title: ung1 UDG + 5-FU Postdigestion Beseq

status: Public on May 15 2014

city: Aurora

first: Jay

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description: BE-seq

data_processing:
Reads were aligned to theUCSC sacCer1 genome using bowtie2
BAM alignment files were processed to genome coverage in bedGraph format using bedtools
bedgraph files were displayed in the UCSC Genome Browser
Genome_build: sacCer1, E. coli K12
Supplementary_files_format_and_content: Genome coverage in bedGraph format

source_name: S. cerevisiae

growth_protocol: Yeast cells were grown in YEPD at 30˚ to an OD600 ~1.0

extract_protocol:
genomic DNA was isolated using SDS and proteinase K followed by RNAseA treatment and DNA precipitation
genomic DNA was treated with Beseq enzymes as stated for samples above.  Samples were treated with NEB end repair kit.  Samples were A-tailed using Klenow exo- from Enzymatics.  Samples were ligated with Illumina Truseq adapters using Enzymatics T4 DNA ligase.  Samples were size selected with Invitrogen size select gels.  Samples were PCR amplified using barcoded Illumina Truseq primers and Ampure bead purified.  Samples were quantitated with Qubit before sequence submission.

treatment_protocol: Cells were arrested in S-phase with alpha factor

value: MATalpha can1∆::STE2pr-Sp_his5 lyp1∆ ura3∆0 leu2∆0 his3∆1 met15∆0 ung1::natMX dut1-1::URA3

tag: enzyme treatment

value: UDG-New England Biolabs, Y7092 starter strain from Dr. C. Boone


title: ung1 UDG Postdigestion DNA control

type: SRA

middle: R.

country: USA

description: BE-seq

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

tag: strain

value: MATalpha can1∆::STE2pr-Sp_his5 lyp1∆ ura3∆0 leu2∆0 his3∆1 met15∆0 ung1::natmx


title: Afu UDG Predigestion Beseq replicate 2 (BG234)

description: BE-seq

value: MATa leu2-3-112 trp1-289 his7-2 ura3-52 lys1-1 ade2∆ dut1-1 ung1∆::URA3 bar1Δ::kanMX hENt::LEU

value: UDG-New England Biolabs, yeast strain from Dr. S. Boiteux


title: Afu UDG Predigestion Beseq replicate 1 (Y7092)

description: BE-seq


title: 6-4pp Beseq replicate 2

description: BE-seq

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 bar1Δ::LEU2

value: UVDE-lab generated and A. thaliana 6-4 photolyase from Dr. Zhong


title: CPD Beseq replicate 2

description: BE-seq

value: UVDE-lab generated and  E.coli CPD from Dr. Zhong


title: batch5_chrom2_LoVo_IgG_Mouse_control

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4

organism: Homo sapiens

source_name: LoVo

growth_protocol: LoVo (ATCC CCL-229) colon adenocarcinoma cells were cultured in DMEM supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol:
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.
Libraries were constructed according to Illuminas standard protocol. The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane. Sequencing was performed using one lane of Illumina GAIIx, or alternatively, samples were indexed with DNA barcodes and four to six different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads).

tag: cell line

value: LoVo

tag: cell type

value: colon adenocarcinoma

tag: antibody

value: mouse IgG :Santa Cruz Biotechnology, Inc. :sc-2025

tag: sample type

value: control


title: CPD Beseq replicate 1

description: BE-seq

value: UVDE-trevigen  Vibrio cholera CPD from Dr. Sancar


title: batch5_chrom2_LoVo_IgG_Goat_control

value: goat IgG :Santa Cruz Biotechnology, Inc. :sc-2028


title: batch5_chrom2_LoVo_IgG_Rabbit_control

value: rabbit IgG :Santa Cruz Biotechnology, Inc. :sc-2027


title: batch5_chrom1_LoVo_IgG_Goat_control


title: batch5_chrom1_LoVo_IgG_Rabbit_control


title: batch5_chrom1_LoVo_IgG_Mouse_control


title: batch4_chrom3_LoVo_IgG_Goat_control


title: batch4_chrom2_LoVo_IgG_Rabbit_control


title: batch4_chrom3_LoVo_IgG_Rabbit_control


title: batch3_chrom2_LoVo_IgG_Mouse_control


title: batch3_chrom2_LoVo_IgG_Goat_control


title: batch4_chrom1_LoVo_IgG_Mouse_control


title: batch4_chrom2_LoVo_IgG_Mouse_control


title: batch4_chrom1_LoVo_IgG_Rabbit_control


title: batch4_chrom3_LoVo_IgG_Mouse_control


title: batch3_chrom1_LoVo_IgG_Rabbit_control


title: batch3_chrom2_LoVo_IgG_Rabbit_control


title: batch3_chrom1_LoVo_IgG_Goat_control


title: batch3_chrom1_LoVo_IgG_Mouse_control


title: Corrected-FA NSCs

city: La Jolla

first: Nongluk

last: Plongthongkum

state: California

address: 9500 Gilman Drive, MC0412, PFBH402

department: Bioengineering

institute: University of California, San Diego

data_processing:
The libraries were sequenced by Illumina HiSeq2000. Illumina OLB was used for base-calling.
Adaptor sequences (27bp from 5' end) were trimmed from bisulfite reads prior to mapping
Bisulfite reads were single-end mapped using the protocol from Diep et al, Nature Methods 2012. Briefly, all 'C's were replaced by 'T's in reads and mapped to a reference with all 'C's converted to 'T's. After mapping, the modified reads were replaced by the original reads then pileup files were generated using SAMTOOLS
Methylation levels were calculated as the number of cytosines over the total thymines and cytosines for CpGs.
CpG sites with at least 10 depth of coverage were reported in final processed file (BED format)
Genome_build: hg19
Supplementary_files_format_and_content: BED formated (tab-delimited) text files include chromosome position and methylation fraction value for each CpG in each subject

source_name: gene-corrected Fanconi Anemia neural stem cells

growth_protocol: Cultures were  maintained in Neural Stem cell Maintenance Medium (NSMM) containing 50% Advanced DMEM/F12, 50% Neurobasal, 1x N2, 1x B27, 2 mM GlutaMAX, 10 ng/mL hLIF, 3 μM CHIR99021, and 2 μM SB431542

extract_protocol:
Genomic DNA was extracted from the cell pellet using QIAGEN DNeasy Blood and Tissue kit. Approximately 1 µg of genomic DNA was bisulfite converted with Zymo EZ DNA Methylation-Lightning kit
Bisulfite padlock probes capture and sequencing (Diep et al, 2012). Briefly,  approximately 250ng of bisulfite converted genomic DNAs were mixed with normalized amount of genome-wide scale padlock probes and oligo suppressors. The padlock probes annealing to targets were polymerized and ligated resulting in circularized DNA. The bisulfite sequencing libraries were generated by library-free BSPP protocol as described (Dinh et al. 2012). Two-thirds of the circularized DNA of each captured reaction were directly amplified and barcoded. The bisulfite sequencing libraries were purified with AMPure magnetic beads, pooled in equimolar ratios, size selected with 6% polyacrylamide gel, and sequenced by Illumina HiSeq (paired-end 110bp)

value: iPSC-derived neural stem cells


title: WT NSCs

source_name: wild type neural stem cells


title: Hela cell CFIm25 knock down rep1

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

library_source: transcriptomic

data_processing:
Uniquely aligned to the reference genome using TopHat 2.0.10 with provided Ensembl GTF gene annotation
Calculate the coverage Wig/bedgraph file based on Aligned BAM files using tool wiggles from TopHat package
Genome_build: hg19
Supplementary_files_format_and_content: Read coverage Wig/bedgraph files for 4 samples

molecule: total RNA

source_name: Hela

extract_protocol:
RNA was isolated using TriZol reagent and ~10 ug was submitted to LC Sciences for Sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: CFIm25 knockdown

value: HeLa


title: FA NSCs

source_name: Fanconi Anemia neural stem cells


title: Hela cell wild type rep2


title: Hela cell wild type rep1


title: Hela cell CFIm25 knock down rep2


title: E. coli UDG Predigestion Beseq (normalized)

description: BE-seq

organism: Escherichia coli

source_name: E. coli

value: CJ236:FΔ(HindIII)::cat (Tra+ Pil+ CamR)/ ung-1 relA1 dut-1 thi-1 spoT1 mcrA

value: CJ236 from New England Biolabs


title: HCT116_GROseq_DMSO_30min_p53+/+

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

description:
nascent RNA
GROseq

data_processing:
Two biological replicates of Nutlin-treated and DMSO-treated (control) samples were combined.
Reads were mapped to the human genome (hg19 downloaded from bowtie website) using bowtie (version 0.12.7) with the command bowtie -S -t -v 2 –-best.
sam file  was then processed by samtools view -bS –o and samtools sort to create a sorted bam file (version 0.1.16).
Calculations were done exactly as in (Core et al., 2008) unless otherwise noted. Gene annotations (hg19) were downloaded from: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz .
RefSeq genes shorter than 1 kb were not used except for microRNAs, whose coordinates were expanded by 500 on both sides. Number of reads in the gene body (1kb from transcription start site (TSS) to the end of the annotation) and number of reads around the promoter (-100 to +400 bp from annotated TSS) were counted by the program coverageBed v2.12.0. A program to calculate fpkm, pausing indexes, gene activity, and promoter activity was written and run on python 2.6. Fisher’s exact test was done using the python module fisher 0.1.4 downloaded from https://pypi.python.org/pypi/fisher/. Genes that are differentially expressed were determined in R version 2.13.0 using DEseq v1.4.1 (Anders and Huber, 2010). Settings for DEseq were cds <- estimateSizeFactors( cds ), method='blind', sharingMode='fit-only'. Genes were called as differentially transcribed if they had an adjusted p-value less than or equal to 0.1.  Manual curation was used to choose the most parsimonious isoform for the Nutlin versus control (DMSO) comparisons. For genes only differentially expressed across cell lines, we utilized the isoform with the highest fold change (p53+/+ control versus p53 -/- controls).  For all other genes we used the isoform identifier with the highest fold change between p53+/+ control and p53+/+ Nutlin.
Genome_build: hg19
Supplementary_files_format_and_content: bed files, but with many many more columns including fpkms for every gene body, read counts for every gene body, pausing indexs(2 methods of calculating), divergance indexs (2 methods of calcualting), distance from a chip-seq site, microarray data and more.
Supplementary_files_format_and_content: coverageBed from Bedtools:
Supplementary_files_format_and_content: 1. chromosome
Supplementary_files_format_and_content: 2. start
Supplementary_files_format_and_content: 3. stop
Supplementary_files_format_and_content: 4. name
Supplementary_files_format_and_content: 5. The number of reads in region.
Supplementary_files_format_and_content: 6. The number of bases in region which had a read.
Supplementary_files_format_and_content: 7. The length of the region.
Supplementary_files_format_and_content: 8. The fraction of bases in region which had a read.

growth_protocol: HCT116 cells were grown in McCoys 5A media and passaged two days in a row prior to treatment. We found passaging HCT116 cells twice before the experiment resulted in less clumping of the cells and therefore better nuclei isolation.

extract_protocol: Nuclei were isolated, nuclear run on was preformed with BrUTP, RNA was isolated using trizol, RNA was hydrolized with NaOH to a average size of 200, DNAse treated and anartic Phosphate was used to remove  5´ phosphate groups. Nascent RNA was IP with anti-BrdU, then poly A tail was added to the RNA. 3' phosphates were removed using T4 PNK. The RNA was then IP again. RNA was reverse transcribed, size selected (200-650bp), circularized, relinerized, PCRed, again size selected, and sent to the Illumina HiSeq2000 instrument for 50bp read sequencing.

