title: RNA-seq; Sample 30_HTS583


title: Wild Type

status: Public on Feb 28 2014

type: SRA

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

library_source: transcriptomic

data_processing:
Read Alignment: Bowtie v 1.0.0, default parameters
Unaligned reads filtered: Samtools v0.1.18, options:  view -F 0x04
Mapped reads intersecting with exons & miRNAs found: BEDTools (intersectBed) v2.12.0 - target BED files from UCSC genome browser
Count reads intersecting with features (standard Linux tools - awk, sort, uniq)
Genome_build: hg18
Supplementary_files_format_and_content: BED, reads intersecting with exons and miRNAs, Excel file (read counts)

molecule: total RNA

organism: Homo sapiens

source_name: HEK293 cells

growth_protocol: The human embryonic kidney cell line HEK293 was maintained and passaged according to established cell culture conditions

extract_protocol:
RNA and DNA were isolated using Trizol according to standard methodology. The RNA was quality tested and size selected on a denaturing polyacrylamide gel (19-29 bases).
Tagged 3’ adaptors and 5’ adaptors were ligated to the recovered RNA to ensure strand specificity. The material was used for cDNA synthesis.

treatment_protocol: When the cells were about 80% confluent, the medium in one well was replaced and 100 μg/ml ethyl methanesulfonate (EMS; Sigma) was added. Cells were grown in the presence of EMS for 24 hours followed by a 24 hour recovery period in fresh medium.

tag: cell line

tag: cell type

value: human embryonic kidney cells

tag: exposed to

tag: exposure length


title: HCT116-DNaseI_3

city: New York

first: Matthew

middle: T

last: Maurano

state: NY

address: 435 East 30th Street

department: Institute for Systems Genetics

country: USA

institute: NYU School of Medicine

library_source: genomic

data_processing:
Methylation values: Capture bisulfite reads were mapped to the human genome (hg19) using Bismark (Krueger and Andrews 2011) and bowtie2 beta 6 (Langmead et al. 2009) with the options “-n 1” and excluding duplicate reads and combining reads from the top and bottom strands. Methylation was monitored at CpGs with ≥8 read coverage, and averaged for all CpGs within the 150 bp window at each CTCF site.
Peak: ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. DNase data used unthresholded hotspots.
Density: Smoothed density tracks were generated using bedmap (http://code.google.com/p/bedops/) to count the number of tags overlapping a sliding 150-bp window, with a resolution of 20 bp (Neph et al. 2012a). Density tracks for display were normalized for sequencing depth by a global linear scaling to 10 million tags.
Alignment: ChIP-seq and DNase data were mapped to the human genome (GRCh37/ hg19) using bowtie (Langmead et al. 2009) with the options ‘‘bowtie -n 2 -m 1 -e 70 --best’’ allowing up to three mismatches. Reads mapping to multiple locations were then excluded, and reads with identical 5’ ends and strand were presumed to be PCR duplicates and were excluded using Picard MarkDuplicates.
Genome_build: hg19
Supplementary_files_format_and_content: .bed: peak locations generated using the hotspot algorithm; .bed proportion of bisulfite tags indicating methylation per CpG (proportion methylation in bed score column, number of total reads in 7th column) .bw: the number of tags overlapping a sliding 150-bp window, with a resolution of 20 bp; .bam: tags mapped to the human genome

molecule: genomic DNA

source_name: HCT116 colorectal cancer cells

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.

extract_protocol:
Digital DNaseI was performed by DNaseI digestion of intact nuclei, isolating DNaseI 'double-hit' fragments as described in Sabo et al. (2006), 20-50 ng of DNA was end-repaired, adenine ligated to Illumina adapters was added, and then a Solexa library was made for sequencing.
20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and then a Solexa library was made for sequencing.

tag: experiment

value: Dnase-Hypersensitivity

tag: treatment

value: No special treatment

tag: replicate


title: H3K4me2_ChIP-seq; Sample 27_HTS722

status: Public on Feb 27 2014

city: Corvallis

first: Kristina

middle: M

last: Smith

state: OR

department: Biochemisty and Biophysics

institute: Oregon State University

data_processing:
Basecalls were made with RTA1.8_CASAVA1.7
ChIPSeq reads were trimmed of adapter sequence and mapped to the F. graminearum genome with BWA software using default options
RNASeq reads were trimmed of adapter sequence and mapped to the F. graminearum genome with Tophat software with options (-a 5 -m 1 -i 30 -I 2000)
samtools were used to convert BWA or Tophat output to sorted bam files
cufflinks v2.1.1 was used (--max-bundle-length 20000 -I 2000 --min-intron-length 30) to calculate FPKM values for Broad assembly 3 transcripts from sorted bam files of RNA-seq reads
Genome_build: Broad chromosome assembly 3
Supplementary_files_format_and_content: ChIP-seq processed files are tab delimited EpiChIP output containing gene name, NLCS value
Supplementary_files_format_and_content: RNA-seq processed files are tab delimited cufflinks output containing gene name, FPKM value

organism: Fusarium graminearum

source_name: mycelium

extract_protocol: DNA obtained by ChIP was end-repaired and ligated to adapters as described elsewhere {Pomraning, 2012 #12099}. Fragments (300 to 500 bp long) were gel-purified and amplified by 21-24 cycles of PCR with Phusion polymerase (Finnzymes Oy, NEB) and Illumina PCR primers {Pomraning, 2012 #12099}.

tag: strain number

tag: genotype

value: DELkmt6::neoR kmt6+::HygR

tag: nitrogen level

value: high

tag: antibody

value: Millipore 07-030


title: H3K4me2_ChIP-seq; Sample 28_HTS724


title: HCT116-DNMT3BKO-CTCF_1

source_name: HCT116 colorectal cancer cells DNMT3BKO

extract_protocol:
Cells were crosslinked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 degrees C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross linking in immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and then a Solexa library was made for sequencing.
20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and then a Solexa library was made for sequencing.

value: CTCF ChIP-seq


title: H3K27me3_ChIP-seq; Sample 26_HTS725

value: Active Motif 39155


title: HeLa

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: A TAIL-seq sample from HeLa

data_processing:
Library strategy: TAIL-seq
The base calls and signal intensities were acquired from HiSeq 2500 after processing by Illumina RTA 1.17.21.3. The read 1 sequences were aligned to the common contaminants set, which is composed of rDNA repeat units (GenBank accession BK000964.1 for NIH3T3 and U13369.1 for HeLa), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences, and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP 2013-03-31 with maximum 5% mismatches allowed. Clusters with any match to the contaminants were removed from the subsequent analyses. The sequences having completely identical nucleotides in the 21st to 35th cycle in read 1 (representative region of the insert) and the 1st to 15th cycle in read 2 (degenerate bases in 3′ adapter) are deduplicated by leaving only a cluster with the maximum PHRED quality sum of read 1. The degenerate and fixed delimiter sequence in 3′ adapter was clipped out from read 2 by searching perfect match of delimiter sequence (‘GTCAG’ as in the direction of read 2) between the 14th and 16th cycles in read 2. The clusters missing a delimiter sequence or having low diversity in degenerate region (at least two occurrences for all of A, C, G and T) were removed from further analyses.
The fluorescence signal intensities were processed into “Normalized T signal” as described in fig. S1A. The signals from a spike-in sample were purified with an outlier filter based on robust Mahalanobis distance (mvoutlier package 1.9.9; quan=0.5, alpha=0.025). Random 500 clusters per each spike-in were chosen for parameter calculation of a Gaussian mixture hidden Markov model (GMHMM). We trained the model using Baum-Welch algorithm implemented in the GHMM library (http://ghmm.org) with topology and initial parameters shown in fig. S1A and table S7 and S8 (1,000 iterations). The procedure was iterated to maximize likelihood, not using any property (eg. designed length of poly(A) tail) of spike-ins. Normalized T signals outside the range of [-5, 5] were clipped into the range for both training and later calculations.
The length of poly(A) tails were first measured with base call-based “Strategy II” described in fig. S1A. For clusters with the measured length is shorter than 8 nt, the length is called as the final poly(A) tail length. For the others, normalized T signals starting from the first position in T-stretch detected by Strategy II were analyzed with the GMHMM. The hidden states were decoded with the standard Viterbi algorithm implemented in the GHMM library. The number of cycles with state 1 and 2 was called as the length of poly(A) tail. For the estimation of performance, we applied the process to all spike-in samples except the clusters used for the parameter fitting of the model.
The remaining reads after contaminant filter and the first duplication filters were then aligned to the genome sequences (UCSC mm10 for NIH3T3 and UCSC hg19 for HeLa, positions of splicing junctions were processed from the UCSC Genome Browser database for version of Jan 24, 2013) using GSNAP 2013-03-31. Three different versions of alignments to genome were used in this study. (1) R1 alignment: using only the full read 1 sequences which are 51 nt long. This was used for identification of a cluster. (2) R2 short alignment: using only 40 nt right next to the 3′ adapter of read 2. This was used in searching for the poly(A)-free 3′ hydroxyl ends. (3) paired alignment: using the full read 1 sequences and part of read 2 sequences trimmed of degenerate bases and delimiter. We filtered out poly(A) stretches encoded from genome using this alignment set. All the alignments were performed with maximum mismatches of 5%, minimum mapping quality of 3. All multi-mapped reads were removed. The remaining PCR artifacts with few mismatches were removed again using the R1 alignment with 15 degenerate bases inside the 3′ adapter region. To detect that kind of artifacts, we clustered the R1 alignments with maximum distance between mapped positions of 10 bp, they were then clustered again within the first cluster using degenerate bases from read 2 of respective reads with CD-HIT-EST 4.5.4 (word size=6, sequence identity=0.85). For a set of detected duplicates, we chose a read with maximum sum of PHRED quality in read 1 to leave.
For classification and transcript-level analyses, we compiled reference annotations for human and mouse using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The R1 alignments were annotated with intersection with the compiled annotations using BEDTools {Quinlan, 2010 #66}. When multiple annotations were overlapped to an alignment, we chose a class for the statistics requiring exclusive assignment of a genomic source type by the following priority: miRNA, rRNA, tRNA, Mt-tRNA, snoRNA, scRNA, srpRNA, snRNA, lncRNA, RNA, ncRNA, misc_RNA, Cis-reg, ribozyme, RC, IRES, frameshift_element, LINE, SINE, Simple_repeat, Low_complexity, Satellite, DNA, LTR, CDS, 3′ UTR, 5′ UTR, intron, Other, Unknown (higher priority first). The transcript-level analyses were performed using our custom non-redundant RefSeq (nrRefSeq) transcript set, which is a reduced set retaining only the longest isoform or transcript when regions overlap with each other. The positions of read 1 in nrRefSeq transcripts were positioned with BEDTools intersection between alignments to genome sequences and nrRefSeq annotation set, and then translated to the transcript-level coordination with in-house software.
As poly(A) tails were initially detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3′ end modification of poly(A) tails was limited to the last 30 nucleotides of insert. To exclude A stretches obviously encoded from genomic sequence (with or without 3′ end modifications), we masked detected poly(A) tail ranges with read 2 alignments so that the 3′-most position of alignable (not clipped) is eliminated from poly(A) tail or its 3′ end modifications. All statistics regarding transcript-level modification rates were calculated for transcripts having more than 200 tags with poly(A) tails longer than 8 nt.
Genome_build: hg19 for HeLa, mm10 for NIH3T3
Supplementary_files_format_and_content: The .csv files contain the poly(A) tail length distribution and 3' end modification frequencies next to poly(A) tails for all detected transcripts with >= 30 poly(A)+ tags

source_name: HeLa

extract_protocol:
Total RNAs were extracted from NIH3T3 or HeLa cells by TRIzol reagent (Invitrogen, 15596-018) and purified by RNeasy MinElute column (Qiagen, 74204) according to manufacturer’s instruction.
The RNA was depleted of rRNA by using Ribo-zero kit (Epicentre, MRZH11124), ligated to 3′ adapter and partially digested by RNase T1 (Ambion, AM2283). The fragmented RNAs were pull-downed with streptavidin beads (Invitrogen, 11206D), and phosphorylated by PNK reaction (Takara, 2021B) and gel purified in the range of 500 – 1000 nucleotides. The purified RNAs were ligated to 5′ adapter, subjected to reverse-transcription (Invitrogen, 18080085) and amplified by PCR using Phusion DNA polymerase (Thermo, F-530L). PCR products were gel purified again. All adapters and primers are synthesized by IDT.

