title: Glial cell line Even

description: ChRIP seq file using Hotchon even probeset

value: embryonic whole brain


title: Glial cell line Odd

status: Public on Dec 01 2015

type: SRA

city: Porltand

first: Herman

middle: Scott

last: Stadler

state: OR

address: 3101 SW Sam Jackson Park Rd

country: USA

institute: Shriners Hospital

description: ChIRP seq file using Hotchon odd probeset

library_source: genomic

data_processing:
library strategy: chromatin isolation by RNA purification sequencing (ChIRP-seq)
Fastq files were assembled against MM9 mouse reference genome using using bowtie-0.12.9 (Langmead et al., 2009) and normalized to the total read count.  Even and odd Hotchon ChIRP samples were merged by taking the minimum value of the even and odd tracks at each genomic position.  The mouse glial cell line that does not express Hotchon was used as a control to identify false hybridization peaks detected by the Hotchon-specific even and odd probe pools.  Peaks were called by MACS (Zhang et al., 2008) using the Hotchon ChIRP merge sample and the DNA input, with an initial threshold p-value ≤ 5.9 x 10-57 corresponding to 775 peaks based on visual inspection of the peaks using the UCSC Genome Browser.
Genome_build: mm9
Supplementary_files_format_and_content: Called peaks were processed as big wig files and converted to bed file format for viewing in the UCSC genome browser

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse brain

extract_protocol:
Twenty five oligonucleotide probes corresponding to the murine Hotchon transcript were selected using the Stellaris Probe Designer Software set to masking level 5 to ensure the maximal level of probe specificity (biosearchtech.com) (Supplemental File).  The oligonucleotide sequences selected by the software were synthesized with an 18-atom hexa-ethyleneglycol spacer followed by a biotin tag located at the 3’ end of each oligonucleotide and purified by HPLC by Integrated DNA Technologies (Corallville, IA).   The distal half of mouse embryonic limb buds at embryonic day (E) 11 were dissected and digested for 10 minutes in sterile PBS containing 0.1% trypsin and 0.1% collagenase at 37 degrees Celsius as described (Owens and Solursh, 1982).  The digested limb buds were dissociated into a single cell suspension by passing them through a 70 µm nylon mesh and fixed in 1% glutaraldehyde as described (Chu et al., 2011.  Approximately 2000 embryonic limb buds were required to produce the 200mg cells needed for each for each ChIRP assay (Chu et al., 2011).  Cell lysis and chromatin shearing were accomplished using a Bioruptor instrument (Diagenode Denville, NJ) as previously described (Chu et al., 2011).  Once sheared, the chromatin was hybridized with the biotin-tagged Hotchon oligonucleotide probes which were divided into even and odd probe pool sets as described (Chu et al., 2012).  As a control, chromatin from E15.5 murine glial cells (a kind gift from Dr. Peter Hurlin), that do not express the Hotchon, were used in parallel assays and hybridized with the same Hotchon even and odd probe pool sets.   After hybridization the chromatin-Hotchon probe complexes were isolated using magnetic streptavidin beads as described (Chu et al., 2011).  DNA from isolated chromatin was purified using phenol/chloroform extraction followed by DNA precipitation as described (Chu et al., 2011).  The precipitated DNA was quantified using a Qubit 2.0 DNA fluorometer (Life Technologies) and submitted to Elim Biopharm (Hayward, CA) for library preparation and next generation sequencing using an Ilumina HiSeq 2500 sequencer (Illumina San Diego, CA).
Libraries were constructed for next generation sequencing using the Illumina library preparation kit as described by the manufacturer.

tag: strain

value: Swiss Webster

tag: developmental stage

tag: tissue source

value: embryonic mouse brain


title: e9.5 EPC RNA-Seq (3)

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: library barcode: ATGTCA

library_source: transcriptomic

data_processing:
Reads were aligned to mm9 using STAR v2.4.0 (Dobin A, et al. Bioinforma Oxf Engl. 2013;29: 15–21) with default parameters, and then bam files for technical replicates were combined using the samtools (Li H, et al.  Bioinformatics, 25, 2078-9) merge function.
FPKMs were estimated, and genes with significant differential expression between e7.5 and e9.5 were determined using Cufflinks v2.2.1 and Cuffdiff v2.2.1 (Trapnell C, et al. Nat Biotechnol. 2010;28: 511–515. ) with default parameters and a mask file specifying that rRNA, tRNA, and mitochondrial RNA from mm9 should be ignored.
Genome_build: mm9
Supplementary_files_format_and_content: allReplicate_FPKMs.txt: contains FPKM values for each condition and each replicate.  1st row contains column names.

molecule: total RNA

source_name: Placenta

extract_protocol:
Ectoplacental cone (EPC) tissue was dissected from embryos at e7.5 and e9.5, obtained from timed pregnant CD-1 mice (Charles Rivers Labs).   The EPC was separated from the maternal decidua, embryo, and other extraembryonic tissue.  RNA was isolated using the Qiagen RNeasy Micro Kit, following the manufacturer’s protocol.  RNA quality was assessed using the Agilent Bioanalyzer, and all samples had a RIN score ≥ 8.7.
mRNA was isolated and prepared for sequencing using Illumina’s TruSeq Stranded mRNA Sample Prep Kit, following the manufacturer’s protocol, and starting with 1ug total RNA.  6 libraries (3 biological replicates at each time point) were pooled and the pooled sample was run on two lanes (technical replicates).

tag: tissue

value: placenta

tag: age


title: e9.5 EPC RNA-Seq (2)

description: library barcode: CCGTCC


title: e7.5 EPC RNA-Seq (3)

description: library barcode: CAGATC


title: e9.5 EPC RNA-Seq (1)

description: library barcode: GTCCGC


title: e7.5 EPC RNA-Seq (2)

description: library barcode: CTTGTA


title: PPAR delta E411P rep3

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Striatum

extract_protocol:
Striatum were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared by BGI for sequencing using standard Illumina protocols

value: Striatum

tag: genotype

value: PPAR delta E411P +; Nestin-Cre +


title: ChIP-seq IRF4 Pre-PB [25440]

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
For determining the regulatoy landscape and overall number of peaks, we used the MACS program version 1.3.6.1 with default parameters, a genome size of 2,654,911,517 bp (mm9) and a mixture of pro-B and mature B cell input control sample. For H3K27me3 ChIP-seq samples, we used SICER () and for de novo motif prediction analysis, we used SISSRS ().
For analysis of differential gene expression, the RNA-seq samples were cut down to a read length of 44 bp and aligned to the mouse transcriptome using the TopHat version 1.4.1. The number of reads per gene was counted using the HTseq version 0.5.3 with the overlap resolution mode option set to ‘union’. Between-batch variation was reduced with applying the R package EDAseq 1.0.0 (ref. 29). Genes with less than 10 counts per sample on average were excluded. For the remaining genes, all RefSeq transcripts assigned to the same gene were investigated, and cases, where the GC content differed by 10% or more between transcripts assigned to the same gene, were removed. If the difference was smaller than 10%, the average GC content across the transcripts were used as GC content input to EDASeq. EDASeq was run with default parameters. The GC-normalized EDAseq output was rounded, and the results were used as input for the downstream count-based analysis. The ex vivo samples showed no batch effect, and no GC normalization was performed. The ex vivo and in vitro data were analyzed separately using the R package DESeq version 1.8.3. To this end, the samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.1 were called as differentially expressed. Due to the strong batch effects in the in vitro data set, RPM and RPKM were not calculated. Instead, the GC-normalized rounded counts (EDAseq output) were used to calculate the GC-normalized RPM and GC-normalized RPKM. The calculations were done as for RPM and RPKM with the only difference that the GC-normalized data was used instead of the raw counts.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base; text tab delim = RPKM values in ASCII text format tab delimited

source_name: ChIP-seq IRF4 Pre-PB

extract_protocol:
phenol-chloroform extraction
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext Ultra End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer’s guidelines.

tag: strain background

tag: genotype/background

value: Wild-type

tag: cell preparation

value: 4-day LPS stimulation, MACS sorted

tag: cell type

value: Pre-PB

tag: cell sorting strategy

value: CD138– MACS sorted

tag: chip antibody

value: Irf4 Ab, SantaCruz SC6059X, lot:E0608


title: PPAR delta E411P rep2


title: e7.5 EPC RNA-Seq (1)

description: library barcode: AGTCAA


title: PPAR delta E411P rep1


title: Bio-ChIP-seq PU.1 PB [24486]

source_name: Bio-ChIP-seq PU.1 PB

value: PU.1(Bio/Bio) R26(BirA/BirA)

value: PB

value: Streptavidin


title: ATAC-seq Pre-PB [25427]

data_processing:
library strategy: ATAC-seq
For determining the regulatoy landscape and overall number of peaks, we used the MACS program version 1.3.6.1 with default parameters, a genome size of 2,654,911,517 bp (mm9) and a mixture of pro-B and mature B cell input control sample. For H3K27me3 ChIP-seq samples, we used SICER () and for de novo motif prediction analysis, we used SISSRS ().
For analysis of differential gene expression, the RNA-seq samples were cut down to a read length of 44 bp and aligned to the mouse transcriptome using the TopHat version 1.4.1. The number of reads per gene was counted using the HTseq version 0.5.3 with the overlap resolution mode option set to ‘union’. Between-batch variation was reduced with applying the R package EDAseq 1.0.0 (ref. 29). Genes with less than 10 counts per sample on average were excluded. For the remaining genes, all RefSeq transcripts assigned to the same gene were investigated, and cases, where the GC content differed by 10% or more between transcripts assigned to the same gene, were removed. If the difference was smaller than 10%, the average GC content across the transcripts were used as GC content input to EDASeq. EDASeq was run with default parameters. The GC-normalized EDAseq output was rounded, and the results were used as input for the downstream count-based analysis. The ex vivo samples showed no batch effect, and no GC normalization was performed. The ex vivo and in vitro data were analyzed separately using the R package DESeq version 1.8.3. To this end, the samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.1 were called as differentially expressed. Due to the strong batch effects in the in vitro data set, RPM and RPKM were not calculated. Instead, the GC-normalized rounded counts (EDAseq output) were used to calculate the GC-normalized RPM and GC-normalized RPKM. The calculations were done as for RPM and RPKM with the only difference that the GC-normalized data was used instead of the raw counts.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base; text tab delim = RPKM values in ASCII text format tab delimited

source_name: ATAC-seq Pre-PB

extract_protocol:
Qiagen MinElute Kit
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext Ultra End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer’s guidelines.