treatment_protocol: Cells were plated at a concentration of 10 x 106 on 15 cm plates and treated 24 hours later with media containing either Nutlin-3a (10μM) or the equivalent amount of vehicle (DMSO) for 1 hour or 30 min.

value: DMSO

value: Santa Cruz anti-BrdU beads sc-32323-ac

tag: genotype

value: wild type


title: HCT116_GROseq_Nutlin_30min_p53+/+

description:
nascent RNA
GROseq

value: Nutlin


title: HCT116_GROseq_Nutlin_p53-/-

description:
GROseq
eRNAmaster042513marked042513.txt
master040413.txtplusdeseqmicroarray091113.txtmarked092313.txt1groseqpername_maxfcnutlinoverdmso.txt
master040413.txtplusdeseqmicroarray091113.txtmarked092313.txt

data_processing:
Two biological replicates of Nutlin-treated and DMSO-treated (control) samples were combined.
Reads were mapped to the human genome (hg19 downloaded from bowtie website) using bowtie (version 0.12.7) with the command bowtie -S -t -v 2 –-best.
sam file  was then processed by samtools view -bS –o and samtools sort to create a sorted bam file (version 0.1.16).
Calculations were done exactly as in (Core et al., 2008) unless otherwise noted. Gene annotations (hg19) were downloaded from: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz .
RefSeq genes shorter than 1 kb were not used except for microRNAs, whose coordinates were expanded by 500 on both sides. Number of reads in the gene body (1kb from transcription start site (TSS) to the end of the annotation) and number of reads around the promoter (-100 to +400 bp from annotated TSS) were counted by the program coverageBed v2.12.0. A program to calculate fpkm, pausing indexes, gene activity, and promoter activity was written and run on python 2.6. Fisher’s exact test was done using the python module fisher 0.1.4 downloaded from https://pypi.python.org/pypi/fisher/. Genes that are differentially expressed were determined in R version 2.13.0 using DEseq v1.4.1 (Anders and Huber, 2010). Settings for DEseq were cds <- estimateSizeFactors( cds ), method='blind', sharingMode='fit-only'. Genes were called as differentially transcribed if they had an adjusted p-value less than or equal to 0.1.  Manual curation was used to choose the most parsimonious isoform for the Nutlin versus control (DMSO) comparisons. For genes only differentially expressed across cell lines, we utilized the isoform with the highest fold change (p53+/+ control versus p53 -/- controls).  For all other genes we used the isoform identifier with the highest fold change between p53+/+ control and p53+/+ Nutlin.
Genome_build: hg19
Supplementary_files_format_and_content: bed files, but with many many more columns including fpkms for every gene body, read counts for every gene body, pausing indexs(2 methods of calculating), divergance indexs (2 methods of calcualting), distance from a chip-seq site, microarray data and more.

extract_protocol:
Trizol
Nuclei were isolated, nuclear run on was preformed with BrUTP, RNA was isolated using trizol, RNA was hydrolized with NaOH to a average size of 200, DNAse treated and anartic Phosphate was used to remove  5´ phosphate groups. Nascent RNA was IP with anti-BrdU, then poly A tail was added to the RNA. 3' phosphates were removed using T4 PNK. The RNA was then IP again. RNA was reverse transcribed, size selected (200-650bp), circularized, relinerized, PCRed, again size selected, and sent to the Illumina HiSeq2000 instrument for 50bp read sequencing.

treatment_protocol: Cells were plated at a concentration of 10 x 106 on 15 cm plates and treated 24 hours later with media containing either Nutlin-3a (10μM) or the equivalent amount of vehicle (DMSO) for 1 hour.


title: UDG Postdigestion Beseq

description: BE-seq

value: MATa leu2-3-112 trp1-289 his7-2 ura3-52 lys1-1 ade2∆ dut1-1 ung1∆::URA3 bar1Δ::kanMX hENt::LEU

value: UDG-New England Biolabs, yeast strain from Dr. S. Boiteux


title: HCT116_GROseq_DMSO_p53+/+


title: UDG Predigestion Beseq

description: BE-seq

value: UDG-New England Biolabs, yeast DNA from Dr. S. Boiteux


title: 008CHep3BpolyARNA

city: Oakland

first: Elizabeth

last: Theusch

state: CA

address: 5700 Martin Luther King Jr Way

institute: CHORI

data_processing:
Base calling was performed with CASAVA.
100 bp paired-end reads were concatenated and duplicate fragments were removed before being split back into 100bp pairs.
Reads were aligned to hg19 using Tophatv2.0.4 with Ensemblv67 reference transcriptome allowing 4 mismatches.
Novel splice junctions were identified by comparing Tophat output with known gene annotations.
Genome_build: hg19
Supplementary_files_format_and_content: The junctions.bed file is a bed file format showing all of the splice junctions observed in the RNA-seq library and the number of reads crossing each junction.

molecule: polyA RNA

source_name: Hep3B cells

extract_protocol:
Cells were homogenized using QIAshredders (QIAGEN), and total RNA was extracted using the PureLink® RNA Mini Kit (Life Technologies). mRNA was isolated through two rounds of purification from 10mg total RNA using the MicroPoly(A)Purist Kit (Ambion)
A paired-end RNA-seq library was prepared following Illumina’s protocol with a few modifications. RNA fragmentation time was reduced from 5 minutes to 30 seconds to obtain a longer library fragment size.  cDNA was synthesized using random primers, and after end repair, dA-tailing, adapter ligation and gel purification of ~450bp fragments, libraries were amplified using indexed primers with 15 PCR cycles. A second round of gel purification was performed before sequencing.


title: ABRF-ILMN-RNA-C-4

status: Public on May 14 2014

city: New York

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

description:
Agilent Universal Human Reference RNA, Catalog #740000 and FirstChoice® Human Brain Reference Total RNA, Lot #105P055201A, Cat #6050
Pooled RNA Sample of 3/4 ABRF Sample A and 1/4 ABRF Sample B

data_processing:
STAR Aligner v2.3.0 Long
Read counts were calculated using the Rmake pipeline (http://physiology.med.cornell.edu/faculty/mason/lab/r-make/) with Gencode v12 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Counts table

source_name: ABRF-ILMN-RNA-C

extract_protocol:
NA
PolyA; RNA libraries were prepared for sequencing using standard unstranded PolyA Illumina protocols with TruSeq RNA Sample Preparation Kit v2

tag: tissue

value: Pooled tumor

tag: reference rna

value: Agilent Universal Human Reference RNA

tag: reference rna cat. #

tag: reference rna 2

tag: reference rna 2 cat. #

tag: reference rna 2 lot #


title: ABRF-ILMN-RNA-D-4

description:
Agilent Universal Human Reference RNA, Catalog #740000 and FirstChoice® Human Brain Reference Total RNA, Lot #105P055201A, Cat #6050
Pooled RNA Sample of 1/4 ABRF Sample A and 3/4 ABRF Sample B

source_name: ABRF-ILMN-RNA-D

value: Brain


title: ABRF-ILMN-V-A-2

description: Pure Human Reference RNA Sample from Agilent, Inc.

source_name: ABRF-ILMN-V-A

extract_protocol:
NA
Ribo-Depleted; Following ribo-depletion, all recovered RNA was processed using the Illumina TruSeq RNA Sample Preparation Kit v2 protocol at the “elute-fragment-prime” step, followed by the standard TruSeq protocol.  Completed libraries were evaluated by DNA quantitation and Bioanalyzer analysis, and then submitted to a single core laboratory site for sequencing.  Sequencing libraries were constructed with barcodes to allow multiplexing of 12 samples per lane, pooled to target 200 million clusters per channel and 100 million reads per library, and distributed over multiple channels of three flow cells to normalize for lane and run variability.  Sequencing was carried out on Illumina HiSeq 2500 instruments using protocols HCS 1.5.15.1 and RTA 1.13.48.


title: ABRF-ILMN-V-A-1


title: ABRF-ILMN-V-B-1

description: Pure Human Brain Reference RNA Sample from Ambion, Inc.

source_name: ABRF-ILMN-V-B

value: FirstChoice® Human Brain Reference Total RNA

tag: reference rna lot #


title: ABRF-ILMN-V-B-3


title: ABRF-ILMN-V-A-3


title: ABRF-ILMN-RNA-D-2


title: ABRF-ILMN-RNA-C-2


title: ABRF-ILMN-RNA-B-4

source_name: ABRF-ILMN-RNA-B


title: ABRF-ILMN-RNA-D-1


title: ABRF-ILMN-V-B-2


title: ABRF-ILMN-RNA-C-3


title: ABRF-ILMN-RNA-B-3


title: ABRF-ILMN-RNA-B-1


title: ABRF-ILMN-RNA-D-3


title: ABRF-ILMN-RNA-C-1


title: HCT116_GROseq_Nutlin_p53+/+

value: control


title: HCT116_GROseq_DMSO_p53-/-


title: ABRF-ILMN-RNA-A-2

source_name: ABRF-ILMN-RNA-A


title: ABRF-ILMN-RNA-A-4


title: ABRF-ILMN-RNA-A-3


title: ABRF-ILMN-RNA-A-1


title: ABRF-ILMN-RIBO-D-4

description:
Agilent Universal Human Reference RNA, Catalog #740000 and FirstChoice® Human Brain Reference Total RNA, Lot #105P055201A, Cat #6051
Pooled RNA Sample of 1/4 ABRF Sample A and 3/4 ABRF Sample B

source_name: ABRF-ILMN-RIBO-D


title: ABRF-ILMN-RIBO-D-3


title: ABRF-ILMN-RIBO-D-1


title: J1_NT_Klf4

status: Public on May 16 2014

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description: Library was prepared by Nextera XT kit

data_processing:
Basecalls performed using CASAVA version 1.7
Raw data from the replicates were merged.
Raw data was filtered by the following steps:  reads were filtered if the average base quality score <20 and duplicate reads removed (based on identical sequences)
Reads were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bowtie (v0.12.8 using the following parameters:  -v 2 -m 1)
Mapped data was filtered to remove hits with >2 mismatches to the reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file per sample per strand showing normalized mapped read coverage; generated by BEDtools genomeCoverageBed and bedGraphToBigWig.
Supplementary_files_format_and_content: Ino80 peak bed files were generated by SICER v1.1 (redundancy threshold=1, window size=200, gap size=800, fragment size=300, FDR=1e-6)

organism: Mus musculus

source_name: cell line

growth_protocol: J1 cell were maintianed in ESGRO medium. Cell were cultured in M15 medium when ChIP was performed.

extract_protocol:
Cells were fixed with 1% formaldehyde, sonicated and precipitated by Ino80, Oct4, Klf4, Med1, or Pol2 antibodies. Then precipitated DNA was reverse crosslinked, extracted and quantified for library.
Library was prepared by TruSeq DNA Sample Prep kit (Illumina) or Nextera XT DNA sample prep kit (Illumina) according to the manufacturer's protocol.

