly(A) selected mRNA

data_processing:
General: Illumina Casava 1.8.2 software were used for basecalling.
General: Reads were aligned to the hg19 genome assembly using bowtie version 1.0 with at most 2 mismatch allowed -n 2 -g 1.
A: PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings.
B and C: RIP and Ribosome profiling were mapped by Tophat version 2.0 and analyzed by DESeq to generate RPKM
D and E: mRNA lifetime data were mapped by Tophat version 2.0, analyzed by Cuffidff version 2.0 to calculate RPKM, then re-normalized by ERCC spike-in control
F: RNASeq data were mapped by Tophat version 2.0 and followed by Cuffdiff version 2.0 for differential expression test.
All other following calculation steps were illustrated in processed files.
Genome_build: hg19
Supplementary_files_format_and_content: rpkm and peaks

source_name: HeLa cell

extract_protocol:
Extract total RNA by Rneasy kit (QIAGEN), Dnase I treated, then add ERCC RNA spike-in control
Truseq stranded mRNA sample prepration kit (illumina)

value: HeLa

value: 40nM siRNA knock-down for 48h, then add actinomycin for 3h


title: mRNA lifetime-SiControl-TI-0h E1

description: Poly(A) selected mRNA

value: 40nM siRNA knock-down for 48h, then add actinomycin for 0h


title: mRNA lifetime-SiYTHDF2-TI-3h D5

description: Poly(A) selected mRNA

extract_protocol:
Extract total RNA by Rneasy kit (QIAGEN), Dnase I treated, then add ERCC RNA spike-in control
Truseq RNA sample prepration kit (illumina)


title: mRNA lifetime-SiControl-TI-6h E3

description: Poly(A) selected mRNA

value: 40nM siRNA knock-down for 48h, then add actinomycin for 6h


title: mRNA lifetime-SiControl-TI-0h D1

description: Poly(A) selected mRNA

extract_protocol:
Extract total RNA by Rneasy kit (QIAGEN), Dnase I treated, then add ERCC RNA spike-in control
Truseq small RNA sample prepration kit (illumina)


title: S. paradoxus poly-A selected mRNA fragments

city: Stanford

first: Carlo

middle: G.

last: Artieri

state: California

address: Herrin Labs Rm. 309

department: Biology

institute: Stanford University

description: Poly-A selected mRNA

data_processing:
Bases were called using Illumina CASAVA version 1.8.2  and only reads passing the software's quality filter were retained.
S. cerevisiae and S. paradoxus genome assemblies, annotations, and orthology assignments were obtained from (Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. 2011. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) 1:11-25.). For all analyses, we focused only on the nuclear genome. From the list of genes orthologous between S. cerevisiae and S. paradoxus, we identified those that in both species a) began with an ATG and terminated in a canonical stop codon (TAA, TAG, TGA), b) had a sequence length that was divisible by three, c) lacked in-frame stop codons, d) lacked any ‘N’ nucleotides in their genomic sequence, e) were annotated as either possessing or lacking introns in both species, and f) possessed at least 100 uniquely mappable nucleotides. Furthermore, we required that the lengths of both orthologs be within 50% of one another and excluded genes that were annotated as having a different number of introns in the Scannell et al. (2011) S. cerevisiae annotation than in the Saccharomyces Genome Database (SGD) annotation available as of 14 August 2012. The Scannell et al. (2011) annotation provides spliced, processed mRNA sequences for each annotated gene, however the positions of introns are not indicated in the genomic annotation files. These were obtained by using BLAT (Kent WJ. 2002. BLAT--the BLAST-like alignment tool. Genome Res 12: 656-664.) to map each species’ mRNA to its respective genome. Intron flanking segments of 84 of the 105 intron containing mRNAs mapped uniquely and were retained for analysis. Finally we eliminated orthologs for LYS2 (Scer_2.299) as its knockout in the S. cerevisiae parental strain was used as a selectable marker as well as CTR3 (Scer_12.598) as it is interrupted by a Ty2 transposon in BY strains of S. cerevisiae. Our final analysis set contained 4,640 orthologs between the two parental species.    Reads from both mRNA and Ribofootprint fractions were mapped to the S. cerevisiae and S. paradoxus genome assemblies of Scannell et al. (2011) in a strand-specific manner using the iterative method described in Ingolia (Ingolia NT. 2010. Genome-Wide Translational Profiling by Ribosome Footprinting. In Methods in Enzymology Vol. 470 [eds. J Weissman, C Guthrie, GR Fink], pp. 119–142. Academic Press, Waltham, Massachusetts.) in order to enrich for ribosome protected fragments and account for spurious adenine (A) bases added to the 3' ends of reads by the oligo-dT mediated reverse transcription. We first excluded any reads that, when trimmed to 23 bases from the 5' end, mapped to the complete rDNA sequence of S. cerevisiae allowing 3 mismatches and a maximum of 20 mapping locations using Bowtie version 0.12 (Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.). Remaining reads from the parental mRNA samples were mapped to their respective genomes allowing no multimappers, and a single mismatch. Mapping reads were filtered such that no more than 30 bp (31 bp if the 3' most base ended with an A), and no less than 27 bp (28 if the 3' most base was an A) from the 5' end of the read mapped uniquely. These were used to reannotate the genome assemblies by identifying nucleotides that were overlapped by at least 10 reads differing at a specific nucleotide with the reference genomes at a frequency >= to 0.8, and that did not introduce nonsense mutations in annotated genes (the absence of true nonsense mutations was confirmed in the five cases where substitutions were detected by the presence of abundant Ribo fraction read coverage 3' of the putative stop codon). This identified 239 and 605 differences between our data and the S. cerevisiae and S. paradoxus assemblies, respectively. Replicate reads from both fractions were then mapped to a concatenation of the updated assemblies, as above, but allowing no mismatches.    S. cerevisiae and S. paradoxus show sufficient divergence at the nucleotide level (~5%) that the 27-30 nt RNA fragments produced by the riboprofiling protocol mapped uniquely to most genomic regions (~87% when accounting for non-unique regions both within and between the two genomes). Therefore, all analyses of coverage were restricted to locations where all possible reads spanning the nucleotide of interest would map uniquely. Non-unique mapping nucleotides were identified by truncating each of the species’ genomes into overlapping 27 bp fragments in single-base increments along each chromosome. These fragments were then mapped back to the concatenation of the two species genomes using Bowtie allowing no mismatches and retaining all reads mapping to more than a single location (multi-mapping reads). Any position in the concatenated genomes that was represented in a multi-mapping 27 bp segment was removed from further analysis. Furthermore, we removed all nucleotides within 27 bp of a splice junction as junction-spanning reads were likely to be underrepresented in our short read lengths. Mapping reads were assigned to genomic locations (CDS, 5' and 3' UTRs, or introns) based on the position of their 5' most base (Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218–223.): CDS, 16 bases upstream of the first nucleotide and 16 bases upstream of the last nucleotide; 5' UTR, first base of the UTR to 17 bases upstream of the stop codon; 3' UTR, 13 bases upstream of the first nucleotide to 15 bases upstream of the last nucleotide; intron, first base of the intron to 8 nucleotides before the last base. Note that our positions differ slightly from those of Ingolia et al. (2009).

