title: M3_s_7_sequence_aligned.fastq

source_name: Renal carcinoma tissue

value: Metastatic


title: N4_2_s_3_sequence_aligned.fastq

status: Public on Jul 31 2015

type: SRA

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

library_source: transcriptomic

data_processing:
Basecalling was done using Illumina CASAVA v1.4
Sequences were adaptor trimmed and aligned to hg18 genome using Novoalign V2.0.
Known piRNA sequences were downloaded from a publically available piRNA database (RNAdb: http://research.imb.uq.edu.au/rnadb/). The hg18 genome loci that matched perfectly to the piRNA sequences were identified and piRNA expression levels were counted using R scripts.
Genome_build: hg18
Supplementary_files_format_and_content: text format containing expression counts

molecule: total RNA

organism: Homo sapiens

source_name: Nomral renal tissue

extract_protocol:
Total RNA was isolated using the Recover All Total Nucleic Acid Isolation Kit (Ambion, Austin, TX, USA), following the manufacturers' protocols.
Libraries were prepared according to Illumina's instructions

tag: Stage

value: Normal


title: Wilt stress (WS)

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

country: India

institute: Delhi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Images obtained from Illumina GA IIx were converted into text files using genome analyzer pipeline software provided with the genome analyser. The UEA small RNA workbench v2.4 was then used for further analysis. Briefly, after trimming of adapter sequences, tags of length ranging from 16-30 nt were used to remove all non-small RNA sequences like low complexity sequences (simple sequence repeats) and degradation species (fragments of tRNA, rRNA, snRNA, snoRNA). The putative small RNA reads thus obtained were screened for the presence of conserved miRNAs based on their perfect homology with miRBase version 18. The remaining dataset was mapped onto the chickpea genome (from NCBI Genome: PRJNA175619), ESTs database (from NCBI) and transcriptome dataset (from chickpea transcriptome database, CTDB). The flanking sequences of varying length on both sides of the mapping position were extracted and processed for prediction of secondary hairpin structure. Secondary structures fulfilling the miRNA hairpin structure criteria were listed as conserved (already reported in miRBase v 20) and chickpea novel miRNAs.
Genome_build: ASM33114v1
Supplementary_files_format_and_content: abundance measurements

organism: Cicer arietinum

source_name: Wilt stress (WS)

growth_protocol: Plants of ICC4958 cultivar were grown on a 16 h day/8 h night photoperiod cycle at 25±2ºC growth conditions in pots.

extract_protocol:
Tissues obtained from each stress were pooled and enriched low molecular weight (LMW) RNA was isolated using GITC-LiCl method (Chomczynski and Sacchi, 1987) with some modifications. Tissue was homogenized in liquid nitrogen and total RNA was extracted using GITC buffer and phenol-chloroform purification steps followed by ethanol precipitation. Total RNA was re-precipitated with lithium chloride to extract low molecular weight RNA.
Small RNA libraries were prepared utilizing Illumina small RNA sample preparation kit v1 according to manufacturer’s instructions. Briefly, equal amount of enriched-LMW RNA (50 μg) was size fractionated on 15% TBE-urea gel and small RNA fraction (18-40 nt) was excised and purified. RNA adapters were ligated on both ends using T4 RNA ligase followed by cDNA preparation utilizing Superscript II (Invitrogen, USA). The prepared cDNA was PCR amplified and the amplicon of approximately 100 bp was excised from a 6% TBE gel. The quality and quantity of prepared libraries was evaluated utilizing DNA 1000 kit on a Bioanalyzer (Agilent, USA).

treatment_protocol: Fourteen day old seedlings were subjected to biotic and abiotic stress separately. For wilt stress two-week-old plants grown in hydroponic condition were subjected to toxin isolated from fungus Fusarium oxysporum f.sp. ciceris for one day. For salt stress, roots of two-week-old seedlings were immersed in 150 mM NaCl solution for 12 h. Untreated seedlings were taken as control. Whole seedlings were harvested, snap-frozen in liquid nitrogen and stored at -80°C.