tag: vendor/catalog#

tag: transfection

value: lentiviral mediated-shRNA against non-targeting NT


title: ABRF-ILMN-RIBO-C-4

source_name: ABRF-ILMN-RIBO-C


title: ABRF-ILMN-RNA-B-2


title: ABRF-ILMN-RIBO-C-1


title: ABRF-ILMN-RIBO-B-4

source_name: ABRF-ILMN-RIBO-B


title: ABRF-ILMN-RIBO-B-2


title: ABRF-ILMN-RIBO-C-2


title: ABRF-ILMN-RIBO-B-1


title: ABRF-ILMN-RIBO-C-3


title: ABRF-ILMN-RIBO-A-3

source_name: ABRF-ILMN-RIBO-A


title: ABRF-ILMN-RIBO-B-3


title: ABRF-ILMN-RIBO-A-2


title: ABRF-ILMN-RIBO-A-4


title: ABRF-ILMN-R-A-2

source_name: ABRF-ILMN-R-A


title: ABRF-ILMN-R-B-3

source_name: ABRF-ILMN-R-B


title: ABRF-ILMN-N-AR-2

source_name: ABRF-ILMN-N-AR

extract_protocol:
NA
Rnase, RiboDep; exposure to 1 ng/ul RNase A for a sufficient time period to result in a RIN of 3, with the RNase then neutralized with 10 ul RNase Inhibitor (RiboLock EO0381, Thermo Scientific)


title: ABRF-ILMN-R-B-2


title: ABRF-ILMN-R-A-1


title: ABRF-ILMN-R-A-3


title: 6-4pp Beseq replicate 1

description: BE-seq

source_name: S. cerevisiae

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 bar1Δ::LEU2

tag: enzyme treatment

value: UVDE-trevigen  Xenopus laevis 6-4 photolyase- Sancar


title: ABRF-ILMN-RIBO-A-1


title: ABRF-ILMN-R-B-1


title: ABRF-ILMN-N-BR-2

source_name: ABRF-ILMN-N-BR


title: ABRF-ILMN-N-BR-3


title: ABRF-ILMN-N-BR-1


title: ABRF-ILMN-RIBO-D-2


title: ABRF-ILMN-N-AH-1

source_name: ABRF-ILMN-N-AH

extract_protocol:
NA
Heat Degraded, RiboDep; heat treatment in deionized water at 99.C for 10 min


title: ABRF-ILMN-M-AS-3

source_name: ABRF-ILMN-M-AS

extract_protocol:
NA
Sonication, RiboDep; sonication within a Covaris S2 MicroVial for 6 x 55 sec at 5% DC,  intensity 3, and 100 c/b


title: ABRF-ILMN-M-AS-2


title: ABRF-ILMN-M-AS-1


title: ABRF-ILMN-M-AH-3

source_name: ABRF-ILMN-M-AH


title: ABRF-ILMN-M-AH-2


title: ABRF-ILMN-M-AH-1


title: ABRF-ILMN-L-B-3

source_name: ABRF-ILMN-L-B


title: ABRF-ILMN-L-B-2


title: ABRF-ILMN-N-AR-1


title: ABRF-ILMN-L-A-1

source_name: ABRF-ILMN-L-A


title: ABRF-ILMN-L-A-3


title: ABRF-ILMN-L-A-2


title: Nitrogen 48h replicate1

city: Qingdao

first: Jian

last: Xu

state: Shandong province

address: No.189 Songling Rd, LaoShan District

department: BEGC

country: China

institute: QIBEBT-CAS

data_processing:
To ensure quality, the raw data (2×90bpPE reads) was modified by following 2 steps: first the adapter pollutions in reads were deleted, and then because the sequence qualities of Illumina reads degrade quickly toward the 3’ end, all reads were trimmed from the 3’ end until the 3’-end-most position with Phred-equivalent score was 20 or greater. These filtered Illumina reads with 75bp length were aligned to the N.oceanica draft genome with Tophat (version 2.0.4, allowed no more than two segment-mismatches) and reads mapped to more than one location were excluded. Thirdly, the short read mapping results from TopHat was used for the following differential gene expression analysis with Cufflinks (version 2.0.2).
Genome_build: de novo assembly of Nannochloropsis oceanica IMET1 (http://www.bioenergychina.org:8989/indexs/IMET_index.html)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: nuclear RNA

organism: Nannochloropsis oceanica

source_name: Nitrogen 48h whole cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into modified f/2 liquid medium, which was prepared as follows:35 g/l sea salt, 1 g/l NaNO3, 67 mg/1 NaH2PO4*H2O, 3.65 mg/l FeCl3*6H2O, 4.37 mg/l Na2EDTA*2H2O, trace metal mix (0.0196 mg/l CuSO4*5H2O, 0.0126 mg/l NaMoO4*2H2O, 0.044 mg/l ZnSO4*7H2O, 0.01mg/l CoCl2, 0.36 mg/l MnCl2*4H2O) and vitamin mix(5 mg/l VB12, 5 mg/l Biotin and 1 mg/l Thiamine HCl). The cells were grown in liquid cultures under continuous light (approximately 50 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 1.5% CO2 in air.

extract_protocol: Algal total RNAs under the above conditions were extracted using Trizol reagents (Invitrogen). For RNA-Seq, the poly (A) containing mRNA molecules were purified using Sera-mag Magnetic Oligo(dT) Beads (Thermo Scientific) and was fragmented into 200- to 300-bp fragments by incubation in RNA Fragmentation Reagent (Ambion)according to the manufacturer’s instructions. The fragmented mRNA was then purified away from the fragmentation buffer by Agencourt®RNAClean beads (Beckman Coulter). The purified, fragmented mRNA was then converted into double-stranded cDNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) by priming with random hexamers. Strand nonspecific transcriptome libraries were prepared using NEBNext® mRNA Library Prep Reagent Set(New England Biolabs) and sequenced for 2×90bprun(paired-end, PE) using Illumina HiSeq2000.

treatment_protocol: Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 50 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 1.5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in nitrogen replete medium (Control condition or C) and nitrogen deprived medium (N deficiency or N) with 50µmol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 4h, 6h, 12h, 24h and 48h. Three biological replicates of algal cultures were established under each of the above “C” and “N” conditions, respectively. In total, 36 samples collected at six time points (3h,4h,6h,12h,24h and 48h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.

tag: strain

value: whole cells


title: Soybean Cotyledon Stage Seed Coat Outer Integument-Biological replicate 2

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file.  The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max gene models (v1.1) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 4 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. Normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: Glyma V1.1 (http://www.ncbi.nlm.nih.gov/assembly/GCF_000004515.3)
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for each sample. Please note that the identifiers in the file are traceable at phytozome genome browser (http://www.phytozome.net/cgi-bin/gbrowse/soybean/) or at soybase database (http://soybase.org/).

organism: Glycine max

growth_protocol: Soybean plants were grown at the UC Davis Greenhouses with a 16:8 day:night cycle at 22°C-30°C. Seeds were germinated in Modified UC Mix (equal parts of ground canadian sphagnum, horticultural grade sand, white pumice, redwood compost) for 10 days.  Individual seedlings were transfered to 1 gallon pots where they were grown for an additional 3 weeks before being transplanted to 3 gallon pots.  Plants were watered as needed with water containing 190 ppm Nitrogen, 40 ppm Phosphorus and 140 ppm Potassium and micronutrients.

extract_protocol:
Soybean seeds (Williams 82) were fixed in 3:1 ethanol:acetic acid for 16-20 hours at 4°C, then dehydrated with 75% ethanol, 85% ethanol, 95% ethanol, and three times with 100% ethanol, each wash in one hour intervals. Then they were infiltrated with 3:1 ethanol-xylenes, 1:1 ethanol-xylenes, 1:3 ethanol-xylenes, and three times with 100% xylenes, dilution in two hour intervals. They were then infiltrated with molten paraffin at 60 deg  C for 1-4 days, depending on the size of the tissue. Laser capture microdissection was used to isolate specific compartments of the seed after tissues were sectioned in 5-10um sections. Total RNA was isolated with Ambion RNaqueous-Micro kit (Grand Island, NY) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300.
Amplification was performed using NuGen Ovation Pico WTA V1 (San Carlos, CA), starting with 15ng total RNA. Double-stranded cDNA was generated using the NuGen WT-Ovation Exon-Module (San Carlos, CA). Illumina-complatible libraries were made starting with 150 ng double-stranded cDNA using Kumar et al. (Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN and Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. doi: 10.3389/fpls.2012.00202) Supplemetary Methods 1 library preparation protocol, starting at Day 2.  The following modifications were done: the Illumina TruSeq DNA Sample preparation kit adapters were used (1/25 dilution) and the Agilent Pfu Turbo Cx hotstart DNA polymerase was used for the PCR enrichment step (15 cycles).  Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: William 82

value: seeds ranging 3.0-3.5mm in length

tag: compartment

value: cotyledon Stage Seed Coat Outer Integument


title: Soybean Cotyledon Stage Suspensor-Biological replicate 2

source_name: Soybean Cotyledon Stage Suspensor

value: cotyledon Stage Suspensor


title: Soybean Cotyledon Stage Suspensor-Biological replicate 3


title: Soybean Cotyledon Stage Seed Coat Inner Integument-Biological replicate 3

value: cotyledon Stage Seed Coat Inner Integument


title: Nitrogen 24h replicate2

source_name: Nitrogen 24h whole cells


title: Nitrogen 48h replicate3


title: Nitrogen 24h replicate3


title: Nitrogen 48h replicate2


title: Soybean Cotyledon Stage Seed Coat Hilum-Biological replicate 3

source_name: Soybean Cotyledon Stage Seed Coat Hilum

value: cotyledon Stage Seed Coat Hilum


title: Soybean Cotyledon Stage Seed Coat Inner Integument-Biological replicate 2


title: Soybean Cotyledon Stage Seed Coat Inner Integument-Biological replicate 1


title: Nitrogen 24h replicate1


title: Soybean Cotyledon Stage Seed Coat Hilum-Biological replicate 1


title: Nitrogen 12h replicate3

source_name: Nitrogen 12h whole cells


title: Soybean Cotyledon Stage Seed Coat Epidermis-Biological replicate 3

value: cotyledon Stage Seed Coat Epidermis


title: Nitrogen 12h replicate2


title: Nitrogen 6h replicate3

source_name: Nitrogen 6h whole cells


title: Soybean Cotyledon Stage Seed Coat Epidermis-Biological replicate 1


title: ABRF-ILMN-L-B-1


title: Soybean Cotyledon Stage Seed Coat Endothelium-Biological replicate 3

value: cotyledon Stage Seed Coat Endothelium


title: Soybean Cotyledon Stage Seed Coat Epidermis-Biological replicate 2


title: Nitrogen 6h replicate1


title: Soybean Cotyledon Stage Seed Coat Hilum-Biological replicate 2


title: Soybean Cotyledon Stage Seed Coat Endothelium-Biological replicate 1


title: Soybean Cotyledon Stage Seed Coat Endothelium-Biological replicate 2


title: Nitrogen 4h replicate2

source_name: Nitrogen 4h whole cells


title: Nitrogen 3h replicate2

source_name: Nitrogen 3h whole cells


title: Soybean Cotyledon Stage Endosperm-Biological replicate 3

source_name: Soybean Cotyledon Stage Endosperm

value: cotyledon Stage Endosperm


title: Soybean Cotyledon Stage Suspensor-Biological replicate 1


title: Soybean Cotyledon Stage Seed Coat Outer Integument-Biological replicate 1


title: Soybean Cotyledon Stage Seed Coat Outer Integument-Biological replicate 3


title: Soybean Cotyledon Stage Endosperm-Biological replicate 2


title: Nitrogen 3h replicate3


title: Nitrogen 3h replicate1


title: Control 48h replicate2

source_name: Control 48h whole cells


title: Control 48h replicate1


title: Soybean Cotyledon Stage Endosperm-Biological replicate 1


title: Control 24h replicate2

source_name: Control 24h whole cells


title: Nitrogen 6h replicate2


title: Control 48h replicate3


title: Control 24h replicate1


title: Nitrogen 4h replicate3


title: Control 12h replicate3

source_name: Control 12h whole cells


title: Soybean Cotyledon Stage Embryo Proper Cotyledon-Biological replicate 3

value: cotyledon Stage Embryo Proper Cotyledon


title: Control 12h replicate2


title: Control 6h replicate3

source_name: Control 6h whole cells


title: Nitrogen 4h replicate1


title: Control 6h replicate2


title: Control 12h replicate1


title: Soybean Cotyledon Stage Embryo Proper Cotyledon-Biological replicate 1


title: Soybean Cotyledon Stage Embryo Proper Cotyledon-Biological replicate 2


title: Control 24h replicate3


title: Soybean Cotyledon Stage Embryo Proper Axis-Biological replicate 3

value: cotyledon Stage Embryo Proper Axis


title: Soybean Cotyledon Stage Embryo Proper Axis-Biological replicate 2


title: Control 4h replicate2

source_name: Control 4h whole cells


title: Control 4h replicate1


title: Control 4h replicate3


title: Soybean Cotyledon Stage Embryo Proper-Biological replicate 3

source_name: Soybean Cotyledon Stage Embryo Proper

value: cotyledon Stage Embryo Proper


title: Soybean Cotyledon Stage Embryo Proper-Biological replicate 2


title: Control 6h replicate1


title: rpd3 sir2

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, , allowing only perfect matches
Alignement against rDNA repeats were performed using a sequence retrieved on SGD (http://www.yeastgenome.org) by entering the coordinates ChrXII:459797..468931 into GBrowse or Gene/Sequence Resources.
Genome_build: sacCer3 or rDNA sequence (9.1 kb)
Supplementary_files_format_and_content: BED files