value: Blimp1(GFP/+) Cd23(Cre/+)

value: 4-day LPS stimulation, FACS sorted

value: CD138+GFP+ FACS-sorted


title: WT rep2

value: wild type


title: WT rep3


title: WT rep1


title: RNA-seq Pre-PB [26934]

molecule: polyA RNA

source_name: RNA-seq Pre-PB

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext Ultra End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer’s guidelines.

tag: genotype/variation

value: 4-day LPS stimulation GSK343 treated

value: CD138–GFP+ FACS-sorted


title: RNA-seq Pre-PB [26933]


title: C57.2_mouse

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

data_processing:
3' ends were trimmed for low quality bases using trim_seq with the settings (www.biopieces.org)
Reads were mapped to the mouse genome (build mm9) using Bismark and Bowtie2 with the options -N 1 -D 30
PCR duplicates were removed from mapped reads using deduplicate_bismark_alignment_output.pl
Methylation values extracted using bismark_methylation_extractor with the setttings --ignore_r2 2
CpG methylation values were finally merged into a single value per CpG
Genome_build: mm9
Supplementary_files_format_and_content: processed data files consist of single CpGs and their methylation score from overlapping reads with at least 6 reads covering the cytosine.

source_name: Adult Liver

extract_protocol: Liver (left lateral lobe) was extracted from saccrificed mice. DNA was extracted using Phenol : Chloroform : EtOH precipitation.

value: Avy

value: 22 weeks

tag: coat colour

value: Black


title: C57.3_mouse


title: RNA-seq Pre-PB [26931]

value: 4-day LPS stimulation DMSO treated


title: Untreated

city: Vancouver

first: Brad

last: Hoffman

state: BC

country: Canada

institute: University of British Columbia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie2 v2.2.1
Transcript splice junctions were determined using Tophat v2.0.11
Transcripts were assembled and differences in expression were determined using Cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: RNA_seq differential expression
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie2 v2.2.1
The aligned reads were used to identify enriched regions using ChromHMM
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq enriched peaks in bed format

source_name: Islets

growth_protocol: Untreated pancreatic islets were cultured for four days in RPMI

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 800ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After isolation islets were allowed to recover for 4-6 hours and were then cultured in RPMI for four days.

value: 8-12 Weeks

value: Islets


title: RNA-seq Pre-PB [26932]

value: Pre-PB


title: Cytokine Treated

growth_protocol: Cytokine-treated pancreatic islets were cultured for four days in RPMI

treatment_protocol: After isolation islets were allowed to recover for 4-6 hours and were then treated with 1.6ng/ml IFNγ, 0.25ng/ml IL-1β and 0.16ng/ml TNFα in RPMI for four days.


title: Limb Mesenchyme Odd

source_name: Mouse limb bud

value: Swiss Webster

value: limb bud


title: Pseudoagouti_mouse

value: Pseudoagouti


title: RNA-seq Pre-PB [11954]

value: Blimp1(GFP/fl) Cd23(Cre/+)

value: CD138–GFP+CD22hi FACS-sorted


title: RNA-seq Pre-PB [11749]

value: 4-day LPS stimulation, FACS sorted


title: Yellow_mouse

value: Yellow


title: C57.1_mouse


title: RNA-seq Pre-PB [11951]

value: Blimp1(GFP/+) Cd23(Cre/+)


title: Islets_cyto_K4me1

extract_protocol:
Islets were dispersed, fixed with formaldyhyde and lysed. DNA was fragmented using a bath sonicator and bound to anti-bodies and beads. Bound DNA/protein complexes were eluted from the beads and prepared for library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: antibody

value: H3K4me1 (Abcam)


title: RNA-seq Plasma cell [17013]

source_name: RNA-seq Plasma cell

value: Ex vivo, FACS sorted

value: Plasma cell

value: CD28+CD138+GFP+Lin- FACS-sorted


title: RNA-seq Plasma cell [17014]


title: RNA-seq Pre-PB [11746]

value: CD138–GFP+ FACS-sorted


title: RNA-seq PB [11952]

source_name: RNA-seq PB

value: PB

value: CD138+GFP+ FACS-sorted


title: RNA-seq Act B cell [11748]

source_name: RNA-seq Act B cell

value: Act B cell

value: CD138–GFP– FACS-sorted


title: RNA-seq Mature B cell [16185]

source_name: RNA-seq Mature B cell

value: Wild-type

value: Mature B cell

value: B220+CD19+IgDhi FACS-sorted


title: RNA-seq Act B cell [11953]


title: RNA-seq PB [11747]


title: RNA-seq Mature B cell [16186]


title: H3K4me3 PB [13028]

source_name: H3K4me3 PB

value: B220intGFP+ FACS sorted


title: H3K4me3 Act B cell [13029]

source_name: H3K4me3 Act B cell

value: B220+GFP- FACS sorted


title: H3K4me2 Act B cell [13027]

source_name: H3K4me2 Act B cell

value: 4-day LPS stimulation, FACS sorted


title: H3K27me3 PB [13010]

source_name: H3K27me3 PB

value: H3K27me3 Ab TJ crude serum


title: H3K27me3 Act B cell [13011]

source_name: H3K27me3 Act B cell


title: H3K4me2 PB [13026]

source_name: H3K4me2 PB


title: OE1648 mm skin 30months rep2

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species
Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor
Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation
Genome_build: D. rerio: danRer7; M. musculus: mm9
Supplementary_files_format_and_content: Excel file include raw counts and RPKM values for each sample

source_name: total RNA extracted from skin

extract_protocol:
D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater (Qiagen, Hilden, Germany) at 80 °C. Total RNA was isolated with TRIzol (Life Technologies, Darmstadt, Germany) according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol (Qiagen) by subsequently adding 100 μl chloroform. Following phase separation, the aqueous phase was transferred into a fresh tube, then 0.16 volume NaAc (2 M, pH 4.0) and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water (GIBCO) and stored at –80°C until use.
D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA-Seq sample prep kit (Illumina, San Diego, CA, USA) following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.

value: 30 months

value: skin


title: OE1647 mm skin 30months rep1


title: OE1654 mm skin 15months rep6

value: 15 months


title: OE1653 mm skin 15months rep5


title: OE1655 mm skin 30months rep3


title: OE1644 mm skin 2months rep3

value: 2 months


title: OE1646 mm skin 2months rep5


title: OE1652 mm skin 15months rep4


title: OE1649 mm skin 15months rep1


title: OE1645 mm skin 2months rep4


title: OE1651 mm skin 15months rep3


title: OE1643 mm skin 2months rep2


title: OE1656 mm skin 30months rep4


title: OE1642 mm skin 2months rep1


title: OE1650 mm skin 15months rep2


title: Col-H3K23ac

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

description: Genomic DNA isolated from immnuoprecipitated chromatin using H3K23ac antibody (07-355 Millipore)

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10/MSU7.0 genome, with default parameters. Reads mapping to identical positions in the genome  were collapsed into one read.
Genome_build: TAIR10 for Arabidopsis; MSU7.0 for Rice
Supplementary_files_format_and_content: bigwig file generated by UCSC "bedGraphToBigWig" scipts

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis plants were grown on soil at 21 degree under continuous light for 2 weeks. Oryza sativa was grown on MS medium at 28 degree under short day condition (8hrs light and 16hrs dark)

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850
ChIP library was constructed by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330)

tag: cultivar

value: leaf


title: Col-H4K16ac

description: Genomic DNA isolated from immnuoprecipitated chromatin using H4K16ac antibody (07-329 Millipore)


title: Col-H3

description: Genomic DNA isolated from immnuoprecipitated chromatin using H3 antibody (ab1791 abcam)


title: Lys1/2

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

description: protein associated DNA

data_processing:
In brief, all samples were sequenced on an Illumina Genome Analyzer (GAIIx). Quality score and nucleotide composition at each position of the sequenced tags were assessed by box and bar plotting using FastX-Toolkit standard functions.
All samples were aligned to human genome (hg19, GRCh37) using Bowtie aligner (allowing 2 mismatches, keeping uniquely aligned reads only)
Piles of tags with same coordinates, due to artifacts of PCR or unannotated regions of the genome were removed according to a thresholding method.
Uniquely aligned tags were further elongated after estimating optimal elongation size in silico and enabling to use the original fragment length for further processing.
Sample was input subtracted and signals were scaled according to the mean signal..
The number of tags covering each nucleotide of the genome was computed and averaged in bins of 50 nucleotides. The scores of bins were rescaled (after input subtraction when applicable) to reduce over-representation of particular genomic regions and signal/noise ratio.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: wiggle format, scores of  binding of RNA Pol II containing a lysine methylated CTD.

organism: Homo sapiens

source_name: Raji B-cell line

growth_protocol: Raji B-cells were grown in RPMI medium supplemented with 10% FCS, 100 µg/ml streptomycin, 100 U/ml penicillin and 2 mM L-glutamine at 37°C with 8% or 5% CO2. Stable transfected Raji cell lines were selected and maintained by G418 (Invitrogen) (Chapman et al., 2005). The expression of the recombinant Rpb1 was induced by the removal of tetracycline. The endogenous RNAPII was poised by α-amanitin (2 µg/ml).

extract_protocol: Raji cells were crosslinked at room temperature by adding 1/10th volume of crosslinking solution (11% formaldehyde, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 50 mM Hepes pH 7.8) to the cell culture medium for 10 min. The reaction was stopped by the addition of 250 mM glycine for 5 min. Afterwards the cells were washed twice with PBS. 5 x 107 cells were lysed in 2,5 ml LB1 (50 mM Hepes, pH 7.5, 140 mM NaCl, 1 mM EDTA, pH 8.0, 10% Glycerol, 1% NP-40, 0.5% Triton X-100, 1 x phosphatase inhibitors, 1 x EDTA‐free protease inhibitors (Roche)) for 20 min at 4°C on a shaker. The cells were spun down (5 min, 4°C, 1350 g) and washed with LB2 (200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 10 mM Tris pH 8.0, 1 x phosphatase inhibitors, 1 x EDTA‐free protease inhibitors) for 20 min at 4°C. The samples were spun down again and suspended in 1.5 ml LB3 (1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 10 mM Tris pH 8.0, 100 mM NaCl, 0.1 % Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1 x phosphatase inhibitors, 1 x EDTA‐free protease inhibitors). The samples were sonicated with a Misonix 4000 (Misonix Inc.) sonicator for 14 cycles (30 sec on, 30 sec off, amplitude 40). Triton X-100 was added to a final concentration of 1% and the chromatin was collected by centrifugation (20 000 g, 20 min, 4°C). An aliquot of 50 µl was taken as input control. The input was mixed with an equal volume of 2 x elution buffer (100 mM Tris pH 8.0, 20 mM EDTA pH 8.0, 2 % SDS) and incubated at 65°C for 13-15 h. The sample was diluted with same volume of TE (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0) and digested by RNase A (0.2 µg/ml, 2 h, 37°C) and Proteinase K (0.2 µg/ml, 2 h, 55°C). DNA was purified by two phenol:chloroform:isoamylalcohol (25:24:1, pH 8.0) extractions steps and a subsequent PCR column purification (Qiagen). DNA fragmentation was controlled on a 2% agarose gel.