organism: Saccharomyces paradoxus

source_name: YPD medium log-phase growth collected

growth_protocol: All samples and replicates were derived from single-colonies grown for at least 16 hours in 750 ml of YPD medium at 30°C and collected during log phase (OD600 0.5 - 0.7).

extract_protocol: Ribosome profiling next-generation sequencing (NGS) libraries were prepared as detailed in [Ingolia NT. 2010. Genome-Wide Translational Profiling by Ribosome Footprinting. In Methods in Enzymology Vol. 470 (eds. J Weissman, C Guthrie, GR Fink), pp. 119–142. Academic Press, Waltham, Massachusetts] with the following modifications: Cryo-grinding of lysates was performed in a Retsch Mixer-Mill MM 301 (Retsch Technology GmbH) at maximum frequency for two 1.5 minute cycles with immersion in liquid N2 before grinding, in between cycles, and following grinding. After purification of the cryo-ground lysate, RNA abundance was determined from the A260 measured using a Nanodrop 2000c (Thermo Scientific) and 1000 µg of RNA was subjected to density gradient centrifugation for monosome isolation. Gradients were fractionated and fractions corresponding to the 80S monosome were collected using a Biocomp Instruments Gradient Station attached to a Foxy Jr Fraction Collector (Teledyne Isco). Total RNA was isolated from the purified lysate using the Epicenter MasterPure™ Yeast RNA Purification Kit beginning with 500 µg of lysate RNA diluted to 125 µl using polysome lysate buffer. Following circularization, the libraries were subjected to an rRNA subtraction step as described in [Brar GA, et al. 2012. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 335: 552–557].

tag: strain

value: S. paradoxus CBS432

tag: ploidy

value: Diploid


title: mRNA lifetime-SiControl-TI-6h D3

description: Poly(A) selected mRNA


title: mRNA lifetime-SiControl-TI-3h D2

description: Poly(A) selected mRNA


title: mRNA lifetime-SiYTHDF2-TI-3h E5

description: Poly(A) selected mRNA


title: lincFoxf1a_E14-5_Lung_10WT

tag: genotype/variation

value: Lung


title: DSQ-RNA-muscle

city: Bei Jing

first: Shilin

last: Tian

address: Xueqing Road

department: genome research

institute: Novogene Bioinformatics Technology CO.ltd

data_processing:
Illumina Casava1.82 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ground tit whole genome using Tophat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ground tit genome assembly (PRJNA179234 available on Mar 1, 2014)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Pseudopodoces humilis

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: muscle


title: mRNA lifetime-SiYTHDF2-TI-0h E4

description: Poly(A) selected mRNA


title: mRNA lifetime-SiYTHDF2-TI-6h E6

description: Poly(A) selected mRNA


title: Ribosome profiling rep2-SiYTHDF2-input-polyA C9

description: Poly(A) selected mRNA

extract_protocol:
Extract by trizol, poly-dT beads pull-down
Truseq small RNA sample prepration kit (illumina)

value: 40nM siRNA knock-down for 48h


title: Ribosome profiling rep2-SiYTHDF2-RPF C8

description: Ribosome-bound mRNA

extract_protocol:
Isolate from surcrose gradient, recovered by trizol
Truseq small RNA sample prepration kit (illumina)


title: Ribosome profiling rep2-SiYTHDF2-input-ribominus C10

description: rRNA removal RNA

extract_protocol:
Extracy by trizol, then rRNA removal
Truseq small RNA sample prepration kit (illumina)


title: mRNA lifetime-SiYTHDF2-TI-0h D4

description: Poly(A) selected mRNA


title: Ribosome profiling rep2-SiControl-input-polyA C6

description: Poly(A) selected mRNA


title: Ribosome profiling rep1-SiYTHDF2-RPF C3

description: Ribosome-bound mRNA


title: Ribosome profiling rep2-SiControl-RPF C5

description: Ribosome-bound mRNA


title: Ribosome profiling rep2-SiControl-input-ribominus C7

description: rRNA removal RNA


title: mRNA lifetime-SiYTHDF2-TI-6h D6

description: Poly(A) selected mRNA


title: Ribosome profiling rep1-SiControl-RPF C1

description: Ribosome-bound mRNA


title: YTHDF2-RIP-input ribominus B4

description: RNA after rRNA removal

extract_protocol:
Extract by trizol, then rRNA removal
Truseq stranded mRNA sample prepration kit (illumina)

value: over-express N-terminal flag-tagged YTHDF2 for 24h(0.75ug plasmid/mL)


title: Ribosome profiling rep1-SiControl-input-polyA C2

description: Poly(A) selected mRNA


title: YTHDF2-RIP-input polyA B3

description: Poly(A) selected mRNA

extract_protocol:
Extract by trizol, then poly-dT beads pull-down
Truseq stranded mRNA sample prepration kit (illumina)

value: over-express N-terminal flag-tagged YTHDF2 for 24h (0.75ug plasmid/mL)


title: YTHDF2-RIP-IP-rep1 B1

description: RNA IP with YTHFD2

extract_protocol:
anti-flag-beads IP, recovered by trizol
Truseq stranded mRNA sample prepration kit (illumina)


title: YTHDF2-RIP-IP-rep2 B2

description: RNA IP with YTHFD2


title: YTHDF2-PAR-CLIP-rep2 A2

description: small RNA fragments crosslinked with YTHDF2

extract_protocol:
fed with 4SU, UV crosslink, partial digested by RNase T1, anti-flag-beads IP, recovered by trizol
Truseq small RNA sample prepration kit (illumina)


title: M3_new-IP-2

first: Dali

department: Department of Chemisty

description: RNA IP against m6A

data_processing:
PAR-CLIP sequencing reads were trimmed of 3’ adaptors. Reads shorter than 13bp were discarded.
Trimmed reads were aligned to human genome hg18 by Bowtie(cite) software. First 36bp were used as seed sequence. Two mismatch were allowed
PARalyzer was used to detect Par-Clip read groups and binding sites.
RNA-seq and m6A-seq reads were aligned to human genome hg18 by Tophat
M6A enriched region were detected by MACS software. RNA-Seq data(no IP, input RNA) in the same condition was used as input information
Genome_build: hg18
Supplementary_files_format_and_content: for each par-clip sample,csv filescontain Par-Clip read groups(*groups) and binding sites(*cluster), Format for groups file:Chromosome,Strand,GroupStart,GroupEnd,GroupID,GroupSequence,ReadCount,ConversionLocationCount,ConversionEventCount; Format for clusters file: Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ModeScore,ConversionLocationCount,ConversionEventCount,NonConversionEventCount
Supplementary_files_format_and_content: for each m6A IP sample,bed files contain m6A enriched peaks. Format:chr start end peakID peakScore

source_name: HeLa

growth_protocol: Human HeLa cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100× Pen Strep (Gibco, 15140).