source_name: rpd3 sir2_Mnase-seq

growth_protocol: Cells were grown on YPD at 25°C

extract_protocol:
Micrococal nuclease digestion was performed as described in Rando (2010) Methods in Enzymology 470, 105-108
Libraries were constructed using standard Illumina kits and protocols

treatment_protocol: Asynchronous cells were collected for Mnase-seq analysis

tag: strain background

tag: genotype/variation

value: rpd3 sir2


title: wt

value: wild type


title: Control 3h replicate2

source_name: Control 3h whole cells


title: Soybean Cotyledon Stage Embryo Proper-Biological replicate 1


title: CP190, dCTCF RNAi

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

description: ChIP-seq

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.
Genome_build: DM3
Supplementary_files_format_and_content: wig files were generated using MACS1.4.9alpha2

organism: Drosophila melanogaster

source_name: Kc167 cells

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC.  After washing and eluting from beads the crosslinking was reversed and DNA was isolated.
To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

treatment_protocol: No treatment

tag: cell line

tag: chip antibody

tag: treatment

value: dCTCF RNAi


title: Input, dCTCF RNAi

description: ChIP-seq

value: Input


title: Control 3h replicate3

tag: tissue

value: whole cells


title: BirA

city: Athens

first: Giorgio

middle: L

last: Papadopoulos

state: Attiki

address: 34 Fleming Street

department: Molecular Oncology

country: Greece

institute: BSRC 'Alexander Fleming'

description:
Sample 3
Strept/bio-ChIP seq

data_processing:
Library strategy: Streptavidin-mediated pulldown
Sequenced reads were aligned to the hg18 genome assembly using bowtie.2 version 2.1.0 with the following configurations: -p 2 -q  -k 1 -S
bioTF2-I replicates were merged into one single reads dataset (cat reads_of_TF2I_clone1.sam reads_of_TF2I_clone2.sam >reads_of_reps_1_and_2_hg18.sam)
Peaks were called using MACS version 1.4.1 with the following setting: macs14 -t reads_of_reps_1_and_2_hg18.sam -c reads_of_BirA.sam  -g hs -n TF2I_5_and_18 -w -S
The Galaxy online liftOver tool was used to create the bioTF2I_peaks_hg19.bed from the bioTF2I_peaks_hg18.bed file produced by MACS.
Genome_build: hg18
Supplementary_files_format_and_content: bioTF2I_peaks_hg18.bed file was created using MACS14, bioTF2I_peaks_hg19.bed file was created using liftOver (see supplementary files linked to Series record)

source_name: K562 cells_expressing BirA

growth_protocol: K562 cells were grown in RPMI 1640 (Corning, Cellgro) containing 10% feta bovine serum and 1% penicillin-streptomycin at a density of 1x105 to 2x106 cells/ml. 4x 107 cells were subjected to streptavidin mediated pull down

extract_protocol:
K562 cells were crosslinked with 1% formaldehyde for 7 min. Then glycine was added to final concentration of 125 mM. The lysates were subjected to sonication and pull down using streptavidin coated magnetic beads. The DNA was iolated and purified using standard procedures.
Libraries were prepared using the Illumina Multiplexing Sample Preparation guide (www.illumina.com).

treatment_protocol: No special treatment

value: BirA stably transfected

value: none (streptavidin mediated pull down)


title: bioTF2-I clone 2

description:
Sample 2
Strept/bio-ChIP seq

source_name: K562 cells_expressing bioTF2-I clone 2

value: BirA/bioTF2-I stably transfected


title: Condensin II (CAPH2), dCTCF RNAi

description: ChIP-seq

value: Condensin II (CAPH2)


title: Cohesin (Rad21), dCTCF RNAi

description: ChIP-seq

value: Cohesin (Rad21)


title: dTFIIIC220, dCTCF RNAi

description: ChIP-seq


title: Endoderm G1/S phase (day6-3 h)

first: Edward

last: Chuong

address: 596 UCB

institute: University of Colorado Boulder

description:
X6.3
3' RNA-seq
Post H9 hESC (passage 51) differentiated to endoderm day 6

data_processing:
Basecalls performed using CASAVA version 1.5.
Reads were aligned to hg18 using Bowtie 0.12.7 with the settings --best --strata -k 10 -S --chunkmbs 190.
Using Unipeak v1.0, Bowtie alignments were filtered by posterior probability (sam_map.pl from Unipeak), and transcription region peaks were called using default settings.
Regions were associated with the nearest 3' UTR of genes annotated by UCSC knownGene hg18.
Regions >5kb from a 3' UTR were annotated as "NOVEL" regions.
Multiple regions associated with a gene were pooled together.
Counts were normalized using the Variance Stabilized Data method in DESeq 1.5.24.
Genome_build: NCBI36
Supplementary_files_format_and_content: GS47117_regions.annotated.vsd.txt: Text  file of 3'Seq regions with genomic coordinates, gene name, and normalized scores for each timepoint.

source_name: hESC-derived endoderm cells, G1/S

growth_protocol: Undifferentiated hESCs were passaged on growth factor reduced matrigel and cultured in hESC media conditioned overnight on primary MEF (CM).

extract_protocol:
Sequencing libraries were generated by first isolating total RNA using RNeasy Plus Mini Kit (Qiagen) and then purifying mRNA using Dynabeads® Oligo (dT)25 (Invitrogen) according to the manufacturer's instructions.
3' RNA-Seq libraries were prepared as previously described (Beck et al., PLOS One 2010). Briefly, mRNA was heat sheared for 7 minutes to produce an average fragment size range of 300-500 bp, then used to generate cDNA libraries using a custom oligo dT primer containing Illumina-compatible adapter sequence. cDNA fragments were end-repaired and ligated to standard Illumina adapters. Products were PCR amplified for 15 cycles, and purified using Qiagen MinElute columns. Library quality was assessed using Bioanalyzer and Qubit, and sequenced on the Genome Analyzer IIx.

treatment_protocol: Differentiation was initiated by adding 100 ng/ml activin A in RPMI 1640 supplemented with Glutamax, penicillin/streptomycin. FBS concentrations were 0% for the first 24 h, 0.2% for the second 24 h, and 2.0% for subsequent days. Cells were treated for 6 days, with medium changed once at day 3.

tag: cell type

value: hESC-derived endoderm cells

tag: cell cycle phase


title: Endoderm S phase (day6-6 h)

description:
X6.6
3' RNA-seq
Post H9 hESC (passage 51) differentiated to endoderm day 6

source_name: hESC-derived endoderm cells, S

value: S (day6-6 h)


title: Soybean Cotyledon Stage Embryo Proper Axis-Biological replicate 1

value: William 82

value: seeds ranging 3.0-3.5mm in length


title: Endoderm G1 phase (day6-0 h)

description:
X6.0
3' RNA-seq
Post H9 hESC (passage 51) differentiated to endoderm day 6

source_name: hESC-derived endoderm cells, G1


title: Control 3h replicate1


title: Nitrogen 12h replicate1

source_name: Nitrogen 12h whole cells


title: hESCs S phase (day0-3 h)

description:
X0.3
3' RNA-seq
H9 hESCs passage 51

source_name: human embryonic stem cells, S

value: embryonic stem cells

value: S (day0-3 h)


title: sir2


title: hESCs G1/S phase (day0-2 h)

description:
X0.2
3' RNA-seq
H9 hESCs passage 51

source_name: human embryonic stem cells, G1/S


title: rpd3


title: Chromator

description: ChIP-seq


title: GAF

description: ChIP-seq


title: Condensin II (CAPH2) Interphase

description: ChIP-seq


title: Condensin I (Barren) Interphase

description: ChIP-seq


title: hESCs G1 phase (day0-0 h)

description:
X0.0
3' RNA-seq
H9 hESCs passage 51

source_name: human embryonic stem cells, G1


title: 2-cell_fCAB-Seq

city: Beijing

first: Lu

email: share.luwang@gmail.com, liuj@big.ac.cn

address: No.1 Beichen West Road

institute: Beijing Institute of Genomics

description: library strategy: fCAB-Seq

data_processing:
Illumina Casava 1.82 software was used for basecalling.
Once the sequencing data was obtained from Hiseq-2000, the raw data will be analyzed by the standard combined pipeline in the lab including five steps: 1) finding reads hit by adaptor sequence with a custom pair-wise alignment script, 2) low-quality base trimming by Trimmomatic with default parameters, 3) mapping paired-end methylC-seq reads by Bismark (version 0.7.8) with stringent parameters: -N 1 –X 600, 4) removing duplicates by using Picard program, 5) trimming the overlapped part of paired-end reads from one end.
Quantification of methylation levels of CpGs: For CpG i, define mi as the number of reads showing methylation over position i (both strands). Define ui as the number of reads showing lack of methylation over CpG i. The methylation level is estimated as mi/(mi + ui), which is an estimate of the probability that CpG i is methylated in a molecule sampled randomly from the cell population. Because CpG methylation is symmetric, mi and ui include observations associated with the cytosines on both strands for the i-thCpG.
Genome_build: mm10
Supplementary_files_format_and_content: Format: bed; content: Methylation level for each CpG site plus 2 columns representing the numbers of Cs and Ts. For strand-specific files, the position of each CpG site is displayed as the C position in Watson strand.
Supplementary_files_format_and_content: Besides mm10 (C57BL/6J), a DBA/2J reference was constructed using a custom script by replacing all the SNPs between DBA/2J strain and C57BL/6J strain for mapping. A custom script was used to track maternal and paternal DNA using the SNPs between these two strains.

source_name: 2-cell embryos

extract_protocol:
fCAB-Seq: Hydroxylamine protection of 5fC in sonicated DNA (two-cell) was performed as previously described (Song et al., 2013). Then, hydroxylamine-protected DNA was treated with bisulfite conversion.
Mouse gametes and embryos were collected at minimal volume and frozen.  DNA was extracted using QIAamp DNA Mini Kit (QIAGEN) and RNA was isolated using RNeasy Micro Kit (QIAGEN).

value: 2-cell embryo


title: 2-cell_TAB-Seq

description: library strategy: TAB-Seq

extract_protocol:
TAB-Seq: Purified and sonicated genomic DNA with spike-in controls was glucoslyated and oxidized using 5hmC TAB-Seq Kit (WiseGene) according to the manufacturer’s instructions. Prepared DNA was subjected to library construction following the standard protocol of methylC-Seq library preparation.
Mouse gametes and embryos were collected at minimal volume and frozen.  DNA was extracted using QIAamp DNA Mini Kit (QIAGEN) and RNA was isolated using RNeasy Micro Kit (QIAGEN).