tag: cultivar

tag: tissue

value: 14-day old whole seedling


title: N17_2_s_6_aligned_short_fullLength.fastq


title: M4_novoaligned_recreated_old.fastq


title: Control (C)

source_name: Control (C)


title: TP_Case-1_miRNA-seq

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

country: China

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sscrofa10.2.72 whole genome using bowtie v0.12.5 and  mirdeep2_0_0_2
All of the clean reads were initially searched against miRBase20.0 to identify known miRNAs and miRNA hairpins;unmappable reads subsequently were annotated and classified by reference to non-coding RNAs in the NONCODE database (version3.0), and Rfam (version11.0) database
We provided the known mature miRNA for pig, human, mouse, cow, sheep (326,257,1908,783,153, respectively) from miRBase 20.0 for use in software mirdeep2_0_0_2 to predict the pig novel  miRNA.
Transcripts per million (TPM) was calculated in the edgeR package using a protocol from Li et al., Bioinformatics, 2010. This is a two-step procedure of TPM normalization between compared libraries. First, the normalization factors were calculated by edgeR for each library. Second, the normalized read counts were calculated by the following formula: normalized read counts = mapped read count/Total reads × 106.
Genome_build: Sscrofa10.2.72
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample …

organism: Sus scrofa

extract_protocol:
Hearts were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Tibetan pig

value: heart

tag: age

value: 6 months

tag: Sex

value: male


title: L12_s_7_aligned_short_fullLength.fastq

value: Localized


title: Salt stress (SS)

source_name: Salt stress (SS)


title: E6_s_4_sequence_aligned.fastq

value: Locally extensive


title: YP_Control-1_miRNA-seq

value: Yorkshire pig


title: E2_s_1_sequence_aligned.fastq


title: L89-2_s_5_sequence_aligned.fastq


title: M2s_7_sequence_aligned.fastq


title: TP_Case-2_miRNA-seq


title: DM2 Sample_frontalcortex_polyASeq_1

status: Public on Jul 30 2015

city: Gainesville

first: Maurice

last: Swanson

state: Florida

address: 2033,Mowry Road

department: Molecular genetics and microbiology

institute: University of Florida

description:
processed data file: DM2_polyAseq_human_frontal_cortex_3BRs.bedGraph available in polyASeq.bedGraph.tar
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
PolyA-seq on DM2 human frontal cortex
Human brain autopsy
Oligo(dT) reverse transcribed RNA

data_processing:
For polyA-seq, the raw sequencing reads were mapped to the reference genome (hg19 and mm10) using OLego (Wu et al., 2014) and processed as previously described (Derti et al., 2012; Batra et al., 2014) with modifications.  Mapping used a 13 nt seed sequence and allowed a max of 2 mismatches while specifying antisense orientation.  The potential polyA sites were recorded as the 3’end of the reverse complement read.  BedGraph files were generated and three biological replicates were pooled.  Internal priming sites representing mis-aligning of oligo(dT) were removed by filtration step that analyzed nucleotide sequence downstream of potential polyA sites.  After filtration, polyA sites were filtered by robustness and number of reads (≤ 10 reads), nearby reads were clustered (within ≤ 25 nt), and polyA sites were assigned to genes, including extended 3’ UTRs (1 kb).  The usage of each site was then quantified and the relative usage of different sites within each gene was analyzed by pairing of sites.  Differential usage between groups was identified by statistical analysis (Fisher’s exact test followed by Benjamini correction) and significant changes were reported (FDR ≤ 0.05, dI ≥ I0.15I).
genome build: hg19
processed data files format and content: PolyA-seq data are represented in bedgraph file format representing computationally combined samples per group after filtration and data processing (available on series record).

source_name: PolyA-seq on brain tissue

extract_protocol: For polyA-seq, total RNA (4 μg) was extracted using Trizol reagent and used as starting template for library preparation.

tag: disease status

value: Brain

tag: tissue compartment

value: frontal cortex


title: DM2 Sample_frontalcortex_polyASeq_2


title: M22_s_4_aligned_short_fullLength.fastq


title: M16_s_3_aligned_short_fullLength.fastq


title: L91-2_s_6_sequence_aligned.fastq


title: DM1 Sample_frontalcortex_polyASeq_1

description:
processed data file: DM1_polyAseq_human_frontal_cortex_3BRs.bedGraph available in polyASeq.bedGraph.tar
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
PolyA-seq on DM1 human frontal cortex
Human brain autopsy
Oligo(dT) reverse transcribed RNA


