title: 11-12hr_RNAseq_rep2

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description: GRH- RNA-seq

data_processing:
Basecalls performed using CASAVA1.8.2
All analyses were done on the Galaxy online platform
Raw ChIP reads were trimmed for quality by sliding window with a minimum score of 28
ChIP reads were aligned to the dm3 genome assembly using Bowtie with maximum of 2 mismatches and unmapped reads were removed.  Additional mapping was done using the dm6 genome and these re-mapped sequences are provided as bam files.
ChIP peaks were called with MACS with a p-value cutoff of 1e-6, MFOLD renrichment ratio of 5, Tag size of 80, and calculating the maximum lambda as local lambda at 1000, 2500, and 5000bp
Raw RNA-seq reads weere trimmed for quality by sliding window with a minimum score of 28
Reads were aligned to the dm3 geneome assembly using TopHat using default settings
Cufflinks was used to assemble transcripts and estimate FPKM for TopHat-aligned data
Cuffmerge was used to merge together resultant Cufflinks files (as GTF files)
Fold change between experimental conditions (with or without GRH) was calculated using CuffDiff, using the TopHat and Cuffmerge files produced in previous steps.
Genome_build: dm3 or dm6
Supplementary_files_format_and_content: BED: File produced by MACS peak calling software. File contains genomic regions corresponding to ChIP peaks (mapped to dm3)
Supplementary_files_format_and_content: WIG: File produced by MACS peak calling software. Contains profile data of genome from ChIP-seq experiment (mapped to dm3)
Supplementary_files_format_and_content: TABULAR: File produced by CuffDiff softare for assessing RNA-seq data. Fold change, p-value, and q-values are given for each gene or locus that describes the change in gene expression between experiment conditions.
Supplementary_files_format_and_content: BAM: File produced by Bowtie mapping software. File is mapped to "dm6" Drosophila genome

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: For ChIP-seq experiments, wild type OreR embryos at various stages were collected. To deplete zygotic GRH, two mutants (grhIM and grhB37) were balanced over CyO, sChFP and embryos were scored for fluorescence. To deplete maternal GRH, germline clones were produced as described in Harrison et al., 2010 using the FLP-FRT system described in Chou and Perrimon, 1996

extract_protocol:
ChIP-seq: Embryos were collected, fixed in formaldehyde, chromatin was isolated, and the chromatin was immunoprecipitated as described in Li et al., 2008. Immunoprecipitation was done using two antibodies against Grainy head and an input sample was also collected for sequencing. RNA-seq: Embryos depleted of either maternal or zygotic GRH as well as sibling controls were collected and examined to determine the stage. 7 embryos were collected for each set and lysed in TRIzol reagent (Life Technologies) supplemented with 150 µg/ml glycogen. RNA was extracted and cDNA libraries were prepared using the Illumina Truseq RNA sample prep kit.
ChIP-seq libraries were prepared using standard Illumina protocols and RNA-seq libraries were prepared using Illumina Truseq RNA sample prep kit according to manufacterer's instructions

value: zygotic grh depletion

tag: Stage

value: 11-12 hours after egg laying


title: 15-16hr_RNAseq

status: Public on Feb 02 2017

type: SRA

country: USA

description: GRH- RNA-seq

library_source: transcriptomic

molecule: total RNA

tag: strain

value: 15-16 hours after egg laying


title: 11-12hr_RNAseq_rep1

description: GRH- RNA-seq


title: Maternal_RNAseq_rep2

description: GRH- RNA-seq

value: maternal grh depletion

value: 2-3 hours after egg laying


title: KR_51

city: Poznań

first: Michal

last: Kabza

address: ul. Fredry 10

country: Poland

institute: Poznan University of Medical Sciences

data_processing:
Short reads were trimmed using Trimmomatic version 0.32
Reads matching rRNAs were removed using Bowtie version 1.0.1
Reads were mapped to the reference genome using STAR version 2.4.0j
Mapped reads were assembed into transcripts using StringTie version 1.0.4
Assembled reads were merged with reference annotations using Cuffmerge version 2.2.1
Expression of genes and transcripts was estimated using Kallisto version 0.42.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Merged annotations created by Cuffmerge (GFF3 format); tab-delimited text files containing expression values of genes and transcripts (TPM values and raw estimated read counts)

organism: Homo sapiens

source_name: Cornea

extract_protocol:
The corneas were transferred to 400 µl of lysis solution (Norgen Biotek, Thorold, ON, Canada) in a 2-mL microtube with Lysing Matrix D (MP Biomedicals, Irvine, CA, USA) and homogenized using a FastPrep®-24 Instrument (MP Biomedicals). Further total RNA extraction and purification steps were performed according to the manufacturer’s instructions supplied with a Total RNA Purification Kit (Norgen Biotek). To maximize the removal of residual DNA that could affect downstream analyses, an on-column DNase I (Zymo Research, Irvine, CA, USA) treatment was performed.
Libraries were prepared with a TruSeq Stranded Total RNA LT with Ribo-Zero™ Human/Mouse/Rat Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol, with slight modifications.

tag: disease state

value: non-KTCN

tag: study

value: discovery

tag: tissue

value: cornea


title: Input_MNase_shGFP

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

library_source: genomic

data_processing:
Sequencing data was acquired through the default Illumina pipeline using Casava v1.8.
ChIP-seq reads were aligned to the mouse genome (UCSC mm9) using the Bowtie aligner v0.12.9 allowing uniquely mapping reads only and allowing up to two mismatches (Langmead, 2009). RNA-seq reads were aligned to the mouse genome UCSC mm9 and to gene annotations from Ensembl 67 using TopHat v2.0.13 (Trapnell et al., 2009), using option –g 1 –x 1.
ChIP-seq reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million; RPM). RNA-seq reads were normalized to total reads aligned (reads per million; RPM) to generate bigWig files.
Peak detection was done using MACS v1.4.2 (Zhang et al., 2008). Associated control samples were used to determine statistical enrichment at p<1e-5. For down stream analysis, peaks were further filtered with p < 1e-8 and FDR < 0.05.
R package edgeR 3.0.8 was used to perform differential expression analysis at p-value < 1e-3 (Robinson et al., 2010).
For 4C seq, reads were demultiplexed by allowing no mismatch in library index and 1 mismatch in viewpoint sequences. The library index were trimmed before mapping. 4cseqpipe were used for alignment (van de Werken HG et al., 2012).
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq, RNA-Seq, and 4C samples

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: Mouse V6.5 ES cells were grown in DMEM supplemented with 15% FBS (HyClone), 2 mM L-glutamine, 0.1 mM nonessential amino acids (Stemcell Technologies) and 1,000 U/ml recombinant LIF (Millipore). Hanging drop method was used to form embryoid bodies (EBs) by culturing 1000 mouse ES cells in 25 µl differentiation medium (without LIF) on the lid of 150 mm culture dish for indicated days.

extract_protocol:
ChIP assays were performed as previously described (Lee et al., 2006) . Briefly, 2-5x10^7 cells were crosslinked with 1% paraformaldehyde (Electron microscropy science #15710) at room temperature for 10 min and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody. Total RNA was extracted with Trizol (Invitrogen #15596), treated with DNAase I (NEB #M0303) for 20 min at room temperature and purified with RNeasy Mini kit (Qiagen #74106).Circular Chromosome Conformation Capture (4C) technique was performed as described (van de Werken et al., 2012, Methods Enzymol). Cross-linked chromatin was digested with HindIII, ligated under diluted conditions.  Cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions.For each viewpoint approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer’s specifications.  4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline according to (van de Werken et al., 2012, Methods Enzymol).
ChIP-seq and RNA-seq libraries were constructed by following instrucitons in KAPA HTP Library Preparation Kits (Kapa Biosystems, #KK8234) and TruSeq Stranded Total RNA Library Prep kits with Ribo-Zero Human/Mouse/Rat (Illumina, #RS-122-2201 and #RS-122-2202), respectively. Indexed primers for ChIP-seq libraries are from Bioo Scientific (#514104 ). For 4C-seq, Cross-linked chromatin was digested with HindIII, ligated under diluted conditions.  Cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions. For each viewpoint, approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer’s specifications.

treatment_protocol: Mouse ES cells were infected with lentivial shRNA against either Mll2 or Menin in the presense of 4ug/ml polybrene for 12 hours and then seleted with 1.5 ug/ml puromycinfor 48h before harvest for ChIP-seq or RNA-seq experiments. For rescue experiment, mouse ES cells were electroporated with indicated plasmids and selected with 400 µg/ml G418 for 3 days.

tag: cell type

value: V6.5 mES

tag: genotype/variation

value: wild type

tag: chip antibody

tag: lentiviral shrna infection

value: shGFP


title: KR_53


title: Input_MNase_shMll2


title: H3K4me3_MNase_shMll2

value: H3K4me3 (Homemade, #28)


title: KR_50


title: KR_61


title: Maternal_RNAseq_rep1

description: GRH- RNA-seq


title: KR_38


title: KC_52

value: KTCN


title: H3K4me3_MNase_shGFP


title: 15-16hr_input

tag: antibody


title: KC_45


title: KC_43


title: 11-12hr_input


title: Prdm1_4C

description: library strategy: 4C-seq

data_processing:
Sequencing data was acquired through the default Illumina pipeline using Casava v1.8.
ChIP-seq reads were aligned to the mouse genome (UCSC mm9) using the Bowtie aligner v0.12.9 allowing uniquely mapping reads only and allowing up to two mismatches (Langmead, 2009). RNA-seq reads were aligned to the mouse genome UCSC mm9 and to gene annotations from Ensembl 67 using TopHat v2.0.13 (Trapnell et al., 2009), using option –g 1 –x 1.
ChIP-seq reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million; RPM). RNA-seq reads were normalized to total reads aligned (reads per million; RPM) to generate bigWig files.
Peak detection was done using MACS v1.4.2 (Zhang et al., 2008). Associated control samples were used to determine statistical enrichment at p<1e-5. For down stream analysis, peaks were further filtered with p < 1e-8 and FDR < 0.05.
R package edgeR 3.0.8 was used to perform differential expression analysis at p-value < 1e-3 (Robinson et al., 2010).
Reads were demultiplexed by allowing no mismatch in library index and 1 mismatch in viewpoint sequences. The library index were trimmed before mapping. 4cseqpipe were used for alignment (van de Werken HG et al., 2012). The 4cseqpipe (van de Werken HG et al., 2012) generated figures directly from the alignment files.
Genome_build: mm9

extract_protocol:
ChIP assays were performed as previously described (Lee et al., 2006) . Briefly, 2-5x10^7 cells were crosslinked with 1% paraformaldehyde (Electron microscropy science #15710) at room temperature for 10 min and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody. Total RNA was extracted with Trizol (Invitrogen #15596), treated with DNAase I (NEB #M0303) for 20 min at room temperature and purified with RNeasy Mini kit (Qiagen #74106).Circular Chromosome Conformation Capture (4C) technique was performed as described (van de Werken et al., 2012, Methods Enzymol). Cross-linked chromatin was digested with HindIII, ligated under diluted conditions.  Cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions.For each viewpoint approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer’s specifications.  4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline (van de Werken et al., 2012, Methods Enzymol).
ChIP-seq and RNA-seq libraries were constructed by following instructions in KAPA HTP Library Preparation Kits (Kapa Biosystems, #KK8234) and TruSeq Stranded Total RNA Library Prep kits with Ribo-Zero Human/Mouse/Rat (Illumina, #RS-122-2201 and #RS-122-2202), respectively. Indexed primers for ChIP-seq libraries are from Bioo Scientific (#514104 ). For 4C-seq, Cross-linked chromatin was digested with HindIII, ligated under diluted conditions.  Cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions. For each viewpoint, approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer’s specifications.