title: Cohesin (Rad21)

description: ChIP-seq


title: dTFIIIC220 biological replicate 3

description: ChIP-seq


title: PGC_male_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: E135M1_*.fastq.gz, E135M2_*.fastq.gz, E135M3_*.fastq.gz, E135M4_*.fastq.gz [SRR1286816-SRR1286819]; replicate2: E135M5_*.fastq.gz, E135M6_*.fastq.gz [SRR1286820,SRR1286821]

data_processing:
Illumina Casava 1.82 software was used for basecalling.
Once the sequencing data was obtained from Hiseq-2000, the raw data will be analyzed by the standard combined pipeline in the lab including five steps: 1) finding reads hit by adaptor sequence with a custom pair-wise alignment script, 2) low-quality base trimming by Trimmomatic with default parameters, 3) mapping paired-end methylC-seq reads by Bismark (version 0.7.8) with stringent parameters: -N 1 –X 600, 4) removing duplicates by using Picard program, 5) trimming the overlapped part of paired-end reads from one end.
Quantification of methylation levels of CpGs: For CpG i, define mi as the number of reads showing methylation over position i (both strands). Define ui as the number of reads showing lack of methylation over CpG i. The methylation level is estimated as mi/(mi + ui), which is an estimate of the probability that CpG i is methylated in a molecule sampled randomly from the cell population. Because CpG methylation is symmetric, mi and ui include observations associated with the cytosines on both strands for the i-thCpG.
Genome_build: mm10
Supplementary_files_format_and_content: Format: bed; content: Methylation level for each CpG site plus 2 columns representing the numbers of Cs and Ts. For strand-specific files, the position of each CpG site is displayed as the C position in Watson strand.

source_name: E13.5 male PGCs

extract_protocol:
MethylC-Seq: Purified DNA spiked in with 0.1% unmethylated cl857 Sam7 lambda DNA (Promega) was sonicated using the microtube protocol-300 of Covaris S2 (Applied Biosystems). End-repair, dA-tailing and ligation were performed using the NEBNext End Repair Module, dA-Tailing Module and NEB T4 ligase. The adaptor-ligated DNA with insert size larger than 200 bp was selected by gel electrophoresis. Bisulfite conversion was performed using the EZ DNA methylation Gold Kit (Zymo Research) according to the manufacturer’s instructions. The time of 64°C incubation was 2 hr for some libraries. Bisulfite- treated DNA was amplified using ZymoTaq DNA Polymerase or KAPA HiFi HotStart Uracil+ ReadyMix with 14-15 cycles.
Mouse gametes and embryos were collected at minimal volume and frozen.  DNA was extracted using QIAamp DNA Mini Kit (QIAGEN) and RNA was isolated using RNeasy Micro Kit (QIAGEN).

value: B6; 129S4-Pou5f1tm3Jae/J

value: E13.5 male PGC


title: bioTF2-I clone 1

description:
Sample 1
Strept/bio-ChIP seq

source_name: K562 cells_expressing bioTF2-I clone 1


title: Condensin I (Barren) Asynchronous

description: ChIP-seq


title: E7.5_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: E751_*.fastq.gz, E752_*.fastq.gz, E753_*.fastq.gz [SRR1286806-SRR1286808]; replicate2: E754_*.fastq.gz [SRR1286809]

source_name: E7.5 embryos

value: E7.5 embryo


title: CP190

description: ChIP-seq


title: dTFIIIC220 biological replicate 2

description: ChIP-seq


title: dTFIIIC220 biological replicate 1

description: ChIP-seq


title: PGC_female_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: E135F1_*.fastq.gz, E135F2_*.fastq.gz, E135F3_*.fastq.gz, E135F4_*.fastq.gz [SRR1286810-SRR1286813]; replicate2: E135F5_*.fastq.gz, E135F6_*.fastq.gz [SRR1286814,SRR1286815]

source_name: E13.5 female PGCs

value: B6; 129S4-Pou5f1tm2Jae/J

value: E13.5 female PGC


title: E6.5_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: E651_*.fastq.gz, E653_*.fastq.gz, E654_*.fastq.gz, E655_*.fastq.gz, E656_*.fastq.gz, E657_*.fastq.gz [SRR1286797, SRR1286799-SRR1286803]; replicate2 (in-spike controls contain lambda DNA whose Cs in CG context are methylated): E652_*.fastq.gz, E658_*.fastq.gz, E659_*.fastq.gz [SRR1286798,SRR1286804,SRR1286805]

source_name: E6.5 embryos

value: E6.5 embryo


title: ICM_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: ICM1_*.fastq.gz [SRR1286792]; replicate2: ICM2_*.fastq.gz, ICM3_*.fastq.gz, ICM4_*.fastq.gz, ICM5_*.fastq.gz [SRR1286793-SRR1286796]

source_name: E3.5 inner cell mass

value: Inner cell mass


title: 4-cell_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: 4cell1_*.fastq.gz, 4cell2_*.fastq.gz, 4cell3_*.fastq.gz, 4cell4_*.fastq.gz, 4cell5_*.fastq.gz, 4cell6_*.fastq.gz, 4cell7_*.fastq.gz [SRR1286783-SRR1286789]; replicate2: 4cell8_*.fastq.gz, 4cell9_*.fastq.gz [SRR1286790-SRR1286791]

source_name: 4-cell embryos

value: 4-cell embryo


title: sperm_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: sperm1_*.fastq.gz, sperm2_*.fastq.gz [SRR1286765-SRR1286766]; replicate2: sperm3_*.fastq.gz [SRR1286767]; replicate3: sperm4_*.fastq.gz, sperm5_*.fastq.gz, sperm6_*.fastq.gz, sperm7_*.fastq.gz, sperm8_*.fastq.gz, sperm9_*.fastq.gz [SRR1286768-SRR1286773]

source_name: sperm

value: sperm


title: m15.5 AVC Scx WT2

city: Oxford

first: Damien

last: Barnette

state: Oxfordshire

address: Sherrington Building

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina HiSeq 2000
Tophat 1.4.1 software was used to align the library reads to the UCSC Mouse (mm9) reference genome
EasyRNASeq version 1.6 was used to count reads mapping within Ensembl version 66 exons, and calculate normalized counts for each gene
RPKM values were calculated using easyRNASeq
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing detected genes with ensembl gene ID, Chromosome name, Gene start and end base pair, gene name, description, fold changes, FDR values, p vlaues, and normalized RPKM values

source_name: Scx+/+, atrioventicular canal region

extract_protocol:
Total RNA from atrioventricular valve regions were using 200uL Trizol reagent.  Sample precipitated overnight at -20 degrees Celsius with 1uL of glycogen. And RNA pellet resuspended in 20uL of pure water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: organ

value: heart

value: atrioventricular canal region

tag: genotype

value: wildtype


title: oocyte_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: oocyte1_*.fastq.gz [SRR1286759]; replicate2: oocyte2_*.fastq.gz, oocyte3_*.fastq.gz, oocyte4_*.fastq.gz, oocyte5_*.fastq.gz, oocyte6_*.fastq.gz [SRR1286760-SRR1286764]

source_name: MII oocytes

value: MII oocyte


title: m15.5 AVC Scx WT1


title: Condensin I (CAPH2) Asynchronous

description: ChIP-seq

source_name: Kc167 cells


title: m15.5 AVC Scx Null3

source_name: Scx-/-, atrioventicular canal region

value: Scx null


title: m15.5 AVC Scx WT3


title: m15.5 AVC Scx Null2


title: m15.5 AVC Scx Null1


title: RBPJ in asynchronous rep2

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7 using option of --best -v 2 --strata -m 1
Peaks were called using Homer with a defalt option
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated after peak calling

growth_protocol: DMEM, 10% FBS, 5% CO2

extract_protocol:
After wash steps, cells were resuspended in lysis buffer and proceeded to the sonication with 40% power amplitude, 30sec, 12 times total. Cell debris was removed by 10 min centrifuge, 15,000 rpm at 4℃. Extracted chromatin supernatant was used for the following chromatin immunoprecipitation or frozen in -80℃ for storage.
To generate the library from ChIP experiemtn, ChIP-Seq Library Protocol with multiplexing was used. This protocol was developed before Illumina released its multiplex truSeq ChIP-seq kit, and the details can be found on http://ngsc.med.upenn.edu/. According to the protocol, 10 ng of ChIP DNA product was used to start the library construction.

treatment_protocol:
Murine embryonic carcinoma F9 cells were harvested and fixed in 1% formaldehye, 10 min. Glycine was added to final 125mM to quench the fixation. Cells were pelleted and washed with PBS and wash buffers. After wash steps, cells were resuspended in lysis buffer and proceeded to the sonication with 40% power amplitude, 30sec, 12 times total. Cell debris was removed by 10 min centrifuge, 15,000 rpm at 4°C. Extracted chromatin supernatant was used for the following chromatin immunoprecipitation or frozen in -80°C for storage. A portion of the chromatin supernatant was reverse crosslinked and total DNA was purified by PCR purification kit. According to the measurement from this pilot DNA quantification, 70 μg of DNA was used to incubate with anti-RBPJ antibody (raised in our laboratory) or with same amount of IgG as the negative control. BSA coated protein A agarous beads were used to obtain the ChIP product. Chromatin was reverse crosslinked at 65°C 16hours, and DNA was purified by PCR purification kit.
ChIP protocol: 70  μg soluble chromatin was  incubated with anti-RBPJ antibody (rasied in our laboratory) or with same amount of IgG as the negative control. BSA coated protein A agarous beads were used to obtain the ChIP product. Chromatin was reverse crosslinked at 65℃ 16hours, and DNA was purified by PCR purification kit.
For generating anti-mRBPJ antibodies, GST-mRBPJ was expressed in SF9 cells and purified using glutathione sepharose chromatography.  The rabbit anti-RBPJ polyclonal antibody was generated by Cocalico Biologicals, Inc.

value: murine embryonic carcinoma cells; testicular teratoma

tag: cell cycle stage

value: cycling cells (containing 95% interphase and 5% mitosis cells)

tag: antibody

value: anti-RBPJ antibody (custom-made)


title: RBPJ in mitosis rep2

value: mitotic cells


title: input in asynchronous

description: Sample 3

extract_protocol:
After wash steps, cells were resuspended in lysis buffer and proceeded to the sonication with 40% power amplitude, 30sec, 12 times total. Cell debris was removed by 10 min centrifuge, 15,000 rpm at 4℃. Extracted chromatin supernatant was used for the following chromatin immunoprecipitation or frozen in -80C for storage.
To generate the library from ChIP experiemtn, ChIP-Seq Library Protocol with multiplexing was used. This protocol was developed before Illumina released its multiplex truSeq ChIP-seq kit, and the details can be found on http://ngsc.med.upenn.edu/. According to the protocol, 10 ng of ChIP DNA product was used to start the library construction.

treatment_protocol:
Murine embryonic carcinoma F9 cells were harvested and fixed in 1% formaldehye, 10 min. Glycine was added to final 125mM to quench the fixation. Cells were pelleted and washed with PBS and wash buffers. After wash steps, cells were resuspended in lysis buffer and proceeded to the sonication with 40% power amplitude, 30sec, 12 times total. Cell debris was removed by 10 min centrifuge, 15,000 rpm at 4°C. Extracted chromatin supernatant was used for the following chromatin immunoprecipitation or frozen in -80°C for storage. A portion of the chromatin supernatant was reverse crosslinked and total DNA was purified by PCR purification kit. According to the measurement from this pilot DNA quantification, 70 μg of DNA was used to incubate with anti-RBPJ antibody (raised in our laboratory) or with same amount of IgG as the negative control. BSA coated protein A agarous beads were used to obtain the ChIP product. Chromatin was reverse crosslinked at 65°C 16hours, and DNA was purified by PCR purification kit.
For generating anti-mRBPJ antibodies, GST-mRBPJ was expressed in SF9 cells and purified using glutathione sepharose chromatography.  The rabbit anti-RBPJ polyclonal antibody was generated by Cocalico Biologicals, Inc.
ChIP protocol: 70  μg soluble chromatin was  incubated with anti-RBPJ antibody (rasied in our laboratory) or with same amount of IgG as the negative control. BSA coated protein A agarous beads were used to obtain the ChIP product. Chromatin was reverse crosslinked at 65℃ 16hours, and DNA was purified by PCR purification kit.