value: HeLa

value: human cervical cancer cell line


title: HeLa-miR-1-6h

description: TAIL-seq for HeLa cell line 6h post-transfection of miR-1

data_processing:
The base calls and signal intensities were acquired from HiSeq 2500 after processing by Illumina RTA 1.17.21.3. The read 1 sequences were aligned to the common contaminants set, which is composed of rDNA repeat units (GenBank accession BK000964.1 for NIH3T3 and U13369.1 for HeLa), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences, and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP 2013-03-31 with maximum 5% mismatches allowed. Clusters with any match to the contaminants were removed from the subsequent analyses. The sequences having completely identical nucleotides in the 21st to 35th cycle in read 1 (representative region of the insert) and the 1st to 15th cycle in read 2 (degenerate bases in 3′ adapter) are deduplicated by leaving only a cluster with the maximum PHRED quality sum of read 1. The degenerate and fixed delimiter sequence in 3′ adapter was clipped out from read 2 by searching perfect match of delimiter sequence (‘GTCAG’ as in the direction of read 2) between the 14th and 16th cycles in read 2. The clusters missing a delimiter sequence or having low diversity in degenerate region (at least two occurrences for all of A, C, G and T) were removed from further analyses.
The fluorescence signal intensities were processed into “Normalized T signal” as described in fig. S1A. The signals from a spike-in sample were purified with an outlier filter based on robust Mahalanobis distance (mvoutlier package 1.9.9; quan=0.5, alpha=0.025). Random 500 clusters per each spike-in were chosen for parameter calculation of a Gaussian mixture hidden Markov model (GMHMM). We trained the model using Baum-Welch algorithm implemented in the GHMM library (http://ghmm.org) with topology and initial parameters shown in fig. S1A and table S7 and S8 (1,000 iterations). The procedure was iterated to maximize likelihood, not using any property (eg. designed length of poly(A) tail) of spike-ins. Normalized T signals outside the range of [-5, 5] were clipped into the range for both training and later calculations.
The length of poly(A) tails were first measured with base call-based “Strategy II” described in fig. S1A. For clusters with the measured length is shorter than 8 nt, the length is called as the final poly(A) tail length. For the others, normalized T signals starting from the first position in T-stretch detected by Strategy II were analyzed with the GMHMM. The hidden states were decoded with the standard Viterbi algorithm implemented in the GHMM library. The number of cycles with state 1 and 2 was called as the length of poly(A) tail. For the estimation of performance, we applied the process to all spike-in samples except the clusters used for the parameter fitting of the model.
The remaining reads after contaminant filter and the first duplication filters were then aligned to the genome sequences (UCSC mm10 for NIH3T3 and UCSC hg19 for HeLa, positions of splicing junctions were processed from the UCSC Genome Browser database for version of Jan 24, 2013) using GSNAP 2013-03-31. Three different versions of alignments to genome were used in this study. (1) R1 alignment: using only the full read 1 sequences which are 51 nt long. This was used for identification of a cluster. (2) R2 short alignment: using only 40 nt right next to the 3′ adapter of read 2. This was used in searching for the poly(A)-free 3′ hydroxyl ends. (3) paired alignment: using the full read 1 sequences and part of read 2 sequences trimmed of degenerate bases and delimiter. We filtered out poly(A) stretches encoded from genome using this alignment set. All the alignments were performed with maximum mismatches of 5%, minimum mapping quality of 3. All multi-mapped reads were removed. The remaining PCR artifacts with few mismatches were removed again using the R1 alignment with 15 degenerate bases inside the 3′ adapter region. To detect that kind of artifacts, we clustered the R1 alignments with maximum distance between mapped positions of 10 bp, they were then clustered again within the first cluster using degenerate bases from read 2 of respective reads with CD-HIT-EST 4.5.4 (word size=6, sequence identity=0.85). For a set of detected duplicates, we chose a read with maximum sum of PHRED quality in read 1 to leave.
For classification and transcript-level analyses, we compiled reference annotations for human and mouse using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The R1 alignments were annotated with intersection with the compiled annotations using BEDTools {Quinlan, 2010 #66}. When multiple annotations were overlapped to an alignment, we chose a class for the statistics requiring exclusive assignment of a genomic source type by the following priority: miRNA, rRNA, tRNA, Mt-tRNA, snoRNA, scRNA, srpRNA, snRNA, lncRNA, RNA, ncRNA, misc_RNA, Cis-reg, ribozyme, RC, IRES, frameshift_element, LINE, SINE, Simple_repeat, Low_complexity, Satellite, DNA, LTR, CDS, 3′ UTR, 5′ UTR, intron, Other, Unknown (higher priority first). The transcript-level analyses were performed using our custom non-redundant RefSeq (nrRefSeq) transcript set, which is a reduced set retaining only the longest isoform or transcript when regions overlap with each other. The positions of read 1 in nrRefSeq transcripts were positioned with BEDTools intersection between alignments to genome sequences and nrRefSeq annotation set, and then translated to the transcript-level coordination with in-house software.
As poly(A) tails were initially detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3′ end modification of poly(A) tails was limited to the last 30 nucleotides of insert. To exclude A stretches obviously encoded from genomic sequence (with or without 3′ end modifications), we masked detected poly(A) tail ranges with read 2 alignments so that the 3′-most position of alignable (not clipped) is eliminated from poly(A) tail or its 3′ end modifications. All statistics regarding transcript-level modification rates were calculated for transcripts having more than 200 tags with poly(A) tails longer than 8 nt.
Genome_build: hg19
Supplementary_files_format_and_content: The csv files contain the poly(A) tail length distribution and 3' end modification frequencies next to poly(A) tails for all detected transcripts with >= 30 poly(A)+ tags

growth_protocol: HeLa cells were maintained in DMEM (Welgene) supplemented with 10% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted from NIH3T3 or HeLa cells by TRIzol reagent (Invitrogen, 15596-018) and purified by RNeasy MinElute column (Qiagen, 74204) according to manufacturer’s instruction.
The RNA was depleted of rRNA by using Ribo-zero kit (Epicentre, MRZH11124), ligated to 3′ adapter and partially digested by RNase T1 (Ambion, AM2283). The fragmented RNAs were pull-downed with streptavidin beads (Invitrogen, 11206D), and phosphorylated by PNK reaction (Takara, 2021B) and gel purified in the range of 500-1000 nucleotides. The purified RNAs were ligated to 5′ adapter, subjected to reverse-transcription (Invitrogen, 18080085) and amplified by PCR using Phusion DNA polymerase (Thermo, F-530L). PCR products were gel purified again. All adapters and primers are synthesized by IDT.

treatment_protocol: HeLa cells were transfected with 50 nM of synthetic miR-1 duplex using Lipofectamine 2000 (Life Technologies). Total RNAs were extracted at 0, 3, 6, and 9 hr after transfection. miR-1 guide 5′- UGGAAUGUAAAGAAGUAUGUA-3′;; miR-1 passenger 5′-CAUACUUCUUUACAUUCCAUU- 3′.

value: human cervical cancer cells

tag: transfected with

value: synthetic miR-1 mimic

tag: time point

value: 6hrs post-transfection


title: HCT116-CTCF_1

description: This biological replicate have been previously released in GSE30263, but the data has been reprocessed to be consistent wit the new data in this study.


title: H3K4me3_ChIP-seq; Sample 24_HTS638

value: abcam ab 8580


title: P

city: Lanzhou

first: Ruiqing

last: Zhu

state: Gansu

address: DingxiSouth Road 197

department: Instituye of biology

country: China

institute: Gansu Academy of Sciences

data_processing:
Sequencing-received raw image data were transformed by base calling into sequence data. Prior to mapping reads to the reference database, all sequences were filtered to remove 3′ adaptor sequence, low quality sequences (tags with unknown sequences ‘N’), tags with a copy number of 1 (probably sequencing error), and tags which are too long or too short, leaving clean tags of 21 nt. For annotation, all clean tags were mapped to the reference sequences, and a mismatch of only 1 bp was considered.
The clean reads mapped to reference database from multiple genes were filtered.
The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags)

organism: Reaumuria songarica

source_name: leaf

growth_protocol: The three-year-old plants were transferred to a greenhouse under the following conditions: 150 µmol m-2∙s-1 (fluorescent tubes), photoperiod 16 h light/8 h darkness, day/night temperature of 25/20 °C. The plants were washed with deionized water to remove surface contaminants. Soil attached to roots was also rinsed off with deionized water, and then the plants were cultivated in 1/8 Murashige and Skoog medium solution with insufflating air for two weeks to accommodate the liquid environment during treatments.

extract_protocol:
CTAB-method
library construction, and sequencing were carried out at Beijing Genome Institute at Shenzhen, China. An extract of 8 μg of total RNA was obtained and treated with oligo(dT) magnetic bead adsorption to purify mRNA; oligo(dT) was then used as a primer to synthesize the first- and second-strand cDNA. The 5′-ends of tags can be generated by two types of endonuclease: NlaIII or DpnII. Then, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and severs the CATG sites. Fragments other than the 3′-cDNA fragments connected to oligo(dT) beads are washed away, and the Illumina adaptor 1 is ligated to the sticky 5′-end of the digested bead-bound cDNA fragments. The junction of the Illumina adaptor 1 and the CATG site constitutes the recognition site of MmeI, which is a type of endonuclease with separate recognition and digestion sites; it breaks 17 bp downstream of the CATG site, producing tags with adaptor 1. After removal of 3′ fragments with magnetic beads precipitation, the Illumina adaptor 2 is ligated to the 3′-ends of tags, acquiring tags with different adaptors of both ends to form a tag library.

treatment_protocol: The experiment was arranged with two treatments (untreated and PEG-treated) and three replications. The untreated samples were maintained with the cultivating conditions as described previously. For drought treatment, 15% PEG6000 was added to the solution for dissolving. All the plants were treated for 12 h, from 6:00 to 18:00.