tag: cell line

value: mES

tag: viewpoint


title: 5-6hr_input

value: 5-6 hours after egg laying


title: KC_40


title: KC_39


title: KC_37


title: 2-3hr_input


title: RNA_EB9d_Mll2KO

data_processing:
Sequencing data was acquired through the default Illumina pipeline using Casava v1.8.
ChIP-seq reads were aligned to the mouse genome (UCSC mm9) using the Bowtie aligner v0.12.9 allowing uniquely mapping reads only and allowing up to two mismatches (Langmead, 2009). RNA-seq reads were aligned to the mouse genome UCSC mm9 and to gene annotations from Ensembl 67 using TopHat v2.0.13 (Trapnell et al., 2009), using option –g 1 –x 1.
ChIP-seq reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million; RPM). RNA-seq reads were normalized to total reads aligned (reads per million; RPM) to generate bigWig files.
Peak detection was done using MACS v1.4.2 (Zhang et al., 2008). Associated control samples were used to determine statistical enrichment at p<1e-5. For down stream analysis, peaks were further filtered with p < 1e-8 and FDR < 0.05.
R package edgeR 3.0.8 was used to perform differential expression analysis at p-value < 1e-3 (Robinson et al., 2010).
Reads were demultiplexed by allowing no mismatch in library index and 1 mismatch in viewpoint sequences. The library index were trimmed before mapping. 4cseqpipe were used for alignment (van de Werken HG et al., 2012). The 4cseqpipe (van de Werken HG et al., 2012) generated figures directly from the alignment files.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

source_name: mouse embryoid bodies(EB)

value: EB

tag: time


title: 15-16hr_GRH_ChIPseq

description: GRH ChIP-seq

value: GRH


title: RNA_EB6d_Mll2WT_rep1


title: KC_35


title: 15-16hr_1-441GRH_ChIPseq

description: 1-441GRH ChIP-seq


title: RNA_EB6d_Mll2_Y2602A


title: RNA_EB6d_Mll2KO_rep1


title: RNA_EB6d_Mll2_mCXXC

value: Mll2 mCXXC/mCXXC


title: 5-6hr_1-441GRH_ChIPseq

description: 1-441GRH ChIP-seq


title: 11-12hr_1-441GRH_ChIPseq

description: 1-441GRH ChIP-seq

value: 11-12 hours after egg laying


title: RNA_EB6d_Mll2KO_rep2


title: RNA_EB6d_Mll2WT_rep2


title: 11-12hr_GRH_ChIPseq

description: GRH ChIP-seq


title: RNA_EB9d_Mll2WT


title: RNA_EB3d_Mll2WT


title: KC_47


title: 2-3hr_GRH_ChIPseq

description: GRH ChIP-seq


title: RNA_EB3d_Mll2KO


title: RNA_EB0d_Mll2WT_rep1


title: 2-3hr_1-441GRH_ChIPseq

description: 1-441GRH ChIP-seq


title: RNA_EB0d_Mll2KO_rep2


title: WT_665K_RRBS

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using the Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/)  allowing two alignment mismatches (n 2).
Resulting SAM aligment files were sorted to be used in as input in further steps.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 5X coverage. We use methylKit  to compute methylation ratios  and  differential methylation analysis  (http://code.google.com/p/methylkit/)
Genome_build: mm10
Supplementary_files_format_and_content: Differentially methylated regions (DMR) table obtained from Methylkit processing of the SAM files yieldedby Bismark alignment. Each table representes the following parameters: Chromosome (chr), start and end coordinates of the methylated region (start, end), strand location (strand), probability value "pvalue", adjusted p-value "qvalue", differential methylation score "meth.diff". Only regions with a meth.diff score over 20 or under -20, and a qvalue under 0.05, where considered as differentially methylated (Hyper- or Hypo- methylated respectively).

source_name: Liver

growth_protocol: Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.

extract_protocol:
DNA was extracted from the livers using AllPrep DNA/RNA Mini Kit
RRBS/MspI+TaqαI, followed by a modified NEXTflex™ Bisulfite-Seq Kit (Illumina Compatible,  Bioo Scientific Corp Catalog #5119-01). Samples were multiplexed according to Illumina's recommendations and experimental design.

value: Liver

tag: genotype

value: MAT1A WT

tag: age

value: 10 month

tag: treatment

value: no treatment


title: WT_666K_RRBS


title: RNA_EB0d_Mll2KO_rep1


title: WT_663K_RRBS


title: WT_664K_RRBS


title: WT_661K_RRBS


title: WT_660K_RRBS


title: 5-6hr_GRH_ChIPseq

description: GRH ChIP-seq


title: WT_658K_RRBS


title: MKS_990I_RRBS

value: MAT1A KO

value: SAMe supplementation


title: RNA_EB0d_Mll2_mCXXC


title: RNA_Mll2KO_rep1


title: RNA_Mll2KO_rep2


title: RNA_Mll2_Y2602A_F1


title: RNA_Mll2_Y2602A_F4


title: MKS_324K_RRBS


title: MKS_986I_RRBS


title: RNA_Mll2WT_rep1


title: RNA_Mll2_mCXXC_F4


title: RNA_EB0d_Mll2WT_rep2


title: MKS_849G_RRBS


title: MKS_322K_RRBS


title: MKP_409G_RRBS

value: Placebo


title: Input_Mll2WT

value: wild type


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Klhdc4 knockdown (T0904), replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TTCCAAGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab

data_processing:
CASAVA 1.8 was used for base calling.
Fastq files contain demultiplexed reads which were assigned to the appropriate treatment by matching to expected forward and reverse barcodes (sequenced in dedicated reads; not supplied).
Forward and reverse event reads were mapped to custom junction libraries representing all expected splice variants (supplied as processed files), using bowtie with settings --best -v 3 -k 1 --trim3 26 --trim5 20. Trimming was done to remove lower-quality, uninformative ends and because forward reads had a missing base call at position 11 due to a power outage. Junction libraries were first constructed from NCBIm37/mm9 gene annotations, and then refined based on the results of de novo mapping of the reads from one full Illumina lane from each cell line using tophat (default settings with -i 40 and providing Ensembl transcript annotations for NCBIm37), after quality trimming (minimum MAPQ of 33) from the 3'-end with the fastx toolkit. Mapped reads were counted per junction.
Alternative splicing analysis: Percent-spliced-in (PSI) values were calculated for each alternative exon, or part thereof in the case of alternative 5'-/3'-splice sites ('event'), from read tallies as follows: PSI was calculated independently from forward and reverse reads as the percentage of reads supporting inclusion divided by the total number of reads for the event. For alternative 5'/3'-ss events that were part of an alternative exon (Foxm1.A2, Mta1.A1, Uspl1.A3), the PSI was instead calculated with reference to the total reads supporting inclusion of that exon in order to assess independent regulation of alternative splice site usage. Only the read direction in which all reads unambiguously supported either inclusion or exclusion of an event was used, and the average if that applied for both. Exploratory analysis revealed that PSI values showed low-level batch effects per 96-well plate which we moderated by subtracting a weighted plate median in which negative controls (siNT and mock treatment) were given 20x more weight than other samples. To derive variances, and because PSI values are not nearly normally distributed but roughly follow a beta distribution, we elected to fit a beta distribution to each pair of replicate treatments, as well as to all negative controls from both replicates, using maximum-likelihood fitting as implemented in the fitdistr() function from the R package MASS {Venables & Ripley, Modern Applied Statistics with S (2002)}. Iterative optimization of shape parameters was initiated with settings x=PSI, shape1=1, shape2=1, method=”L-BFGS-B”, lower=0.01, and upper=mean number of reads supporting each PSI value. A modified Strictly Standardized Mean Difference (SSMD {Zhang, Genomics (2007)}) was then calculated based on the formula: SSMD = (μt – μc)/SQRT(vart + varc) where μt and μc are the means (corresponding to the PSI), and vart and varc the variances of the beta distributions fitted to the treatment replicates and negative controls, respectively. Events for which not all reads from at least one direction were informative (Mff.A2, Tead1.A2) were excluded from further analysis, as were events in individual treatments with less than 20 reads in one or both replicates (~9% of all event x treatment combinations). Additionally, the following events were removed from further splicing analysis: expression only events or constitutive exons, Fgf4, Gapdh, Srpk2, Srrm4; events with consistently low read counts: Atg13.A1, H2afy.A2, Tcf7l1 (N2A only), Dnmt3b (N2A only); or because measured inclusion was biased by differential length of isoforms:, Fgfr1, Sall4.
Expression analysis: Read counts from all splice variants of each gene were used to estimate relative mRNA expression levels, reads per million reads (RPMs). Differential expression analysis based on raw read counts was performed using the generalized linear models workflow from the R package edgeR. Plate, position (edge/interior) and treatment were used as design factors (where all treatments of each type of control were treated as replicates.) Models fitted using estimateDisp() to estimate the common, trended, and tag-wise dispersion for the CGR8 and N2A data separately. Subsequently, differences attributable to treatment, plate, or position contrasts were extracted with glmLRT() and represented as log2-fold changes with associated FDR. Fold-changes for treatments are relative to the siNT and mock-treatment controls.
Genome_build: NCBIm37/mm9
Supplementary_files_format_and_content: Processed files are either tab-delimited  tables (.tab) or FASTA files (.fa). KnockdownAnnotation.tab contains treatment annotations and well/plate positions. ScreenJuncUp.20-77.tab and ScreenJuncDn.20-77.tab contain the custom junction upstream and downstram junction libraries, respectively, and ScreenEvent_junctions.tab contains the information which junctions were used to calculate PSI for each event. PSI.SSMD.CGR8.tab and PSI.SSMD.N2A.tab contain raw PSI of each replicate and final SSMD. Reads_perEvent_CGR8.tab and Reads_perEvent_N2A.tab contain raw read counts on which expression analyis was based, and Expression.CGR8.treatments.tab and Expression.N2A.treatments.tab contain modeled relative abundance and fold-change with associated FDR for each treatment type.