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.
TruSeq RNA Sample Preparation Kit (Illumina)
refer to specific columns
refer to specific columns

treatment_protocol:
Scrambled control or siRNAs against METTL3, METTL14, and WTAP were transfected into HeLa cells, respectively, by using Lipofectamine RNAiMAX reagent (Invitrogen).
refer to specific columns

tag: technology

tag: sample ip type

value: m6A-antibody (202003; Synaptic Systems)

tag: antibody

tag: antibody manufacturer

value: Synaptic Systems

tag: antibody catalog #

tag: condition

value: M3 knock-down batch2


title: M3_new-Input-1

description: no IP (input RNA)

value: no IP (input RNA)


title: M3_new-Input-2

description: no IP (input RNA)


title: YTHDF2-PAR-CLIP-rep1 A1

tag: treatment


title: Ribosome profiling rep1-SiYTHDF2-input-polyA C4

description: Poly(A) selected mRNA


title: YTHDF2-PAR-CLIP-rep3 A3


title: M3_new-IP-1

description: RNA IP against m6A


title: WTAP-IP-1

description: RNA IP against m6A


title: C_new-Input-2

description: no IP (input RNA)


title: C_new-IP-1

description: RNA IP against m6A


title: C_new-Input-1

description: no IP (input RNA)


title: WTAP-IP-2

description: RNA IP against m6A


title: M14-IP-2

description: RNA IP against m6A

value: M14 knock-down


title: WTAP-Input-1

description: no IP (input RNA)


title: WTAP-Input-2

description: no IP (input RNA)


title: C_new-IP-2

description: RNA IP against m6A


title: M14-IP-1

description: RNA IP against m6A


title: DSQ-RNA-liver

value: liver


title: M14-Input-1

description: no IP (input RNA)

value: HeLa


title: C-IP-2

description: RNA IP against m6A

value: Control


title: C-Input-1

description: no IP (input RNA)


title: Hybrid poly-A selected mRNA fragments replicate 1

description: Poly-A selected mRNA

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

value: S. cerevisiae BY4176 (MAT-alpha lys2 ura::KAN) x S. paradoxus CBS432(MATa ura::HYG)


title: M14-Input-2

description: no IP (input RNA)


title: Hybrid poly-A selected mRNA fragments replicate 2

description: Poly-A selected mRNA


title: C-IP-1

description: RNA IP against m6A


title: C-Input-2

description: no IP (input RNA)


title: Hybrid ribosome protected fragments replicate 2

description: Ribosome protected RNA


title: 6SG-WTAP-1_parClip

description: RNAs bond to WTAP were purified and sequenced by 6SG PAR-CLIP

extract_protocol:
HeLa cells were transfected with the plasmid containing flag-tagged WTAP by using Lipofectamine2000 (Invitrogen). PAR-CLIP was performed as in Hafner et. al 2010 Cell, but with the anti-Flag magetic beads for immunoprecipitation.
TruSeq Small RNA Sample Preparation Kit (Illumina)
refer to specific columns
refer to specific columns

treatment_protocol:
HeLa cells were incubated with 6-thioguanosine (6SG) for 16 h before crosslinking.
refer to specific columns

value: PAR-CLIP

tag: ribonucleoside analog

tag: transfection

value: flag-tagged WTAP

value: WTAP overexpression


title: 6SG-WTAP-2_parClip

tag: cell line


title: Hybrid ribosome protected fragments replicate 1

description: Ribosome protected RNA

value: Diploid


title: 6SG-M14-2_parClip

description: RNAs bond to M14 were purified and sequenced by 6SG PAR-CLIP

extract_protocol:
HeLa cells were transfected with the plasmid containing flag-tagged METTL14 by using Lipofectamine2000 (Invitrogen). PAR-CLIP was performed as in Hafner et. al 2010 Cell, but with the anti-Flag magetic beads for immunoprecipitation.
TruSeq Small RNA Sample Preparation Kit (Illumina)
refer to specific columns
refer to specific columns

value: flag-tagged METTL14

value: M14 overexpression


title: 6SG-M14-1_parClip


title: 6SG-M3-2_parClip

description: RNAs bond to M3 were purified and sequenced by 6SG PAR-CLIP

extract_protocol:
HeLa cells were transfected with the plasmid containing flag-tagged METTL3 by using Lipofectamine2000 (Invitrogen). PAR-CLIP was performed as in Hafner et. al 2010 Cell, but with the anti-Flag magetic beads for immunoprecipitation.
TruSeq Small RNA Sample Preparation Kit (Illumina)
refer to specific columns
refer to specific columns

value: flag-tagged METTL3

value: M3 overexpression


title: 4SU-WTAP-2_parClip

description: RNAs bond to WTAP were purified and sequenced by 4SU PAR-CLIP

treatment_protocol:
HeLa cells were incubated with 4-thiouridine (4SU) for 16 h before crosslinking.
refer to specific columns


title: 4SU-M14-2_parClip

description: RNAs bond to M14 were purified and sequenced by 4SU PAR-CLIP


title: 4SU-WTAP-1_parClip


title: 6SG-M3-1_parClip


title: 4SU-M14-1_parClip


title: 4SU-M3-2_parClip

description: RNAs bond to M3 were purified and sequenced by 4SU PAR-CLIP


title: 4SU-M3-1_parClip


title: Input

status: Public on Nov 28 2013

city: Nijmegen

first: Gert Jan

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

data_processing:
Basecalling was performed using Illumina CASAVA
Filtering was performed using the default Illumina Chastity Filter
Read were aligned to the Xenopus tropicalis genome (version JGI 7.1) using bwa
Genome_build: JGI 7.1
Supplementary_files_format_and_content: BED alignment files were generated from the alignments produced by bwa, duplicates were marked using bamUtil version 1.0.2 and filtered out, all reads mapping to multiple genomic positions were filtered out; _peaks.bed files were produced from the PeakRanger summit file and post-processed to show both region and summit while still being valid BED format, region coordinates are present in column 2 and 3, summit coordinates are present in columns 7 and 8 using the thickStart and thickEnd properties of the BED format; wig files were generated by normalizing experiments between developmental stages per antibody by random removal of reads, extending the reads in the BED file to 300bp and calculating the average number of reads in 10 bp windows.

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 3% cysteine and collected at the indicated stage.

extract_protocol: Embryos (n=300-600) were fixed in 1% formaldehyde for 30 minutes at the indicated developmental stage. Embryos were subsequently washed in 125 mM glycine / 25% Marc's modified Ringer's medium (MMR)  and twice in 25% MMR, homogenized in sonication buffer (20 mM Tris•HCl, pH 8/10 mM KCl/1mM EDTA/10% glycerol/5 mM DTT/0.125% Nonidet P-40, and protease inhibitors), sonicated using a Bioruptor sonicator (Diagenode), centrifuged, and supernatants were frozen. ChIP extract was diluted with IP buffer (50 mM Tris•HCl, pH 8/100 mM NaCl/2mM EDTA/1 mM DTT/1% Nonidet P-40, and protease  inhibitors) and incubated with 1-5 µg of antibody; 12.5 µl Prot A/G beads (Santa Cruz) was added and incubated for 15 hours on a rotating wheel at 4°C. The beads were subsequently washed in ChIP1 buffer (IP buffer plus 0.1% sodium deoxycholate), ChIP2 buffer (ChIP1 buffer with 500 mM NaCl final concentration), ChIP3 buffer (ChIP1 buffer with 250 mM LiCl), ChIP1 buffer, and TE buffer (10 mM Tris, pH 8/1 mM EDTA). The material was eluted in 1% SDS in sodium carbonate, cross-linking was reversed by adding  16 µl NaCl and incubating at 65°C for 5 h, DNA was phenol extracted and    precipitated. The following antibodies were used: α-H3K4me3 (Abcam     ab8580), α-H3K27me3 : (Upstate/Millipore 07-449), α-H3K4me1 (Diagenode CS-037-100), Jarid2 (Abcam ab48137), EZH2 (Active Motif 39103), RNAPII (Diagenode AC-055-100). For all ChIP-seq samples three independent biological replicates of difference chromatin isolations were pooled.