tag: age

value: 15% PEG for 12h


title: H3K4me3_ChIP-seq; Sample 23_HTS636

value: low


title: H3K4me2_ChIP-seq; Sample 21_HTS485


title: H3K27me3_ChIP-seq; Sample 15_HTS486


title: H3K4me2_ChIP-seq; Sample 19_HTS405


title: H3K36me3_ChIP-seq; Sample 16_HTS637

value: abcam ab 9050


title: H3K27me3_ChIP-seq; Sample 25_HTS723


title: H3K27me3_ChIP-seq; Sample 14_HTS484


title: H3K4me3_ChIP-seq; Sample 10_HTS632

value: FMF1 (FGSC9075)

value: WT


title: H3K4me3_ChIP-seq; Sample 11_HTS634


title: RNA-seq; Sample 29_HTS582

extract_protocol: mRNA was isolated using a Poly(A)Purist MAG kit (Ambion). We removed DNA by treatment with RNase-free DNAase (Qiagen), followed by column clean-up according to manufacturers instructions. We used Illumina TruSeq RNA Sample Preparation kits to make RNA-seq libraries


title: H3K4me2_ChIP-seq; Sample 9_HTS716


title: H3K4me2_ChIP-seq; Sample 8_HTS714


title: H3K4me2_ChIP-seq; Sample 6_HTS479


title: H3K4me2_ChIP-seq; Sample 7_HTS481


title: H3K36me3_ChIP-seq; Sample 5_HTS635


title: H3K4me2_ChIP-seq; Sample 20_HTS483


title: H3K27me3_ChIP-seq; Sample 1_HTS480


title: H3K4me2_ChIP-seq; Sample 22_HTS718


title: third_OSVZ_17ext

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

state: California

address: UC Santa Barbara

department: NRI

institute: UCSB

data_processing:
the reads were corrected with SOLiD(TM) Accuracy Enhancer Tool (SAET) v.2.2 by nosampling and 3 globalrounds
the reads were aligned to human miRNA precusors from miRBase version 16 by using SOLiD small RNA pipeline version 0.5, reads aligned with muliti miRNA species were filtered
reads aligned with muliti miRNA species were filtered and read count for each miRNAs were collected with Perl scripts
Genome_build: miRBase 16
Supplementary_files_format_and_content: tab-delimited text file for miRNA profiling

organism: Macaca fascicularis

source_name: Third Replicate Outer Sub Ventricular Zone Ext, E82 area 17

growth_protocol: Microdissection was performed on a LEICA LDM7000 equipped with a UV laser. Seven brain regions (VZ17, OSVZ17int, OSVZ17ext, CP17, VZ18, OSVZ18, CP18). OSVZ17int corresponds to the inner (apical) third of OSVZ 17 and OSVZ17ext to the most outer (basal) third of OSVZ 17, located immediately below the Outer Fiber Layer (Smart et al., 2002; Betizeau et al., 2013)

extract_protocol:
RNA was extracted from each section by microRNeasy kit from Qiagen with DTT to stabilize RNA
Libraries were prepared with SOlID Total RNA-seq kit (mirRNA library size selection)

tag: tissue

value: developing brain

tag: brain region


title: third_CP_18

source_name: Third Replicate Cortical Plate, E82, area 18


title: third_OSVZ_18

source_name: Third Replicate Outer Sub Ventricular Zone, E82 area 18


title: third_VZ_17

source_name: Third Replicate Ventricular Zone, E82, area 17


title: second_VZ_18

source_name: Second Replicate Ventricular Zone, E79, area 18


title: third_OSVZ_17int

source_name: Third Replicate Outer Sub Ventricular Zone Int, E82 area 17


title: third_CP_17

source_name: Third Replicate Cortical Plate, E82, area 17


title: H3K27me3_ChIP-seq; Sample 3_HTS717


title: H3K4me2_ChIP-seq; Sample 18_HTS403


title: second_OSVZ_18

source_name: Second Replicate Outer Sub Ventricular Zone, E79 area 18


title: H3K27me3_ChIP-seq; Sample 13_HTS406


title: second_VZ_17

source_name: Second Replicate Ventricular Zone, E79, area 17


title: second_CP_18

source_name: Second Replicate Cortical Plate, E79, area 18


title: H3K36me3_ChIP-seq; Sample 17_HTS639


title: H3K27me3_ChIP-seq; Sample 12_HTS404


title: first_VZ_18

source_name: Ventricular Zone, E80, area 18


title: second_OSVZ_17_ext

source_name: Second Replicate Outer Sub Ventricular Zone Ext, E79 area 17


title: second_CP_17

source_name: Second Replicate Cortical Plate, E79, area 17


title: first_OSVZ_17int

source_name: Outer Sub Ventricular Zone Int, E80 area 17


title: H3K36me3_ChIP-seq; Sample 4_HTS633

source_name: mycelium


title: first_CP_17

source_name: Cortical Plate, E80, area 17


title: first_VZ_17

source_name: Ventricular Zone, E80, area 17


title: first_OSVZ_18

source_name: Outer Sub Ventricular Zone, E80 area 18


title: first_OSVZ_17ext

source_name: Outer Sub Ventricular Zone Ext, E80 area 17


title: H3K27me3_ChIP-seq; Sample 2_HTS482


title: mir124-3p_Illumina-2

description:
L006
RISC trap Immunoprecipitation

data_processing:
Library strategy: RISC trap immunoprecipitation
SOLiD data were aligned by Bioscope 2 and tophat2 was used for Illumina data
reads from both strands were count for each gene
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file for mRNA profiling

molecule: polyA RNA

source_name: HEK 293 cells

growth_protocol: RISC trap immunoprecipitation (Cambronne, et al  2012 PNAS)

extract_protocol:
RNA was extracted by trizol
Libraries were prepared with SOlID Total RNA-seq kit (whole transtriptome library size selection).

value: HEK 293


title: mir124-3p_Illumina-3

description:
L007
RISC trap Immunoprecipitation


title: mir124-3p_Illumina-1

description:
L008
RISC trap Immunoprecipitation


title: GRO-seq_TNFα_120m_2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: GRO-seq in AC16 cells treated for 120 minutes with TNFα (New submission, Processed and Sequenced together with the above 6 samples in GSE41323 )

data_processing:
Library strategy: GRO-Seq
Alignment: Short-reads were aligned to the human reference genome (hg19), including autosomes, X-chromosome, and one complete copy of an rDNA repeat (GenBank ID: U13369.1).  The SOAP2 software package (Li et al., 2009) was used to align reads with the following options: (1) all non-unique mappings were removed (-r 0), (2) three mismatches were allowed in each mapped read (-v 3), (3) low-quality reads with more than 10 ambiguous bases were removed (-N 10), and (4) for reads failing to align over the entire length of the read, the first 32 bp was used (-l 32).  SOAP2 output was processed using custom Perl scripts, and imported into R for most the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed

growth_protocol: AC16 human adult ventricular cardiomyocyte cells (Davidson et al. 2005) from the American Type Cell Culture (ATCC) were maintained in DMEM F-12 supplemented with 12.5% fetal bovine serum.

extract_protocol:
For the vehicle /α-amanitin samples, the isolated nuclei were treated with Vehicle DMSO or 1 μg/ml α-amanitin  for 15 minutes on ice prior to the run-on reaction. Nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of NTPs and 0.5% Sarkosyl in run-on buffer to allow a run-on of ~100 nucleotides.  The reaction was stopped by incubation with DNase I, followed by incubation with proteinase K.  Newly synthesized nascent RNAs were isolated by acid phenol-chloroform extraction, followed by ethanol precipitation.  After re-dissolving, the isolated RNAs were base-hydrolyzed with 0.2 N NaOH and the reaction was neutralized by the addition of 500 mM Tris×HCl, pH 6.8.  The base-hydrolyzed RNAs were subjected to BioRad P-30 chromatography for buffer exchange.  The isolated and base hydrolyzed RNAs were subjected to three bead binding steps where the bromo-UTP incorporated nascent RNAs (BrU-RNAs) were enriched using anti-bromo-deoxy-U antibody conjugated beads.  After each binding step, the BrU-RNAs were eluted, acid phenol-chloroform extracted, and precipitated.  Each of the three bead binding steps also contained additional manipulations.  After the first binding step, the BrU-RNAs were treated with tobacco acid pyrophosphatase to remove 5’-methyl guanosine caps, then with T4 polynucelotide kiase to remove 3’-phosphate group at low pH.  The BrU-RNAs were treated with T4 PNK again at high pH in the presence of ATP to add 5’-phosphate group.  5’-adaptors were added to the end-repaired BrU-RNAs by T4 RNA ligase.  After the addition of the 5’-adaptors, the BrU-RNAs were subjected to the second bead binding step to remove excessive adaptors and further enrich the BrU-RNAs.  After the second bead binding step, 3’ adaptors were ligated by T4 RNA ligase, followed by the third bead binding.
The affinity purified 5’- and 3’-adaptor-ligated BrU-RNAs were reverse transcribed into cDNAs usining annealed RT-oligo and Super Scripts III reverse transcriptase.  The RNAs were then degraded by incubation with RNase cocktail.  The cDNAs were then subjected to PCR-amplification using Phusion DNA Polymerase with small RNA PCR primers.  Samples of the amplified product were analyzed on a 2% agarose gel to assess yield and size.  The remaining samples were extracted by phenol:chloroform:isoamyl alcohol (25:24:1).  The purified product were run on a 6% native PAGE gel for further purification. The gel was stained with SYBRE gold and the DNA product were visualized using a Dark Reader transilluminator.  The bands between size 100 bp to 250 bp were cut out and the DNAs were eluted from the gel by incubating overnight in elution buffer.  The eluted DNAs were extracted again with phenol-chloroform, resuspended in water, and quantified using a Nanodrop.  The final libraries were then sequenced using an Illumina Genome Analyzer. The libraries generated from vehicle/α-amanitin-treated nuclei were amplified with indexed primers containing barcodes according to the Illumina TrueSeq small-RNA library prep kit, then sequenced using an Illumina HiSeq 2000.

treatment_protocol: AC16 cells were plated at a density of 3 x 106 cells per 15 cm diameter dish in DMEM F-12 supplemented with 12.5% fetal bovine serum., using two dishes per experimental condition. For TNFα treatments, the cells were grown to 75% confluence, switched to serum-free medium for 24 hours, and then treated with TNFα (25 ng/ml) for the indicated time.

value: cardiomyocytes

value: TNFα


title: GRO-seq_TNFα_10m_2

description: GRO-seq in AC16 cells treated for 10 minutes with TNFα (the same as GSM1014634 )


title: GRO-seq_Vehicle_2

description: GRO-seq in AC16 cells treated for 0 minutes with TNFα (the same as GSM1014632)


title: GRO-seq_TNFα_30m_2

description: GRO-seq in AC16 cells treated for 30 minutes with TNFα(the same as GSM1014636 )


title: GRO-seq_TNFα_120m_1


title: GRO-seq_TNFα_10m_1

description: GRO-seq in AC16 cells treated for 10 minutes with TNFα (the same as GSM1014633)


title: s24_10h

city: Tianjin

first: Bang

last: Wang

address: 32 Xi Qi Dao, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description:
Prochlorococcus MED4 (or CCMP 1986)
AMP medium with 24 mM Sodium bicarbonate for inducing 10h

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality reads
Clean reads were mapped to whole genome of Prochlorococcus MED4 (GenBank: NC_005072) using bowtie2 version 2.1.0 with parameters -p 8 -N 1 -X 250. The alignment results were stored in SAM format files for subsequent analysis.
The reads that were properly mapped to gene region were calculated by BEDtools using SAM files and gene annotation as input.
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM).
Genome_build: ASM1146v1
Supplementary_files_format_and_content: tab-delimited text files including sysName, start_site, end_site, strand, reads, RPKM