source_name: Neuroblastoma cells

growth_protocol: CGR8 mouse embryonic stem cells (ESCs) were cultured as described previously on gelatin-coated plates (Gabut et al., Cell (2011), Han  et al., Nature (2013)). Mouse neuroblastoma (N2A) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin. All cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Forty-eight hours post-transfection, total RNA were purified from cultured cells using RNeasy Plus 96 Kit (Qiagen), as per the manufacturer’s instructions.
For each sample, a multiplex RT-PCR assay was first applied to simultaneously amplify 50 AS and/or expression events in a single reaction. The multiplex RT-PCR reaction was carried out in 96-well plates using the OneStep RT-PCR kit (Qiagen) as recommended by the manufacturer, with the following changes: reactions were performed in a volume of 20 uL with 2 uL of the purified total RNA as input, and a mixture of 50 pairs of primers was added to each reaction with a final concentration of 0.25 uM for each individual forward and reverse primer. Four identical Veriti 96-well Thermal Cyclers (Applied Biosystems) were used with the following conditions: 50°C for 30 minutes, 95°C for 15 minute, 30 cycles of 94°C for 40 seconds, 58°C for 1 minute (slow ramp rate), 72°C for 3 minutes, and a final extension step at 72°C for 10 minutes. Two sets of barcodes were incorporated into forward and reverse primers, respectively, after the universal adaptors and added to the amplicons in the second PCR reaction to allow demultiplexing all reads that were derived from a particular treatment. Primers sequences were: forward primer, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT (N denotes i5 barcode); reverse primer, CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (N denotes i7 primer). The second PCR was performed using Phusion High-Fidelity DNA Polymerase (Thermo Scientific), as per the manufacturer’s instructions. For each 20 uL of reaction, 1 uL of the multiplex RT-PCR reaction products was used as templates. The thermal cycling conditions were as follows: 98°C for 30 seconds, 15 cycles of 98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, and a final extension step at 72°C for 5 minutes. The resulting libraries were pooled and sequenced.

treatment_protocol: Twenty-four hours prior to transfection, CGR8 and N2A cells were seeded in 96-well plates, 3000 and 5000 cells per well, respectively. Cells were transfected with the SMARTpool siRNAs at 50 nM final concentration using DharmaFECT1 reagent (Dharmacon), as recommended by the manufacturer.


title: RNA_EB0d_Mll2_Y2602A


title: RNA_Mll2_mCXXC_F1


title: Input_shMll2_2


title: Input_shGFP_2

value: shGFP


title: MKP_028J_RRBS


title: WT_659K_RRBS


title: Input_Mll2KO


title: MKP_024J_RRBS


title: RNA_Mll2WT_rep2


title: MKP_021J_RRBS


title: Input_Mll2_Y2604A_F4


title: Input_Mll2_mCXXC_F4


title: Input_Mll2_Y2604A_F1


title: siDDX5_17_N2

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

country: France

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

data_processing:
Data generated with an Illumina HiSeq 2500 platform
Sequenced reads were trimmed for adaptor sequence with cutadapt and low quality bases (Q<20)  with prinseq
Mapping and count with Tophat
Splicing  analysis with FARLINE pipeline (publication in progress)
Genome_build: hg18
Supplementary_files_format_and_content: excel file containing splicing events differentially observed in DDX5-17 Vs control (events : acceptor, donor, mutually exclusive, multi exon skipping)

extract_protocol:
total RNA were extracted as described previously (Dardenne Cell Rep 2014)
RNA libraries were prepared for sequencing using standard Illumina protocols. rRNA were depleted with the "TruSeq Stranded Total RNA with Ribo‐Zero Gold" kit.

treatment_protocol: MCF-7 cells were transfected with siRNA targeting both DDX5 and DDX17 RNA helicases

tag: transfected with


title: Input_Mll2_mCXXC_F1


title: Mll2_shGFP_2

value: Mll2 (Homemade, #9173)


title: Mll2_Mll2WT

tag: rescue experiment

value: Halo


title: Mll2_Mll2_Y2602A_F1

value: mES


title: Mll2_Mll2_mCXXC_F4


title: siCTL_N1

source_name: MCF7_siRNA control

value: breast cancer cells

value: siRNA control


title: Mll2_Mll2KO


title: MKP_408G_RRBS


title: Mll2_Mll2_mCXXC_F1


title: H3K4me3_Mll2KO

value: H3K4me3 (Homemade, #28)


title: siCTL_N2


title: H3K4me3_Mll2_Y2602A_F4


title: H3K4me3_Mll2_Y2602A_F1


title: Mll2_shMll2_2


title: MKP_030J_RRBS


title: H3K4me3_Mll2WT


title: H3K4me3_Mll2_mCXXC_F4

value: Mll2 mCXXC/mCXXC


title: siDDX5_17_N1

value: siRNA targeting both DDX5 and DDX17 RNA helicases


title: PLP_PELO_0hrs_rep2

city: Baltimore

first: Eric

middle: W

last: Mills

state: Maryland

address: 725 N. Wolfe St

institute: Johns Hopkins University School of Medicine

data_processing:
Basecalls were made using CASAVA 1.8
rRNA-derived reads were subtracted using Bowtie 2 version 2.2.6
non-rRNA Reads were aligned to hg19 using TopHat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: Primary_PLT_RNA.txt: Per-transcript read counts for Primary_PLT_RNA_rep1 and Primary_PLT_RNA_rep2
Supplementary_files_format_and_content: PLP_timecourse_RNA.txt: Per-transcript RPKM data for PLP_timecourse_RNA samples

source_name: platelet-like particle (PLP)

growth_protocol: Cells were grown as described in Mills EW et al., 2017

extract_protocol:
Samples were extracted as described previously in Ingolia et al., 2014
RNA-Seq libraries were prepared as described previously in Ingolia et al., 2014 using the TruSeq stranded RNA-Seq protocol

value: cell line

tag: drug treatment

value: 0.05ng Promega Firefly luciferase per 100ng Total RNA

tag: rrna depletion

value: RiboZero-Gold rRNA depletion


title: PLP_PELO_1hr


title: PLP_PELO_2hrs


title: H3K4me3_Mll2_mCXXC_F1


title: PLP_PELO_6hrs


title: PLP_PELO_0hrs_rep1


title: PLP_GFP_4hrs


title: Mll2_Mll2_Y2602A_F4


title: PLP_PELO_4hrs


title: PLP_GFP_0hrs_rep2


title: PLP_GFP_0hrs_rep1


title: PLP_GFP_1hr


description:
RNA-Seq
primary epidermis wild type RNA-Seq replicate 1

data_processing:
Basecalls were made using CASAVA 1.8
rRNA-derived reads were subtracted using Bowtie 2 version 2.2.6
non-rRNA Reads were aligned to hg19 using TopHat v2.0.10
Genome_build: mm9
Supplementary_files_format_and_content: see read me file via the Series record

source_name: epidermis

growth_protocol: Cells were grown as described in Liakath-Ali et al., 2017

extract_protocol:
Samples were extracted as described previously in Ingolia et al., 2014
Ribo-prof and RNA-Seq libraries were prepared as described previously in Ingolia et al., 2014

value: primary cell type


title: PLP_GFP_6hrs


description:
RNA-Seq
primary epidermis Pelota knockout RNA-Seq replicate 1


title: PLP_GFP_2hrs


title: primary platelet RNA-Seq replicate 2

description: primary platelet RNA-Seq replicate 2

source_name: platelet


title: primary platelet RNA-Seq replicate 1

description: primary platelet RNA-Seq replicate 1


description:
Ribo-Prof
primary epidermis wild type Ribo-Prof replicate 1


description:
Ribo-Prof
primary epidermis Pelota knockout Ribo-Prof replicate 2


description:
RNA-Seq
primary epidermis Pelota knockout RNA-Seq replicate 2


description:
Ribo-Prof
primary epidermis Pelota knockout Ribo-Prof replicate 1


description:
Ribo-Prof
primary epidermis wild type Ribo-Prof replicate 2


title: Pol II ChIP DNA

city: Toulouse

first: Beata

last: Jady

address: 118 route de Narbonne

department: Laboratoire de Biologie Moléculaire Eucaryote

institute: CNRS

data_processing:
Bustard Version 1.9.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to Hg18 human genome using BWA v0.5.6 (r1303) with --bwaoptions=-t 2 -q10
Peak Calling with MACS2 callpeak, Galaxy version  2.1.0.20151222.0 with parameters --format BAMPE --gsize 2451960000 --bw=300 --bdg --qvalue 0.05
bigWig files were created with wig_to_bigWig Galaxy Tool version 1.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: tabular for called peaks
Supplementary_files_format_and_content: BedGraph
Supplementary_files_format_and_content: bigWig

source_name: HeLa cells stably expressing Flag-LARP7

growth_protocol: DMEM supplemented with 10% serum and antibiotics

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies.
Library prepared using Illumina's TruSeq ChIP Library Preparation Kit and following the instructions of the fabricant

treatment_protocol: 1% formaldehyde cross-linking

tag: antibody used

tag: beads

value: Pansorbin cells


title: Control for Pol II ChIP DNA

value: no antibody


title: Flag-Larp7 ChIP DNA

value: M2-Sigma + rabbit anti-mouse


title: nod_btm2_0406

city: Cambridge

first: Arnon

last: Arazi

state: MA

address: 415 Main Street

institute: Broad Institute

description: Bottom beta cells; included in batch #1.

data_processing:
Mapping of reads to mouse reference transcriptome mm9 and quantification of mRNA expression levels was done using RSEM (Li and Dewey, 2011).
Identification of differentially expressed genes was performed using the Bioconductor package EdgeR (Robinson et al., 2010), employing a generalized linear model taking into account both the technical batch and the cell type. The resulting p-values were adjusted using Benjamini and Hochberg’s procedure for controlling the false discovery rate (FDR) (Benjamini and Hochberg, 1995).
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files specify, for each gene, its symbol and the expcted count estimated by RSEM

source_name: Primary beta cells sorted from NOD mice (8-10wk)

extract_protocol:
Subpopulations of beta cells (Top and Btm) were sorted from 8-10-wk-old NOD mice. Cell viability and concentration was assessed by the Countess Automated Cell Counter (ThermoFisher Scientific).
Reverse transcription and cDNA amplification were performed from approximately 1,000 cells using SMARTer Ultra Low RNA kit (Clontech). Sequencing libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina). Libraries were pooled and sequenced.