tag: cell type

value: whole embryo

tag: developmental stage

value: tailbud (stage 30)


title: RNAPII_gastrula

value: gastrula (stage 12)

tag: chip antibody

value: RNAPII (Diagenode, AC-055-100)


title: H3K4me1_blastula

value: blastula (stage 9)

value: H3K4me1 (Diagenode CS-037-100)


title: EZH2_blastula

value: EZH2 Active Motif 39103


title: RNAPII_tailbud


title: RNAPII_neurula

value: neurula (stage 16)


title: Jarid2_blastula

value: Jarid2 (Abcam ab48137)


title: H3K4me3_tailbud

value: H3K4me3 (Abcam,  ab8580)


title: H3K4me3_neurula


title: H3K27me3_gastrula

value: H3K27me3 (Upstate/Millipore, 07-449)


title: RNAPII_blastula


title: H3K27me3_tailbud


title: H3K4me3_blastula


title: H3K4me3_gastrula


title: HS578T, input DNA

city: Boston

first: Xiaole

middle: Shirley

last: Liu

state: MA

address: 450 Brookline Avenue, CLS 11007

department: Department of Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute, Harvard School of Public Health

description: treated by hypoxia and glucose deprivation

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with the following parameters: bowtie -S -m 1 *.fastq  *.sam.
Sam format files were converted to bed format; mapped reads of treat and input files were randomly sampled to the same depth.
Mapped reads of ChIP-seq replicates were pre-processed by MACS as instructed by the IDR pipeline. The MACS-identified peaks were integrated using default parameters and reproducible peaks were obtained at IDR cutoff 20%.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using MACS; scores represent tag pileup over each position.Bed files of peak positions were generated by MACS and IDR.

source_name: breast cancer cells

growth_protocol: All breast cancer cells were cultured according to Neve et al. (Cancer Cell 2006). Following retroviral or lentiviral infection, cells were maintained in the presence of puromycin (2 ug/ml) (Sigma).

extract_protocol:
ChIP was performed as previously described by Chen et al. (Cell 2008).
The ChIP-seq library was prepared using ChIP-Seq DNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: For all hypoxia experiments, cells were maintained in an anaerobic chamber (Coy laboratory) with 0.1% O2. For glucose deprivation experiments, cells were maintained in DMEM without glucose medium (Gibco) with 10% FBS (Gibco) and 50 units/ml of penicillin/streptomycin.

value: triple negative breast cancer cells


title: HS578T, XBP1_ChIPSeq, treated by hypoxia and glucose deprivation, biological replicate  2

value: XBP1 (Biolegend, 619502)


title: MDA-MB-231, XBP1_ChIPSeq, treated by hypoxia and glucose deprivation, biological replicate 2


title: T47D, XBP1_ChIPSeq, treated by hypoxia and glucose deprivation, biological replicate  2

value: ER positive breast cancer cells


title: MDA-MB-231, XBP1_ChIPSeq, untreated, biological replicate 2

description: untreated


title: S. cerevisiae poly-A selected mRNA fragments

description: Poly-A selected mRNA

organism: Saccharomyces cerevisiae

value: S. cerevisiae BY4176

value: Haploid


title: H3K27me3_neurula


title: Whole-cell-extract of primed WIBR3 embryonic stem cells

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to hg19 reference genome using bowtie version 1.0.0. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read (flags -a -m 1 --best --strata -v 1)
To rule out sequencing depth bias, the aligned sequences were down-sampled such that all samples had the same number of aligned reads. Human samples of the marks H3K4me3, H3K27me3, H3K4me1 and H3K27ac, as well as whole-cell extract, were down-sampled to include 3,750,000 aligned reads. H3K9me3 samples were down-sampled to 5,900,000 aligned reads.
Peaks were detected with MACS version 1.4.1, with whole-cell-extract used for control
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain enriched peaks detected by MACS version 1.4.1

source_name: hES Cells

growth_protocol: Cells were grown on vitronectin+gelatin or MEF. Rock inhibitor was added 2-24 hours before splitting with trypsin.

extract_protocol:
 Approximately 40 × 106 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature), and then quenched with glycine (5 min at room temperature). Fixed cells were lysed in 50 mM HEPES KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4 °C (Roche), centrifuged at 950g for 10 min and resuspended in 0.2% SDS, 10 mM EDTA, 140 mM NaCl and 10 mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at −4 °C to size ranges between 200 and 800 bp, and precipitated by centrifugation. 10 μg of each antibody was pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 h at room temperature. Beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250 mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65 °C. Eluate was treated sequentially with RNase A (Roche) for 30 min and proteinase K (NEB) for 2 h, and then incubated at 65 °C for 4 h. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881)
140ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed twice on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 100ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 12 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer and KAPA HiFi matermix) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

value: WCE

value: hES Cells


title: H3K9me3 marks of naïve WIBR3 embryonic stem cells

value: anti-H3K9me3 (ab8898, Abcam)


title: H3K27ac marks of primed WIBR3 embryonic stem cells

value: anti-H3K27acetyl (ab4729, Abcam)


title: H3K9me3 marks of primed WIBR3 embryonic stem cells


title: H3K27me3 marks of primed WIBR3 embryonic stem cells

value: anti-H3K27me3 (07-449, Millipore)


title: H3K4me1 marks of primed WIBR3 embryonic stem cells

value: anti-H3K4me1 (ab8895, Abcam)


title: H3K4me3 marks of primed WIBR3 embryonic stem cells

value: anti-H3K4me3 (ab8580, Abcam)


title: Whole-cell-extract of naïve WIBR3 embryonic stem cells


title: H3K27ac marks of naïve WIBR3 embryonic stem cells


title: H3K4me1 marks of naïve WIBR3 embryonic stem cells


title: H3K27me3 marks of naïve WIBR3 embryonic stem cells


title: H3K4me3 marks of naïve BGO1 embryonic stem cells


title: H3K4me3 marks of naïve WIBR3 embryonic stem cells


title: H3K27me3_blastula

value: whole embryo

value: blastula (stage 9)


title: Whole-cell-extract of primed C1 induced stem cells

source_name: iPS Cells

value: iPS Cells


title: H3K27ac marks of naïve BGO1 embryonic stem cells


title: H3K27me3 marks of naïve BGO1 embryonic stem cells


title: Whole-cell-extract of naïve BGO1 embryonic stem cells


title: H3K27ac marks of primed C1 induced stem cells


title: H3K27me3 marks of primed C1 induced stem cells


title: H3K4me3 marks of primed C1 induced stem cells


title: Whole-cell-extract of naïve C1 induced stem cells


title: H3K4me1 marks of primed C1 induced stem cells


title: H3K9me3 marks of naïve C1 induced stem cells


title: H3K9me3 marks of naïve BGO1 embryonic stem cells


title: H3K27ac marks of naïve C1 induced stem cells


title: H3K4me3 marks of naïve C1 induced stem cells


title: H3K27me3 marks of naïve C1 induced stem cells


title: RA1_input_ear_YFP

status: Public on Nov 27 2013

city: St. Louis

first: Andrea

middle: L

last: Eveland

address: 975 N. Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Illumina GAII and HiSeq 2000 sequencing with SR50 were performed by the OSUCCC Nucleic Acid Shared Resource (The Ohio State University)
All image processing and base calling was done with the Illumina Real Time Analysis software as the run progressed.  Binary basecall files were then transferred to a shared Linux server for further processing and archival.  The latest version of the Illumina processing software CASAVA was used to generate fastq files.
ChIP-seq reads were aligned to the maize reference genome (AGPv2) and peak calling was performed with MACS version 1.4.0rc2 using only uniquely mapped reads.  Peaks were identified as significantly enriched (p<1e-05) in each of the ChIP-seq libraries compared to input DNA.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Processed data files are output of MACS.1.4.0.  The peaks.bed file includes (from left to right columns) chromosome, peak start, peak stop, -10*log10(pval).  The summits.bed file includes (from left to right columns) chromosome, summit start, summit stop, tag pileup at summit.