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

source_name: Prochlorococcus MED4

growth_protocol: The cells were cultured on Pro99 medium based on Indian Ocean seawater or transferred to AMP (Artificial Medium for Prochlorococcus) with 6 mM or 24 mM bicarbonate in 21 °C with an irradiance of 28 μmol quanta m-2s-1

extract_protocol:
Before RNA extraction, cells were treated with 150 ml 10 mM Tris-HCl (pH 7.5), 2 ml RNase inhibitor (20 u/uL, AM2696), and 1 ml Readylysis lysozyme (EPICENTRE, Cat#R1810). Total RNA extraction was extracted by using the mirVana miRNA kit (Ambion). DNA was removed using Turbo DNA-free™ Kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Before the experiment, cell cultures were maintained under continuous light at log-phase for five generations. And then log-phase cell cultures were inoculated into specific growth conditions for subsequent research at cell cultures:medium volume ratio of 8:100

tag: growth condition

tag: time

tag: strain


title: s6_5h

description:
Prochlorococcus MED4 (or CCMP 1986)
AMP medium with 6 mM Sodium bicarbonate for inducing 5h

value: AMP medium with 6 mM Sodium bicarbonate


title: s24_5h

description:
Prochlorococcus MED4 (or CCMP 1986)
AMP medium with 24 mM Sodium bicarbonate for inducing 5h


title: esl3d

description:
Prochlorococcus MED4 (or CCMP 1986)
Pro99 medium for 3d

value: Pro99 medium


title: amp3d

description:
Prochlorococcus MED4 (or CCMP 1986)
AMP medium for 3d

value: AMP medium


title: esl1d

description:
Prochlorococcus MED4 (or CCMP 1986)
Pro99 medium for 1d


title: esl10d

description:
Prochlorococcus MED4 (or CCMP 1986)
Pro99 medium for 10d


title: esl4d

description:
Prochlorococcus MED4 (or CCMP 1986)
Pro99 medium for 4d


title: first_CP_18

source_name: Cortical Plate, E80, area 18


title: GRO-seq_Vehicle_1

description: GRO-seq in AC16 cells treated for 0 minutes with TNFα (the same as GSM1014631)

tag: cell line

tag: cell type


title: esl8d

description:
Prochlorococcus MED4 (or CCMP 1986)
Pro99 medium for 8d


title: RNA Pool 21 Lane 5 NGD

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: 1190 Hornby Street

country: Canada

institute: PROOF Centre of Excellence

data_processing:
Illumina Casava 1.7 software used for basecalling.
Alignment: sequenced reads were mapped to the hg18 reference genome using tophat v1.3.2 with parameters -r 250 -p 8.
Quantification of Transcript Expression: Fragments Per Kilobase of exon per Megabase of library size (FPKM) were computed using Cufflinks (Trapnell et al., Nature Biotechnology, 2010).
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all 66803 UCSC transcripts for each sample.

source_name: PAXgene blood

extract_protocol:
Peripheral venous blood samples for 6 healthy volunteers (3 male and 3 female) were collected into PAXgene™ Blood RNA tubes (PreAnalytiX GmbH- BD Biosciences, Mississauga, ON, Canada) and BD vacutainer plastic EDTA tubes (BD Biosciences). Each subject donated 7 PAXgene™ blood samples and 1 EDTA blood sample. An aliquot of the EDTA collected blood was processed for total and differential cell counts on a Cell-Dyn automated hematology analyzer (Abbott, IL, USA). For each subject, 3 of the 7 PAXgene™ tubes were pooled. Total RNA was isolated from these subject-specific pooled samples, resulting in 6 subject-specific total RNA samples. The remaining 4 tubes were pooled across all subjects and total RNA isolated from this single pooled sample to create a single pooled total RNA sample, which was then aliquoted out to create 6 technical replicate total RNA samples. Total RNA, including small RNAs, was purified from PAXgene™ collected blood using the PAXgene™ Blood miRNA Kit (cat#763134, Qiagen, Chatsworth, CA, USA) according to manufacturer's protocols. The quality and yield of the isolated RNA was assessed using a NanoDrop8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The 12 RNA samples (6 biological replicates and 6 technical replicates) were each further divided into two and either submitted to globin transcript depletion or not.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The 12 total RNA aliquots (6 biological replicates, 6 technical replicates) destined for globin transcript depletion were further processed as follows. RNA was concentrated using RNeasy MinElute Cleanup Kit (cat#74204, Qiagen) to reduce sample volume before globin transcript depletion. Human alpha and beta globin mRNA was then depleted from total RNA using the GLOBINclear kit (cat#AM1980, Ambion- Applied Biosystems, Mississauga, ON, Canada) and following the manufacturer's protocols. Prior to sequencing, the amount and quality of all 24 RNA samples were assessed using a NanoDrop8000 Spectrophotometer and Agilent 2100 Bioanalyzer.

value: blood

tag: index

value: GCAAGG

value: SLX-Transcriptome

value: Illumina Index

tag: library

tag: flowcell

tag: lane

value: NGD

tag: pool

value: TRUE

tag: Sex

tag: mono (10e9/l)

tag: baso (10e9/l)

tag: rna volume (ul)

tag: rna amount (ng)

tag: rna concentration (ng/ul)

tag: nanodrop 260/280

tag: nanodrop 260/230

tag: rin

tag: total reads

tag: mapped reads


title: RNA Pool 24 Lane 5 NGD

tag: tissue

value: ATGTCA

tag: treatment


title: second_OSVZ_17_int

source_name: Second Replicate Outer Sub Ventricular Zone Int, E79 area 17

tag: brain region


title: RNA Pool 23 Lane 5 NGD

tag: index

value: TGCCAT

tag: library

tag: flowcell


title: RAD21_ChIPseq

city: Montreal

first: Josée

last: Dostie

state: QC

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

institute: McGill University

description: BARCODE ChIP-seq library. BARCODE adaptor was used for generating the each library. In raw data file, barcode seuquence was including in first 4 bps in each sequence reads.

data_processing:
For BARCODE ChIP-sequencing library, we used the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/ (Version 0.0.13)) to split the reads according to the specific nucleotide barcode in first 4bp of sequence reads. Before mapping to the genome, we trimmed the first 4bps nucleotide of each reads. Low quality reads were trimmed to 25bps.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie (version 0.2.7). One mismatch was allowed to the unique mapped reads (option: -v 1 -m 1).
For peak calling, HOMER tools (http://http://homer.salk.edu/homer/chipseq/) were used.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated by HOMER program. Score was normalized to tags per 1e7 reads.

source_name: THP-1 RAD21 ChIPseq

growth_protocol: THP-1 cells were cultured in Roswell Park Memorial Institute medium (RPMI 1640; Invitrogen™, Burlington, ON, Canada) supplemented with 10% fetal bovine serum (HyClone, Logan, UT, USA). The medium was made ‘complete’ by adding 50 µM of 2-mercaptoethanol (Invitrogen™), 1 mM sodium pyruvate (Invitrogen™), 10 mM HEPES (Invitrogen™) and 1% penicillin–streptomycin (Invitrogen™). The cell cultures were grown in a controlled environment at 37°C in 5% CO2 atmosphere.

extract_protocol:
Protein-DNA complexes were immunoprecipitated from sonicated chromatin extract by the specific antibody.
ChIP-seq DNA sample prep kit (Illumina, catalog number 1003473) according to the manufacturer’s protocol. For BARCODE ChIP-seq library we used the BARCODE adaptor for generating the library (BARCODE adaptor: PMID 19159457).

tag: cell line

tag: cell type

value: monocytic cell

tag: genotype

tag: chip antibody

value: RAD21 :ab992 Abcam Lot GR12688


title: GRO-seq_TNFα_30m_1

description: GRO-seq in AC16 cells treated for 30 minutes with TNFα (the same as GSM1014635 )

tag: time point


title: RNA Pool 22 Lane 5 NGD

value: TACAGC

tag: lane

tag: pool

tag: Sex

tag: mono (10e9/l)

tag: baso (10e9/l)

tag: rna volume (ul)

tag: rna amount (ng)

tag: rna concentration (ng/ul)


title: Subject  6 Lane 5 NGD

tag: tissue

value: AGTTCC

tag: treatment

value: FALSE

value: female

tag: nanodrop 260/280

tag: nanodrop 260/230

tag: rin

tag: total reads

tag: mapped reads


title: Subject  5 Lane 5 NGD

tag: index

value: TGAATG

tag: library

tag: flowcell


title: Subject  4 Lane 5 NGD

value: TAATCG

tag: lane

tag: pool


title: Subject  3 Lane 5 NGD

value: GATGCT

tag: Sex

value: male

tag: mono (10e9/l)


title: RNA Pool 23 Lane 2 NGD

value: blood

tag: baso (10e9/l)

tag: rna volume (ul)


title: RNA Pool 24 Lane 2 NGD

value: SLX-Transcriptome

tag: rna amount (ng)

tag: rna concentration (ng/ul)


title: RNA Pool 21 Lane 2 NGD

tag: tissue

value: GCAAGG

value: Illumina Index

tag: treatment


title: RNA Pool 22 Lane 2 NGD

value: NGD

value: TRUE

tag: nanodrop 260/280

tag: nanodrop 260/230


title: Subject  2 Lane 5 NGD

value: CTAGCT

tag: rin

tag: total reads


title: s6_10h

description:
Prochlorococcus MED4 (or CCMP 1986)
AMP medium with 6 mM Sodium bicarbonate for inducing 10h

tag: growth condition

value: AMP medium with 6 mM Sodium bicarbonate

tag: time

tag: strain


title: Subject  1 Lane 5 NGD

tag: index

value: CCAACA

tag: library

tag: flowcell

tag: lane

tag: mapped reads


title: RNA Pool 20 Lane 2 NGD

value: CTATAC

tag: pool

tag: Sex

tag: mono (10e9/l)

tag: baso (10e9/l)

tag: rna volume (ul)


title: NPC_XY_mB4

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Illumina Casava1.8 software used for basecalling.
SNP sites between 129S1/SvImJ and Cast/EiJ mouse strains were collected from the Sanger mouse genome project (Keane et al., 2011) and dbSNP (v128; (Sherry et al., 2001)) databases.
Paired-end 100bp RNAseq reads from each sample were mapped to the mouse genomes using the TopHat software (v1.4.0). RefSeq gene annotation from UCSC genome browser was used as the reference for known junction sites when performing spliced alignments. Only unique alignments with a maximum of 2 mismatches were reported.
Transcriptome assembly was performed in all 12 samples using the Cufflinks software (v1.3.0). Expression of each gene/transcript was measured in Fragments Per Kilobase of transcript per Millions mapped reads (FPKM).
The Pileup program in Samtools ((0.1.18) was used to extract base-pair information at each genomic position from genome alignment files. At each SNP site, the number of bases matching each genotype was counted to obtain the abundance of the 129 and Cast alleles. The 129- and Cast- specific gene abundance was computed by summing up the 129- and Cast- specific abundance of all exonic SNPs within the gene respectively
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, allelic read abundance, allelic read ratio of genes for each Sample. Replicates were only used to compute the degree of over-dispersion.

organism: Mus musculus

source_name: Neural progenitor cells

extract_protocol:
Total RNAs were prepared using Trizol Reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: ES-derived neural progenitor cells

value: Male


title: NPC_XY_mG3


title: NPC_XY_mC3_replicate

description: Replicates were only used to compute the degree of over-dispersion.