tag: sample type

value: input control


title: input in mitosis

description: Sample 4


title: RBPJ in asynchronous rep1

description: Sample 1


title: rhesus_36_M

city: Leipzig

first: Zhisong

last: He

address: Deutscher Platz 6

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

data_processing:
For transcript assembly, TopHat2 was used with default parameters to align all sequenced reads to the human genome (hg19).
Using the GENCODE v16 annotation, all sequeced transcripts overlapping annotated transcripts were removed.
To estimate gene expression including both protein-coding genes and lincRNAs in human and macaque, a human-macaque consensus genome based on a pairwise whole-genome alignment of the human (hg19) and the rhesus macaque (rheMac3) genomes was constructed.
Reads in both, human and macaque samples were mapped to the consensus genome using STAR with default parameters.
Gene expression was quantified using RPKM = n*1000*100/L/N, where n is the number of reads aligned to exon regions, and L is the length of exons regions, N is the total number of reads in the sample.
Genome_build: GENCODE 16; hg19; GCA_000230795.1; consensus genome
Supplementary_files_format_and_content: rpkm_human.tsv is a table showing gene expression (in RPKM) of each gene in each human PFC sample. rpkm_macaque.tsv is a similar table but showing information in macaque PFC samples.
Supplementary_files_format_and_content: All the ENSG* IDs in the GENE_ID column are correspond to GENCODE v16 gene IDs (not transcript IDs). The "CUFF.*" IDs are novel lincRNAs we identified. Please see the file named "novel_lincrna.gtf", which involves the information of them.

organism: Macaca mulatta

source_name: prefrontal cortex (PFC)

extract_protocol:
Total RNA was extracted by a Trizol (Invitrogen) procedure according to the manufacturer’s instructions. All RNA quality was assessed using an Agilent 2100 Bioanalyser.
Sequencing libraries were prepared using the Truseq RNA-Seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
Polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded complementary DNA were repaired. After 3′-end adenylation of these products, Illumina Single-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were then PCR-amplified (15 cycles). The RNA-seq libraries were sequenced (100 cycles) on the Illumina Hiseq 2000 platform.

tag: Sex

value: male

tag: age (year)

tag: age (day)


title: rhesus_35_M


title: rhesus_37_M


title: rhesus_38_M


title: rhesus_30_M


title: rhesus_31_M


title: rhesus_39_M


title: rhesus_32_M


title: rhesus_34_M


title: rhesus_40_M


title: rhesus_29_M


title: rhesus_33_M


title: rhesus_28_M


title: 2-cell_MethylC-Seq

description:
library strategy: MethylC-Seq
replicate1: 2cell1_*.fastq.gz, 2cell2_*.fastq.gz, 2cell3_*.fastq.gz, 2cell4_*.fastq.gz [SRR1286774-SRR1286777]; replicate2 (match for 2cell_fCAB-Seq): 2cell5_*.fastq.gz, 2cell6_*.fastq.gz, 2cell7_*.fastq.gz, 2cell8_*.fastq.gz, 2cell9_*.fastq.gz [SRR1286778-SRR1286782]

tag: strain

value: 2-cell embryo


title: rhesus_27_M


title: rhesus_25_M


title: rhesus_24_M


title: rhesus_22_M


title: rhesus_21_M


title: rhesus_23_M


title: rhesus_26_M


title: rhesus_20_M


title: rhesus_19_M


title: human_40_M


title: RBPJ in mitosis rep1

description: Sample 2


title: human_39_M


title: rhesus_17_M


title: human_38_M


title: rhesus_16_M


title: rhesus_14_M


title: human_36_M


title: human_35_M


title: rhesus_15_M


title: human_37_M


title: human_32_M


title: rhesus_11_M


title: human_31_F

value: female


title: rhesus_13_M


title: rhesus_09_M


title: human_30_M


title: human_29_M


title: rhesus_08_M


title: human_26_F


title: rhesus_06_M


title: human_28_M


title: rhesus_07_M


title: rhesus_05_M


title: human_27_F


title: rhesus_10_M


title: rhesus_04_M

description: they are fetal samples before birth. The absolute value of their age shows the number of days before their expected birth.


title: human_24_M


title: human_23_M


title: human_25_M


title: rhesus_18_M


title: rhesus_02_M


title: rhesus_12_M


title: human_33_F


title: human_21_M


title: rhesus_01_F


title: human_20_U


title: human_19_F


title: human_18_F


title: human_17_M


title: human_16_M


title: ABRF-454-UI-A-1

data_processing:
STAR Aligner v2.3.0 Regular
Read counts were calculated using the Rmake pipeline (http://physiology.med.cornell.edu/faculty/mason/lab/r-make/) with Gencode v12 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Counts table

extract_protocol:
NA
Poly A; Library synthesis and sequencing was performed with MAQC A and MAQC B samples at three core laboratory sites.  Each site constructed one cDNA library from each of the polyA-enriched RNA samples.  Enriched RNA (200 ng) was reduced to 19 µl in a vacuum centrifuge at 60 oC, followed by library construction using  the Roche cDNA Rapid Library Preparation Method Manual XL+ (May 2011) with the following modifications: (1) RNA Fragmentation Reagent kit (AM#8740, Life Technologies) was used in place of the RNA Fragmentation Solution; (2) all magnetic particle concentrator (MPC) pelleting steps were held for 2 minutes; (3) Roche rapid library multiplex identifier (RL-MIDs) adaptors were used for the adaptor ligation step; (4) the final libraries were quantified using a Qubit fluorometer (Life Technologies) and average fragment sizes were determined by analyzing 1 µl of the libraries on the Agilent Bioanalyzer 2100 using a High-Sensitivity DNA LabChip; and (5) the library concentrations were determined using the average fragment size from the Bioanalyzer analysis.  Final samples were diluted to 1x108 molecules/µl in Tris-HCl pH 8 buffer with 0.001% Tween-20.

value: Pooled Tumor Tisue

tag: reference rna

value: Agilent Universal Human Reference RNA

tag: reference rna cat. #


title: ABRF-454-PSU-B-1

value: Brain

value: FirstChoice® Human Brain Reference Total RNA, Lot #105P055201A, Cat #6050

tag: reference rna lot #


title: ABRF-454-PSU-A-2


title: ABRF-454-UI-A-2


title: ABRF-454-UI-B-1


title: human_14_M


title: ABRF-454-PSU-A-1


title: human_15_F


title: ABRF-454-PSU-B-2


title: human_12_F


title: human_11_F


title: ABRF-454-CNL-B-2


title: human_13_F


title: ABRF-454-CNL-B-1


title: human_10_M


title: rhesus_03_M


title: human_09_M


title: ABRF-454-CNL-A-1


title: ABRF-454-CNL-A-2


title: human_08_M


title: wt WCE #2

description: Whole-cell extract

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
BrdU-IP-seq reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, , allowing only perfect matches
Alignement against rDNA repeats were performed using a sequence retrieved on SGD (http://www.yeastgenome.org) by entering the coordinates ChrXII:459797..468931 into GBrowse or Gene/Sequence Resources.
Nucleosomes were positioned using NSeq ( Nellore et al. (2012). Front Genet 3, 320.)
Genome_build: sacCer3
Supplementary_files_format_and_content: SGR files correspond to signal log ratio smoothed with a 1000 bp window and a 100 bp step

source_name: wild type_WCE

extract_protocol:
For immunoprecipitation of BrdU-labelled DNA, 1.5x10^9 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA. For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp.
Libraries were constructed using standard Illumina kits (TruSeq SBS Kit v3) and protocols

treatment_protocol: Samples were released from alpha-factor arrest in the presence of 200 mM HU (hydroxyurea).

tag: strain background

tag: genotype/variation

value: wild type


title: human_07_M


title: wt WCE #1

description: Whole-cell extract


title: human_06_M


title: rpd3 sir2 #2

description: BrdU IP

source_name: rpd3 sir2 _BrdU IP

value: rpd3 sir2


title: human_05_M


title: ABRF-PGM-PSU-B-2

data_processing:
STAR Aligner v2.3.0 long
Read counts were calculated using the Rmake pipeline (http://physiology.med.cornell.edu/faculty/mason/lab/r-make/) with Gencode v12 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Counts table

source_name: ABRF-PGM-PSU-B

extract_protocol:
NA
Poly A; Whole transcriptome library preparation was performed using 5-10 ng of fragmented enriched polyA RNA according to the manufacturer’s protocol (Ion Total RNA-Seq Kit V2 protocol #4476286B Life Technologies).  Size selection of a 315 bp product was performed using a standard Pippin prep protocol (Sage Science) followed by purification with AMPure beads (Beckman-Coulter Genomics).  The synthetic ERCC 1 and ERCC 2 control RNA library construction was performed directly from 30 ng of the non-polyA enriched sample.

tag: tissue

value: FirstChoice® Human Brain Reference Total RNA


title: rpd3 #2

description: BrdU IP

source_name: rpd3 _BrdU IP


title: human_04_F


title: ABRF-PGM-PSU-B-1


title: human_03_F


title: wt #2

description: BrdU IP

source_name: wild type_BrdU IP


title: ABRF-PGM-NIH-B-2

source_name: ABRF-PGM-NIH-B


title: human_02_M


title: human_01_M


title: sir2 #2

description: BrdU IP

source_name: sir2 _BrdU IP


title: rpd3 #1

description: BrdU IP


title: ABRF-PGM-PSU-A-1

source_name: ABRF-PGM-PSU-A

value: Pooled Tumor


title: rpd3 sir2 #1

description: BrdU IP


title: ABRF-PGM-PSU-A-2


title: ABRF-PGM-NIH-B-1


title: ABRF-PGM-NIH-A-2

source_name: ABRF-PGM-NIH-A


title: ABRF-PRO-NCI-C-1

description: Pooled RNA Sample of 3/4 ABRF Sample A and 1/4 ABRF Sample B

source_name: ABRF-PRO-NCI-C

extract_protocol:
NA
Poly A; Libraries were prepared from 1 ug of MAQC A, B, C, and D RNA containing ERCC controls using either polyA enrichment (as described for PGM) or ribo-depletion using Ribo-Zero Magnetic Kit (MRZH11124, Epicentre). After enrichment, 8-9 ng of polyA mRNA or 150 ng of ribo-depleted RNA was used for ligation reactions. The size selection step was adjusted to 220 bp using a standard Pippin Prep protocol, generating library competent molecules with a template insert size of approximately 150 bp. The Ion Total RNA-seq Kit v2 (4476286 Rev D, Life Technologies) was used to prepare the MAQC libraries for sequencing.  The resulting material was quantified using the Agilent Bioanalyzer High Sensitivity Chip.

tag: reference rna 2

tag: reference rna 2 cat. #

tag: reference rna 2 lot #


title: wt #1

description: BrdU IP


title: ABRF-PRO-NCI-D-1

description: Pooled RNA Sample of 1/4 ABRF Sample A and 3/4 ABRF Sample B

source_name: ABRF-PRO-NCI-D


title: ABRF-PGM-NIH-A-1

description: Pure Human Reference RNA Sample from Agilent, Inc.


title: ABRF-PRO-NCI-B-1

description: Pure Human Brain Reference RNA Sample from Ambion, Inc.