title: Control Sample_frontalcortex_polyASeq_3

description:
processed data file: Control_polyAseq_human_frontal_cortex_3BRs.bedGraph available in polyASeq.bedGraph.tar
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
PolyA-seq on control human frontal cortex
Human brain autopsy
Oligo(dT) reverse transcribed RNA

value: control


title: Control Sample_frontalcortex_polyASeq_2


title: Control Sample_frontalcortex_polyASeq_1


title: DM2 Sample_hippocampus_polyASeq_3

description:
processed data file: DM2_polyAseq_human_hippocampus_3BRs.bedGraph available in polyASeq.bedGraph.tar
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
PolyA-seq on DM2 human hippocampus
Human brain autopsy
Oligo(dT) reverse transcribed RNA

value: hippocampus


title: DM2 Sample_hippocampus_polyASeq_2


title: L7_novoaligned_recreated_old.fastq


title: DM1 Sample_hippocampus_polyASeq_3

description:
processed data file: DM1_polyAseq_human_hippocampus_3BRs.bedGraph available in polyASeq.bedGraph.tar
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
PolyA-seq on DM1 human hippocampus
Human brain autopsy
Oligo(dT) reverse transcribed RNA


title: L13_s_6_sequence_aligned_clean.fastq


title: N18_s_7_sequence_aligned.fastq


title: L31_s_8_aligned_short_fullLength.fastq


title: E5_s_3_sequence_aligned.fastq


title: DM2 Sample_hippocampus_polyASeq_1


title: E3_s_2_aligned_short_fullLength.fastq


title: DM2 Sample_frontalcortex_polyASeq_3


title: DM1 Sample_frontalcortex_polyASeq_3


title: DM1 Sample_frontalcortex_polyASeq_2


title: Control Sample_hippocampus_polyASeq_3

description:
processed data file: Control_polyAseq_human_hippocampus_3BRs.bedGraph available in polyASeq.bedGraph.tar
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
PolyA-seq on control human hippocampus
Human brain autopsy
Oligo(dT) reverse transcribed RNA


title: E1_s_1_aligned_short_fullLength.fastq


title: Control Sample_hippocampus_polyASeq_2


title: Control Sample_frontalcortex_HITS_CLIP_2

description:
more processed data files available on series record: dCLIP.frontalcortex.bedgraph.tar, Control_3BRs_MBNL2_CLIP_FCx_hg19c_wiggle.bedgraph.gz
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
HITS-CLIP of MBNL2 from control human frontal cortex
Human brain autopsy
Immunoprecipitated RNA

data_processing:
For HITS-CLIP, Illumina FASTQ sequencing files were groomed to Sanger format, PCR duplicate reads were collapsed, sequences were trimmed (5 nt from the 5’end and 3 nt from the 3’ end), 3’-adaptors were clipped, and the resulting files were combined with quality scores and converted from BAM to SAM format.  The processed sequencing files were mapped to the human genome ( hg19) using BWA  and reads mapped to the same chromosomal location were collapsed. For visualization in the UCSC Genome Browser, bedgraph files were generated with conversion to units of reads per kilobase per million (RPKM).  Bedgraph files were also generated from BED files representing three biological replicates per group (control, DM1, DM2). BedGraph files for individual samples are available on the sample record. Bedgraph files with data for the pooled biological replicates can be found on the series record. Significant peaks (>3 overlapping CLIP tags) were ranked by peak height and intervals were annotated to determine the binding distribution.
Differential CLIP was used to further process the MBNL2 CLIP files and analysis was performed as previously described (Wang et al., 2014) with modifications.  After MA plot normalization and processing, the following code and modified parameters were used to define differential binding: perl /path/to/dCLIP1.6/bin/dCLIP.pl -f1 dCLIP1.5/path/RBP_disease.sam -f2 dCLIP1.5/path/RBP_control.sam dCLIP1.5/path/output -mut "T2C, del" -filter 20. (-f1, SAM file for disease; -f2, SAM file for control; -m1, minimum number of reads in a cluster for disease (5 reads); -m2, minimum number of reads in a cluster for control (5 reads); -mut, CIMS designated as T>C substitution or deletion ("T2C, del"); -filter, minimum sum of reads per cluster from both conditions (20 reads). Output files were generated including summary.bed files with coordinates of all identified clusters; .bedgraph files for genome browser visualization of normalized CLIP clusters, and .txt files containing coordinates, significance, and differential values of all identified clusters. To generate annotated .txt files, the .txt files were intersected using the Bedtools software tool -intersectBed with hg19 Refseq bed file (from the UCSC Genome Browser).  The dCLIP output files are available on the series record. Annotated files were filtered by threshold differential value and events with greater than 0.95 probability to identify significant differential binding events
genome build: hg19
processed data files format and content: MBNL2 HITS-CLIP data are represented in bedgraph file format and include each individual biological replicate (on sample record) and computationally combined samples per group (3BRs) (on series record). The dCLIP analysis produced bedgraph files representing normalized clusters of MBNL2 CLIP tags per group (control, DM1, DM2) divided into positive and negative DNA strands for visualization (available on series record).