value: Female


title: NPC_XX_C2_replicate


title: Subject  5 Lane 2 NGD

tag: tissue

value: TGAATG

tag: treatment

value: FALSE

value: female

tag: rna amount (ng)

tag: rna concentration (ng/ul)

tag: nanodrop 260/280

tag: nanodrop 260/230


title: Subject  6 Lane 2 NGD

tag: index

value: AGTTCC

tag: rin

tag: total reads


title: RNA Pool 20 Lane 5 NGD

value: blood

tag: library

tag: flowcell

tag: lane


title: Subject  3 Lane 2 NGD

value: GATGCT

value: SLX-Transcriptome

tag: pool

tag: Sex

value: male

tag: mapped reads


title: Subject  4 Lane 2 NGD

value: TAATCG

value: Illumina Index

value: NGD

tag: mono (10e9/l)

tag: baso (10e9/l)

tag: rna volume (ul)


title: NPC_XY_mC3

tag: cell type

tag: strain


title: RNA Pool 19 Lane 2 NGD

tag: tissue

value: CCACGC

tag: treatment

value: TRUE

tag: rna amount (ng)

tag: rna concentration (ng/ul)


title: Subject  2 Lane 2 NGD

tag: index

value: CTAGCT

tag: nanodrop 260/280

tag: nanodrop 260/230

tag: rin


title: Subject  1 Lane 2 NGD

value: CCAACA

tag: library

tag: flowcell

tag: lane

tag: total reads


title: ES_XX_F1-21.6

source_name: Embryonic stem cells

value: Embryonic stem cells

tag: Sex


title: NPC_XX_E1.2

value: ES-derived neural progenitor cells

value: Female


title: NPC_XY_mE6

value: Male


title: RNA Pool 11 Lane 4 GD

value: AGGCCG

value: GD

tag: pool

tag: mono (10e9/l)

tag: baso (10e9/l)

tag: mapped reads


title: NPC_XX_G4

tag: cell type

tag: strain


title: NPC_XX_C2


title: RNA Pool 9 Lane 4 GD

tag: tissue

value: blood

value: AACTTG

tag: treatment

tag: rna volume (ul)

tag: rna amount (ng)


title: RNA Pool 8 Lane 4 GD

tag: index

value: TAGCTT

value: SLX-Transcriptome

tag: rna concentration (ng/ul)

tag: nanodrop 260/280

tag: nanodrop 260/230


title: NPC_XX_129


title: RNA Pool 7 Lane 4 GD

value: CGATGT

tag: library

tag: flowcell

tag: lane

tag: rin


title: Subject  4 Lane 4 GD

value: ACCCAG

value: Illumina Index

tag: pool

value: FALSE

tag: Sex

value: female

tag: mono (10e9/l)

tag: total reads


title: Subject  6 Lane 4 GD

value: CAAAAG

tag: baso (10e9/l)

tag: mapped reads


title: Subject  5 Lane 4 GD

tag: tissue

value: AGCGCT

tag: treatment


title: ES_XY_F1-23

tag: cell type

value: Embryonic stem cells

tag: strain


title: RNA Pool 12 Lane 1 GD

tag: index

value: CAACTA

value: TRUE

tag: rna volume (ul)

tag: rna amount (ng)

tag: rna concentration (ng/ul)


title: Subject  3 Lane 4 GD

value: AACCCC

tag: library

tag: flowcell

value: male

tag: nanodrop 260/280

tag: nanodrop 260/230


title: RNA Pool 19 Lane 5 NGD

value: CCACGC

tag: lane

value: NGD

tag: pool

tag: Sex

tag: rin


title: Subject  2 Lane 4 GD

value: blood

value: GATCAG

value: GD

tag: mono (10e9/l)

tag: baso (10e9/l)

tag: total reads

tag: mapped reads


title: RNA Pool 8 Lane 1 GD

tag: tissue

value: TAGCTT

value: SLX-Transcriptome

tag: treatment


title: RNA Pool 9 Lane 1 GD

tag: index

value: AACTTG

value: Illumina Index

tag: rna volume (ul)


title: RNA Pool 10 Lane 1 GD

value: ACCGGC

tag: rna amount (ng)

tag: rna concentration (ng/ul)


title: Subject  1 Lane 1 GD

value: ATCACG

tag: library

tag: flowcell

value: FALSE


title: Subject  4 Lane 1 GD

value: ACCCAG

value: female

tag: nanodrop 260/280

tag: nanodrop 260/230


title: GRO-seq_α-amantin_2

description: GRO-seq in AC16 cells, treated the nuclei for 15 minutes with a-amanitin on ice prior nuclear run-on reaction.

tag: cell line

tag: cell type

value: cardiomyocytes

value: α-amanitin


title: Subject  1 Lane 4 GD

tag: lane

tag: pool

tag: Sex

value: male

tag: rin


title: RNA Pool 10 Lane 4 GD

value: TRUE

tag: mono (10e9/l)

tag: baso (10e9/l)

tag: total reads

tag: mapped reads


title: GRO-seq_α-amanitin_1

tag: treatment


title: Subject  3 Lane 1 GD

tag: tissue

tag: index

value: AACCCC

tag: rna volume (ul)

tag: rna amount (ng)


title: GRO-seq_control_2

description: GRO-seq in AC16 cells, treated the nuclei for 15 minutes with vehicle DMSO on ice prior nuclear run-on reaction.

value: control


title: Subject  5 Lane 1 GD

value: blood

value: AGCGCT

tag: library

tag: flowcell

tag: rna concentration (ng/ul)

tag: nanodrop 260/280


title: RNA Pool 11 Lane 1 GD

value: AGGCCG

tag: lane

value: GD

tag: nanodrop 260/230


title: Pol II_ChIP-seq_TNFα_2

description: ChIP-enriched DNA from AC16 cells after 30min of TNFα treatment

data_processing:
The ChIP-seq reads were aligned to the hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to (1) “bed” files for later Metagene and read-density analyses and (2) “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using the BEDTools software package  (Quinlan et al, 2010) and PeakRanger software package (Feng et.al, 2011).
genome build: hg19

source_name: Pol II_ChIP-seq_TNFα

extract_protocol:
AC16 cells were seeded at ~3 x 106 cells per 15 cm diameter plate and treated as described above.  The cells were cross-linked with 1% paraformaldehyde in PBS for 10 minutes at 37°C and quenched in 125 mM glycine in PBS for 5 minutes at 4°C.  The cells were then collected and lysed in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and 1x RCPIC).  A crude nuclear pellet was collected by centrifugation, resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 7.9, 1 mM DTT, and 1x RCPIC), and incubated on ice for 10 minutes.  The chromatin was sheared at 4°C by sonication using a Bioruptor UC200 at the high setting for four 5-minute cycles of 30 seconds on and 60 seconds off to generate chromatin fragments of ~300 bp in length.  The soluble chromatin was diluted 1:10 with dilution buffer (20 mM Tris-HCl, pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT and 1x RCPIC) and pre-cleared with protein A agarose beads.  The pre-cleared supernatant was used in immunoprecipitation reactions with antibodies against the factor of interest or with rabbit IgG as a control.  The immunoprecipitated material was washed once with low salt wash buffer (20 mM Tris-HCl, pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM aprotinin, and 1 mM leupetin), once with high-salt wash buffer (20 mM Tris-HCl, pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM aprotinin, and 1 mM leupetin), once with LiCl wash buffer (10 mM Tris-HCl, pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM aprotinin, and 1 mM leupetin), and once with 1x Tris-EDTA (TE).  The immunoprecipitated material was eluted in elution buffer (100 mM NaHCO3, 1% SDS) and was then digested with proteinase K and RNase H to remove protein and RNA, respectively.  The immunoprecipitated genomic DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. The immunoprecipitated DNA was purified further using the MinElute PCR Purification Kit from Qiagen.
After purification, 50 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, as previously described  {Robertson, 2007 #41}, with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter).  The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: AC16 cells were plated at a density of 3 x 106 cells per 15 cm diameter dish in DMEM F-12 supplemented with 12.5% fetal bovine serum., using two dishes per experimental condition. For TNFα treatments, the cells were grown to 75% confluence, switched to serum-free medium for 24 hours, and then treated with TNFα (25 ng/ml) or vehicle for 30min.

tag: cell type

tag: antibody

value: RNA Pol II

tag: cell line

value: TNFα


title: GRO-seq_control_1


title: Pol II_ChIP-seq_Vehicle_2

description: ChIP-enriched DNA from AC16 cells in vehicle treated condition

source_name: Pol II_ChIP-seq_Vehicle

value: vehicle


title: Pol II_ChIP-seq_Vehicle_1


title: Subject  6 Lane 1 GD

value: CAAAAG

value: SLX-Transcriptome

value: Illumina Index

tag: pool

tag: Sex

tag: mono (10e9/l)

tag: baso (10e9/l)

tag: rin


title: p65_ChIP-seq_TNFα_2

tag: treatment


title: Pol II_ChIP-seq_TNFα_1


title: p65_ChIP-seq_TNFα_1


title: p65_ChIP-seq_Vehicle_2


title: p65_ChIP-seq_Vehicle_1


title: mir124-3p_Solid-1

description:
8
RISC trap Immunoprecipitation

value: HEK 293


title: RNA Pool 7 Lane 1 GD

tag: tissue

tag: index

value: CGATGT

tag: rna volume (ul)

tag: total reads

tag: mapped reads


title: Replicate mir1271-5p

description:
Sample2
RISC trap Immunoprecipitation


title: mir550-3p

description:
550abio1
RISC trap Immunoprecipitation


title: mir1271-5p

description:
Sample1
RISC trap Immunoprecipitation


title: mir1260a-5p

description:
Sample7
RISC trap Immunoprecipitation


title: Subject  2 Lane 1 GD

value: GATCAG

tag: library

tag: flowcell

value: FALSE

tag: rna amount (ng)

tag: rna concentration (ng/ul)

tag: nanodrop 260/280


title: RNAPII_MCF7

city: Sherbrooke

last: Gévry

state: Québec

address: 2500 boulevard de l'université

institute: Université de Sherbrooke

description: Sample 4

data_processing:
Reads were aligned to the Human Reference Genome (assembly hg18) using BWA version 0.6.1 (Li and Durbin, 2010).
Only sequence reads that were uniquely mapped to the genome and with a MAQ mapping quality score >10 were used for the analysis.
Aligned tags were converted to WIG files by F-Seq (Boyle et al. 2008)
Genome_build: hg18
Supplementary_files_format_and_content: wig files containing aligned tags

growth_protocol: MCF7 cells were grown to 70% of confluence in DMEM with 10% FBS.

extract_protocol:
For ChIP and FAIRE assays, DNA was extracted according to Svotelis et al. (Methods Mol Biol., 2009) and to Eeckhoute et al. (Genome Res., 2009) with few modifications. In brief, ~20-30.106 cells were cross-linked using 1.1% formaldehyde for 10 or 30 min at RT in 20ml of PBS 1X, reaction was quenched with 1ml of 2.5M Glycine. Cells were lysed with SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris–HCI of pH 8.1) during 30 min at 4°C and sonicated to have DNA fragment size between 200 and 300 bp. For ChIP, lysate was incubated overnight at 4°C on a rotator with 5µg of antibody. 35 µl of protein-A magnetic beads (Invitrogen) were added during 2h before washing with TSE-150 (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris–HCl of pH 8.1, 150 mM NaCl), TSE-500 (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris of pH 8.1, 500 mM NaCl), LiCl detergent (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris of pH 8.1) and three times with TE 1X. For FAIRE, soluble chromatin was subjected to three consecutive phenol-chloroform extractions. DNA was then reverse-crosslinked overnight at 65ºC and treated with RNAse A for 30 min at 37°C, followed by Proteinase K for 2 h at 37°C. After purification, DNA was quantified with Picogreen (Invitrogen) before library preparation.
Libraries were prepared according to Illumina's instructions. Briefly, 10 ng (ChIP-seq) or 50 ng (FAIRE-seq) of DNA were end-repaired using a combination of T4 DNA polymerase and T4 polynucleotide kinase (Enzymatics). DNA fractions of ~300 bp were selectively isolated with solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure, Beckman Coulter). After adapter ligation, DNA was PCR amplified with Illumina primers, the quality and quantity of each DNA library was analyzed using Agilent Bioanalyser before sequencing on HiSeq (Illumina) following the manufacturer's protocols.

treatment_protocol: MCF7 cells were maintained in DMEM without phenol red and supplemented with 5% charcoal–dextran-treated FBS for 4 days prior to their use in estradiol (E2) treatment (10-7M, 30 min).