tag: cell line

value: Raji B-cell line

tag: library strategy

value: ChIP-seq


title: Input ChIP-Seq

first: Patricia

middle: J

last: Kiley

address: 420 Henry Mall, Room 1135 Biochemistry Building

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

data_processing:
Reformat Illumina files to Sanger format, FASTQ Groomer
Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
Call peaks to and FDR 0.1, MOSAiCs
Deconvolute peaks in close proximity, dPeak
Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
Scale data set to 20 million reads
Genome_build: Escherichia coli MG1655 K-12 genome version U00096.2
Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment

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

source_name: Combined input

growth_protocol: Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of ~0.3-0.35).

extract_protocol:
Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.

treatment_protocol:
Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.

value: Combined input

tag: growth medium


title: Fur IP ChIP-Seq Anaerobic, Iron Deficient A

source_name: Anaerobic, Iron Deficient cultures

value: {delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12

value: MOPS minimal glucose media containing 1 µM FeSO4

value: Custom anti-Fur polyclonal antibody


title: Fur IP ChIP-Seq Anaerobic, Iron Deficient B

value: {delta}tonB, {delta}feoA, {delta}zupT K12


title: Fur IP ChIP-Seq Anaerobic C

source_name: Anaerobic cultures

value: Wild-type

value: MOPS minimal glucose media containing 10 µM FeSO4


title: Fur IP ChIP-Seq Anaerobic B


title: Fur IP ChIP-Seq Aerobic C

source_name: Aerobic cultures


title: 3 SAFB1 iCLIP

city: Bristol

first: James

last: Uney

address: Medical School, University Walk

department: School of Clinical Sciences

country: United Kingdom

institute: University of Bristol

description: 3 SAFB1

data_processing:
Library strategy: CLIP-Seq
Data was processed using RTA version 1.13.48, with default filter and quality settings.
The reads were demultiplexed (allowing no mismatches in the index sequence) with CASAVA 1.8.2
The random bar-code sequences for the individual experiments were applied using the following RT primers: 5’-phosphate-NNXXXXNNNAGATCGGAAGAGCGTCGTGGATCCTGAACCGC-3’ where the unique experimental identifier (XXXX) was as follows: AACC, ACAC and AGGT for the anti-SafB1 antibody (Bethyl) experiments and CGAC for a no antibody control.
The random barcodes were registered and PCR-duplicates were removed along with any reverse-primer sequences.
The filtered iCLIP tag sequences were mapped to the human genome sequence (version hg19/GRCh37) allowing one mismatch using Bowtie version 1.0.1. Comparing cross-link nucleotide positions from three independent replicates assessed reproducibility, and allowed the z-score analysis of enriched pentamers at cross-link nucleotides to be calculated
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Gene coordinates (columns 1-4), gene name, gene segment type and biotype, and tag sums for each expt

growth_protocol: SHSY-5Y cells were grown using standard cell culture techniques in DMEM-F12 media supplemented with 10% FBS

extract_protocol:
iCLIP was performed with partial RNase I digestion and following SDS-PAGE analysis of immunoprecipitated SAFB1 the cross-linked RNA was extracted, reverse-transcribed and PCR-amplified. (For detailed protocol see reference Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J: iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. Journal of visualized experiments : JoVE 2011(50))
The iCLIP procedure introduces Illumina sequencing primer sequences into the cDNA libraries (Konig et al. Journal of visualized experiments : JoVE 2011(50)) during the reverse transcription and PCR-amplification steps.
High-throughput sequencing of iCLIP cDNA was performed on a HiSeq 2500 high output mode using v3 Illumina chemistry.

treatment_protocol: SHSY5Y neuroblastoma cells were irradiated once with 400 mJ/cm2 at 254 nm in a Stratalinker 1800 and SAFB1 was immunoprecipitated with protein G Dynabeads (Invitrogen) conjugated to rabbit anti-SafB1 antibody  (Bethyl laboratories Inc., A300-811A). The region corresponding to 140-200 kDa complexes was excised from the membrane to isolate the RNA and high-throughput sequencing of iCLIP cDNA was performed using Illumina GA2

value: Neuroblastoma

value: Bethyl SAFB1


title: Mock

city: YangLing

first: Juan

last: Huang

state: Shaanxi

address: NO. 3. WeiHui Road

department: College of Agronomy

country: China

institute: Northwest Agriculture & Forestry University

data_processing:
the libraries were sequenced using Illumina HiSeq™ 2000, producing the raw data.
Clean tags were acquired from raw sequences after removing (1) 39 bp adaptor sequences, (2) empty reads, (3) low-quality tags with unknown sequences ‘‘N’’, (4) tags unequal to 21bp, and (5) tags with only one copy number.
All clean tags were mapped to the reference sequences and only 1bp mismatch was considered.
Unambiguous clean tags were obtained by filtering clean tags which mapped to multiple reference sequences.
The number of unambiguous clean tags for each gene was calculated and then normalized to TPM
Genome_build: we used an integrated reference gene database with 104,831 sequences for tag mapping. The unambiguous tags that can’t be mapped to reference genes were subsequently mapped to the D genome (Gossypium raimondii)
Supplementary_files_format_and_content: Text files include lengths and counts of each distinct reads.

organism: Gossypium hirsutum

source_name: Plants 3 hours after treatment with Mock (double distilled water)

growth_protocol: Seeds of Gossypium hirsutum L. ecotype CCRI10 were cultured in a mix of sand and nutritional soil in a culture room under white fluorescent light (16h light/8h dark) with day/night temperatures of 30/22℃.

extract_protocol:
Total RNA was extracted using the EASYspin Plant Total RNA Extraction Reagent (Aidlab, BeiJing, China) in accordance with the manufacturer’s instruction and stored at −70°C freezer. RNA samples with A260/A280 ≥ 1.8, A260/A230≥1.8, and RIN ≥6.5 were considered acceptable for library construction.
Poly(A)-containing mRNA was purified from six micrograms total RNA by oligo(dT) magnetic adsorption beads and cDNA was synthesized using oligo(dT) as primer. The bead-bound cDNA was firstly digested with restriction enzyme NlaⅢ, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to oligo(dT) beads were washed away and the Illumina adaptor 1 was ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The 3′cDNA fragments attached to the oligo(dT) beads were subsequently digested with restriction enzyme MmeⅠ, which recognizes the junction of Illumina adaptor 1 and CATG site and cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 was ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form tag libraries. After linear PCR amplification, fragments were purified by PAGE Gel electrophoresis. The quantification and qualification of the sample libraries were controlled by Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System.

treatment_protocol: 20 days after germination, plants with robust and consistent growth condition were irrigated with 100μM SNP, 250μM SNP, 10μM cPTIO respectively under continuous light.

tag: ecotype

value: cotyledon


title: 100μM SNP

source_name: Plants 3 hours after treatment with 100μM SNP

tag: tissue


title: No Antibody iCLIP

description: 4 No antibody


title: 10μM cPTIO

source_name: Plants 3 hours after treatment with 10μM cPTIO


title: 1 SAFB1 iCLIP

description: 1 SAFB1


title: 2 SAFB1 iCLIP

description: 2 SAFB1


title: 250μM_SNP_Replicate

source_name: Plants 3 hours after treatment with 250μM SNP (replicate of sample 3)


title: 250μM SNP

source_name: Plants 3 hours after treatment with 250μM SNP


title: wild type 3' end ligated

city: Stony Brook

first: Janet

last: Leatherwood

state: New York

address: 343 Life Sciences Building

department: Microbiology

institute: Stony Brook University

description:
processed data file: WT.tab
Sample 15

data_processing:
Basecalling with MiSeq Control Software v. 2.4.0.4
demultiplexing and fastq files generation with MiSeq Reporter v2.4
fastq files aligned to genome and transcriptome using Tophat-2.1.0
bam files sorted and indexed using Samtools1.2
fpkm for each annotation generated by cuffnorm and cuffdiff from the cufflinks suite v2.2.1
3' end ligation libraries fastq files were aligned to the genome using Bowtie-2.2.2
raw counts for region between 9500 and 10,100 on chromosome III using mpileup function of Samtools1.2
Genome_build: Schizosaccharomyces_pombe.ASM294v2.26
Supplementary_files_format_and_content: tab-delimited text files include combined fpkm of each annotation from replicates of samples (1,2,3,4,5,6,9,10,13,14) generated by cuffdiff, and separate fpkms for each gene in the replicates generated by cuffnorm; tab-delimited text files contain chromosome III coordinates and raw counts for 3' end ligated libraries

organism: Schizosaccharomyces pombe

source_name: vegetatively growing fission yeast

growth_protocol: All strains were grown in liquid YES media at 32°C until mid-log phase and harvested for RNA isolation, except: dis3-4 and rrp6-cat dis3-4 temperature-senstive mutants were grown at 23°C till mid-log phase and then shifted to 30°C for 1h before harvesting for RNA isolation

extract_protocol:
RNA was isolated using Ambion Ribopure™ RNA purification kit, yeast Cat# AM1926
RNA-Seq libraries for polyA selected RNA was made using NuGen Ovation Universal kit, Part# 0343 which uses dUTP to make stranded RNA-Seq libraries
RNA-Seq libraries by 3' end ligation of adapter and stranded sequencing using dUTP method