organism: Zea mays

source_name: ear primordia

growth_protocol: Tassel primordia were harvested ~4 weeks after planting, and immature ears were harvested after 6 weeks.  Analysis of plant phenotypes in F1BC2 families segregating for the transgene and ra1 mutants, showed transgenic constructs were capable of complementing the mutant.

extract_protocol:
ChIP preparation were performed as previously described (Bolduc et al. 2012; Morohashi et al. 2012).  Anti-GFP (ab290, Abcam) and anti-HA (H3663, Sigma) antibodies were used for immunoprecipitation of RA1-YFP and RA1-HA, respectively, and protein A agarose/salmon sperm DNA beads (16-157, Millipore) were used to precipitate antibody complexes.
ChIP-seq library preparation were performed as previously described (Bolduc et al. 2012; Morohashi et al. 2012).  ChIP DNA was subjected to end repair and A-base addition, followed by ligation with Illumina adapters made by annealing Mltplx_short and Mltplx_long oligos.  Library amplification was performed by PCR using Phusion Hot Start II High-Fidelity DNA Polymerase (F549L, Thermo Scientific) with MltplxPCR1.0 and PCR2.0_indx1 to 7, followed by gel-size fractionation to obtain 200-500bp fragments.

treatment_protocol: We created two native translational fusion constructs to drive the expression of tagged RA1 proteins in the endogenous expression domain.  We fused the YFP and HA-FLAG tags in frame with the RA1 coding sequence at the N-terminus.  Constructs were transformed into the HiII genetic background at the Iowa State University Plant Transformation Facility (Ames, IA).  T0 generation transformed plants were crossed to the ra1-R mutant.  T1 plants were then backcrossed to create a T2 generation segregating 1:1 for the transgene and for ra1.

tag: transgene

value: input

tag: tissue

value: ear primordia (pool)

tag: genotype

value: ra1/ra1 B73


title: RA1_ChIPseq_ear_YFP

value: YFP


title: ra1_2mm_ear.2

data_processing:
Libraries were quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip, and sequenced using the Illumina GAII platform at the CSHL Genome Center.
All image processing and base calling was done with the Illumina Real Time Analysis software on the HiSeq as the run progressed.  Binary basecall files were then transferred to a shared Linux server for further processing and archival.  The latest version of the Illumina processing software CASAVA was used to generate fastq files.
The Tuxedo suite (Trapnell et al. 2010) was used for mapping and analysis of RNA-seq data.  Tophat (version 1.2.0) was used to align reads to the maize reference genome (AGPv2) based on an a priori set of 110,028 predicted maize gene models (Working Gene Set v5b.60; maizesequence.org).  Cuffdiff (version 1.0.2) was used to analyze differential expression using a high-confidence subset of 39,656 maize gene models, the Filtered Gene Set (FGS v5b.60; maizeseqeunce.org).  Gene-level expression values are represented by Fragments Per Kilobase exon per Million reads mapped (FPKM) and a consensus FPKM was determined for each gene based on its representation across biological replicates (Trapnell et al. 2010).  Further details are provided in Supplemental Methods in associated Eveland et al. paper.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Processed data files from Cufflinks output can be found for each sample - FPKM values at both gene level and transcript isoform level are provided.  Consolidated (combined) files from Cuffdiff output are also provided and give the FPKM values and 95% confidence intervals for expression of each gene across replicates and between developmental stages or genotypes.  All are tab-delimited txt files.

growth_protocol: For the wild-type ear and tassel developmental series, greenhouse-grown B73 inbred plants were used.  For ramosa mutant series, segregating families (1:1) of ra1-R, ra2-R, and ra3-fea1 mutant alleles, all introgressed at least 6 times into the B73 inbred background, were grown at CSHL Uplands Farm.  Field-grown plants were genotyped and collected 6-7 weeks after germination (V7-V8 stage).

extract_protocol:
Total RNA was extracted using the Qiagen RNAeasy kit
RNA-seq libraries were constructed based on methods used in Li et al., Nature Genetics (2008)
RNA-seq libraries are paired end and are not strand-specific

treatment_protocol: Ear and tassel tissues were dissected as described above in "overall design".

value: pool of ra1 mutant ear primordia

tag: Stage

value: ra1/ra1 (in B73)


title: RA1_input_tassel_YFP

source_name: tassel primordia

value: tassel primordia (pool)


title: H3K4me1 marks of naïve BGO1 embryonic stem cells


title: ra1_2mm_ear.1


title: RA1_input_ear_HA


title: ra3_2mm_ear.1

value: pool of ra3 mutant ear primordia

value: ra3/ra3 (in B73)


title: wt_2mm_ear.3

value: pool of B73 ear primordia


title: H3K9me3 marks of primed C1 induced stem cells

value: anti-H3K9me3 (ab8898, Abcam)


title: RA1_ChIPseq_tassel_HA

value: HA


title: RA1_input_tassel_HA


title: RA1_ChIPseq_tassel_YFP


title: ra3_2mm_ear.3


title: ra3_2mm_ear.2


title: ra2_2mm_ear.2

value: pool of ra2 mutant ear primordia

value: ra2/ra2 (in B73)


title: ra2_2mm_ear.3


title: ra2_2mm_ear.1


title: ra1_2mm_ear.3


title: ra3_1mm_ear.2


title: ra1_1mm_ear.2


title: ra2_1mm_ear.1


title: wt_2mm_ear.1


title: wt_2mm_ear.2


title: wt_1mm_ear.2


title: RA1_ChIPseq_ear_HA


title: wt_1mm_ear.1


title: tassel_stg1.2

value: pool of whole B73 tassels (1-2mm)

value: wild-type B73


title: tassel_stg3.1

value: pool of whole B73 tassels (5-7mm)


title: tassel_stg2.1

value: pool of whole B73 tassels (3-4mm)


title: tassel_stg3.2


title: ra1_1mm_ear.1


title: tassel_stg2.2


title: WT day 6 post infection 4

first: Amanda

last: Marchiando

address: 545 First Ave

department: Skirball Institute

institute: NYU School of Medicine

data_processing:
base calling, alignment to mouse reference genome mm9, and gene expression quantification  with Illumina CASAVA v.1.8.2
all genes with expression counts below one base pair per million in the majority of replicates in all treatments have been removed
normalization and differential expression computed with BioConductor package edgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text containing per-gene counts of RNA-seq bases