source_name: ABRF-PRO-NCI-B


title: sir2 #1

description: BrdU IP


title: ABRF-PRO-MSK-B-3

source_name: ABRF-PRO-MSK-B


title: ABRF-PGM-MSK-B-1

source_name: ABRF-PGM-MSK-B


title: ABRF-PRO-MSK-B-2


title: ABRF-PGM-MSK-B-2


title: ABRF-PRO-MSK-B-1


title: ABRF-PGM-MSK-B-3


title: ABRF-PGM-MSK-A-3

source_name: ABRF-PGM-MSK-A


title: ABRF-PRO-MSK-A-3

source_name: ABRF-PRO-MSK-A


title: ABRF-PGM-MSK-A-2


title: ABRF-PRO-MSK-A-1


title: ABRF-PGM-MSK-A-1


title: ABRF-PGM-PSU-E-1

description: Reference ERCC spike-ins

organism: synthetic construct

source_name: ABRF-PGM-PSU-E

value: Synthetic

value: Reference ERCC 1


title: ABRF-PGM-PSU-F-1

description: Reference ERCC spike-ins

source_name: ABRF-PGM-PSU-F

value: Reference ERCC 2


title: ABRF-PRO-MSK-A-2


title: ABRF-PGM-NIH-F-1

description: Reference ERCC spike-ins

source_name: ABRF-PGM-NIH-F


title: ABRF-PGM-NIH-E-1

description: Reference ERCC spike-ins

source_name: ABRF-PGM-NIH-E


title: ABRF-PGM-MSK-E-1

description: Reference ERCC spike-ins

source_name: ABRF-PGM-MSK-E


title: ABRF-PGM-MSK-F-1

description: Reference ERCC spike-ins

source_name: ABRF-PGM-MSK-F


title: ABRF-PRO-NCI-A-1

source_name: ABRF-PRO-NCI-A


title: ABRF-PGM-MSK-F-2

description: Reference ERCC spike-ins


title: control

status: Public on May 13 2014

city: guang zhou

first: ling

last: li

address: South China Normal University, Guangzhou, P.R. China

institute: south china normal universty

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (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.
Supplementary_files_format_and_content: tab-delimited files include RPKM values for each Sample
Supplementary_files_format_and_content:DiffExprAnalysis_1.5_fold_.xlsx.gz: differentially expressed genes(>1.5 fold)

organism: Arachis hypogaea

source_name: leaf

growth_protocol: A sequences library of Yueyou7 were constructed at first. Then the profile of diffentialy expressed genes (DEGs) under three different treatments (control, water deficit without ABA, and water deficit with ABA)  were conducted based on above sequence library. For sequencing library construction, plants were grown under normal conditions, as described previously [14, 17], Seeds were planted in soil and kep in the greenhouse at temperature of 25-30℃ and water well. Three tissues (leaves, roots, and stems) were collected at three development stages (four-leaf, flowering and podding stages), respectively. Then all of these tissues were mixed to extract the total RNA for sequence library construction.

extract_protocol: Total RNA was extracted from 100 mg of plant material, and RNA integrity was checked by gel electrophoresis. Also RNA quality was checked and RNA was quantified using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA) and Nanodrop ND-1000 (Thermo Scientific, Waltham, USA).

treatment_protocol: For DEGs study, two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 µmol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel.

value: leaf

tag: age

value: two-week-old plants


title: water deficit without ABA treatment


title: water deficit with ABA treatment


title: RHP229

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

data_processing:
Data was mapped to hg19 using tophatv2 with default parameters. The unmapped mates of reads that mapped to TCR variable regions were then mapped to a synthetic VJ database consiting of all possible V-J junctions using bowtie
Genome_build: hg19
Supplementary_files_format_and_content: data files contain individual information on which v-j junctions were found, and the DNA sequence of the junction, for TRAV1-2 junctions only

source_name: lymphocytes from PBMC

extract_protocol:
RNA was extracted using the mirVana miRNA Isolation Kit - Life Technologies; 300 ng of total RNA were used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols and the Illumina TruSeq RNA v2

tag: celltype

value: lymphocytes


title: RHP483


title: RHP256


title: RHP480


title: RHP240


title: RHP241


title: RHP201


title: RHP462


title: ABRF-454-UI-B-2


title: RHP200


title: RHP177


title: RHP074


title: RHP050


title: RHP062


title: RHP033


title: RHP005


title: RHP015


title: RHP028


title: RHP217


title: KYSE70 shTP63(2) Day 4

city: Boston

first: Shouyong

last: Peng

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Sample 5

data_processing:
Aligned to human reference genome (hg19) and exon-exon junctions (ensembl v64) with PRADA pipeline.
Transcriptome was collapsed to gene level using the GENCODE v12 transcriptome model.
RPKM values were generated by RNA-seQC for each experiment, log2 transformed (log2 (RPKM+1)), and quantile-normalized.
Gene expressions for each condition (shSOX2, and shTP63) were represented by the mean of duplicates, and were used to calculate the log2 fold change between two experimental conditions.
Genome_build: hg19 for human genome, ensembl v64 for exon-exon junctions.
Supplementary_files_format_and_content: Matrix text file, quantile-normalized log2 (RPKM+1)) values for each sample

source_name: KYSE70_shTP63_Day 4

extract_protocol: For each sample, polyA+ RNA was isolated from 5 ug of total RNA using Dynabeads mRNA DIRECT Kit (Ambion). RNA was fragmented by incubation at 98 °C for 41 min in 1× RNA restoration buffer (Ambion). cDNA was synthesized with 20-40 ng of polyA+ RNA with a peak length around 600-700 bases with the use of SuperScript III Reverse Transcriptase, SuperScript Double-Stranded cDNA Synthesis kit, and random primers (Invitrogen). Primers were annealed at room temperature for 10 min followed by first strand synthesis for 1 h at 50°C and second strand synthesis for 2.5 h at 16°C. Following cDNA size selection with 1.8× AMPure XP beads (Beckman Coulter), end repair, and A-tailing, adapter ligation was performed using the TruSeq DNA Sample Preparation kit (Illumina) according to manufacturer’s instruction. Adaptor-ligated cDNAs were cleaned up with 0.8× AMPure XP beads followed by 8 cycles of PCR with primers complementary to the adaptor sequences with indexes. The PCR products were purified with 0.8× AMPure XP beads and then subject to HiSeq 2000 sequencing.

treatment_protocol: Doxycycline 50ng/ml for 4 days

tag: cell line

tag: cell type

value: human esophageal squamous carcinoma cells

value: stably expressing pLKO-Tet-On-shTP63

tag: treated with

value: 50ng/ml of doxycyline for 4 days


title: KYSE70 shTP63(2) Day 0

description: Sample 4

source_name: KYSE70_shTP63_Day 0


title: KYSE70 shTP63(1) Day 4

description: Sample 6


title: KYSE70 shSOX2(2) Day 0

description: Sample 1

source_name: KYSE70_shSOX2_Day 0

value: stably expressing pLKO-Tet-On-shSOX2


title: Wildtype Adult OE 1

city: La Jolla

first: Miles

middle: F

last: Wilkinson

address: 9500 Gilman Dr

institute: The University of California, San Diego

description: sample_1 (wt)

data_processing:
1) Used TopHat2/Bowtie2 algorithms to align FASTQ reads to mm9 genome
2) Cuffdiff to generate transcriptome and calculate FPKM for each gene that encodes for olfactory receptors.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm values

source_name: olfactory epithelium

extract_protocol:
Trizol RNA isolation
libraries were constructed according to Illumina TruSeq protocol

tag: developmental stage

value: adult

value: olfactory epithelium


title: Wildtype Adult OE 2

description: sample_2 (3bko)


title: KYSE70 shSOX2(2) Day 4

description: Sample 2

source_name: KYSE70_shSOX2_Day 4


title: KYSE70 shSOX2(1) Day 4

description: Sample 3


title: RHP197


title: Adult replicate B

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: biological replicate 2

data_processing:
We trimmed low-quality nucleotides from the end of each read (Phred score <=2)
Reads were aligned to the mm9 genome using Tophat v.2.0.6 with no novel junctions
FPKM values were found by CuffDiff on each pair of biological replicates
Genes that were differentially expressed between adults and neonates were found by running CuffDiff on the adult and neonatal samples
Genome_build: mm9
Supplementary_files_format_and_content: FPKM text files contain expression level measurements from running CuffDiff on the biological replicates. The differential expression file was generated by running CuffDiff on the pairs of adult and neonatal samples, where sample 1 = adult  and sample 2 = neonate.

source_name: CD8+ T cells

extract_protocol:
RNA was isolated using Trizol (Invitrogen), following the protocol
Libraries were prepared with Illumina's TruSeq RNA prepration kit according to protocol

treatment_protocol: Naïve CD8+ T cells were collected from adults and neonates using magnetic beads. The donors expressed CD45.2, and the adults also expressed Thy1.1. Equal numbers of adult and neonatal cells were then co-transferred into an adult recipient mouse, who was subsequently infected with Listeria. Seven days post-infection, cells were sorted based on the CD45.2 and Thy 1.1 markers to differentiate between the adult and neonatal donor cells.

value: B6-Thy1.1/CyJ  gBT-I TCR

value: 2-3 months

value: CD8+ T cells

value: Adult


title: Adult replicate A

description: biological replicate 1


title: WT

status: Public on May 12 2014

city: Tianjin

first: Xuexia

last: Zhou

address: 154 Anshan Road

department: Tianjin Neurological Institute

institute: Tianjin Medical University General Hospital

description: Sample 1

data_processing:
Images generated by sequencers are converted by base calling into nucleotide sequences.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The clean reads were then aligned to the reference mouse genome and the corresponding annotated genes using the TopHat.
In the alignment, preliminary experiments were performed to optimize the alignment parameters to provide the most information on the alternative splicing events.
Genome_build: Mm9
Supplementary_files_format_and_content: tab-delimited text file includes the splicing loci on chrosome, gene name, ensemble ID, splicing types, and stantistially values for alternative splicing events between the two samples

source_name: WT_MEF cells

extract_protocol:
Cells were harvested and total RNA was extracted by Trizol reagent. Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected.
Libraries for paired-end sequencing were prepared using mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

value: wide type (WT)

value: embryonic tissues

value: Embryonic fibroblast cells


title: Neonate replicate B

description: biological replicate 2

value: 6-7 days

value: neonate


title: Neonate replicate A

description: biological replicate 1


title: pec_ptp1b_wt_+il10_rep2

city: Shenzhen

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

institute: Southern University of Science and Technology

data_processing:
rsem-calculate-expression --phred64-quals -seed-length 28 --bowtie-m 50
Only keep genes >1.0 in >=2 samples
EDASeq: withinLaneNormalization(data, "gc", which="full")
EDASeq:betweenLaneNormalization(data, which="full")
mean expression values between replicates
Genome_build: mm9
Supplementary_files_format_and_content: TSV file containing gene annotations (Ensembl) and expression values in normalised abundance estimates

source_name: Peritoneal macrophages

extract_protocol:
TRIzol
Illumina Standard protocol

treatment_protocol: Peritoneal cells were allowed to adhere to plastic for 24 hours

tag: genotype

value: wildtype

tag: treatment

value: +IL-10 (100ng/ml) 4 hours


title: pec_ptp1b_ko_+il10_rep2

tag: strain


title: oocyte_RNA-Seq

last: Wang

data_processing:
Paired reads were aligned with Tophat software against Mus musculus UCSC mm10 references.
Fragments per kilobase of exon per million fragments mapped (FPKM) were calculated using Cufflink.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for 1 Sample

source_name: MII oocytes

extract_protocol:
Metaphase II oocytes were collect by removing all somatic contaminants. Sample for RNA isolation was collected in Buffer RLT (RNeasy Micro Kit from QIAGEN).
The RNA-seq libraries were constructed as described (Tang et al., 2010). Briefly, reverse transcription was carried out at the first step. Then, free primers were removed by exonmulease I and a polyA tail was added to the 3' end of the first-strand cDNAs by terminal deoxynucleotidyl transferase. The cDNAs were amplified by PCR and subjected to construct a sequencing library sequenced by Illumina HiSeq 2000.