value: wild type

tag: growth temperature

tag: strain

value: S. pombe strain CHP1365


title: rrp6Δ 3' end ligated

description:
processed data file: 1704.tab
Sample 16

tag: genotype

value: S. pombe strain JLP1704


title: rrp6-cat dis3-4 23°C rep-2

description:
processed data file: fpkm_cuffnorm.txt
Sample 12

value: rrp6-cat dis3-4

value: S. pombe strain JLP1863


title: dis3-4 30°C  rep-1

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 9

value: S. pombe strain JT449


title: rrp6-cat dis3-4 30°C  rep-1

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 13


title: dis3-4 30°C rep-2

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 10


title: dis3-4 23°C rep-2

description:
processed data file: fpkm_cuffnorm.txt
Sample 8


title: dis3-4 23°C  rep-1

description:
processed data file: fpkm_cuffnorm.txt
Sample 7


title: rrp6-cat rep-1

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 5

value: S. pombe strain JLP1708


title: rrp6-cat rep-2

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 6


title: rrp6Δ rep-2

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 4


title: rrp6Δ  rep-1

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 3


title: wild type rep-1

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 1


title: Fur IP ChIP-Seq Aerobic B


title: rrp6-cat 3' end ligated

description:
processed data file: 1708.tab
Sample 17


title: rrp6-cat dis3-4 30°C rep-2

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 14


title: mut-0h

city: Barcelona

first: Jose

last: Ayte

address: Doctor Aiguader 88

country: Spain

institute: Universitat Pompeu Fabra

description: Control sample (untreated cells)

data_processing:
Sequenced reads were trimmed for adaptor sequence by using Tagdust
Filtered reads were mapped to the reference genome by using Tophat splice mapper (v2.0.5) using the annotation defined in Ensembl database (version ASM294 v1.15)
Mapped reads were filtered removing the muli-mapped ones by using samtools
For each intron, the number of split and unsplit reads that mapped to the splice junction (defined as the three bases around the 5’ exon junction) were counted, and the base-2 logarithm of the ratio between the two values was calculated. This value is called the Relative Splicing Efficiency Index (RSEI). If the RSEI was positive, then more reads indicated spliced mRNA than unspliced pre-mRNA. On the other hand, a negative RSEI indicates more unspliced than spliced RNA.
Genome_build: ASM294v1
Supplementary_files_format_and_content: excel file a table with chromosome, start and end of each splicing site, gene name, strand, number of tags (that maps univocally) in each condition and corresponding log2 ratio. A pseudocount of 1 was added to both numerator and denominator,.

source_name: Untreated cells

growth_protocol: Cells were gronw in standard EMM media to grow S. pombe

extract_protocol:
RNA was isolated using standard protocols for S pombe
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell were treated with the ATP analog 1NM-PP1 for 30 min, 60 min or left untreated

tag: mutation

value: Prp4 kinase conditional mutant

tag: time from induction

value: 0 h

tag: treatment

value: Control sample


title: rrp6-cat dis3-4 23°C  rep-1

description:
processed data file: fpkm_cuffnorm.txt
Sample 11


title: obe2/Df_rep2

city: New York

first: Jennifer

last: Zallen

state: NY

address: 1275 York Avenue

department: Developmental Biology

institute: Sloan Kettering Institute

data_processing:
RNA sequencing was carried out by the New York Genome Center using the HiSeq2500 platform (Illumina) with 50-bp paired-end reads and >20 million reads per sample.
Sequenced libraries were mapped to the Drosophila genome (DM3; UCSC Genome Browser) using the RNA-Seq aligner STAR (v_2.3.1z).
Differential analysis of gene and transcript expression was performed using Cuffdiff 2 (v_cufflinks-2.1.1; Trapnell et al., 2013).
Genome build: UCSC dm3
Supplementary_files_format_and_content:
Excel file with a matrix of normalized gene counts for all nine samples.
Excel file with differential expression analysis between obe1/obe2 mutants compared to WT (triplicate).
Excel file with differential expression analysis between obe2/Df mutants compared to WT (triplicate).

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Parental flies were raised under standard laboratory conditions (18C-25C). Embryos aged 3 h were collected on apple juice plates at 25C.

extract_protocol:
Embryos were ground in microfuge tubes in 50 ul Trizol reagent using plastic pestles. An additional 450 ul Trizol was then added and the samples were incubated for 5 min at RT. Next, 100 ul chloroform was added, and the samples were incubated for 3 min at RT. The samples were centrifuged at 12,000 g for 15 min to separate the aqueous and organic phases. At this point the standard Trizol protocols for total RNA extraction were followed.
Sample libraries were generated using TruSeq RNA Library Preparation Kit v2.

treatment_protocol: Approximately 50 late stage 5/early stage 6 embryos were manually selected, dechorionated and stored in 50 ul Trizol reagent. RNA from each genotype was isolated in triplicate.

value: Progeny of transheterozygous obe2/Df females crossed to obe2/+ males

tag: developmental stage

value: late stage 5/early stage 6 embryos


title: obe2/Df_rep3


title: obe1/obe2_rep3

value: Progeny of transheterozygous obe1/obe2 females crossed to obe2/+ males


title: OreR_rep1

value: Oregon R


title: mut-30min

description: Cells were treated for 30 minutes with the ATP analog to inhibit Prp4

source_name: Treated cells for 30 min

value: 30 min

value: Prp4 inhibited for 30 minutes


title: Ubx_bc3_r2

city: Montreal

first: Nicole

last: Francis

state: Quebec

address: 110 Ave des Pins Ouest

institute: IRCM/University of Montreal

description:
4C sequenced reads
primer sequence: CCAACTCGGCATTGTACGGTAA

data_processing:
library strategy: 4C-Seq
Sequenced reads in fastq files were trimmed from the 5' end to remove barcode and primer sequences up  to the 4C ligation junction. They were further trimmed from the 3' end to 35 bp.
Trimmed reads were aligned to the Drosophila genome using bowtie2.
Aligned reads were mapped to NlaIII-DpnII  fragments using the "bowtieToReTab.pl" Perl script that is part of the fourSig suite. This step generates Tab files that are the input for fourSig analysis.
Tab files were analyzed with fourSig, using the “mappability” function.  The output files from this analysis consist of the chromosomal position of the windows with detected interactions and a score (1, 2, or 3) assessing the contact, with a score of 1 being the most broad/stringent category (see Williams et al., 2014).  These files can be directly uploaded into a genome browser (as bed files) for visualization of chromatin contacts.
Genome_build: dm3
Supplementary_files_format_and_content: Files are text files, set up in a bed format with a track header and consisting of 4 columns:  chromosome, start, end, fourSig score (1, 2, or 3). Note that only contacts with score of 1 were presented or used for analysis.

source_name: Drosophila S2 cells

growth_protocol: Drosphila S2 cells were grown in ESF-9 media in 10 cm dishs at 27 C

extract_protocol:
Cells were cross-linked with formaldehyde and processed for 4C, according to  van de Werken et al., 2012.  NlaIII was used as the first restriction enzyme, and DpnII as the second.
After 3 days of induction, Drosophila S2 cells and S2 cells expressing Ph-WT or Ph-ML were crosslinked with 1% formaldehyde for 10 minutes. Nuclei were prepared by incubating fixed cells in Buffer A (20 mM HEPES pH 7.5, 1.5 mM MgCl2, 10 mM KCl and 0.1% NP40) for 12 min on ice, douncing 60 times and centrifuging at 150 g for 1 min. at 4oC. The supernatant was centrifuged at 1000 g for 10 min, and pelleted nuclei were washed with PBST. 4C-seq was carried out as described elsewhere (van de Werken et al., 2012). Briefly, Nuclei were resuspended in 180 µl of water and 20 µl of 10x NLAIII buffer. Nuclei were digested with NlaIII for 20 h at 37oC in a thermo-shaker set at 1000 rpm. NlaIII was inactivated by incubating samples at 65oC for 10 min. Digested DNA was ligated with T4 DNA ligase overnight at 16o C. Ligation mixture was treated with Proteinase K, crosslinks were reversed by overnight incubation at 65o C, and RNase A treatment was performed for 30 min. at 37o C. Phenol chloroform extracted and ethanol precipitated DNA was digested with DpnII for 7 h. at 37o C in a thermo-shaker set at 1000 rpm. DpnII was inactivated by incubating samples at 65o C for 15 min., and DNA was ligated with T4 DNA ligase overnight at 16o C. DNA was purified by phenol chloroform extraction and ethanol precipitation and resuspended in 30 µl of water. 20 ng of DNA per 50 uL of PCR reaction mixture was amplified for 30 cycles by expanded long range DNA polymerase (Roche) using indexed viewpoint primers. 100 base pair single end reads were sequenced at the Genomics Platform, University of Genève. Primer sequences are in Table II. Note that our primer design is atypical in that the sequenced primer corresponds to the secondary (DpnII) junction rather than the primary (NlaIII) one.The 4C-seq read structure is as follows:  barcode (6bp)--viewpoint specfic primer--11-12 bp--GATC (DpnII junction)--captured sequence.

treatment_protocol: Protein expression was induced by adding 0.5mM copper sulphate for 3 days

value: S2 expressing Ph-ML (SAM mutant)


title: obe1/obe2_rep2


title: OreR_rep3


title: OreR_rep2


title: Ubx_bc2_r2

value: S2 expressing Ph-wild type


title: Ubx_bc1_r2


title: Ubx_bc3_r1


title: Fab6_bc3_r2

description:
4C sequenced reads
primer sequence: CGTTGATGGTTCGGGGTATTATCT


title: Fab6_bc2_r2


title: obe2/Df_rep1


title: Fab6_bc1_r2


title: obe1/obe2_rep1


title: Ubx_bc1_r1


title: Fab6_bc1_r1


title: Fab6_bc2_r1


title: mut-60min

description: Cells were treated for 60 minutes with the ATP analog to inhibit Prp4

source_name: Treated cells for 60 min

value: 60 min

value: Prp4 inhibited for 60 minutes


title: AbdB_bc3_r2

description:
4C sequenced reads
primer sequence: TGGTGGATGAACTCCCCAAAA


title: Fab6_bc3_r1


title: wild type rep-2

description:
processed data file: fpkm_cuffdiff.txt, fpkm_cuffnorm.txt
Sample 2

value: wild type

value: S. pombe strain CHP1365


title: AbdB_bc2_r2


title: Abdb_bc3_r1


title: Abdb_bc2_r1


title: Abdb_bc1_r1


title: Ubx_bc2_r1


title: ARID3B-KD_KDM4C

city: Taipei

first: Tsai-Tsen

last: Liao

state: State...