tag: strain

value: NOD mice

tag: tissue

value: Pancreas

tag: cell type

value: primary beta cells purified by cell sorting


title: Control for Flag-Larp7 ChIP DNA

value: rabbit anti-mouse


title: nod_btm1_0406


title: nod_btm1_0425

description: Bottom beta cells; included in batch #2.


title: Input DNA


title: nod_btm2_0425

description: Bottom beta cells; included in batch #2


title: nod_top3_0406

description: Top beta cells; included in batch #1.


title: nod_top1_0425

description: Top beta cells; included in batch #2.


title: nod_top1_0406

description: Top beta cells; included in batch #1.


title: nod_top3_0425

description: Top beta cells; included in batch #2.


title: old ISCs, rep2

city: Ulm

first: Petra

last: Pandur

address: Albert-Einstein-Allee 11

department: Institute for Biochemistry and Molecular Biology

country: Germany

institute: University of Ulm

data_processing:
All sequencing libraries were quantified on a Qubit fluorometer and equimolar amounts of all six libraries were pooled and loaded onto two lanes of an Illumina single-read flow cell and bound molecules were clonally amplified on a cBot instrument. The first 58 nt from each fragment were sequenced on an Illumina Genome Analyzer IIx. To increase the number of reads for each sample, three additional 50 nt sequencing runs on a mySeq instrument were performed. The raw base calls were simultaneously demultiplexed and transformed into fastq files, containing the sequence and an ASCII-coded PHRED quality score for each sequence read.
The fastq files of each sample were trimmed using the fastx clipper tool (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads shorter than 20 nt were discarded. The clipped fastq files were checked for read quality using the fastqc quality control tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were aligned against the genome sequence using bowtie (Langmead et al., 2009). The Ensembl genes were retrieved from the UCSC genome browser.
Statistical data analysis was performed with the bioconductor package "edgeR" (Robinson et al., 2010). The raw count data were normalized based on CPM to account for differences in sequencing depth. Features with less than 1 CPM in less than 2 samples were removed from the data set, since here valid statistical assessment of differential expression is not possible. The remaining data were subjected to principal component analysis (PCA) to visualize the overall data structure. The clear separation between the two groups (young and old) indicates specific differences in the expression profiles. Discrete count data as obtained by RNAseq follow a Negative Binominal (NB) distribution. The experimental group "age" was used to fit the NB model and estimate the common dispersion. An exact test was performed to calculate the p-values for differential expression. The resulting p-values are adjusted for multiple testing according to Benjamini and Hochberg (1995) to calculate the FDR.
Genome_build: D. melanogaster genome, version BDGP R5/dm3 using tophat v1.2.0 (Trapnell et al., 2009)
Supplementary_files_format_and_content: The E12R027_genelists.xlsx file contains the data described in the data processing steps

source_name: midgut

extract_protocol:
Young and old midguts were dissociated and ISCs were isolated by FACS as described in Tauc et al. (2014). The ISCs were collected into RNAlater solution (Ambion), snap-frozen in liquid nitrogen and sent to MFT Services (Tübingen) for RNA isolation and sequencing. Sequencing libraries were prepared with the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) according to the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: fly line (genotype)

value: esg-GAL4, UAS-GFP                    (yw; esg-GAL4 NP5130, UAS-GFP, UAS-GFPnlacZ (N 1099))

value: midgut


title: young ISCs, rep2

value: 6 - 8 days


title: old ISCs, rep1


title: M393_IP_ChIPseq1

city: Iowa City

first: Ryan

last: Baxley

state: IA

address: 3159C MERF 375 Newton Rd

department: Biochemistry

institute: University of Iowa

data_processing:
Alignment: Sequence reads were obtained and mapped to the Drosophila (dm3) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Partek Genomics Suite version 6.5 (Partek Inc., St. Louis, MO, USA, www.partek.com)
Calling binding sites: For each dataset, the overlap with known Su(Hw) binding sites (Soshnev et al., 2012) was inspected using the UCSC genome browser following adjustment of fold enrichment (IPvsIgG). For ChIPseq1 a 3-fold cutoff and for ChIPseq2 a 1.5-fold cutoff were used to generate the final list of called Su(Hw) binding sites identified.
Genome_build: dm3
Supplementary_files_format_and_content: txt files include the list of called binding sites in each sample, bed generated from WIG data for IP and IgG for each sample are included

source_name: Ovaries

growth_protocol: Newly eclosed virgin female flies were collected in the morning and dissected within 6 hours of eclosion.

extract_protocol:
Ovaries were cross-linked with 1.8% formaldegyde and Su(Hw)-DNA complexes were isolated with anti-Su(Hw) guinea pig antibody (Baxley et al., 2011).
Single-end libraries for Illumina high-throughput sequencing were prepared from ~100ng of DNA from each fraction (Cincinnati Children's Hospital Medical Center Genetic Variation and Gene Discovery Core Facility, Cincinnati, OH, USA)

treatment_protocol: Dissected ovaries were kept on ice following dissection and frozen at -80C for storage.

tag: tissue age

value: Newly eclosed (>6hr old)


title: Georgecraigius atropalpus replicate 1

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description:
processed data file: non_reference_mCG_estimates.tsv
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: None
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Aedes atropalpus

source_name: genomic DNA

extract_protocol:
DNA was isolated using a Qiagen Dneasy Mini kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations.
Libraries were prepared following the steps provided in Urich et al. (2015; Nature Protocols)

value: Whole animal

tag: social behavior

value: Solitary

value: Lab colony


title: Pemphigus populicaulis replicate 3

organism: Pemphigus populicaulis


title: Pemphigus populitransversus replicate 2

organism: Pemphigus populitransversus

value: Presocial


title: Pemphigus populicaulis replicate 4


title: Pemphigus populitransversus replicate 3


title: Pemphigus populitransversus replicate 4


title: Pemphigus populitransversus replicate 1


title: M393_IgG_ChIPseq1


title: Pyractomena borealis replicate 4

organism: Pyractomena borealis


title: Reticulitermes flavipes replicate 4

organism: Reticulitermes flavipes

value: Whole animal (guts discarded)

value: Eusocial


title: old ISCs, rep3


title: Pemphigus populicaulis replicate 2


title: Reticulitermes flavipes replicate 2


title: Reticulitermes flavipes replicate 3


title: Reticulitermes flavipes replicate 1


title: young ISCs, rep3


title: M393_IP_ChIPseq2


title: young ISCs, rep1


title: Pemphigus obesinymphae replicate 4

organism: Pemphigus obesinymphae


title: Pemphigus populicaulis replicate 1


title: Pyractomena borealis replicate 2


title: M393_IgG_ChIPseq2


title: Pyractomena borealis replicate 1


title: Polistes carolina replicate 3

description:
processed data file: allc_Polistes_carolina_to_Polistes_canadensis.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: http://www.ncbi.nlm.nih.gov/genome/?term=Polistes+canadensis%5Borgn%5D
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Polistes carolina

value: WT


title: Polistes carolina replicate 2


title: Pyractomena borealis replicate 3


title: Polistes carolina replicate 4


title: Pemphigus obesinymphae replicate 3


title: Aedes aegypti replicate 1

description:
processed data file: allc_Aedes_aegypti.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: https://www.vectorbase.org/organisms/aedes-aegypti
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Aedes aegypti


title: Leucophaea maderae replicate 4

organism: Rhyparobia maderae


title: Periplaneta americana replicate 4

organism: Periplaneta americana


title: Toxorhynchites amboinensis replicate 1

organism: Toxorhynchites amboinensis


title: Leucophaea maderae replicate 3


title: Periplaneta americana replicate 3


title: Pemphigus obesinymphae replicate 2


title: Reticulitermes virginicus replicate 1

organism: Reticulitermes virginicus


title: Periplaneta americana replicate 2


title: Pemphigus obesinymphae replicate 1


title: Microplitis mediator replicate 1

description:
processed data file: allc_Microplitis_mediator_to_Microplitis_demolitor.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: http://www.ncbi.nlm.nih.gov/genome/?term=Microplitis+demolitor%5Borgn%5D
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Microplitis mediator


title: Leucophaea maderae replicate 1


title: Eublaberus posticus replicate 4

organism: Eublaberus posticus


title: Periplaneta americana replicate 1


title: Heliothis virescens replicate 1

organism: Heliothis virescens


title: Eublaberus posticus replicate 3


title: Eublaberus posticus replicate 2


title: Eublaberus posticus replicate 1


title: Chrysodeixis includens replicate 4

organism: Chrysodeixis includens


title: Blattella germanica replicate 1

description:
processed data file: allc_Blattella_germanica.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: https://www.hgsc.bcm.edu/arthropods/german-cockroach-genome-project
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Blattella germanica


title: Helicoverpa zea replicate 1

organism: Helicoverpa zea


title: Anopheles gambiae replicate 1

description:
processed data file: allc_Anopheles_gambiae.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: https://www.vectorbase.org/organisms/anopheles-gambiae
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Anopheles gambiae


title: Aphidius ervi replicate 1

organism: Aphidius ervi


title: Chrysodeixis includens replicate 3


title: Chrysodeixis includens replicate 2


title: Aphis craccivora replicate 1

organism: Aphis craccivora


title: Polistes carolina replicate 1


title: Blaptica dubia replicate 4

organism: Blaptica dubia


title: Anastrepha suspensa replicate 1

organism: Anastrepha suspensa


title: Leucophaea maderae replicate 2


title: Culex quinquefasciatus replicate 1

description:
processed data file: allc_Culex_quinquefasciatus.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: https://www.vectorbase.org/organisms/culex-quinquefasciatus
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Culex quinquefasciatus


title: Blaptica dubia replicate 3


title: Chrysodeixis includens replicate 1


title: Blattella asahinai replicate 4

description:
processed data file: allc_Blattella_asahinai_to_Blattella_germanica.tsv.bz2
MethylC–seq

organism: Blattella asahinai


title: Blaptica dubia replicate 2


title: Cryptocercus garciai replicate 3

organism: Cryptocercus garciai

value: Subsocial


title: Blaptica dubia replicate 1


title: Microplitis demolitor replicate 1

description:
processed data file: allc_Microplitis_demolitor.tsv.bz2
MethylC–seq

organism: Microplitis demolitor


title: Blattella asahinai replicate 3


title: Cryptocercus garciai replicate 4


title: Aedes albopictus replicate 1

description:
processed data file: allc_Aedes_albopictus.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: https://www.vectorbase.org/organisms/aedes-albopictus
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Aedes albopictus


title: Cryptocercus garciai replicate 1


title: Blattella asahinai replicate 2


title: Acyrthosiphon pisum replicate 1

description:
processed data file: allc_Acyrthosiphon_pisum.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: https://www.hgsc.bcm.edu/arthropods/aphid-genome-project
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Acyrthosiphon pisum


title: Cryptocercus garciai replicate 2


title: Copidosoma floridanum replicate 1

description:
processed data file: allc_Copidosoma_floridanum.tsv.bz2
MethylC–seq

data_processing:
Data was mapped to genome assemblies of each species. If a species did not have an assembled genome, a closely related species (i.e., within same genus) was used. Alternatively, if no closely related species was available, DNA methylation levels were estimated using FASTmC (Bewick et al., 2015; G3)
MethylC-seq analysis was performed as described in Schmitz et al. (2013; Genome Research).
genome build: http://www.ncbi.nlm.nih.gov/genome/?term=Copidosoma+floridanum%5Borgn%5D
processed data files format and content: Tab delimited text file. Please see metafile.txt for column headers for allc*.tsv.bz2 processed data files. Please see metafile2.txt for column headers for non_reference_mCG_estimates.tsv. The text files with the processed data are available in a tar archive on the series record.