value: MII oocyte


title: pec_ptp1b_wt_+il10_rep1


title: pec_ptp1b_ko_+il10_rep1


title: pec_ptp1b_wt_untreated_rep1

value: Mock


title: pec_ptp1b_ko_untreated_rep2


title: pec_ptp1b_ko_untreated_rep1


title: GTW-2

city: Geneva

first: Denis

last: Basquin

state: Geneva

address: 30 Quai Ernest-Ansermet

department: Genetics & Evolution

country: Switzerland

institute: University of Geneva

data_processing:
Base calling Pipeline : HiSeq Control Soft. V.1.4.8 ; RTA 1.12.4.2 ; CASAVA 1.8.2
Sequenced inserts of 19 to 29 nucleotides were trimmed for adaptor sequence and mapped to the Dmel5.47 reference genome (dmel-all-chromosome-r5.47, dmel-all-intergenicr5.47, dmel-all-miRNA-r5.47, dmel-alltransposon-r5.47, dmel-all-tRNA-r5.47, hairpin_dme) using Burrows-Wheeler Alignment tool v.0.5.9
Inserts of size 23 to 29 nucleotides mapped to piRNA clusters (unique positions with 0 mismatches) and transposon sequences (allowing 1 mismatche) were recovered using Samtools v.0.1.17
Quantification of inserts overlapping the piRNA clusters and transposon sequences was done using SeqMonk v0.19 software (Babraham Bioinformatics), and libraries were normalized for comparison to miRNAs
Genome_build: Dmel 5.47
Supplementary_files_format_and_content: tab-delimited text files include the name and positions of the piRNA clusters or transposons, the read count quantifications and normalized value for each sample.

source_name: Ovary

growth_protocol: Flies were growth at 25°C

extract_protocol:
Small RNAs were extracted from heterozygous and homozygous Su(var)3-7R2a8 mutants ovaries using RNeasy Mini Kit (Qiagen) followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols. RNA fractions ranging from 15-30 nucleotides were isolated and purified from 15% polyacrylamide gels, modified by sequential ligation of 3’ and 5’ adapters. The constructs were purified again on an acrylamide gel to remove emtpy adapters and then reverse-transcribed and PCR-amplified. High-throughput sequencing was performed on a Illumina HiSeq 2000 (1x50 cycles) (FASTERIS SA, Switzerland).

value: 3-day old

tag: gender

value: female


title: E14-d0_RNA-seq

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
For hairpin-bisulfite sequencing data, each read was searched for adaptor and hairpin sequences with cross_match. Additional search on the 3’-end of sequence reads was conducted to eliminate any sub-string derived from hairpin sequence adaptor. After adaptor removal, sequence reads shorter than 40 bp were excluded from further analysis. To remove reads that are likely to be not bisulfite converted, read pairs with more than 3 methylated non-CpG in either arm were discarded.
Following steps were taken to retrieve and map the original sequences onto reference genome: 1) the two arms for each read pair were first subjected to C->T and G->A conversion, and then globally aligned using Needleman-Wunsch algorithm; 2) the sequence reads with identity less than 90% between two arms were discarded; 3) after trimming the overhangs of the aligned sequences, original sequences were recovered according to the alignment information; 4) the recovered original sequences were mapped to mouse genome using bowtie with parameters ( -n 2 –l 40 –k 1 –m 1 --best), and only uniquely mapped reads were retained.
The methylation patterns for all cytosines were extracted based on the mapping result and the raw sequences. To eliminate the influence of SNP on the data analysis, the methylation pattern calling for nucleotide bases inconsistent with reference genome were masked.
For the RNA-seq data, all the pair-end reads were mapped to the mouse reference genome using TopHat (version 2.0.3). Genome annotation files with GTF format for Known Genes were downloaded from UCSC. Reads per kilobase of transcript per million reads (RPKM) values were calculated for each gene using Cufflinks software (version 2.0.2) with default parameters and normalized using quantile method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include methylation level and methylation fidelity for each CpG dyads; tab-delimited text files include methylation level for cytosines in CHG and CHH context. tab-delimited text files include RFKM for each transcript.

source_name: Embryonic stem cell

growth_protocol: Mouse ES cells (E14TG2a) were maintained on gelatin-coated dishes in ATCC-formulated Dulbecco's Modified Eagle's Medium (ATCC), supplemented with 0.1 mM of 2-mercaptoethanol, 10% fetal bovine serum (StemCell Technologies), 2mM L-glutamine, 0.1mM MEM nonessential amino acid, 100U/ml penicillin, 10µg/mlstreptomycin, and 10ng/ml LIF (StemCell Technologies). The mES cells were passaged every 2 days at a ratio of 1:5 by washing with PBS, dissociating with 0.25% trypsin (GIBCO) for 3 min at 37°C, and resuspending in mES media. Media were changed daily. The nondifferentiated state of mES cells was measured using the Alkaline Phosphatase Kit from Stemgent.

extract_protocol:
Mouse ES cell genomic DNA was isolated using DNeasy Blood and Tissue kit (Qiagen, Frederick, MD). Total RNA was extracted with the miRNeasy extraction kit (Qiagen, Frederick, MD).
Ten-microgram mouse genomic DNA was spiked with 0.01% unmethylated cl857 Sam7 Lambda DNA (Promega) and sonicated to 200bp fragments with Covaris S2 (AB). After purification (PureLink® PCR Purification Kit, Invitrogen), DNA fragments were then subjected to end repair with the end repair enzyme mix (NEB), dA tailing using Klenow 3’-5’ exo- (NEB) with purification at each step. Ligation to Biotin-modified hairpin adapter (P-CGCCGGCGGCAAG/iBiodT/GAAGCCGCCGGCGT) and Illumina TruSeq adapters were performed using T4 DNA ligase (NEB) overnight. Adapter-ligated DNA was digested with MseI and MluCI (NEB) for 1h at 37°C. After purification, DNA fragments were then pulled down using Dynabeads® MyOne™ Streptavidin C1 beads (Invitrogen). Bisulfite conversion was performed using the EpiTect Bisulphite Kit (Qiagen). After bisulfite conversion, the single-stranded uracil-containing DNA was subjected to 12 cycles of PCR reaction with Illumina TruSeq PCR primers (with specific index) and 2.5 U Pfu TurboCx Hotstart DNA polymerase (Agilent) to recover enough DNA for sequencing. After purification, size selection of 400-600 bp fragments was conducted with LabChip XT DNA Assay (Caliper) to yield longer sequences that are more amenable for unambiguous mapping to the reference sequence. RNA-seq libraries were constructed according to Illumima protocol and sequenced with the Illumina Hiseq 2000.

treatment_protocol: To induce differentiation, the mES cells were passaged and then cultured in ES cell culturing media without LIF. Media were changed every 2 days.

tag: cell subtype

value: undifferentiated state

value: 0 day of undifferentiated


title: E14-d6_hairpin-BS

value: spontaneous differentiated state

value: 6 day of spontaneous differentiated


title: E14-d0_hairpin-BS


title: GTW-1


title: SK-HEP-1, 4U, miRNA (SOLiD 5500xl)

status: Public on May 10 2014

city: Taipei

first: mike

last: thang

state: Taipei

address: 128 Academia Road, Section 2, Nankang

department: Genome Research Center

country: Taiwan

institute: Academia Sinica

description:
microRNA; small RNA-Seq
4U
Processed data file: miRNA_solid5500.txt

data_processing:
miRNA data utilized in-house built miRNA pipeline combined with publicly available tools such as bowtie and cutadapt for pre data processing.
Sequenced reads were then trimmed for adaptor sequence, low-quality sequence or low-complexity or reads shorter than 16 bp and longer than 30 bp, then mapped to mm9 for the CL2 samples and hg19 for the human sample whole genome using bowtie v0.12.7 with perfect match for known miRNA detection. Transcripts Per Million (TPM) were calculated.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files. 'Transcriptome.txt' includes FPKM values for each mRNA sample; 'miRNA_solid5500.txt', 'miRNA_solid3.txt', and 'fCL_5500.txt' include TPM for each miRNA sample.

source_name: Liver cell line SK-HEP-1, control, 4 hours

growth_protocol: Cells were cultured in DMEM medium with 10% FBS.

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA were isolated from total RNA samples by Poly(A) Purist-MAG kit.
SOLiD™ total RNA-seq kit for whole transcriptome libraries and small RNA libraries kits were used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard SOLiD™protocols.

treatment_protocol: Treated with 0.5 mg/ml Antrodia cinnamomea fruiting body ethanol extracts or 0.5 mg/ml DMSO.

value: DMSO control

tag: time

value: 4 hours


title: SK-HEP-1, 2U, miRNA (SOLiD 5500xl)

description:
microRNA; small RNA-Seq
2U
Processed data file: miRNA_solid5500.txt

source_name: Liver cell line SK-HEP-1, control, 2 hours

value: 2 hours


title: SK-HEP-1, 4T, miRNA (SOLID 3)

description:
microRNA; small RNA-Seq
4T
Processed data file: miRNA_solid3.txt

source_name: Liver cell line SK-HEP-1, Antrodia cinnamomea treated, 4 hours

value: Antrodia cinnamomea


title: SK-HEP-1, 2T, miRNA (SOLiD 5500xl)

description:
microRNA; small RNA-Seq
2T
Processed data file: miRNA_solid5500.txt

source_name: Liver cell line SK-HEP-1, Antrodia cinnamomea treated, 2 hours


title: SK-HEP-1, 4U, miRNA (SOLID 3)

description:
microRNA; small RNA-Seq
4U
Processed data file: miRNA_solid3.txt


title: SK-HEP-1, 4T, miRNA (SOLiD 5500xl)

description:
microRNA; small RNA-Seq
4T
Processed data file: miRNA_solid5500.txt


title: SK-HEP-1, 2U, miRNA (SOLID 3)

description:
microRNA; small RNA-Seq
2U
Processed data file: miRNA_solid3.txt


title: pec_ptp1b_wt_untreated_rep2


title: SK-HEP-1, 4T, mRNA (SOLID 3)

description:
mRNA; RNA-Seq
4T
Processed data file: Transcriptome.txt

data_processing:
mRNA data used Galaxy web portal for abundance measurements. Sequenced reads were then trimmed for adaptor sequence, low-quality sequence or low-complexity mapped to hg19 with 2 mismatches using tophat and cufflinks for abundance measurement.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009 (PMID 19528076). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files. 'Transcriptome.txt' includes FPKM values for each mRNA sample; 'miRNA_solid5500.txt', 'miRNA_solid3.txt', and 'fCL_5500.txt' include TPM for each miRNA sample.


title: BNL CL.2, 4T, miRNA (SOLiD 5500xl)

description:
microRNA; small RNA-Seq
4T
Processed data file: fCL_5500.txt

data_processing:
miRNA data utilized in-house built miRNA pipeline combined with publicly available tools such as bowtie and cutadapt for pre data processing.
Sequenced reads were then trimmed for adaptor sequence, low-quality sequence or low-complexity or reads shorter than 16 bp and longer than 30 bp, then mapped to mm9 for the CL2 samples and hg19 for the human sample whole genome using bowtie v0.12.7 with perfect match for known miRNA detection. Transcripts Per Million (TPM) were calculated.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text files. 'Transcriptome.txt' includes FPKM values for each mRNA sample; 'miRNA_solid5500.txt', 'miRNA_solid3.txt', and 'fCL_5500.txt' include TPM for each miRNA sample.

source_name: Liver cell line BNL CL.2, Antrodia cinnamomea treated, 4 hours

value: BNL CL.2