source_name: colon

growth_protocol: mice were 8 wks old, housed in BSL2 animal facility

extract_protocol:
colon tissue homogenized frozen in trizol, chloroform extraction
TruSeq RNA v2 LS

treatment_protocol: mice were infected with 2x10^9 CFU of C. rodentium at indicated day prior to sacrifice

value: WT

tag: time (dpi)

tag: infection

value: C. rodentium

value: colon

tag: genetic background


title: WT day 6 post infection 2


title: ear_base_FM.2

value: 2mm base of 10mm B73 ear (pool)

value: FM


title: ear_base_FM.1


title: ear_mid_SM.2

value: 1mm middle of 10mm B73 ear (pool)

value: SM


title: WT day 0 post infection 3


title: WT day 6 post infection 1


title: ear_mid_SM.1


title: WT day 15 post infection 3


title: WT day 0 post infection 1


title: ear_tip_IM.SPM.2

value: 1mm tip of 10mm B73 ear (pool)

value: IM/SPM


title: ear_tip_IM.SPM.1


title: WT day 15 post infection 2


title: Atg16L1HM day 15 post infection 3


title: H3K4me1 marks of naïve C1 induced stem cells

value: anti-H3K4me1 (ab8895, Abcam)

value: iPS Cells


title: ra3_1mm_ear.1

value: pool of ra3 mutant ear primordia

value: ra3/ra3 (in B73)


title: Atg16L1HM day 15 post infection 1


title: Atg16L1HM day 6 post infection 2


title: Atg16L1HM day 6 post infection 1


title: ra2_1mm_ear.2

value: pool of ra2 mutant ear primordia

value: ra2/ra2 (in B73)


title: WT day 6 post infection 3


title: WT day 15 post infection 1


title: Atg16L1HM day 15 post infection 2


title: WT_Sucrose_4h_3

city: Berkeley

first: Johan

middle: Philipp

last: Benz

address: 2151 Berkeley Way

department: Energy Biosciences Institute

institute: UC Berkeley

description: Coradetti et al. 2012, PNAS

data_processing:
Libraries were sequenced in SR50 mode on an Illumina HiSeq2000/Illumina Genome Analyzer IIx
Mapping of the reads was done against the current version of the N. crassa OR74A genome (v10) (Galagan et al. 2003) using Tophat v1.2.0 (http://tophat.cbcb.umd.edu/; Langmead et al. 2009).
Transcript abundance was estimated with Cufflinks v0.9.3 in FPKMs (fragments per kilobase of transcript per million mapped reads) using upper quartile normalization and mapping against reference isoforms from the Broad Institute (http://cufflinks.cbcb.umd.edu/; Roberts et al. 2011).
Genes with a multiple-hypothesis adjusted p-value of <0.05 using Cuffdiff where called as significantly differentially expressed between conditions.
Averaged FPKMs of all RNAseq library replicates were hierarchically clustered with the ‘Hierarchical Clustering Explorer’ v3.0 software (http://www.cs.umd.edu/hcil/multi-cluster/hce3.html). Genes with a consistently low expression (<10 FPKMs under all conditions) were not included in the analysis. Data (8664 genes total) were initially normalized row-by-row by standardization (i.e. the deviation from the mean was divided by the standard deviation). The average linkage method (unweighted pair group method with arithmetic mean) was used for cluster generation, with centered Pearson’s correlation as distance/similarity measure. Nodes were arranged with the smaller subtrees kept to the right.
Genome_build: N. crassa OR74A genome (v10)
Supplementary_files_format_and_content: tab-separated values containing the Cufflinks output

organism: Neurospora crassa OR74A

growth_protocol: N. crassa cultures were pre-grown from 10 day-old conidia for 16 hrs at 200 rpm in the light in 100 mL of 1x Vogel’s salts plus 2% (w/v) sucrose using 250 mL shake flasks.

extract_protocol:
Total RNA from fungal mycelia was obtained by bead-beating the tissue with 0.5 mm Zirkonia beads in the presence of TRIzol® (Life Technologies). Total RNA was subsequently DNase treated (Turbo DNA-free; Ambion) and cleaned-up using the Rneasy mini kit (Qiagen).
mRNA was purified from DNase-treated total RNA with Dynabeads® Oligo dT magnetic beads (Invitrogen/Life Technologies). Purified mRNA was fragmented with buffered zinc solution from Ambion (Cat # AM8740). First and second strand cDNA synthesis was carried out using Superscript II Reverse Transcriptase (Invitrogen) and DNA pol I (Invitrogen) and random primers. Illumina sequencing adapters were then ligated to the cDNA, 200bp fragments were purified by gel electrophoresis, and PCR enriched with Pfx DNA polymerase (Invitrogen).

treatment_protocol: To ensure optimal comparability, transfer assays were performed following the procedures described in Coradetti et al. (2012) and Znameroski et al. (2012). The mycelia (16 hr culture) were washed three times in 1x Vogel’s salts without added carbon (NoC) and transferred to 1% (w/v) pectin/OPP or 2% xylan for induction. After an additional 4 hours, the mycelial mass was harvested over a Whatman glass microfiber filter (GF/F) on a Buchner funnel and subsequently flash-frozen in liquid nitrogen to be stored at −80 °C.

tag: strain

value: FGSC 2489

value: mycelia

tag: time after media shift

value: 4 hours

tag: carbon source

value: 2% Sucrose


title: tassel_stg1.1

value: pool of whole B73 tassels (1-2mm)

value: wild-type B73


title: Atg16L1HM day 6 post infection 3

value: C. rodentium

value: colon


title: Atg16L1HM day 0 post infection 3


title: WT_No_Carbon_4h_1

description: Coradetti et al. 2012, PNAS

value: No Carbon


title: WT_No_Carbon_4h_2

description: Coradetti et al. 2012, PNAS


title: WT day 0 post infection 2

value: WT


title: Atg16L1HM day 0 post infection 2


title: Atg16L1HM day 0 post infection 1


title: WT_Pectin_4h_1

description: this study

value: 1% Pectin


title: WT_Pectin_4h_3

description: this study


title: WT_OPP_4h_2

description: this study

value: 1% Orange peel powder


title: WT_No_Carbon_4h_3

description: Coradetti et al. 2012, PNAS


title: WT_Avicel_4h_3

description: Coradetti et al. 2012, PNAS

value: 2% Avicel (microcrystalline cellulose)


title: WT_Avicel_4h_2

description: Coradetti et al. 2012, PNAS


title: WT_OPP_4h_1

description: this study


title: Fetal liver E11.5 Flt3-IL7R- 3

status: Public on Nov 26 2013

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

data_processing:
Alignment by Bowtie (version 0.12.7, option –best) to genome and exon-exon junctions.
Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
Gene expression levels for Refseq transcripts were summarized as reads per kilobase of exon model per million mapped reads (RPKM) and read counts using Rpkmforgenes (Ramskold et al., 2012)
Genome_build: mm9

source_name: Fetal liver, embryonic day 11.5

extract_protocol:
cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".
NEBNext® DNA Library Prep Reagent Set for Illumina®

treatment_protocol: Cell populations isolated by FACS sorting from murine yolk sac, fetal liver or adult bone marrow