tag: cell line

tag: cell type

value: breast adenocarcinoma cells

tag: chip antibody

value: RNAPII

tag: chip antibody vendor

value: Covance

tag: chip antibody cat. #

tag: chip antibody lot #


title: Med12_MCF7

description: Sample 2

value: Bethyl


title: LRH1_MCF7

description: Sample 1

data_processing:
Reads were aligned to the Human Reference Genome (assembly hg18) using BWA version 0.6.1 (Li and Durbin, 2010).
Only sequence reads that were uniquely mapped to the genome and with a MAQ mapping quality score >10 were used for the analysis.
Aligned tags were converted to WIG files by F-Seq (Boyle et al. 2008)
Genome_build: hg18
Supplementary_files_format_and_content: wig files containing aligned tags
Peaks were called using MACS, version 1.4.2

value: R&D


title: mir1180-3p

description:
Sample10
RISC trap Immunoprecipitation


title: Replicate mir3613-5p

description:
Sample4
RISC trap Immunoprecipitation


title: Replicate mir550-3p

description:
550abio2
RISC trap Immunoprecipitation


title: Replicate mir1301-3p

description:
1301Bio2
RISC trap Immunoprecipitation


title: WCE_DNA

source_name: THP-1 WCE ChIPseq

value: monocytic cell

tag: genotype

value: No antibody


title: Replicate mir1180-3p

description:
Sample9
RISC trap Immunoprecipitation


title: Input 8hrs embryo

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: Input control for 8hrs embryo Chip-seq

data_processing:
Sequencing reads were mapped to the zebrafish genome assembly version July 2010 (Zv9), following which peak finding was performed using the QuEST algorithm (Valouev et al., 2008)
Genome Build:
CZE001_zv9-6cols.tags: zv9

organism: Danio rerio

source_name: 8hpf embryos

growth_protocol: Zebrafish of wild type (AB strain) and transgenic line SqET33 (Kondrychyn et al., 2009; Parinov et al., 2004) were maintained according to established protocols (Westerfield, 1993). Embryos were staged according to standard morphological criteria (Kimmel et al. 1995).

extract_protocol: Chromatin Immunoprecipitation (ChIP) was performed according to a published protocol (Wardle et al., 2006) with an addition of a deyolking step according to Link and colleagues (2006), with modifications.

tag: developmental stage

value: 8hpf embryos

tag: tissue

value: Whole embryo

tag: genetic background

value: AB strain

value: wild type

value: Input-control


title: mir1301-3p

description:
1301
RISC trap Immunoprecipitation


title: mir3613-5p

description:
Sample3
RISC trap Immunoprecipitation


title: Zic3 24hrs sorted

description: Zic3 ChIP-seq of sorted cells from 24hr embryo

data_processing:
Sequencing reads were mapped to the zebrafish genome assembly version July 2010 (Zv9), following which peak finding was performed using the QuEST algorithm (Valouev et al., 2008)
Genome Build:
CZE019-24hrs-sorted-zic3-peaks.txt: zv9
CZE019.bed: zv9

source_name: 24hpf embryos

value: 24hpf embryos

value: FACS sorted zic3 expressing cell from 24hpf embryo

value: sqet33 transgenic


title: Input 24hrs

description: Input control for 24hrs Chip-seq

data_processing:
Sequencing reads were mapped to the zebrafish genome assembly version July 2010 (Zv9), following which peak finding was performed using the QuEST algorithm (Valouev et al., 2008)
Genome Build:
CZE020.bed: zv9


title: [RNA-Seq] Young yeast RNA replicate2

status: Public on Feb 26 2014

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

data_processing:
reads mapping by tophat
expression calculated by cufflinks.
Genome_build: sacCer3
Supplementary_files_format_and_content: [RNA-Seq] The tab-delimted .txt file reports gene expression fpkm for all samples (expression.txt linked as supplementary file on Series record).

organism: Saccharomyces cerevisiae

source_name: Young yeast RNA

growth_protocol: Cells were cultured in YEPD (1% yeast extract, 2% peptone, 2% glucose).  Cells were grown exponentially overnight to mid log phase before the initiation of all experiments.  For over-expression of histones H3/H4 under the control of the pGAL1/10 divergent promoters, cells were cultured in YEP plus the indicated carbon source.  Plasmids expressing histones were maintained by growth in synthetic complete media lacking the appropriate amino acid and supplemented with raffinose and galactose for strains carrying galactose inducible promoter fusions.

extract_protocol:
Total RNA isolation was performed using the MasterPure Yeast RNA Isolation Kit from Epicentre Biotechnologies (catalog no. MPY03100) following the manufacturer’s instructions. We included the DNase I digestion steps in our RNA isolation to ensure a purer sample for subsequent analyses. The quality of the RNA was confirmed by Agilent 2100 Bioanalyzer electropherograms. The total RNA was spiked-in with the external RNA Controls Consortium (ERCC) spike-in control mixes (Ambion, 4456740) based on the same number of cells for each sample. The ERCC RNA Spike-In Control Mixes used here comprise a set of 92 polyadenylated transcripts that mimic natural eukaryotic mRNAs. The RNAs range in size from 250–2,000 nucleotides in length and span an approximately 106-fold concentration range. Ribosomal RNA was removed using the ribo-zero rRNA removal kit (Epicentre, MRZH11124).
cDNA libraries were prepared using the ScriptSeqTM v2 RNA-seq library preparation kit (Epicentre, SSV21106)

treatment_protocol:
For isolating old cells, we utilized the mother enrichment program as previously described with slight modification.  The wild type (WT) strain ZHY2 was used for the young and old cell purification. For the overexpression of histones H3/H4, strain JFY087 was used and cells were seeded into 1L of YEP containing 2% raffinose and 0.5% galactose (YEPRG) for histone H3/H4 induction. Briefly, 2x107 cells from YEPD mid-log phase culture were washed twice in 1X PBS, pH 7.4, and resuspended in PBS buffer containing 3 mg ml-1 Ez-link Sulfo-NHS -Lc-Lc biotin (Thermo-scientific))at a final concentration of 2x107 ml.  Cells were incubated at room temperature for 30 min and washed twice in PBS and once in YEPR medium. Biotinylated cells were resuspended in 100 ml YEPR at  2x 106cells and recovered with shaking for 5 h at 30∞C.  These cells were used to seed culture at a density of 2x 104 biotinylated cells per ml in YEPRG. 17-Estradiol (Sigma E2758) was added to a final concentration of 1 ºM to initiate the MEP and cells were cultured at 30∞C  for 36 hours to obtain cells of desired age.  Cells were washed twice in PBS, resuspended at a density of 5x108 cells ml-1 in 1 ml of PBS, and incubated for 30 min at room temperature with 50 ºl streptavidin-coated magnetic beads (MicroMACS, Miltenyi Biotec).  After incubation, cells were washed in PBS, resuspended in 8 ml of PBS, and loaded onto an LS MACS column (Miltenyi Biotec) equilibrated with 5 ml of PBS.  After gravity flow-through of unlabeled cells and debris, columns were washed twice with 8 ml of PBS. The columns were then removed from the magnetic field and aged cells were eluted by gravity flow with 5 ml of PBS.  For the isolation of young cells, biotinylated cells were inoculated into liquid medium and grown overnight to mid-log phase.  Cells were harvested and washed with PBS buffer.  After the cells were incubated with streptavidin-coated magnetic beads for 30 min at room temperature, cells were loaded onto a LS MACS column (Miltenyi Biotec) in the magnetic field.  The flow through was collected and young cells were pelleted for further experiments.
The strains ZHY2 and JFY087 are derivatives of S. cerevisiae S288c (BY4741).

tag: strain

tag: age

value: young

tag: genotype/variation

value: control


title: [Genome-Seq] Old yeast genome replicate2 (MNase-Seq input)

description:
genome_old_rep2
The Genome-Seq samples are the input sequencing for the MNase-Seq data.

data_processing:
reads mapping by bowtie
aboundance (occupancy value in wig file) calculated by DANPOS
Genome_build: sacCer3
Supplementary_files_format_and_content: [Genome-Seq] The .wig file reports reads density on each base pair across the genome.  The value is similar to nucleosome occupancy value in the wig file for MNase-Seq data.

source_name: Old yeast genome

extract_protocol:
The same number of purified young and old cells was subjected to genomic DNA isolation. The masterpureTM yeast DNA purification kit (cat. Nos. MPY80010 and MPY 80200) was used to isolate the genomic DNA.  Briefly, 300 ml of yeast cell lysis solution was added to each cell pellet. 1 ml of 5 mg/ml RNase A was added to each pellet. The cells were resuspended and incubated at 65°C for 15 minutes.  Samples were placed on ice for 5 minutes. 150 ml MPC protein precipitation reagent was added and vortexed. The cellular debris was pelleted by centrifugation for 10 min at 13,200 rpm. The supernatant was added to 500 ml isopropanol and the DNA was pelleted by centrifugation at 13,200 rpm for 10 minutes. The pellet was washed with 0.5 ml 70% ethanol. The ethanol was removed and the pellet was dried at room temperature. The isolated genomic DNA was fragmented using a Covaris sonicator to mimic the size of mononucleosomal DNA fragments for the size selection.
The libraries were generated using a KAPA library preparation kit (KK8200, Illumina Series). During the library construction the same spike-in control described for MNase-seq was included and added proportional to cell number. DNA fragments were size selected between 200-400 bp after ligation of 121 bp adapters.

value: old


title: [Genome-Seq] Old yeast genome replicate1 (MNase-Seq input)

description:
genome_old_rep1
The Genome-Seq samples are the input sequencing for the MNase-Seq data.


title: Zic3 8hrs embryo

description: Zic3 ChIP-seq 8hrs embryo

data_processing:
Sequencing reads were mapped to the zebrafish genome assembly version July 2010 (Zv9), following which peak finding was performed using the QuEST algorithm (Valouev et al., 2008)
Genome Build:
CZE017-8hrs-embryo-zic3-peaks.txt: zv9
CZE017-zv9-zic3-6cols.tags: zv9


title: FAIRE_MCF7

description: Sample 3

data_processing:
library strategy: FAIRE-seq
Reads were aligned to the Human Reference Genome (assembly hg18) using BWA version 0.6.1 (Li and Durbin, 2010).
Only sequence reads that were uniquely mapped to the genome and with a MAQ mapping quality score >10 were used for the analysis.
Aligned tags were converted to WIG files by F-Seq (Boyle et al. 2008)
Genome_build: hg18
Supplementary_files_format_and_content: wig files containing aligned tags

value: breast adenocarcinoma cells


title: [Genome-Seq] Young yeast genome replicate2 (MNase-Seq input)

description:
genome_young_rep2
The Genome-Seq samples are the input sequencing for the MNase-Seq data.

source_name: Young yeast genome


title: [RNA-Seq] Old yeast RNA replicate2

source_name: Old yeast RNA


title: [MNase-Seq] Young yeast nucleosome  replicate3

data_processing:
reads mapping by bowtie
aboundance (occupancy value in wig file) calculated by DANPOS
Genome_build: sacCer3
Supplementary_files_format_and_content: [Mnase-Seq] The .wig file reports nucleosome occupancy data (the content is reads density).

source_name: Young yeast nucleosome

extract_protocol:
The strains were grown in medium at 30°C overnight. The same number of young, old and histone H3/H4 overexpressing cells were collected and the cells were cross-linked with formaldehyde.  The cells were washed twice in 1xPBS buffer and pelleted. Then cells were resuspended in the Zymolyase buffer (1M sorbitol, 50 mM Tris-HCl at pH 7.4, and 10 mM b- Mercaptoethanol) for cell wall digestion with zymolyase-100T. After zymolyase-100T treatment, spheroplasts were pelleted and then resuspended in NP buffer (1M sorbitol, 50 mM NaCl, 10 mM Tris-HCl at pH 7.4, 5 mM MgCl2, 1mM CaCl2 and 0.075% Nonidet P40, and 500 mM spermidine). Micrococcal nuclease (MNase) was added to a final concentration of 1 U MNase/sample. The digestion reactions were incubated at 37°C for 30 min, and were stopped by adding SDS to a final concentration of 1% and EDTA to a final concentration of 10 mM. 5 ml of proteinase K solution was added to each tube. To reverse the formaldehyde cross-links, samples were incubated at 65°C overnight. Samples were extracted with 1 volume phenol/chloroform-IAA and centrifuged at room temperature for 15 min. DNA was precipitated with 2-propanol and washed with 70% ethanol. The pellet was dried at room temperature. 10 ml sterile ddH2O was added to the pellet. Then the DNA was treated with 1 ml RNase A (1mg/ml) at 37°C for 30 min. To check the mononucleosomal DNA fragments and MNase digestion level, electrophoresis was carried out on a 2% agarose gel. Samples were further analyzed on a Bioanalyzer 2100 to determine quality prior to library preparation.
The libraries were generated using a KAPA library preparation kit (KK8200, Illumina Series).  A spike-in control which mimics the size of the mononucleosomal fragment was included during the library construction, and was added according to the number of cells used to isolate the mononucleosomal fragments.  The spike-in control used here comprises a set of three DNA sequences that were each around 150 nucleotides in length, with GC contents that mimic the GC% of the S. cerevisiae genome but with no significant similarity to the yeast genome. DNA fragments were size-selected between 200-400 bp after ligation of 121 bp adapters (Next flexTM DNA Barcodes-6).