address: No.201, Sec.2, Shih-Pai Rd. Peitou, Taipei, Taiwan, 11221, R.O.C

country: Taiwan

institute: Institute of Clinical Medicine

data_processing:
NextSeq500 Control Software Ver.1.3.0(BaseCalling)
Bcl2fastq Ver. 2.1.5.
ConDeTri Ver. 2.1.(ReadsTrimming)
BWA Ver. 0.7.12.(Alignment/mapping)
MACS Ver. 1.4.2.(PeakCalling)
Genome_build: Grch37

source_name: Head and neck cancer cell line OECM1 receving ARID3B-Cas9

growth_protocol: cultivated in RPMI + 10% fetal bovine serum

extract_protocol:
Lysates were clarified by the Pierce Magnetic ChIP Kit and histone-DNA complexes were isolated with antibody.
10 ng DNA was end-repaired, A-tailed and adaptor-ligated following the Illumina's  TruSeq DNA preparation protocol.

tag: cell type

value: Head and neck cancer cell

tag: chip antibody

tag: chip antibody vendor

value: NOVUS

tag: chip antibody cat. #


title: Control rep2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Control

data_processing:
Illumina Casava software used for basecalling.
Reads were mapped to the D. melanogaster genome version dm3 using Tophat2 v2.0.10 with the multithreading option -p 5 and the remaining parameters as the default allowing for two mismatches.  Tophat2 was using bowtie2 v2.1.0.0 as the underlying mapper
Mapped reads were assembled into transcripts with cufflinks v2.1.1 using the multithreading option -p 5 and the remaining options as the defaults.  The gtf used for transcript construction was the flyBase
Aligned reads were used as inputs for cuffdiff2 to determine gene expression levels (FPKM) and differential expression between conditions using the multithreading option -p 8 and the minimum alignment count of 7 (--min-alignment-count 7).  All other parameters were set to the defaults.
Differential expression was tested for dose independent PARylation inhibition results by comparing the combined alignments of samples 2 and 3 (PARylation) to the combined alignments of samples 1 and 4 (control) using cuffdiff2.
Differential expression was tested for dose-independent PARP knockdown results by comparing the combined alignments of samples 5 and 6 (PARP-1 Knockdown) to the combined alignments of samples 1 and 4 (control) using cuffdiff2.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: Genes_FPKMValues.txt is a tab-delimited text file containing the gene ID, locus, and FPKM values for each gene assembled using cufflinks.  PARP-1-KD_tss_group_exp.dff and PARylation_tss_group_exp.diff are the resulting combined dose-independent differential expression results for PARP-1 knockdown and PARylation inhibition, respectively.  These files are output by cuffdiff.  A p-value cutoff of 0.05 was used to determine differentially expressed genes.

source_name: late embryonic stage cells

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

extract_protocol:
RNA was extracted using standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: late embryonic stage cells

tag: passages

value: Control


title: dsRNA-knockdown-500ng rep1

description: PARP-1 Knockdown 500ug

tag: cell line

value: PARP-1 Knockdown 500ug


title: Control rep1

description: Control


title: dsRNA-100ng rep1

description: PARP-1 Knockdown 100ug

value: PARP-1 Knockdown 100ug


title: PJ34-0.3um rep1

description: PARylation inhibited 0.3um

value: PARylation inhibited 0.3um


title: ARID3B-KD_ARID3B

value: BETHYL


title: PJ34-10um rep1

description: PARylation inhibited 10um

value: PARylation inhibited 10um


title: AbdB_bc1_r2


title: Nr16 bcat-1

data_processing:
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) vs. the C. elegans genome WBcel235.74 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: WBcel235.74

organism: Caenorhabditis elegans

source_name: total RNA from whole animals

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of 2 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.

value: Bristol N2

value: Adult (5 days after L4)

tag: agent

value: bcat-1 RNAi


title: Nr15 control

value: control


title: Nr18 bcat-1


title: intra_hemo2

city: Montpellier

first: Guillaume

last: Charriere

address: Place Eugene Bataillon

department: UMR 5244 IHPE

country: France

institute: Universite de Montpellier

data_processing:
In a first step, the RNA-Seq data quality was assessed by including option like reads trimming or merging/split paired-end reads.
In a second step, reads were mapped onto the Vibrio tasmaniensis LGP32 genome sequence , respectively using the SSAHA2 package (Ning et al, 2001) that combines the SSAHA searching algorithm (sequence information is encoded in a perfect hash function) aiming at identifying regions of high similarity, and the cross-match sequence alignment program (Ewing et al, 1998), which aligns these regions using a banded Smith-Waterman-Gotoh algorithm. An alignment score equal to at least half of the read is required for a hit to be retained.
To lower false positives discovery rate, the SAMtools (v.0.1.8) were then used to extract reliable alignments from SAM formatted files.
The number of reads matching each genomic object harbored by the reference genome was subsequently computed with the Bioconductor-GenomicFeatures package.
The Bioconductor-DESeq package with default parameters was used to analyze raw counts data, normalize data and test for differential expression between conditions. Out of the paired-end reads, only mapping results of the first sequencing run reads were used for the DESeq analysis.
Genome_build: Vibrio tasmaniensis LGP32 genome (genome ID: 13995, assembly GCA_000091465.1,NCBI)
Supplementary_files_format_and_content: rawCountData.txt file includes raw read counts for each gene in each Sample (forward and reverse counts).
Supplementary_files_format_and_content: differentialGeneExpression.txt includes DESeq differential expression analysis between the two conditions (control and intra oyster hemocytes bacteria).

organism: Vibrio tasmaniensis

source_name: intra_hemo_bacteria transcriptome

growth_protocol: LGP32 was grown at 20°C in Zobell medium for 10h and washed twice in SSW by centrifugations (10min, 1000g, 20°C). Bacteria were then resuspended in SSW at OD 600 of 0.5 (1.109cfu/mL equivalent).

extract_protocol:
RNA of LGP32 were extracted using the Trizol reagent protocol (Life Technologies). RNA concentration was measured using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc.) and RNA quality was monitored by agarose gel electrophoresis and a 2100 Bioanalyzer (Agilent Technologies Inc.). For each sample, 7 μg of starting material was treated with DNaseI(4 U) (Ambion’s DNA-free™) following the manufacturer instructions. Samples were then enriched in bacterial RNA using the MICROBEnrich™ Kit (Ambion) and bacterial rRNA were then removed by the MICROB Express ™Kit (Ambion) following the manufacturer instructions. Because the MICROBEnrich™ Kit is based on oligonucleotides that are designed to capture rRNAs from mammal species, it is not fully efficient to remove invertebrate rRNAs. Accordingly, we performed a further depletion step using a 5’-phosphate-dependent exonuclease (Terminator, Epicentre), that degrades processed transcripts, following instructions from the manufacturer.
Directional cDNA libraries were constructed from 3 independent experiments and sequenced on an illumina Hiseq 1000, in paired-end reads of 2 x 100 bp (~ 60 x 106 reads per sample).

treatment_protocol: Hemolymph was dispensed in a 6 well-plate at 6 × 10^6 hemocytes per well. After 1h, vibrios were added at a MOI of 100:1. After a 1h phagocytosis, hemocytes were washed 3 times and 500 µl Trizol reagent (Invitrogen) were added to the wells. ~ 40% hemocytes had internalized 50-70 bacteria, with rare bacteria remaining extracellular.

value: bacteria phagocytosis by oyster hemocytes


title: Nr14 bcat-1


title: intra_hemo3


title: control3

source_name: control_bacteria transcriptome

extract_protocol:
For extracellular controls, vibrios were kept for 1h in SSW. As vibrio RNA represents ~10% of the total RNA, in extracellular controls, C. gigas hemocyte RNA was added to LGP32 RNA with a ratio of 1:9.
RNA of LGP32 were extracted using the Trizol reagent protocol (Life Technologies). RNA concentration was measured using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc.) and RNA quality was monitored by agarose gel electrophoresis and a 2100 Bioanalyzer (Agilent Technologies Inc.). For each sample, 7 μg of starting material was treated with DNaseI(4 U) (Ambion’s DNA-free™) following the manufacturer instructions. Samples were then enriched in bacterial RNA using the MICROBEnrich™ Kit (Ambion) and bacterial rRNA were then removed by the MICROB Express ™Kit (Ambion) following the manufacturer instructions. Because the MICROBEnrich™ Kit is based on oligonucleotides that are designed to capture rRNAs from mammal species, it is not fully efficient to remove invertebrate rRNAs. Accordingly, we performed a further depletion step using a 5’-phosphate-dependent exonuclease (Terminator, Epicentre), that degrades processed transcripts, following instructions from the manufacturer.
Directional cDNA libraries were constructed from 3 independent experiments and sequenced on an illumina Hiseq 1000, in paired-end reads of 2 x 100 bp (~ 60 x 106 reads per sample).

treatment_protocol: As a control, washed bacteria were incubated in triplicates in SSW for 1h.


title: Nr13 control


title: control1


title: control2


title: YY rep3

status: Public on Nov 30 2015

city: hefei

first: xiaojin

last: li

state: anhui

address: nongkenan road no. 40

department: Institute of Animal husbandry and veterinary medicine

institute: Anhui academy of agricultural sciences

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the Sscrofa10.2.69 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: Sscrofa10.2.69
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Sus scrofa

source_name: longissimus dorsi muscle

extract_protocol:
Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration.