value: Fetal liver progenitor

tag: genotype/variation

value: wild type

tag: phenotype


title: Fetal liver E11.5 Flt3-IL7R- 2


title: WT_Sucrose_4h_2

description: Coradetti et al. 2012, PNAS


title: WT_Sucrose_4h_1

description: Coradetti et al. 2012, PNAS


title: WT_Avicel_4h_1

description: Coradetti et al. 2012, PNAS


title: Fetal liver E11.5 Flt3+IL7R+ 3


title: Atg16L1HM day 6 post infection 4

city: New York


title: Fetal liver E11.5 Flt3-IL7R- 1


title: Fetal liver E11.5 Flt3+IL7R+ 2


title: WT_Xylan_4h

description: this study

value: 2% Xylan


title: Fetal liver E10.5 Rag1GFP+IL7R+ 3

source_name: Fetal liver, embryonic day 10.5


title: Yolk sac E9.5 Rag1GFP+Il7R+ 3

source_name: Yolk sac embryonic day 9.5

value: Yolk sac progenitor


title: Fetal liver E10.5 Rag1GFP+IL7R+ 2


title: Yolk sac E9.5 Rag1GFP+Il7R+ 2


title: Yolk sac E9.5 Rag1GFP-Il7R- 2


title: Yolk sac E9.5 Rag1GFP-Il7R- 3


title: Adult BM proB2

source_name: Adult BM

value: Adult bone marrow progenitor


title: Fetal liver E10.5 Rag1GFP-IL7R- 1


title: Adult BM CLP3


title: Yolk sac E9.5 Rag1GFP+Il7R+ 1


title: WT_Pectin_4h_2

description: this study

value: FGSC 2489

value: mycelia


title: Yolk sac E9.5 Rag1GFP-Il7R- 1


title: Adult BM proB3


title: Fetal liver E11.5 Flt3+IL7R+ 1


title: RNA_R_DL23_4OHT8h_Rep2

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin, 2009). Non-uniquely placed reads were discarded.
Cisgenome v2.0 software package was used to calculate reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values for all RefSeq annotated genes.
Genome_build: hg19
Supplementary_files_format_and_content: alignment file (chr;start;end;strand)

source_name: DL23 cell line with pcDNA3-HA-FOXO33-ER

growth_protocol: DLD1 and DLD1-F3 cells were grown on RPMI-1640 medium with 10% FCS and standard supplements

extract_protocol:
Sequencing libraries were constructed using SOLiD® Total RNA-Seq Kit (Life technologies) according to the standard protocol recommendations for low input and sequenced on SOLiD sequencer in a multiplexed way to produce 50-bp long reads.
rRNA was depleted using Ribominus (Life Technologies)

value: DL23 cell line with pcDNA3-HA-FOXO33-ER

tag: molecule subtype

value: Ribosome depleted total RNA


title: Fetal liver E10.5 Rag1GFP-IL7R- 2


title: RNA_DL23_nt_Rep2

extract_protocol:
Sequencing libraries were constructed using SOLiD® Total RNA-Seq Kit (Life technologies) according to the standard protocol recommendations for low input and sequenced on SOLiD sequencer in a multiplexed way to produce 50-bp long reads.
To isolate polyadenylated and capped RNA, total RNA was purified using Poly(A)Purist MAG Kit (Life Technologies) according to manufacturer's instructions. Isolated RNA was subsequently re-purified using mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre).

tag: cell line


title: Adult BM LMPP3


title: Fetal liver E10.5 Rag1GFP+IL7R+ 1


title: Adult BM LMPP2


title: Adult BM HSC2

value: Adult bone marrow stem cell

value: LSK CD150+CD48-


title: Adult BM HSC3


title: BXM 10DAP

city: Tucson

first: Xiangfeng

address: 1140 E. South Campus Drive, Marley Building 541C

department: School of Plant Sciences

institute: University of Arizona

data_processing:
Illumina RTA software used for basecalling.
Raw sequence reads were processed into clean full-length reads using the BGI small RNA pipeline. First, all low-quality reads were removed from the raw sequence, and the 3' adapter reads, 5' adapter contaminants, sequences containing the polyA tail and those smaller than 18 nt were also discarded. The remaining high-quality sequences were counted, and the unique sequences with their associated read counts were mapped to the maize genome to infer siRNA loci.
Genome_build: ZmB73_RefGen_v2.tar.gz
Supplementary_files_format_and_content: Compressed tab-delimited text files include counts and length for each sequence

source_name: maize

growth_protocol: Maize B73 and Mo17 inbred lines were grown under greenhouse conditions. Reciprocal crosses and self-pollination were performed as follows: the ears were bagged before silking; when the silks grew to approximately 2 to 3 cm long, the ears were cut at 2cm from the top and the tassels were bagged. Pollination was conducted on the next day using the corresponding pollen. The un-pollinated kernels (0-DAP) and the kernels from the reciprocal crosses of B73 and Mo17 at 3, 5, 7, 10, and 15-DAP were harvested. Endosperm tissues from the 7, 10, and 15-DAP kernels were manually isolated. The endosperm and kernel were harvested from three different ears as three biological replicates and were immediately frozen in liquid nitrogen.

extract_protocol:
The total RNA was isolated from the 36 (12 samples × 3 replicates) groups of plant material using the Trizol method according to the manufacturer’s instructions.
18-30 nts RNAs were gel-purified from total RNA sample, Illumina 5’ and 3’ RNA adapter were sequentially ligated to the RNA fragments and the ligated products were size-selected on denaturing polyacrylamide gels. The adapter-linked RNA was reverse transcribed with small RNA RT primers and amplified with 15 cycles of PCR using small RNA PCR primer 1 and 2 (Illumina). The libraries were sequenced with the Illumina Genome Analyzer.

value: endosperm

tag: age


title: MXB 7DAP


title: RNA_R_DL23_nt_Rep1


title: RNA_R_DL23_nt_Rep2


title: SNP

city: Tai'an

first: Zhongxi

last: Gao

address: Daizong street no. 61

institute: Shandong Agricultural University

data_processing:
Illumina RTA 1.13.48 software used for basecalling.
*_TagCopyNumber.txt: Extraction of tags and tag counting were performed using the Illumina pipeline. To get the high quality tags that we used to analysis, we filtered the potentially erroneous tags (only one copy number, only adaptor sequences, or containing unknown sequences 'N') to get the clean tags. For mapping the clean tags to reference sequences, we get all the possible 17 bases length sequences next to the NlaIII restriction site of the reference sequences, then plus the 4 bases NlaIII recognition site to construct a reference database. The clean tag expression was normalized to TPM (transcripts per million clean tags).
Clean tags were mapped to cucumber genome V1 and the tags mapped to one gene were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM to better measure gene expression level. The genes were analyzed by searching the protein databases nr using blastx (evalue < 0.00001) program. and further analyzed with Blast2go to get GO annotations.
Genome_build: Cucumber genome V1 (http://www.ncbi.nlm.nih.gov/assembly/GCA_000004075.1/)
Supplementary_files_format_and_content: xls files containing gene accession gene expression level, GO analysis, blast nr, mapped-tag and its number.

organism: Cucumis sativus

source_name: NaHCO3 + SNP-treated cucumber leaves

growth_protocol: Cucumber plants were grown in a greenhouse at a cycle of 16 h light and 8 h dark.