source_name: MBNL2 CLIP Brain - Frontal Cortex

extract_protocol: For HITS-CLIP, autopsy-derived frozen brain tissues from control, disease control (ALS), DM1 and DM2 were pulverized in liquid nitrogen, UV crosslinked and fragmented using RNase A. Lysates were denatured, incubated on ice for 10 min, followed by addition of anti-MBNL2 and immunoprecipitation at 4°C for 2 hr.  MBNL2-RNA complexes were size selected, proteinase K treated, and the RNA was purified using RNA phenol chloroform extraction. The MBNL2 antibodies were obtained from Santa Cruz Biotechnology (catalog number SC 136167 (3B4); lot number E3112).


title: DM1 Sample_hippocampus_polyASeq_2


title: DM1 Sample_hippocampus_polyASeq_1


title: Control Sample_hippocampus_polyASeq_1

data_processing:
For polyA-seq, the raw sequencing reads were mapped to the reference genome (hg19 and mm10) using OLego (Wu et al., 2014) and processed as previously described (Derti et al., 2012; Batra et al., 2014) with modifications.  Mapping used a 13 nt seed sequence and allowed a max of 2 mismatches while specifying antisense orientation.  The potential polyA sites were recorded as the 3’end of the reverse complement read.  BedGraph files were generated and three biological replicates were pooled (file is available on the series record).  Internal priming sites representing mis-aligning of oligo(dT) were removed by filtration step that analyzed nucleotide sequence downstream of potential polyA sites.  After filtration, polyA sites were filtered by robustness and number of reads (≤ 10 reads), nearby reads were clustered (within ≤ 25 nt), and polyA sites were assigned to genes, including extended 3’ UTRs (1 kb).  The usage of each site was then quantified and the relative usage of different sites within each gene was analyzed by pairing of sites.  Differential usage between groups was identified by statistical analysis (Fisher’s exact test followed by Benjamini correction) and significant changes were reported (FDR ≤ 0.05, dI ≥ I0.15I).
genome build: hg19
processed data files format and content: PolyA-seq data are represented in bedgraph file format representing computationally combined samples per group after filtration and data processing (available on series record).


title: E4_s_8_sequence_aligned.fastq


title: DM1 Sample_frontalcortex_HITS_CLIP_3

description:
more processed data files available on series record: dCLIP.frontalcortex.bedgraph.tar, DM1_3BRs_MBNL2_CLIP_FCx_hg19c_wiggle.bedgraph.gz
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
HITS-CLIP of MBNL2 from DM1 human frontal cortex
Human brain autopsy
Immunoprecipitated RNA


title: DM2 Sample_hippocampus_HITS_CLIP_2

description:
more processed data files available on series record: dCLIP.hippocampus.bedgraph.tar, DM2_MBNL2_3BRs_hg19c_hip_wiggle.bedgraph.gz
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
HITS-CLIP of MBNL2 from DM2 human hippocampus
Human brain autopsy
Immunoprecipitated RNA

source_name: MBNL2 CLIP Brain - Hippocampus


title: DM1 Sample_frontalcortex_HITS_CLIP_1


title: Control Sample_hippocampus_HITS_CLIP_3

description:
more processed data files available on series record: dCLIP.hippocampus.bedgraph.tar, Control_MBNL2_3BRs_hg19c_hip_wiggle.bedgraph.gz
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
HITS-CLIP of MBNL2 from control human hippocampus
Human brain autopsy
Immunoprecipitated RNA