tag: breed

value: Yorkshire

tag: age

value: 5 months old


title: intra_hemo1


title: YY rep1


title: YY rep2


title: WH rep3

value: Wannanhua


title: WH rep1


title: Control_KDM4C

source_name: Head and neck cancer cell line OECM1 receving Cas9-ctrl

value: Head and neck cancer cell


title: Nr17 control


title: Control_ARID3B


title: H1_TKO_ESC_H3K4me3_IP_R2

city: Utrecht

first: Geert

last: Geeven

state: Utrecht

address: Uppsalalaan 8

department: Biomedical Genomics

country: Netherlands

institute: Hubrecht Institute

description:
Processed data file: H1_TKO_ESC_H3K4me3_R2_peaks.bed.gz
Processed data file: H3K4me3_WT_vs_TKO_diffReps_output.txt.gz

data_processing:
Hi-C : Reads from both ends were mapped separately single end with bwa aln with default parameters. Uniquely mapped reads were sorted and paired by read ID using samtools. Mapped pairs were filtered to remove reads coming from the same or neighboring restriction fragments. Filtered pairs were deduplicated to remove PCR duplicates and valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files.
DNase Hypersensitivity : Aligned reads in bam files are those 36bp reads that aligned uniquely (Bowtie) to the reference (NCBI37/mm9) and contain no more than 2 mismatches. DNaseI-sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004).
DNA methylation HELP tagging data was processed with the WASP pipeline (version 3.0.31 (rev. 3822). Reads were aligned with Illumina's CASAVA and ELAND v. 1.7.0 allowing 2 mismatches in the first 32bp and no more than 10 alignments for each read. HELP angles were computed as described in (Suzuki et al. 2010).
RNA-Seq : We aligned 2x100 paired-end reads of 2 replicate WT ESC RNA-seq libraries and 3 replicate H1 TKO ESC RNA-seq libraries to the reference genome (NCBI37/mm9) with TopHat and used Cufflinks and CuffDiff for differential expression analysis of RNA-seq expression for a non-redundant collection of 20876 known RefSeq transcripts. We considered genes with a marginal p-value smaller than 0.05 and an absolute log2 fold-change  bigger than 1 to be differentially expressed.
ChIP-Seq : Reads from all different libraries were aligned to the reference genome (NCBI37/mm9) with bowtie2 with default settings and the --qc-filter switch. Duplicates were marked using Picard (http://broadinstitute.github.io/picard/) and were removed from the data for subsequent analyses. Regions significantly enriched for H3K4me1, H3K4me3, H3K27me3 and H3K9me3 compared to matched input samples were identified using the MACS2 peak caller with default settings. For the H3K9me3 and H3K27me3 histone marks, the parameter - - broad was set. Analysis of differential ChIP enrichment was done using diffReps with parameters -me gt –pval 0.001 --frag 150.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files; ChIP-Seq peaks called by MACS2 are in peaks.bed.gz files; DNaseI-hypersensitive sites called with the HOTSPOT algorithm in mm9.bed.gz files; DNA methylation HELP angles are in HELP.txt.gz file; RNA-Seq FPKM values are in FPKM.txt.gz file.

source_name: H1 TKO embryonic stem cells, H3K4me3 ChIP

growth_protocol:
Wild-type ES cell line was derived from littermate male blastocysts produced from matings of N7 backcrossed C57BL/6 triple heterozygous H1 mutant parents. The transgenic lines are further described in Fan et al. Cell 2005 (PMID 16377562).
WT and H1 TKO ES cells were grown on irradiated mouse embryonic fibroblasts in DMEM (high glucose, Gibco) with 15% FBS, 1x non-essential amino acids (NEAA; Gibco), 1x penicillin–streptomycin (Gibco), 1:1,000 b-mercaptoethanol (Invitrogen), 1x L-glutamine (Gibco) and 1,000 U/ml leukaemia inhibitory factor (LIF; Gibco).

extract_protocol: TruSeq DNA sample preparation kit (Illumina).

tag: strain/background

value: embryonic stem cell line

tag: genotype/variation

value: H1c, H1d, H1e triple-null


title: H1_TKO_ESC_H3K4me3_IP_R1

description:
Processed data file: H1_TKO_ESC_H3K4me3_R1_peaks.bed.gz
Processed data file: H3K4me3_WT_vs_TKO_diffReps_output.txt.gz


title: H1_TKO_ESC_H3K4me1_IP_R2

description:
Processed data file: H1_TKO_ESC_H3K4me1_R2_peaks.bed.gz
Processed data file: H3K4me1_WT_vs_TKO_diffReps_output.txt.gz

source_name: H1 TKO embryonic stem cells, H3K4me1 ChIP


title: WT_ESC_H3K4me3_IP_R2

description:
Processed data file: WT_ESC_H3K4me3_R2_peaks.bed.gz
Processed data file: H3K4me3_WT_vs_TKO_diffReps_output.txt.gz

source_name: WT embryonic stem cells, H3K4me3 ChIP

value: WT


title: H1_TKO_ESC_H3K4me1_IP_R1

description:
Processed data file: H1_TKO_ESC_H3K4me1_R1_peaks.bed.gz
Processed data file: H3K4me1_WT_vs_TKO_diffReps_output.txt.gz


title: WT_ESC_H3K4me3_IP_R1

description:
Processed data file: WT_ESC_H3K4me3_R1_peaks.bed.gz
Processed data file: H3K4me3_WT_vs_TKO_diffReps_output.txt.gz


title: H1_TKO_ESC_H3K4me1_H3K4me3_input_R2

description:
Processed data file: H1_TKO_ESC_H3K4me1_R2_peaks.bed.gz
Processed data file: H1_TKO_ESC_H3K4me3_R2_peaks.bed.gz

source_name: H1 TKO embryonic stem cells, H3K4me1 H3K4me3 input


title: WT_ESC_H3K4me1_H3K4me3_input_R1

description:
Processed data file: WT_ESC_H3K4me1_R1_peaks.bed.gz
Processed data file: WT_ESC_H3K4me3_R1_peaks.bed.gz

source_name: WT embryonic stem cells, H3K4me1 H3K4me3 input


title: WT_ESC_H3K4me1_IP_R2

description:
Processed data file: WT_ESC_H3K4me1_R2_peaks.bed.gz
Processed data file: H3K4me1_WT_vs_TKO_diffReps_output.txt.gz

source_name: WT embryonic stem cells, H3K4me1 ChIP


title: Month28_2

city: Huddinge

first: Maria

last: Eriksson

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska institutet

data_processing:
Bcl to Fastq was done with bcl2Fastq v1.8.3
Reads were mapped with Tophat v. 2.0.4
Exon count data were obtained with DEXSeq v. 1.14.2
Differential exon usage were identified with DEXSeq v. 1.14.2 with default settings
Genome_build: GRCm38
Supplementary_files_format_and_content: Exon count data from the DEXSeq analysis

source_name: wild-type, thigh skeletal muscle, 28 months

growth_protocol: Mice were housed in the experimental animal facility with a 12-hour light/dark cycle, a temperature of 20-22°C and 50-75% air humidity (Karolinska Hospital, Huddinge, Sweden). They were supplied with R36 pellets (Lactamin, Sweden) and drinking water ad libitum and aged up to desired age.

extract_protocol:
Mice were euthanized by cervical dislocation and the fur was trimmed before the skin was taken and placed into Ca2+ free PBS (d-PBS; Invitrogen). Subcutaneous tissue was removed, and the skin was floated on trypsin (T4424; Sigma-Aldrich) for 2 h at 32°C. After incubation, the epidermis was scraped into S-minimal essential medium (S-MEM; Invitrogen) supplemented with 0.01% soybean trypsin inhibitor (T9128; Sigma-Aldrich) and 0.5% BSA (bovine albumin fraction V solution (7.5%); Invitrogen) and gently mixed with a magnetic stirrer at room temperature for 20 min. The cell suspension was filtered through a 70-mm cell strainer (BD Falcon, Becton Dickinson, Franklin Lakes, NJ, USA), and viable cells were counted after staining with tryphan blue. Keratinocyte total RNA was thereafter  immediatel extracted with Trizol and RNA  integrity was assessed by the Agilent 2100 Bioanalyzer. The RNA quality criteria for proceeding with exon arrays were a 18S/28S ratio above 1.5 and an RNA integrity number (RIN-value) ≥ 8.0. For array hybridization and Whole Transcript Sense Target Labeling Synthesis, 200 ng of RNA was processed using the Gene Chip WT cDNA Synthesis Kit, (Affymetrix)
Illumina standard RNA procedure

tag: strain

tag: age (month)

tag: gender

value: male

tag: tissue

value: skeletal muscle


title: WT_ESC_H3K4me1_IP_R1

description:
Processed data file: WT_ESC_H3K4me1_R1_peaks.bed.gz
Processed data file: H3K4me1_WT_vs_TKO_diffReps_output.txt.gz


title: Month28_1


title: Month18

source_name: wild-type, thigh skeletal muscle, 18 months


title: H1_TKO_ESC_DNaseI_R3

source_name: H1 TKO embryonic stem cells, DNaseI


title: WT_ESC_DNaseI_R3

source_name: WT embryonic stem cells, DNaseI


title: WH rep2


title: H1_TKO_ESC_DNaseI_R2


title: WT_ESC_DNaseI_R2


title: H1_TKO_ESC_DNaseI_R1


title: WT_ESC_DNaseI_R1


title: HE_DAM ctrl

city: Manchester

first: Roshana

middle: S

last: Thambyrajah

address: Wilmslow Road

department: Stem Cell Biology

institute: CRUK Manchester

description:
DamID-PIP
biological replicates 1 and 2

data_processing:
DamID-seq reads were aligned to mouse genome mm9 using SHRiMP2 (default settings)
BayesPeak was applied to the GFI1:DamID, GFI1B:DAM and control DAM samples
Unique test sample peaks with no overlap with the control sample or overlapping peaks with a > 2 fold change (RPKM_test/RPKM_control) were carried forward
We then used Poisson model based scan statistics to identify peak-enriched-regions and pooled adjacent (<300bp) peak-enriched regions
Genome_build: mm9
Supplementary_files_format_and_content: excel file with geneID, gene symbol, biotype, read counts, readcounts Per KB, SS interval for peaks identified for GFI1:DAM and GFI1B:DAM

source_name: HE_DAM ctrl biological replicate 1

growth_protocol: FLK1+ cells were isolated from day 3.25 EBs from GFI1:DAM-, GFI1B:DAM  or a DAM control  AinV18 ES cell line.  HE (TIE-2/c-KIT) comparment  from all the samples were FACS isolated on day 2 after culture. EBs and Cultures grown as decribed in Lancrin et al, 2009 and Steanska et al, 2014

extract_protocol: DNA from each population was extracted and processed for sequencing  as described in Vogel et al, 2007 and sequenced on a Illumina HiSeq 2500 platform

value: hemogenic endothelium


title: HE_GFI1B:DAM

description:
DamID-PIP
biological replicates 1 and 2

source_name: HE_GFI1B:DAM biological replicate 1


title: HE_GFI1:DAM

description:
DamID-PIP
biological replicates 1 and 2

source_name: HE_GFI1:DAM biological replicate 1


title: H1 TKO RNA-Seq R3

description:
Processed data file: WT_H1_TKO_ESC_RNA-Seq_FPKM.txt.gz
Processed data file: WT_ESC_vs_H1_TKO_ESC_RNA-Seq_cuffDiff.txt.gz

source_name: H1 TKO embryonic stem cells

extract_protocol:
Total RNAs were prepared from ES cells adapted to gelatinized dishes using RiboPure RNA purification kits (Ambion).
TruSeq DNA sample preparation kit (Illumina).