organism: Copidosoma floridanum


title: Blattella asahinai replicate 1


title: Panct1 WT - Input

status: Public on Feb 01 2017

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

description: Panct1 ChIRP was done as described in PMID 21963238

data_processing:
library strategy: ChIRP-Seq
Sequencing reads were aligned to murine genome (GRCm38/mm10) with GEM mapper ver. 1.376 and all duplicate alignments were filtered out with MACS2 ver. 2.1.0 filterdup procedure.
Genomic alignments of reads from odd and even samples were combined with help of bedtools ver. 2.17.0 (intersectBed) and all alignments from one sample that do not overlap with any of alignments from the second sample were discarded. Minimum overlap requirement was set to 75% of an alignment length.
Obtained "odd and even" alignments were subject to peak calling and peak refinement procedures by MACS2, using genomic input samples as controls. Peak calling significance threshold was set to p = 1e-3.
The final set of putative Panct1 binding sites obtained from the ChIRP experiment was defined as a set of all peaks from Panct1 WT sample with at least 2-fold higher enrichment than peaks obtained from Panct1 KO.
Genome_build: mm10
Supplementary_files_format_and_content: Panct1.bed.gz contains genomic coordinates of putative Panct1 binding sites. All other bed files contain coordinates of sequencing read alignments, and files with "Odd_and_Even" suffix contain combined and filtered alignments from respective "odd" and "even" probesets.

organism: Mus musculus

source_name: ES cells

growth_protocol: ES cells were routinely grown on FBS supplemented DMEM with LIF, Pen/Strep, Beta mercaptoethanol and Non-essential Amino Acids. Media was changed every day and cells were split every 48 hours.

extract_protocol:
Following crosslinking, chromatin was sonicated, incubated with Biotin labelled probes overnight and pulled down using Streptavidin beads. DNA was then extracted from the beads, treated with RNAse A and RNAse H, proteinase K and finally purified.
Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers’ instructions. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3', Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume. Large-scale amplification of library constructs was performed by using the PCR Enrich Adaptor Ligated cDNA Library module (NEB).

treatment_protocol: Prior to harvesting for ChIRP, cells were treated with Demecolcine (20ng/ml) for 4h and released in normal media for 2h for synchronization in G1.

tag: strain background

tag: genotype/variation

value: Panct1 WT

tag: construct

value: TOBF1 tagged in BAC

value: embryonic stem (ES) cells


title: Panct1 KO - Odd probes ChIRP-Seq

value: Panct1 KO

tag: chirp probe

value: 3' BIOTIN TEG Panct1 odd probes (18 probes)


title: Panct1 WT - Even probes ChIRP-Seq

value: 3' BIOTIN TEG Panct1 even probes (17 probes)


title: Panct1 WT - Odd probes ChIRP-Seq


title: Panct1 KO - Even probes ChIRP-Seq


title: 26695-68-2

city: Bangalore

first: Sumith

last: Kumar

state: Karnataka

address: Department of Biochemistry, Indian Institute of Science, Bangalore, India

country: India

institute: Indian Institute of Science

data_processing:
Non-polyA tailed RNAs were reomoved from non paired-end reads
Sequenced reads were trimmed for adaptor sequence, ribosomal RNAs, transfer RNAs using bowtie v2.2.2, in house Perl scripts and picard tools (version 1.119)
Pre-processed reads were aligned to the Helicobacter pylori 26695 reference genome and gene model downloaded from ENSEMBL using Tophat program version 2.1.1 with default parameters.
After aligning reads with reference gene model, the aligned reads were used for estimating expression of the genes and transcripts using cufflinks program version 2.2.1
Supplementary_files_format_and_content: cufflinks FPKM

organism: Helicobacter pylori 26695

source_name: whole cell RNA

growth_protocol: H. pylori was grown in BHI liquid broth supplemented with 8% horse serum and IsovitaleX. Total RNA was isolated using exponentially growing culture (OD 600 ~ 0.8).

extract_protocol:
RNA was isolated from exponentially growing H. pylori culture using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: R.hpyAII-M2.hpyAII gene deletion (clone-2)


title: 26695-68-1

value: R.hpyAII-M2.hpyAII gene deletion (clone-1)


title: 26695-1

value: wild type


title: SM Dev rep2

city: Los Angeles

first: Haibin

last: Xi

state: CA

address: 615 Charles E Young Dr South, BSRB 257

department: MIMG

institute: UCLA

data_processing:
HiSeq Control Software v2.0 was used for basecalling on an Illumina HiSeq 3000 sequencer
Raw sequencing reads were processed using the packages available through the UCLA Galaxy resources (galaxy.hoffman2.idre.ucla.edu). Low quality bases found in the raw FASTQ files were removed by FASTQ Trimmer (v1.0.0) to ensure high quality base reads examined by FastQC (v0.4). The trimmed reads were mapped to the hg19 reference genome via Tophat for Illumina (v1.3.3) using default settings.
Gene expression values (Fragments Per Kilobase exons per Million mapped reads; FPKM) were obtained through Cufflinks (v2.0.2) using the iGenomes UCSC hg19 gene annotation and the mapped reads generated from Tophat, with default settings in Galaxy.
Differentially expressed gene (DEG) analysis was performed through Cuffdiff (v2.0.2) using the iGenomes UCSC hg19 gene annotation and the mapped reads generated from Tophat. Galaxy default settings were applied for Cuffdiff except that Bias Correction was performed using the hg19 reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample in Cufflinks files. Cuffdiff files also contained fold change and statistics comparing different sample groups (replicates of the same mesoderm type).

organism: Homo sapiens

source_name: Developed Somites at Forelimb Bud Level

extract_protocol:
Different mesoderm tissues were micro-dissected and RNA was extracted using the QIAGEN RNeasy Plus Micro Kit. 10-100 ng of total RNA was used for the sequencing library construction.
The Nugen Ovation RNA-Seq System V2 kit was used to make and amplify cDNA, and the sequencing libraries were constructed followed the standard operation procedures at the UCLA Clinical Microarray Core Facility.

tag: developmental stage

value: 4.5 weeks embryo

value: Developed Somites at Forelimb Bud Level


title: SM Dev rep1

value: 4.5-5 weeks embryo


title: Panct1 KO - Input


title: SM rep2

source_name: Nascent Somites

value: 5 weeks embryo

value: Nascent Somites


title: SM rep1


title: PSM rep1

source_name: Presomitic Mesoderm

value: Presomitic Mesoderm


title: PSM rep2


title: PrEC NOMe-seq

city: Aarhus N

first: Søren

last: Vang

address: Palle Juul-Jensens Boulevard 99

country: Denmark

institute: Department of Molecular Medicine (MOMA)

data_processing:
Library strategy: NOMe-seq
Base calling and demultiplexin performed with standard illumina tools (CASAVA)
Fastq files mapped to hg19 using BSMAP v2.5 (Yuanxin Xi and Wei Li, "BSMAP: whole genome bisulfite sequence MAPping program" (2009)
bigWig files made from bam files using genomeCoverageBed (kent tools) and wigToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files giving read depth genome wide

source_name: Prostate epithelial cells (normal)

growth_protocol: LNCaP cells were grown in RPMI 1640 with L-glutamine supplemented with 10% fetal bovine serum, 100 U/ml penicillin and 100  g/ml streptomycin. PrEC cells were grown in Prostate Epithelial Cell Basal Medium (ATCC) supplemented with Prostate Epithelial Cell Growth Kit (ATCC).

extract_protocol:
Exponentially growing cells were washed with PBS, trypsinized, and incubated with ice-cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, and 0.5% NP-40) for 5 min on ice to isolate intact nuclei. Nuclei were washed with ice-cold wash buffer (10 mM Tris, pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA), resuspended in ice-cold 1x GpC buffer (New England BioLabs), and treated with 200 units of M.CviPI enzyme supplemented with1.5 xL S-adenosylmethionine (SAM) for 7.5 min with a boost of 100 units enzyme and 0.75 _L SAM for an additional 7.5 min. Genomic DNA was isolated by standard phenol-chloroform extraction and ethanol precipitation.
WGBS libraries were generated using 2-5 µg of DNA and sequenced on the HiSeq2000 performed by the USC Epigenome Center (Blatter et al., Genome Biol. 2014;15:469)
WGBS libraries were prepared based on previously described (Berman et al 2012) and according to Illumina's recommendation.

treatment_protocol: We used the NOMe-seq protocol, which has been developed for simultaneous assessment of nucleosome positioning and DNA methylation genome-wide (Kelly TK et al. Genome Res. 2012;22:2497)

tag: cell line

value: PrEC


title: LNCaP NOMe-seq

source_name: Prostate adenocarcinoma

value: LNCaP


title: Input

data_processing:
Sequencing reads were first subject to adatpter removal and low quality end trimming with Cutadapt package.
Alignment of filtered reads to the mouse genome (mm10 assembly) was performed with Bowtie 2, using '--very-sensitive' parameter.
Peak calling was performed with MACS 2 (using default parameters).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated by MACS2 and compressed into bigWig format using bedtools package, scores represent read pile-up normalized to 1 million reads; bed file contains genomic locations of ChIP-Seq peaks and scores represent q-values, as reported by MACS2

extract_protocol:
Lysates were extracted from sonicated chromatin and processed with indicated Antibodies
Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers’ instructions. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3', Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume. Large-scale amplification of library constructs was performed by using the PCR Enrich Adaptor Ligated cDNA Library module (NEB).