title: CTCF_ChIP-seq

source_name: THP-1 CTCF ChIPseq

value: CTCF :07-729 Millipore Lot. DAM1745366


title: [RNA-Seq] Old yeast with histone over expression, RNA replicate2

value: histone over expression


title: [MNase-Seq] Old yeast nucleosome replicate3

source_name: Old yeast nucleosome


title: [RNA-Seq] Young yeast RNA replicate1


title: [MNase-Seq] Old yeast nucleosome replicate2


title: 4C-Seq for Irx3a promoter in 24hpf zebrafish

status: Public on Feb 24 2014

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing: Mapping: reads were mapped to the Mus musculus (mm9 assembly) or Danio rerio (danRer6 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.

source_name: 24hpf zebrafish embryos

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated manually before fixation.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

treatment_protocol: No treatment

value: whole embryos

tag: promoter


title: [MNase-Seq] Old yeast nucleosome replicate1


title: [MNase-Seq] Old yeast with histone over expression, nucleosome replicate3


title: [MNase-Seq] Old yeast with histone over expression, nucleosome replicate2


title: [RNA-Seq] Old yeast with histone over expression, RNA replicate1


title: [MNase-Seq] Old yeast with histone over expression, nucleosome replicate1


title: [MNase-Seq] Young yeast nucleosome replicate2


title: KI_H3K4me3_Input_sample_2

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using BWA v1.2.3
Data was filtered to keep only uniquely mapped reads
peaks were called using MACS v1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: Processed data include merged Bedgraph files from both biological replicates generated by MACS and tab-delimited peaks called by MACS with p-value e-5. To find uncommon peaks we ran MACS using p = e-2, removed all reads described by common peaks from the alignment file, then ran MACS again with p = e-2 and again identified common peaks. Genomic regions found in common from the two rounds of peak calling were pooled. MACS was run on the data again using p = e-5 and the common peaks were subtracted. These 'uncommon' peaks were considered putative PRDM9 peaks and analyzed further for common features (i.e. motif analysis etc.)

source_name: spermatocytes

growth_protocol: Crude isolation of germ cells was conducted from male mice at 12 days post-partum (dpp). For detailed protocol see publication

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 ul water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix and 14-18 cycles of PCR.

value: 12 days post-partum

tag: strain background

tag: prdm9 allele

value: Cst

tag: ChIP

value: input


title: 4C-Seq for Irx3 promoter in mouse adult brain

source_name: adult mouse brain

growth_protocol: CBA/Ca×C57Bl/10 crosses.

value: adult brain

value: CBA/Ca×C57Bl/10 cross


title: KI_H3K4me3_ChIP_sample_2

description:
H3K4me3_KI_merge_ChIP.bgd
KI_P9uncommonQKI.bed

tag: antibody manufacturer

value: Millipore/EMD

tag: antibody catalog number

tag: antibody lot/batch#


title: KI_H3K4me3_Input_sample_1


title: [RNA-Seq] Old yeast RNA replicate1


title: 4C-Seq for Irx3 promoter in E9.5 mouse_embryos

source_name: E9.5 mouse embryos

growth_protocol: CBA/Ca×C57Bl/10 crosses. Embryos taken at 9.5dpc, taking the day in which the plug was found as 0.5dpc.


title: 4C-Seq for FTO promoter in 24hpf zebrafish

value: FTO


title: RNAseq_shCTRL

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg18 genome using Bowtie version 0.12.7
RNA-seq reads were aligned to the hg18 genome using RUM version 2.0.2
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS; Scores represent the ChIP-seq tag numbers
Supplementary_files_format_and_content: RNA-seq RPKM values were extracted using RUM version 2.02

source_name: U2OS cells

growth_protocol: Cells were maintained in DMEM with 10% FBS,  5% CO2, 37oC.

extract_protocol:
For RNA seq, total RNA was extracted using QiaGen RNAplus kit. ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
Library was contracted by the MD Anderson DNA sequencing Core facility following standard protocol.

treatment_protocol: For stable cell selection, 2ug/ml of puromycin was used selection and subsequent cell maintenance

tag: cell type

value: U2OS Cells

value: shCTRL


title: ChIPseq_POLII-shCTRL

tag: chip antibody

value: POLII, Santa Cruz sc-9001x, lot # E3012


title: [MNase-Seq] Young yeast nucleosome replicate1

value: young


title: ChIPseq_H3K36me3-shZM11


title: 4C-Seq for FTO promoter in mouse adult brain


title: ChIPseq_ZNYMD11-shZM11

value: ZMYND11, home-made


title: ChIPseq_Flag-H3.3

value: Flag-H3.3 stable

value: Flag beads, Sigma A2220


title: [Genome-Seq] Young yeast genome replicate1 (MNase-Seq input)

description:
genome_young_rep1
The Genome-Seq samples are the input sequencing for the MNase-Seq data.

value: control


title: RNAseq_shZMYND11-2


title: RNAseq_shZMYND11-1


title: ChIPseq_S2P-shZM11

value: S2P, Covance MMS-129R


title: Control1_mRNA [RNA-seq]

status: Public on Feb 23 2014

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

description: Control Replicate 1

data_processing:
Illumina pipeline 1.4  was used for base calling
Artefacts were filtered using fastx_artefacts_filter
Reads were aligned to the hg19 Ref-seq transcriptome using bwa 0.5.9 with default parameters
Transcript abundance was extracted out of the aligned file and collated into singe tabular format
Genome_build: hg19 Refseq transcriptome
Supplementary_files_format_and_content: tabular count abundance measurements

growth_protocol: Primary HAECs (human aortic endothelial cells), purchased from Lonza (Walkersville, MD, USA), were cultured in EBM-2 medium (Lonza) containing EGM-2 growth factors and supplements (Lonza) and 10% fetal bovine serum (Gibco).

extract_protocol:
After the incubation, total RNA was isolated using TRIZOL. Genomic DNA contamination was removed by DNAse treatment (Qiagen).
mRNA-Seq libraries were prepared according to Illumina mRNA-Seq library preparation kit (cat # RS-100-0801). Briefly, 8 µg of total RNA was taken for mRNA isolation using poly-T oligo-attached magnetic beads. Poly-A mRNA was fragmented with the presence of divalent cations under elevated temperatures. The mRNA fragments were reverse transcribed via SuperScript II (Invitrogen) with random primers. The second strand was synthesized with addition of RNaseH and DNA Pol I. Double stranded complementary DNA (dscDNAs) were end-repaired, followed by 3’ adenylation and ligation to universal adapters. The ligated cDNA library was separated on a 2.0% agarose gel. Library cDNA fragments in the range of 200 bp ± 10 bp were isolated by gel purification (Qiagen) and amplified with 15 cycles of PCR

value: Primary Human Aortic Endothelial Cells (HAECs)

tag: passage

value: Passage 4-6

tag: treated with

value: none (control)


title: ChIPseq_S2P-shCTRL


title: SAHA1_mRNA [RNA-seq]

description: Treatment Replicate 1

treatment_protocol: HAEC were incubated for 12 hours with 500 nM SAHA.

value: suberoylanilide hydroxamic acid (SAHA)


title: HAEC input control1 [MBD-seq]

data_processing:
Illumina pipeline 1.4  was used for base calling
Reads were aligned to the hg19 genome using bwa 0.5.9 with default parameters
A set of peaks were generated for each sample vs Input using MACS 1.4.1
Genome_build: hg19
Supplementary_files_format_and_content: bed files comparing sample vs Input

source_name: HAEC input control

extract_protocol:
Genomic DNA derived from treated and controls HAECs was fragmented to 150-200bp by Diagnode sonicator and subjected to methylated DNA enrichment using MethylMiner Kit (Invitrogen, ME10035) in triplicate. Briefly, methylated DNA was captured from 500ng of fragmented genomic DNA via binding MBD2 protein coupled to magnetic Dynabeads, which was incubated for 1hr with rotation. The methylated fragments were then eluted in three distinct subpopulation using 0.6M, 1M and 2M salt elution buffers respectively (supplied in MethylMiner kit). Methylated DNA fragments, eluted with 2M salt buffer, were purified and selected for sequencing on the Illumina Genome Analyser.
Libraries were prepared according to the protocols described in the Illumina (San Diego, CA, US) ChIP-seq library preparation kit (cat# IP-102-1001).

treatment_protocol: HAEC were incubated for 12 hours with 500 nM TSA.

tag: passages


title: HAEC CpG TSA3 [MBD-seq]

source_name: HAEC CpG TSA

value: 500 nM TSA for 12hrs


title: HAEC CpG TSA2 [MBD-seq]


title: ChIPseq_ZNYMD11-shCTRL


title: HAEC CpG TSA1 [MBD-seq]


title: HAEC CpG control3 [MBD-seq]

source_name: HAEC CpG control


title: ChIPseq_POLII-shZM11


title: SAHA2_mRNA [RNA-seq]

description: Treatment Replicate 2


title: ChIPseq_H3K36me3-shCTRL


title: Control2_mRNA [RNA-seq]

description: Control Replicate 2


title: KI_H3K4me3_ChIP_sample_1

value: 12 days post-partum

value: Cst


title: HAEC CpG control1 [MBD-seq]


title: HAEC input control2 [MBD-seq]


title: ChIPseq_ZNYMD11

value: WT


title: 4C-Seq for FTO promoter in E9.5 mouse_embryos

tag: tissue

value: whole embryos

value: CBA/Ca×C57Bl/10 cross

value: FTO


title: HAEC input TSA [MBD-seq]

source_name: HAEC input TSA


title: SAHA3_mRNA [RNA-seq]

description: Treatment Replicate 3


title: HAEC CpG control2 [MBD-seq]


title: HAEC H3K9Me3 SAHA1 [ChIP-seq]

description:
HAEC_H3K9Me3_SAHA1_FC046_2
processed data file: HAEC_hg19_H3K9me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K9me3_SAHAvsMock_peaks.bed

data_processing:
Illumina pipeline 1.4  was used for base calling
Reads were aligned to the hg19 genome using bwa 0.5.9 with default parameters
A set of peaks were generated for each ChIP vs Input using MACS 1.4.1
Genome_build: hg19
Supplementary_files_format_and_content: bed files comparing ChIP vs Input

source_name: HAEC H3K9Me3 SAHA

extract_protocol:
After the incubation,HAECs were fixed for 10 minutes with 1% formaldehyde. Glycine (0.125 M) solution was then added for another 10 minutes. Cell pellets were resuspended in SDS lysis buffer containing protease inhibitors. Then cells were sonicated to shear chromatin and ChIP was performed using indicated above antibodies and DynaMag™-2 magnet (Invitrogen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Anti-Histone H3 (tri methyl K9)