title: H1 TKO RNA-Seq R2


title: H1 TKO RNA-Seq R1


title: H1_TKO_ESC_H3K4me1_H3K4me3_input_R1

description:
Processed data file: H1_TKO_ESC_H3K4me1_R1_peaks.bed.gz
Processed data file: H1_TKO_ESC_H3K4me3_R1_peaks.bed.gz


title: WT ESC RNA-Seq R2

source_name: WT embryonic stem cells


title: WT ESC RNA-Seq R1


title: WT_ESC_H3K4me1_H3K4me3_input_R2

description:
Processed data file: WT_ESC_H3K4me1_R2_peaks.bed.gz
Processed data file: WT_ESC_H3K4me3_R2_peaks.bed.gz


title: H1 TKO ESC Hi-C NlaIII

description: library selection: restriction digest

data_processing:
Library strategy: Hi-C
Hi-C : Reads from both ends were mapped separately single end with bwa aln with default parameters. Uniquely mapped reads were sorted and paired by read ID using samtools. Mapped pairs were filtered to remove reads coming from the same or neighboring restriction fragments. Filtered pairs were deduplicated to remove PCR duplicates and valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files.
DNase Hypersensitivity : Aligned reads in bam files are those 36bp reads that aligned uniquely (Bowtie) to the reference (NCBI37/mm9) and contain no more than 2 mismatches. DNaseI-sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004).
DNA methylation HELP tagging data was processed with the WASP pipeline (version 3.0.31 (rev. 3822). Reads were aligned with Illumina's CASAVA and ELAND v. 1.7.0 allowing 2 mismatches in the first 32bp and no more than 10 alignments for each read. HELP angles were computed as described in (Suzuki et al. 2010).
RNA-Seq : We aligned 2x100 paired-end reads of 2 replicate WT ESC RNA-seq libraries and 3 replicate H1 TKO ESC RNA-seq libraries to the reference genome (NCBI37/mm9) with TopHat and used Cufflinks and CuffDiff for differential expression analysis of RNA-seq expression for a non-redundant collection of 20876 known RefSeq transcripts. We considered genes with a marginal p-value smaller than 0.05 and an absolute log2 fold-change  bigger than 1 to be differentially expressed.
ChIP-Seq : Reads from all different libraries were aligned to the reference genome (NCBI37/mm9) with bowtie2 with default settings and the --qc-filter switch. Duplicates were marked using Picard (http://broadinstitute.github.io/picard/) and were removed from the data for subsequent analyses. Regions significantly enriched for H3K4me1, H3K4me3, H3K27me3 and H3K9me3 compared to matched input samples were identified using the MACS2 peak caller with default settings. For the H3K9me3 and H3K27me3 histone marks, the parameter - - broad was set. Analysis of differential ChIP enrichment was done using diffReps with parameters -me gt –pval 0.001 --frag 150.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Valid Hi-C di-tags were recorded in valid_di_tags_txt.gz files; ChIP-Seq peaks called by MACS2 are in peaks.bed.gz files; DNaseI-hypersensitive sites called with the HOTSPOT algorithm in mm9.bed.gz files; DNA methylation HELP angles are in HELP.txt.gz file; RNA-Seq FPKM values are in FPKM.txt.gz file.

source_name: H1 TKO embryonic stem cells, NlaIII


title: WT ESC Hi-C NlaIII

description: library selection: restriction digest

source_name: WT embryonic stem cells, NlaIII


title: Ybx2/3 compound het #2 - mRNP

city: Bar Harbor

first: Elizabeth

last: Snyder

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Reads were aligned to a testis transcriptome via RSEM
Expected counts and TPMs were extracted from RSEM and normalized via RUVSeq
Genome_build: mm10
Supplementary_files_format_and_content: Expected counts in .txt file

source_name: adult whole testis

extract_protocol:
Isolated total, mRNP, and polysome RNA was purified via a RNeasy Mini Column (Qiagen) purification.
100 ng of RNA from each sample. From these mixes, sequencing libraries were constructed using the Stranded Total RNA LT with Ribo-Zero TM Gold Library Prep kit (Illumina)

value: mixed C57B6J/129SvJ

tag: genotype

value: Ybx2/3 compound heterozygote

tag: rna fraction

value: mRNP


title: Ybx2/3 compound het #2 - polysome

value: polysome


title: Sample10_GNS-H3K4me3

city: La Jolla

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
HiSeq Control Software (HCS v2.2.38) and Real Time Analysis (RTA v1.18.61) were used for base calling. Demultiplexing and BCL files conversion to FASTQ files were done by CASAVA v1.8.2.
Fastq files were mapped using bowtie2 v. 2.2.3 and deduplicated using Samtools 0.1.19.
Mapped reads were loaded into Seqmonk (v. v0.27.0) and duplicate reads were removed. Peaks were defined as a contiguous set of reads that were enriched by at least ten-fold. A 50 base pair gap was allowed to prevent large peaks from being broken into multiple small peaks. The number of reads in each peak were counted, corrected for total read count and log transformed.
Genome_build: hg19
Supplementary_files_format_and_content: Text files of peak locations by chromosome and start and stop sites. The sample columns indicate the number of reads in each peak which were counted (corrected for total read count and log transformed).

source_name: human Glioma Tumor Initiating Cells

growth_protocol: Neurobasal media (Invitrogen) supplemented with N2 (Invitrogen), B27 (Invitrogen), and FGF2 (10 ng/ml; preprotech)

extract_protocol:
3*105 cells were fixed using 1% PFA, treated with glycine 0.1M and resuspended in nuclei lysis buffer (SDS 1%, EDTA 100mM, Tris-HCl 50mM pH7.5). Chromatin samples were sonicated with a Branson Digital Sonifier to generate DNA fragments from 200 to 1000 bp, diluted with ChIP RIPA Buffer (Tris-HCl 0.1mM pH7.5, EDTA 1mM, EGTA 0.5mM, Triton X-100 1%, SDS 0.1%, Deoxycolic acid 0.1%, NaCl 140mM) and incubated with Dynabeads Protein A (Invitrogen) coupled to the specific antibody. After overnight incubation, the immunocomplexes were eluted in ChIP elution buffer (Tris-HCl 20mM pH7.5, EDTA 5mM, NaCl 140mM, SDS 1%, proteinase K 40mg/ml) and the crosslinking was reverted overnight at 65ºC. DNA was recovered by phenol/chloroform extraction and quantified by quantitative PCR using SYBR green on an ABI Prism 7300 system.
ChIP DNA was prepared into ChIP-Seq libraries using NEBNext Ultra DNA Library Prep Kit for Illumina according to manufacturer's instructions except adapters were purchased from Bioo Scientific.  Briefly, ChIP DNA was end-repaired, adenylated and adapter ligated. Adapter-ligated DNA was subjected to 12 cycles of PCR using NEB Q5 PCR mastermix. AMPure beads were used to purify sequencing libraries from reactions (Beckman Coulter). ChIP-Seq libraries were quantified using Invitrogen Qubit, Agilent Tape station and Kapa library quantification qPCR kit. Libraries were pooled and sequenced single-end 50bp on Illumina HiSeq 2500.

tag: cell type

value: Glioma Stem Cell

tag: treatment

value: No Treatment

value: iPSC derived


title: Ybx2/3 compound het #1 - polysome


title: Sample8_NPC_p53-H3K4me3

source_name: iPSC-derived human Neural Progenitor Cell with P53 knockdown

tag: chip antibody

value: Neural Progenitor Cell


title: Month28_3


title: Sample6_NPCwt-H3K4me3

source_name: iPSC-derived human Neural Progenitor Cell

value: Inhibition of P53


title: H1 TKO ESC Hi-C DpnII

description: library selection: restriction digest

source_name: H1 TKO embryonic stem cells, DpnII


title: Ybx2/3 compound het #1 - mRNP


title: Ybx2/3 compound het #1 - total RNA

value: total RNA


title: Ybx3 #2 - polysome

value: Ybx3 heterozygote


title: Sample4_NPC_p53-Sox2


title: Sample5_NPC_p53_4F-Sox2

source_name: iPSC-derived human Neural Progenitor Cell, P53 knockdown and inhibition of the PI3K and MAPK signaling pathways

value: Inhibition of P53 and PI3K and MAPK signaling pathways


title: Sample9_NPC_p53_4F-H3K4me3

value: Inhibitionition of PI3K and MAPK signaling pathways


title: Sample2_NPCwt-Sox2

value: Derived by Pollard et al., 2009 Cell Stem Cell, GNS G179. Deposited by Steve Pollard, Austin Smith, Peter Dirks and Ian Clarke at the biorep S.r.l. Catalog number NS00011*B


title: Ybx3 #2 - mRNP


title: Sample3_NPC_4F-Sox2

source_name: iPSC-derived human Neural Progenitor Cell, inhibition of the PI3K and MAPK signaling pathways


title: Ybx3 #1 - polysome


title: Sample7_NPC_4F-H3K4me3


title: Ybx3 #2 - total RNA


title: Sample1_GNS-Sox2

value: IVF derived


title: Ybx3 #1 - mRNP


title: WT ESC Hi-C DpnII

description: library selection: restriction digest

source_name: WT embryonic stem cells, DpnII

value: embryonic stem cell line

value: WT


title: Ybx3 #1 - total RNA

value: mixed C57B6J/129SvJ


title: Ybx2 #2 - polysome

value: Ybx2 heterozygote


title: Ybx2 #2 - mRNP

value: mRNP


title: Ybx2/3 compound het #2 - total RNA

value: Ybx2/3 compound heterozygote


title: Stab1siRNA_d1_2

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

country: Finland

institute: University of Turku

data_processing:
Basecalls performed using the instrument manufacturer’s (Illumina HiSeq2500) Bcl2fastq version 1.8.4 base calling software
the reads were aligned against the human reference genome (hg19 assembly, downloaded from UCSC) using TopHat version 2.0.10
Reads were associated with known genes based on RefSeq annotations derived from UCSC database, the number of associated reads was counted using HTSeq tool (v 0.5.4p3)
Counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package.
For statistical analysis the data were further transformed using the voom approach in the limma package.
R package Limma was used for performing the statistical testing between the groups
Filtering of differentially expressed genes was done using the following thresholds: FC>2.0, p<0,05
Supplementary_files_format_and_content: tab-delimited text files include RPKM values with annotations for each sample

source_name: peripheral blood monocytes

growth_protocol: Blood samples from healthy adults were diluted with HBSS and laid over the Ficoll gradient and centrifuged at 2000 rpm for 20 min and 20oC. The leukocyte containing interface was collected and washed with HBSS three times by centrifuging the cells at 1200 rpm for 10 min at 10oC. Monocytes were enriched using MACS negative selection kit (Monocyte isolation Kit II with CD16) following the manufacturer’s protocol.