tag: chip antibody


title: TOBF1 ChIP-Seq

value: anti GFP antibody (made by David Drechsel lab at MPI-CBG Dresden, Germany)


title: RNA5_20110815

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
Reads were assembled to a reference genome (hg19, European Hapmap (CEU) Major Allele release) using TopHat v1.3.2. The number of mismatches allowed per read was set to 2
PCR duplicates were removed using Picard-tools
non-properly paired and non-uniquely mapped reads were filtered out with SAMtools
Recalibration and local realignment was performed with GATK tools. Calculate transcript abundances using Cufflinks.
Genome_build: hg19

source_name: HL-60, Drug D

growth_protocol: HL-60 cells were maintained in RPMI-1640-HEPES conatining 10% fetal bovine serum (Wisent).

extract_protocol:
At 24 h after the end of drug treatment total RNA was isolated from HL-60 cells using the RNAeasy Plus Mini kit (Qiagen)
TruSeq RNA Sample Prep kit v2 (Illumina)

treatment_protocol: See SAMPLES table for individual sample treatment

value: Cell Line HL-60

tag: Sex

value: Female

tag: age

value: Drug A Replicate2

tag: treatment

value: acute promyelocytic leukemia


title: RNA8_20110815

source_name: HL-60, Drug A+D

value: Control Replicate1


title: RNA6_20110815

value: Drug A Replicate1


title: WT FL Rep 3

city: Melbourne

first: Kevin

middle: Robert

last: Gillinder

state: Victoria

address: 99 Commercial Road

department: Australian Centre for Blood Diseases

country: Australia

institute: Monash University

data_processing:
Base calling was performed with Torrent Suite v4.0.1
[ChIP-seq]
TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4 was used to map reads to the reference genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz)
Fragments mapping to the same position on the same strand were taken to be PCR duplicates and were subsequently discarded, retaining only unique alignments with the highest MAPQ score.
ChIP-seq peaks were called with MACS (v1.4.2) using uniquely mapped ChIP and input sequence alignments.
Significant peaks identified by MACS were further filtered and ranked based on >30 fold-enrichment compared to input, and a false-discovery rate <0.1%. Peaks overlapping regions identified as RNA repeats by the Repeatmasker software were ignored, yielding lists of high-confidence peaks for each sample.
Each peak summit was subsequently annotated with the genomic context, overlapping peaks and central KLF1 binding motif.
[RNA-seq]
Tophat2 (v2.0.10) was used to perform spliced alignment to the reference transcriptome and genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz) using default options with the following additional parameters: -N 4, --read-gap-length 4, --read-edit-dist 4, --read-realign-edit-dist 0, -a 5, -i 50, -g 6, --coverage-search, --microexon-search, --library-type fr-firststrand.
Unaligned sequences were subsequently remapped using TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4.
Successful alignments were merged back into the Tophat2 SAM file.
Alignments of less than 30 nt were discarded.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated and differential expression testing between replicate groups was performed with Cuffdiff2 using default parameters. A mean FPKM cutoff of 1.0 was required in at least one sample and only differentially expressed genes (DEGs) with >2 fold-change were reported.
Genome_build: mm9
Supplementary_files_format_and_content: Nan-KLF1_Annotated_Peaks.csv.gz is a tab-delimited annotated MACS peaks file
Supplementary_files_format_and_content: KLF1_Annotated_Peaks.csv.gz is a tab-delimited annotated MACS peaks file
Supplementary_files_format_and_content: K1-ER_K1-NanER_DEGs.csv.gz reports tab-delimited FPKM values and differential gene expression analysis
Supplementary_files_format_and_content: Nan_FL_DEGs.csv.gz reports tab-delimited FPKM values and differential gene expression analysis

molecule: polyA RNA

source_name: Total Fetal Liver Klf1+/+

growth_protocol: Fetal livers were collected from E14.5 timed matings by dissection, mechanically dissociated and passed through a 27G needle to obtain single cells.

extract_protocol:
Total RNA was extracted from homogenised fetal livers using TRIzol® Reagent (Life Technologies, #15596026). Extracted RNA was subsequently treated with DNase I (New England Biolabs, #M0303L) to remove residual gDNA contamination.
Purified RNA was used to generate Illumina TruSeq Stranded mRNA libraries (Illumina; #RS-122-2101) following removal of globin RNA with the GLOBINclear™ kit for mouse/rat (Ambion®; #AM1981).

value: Primary Fetal Liver

tag: genotype

value: Fetal liver

value: Embryonic day 14.5


title: WT FL Rep 2


title: Nan FL Rep 3

source_name: Total Fetal Liver Nan/+

value: Nan/+


title: Nan FL Rep 2


title: WT FL Rep 1


title: Nan FL Rep 1


title: NSA

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description:
PARP1.narrowPeak
PARP1_MACSpeaks.txt
PARP1_summits.bed
PARP1_rDNA.sgr

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control
Short and low-quality reads were removed from source FASTQ files by cutadapt v.1.8.3 with following options: --minimum-length=20 --quality-cutoff=26
Unique intermediary datasets for rDNA profiling were obtained by tool for removal of duplicates in paired short DNA sequence reads "fastuniq" (PMID 23284954)
Unique reads were mapped to rDNA by bowtie v.1.1.2 with following options: --chunkmbs 1024 --best -m1 to SAM format.
Unmapped reads were removed from SAM files by samtools v.1.2 with the option -F 4, SAM files were converted to BAM files.
BAM files with rDNA alignments were converted to BED files by bamToBed 2.25.0 from BEDtools
BED files were converted to WIG files by Fseq 1.84 with fragment size 200 (fseq -f 200)
WIG files were converted to SGR files by ad hoc Perl script and then NSA profile was used as control and have beed subtracted from PARP1. Result is presented in PARP1_rDNA.sgr file
Mapping to H.sapiens hg19 whole genome was performed as trimmed reads alignment by bwa mem algorithm (v. 0.7.12-r1039)
samtools v.1.2. with options -b -F 4 -q 10 was used to remove unaligned and low quality (MapQ<10) alignments from SAM files and to convert them to BAM paired-end (BAMPE) files.
Peak Calling was performed by MACS2 peak v.2.1.0.20150731, NSA alignment was used as "Control". Additional options -f BAMPE -g hs --call-summits were used to ensure proper format processing, to set сorrect genome size and to obtain peak summits. Results are presented in files PARP1.narrowPak, PARP1_summits.bed. Full MACS2 report is located in the file PARP1_MACSpeaks.txt
Genome_build: Homo sapiens hg19/GRCh37.p13 genome, MFA sequences with High/low complexity regions marked as big/small letters
Genome_build: Human ribosomal DNA complete repeating unit, GenBank Accession number U13369
Supplementary_files_format_and_content: PARP1.narrowPeak contains coordinates of peaks, their scores, signal (fold enrichment) values, pvalues, qvalues. PARP1_summits.bed contains peak summits coordinates and their heights. PARP1_MACSpeaks.txt contains full MACS2 peak caller report.
Supplementary_files_format_and_content: PARP1_rDNA.SGR contains profile of PARP1 along H. sapiens rDNA.

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemente+B29d with 10% inactivated fetal bovine serum (Gibco/BRL, USA), penicillin (100 U/ml), streptomycin (100 ug/ml) and L-glutamine (4 mM). Cells were routinely cultured in 100 mm culture dishes under 5% CO2 in air in a humidified atmosphere at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody using MAGnify™ Chromatin Immunoprecipitation System (Invitrogen). chip antibody: PARP1; chip antibody vendor: Active Motive; chip antibody lot#: 00909001; chip antibody catalog#: 39561.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 -400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: HEK 293 cells were seeded in 10 cm culture plates 1-2 days before experiment in DMEM containing 10% FBS, and used at approximately 60-80% confluency.

tag: strain

value: kidney

value: embryo

value: wild type

value: none (input control)


title: RNA4_20110815

source_name: HL-60, Drug A

tag: tissue

value: Drug D Replicate1

value: 3-deazaneplanocin-A (DZNep)


title: RNA2_20110815

source_name: HL-60, Control

value: Drug A+D Replicate1

value: 5-aza-2'-deoxycytidine (decitabine, 5-AZA-CdR) + 3-deazaneplanocin-A (DZNep)

tag: cell type


title: RNA3_20110815

value: Cell Line HL-60

value: Female

value: Drug D Replicate2


title: PARP1

value: anti-PARP1 antibody (Active Motif; lot# 00909001; catalog# 39561)


title: 26695-2


title: Flag_PAR

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

data_processing:
Library strategy: CRAC
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped
Reads of identical sequence that contained identical 5-nucleotide random barcodes were collapsed
Reads were trimmed and quality controlled using flexbar and aligned to the human genome (Ensembl GRCh 37.75) by Bowtie2 (version 2.2.4)
For PAR-CRAC, only reads containing a single T-C mutation were mapped
Genome_build: Ensembl GRCh 37.75
Supplementary_files_format_and_content: Overview files (.txt) indicate the number of sequence reads mapped to different classes of RNA (feature). The final processed data files (.txt) for the 47S rDNA locus give the feature name, nucleotide position in the feature and in the 47S rRNA, the nuceotide sequence, the number of mapped reads (hits) per nucleotide, the number of substitutions in the reads and in the case of UV crosslinking the number of nucleotide deletions.

source_name: HEK293 cell culture

growth_protocol: Flp-In T-Rex HEK293 cells expressing Flag-His-tagged NKRF or the Flag-His tag only were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal bovine serum.

extract_protocol:
Crosslinked RNA-protein complexes were purified under native (anti-FLAG beads) and denaturing (Ni-NTA) conditions and RNAs associated with Flag-His-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Bohnsack et al., 2012).

treatment_protocol: Expression of tagged proteins was induced by addition of tetracycline for 24 h before crosslinking/harvesting. For PAR-CRAC cells were treated with 100 μM 4-thiouridine for 6 h prior to crosslinking at 365 nm. For UV CRAC, cells were crosslinked as previously described (Sloan et al., 2015).

tag: expressing

value: Flag-His

value: PAR


title: NKRF_PAR

value: Flag-His-NKRF


title: NKRF_UV

value: UV


title: Flag_UV


title: RNA7_20110815

value: Control Replicate2

value: acute promyelocytic leukemia


title: 48h-3

city: Grand Forks

first: Archana

last: Dhasarathy

state: North Dakota

address: 501 N Columbia Rd.