title: DM1 Sample_hippocampus_HITS_CLIP_3

description:
more processed data files available on series record: dCLIP.hippocampus.bedgraph.tar, DM1_MBNL2_3BRs_hg19c_hip_wiggle.bedgraph
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
HITS-CLIP of MBNL2 from DM1 human hippocampus
Human brain autopsy
Immunoprecipitated RNA


title: DM2 Sample_hippocampus_HITS_CLIP_1


title: Control Sample_hippocampus_HITS_CLIP_1


title: DM1 Sample_hippocampus_HITS_CLIP_1


title: DM1 Sample_hippocampus_HITS_CLIP_2


title: 24_2

city: St. Louis

first: James

last: Umen

state: MO

address: 975 N. Warson Rd.

institute: Donald Danforth Plant Science Center

data_processing:
Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20).
Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000).
Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no).
One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs.
Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes.
Genome_build: Chlamydomonas reinhardtii version 5.
Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts
Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates

organism: Chlamydomonas reinhardtii

source_name: Synchronized diurnal cullture

growth_protocol: Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C.  The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling.

extract_protocol:
Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set).
Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe.

treatment_protocol: 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation.

tag: strain

tag: replicate time course

value: Replicate 2

tag: protocol

value: dark

tag: time (zeitgeber)


title: Control Sample_frontalcortex_HITS_CLIP_3


title: 18_2


title: DM1 Sample_frontalcortex_HITS_CLIP_2


title: Control Sample_hippocampus_HITS_CLIP_2


title: 23_2


title: 22_2


title: 21_2


title: 20_2


title: 14.5_2


title: 19_2


title: 15_2


title: 17_2


title: DM2 Sample_hippocampus_HITS_CLIP_3


title: 13_2


title: 14_2


title: 16_2


title: 13.5_2


title: ∆ssrA RNA-seq

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
Reads were de-multiplexed and poly-A tails were removed. Sequence reads were then mapped against the S. Typhimurium 4/74 reference genome using Segemehl with accuracy set to 100%. To increase mapping quality, unmapped reads were sequentially truncated by one nucleotide from the end of the read and were mapped again. This process was iterated until a minimal read length of 20 nucleotides or until a read mapped into a single location on the chromosome.
Genome_build: RefSeq Genome Accession: PRJNA56087 ID: 56087. Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74. Richardson EJ et al., "Genome sequences of Salmonella enterica serovar typhimurium, Choleraesuis, Dublin, and Gallinarum strains of well- defined virulence in food-producing animals.", J Bacteriol, 2011 Apr 8;193(12):3162-3.
Supplementary_files_format_and_content: Graph files (*.gr) are provided showing uniquely mapped sequence reads (without normalization). Ready to load into Integrated Genome Browser (IGB). The file consists of two columns showing nucleotide position on the chromosome and number of reads mapped at each location. "Plus" and "Minus" refer to the two strands of the Salmonella chromosome

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

source_name: RNA from bacteria grown in vitro

growth_protocol: Overnight cultures of Salmonella Typhimurium Str.4/74  were Infected into RAW264.7 murine macrophage cells at an MOI of 1:10 using gentamicin protection assay. The macrophages were lysed after a period of 8 hrs and bacterial RNA was isolated using the standard TRIzol method to obtain the Intra-macrophage Salmonella RNA. As a separate experiment, the gene ssrA was deleted from the 4/74 genome. The mutant was then grown in vitro in PCN media until OD600 of 0.3 and then the bacterial RNA was isolated using the TRIzol method.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and Dnase I digested
cDNA libraries were constructed by vertis Biotechnologie AG (Freising) using an in-house protocol. Total RNA (DNase I digested) was fragmented by ultrasound (4 pulses of 30s at 4°C). The to construct dRNA-seq libraries, these RNA samples were subsequently digested with Terminator Exonuclease (TEX). 3′ ends were subjected to poly(A)-tailing using poly(A) polymerase, pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using an oligo(dT) adapter and M-MLV-RNaseH-reverse transcriptase, following PCR amplification of cDNA using high-fidelity DNA polymerase to ∼20–30 ng/μL. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