extract_protocol:
RNA was extracted from the transfected monocytes using the Nucleo-Spin RNAII Total RNA Isolation Kit (Macherey-Nagel), and the quality of the isolated RNA was checked with the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Purified monocytes  were transfected with Stabilin-1 siRNA and negative control siRNA. The cells were then cultured for 24 hours under non-polarizing culture medium. Stabilin-1 expression was determined by FACS from aliquots of cells to verify the silencing efficacy.

tag: transfection

value: Stabilin-1 siRNA


title: neg.co_d1_3

value: Control siRNA


title: neg.co_d1_2


title: Stab1siRNA_d1_3


title: neg.co_d1_1


title: Ybx2 #1 - mRNP


title: Ybx2 #2 - total RNA


title: Ybx2 #1 - total RNA


title: Wildtype #2 - total RNA

value: wildtype


title: Wildtype #2 - polysome

value: polysome


title: Wildtype #2 - mRNP


title: Wildtype #1 - mRNP


title: Tbet+/-_Rorgt_HIGH rep2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. A linear model was fitted to each gene and empirical Bayes moderated-t p-values were computed relative to a fold-change cut-off of 1.2-fold by using treat. Genes were called differentially expressed if they achieved a false discovery rate of <0.05 and an average RPKM (reads per kilobase per million) of >8 in at least one of the two groups being compared.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized log2-RPKM values for genes

source_name: Intestine

extract_protocol:
Total RNA was prepared from lymphoid cells using an RNeasy mini kit (Qiagen).
cDNA was synthesized from total RNA with OligodT and thermoscript reverse transcriptase (Invitrogen).

value: Intestine

tag: celltype

value: Innate lymphoid cells

value: Tbet+/- with high expression level of Rorgt


title: Tbet+/-_Rorgt_HIGH rep1


title: Wildtype #1 - polysome


title: Wildtype #1 - total RNA

value: total RNA


title: WT_Rorgt_HIGH rep2

value: wild type with high expression level of Rorgt


title: Tbet+/-_Rorgt_INT rep2

value: Tbet+/- with intermediate expression level of Rorgt


title: PARP-1 ChIP-seq replicate 2

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Align(by Bowtie) the reads with their original length and find the uniquely mapped reads by increasing mismatch threshold from 0 to 3
For the reads can not be mapped, we trimmed the reads to 40bp (trimmed off the color from the end), and used the first 40bp color to map the reads. Mismatch threshold is increased from 0 to 3.
For the reads can not be mapped, we further trimmed the reads to 30bp(kept the first 30bp color of the reads), the mismatch threshold is from 0 to 2.
The alignment results from above steps were combined.
Genome_build: dm3
Supplementary_files_format_and_content: tab delimited text files containing combined reads count of uniquely mapped fragment at each genomic position

source_name: late embryonic stage cells

extract_protocol:
MNase digested nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Applied Biosystems protocol for SOLiD4 fragment paired-end sequencing. Briefly, DNA was end-repaired and 5’-phosphorylated by incubation in DNATerminator end-repair kits, as recommended by the manufacturer (Lucigen Corp., Middleton, WI). SOLiD adapters were ligated and the DNA molecules PCR amplified (very low cycle number) and sequenced by using the Applied Biosystems protocol for SOLiD fragment paired-end sequencing. After adapter ligation DNA was PCR amplified with SoLiD primers for less than 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on a SoLid flow cell for cluster generation.

value: late embryonic cells

tag: passages

tag: antibody

value: PARP-1 (Active motif-39559)


title: PARP-1 ChIP-seq replicate 4


title: PARP-1 ChIP-seq replicate 3


title: PARP-1 ChIP-seq replicate 1


title: G166.phf5a_kd_402

city: Cleveland

first: Christopher

middle: G.

last: Hubert

state: OH

address: 9500 Euclid Ave.

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic

description: regulated.phf5a_kd_402.down.G166.list.txt, regulated.phf5a_kd_402.up.G166.list.txt

data_processing:
We used previously published annotations of competing 3' and 5' splice sites, mutually exclusive exons, and skipped exons (Wang et al., 2008). For each splicing event, we assigned it to its most likely parent isoform and assessed whether it was likely to induce nonsense-mediated decay (if it introduced an in-frame stop codon at least 50 bp upstream of a splice junction). We furthermore enumerated all constitutive junctions, where a constitutive junction was defined as a splice junction for which neither the 5' nor 3' splice site was annotated as possibly spliced to another 3' or 5' (respectively) splice site in either Ensembl or UCSC.
We mapped the raw FASTQ files using Bowtie version 0.12.8 (Langmead et al., 2009) and TopHat version 1.3.3 (Trapnell et al., 2009).
We mapped to the genome, all splice junctions in the annotations described above, and all possible splice junctions that could result from skipping of exons in our gene annotations. To reduce the false positive rate of mapping, we did not allow novel junction discovery and furthermore required at least 6 bp of overhang on either side of splice sites.
In order to detect changes in all classes of splicing events with equal statistical power, we used only reads crossing the minimal identifying splice junctions for each event and tested for changes in splicing following PHF5A KD using the binomial proportion test, which is appropriate for RNA-seq data, where the number of reads is variable. We described this approach previously (Bradley et al., 2012). To fairly assess retention of constitutive introns, we treated reads crossing the 5' splice site (the 3' end of the upstream exon) with at least 6 bp of overhang in both the exon and intron as identifying reads. We required p-value < 0.01 and a change of at least 10% in isoform ratio.
We sought to obtain the most comprehensive set of splicing events affected by PHF5A. We therefore took the union of the events detected using the approach described above with events identified with a binomial proportion test on the reads assigned to each isoform by MISO version 0.4.4 (Katz et al., 2010), which uses a Bayesian approach to assign non-identifying reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text containing splicing event coordinates, prediction of nonsense-mediated decay, p-value, and gene information

source_name: glioblastoma

growth_protocol: Grown in serum-free media supplemented with N2, B27, EGF, FGF, L-Glutamine, Sodium Pyruvate, on Laminin coated plates. Samples indicated as CB660 are neural stem cells and samples indicated as either G166 or 0827 are glioblastoma.

extract_protocol:
Trizol
We prepared poly (A)-selected single-end RNA-seq libraries using the Illumina TruSeq protocol and sequenced all libraries on the HiSeq 2000 instrument with a read length of 99 bp.

treatment_protocol: shRNA knockdown using pGIPZ lentivirus followed by puromycin selection of positively infected cells. Clone #861 shRNA sequence is ATAATATGAGACTAGTGGG. Clone #402 shRNA sequence is AGTGTTAAACAAGTAAATG.

value: glioblastoma

tag: lentivirus

value: :pGIPZ

tag: shRNA seq

value: AGTGTTAAACAAGTAAATG


title: MNase-seq replicate 1


title: Tbet+/-_Rorgt_INT rep1


title: G166.phf5a_kd_861

description: regulated.phf5a_kd_861.down.G166.list.txt, regulated.phf5a_kd_861.up.G166.list.txt

value: ATAATATGAGACTAGTGGG


title: WT_Rorgt_INT rep2

value: wild type with intermediate expression level of Rorgt


title: G166.control_kd

value: :control


title: WT_Rorgt_HIGH rep1


title: CB660.phf5a_kd_402

description: regulated.phf5a_kd_402.down.CB660.list.txt, regulated.phf5a_kd_402.up.CB660.list.txt

source_name: neural stem cells

value: neural stem cells


title: Ybx2 #1 - polysome

value: mixed C57B6J/129SvJ

value: Ybx2 heterozygote


title: Stab1siRNA_d1_1

value: Stabilin-1 siRNA


title: CB660.control_kd


title: WT_Rorgt_INT rep1

value: Intestine

value: Innate lymphoid cells


title: Tbet+/-_NCR-Rorgt+CD4- rep2

value: CD4- T cells


title: Tbet+/-_NCR-Rorgt+CD4- rep1


title: WT_NCR-Rorgt+CD4- rep1

value: wild type NCR-Rorgt+CD4-


title: 0827.control_kd


title: WT_NCR-Rorgt+CD4- rep2


title: Tbet+/-_NCR-Rorgt+CD4+ rep1

value: CD4+ T cells


title: Non-targeting RNAseq Replicate5

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

data_processing:
Alignment - tophat -p 8 --library-type fr-firststrand
Quantification - HTSeq- count htseq-count -s reverse -m intersection-strict -i gene_name -
Differential expression analysis - DESeq2 using gencode V16 transcripts ( see differential_expression_test.R in associated code repository)
Genome_build: hg19
Supplementary_files_format_and_content: htseq counts for all genes(rows) x samples (columns)  and depth and length normalized values for each gene (count_data_rpkm.csv)

growth_protocol: Human hepatocellular carcinoma cells (HepG2) were grown in DMEM with 10% Fetal Bovine Serum and penicillin and streptomycin

extract_protocol:
RNA was extracted by Trizol purification and cleaned using a Qiagen RNAeasy column using manufacturers instruction
Strand specific libraries were constructed using the dUTP incorporation method

treatment_protocol: Cells were treated with 50nM siRNA for 72 hours using Lipofectamine RNAimax

tag: cell line

value: hepatocellular carcinoma

tag: sirna vendor

value: Dharmacon

tag: catolog number


title: Tbet+/-_NCR-Rorgt+CD4+ rep2

tag: strain


title: Non-targeting RNAseq Replicate4


title: Non-targeting RNAseq Replicate3


title: Non-targeting RNAseq Replicate6


title: WT_NCR-Rorgt+CD4+ rep1

value: wild type NCR-Rorgt+CD4+


title: WT_NCR-Rorgt+CD4+ rep2


title: Arid2 RNAseq Replicate 4

value: Life Technologies


title: Non-targeting RNAseq Replicate2