institute: University of North Dakota

data_processing:
Sequences were aligned to hg19 genome using TopHat v2.0.13
Sequences were assigned to genes using HTSeq v0.6.0
Differential expression analysis was performed using edgeR v3.10.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files that contain count abundance data for each sample

source_name: Astrocytes

extract_protocol:
RNA extraction protocol not provided.
Library construction protocol not provided.

value: astrocytes

tag: time point

tag: infection status

value: Borrellia burgdorferi infected


title: Untreated-3

value: uninfected control


title: 48h-1


title: Untreated-1


title: 24h-1


title: Untreated-2


title: 24h-2


title: input A used for samples 2, 3 and 4

city: Vienna

first: Heinz

last: Ekker

address: Dr. Bohrgasse 3

country: Austria

institute: VBCF

description: single aphidicolin arrest

data_processing:
Basecalling with Illumina RTA v1.18.61.0
Demultiplexing with BamIndexDecoder vV1.03-184-g590b59e-dirty
Alignment against genome hg19 with bowtie 0.12.5 parameters " -v 2 --best --strata --tryhard   -m 1"
Peak calling using BayesPeak_1.22.0 bin size 1000bp
Genome_build: hg19
Supplementary_files_format_and_content: BED files with called peaks

source_name: Roberts syndrome (vu1199-F SV40)

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 0.2 mM glutamine, penicillin, and streptomycin.

extract_protocol:
Samples were formaldehyde-crosslinked, lysed, sonicated, presipitated, and reverse crosslinked.
Illumina sample libraries were prepared according to NEB protocol E6040

treatment_protocol: Cells were arrested in G1/S phase with aphidicolin (1.2 μg/ml) for 24 hours.

tag: antibody


title: input B used for samples 1, 6 and 7

description: single aphidicolin arrest


title: MCM3

description: single aphidicolin arrest

value: MCM3 (Bethyl, A300-192A)


title: GFP-ESCO2-ΔAB (75-110, 208-212)

description: single aphidicolin arrest

value: GFP-trap beads (Chromotek, gta-200)


title: RNA1_20110815

value: Drug A+D Replicate2


title: GFP-ESCO2-Wild type

description: single aphidicolin arrest


title: AT3-input ChIP-Seq

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

description: AT3-input ChIP-Seq AT-3 mammary tumor cell line

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the mouse reference genome (GRCm38/mm10) using bowtie (2.2.3)
Peak-calling was performed using MACS2.0.10
Genome_build: mm10
Supplementary_files_format_and_content: peaks files

source_name: AT-3 mammary tumor cell line

growth_protocol: Cell lines were cultured in supplemented DMEM based media

extract_protocol:
Lysate were isolated from formaldehyde cross-linked cells and sonicated to release the chromatin, then immunoprecipitated using relevant antibodies.
For BRD4, RNA Polymerase II, IRF1, STAT1, H3K27Ac ChIP-Seq, indexed libraries were prepared using KAPA Hyper Prep Kit for Illumina platforms (Kapa Biosystems) and SeqCap Adapter Kit (Roche). For MYC ChIP-Seq, indexed libraries were prepared using Nugen Ovation Ultralow system (v2, Nugen protocol M01379v3).

treatment_protocol: Cell lines were cultured in the presence of 1000nM JQ1, or DMSO vehicle control. AT-3 were additionally grown in the presence or absence of recombinant mouse interferon-gamma (1ng/mL)

value: AT-3 mammary tumor cell line

value: DMSO vehicle

tag: culture media

value: DMEM-based media (supplemented with 10% FCS, 100U/mL penicillin, 100mg/mL streptomycin)


title: 48h-2


title: 20-h3k27ac-Combo ChIP-Seq

description: 20-h3k27ac-Combo ChIP-Seq AT-3 mammary tumor cell line

value: 1000nM JQ1+ 1ng/mL IFN-γ

value: anti-H3k27Ac (ab4729, Abcam)


title: RS4;11

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

data_processing:
Pipeline Casava version 1.8.2 was run to produce the reads.
Sequences were mapped with tophat 2.0.4 using the hg19 genome built with refSeq hg19 annotation file (-G).
Quantification of the refSeq genes was done using the alignment files and htseq-count [http://www-huber.embl.de/users/anders/HTSeq/doc/count.html] (htseq-count -t exon -m intersection-strict -i gene_id -s no -).
DESeq was used to normalize the data and detect differentially expressed genes for each of the sample types.
In addition, Cuffdiff 2 was run with the above tophat alignment files and the refSeq hg19 annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq.txt is a tab delimited file containing htseq gene quantification counts, DESeq normalized quantification counts and DESeq output containing mean expression,  fold changes and p value.
Supplementary_files_format_and_content: Cuffdiff2_gene_exp.diff.txt is one of the outputs of Cuffdiff2, it  is a tab delimited file  containing the results of differential expression testing between the samples, including  FPKM counts , fold change and p values.

source_name: cell line RS4;11

growth_protocol: Regular RPMI medium with 10% fetal bovine serum

extract_protocol:
Total RNA and was isolated using TRI Reagent®, according to manufacturer instructions.
For each RNA sample, we prepared Illumina mRNA-seq libraries using the TruSeq RNA kit (version 1, rev A), using 1 μg of total RNA

treatment_protocol: Grown to sub confluency

tag: cell attribute

value: Precursor ALL containing the t(4;11) abnormality


title: SEM

source_name: cell line SEM

value: SEM


title: control RNASeq rep1

city: Shanghai

first: Ni

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

data_processing:
Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
Use  Bowtie2  to map clean reads to reference gene and use  BWA to reference genome.
RSEM  was used to computed maximum likelihood abundance estimates. FPKM  method is used in calculated expression level.
Use NOISeq to screen differentially expressed genes between two groups.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

source_name: control RNASeq rep1

growth_protocol: RPMI1640 supplied with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd. Transcriptome reads from RNA-Seq experiments were mapped to the reference genome (hg19) by using BWA/Bowtie tool. Genes expression level is quantified by a software package called RSEM.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment

value: prostate; derived from metastatic site:bone

tag: sirna transfection

value: PC-3 control


title: 19-h3k27ac-IFNy ChIP-Seq

description: 19-h3k27ac-IFNy ChIP-Seq AT-3 mammary tumor cell line

value: 1ng/mL IFN-γ


title: 15-STAT-1-IFNy ChIP-Seq

description: 15-STAT-1-IFNy ChIP-Seq AT-3 mammary tumor cell line

value: anti-STAT1α (sc-345, Santa Cruz Biotechnology)


title: 17-h3k27ac-UT ChIP-Seq

description: 17-h3k27ac-UT ChIP-Seq AT-3 mammary tumor cell line


title: 16-STAT-1-Combo ChIP-Seq

description: 16-STAT-1-Combo ChIP-Seq AT-3 mammary tumor cell line


title: 13-STAT-1-UT ChIP-Seq

description: 13-STAT-1-UT ChIP-Seq AT-3 mammary tumor cell line


title: 14-STAT-1-JQ1 ChIP-Seq

description: 14-STAT-1-JQ1 ChIP-Seq AT-3 mammary tumor cell line


title: siWHSC1 RNASeq rep1

source_name: siWHSC1 RNASeq rep1

value: PC-3 siWHSC1-1


title: GFP-ESCO2-ΔA (75-110)

description: single aphidicolin arrest


title: 12-IRF1-Combo ChIP-Seq

description: 12-IRF1-Combo ChIP-Seq AT-3 mammary tumor cell line

value: anti-IRF1 (sc-497, Santa Cruz Biotechnology, Inc)


title: NALM6

source_name: cell line NALM6

value: Precursor ALL lacking the t(4;11) abnormality


title: 11-IRF1-IFNy ChIP-Seq

description: 11-IRF1-IFNy ChIP-Seq AT-3 mammary tumor cell line


title: siWHSC1 RNASeq rep2

source_name: siWHSC1 RNASeq rep2

value: PC-3 siWHSC1-2


title: GFP-ESCO2-PIP Q374A, I376A, I377A

description: single aphidicolin arrest

value: GFP-trap beads (Chromotek, gta-200)


title: 10-IRF1-JQ1 ChIP-Seq

description: 10-IRF1-JQ1 ChIP-Seq AT-3 mammary tumor cell line


title: control RNASeq rep2

source_name: control RNASeq rep2


title: 8-BRD4-Combo ChIP-Seq

description: 8-BRD4-Combo ChIP-Seq AT-3 mammary tumor cell line

value: anti-Brd4 (ab128874, Abcam)


title: 7-BRD4-IFNy ChIP-Seq

description: 7-BRD4-IFNy ChIP-Seq AT-3 mammary tumor cell line

value: AT-3 mammary tumor cell line


title: 5-BRD4-UT ChIP-Seq

description: 5-BRD4-UT ChIP-Seq AT-3 mammary tumor cell line

value: DMSO vehicle


title: 6-BRD4-JQ1 ChIP-Seq

description: 6-BRD4-JQ1 ChIP-Seq AT-3 mammary tumor cell line

value: DMEM-based media (supplemented with 10% FCS, 100U/mL penicillin, 100mg/mL streptomycin)


title: 9-IRF1-UT ChIP-Seq

description: 9-IRF1-UT ChIP-Seq AT-3 mammary tumor cell line


title: 18-h3k27ac-JQ1 ChIP-Seq

description: 18-h3k27ac-JQ1 ChIP-Seq AT-3 mammary tumor cell line


title: 4-Pol2-Combo ChIP-Seq

description: 4-Pol2-Combo ChIP-Seq AT-3 mammary tumor cell line

value: 1000nM JQ1+ 1ng/mL IFN-γ

value: anti-RNA polymerase II (CTD4H8, Millipore)


title: 3-Pol2-IFNy ChIP-Seq

description: 3-Pol2-IFNy ChIP-Seq AT-3 mammary tumor cell line


title: 2-Pol2-JQ1 ChIP-Seq

description: 2-Pol2-JQ1 ChIP-Seq AT-3 mammary tumor cell line


title: MPV_HEPIV10qc04212016

city: Worcester

first: Shweta

last: Kukreja

address: Aaron Lazare Medical Research Building (LRB) 364 Plantation Street, LRB 9th Floor