extract_protocol:
Samples from Na- and SNP-treated leaves were harvested and immediately frozen in liquid nitrogen, and stored at -80°C. Total RNA was isolated from the frozen leaf with an RNA simple Total RNA Kit (TIANGEN, Beijing, China) according to the manufacturer’s instructions. For DGE profiling, the two individual tag libraries of samples (Na sample and SNP sample) were constructed in parallel. Sequence tags were prepared using Illumina Gene Expression Sample Prep Kit following the manufacturer's instructions. Magnetic beads with oligo(dT) were used to purify poly(A)-containing mRNA and oligo-dT primer was used to sythesize double-stranded cDNA. The bead-bound cDNAs were then digested by endonuclease NlaIII, which recognizes and cuts CATG sites, to generate sticky 5' ends. The cut-off fragments were washed away and the bead-bound fragments were ligated to the Illumina adaptor 1 through the sticky 5' end. The bead-bound fragments with adaptor 1 were then digested by MmeI, which cuts at 17bp downstream of CATG site. After that, the bead-bound fragments without adaptor 1 were removed by magnetic beads precipitation, and the tags with adaptor 1 were purified and ligated to Illumina adaptor 2 through the 3' end of the tag. After 15 cycles of linear PCR amplification, 95bp fragments were purified by 6% TBE polyacrylamide gel electrophoresis to obtain the final tag libraries. After denaturation, the single-stranded DNAs were fixed onto the Illumina Sequencing Chip (flowcell). Four types of nucleotides labeled by four colors were used and sequencing was performed with the method of sequencing by synthesis (SBS) using Illumina HiSeqTM 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jinchun 5

value: leaves

tag: time

value: 12d after treatment

tag: treatment

value: NaHCO3 plus SNP


title: RNA_DL23_4OHT_8h_Rep1


title: MXB 5DAP

value: kernel


title: MXB 10DAP


title: BXM 15DAP


title: Adult BM CLP2


title: BXM 5DAP


title: RNA_DL23_nt_Rep1


title: CHIP_DL23_nt_H3

extract_protocol:
Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD sequencer to produce 50-bp long reads.
4-hydroxy-tamoxifen (4OHT) from Sigma, was dissolved in ethanol and added to cells at a final concentration of 1uM. Cells were treated with PKB inhibitor VIII (Santa Cruz) at a concentration of 10uM. Cells were grown in the absence or 4 hour presence of 4OHT or PKB inhibitor. Three independent batches of chromatin were obtained for all three conditions and mixed, with a total of 80x106 cells per IP. IPs were performed for 16h with the following antibodies: 2.5 ug of H3K4me1, H3K4me3 and H3K27ac and total H3 from Abcam (ab8895, ab8580 and ab4729, ab1791) and 16ug of αFOXO3 (Santa Cruz, H144) for the FOXO3-ER (2) ChIP-seq. The second H3K27ac(2) ChIP-seq was performed on an independent fourth batch of chromatin.

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: MXB15DAP

tag: tissue


title: Fetal liver E10.5 Rag1GFP-IL7R- 3

value: Fetal liver progenitor


title: BXM 7DAP


title: CHIP_DL23_nt_H3_H3K27ac


title: CHIP_DL23_nt_H3_H3K4me1


source_name: NaHCO3-treated cucumber leaves


title: CHIP_DL23_4OHT_4h_H3K4me3


title: CHIP_DL23_4OHT_4h_H3K4me1


title: RNA_DL23_4OHT_8h_Rep2


title: MXB 0DAP


title: BXM 0DAP


title: CHIP_DL23_4OHT_4h_H3K27ac


title: FAIRE_DL23_nt

extract_protocol:
library strategy: FAIRE-seq
Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD sequencer to produce 50-bp long reads.
FAIRE sample was generated from 10x106 DLD1-F3 cells as described in detail (Simon et al., 2012). Briefly, cells were crosslinked in 1% formaldehyde (for 5 minutes at room temperature), lysed, collected in buffer with protease inhibitors (Roche) and dounced with a tight pestle. Nuclei were collected through centrifugation, lysed and DNA was sheared using Biorupter Sonicator. FAIRE DNA was obtained through phenol/chloroform/isoamyl alcohol and chloroform/isoamyl (SIGMA) extraction. DNA was treated with DNase-free RNase and proteinase K (Ambion), decrosslinked overnight at 65C and purified with Qiaquick PCR purification kit (Qiagen).


title: CHIP_DL23_nt_H3_H3K4me3


title: RNA_R_DL23_4OHT8h_Rep1


title: BXM 3DAP


title: SMRT ChIPSeq 5PM (ZT10)

status: Public on Nov 25 2013

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequencing and alignment: Sequencing was done by the Functional Genomics Core at the University of Pennsylvania. Sequence reads were processed and mapped to the mouse genome (mm8) using ELAND pipeline. Before subsequent analysis, edundant reads in each genomic position were condenced into one to avoid possible PCR bias or each sample.
Peak Calling: Peak calling was performed by Homer with default parameters then 1rpm cut-off was applied, where all the redundant reads per position were condensed into one.
Genome_build: mm8
Supplementary_files_format_and_content: peaks

source_name: liver

growth_protocol: Mice were fed ad libum and euthanized at 5 pm (ZT10) and 5 am (ZT22).

extract_protocol:
Whole cell lysates were prepared from cross-linked livers. After sonication, histone-DNA complexes were immunoprecipitated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP Seq DNA Sample Prep Kit (Illumina IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment involved.

value: liver

value: SMRT

tag: chip antibody manufacturer

tag: chip antibody catalog #


title: H3K9ac ChIPSeq HEBI_cohort2

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

description: H3K9ac ChIPSeq HEBI_cohort2

data_processing:
ChIP-seq reads were aligned to the mm8 genome assembly using Bowtie version 0.12.8 with the following configurations: -n 1 -l 30 -m 1.
Peaks were called using HOMER v4.2 with FDR 0.1%.
Genome_build: mm8
Supplementary_files_format_and_content: BigWig files were preduced by HOMER v4.2 using default parameters.

source_name: H3K9ac ChIPSeq HEBI_cohort2

growth_protocol: Adult male HDAC3 floxed mice were intravenously injected with adeno-associated virus (AAV) expressing Cre along with AAV expressing the indicated HDAC3 mutants.

treatment_protocol: Mice were fed ad libum and euthanized at 2-weeks after injection at 5 pm (ZT10).

tag: antibody

value: H3K9ac Millipore 06-942 lot#1973414


title: H3K9ac ChIPSeq WT_cohort2

description: H3K9ac ChIPSeq WT_cohort2

source_name: H3K9ac ChIPSeq WT_cohort2

tag: strain


title: H3K9ac ChIPSeq Cre_cohort2

description: H3K9ac ChIPSeq Cre_cohort2

source_name: H3K9ac ChIPSeq Cre_cohort2


title: SMRT ChIPSeq 5AM (ZT22)


title: H3K9ac ChIPSeq Cre_cohort1

description: H3K9ac ChIPSeq Cre_cohort1

source_name: H3K9ac ChIPSeq Cre_cohort1


title: H3K9ac ChIPSeq WT_cohort1

description: H3K9ac ChIPSeq WT_cohort1

source_name: H3K9ac ChIPSeq WT_cohort1