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: HAEC H3K9Me3 SAHA2 [ChIP-seq]

description:
HAEC_H3K9Me3_SAHA2_FC047_7
processed data file: HAEC_hg19_H3K9me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K9me3_SAHAvsMock_peaks.bed


title: HAEC input control2 [ChIP-seq]

source_name: Endothelial cells

value: No antibody


title: Control3_mRNA [RNA-seq]

description: Control Replicate 3


title: HAEC input SAHA [ChIP-seq]

source_name: HAEC input SAHA


title: HAEC input control1 [ChIP-seq]


title: HAEC H3K9Me3 SAHA3 [ChIP-seq]

description:
HAEC_H3K9Me3_SAHA3_FC049_7
processed data file: HAEC_hg19_H3K9me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K9me3_SAHAvsMock_peaks.bed


title: HAEC H3K9Me3 control3 [ChIP-seq]

description:
HAEC_H3K9Me3_control3_FC049_6
processed data file: HAEC_hg19_H3K9me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K9me3_SAHAvsMock_peaks.bed

source_name: HAEC H3K9Me3 control


title: HAEC H3K9Me3 control1 [ChIP-seq]

description:
HAEC_H3K9Me3_control1_FC046_3
processed data file: HAEC_hg19_H3K9me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K9me3_SAHAvsMock_peaks.bed


title: HAEC H3K9/14ac SAHA2 [ChIP-seq]

description:
HAEC_H3K9K14ac_SAHA2_FC039_3
processed data file: HAEC_hg19_H3Ac_MockvsSAHA_peaks.bed, HAEC_hg19_H3Ac_SAHAvsMock_peaks.bed

source_name: HAEC H3K9/14ac SAHA

value: Anti-acetyl-Histone H3

value: Millipore


title: HAEC H3K9Me3 control2 [ChIP-seq]

description:
HAEC_H3K9Me3_control2_FC047_6
processed data file: HAEC_hg19_H3K9me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K9me3_SAHAvsMock_peaks.bed


title: HAEC H3K9/14ac SAHA1 [ChIP-seq]

description:
HAEC_H3K9K14ac_SAHA1_FC041_7
processed data file: HAEC_hg19_H3Ac_MockvsSAHA_peaks.bed, HAEC_hg19_H3Ac_SAHAvsMock_peaks.bed


title: HAEC H3K9/14ac SAHA3 [ChIP-seq]

description:
HAEC_H3K9K14ac_SAHA3_FC039_6
processed data file: HAEC_hg19_H3Ac_MockvsSAHA_peaks.bed, HAEC_hg19_H3Ac_SAHAvsMock_peaks.bed


title: HAEC H3K4Me3 SAHA3 [ChIP-seq]

description:
HAEC_H3K4Me3_SAHA3_FC049_4
processed data file: HAEC_hg19_H3K4me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K4me3_SAHAvsMock_peaks.bed

source_name: HAEC H3K4Me3 SAHA

value: Histone H3K4me3 antibody

value: Active Motif


title: HAEC H3K4Me3 SAHA1 [ChIP-seq]

description:
HAEC_H3K4Me3_SAHA1_FC046_5
processed data file: HAEC_hg19_H3K4me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K4me3_SAHAvsMock_peaks.bed

value: Primary Human Aortic Endothelial Cells (HAECs)

value: Passage 4-6


title: HAEC H3K9/14ac control2 [ChIP-seq]

description:
HAEC_H3K9K14ac_control2_FC039_2
processed data file: HAEC_hg19_H3Ac_MockvsSAHA_peaks.bed, HAEC_hg19_H3Ac_SAHAvsMock_peaks.bed

source_name: HAEC H3K9/14ac control


title: HAEC H3K4Me3 control3 [ChIP-seq]

description:
HAEC_H3K4Me3_control3_FC049_3
processed data file: HAEC_hg19_H3K4me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K4me3_SAHAvsMock_peaks.bed

source_name: HAEC H3K4Me3 control


title: HAEC H3K4Me3 SAHA2 [ChIP-seq]

description:
HAEC_H3K4Me3_SAHA2_FC047_4
processed data file: HAEC_hg19_H3K4me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K4me3_SAHAvsMock_peaks.bed


title: HAEC H3K4Me3 control1 [ChIP-seq]

description:
HAEC_H3K4Me3_control1_FC046_6
processed data file: HAEC_hg19_H3K4me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K4me3_SAHAvsMock_peaks.bed


title: HAEC H3K4Me3 control2 [ChIP-seq]

description:
HAEC_H3K4Me3_control2_FC047_3
processed data file: HAEC_hg19_H3K4me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K4me3_SAHAvsMock_peaks.bed


title: HAEC H3K9/14ac control3 [ChIP-seq]

description:
HAEC_H3K9K14ac_control3_FC039_5
processed data file: HAEC_hg19_H3Ac_MockvsSAHA_peaks.bed, HAEC_hg19_H3Ac_SAHAvsMock_peaks.bed


title: HAEC input control2

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

treatment_protocol: HAEC were incubated for 12 hours with 500 nM TSA. After the incubation,HAECs were fixed for 10 minutes with 1% formaldehyde. Glycine (0.125 M) solution was then added for another 10 minutes. Cell pellets were resuspended in SDS lysis buffer containing protease inhibitors. Then cells were sonicated to shear chromatin and ChIP was performed using indicated above antibodies and DynaMag™-2 magnet (Invitrogen).

tag: cell line

value: HAEC

value: Primary Human Aortic Endothelial Cells


title: HAEC input control1


title: HAEC input TSA

source_name: HAEC_input_500nM TSA_12h


title: HAEC H3K9/14ac TSA2

source_name: HAEC_H3K9/14ac_500nM TSA_12h

tag: chip antibody cat. no.

tag: chip antibody vendor lot no.


title: HAEC H3K9Me3 TSA1

source_name: HAEC_H3K9Me3_500nM TSA_12h


title: HAEC H3K9Me3 control3


title: HAEC H3K4Me3 TSA1

source_name: HAEC_H3K4Me3_500nM TSA_12h

value: Activ Motif


title: HAEC H3K9Me3 TSA2


title: HAEC H3K4Me3 TSA2


title: HAEC H3K9/14ac control1 [ChIP-seq]

description:
HAEC_H3K9K14ac_control1_FC041_6
processed data file: HAEC_hg19_H3Ac_MockvsSAHA_peaks.bed, HAEC_hg19_H3Ac_SAHAvsMock_peaks.bed


title: HAEC H3K4Me3 control3


title: HAEC H3K4Me3 TSA3


title: HAEC H3K9/14ac control3


title: HAEC H3K9/14ac control2


title: HAEC H3K9/14ac TSA1


title: HAEC H3K9/14ac TSA3


title: Control3_mRNA

extract_protocol: mRNA-Seq libraries were prepared according to Illumina mRNA-Seq library preparation kit (cat # RS-100-0801). Briefly, 8 µg of total RNA was taken for mRNA isolation using poly-T oligo-attached magnetic beads. Poly-A mRNA was fragmented with the presence of divalent cations under elevated temperatures. The mRNA fragments were reverse transcribed via SuperScript II (Invitrogen) with random primers. The second strand was synthesized with addition of RNaseH and DNA Pol I. Double stranded complementary DNA (dscDNAs) were end-repaired, followed by 3’ adenylation and ligation to universal adapters. The ligated cDNA library was separated on a 2.0% agarose gel. Library cDNA fragments in the range of 200 bp ± 10 bp were isolated by gel purification (Qiagen) and amplified with 15 cycles of PCR

treatment_protocol: HAEC were incubated for 12 hours with 500 nM TSA. After the incubation, total RNA was isolated using TRIZOL. Genomic DNA contamination was removed by DNAse treatment (Qiagen).


title: HAEC H3K9Me3 TSA3


title: HAEC H3K9Me3 control2


title: Replicate mir1260a-5p

description:
Sample8
RISC trap Immunoprecipitation

data_processing:
Library strategy: RISC trap immunoprecipitation
SOLiD data were aligned by Bioscope 2 and tophat2 was used for Illumina data
reads from both strands were count for each gene
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file for mRNA profiling

source_name: HEK 293 cells

extract_protocol:
RNA was extracted by trizol
Libraries were prepared with SOlID Total RNA-seq kit (whole transtriptome library size selection).

value: HEK 293


title: HAEC H3K4Me3 control2


title: HAEC H3K4Me3 control1


title: HAEC H3K9/14ac control1


title: Control2_mRNA


title: HAEC H3K9Me3 control1


title: Control1_mRNA


title: TSA3_mRNA

source_name: HAEC_500 nM TSA_12hr

value: 500 nM Trichostatin A (TSA) for 12hr


title: TSA1_mRNA


title: WT_1

city: Sydney

first: Jon

last: Burdach

state: NSW

address: UNSW

department: BABS

institute: University of New South Wales

data_processing:
"Stringent" - Reads were aligned to the mm10 Mus musculus genome using tophat2 (v2.0.4) using the default settings except for the following (-r -40 --segment-length 50 --coverage-search --segment-mismatches 0 -g 50 --genome-read-mismatches 0 --read-mismatches 0 -I 200000 --no-discordant --no-mixed --b2-L 30 --b2-D 10000 --b2-R 100 -n 0 -M) OR;
"Routine" - Reads were aligned to the mm10 Mus musculus genome using tophat2 (v2.0.4) using the default settings except for the following (--no-discordant -M --no-coverage-search --microexon-search -n 3 --genome-read-mismatches 3 --read-mismatches 3 --b2-sensitive -G)
Transcripts were assembled using Cufflinks v2.0.2 and the mm10 annotations were included
Transcripts across all replicates were merged using cuffmerge and differential expression analysis was performed pair-wise on the groups using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files giving results of differential expresison and statistical analysis

source_name: TER119+ E14.5 fetal liver cells

growth_protocol: All mice were housed in standard University of NSW facilities, under SPF conditions

extract_protocol:
RNA extraction was performed using TRI-Reagent, according to manufacturer’s guidelines (Sigma-Aldrich). RNA samples were further purified using RNeasy columns (Qiagen)
Libraries were prepared using 1µg of total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) according to the manufacturer’s instructions.
The six libraries were multiplexed into two lanes using sample specific adapters such that there were three samples per lane.   100 bp paired end reads were sequenced using TruSeq v3 SBS reagents on the HiSeq 2000 (Illumina, San Diego, CA).

treatment_protocol: TER119+ cells were purified from E14.5 fetal liver using Magnetic Activated Cell Sorting with Anti-TER119 MicroBeads (Miltenyi)

tag: strain

value: FVB/NJ

tag: genotype


title: TSA2_mRNA


title: WT_3


title: WT_2


title: KO_3


title: KO_1


title: KO_2


title: CRC_pAplus_1 and 2

status: Public on Feb 22 2014

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
For visualization, Bigwig files were generated using UCSC bedGraphToBigWig from Bedgraph files, which were generated using genomeCoverageBed from Tophat generated .bam. A UCSC browser session with uploaded Bigwig (.bw) track files is used for visualizing gene expression, etc.
Basecalling using Illumina Casava1.8.2 software.
combine two technical replicates control_pAplus_1.txt.gz and control_pAplus_2.txt.gz for further analysis
combine two technical replicates CRC_pAplus_1.txt.gz and CRC_pAplus_2.txt.gz for further analysis
Map to human hg19 reference by using Tophat
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: ha19
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: human CRC patient sample

extract_protocol:
Human paired CRC/control mucosa samples were obtained from Changzheng Hospital, Shanghai under the strict guidance of ethical committee. After frozen, tissue samples were powdered in liquid nitrogen and total RNAs were prepared using Trizol Reagent and treatment with DNase Iadapted from Sambrook, et al, 1989, in Molecular Cloning: A Laboratory Manual, CSHL.
5ug total RNAs from paired human CRC/control mucosa samples were individually used for library preparation with Illumina TruSeq RNA  Samples Prep Kit (v2) according to the manufacturer’s instructions, and then subjected to 1x100 deep sequencing with Illumina HiSeq 2000

value: human

tag: chromosome

value: diploid

value: tissue


title: control_pAplus_1 and 2

source_name: human CRC patient control mucosa