tag: growth condition

value: SalmonellaGrown in PCN media until OD600 0.3

tag: host cells

value: RAW264.7 murine macrophage

tag: sample digestion

value: in vitro RNA + DNase I digestion

tag: genotype

value: ssrA knock-out


title: 11_2

value: light


title: 12_2


title: 12.5_2


title: Intra-macrophage dRNA-seq Replicate 1

source_name: in vivo bacterial RNA

value: Salmonella grown within macrophage

value: in vivo RNA + DNase I digestion + Terminator Exonuclease

value: wild type


title: Intra-macrophage dRNA-seq Replicate 2


title: Intra-macrophage RNA-seq Replicate 2

value: in vivo RNA + DNase I digestion


title: 10_2


title: Sample 18: control (Samples 5-14)

city: New York

first: Leslie

last: Beh

state: NY

department: Biochemistry & Molecular Biophysics

institute: Columbia University

description:
Covaris-sheared genomic DNA from 15hr-starved cells
Tetrahymena genomic DNA, sheared in a sonicator
Used to normalize chromosome copy number in Samples 5 - 14 (inclusive) to obtain processed data file

library_source: genomic

data_processing:
All raw sequencing reads were quality-trimmed (minimum quality score = 20) and length-filtered (minimum length = 40nt) using Galaxy (Giardine et al. 2005; Blankenberg et al. 2010; Goecks et al. 2010) before mapping with Bowtie2 (Langmead and Salzberg, 2012) to the October 2008 build of the Tetrahymena SB210 reference genome (Eisen et al. 2006) using standard settings. Only complete Tetrahymena chromosomes in the genome assembly were included in downstream analyses.
Only mapped read pairs with corressponding fragment sizes of length 122-172bp were used to generate these files. The midpoint of each mapped read pair represents the position of a nucleosome dyad. Per-basepair coverage of nucleosome dyads was calculated across the Tetrahymena genome for each dataset. Following this, the data was normalized by relative chromosome copy number (as determined by sheared genomic DNA-seq), and the whole genome average coverage value. Normalized values were then smoothed with a Gaussian filter of standard deviation = 15. We refer to the resulting values as normalized nucleosome dyads. The provided Processed Data Files (.txt format) thus represent the normalized, smoothed counts of nucleosome dyads in each basepair of the genome. To allow direct comparisons, we applied this analysis pipeline to all samples, including the MNase-digested genomic DNA.
Genome_build: Tetrahymena October 2008 Build
Supplementary_files_format_and_content: NA