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

description: rRNA depleted RNA used to prepare strand specific library

data_processing:
Quality-controlled reads were aligned to the reference genome (Mus musculus/mm10) with Bowtie2 and differential expression was calculated using DESeq2. For multiple comparison adjustments, we used Holm-Bonferroni correction as a more conservative approach.
Genome_build: mM10
Supplementary_files_format_and_content: Excel sheet with normalized gene count

source_name: Hepatocytes from 8 week-old male F1 from NIC fathers

growth_protocol: Eight week-old male F1 animals from control (TA) and nicotine-exposed fathers were anaesthetized using ketamine (100 mg/kg BW) and xylazine (10 mg/kg BW). The abdominal cavity was opened with a transverse incision below the rib cage. The portal vein was dissected with blunt forceps and a 26 G catheter needle was inserted. After cutting the vena cava inferior cranial of the liver, the organ was perfused firstly with 1X HBBS + 200 mM EDTA (10 ml at 7 ml/min) and secondly with 50 ml DMEM containing collagenase type I (0.4 mg/ml) at 7 ml/min. The liver was then removed from the abdominal cavity, put in a petri dish containing culture medium (DMEM, 20% FBS, 1X ITS, 1X Penicillin/Streptomycin, 0.1 mM Dexamethasone, Sigma-Aldrich), and gently dissected to allow release of hepatocytes and supporting cells from connective tissue.After filtration through a 70 mm nylon cell strainer, cells were washed twice with PBS 1X and once with culture media (centrifugation at 500 rpm for 5 min), and plated on a 0.1% gelatin-coated well. Hepatocytes were allowed to adhere to the bottom of the well for three hours. Nonadherent cells were then removed, and fresh culture medium was then added.

extract_protocol:
Total RNA was extracted from Hepatocytes using Trizol method.
RNA from brain and liver was isolated using standard TriZol protocols, followed by rRNA depletion (RiboZero kit, Illumina, Inc.). After first- and second-strand synthesis, adapters were ligated to fragments and amplified using multiplexed PCR primers. Libraries were sequenced on a NextSeq 500 platform from Illumina, Inc.

treatment_protocol: Cells were incubated in culture medium with/without Dexamethasone and DMSO, and harvested at different time points.

tag: gender

value: male

value: Hepatocytes

tag: culture conditions

value: DMSO plus Dexamethasone

tag: culture time

value: 21 hours


title: MPV_HEPIV30qc03122016


title: 1-Pol2-UT ChIP-Seq

description: 1-Pol2-UT ChIP-Seq AT-3 mammary tumor cell line

tag: cell line

tag: chip antibody


title: MPV_HEPIV20qc03122016


title: MPV_HEPIV20qc04212016

source_name: Hepatocytes from 8 week-old male F1 from TA fathers


title: MPV_HEPIV05qc04212016


title: MPV_HEPIV10qc03122016


title: MPV_HEPIV15qc03122016


title: MPV_HEPIV25qc03122016


title: MPV_HEPIV5qc03122016


title: MPV_HEPIV09qc04212016


title: MPV_HEPIV19qc03122016


title: MPV_HEPIV14qc04212016


title: MPV_HEPIV13qc04212016

value: 3 hours


title: MPV_HEPIV24qc03122016


title: MPV_HEPIV28qc03122016


title: MPV_HEPIV08qc04212016


title: MPV_HEPIV14qc03122016


title: MPV_HEPIV19qc04212016


title: MPV_HEPIV18qc03122016


title: MPV_HEPIV8qc03122016


title: MPV_HEPIV04qc04212016


title: MPV_HEPIV4qc03122016


title: MPV_HEPIV03qc04212016


title: MPV_HEPIV23qc03122016


title: MPV_HEPIV13qc03122016


title: MPV_HEPIV29qc03122016


title: MPV_HEPIV27qc03122016

value: 1 hour


title: MPV_HEPIV3qc03122016


title: MPV_HEPIV7qc03122016


title: MPV_HEPIV07qc04212016


title: MPV_HEPIV22qc03122016


title: MPV_HEPIV02qc04212016


title: MPV_HEPIV9qc03122016


title: MPV_HEPIV15qc04212016


title: MPV_HEPIV17qc03122016


title: MPV_HEPIV12qc04212016


title: MPV_HEPIV17qc04212016


title: MPV_HEPIV18qc04212016


title: MPV_HEPIV12qc03122016


title: MPV_HEPIV16qc04212016

value: 0 hours


title: MPV_HEPIV21qc03122016


title: MPV_HEPIV11qc03122016


title: MPV_HEPIV01qc04212016


title: MPV_HEPIV1qc03122016


title: MPV_HEPIV06qc04212016


title: MPV_HEPIV16qc03122016


title: MPV_HEPIV11qc04212016


title: MPV_HEPIV26qc03122016


title: MPV_HEPIV6qc03122016


title: MPV_HEPIV2qc03122016


title: MPV_HEPIV07QC07072016

value: 2 hours


title: MPV_HEPIV13QC07072016


title: MPV_HEPIV19QC07072016


title: MPV_HEPIV11QC08152016

value: DMSO minus Dexamethasone


title: MPV_HEPIV26QC08152016


title: MPV_HEPIV01QC07072016


title: MPV_HEPIV01QC08152016


title: 24h-3

value: astrocytes

value: Borrellia burgdorferi infected


title: MPV_HEPIV06QC08152016


title: MPV_HEPIV21QC08152016


title: H3K4me3 in Lgr5-Tspan8hi rep2

first: Casey

last: Ah-Cann

address: 1G Royal Parade, Parkville

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Rsubread package (version 1.20.3, Liao et al. Bioinformatics, 2014) was used for read mapping and summarisation.
Sequenced reads were mapped using the align function with default parameters.
Gene-level summarisation was carried out using the featureCounts and in-built mm10 annotation.
Counts for H3K27me3 were summarised across the genebody.
Counts for H3K4me3 were summarised over the promoter region of genes.
Genome_build: mm10
Supplementary_files_format_and_content: Text files containing Entrez gene identifiers and counts were extracted from the output generated by Rsubread.

source_name: FACS-sorted cells from mouse mammary gland

growth_protocol: Basal cells defined by Lgr5 and Tspan8 expression were directly isolated from the mammary glands of females.

extract_protocol:
Cells were lysed and the chromatin was sheared to a size range of 200 to 400 bp using Covaris M220 sonicator. Sheared chromatin was diluted and incubated at 4°C overnight with antibodies against Histone H3 trimethyl Lys4 (K4, Millipore #07-473), Histone H3 trimethyl Lys27.
ChIP samples were prepared and indexed for Illumina sequencing using the TruSeq DNA sample Prep Kit.

treatment_protocol: No treatment.

tag: sample

tag: subpopulation

value: Mammary gland

tag: antibody vendor/catalog

value: Millipore #07-473

tag: genetic background


title: H3K4me3 in Lgr5+Tspan8- rep2

tag: tissue


title: H3K4me3 in Lgr5-Tspan8- rep2


title: H3K4me3 in Lgr5-Tspan8- rep1


title: H3K4me3 in Lgr5-Tspan8hi rep1


title: H3K4me3 in Lgr5+Tspan8hi rep2


title: H3K4me3 in Lgr5+Tspan8hi rep1


title: H3K27me3 in Lgr5-Tspan8- rep1

value: Millipore #07-449


title: H3K27me3 in Lgr5-Tspan8- rep2


title: H3K27me3 in Lgr5-Tspan8hi rep1


title: H3K27me3 in Lgr5+Tspan8- rep2


title: H3K27me3 in Lgr5+Tspan8hi rep1


title: H3K27me3 in Lgr5+Tspan8hi rep2


title: H3K27me3 in Lgr5-Tspan8hi rep2


title: MPV_HEPIV16QC08152016

tag: strain


title: Input control in Lgr5-Tspan8hi rep2

value: none (input)


title: Input control in Lgr5-Tspan8- rep2


title: Input control in Lgr5-Tspan8- rep1


title: Input control in Lgr5+Tspan8- rep1


title: Input control in Lgr5-Tspan8hi rep1


title: Input control in Lgr5+Tspan8hi rep1


title: H3K4me3 in Lgr5+Tspan8- rep1


title: non-neutralizer controller 3

city: Cambridge

first: Xu

middle: G

last: Yu

state: Massachusetts

address: 400 Technology sqr

institute: Ragon Institute of MGH, MIT and Harvard

description:
NN3
raw reads indexing length: 8

data_processing:
FASTQ files were obtained by Illumina demultiplexing pipeline. STAR and RSEM were used to align to HG38 and to calculate the raw counts for genes, respectively.
Genome_build: HG38
Supplementary_files_format_and_content: raw counts

source_name: dendritic cell

extract_protocol:
Total RNA was extracted using a commercial kit recommended for low numbers of cells (mirVanaTM Isolation Kit; Life TechnologiesTM)
According to Trombetta et al CPMB 2014
Whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2.

tag: phenotype

value: non-neutralizer controllers


title: non-neutralizer controller 2

description:
NN2
raw reads indexing length: 8


title: non-neutralizer controller 1

description:
NN1
raw reads indexing length: 8


title: Pool3_Index5_ACAGTG_L007_R1_001

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
bcl2fastq v1.8.4 used for Basecalling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence ends and filtered by sequence size (<15) using PRINSEQ v0.20.3
Reads were mapped with the aligner segemehl with the -H 1 parameter enabled to the Nothobranchius furzeri genome published by Reichwald et al Cell 2015
Reads were counted using rnacounter with parameters -s -m raw
Genome_build: nfurzeri_genebuild_v1
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

organism: Nothobranchius furzeri

source_name: Embryo

extract_protocol:
The organs of the fishes were dissected and transferred into 2 ml tubes with 1 ml cooled QIAzol (Qiagen, Hilden, Germany) and one 5 mm stainless steel bead (Qiagen) was added. Homogenization was performed using a TissueLyzer II (Qiagen) at 30 Hz for 3x 1 min. After incubation for 5 min at room temperature 200 µl chloroform was added. The tube was shaken for 15 s and incubated for 3 min at room temperature. Phase separation was achieved by centrifugation at 12,000x g for 20 min at 4°C. The aqueous phase was transferred into a fresh cup and 10 µg of Glycogen (Invitrogen, Darmstadt, Germany), 0.16x volume NaAc (2 M; pH 4.0) and 1.1x volume isopropanol were added, mixed thoroughly and incubated for 10 min at room temperature. The RNA was precipitated by a centrifugation step with 12,000 x g at 4°C for 20 min. The supernatant was removed and the pellet was washed with 80% Ethanol twice and air dried for 10 min. The RNA was resuspended in 20 µl DEPC-treated water by pipetting up and down, followed by incubation at 65°C for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80°C until use.
Sequencing procedure was done using Illumina methodology [Bentley et al, 2008]. Around 1 µg of total RNA was used for library preparation (Illumina, TruSeq™ small RNA Sample Prep Kit) using the manufacturer’s description.

value: Embryo

tag: age

value: two weeks postfertilization plus diapause


title: neutralizer controller 4

description:
NT4
raw reads indexing length: 8

value: neutralizer controllers