molecule: genomic DNA

organism: Tetrahymena thermophila

source_name: Naked genomic DNA

growth_protocol:
Log-phase/starved in vivo samples: 1000ml of Tetrahymena thermophila wild-type strain SB210 (Tetrahymena stock center) was grown in 1xSPP at 30 oC with shaking at 100 rpm to a log-phase density of ~ 35x104 cells/ml.  To obtain starved samples, the cells were centrifuged at 1100 g for 2 min, resuspended in 1.75 volumes of 10 mM Tris pH 7.5, and incubated at 25 oC without shaking for 15 hr.
in vitro samples (reconstituted chromatin): Genomic DNA for reconstitution experiments was obtained from macronuclei of starved Tetrahymena cells. Macronuclei were isolated from starved Tetrahymena cells, and incubated in lysis buffer at 55 oC for 16 hr. Samples were purified through phenol-chloroform extraction and ethanol precipitation, and subsequently RNase-treated. ~45μg genomic DNA was then sheared to 850 bp – 2 kb using a Covaris LE220 sonicator. This size range is in accordance with previously published in vitro reconstitution experiments (Valouev et al. 2011). Sheared DNA was end-repaired with 20 U DNA polymerase I (NEB), 60 U T4 DNA polymerase (NEB), 0.4mM dNTP, and 200 U T4 polynucleotide kinase (NEB) in a total volume of 400 μl at 20 oC for 40 min. The sample was then purified through phenol-chloroform extraction and ethanol precipitation, and then resuspended in nuclease-free water. To obtain Tetrahymena histone octamers for in vitro reconstitution, macronuclei were first isolated from 1.4 x 109 cells as described earlier. Histones were subsequently acid-extracted, as previously described (Wiley et al. 2000). Briefly, 4.39 ml 0.4 N H2SO4 was added at a ratio of 4.39 ml per 108 macronuclei, and incubated at 4 oC for 3 hr with gentle shaking. The suspension was then cleared by centrifugation at 4000 g for 10 min. Perchloric acid was added to the resulting supernatant, at a final concentration of 5.4 % (w/w), and incubated on ice for 1hr. This treatment solubilized histone H1, greatly reducing contamination of the core histone preparation. Samples were then centrifuged at 4000g for 10min, and the pellet was washed with 0.1% (w/w) HCl in cold acetone, and subsequently with unacidified cold acetone. After air-drying at room temperature for 1 hr, the histone pellet was dissolved in unfolding buffer (7 M guanidinium HCl, 50 mM Tris pH 7.5, 10 mM DTT) and refolded into octamers through dialysis against 4 changes of 1L refolding buffer (2 M NaCl, 20 mM Tris pH 7.5, 1 mM EDTA pH 8, 5 mM β-mercaptoethanol) as previously described (Luger et al. 1999). Subsequently, the sample was cleared by centrifugation at 17,900 g for 5 min, before loading onto a Superdex-200 size exclusion column, equilibriated with refolding buffer. Purified histone octamer fractions were pooled, concentrated using Vivaspin 500 columns (GE Healthcare), and subsequently flash-frozen in 50 % glycerol. Together, the sheared macronuclear genomic DNA and purified histone octamers were used for Tetrahymena chromatin assembly through salt gradient dialysis (Luger et al. 1999). Reconstitution experiments were either performed in a 50ul reaction volume (designated as "invitro 1"), or scaled up 3-fold in a 150ul reaction volume (designated as "invitro 2")
MNase-digested genomic DNA sample: genomic DNA was obtained from log-phase cells (grown in 1xSPP at 30 oC with shaking at 100 rpm to a density of ~ 35x104 cells/ml). Macronuclei were isolated, and incubated in lysis buffer at 55 oC for 16 hr. Genomic DNA was purified through phenol-chloroform extraction and ethanol precipitation, and subsequently RNase-treated.

extract_protocol:
Preparations were performed as described (Jacob et al. 2004), with minor modifications. Log-phase or starved cells were centrifuged at 1000 g for 5 min, and resuspended in 70 ml TMS (10 mM Tris pH 7.5, 10 mM MgCl2, 3 mM CaCl2, 0.25 M sucrose, 1 mM DTT, 0.16 % [v/v] NP40). The culture was lysed in a Waring PBB212 Blender at the “High” setting for 25 sec, as previously described (Gorovsky et al. 1975). Formaldehyde was simultaneously added to a final concentration of 1% (v/v), at the onset of blending. The resulting cell lysates were stirred on ice for 15 min before quenching with 125 mM glycine, and subsequent stirring on ice for an additional 10 min. These fixation and quenching steps were omitted in experiments to prepare native chromatin. Sucrose was then added at 0.816 g per ml lysate, with constant stirring on ice for 10 min. Upon complete dissolution of sucrose, the lysates were cleared by centrifugation at 9000 g for 30 min. The resulting macronuclear pellet was washed in buffer A (15 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 2 mM CaCl2, 0.5 mM spermidine trihydrochloride, 0.15 mM spermine tetrahydrochloride, 1 mM DTT), centrifuged at 1200 g for 2 min, and resuspended in 1ml buffer A. An 830 μl aliquot of macronuclei was pre-incubated at 37 oC for 5 min. From this, 100 μl macronuclei was withdrawn and mixed with 52 μl lysis buffer (300 mM NaCl, 30 mM Tris pH 8, 75 mM EDTA, 1.5 % (w/v) SDS, 1.5 mg/ml Proteinase K) to serve as an undigested control. Subsequently, 2,000 Kunitz units of MNase (NEB) were added to the macronuclei, and incubated at 37oC for 45s, 1 min 15 s, 2 min 30 s, 5 min, 7 min 30s, 10min, and 15 min respectively. At each time point, 100 μl macronuclei was withdrawn and mixed with 52 μl lysis buffer. All samples were incubated at 65 oC overnight to reverse formaldehyde crosslinks and digest proteins. DNA was subsequently purified through phenol-chloroform extraction, then ethanol-precipitated, and resuspended in buffer EB (Qiagen). 1μl of DNA from each sample was run on a 2 % agarose-TAE gel to check the progression of MNase digestion. The sample with ~80 % mononucleosomal and ~20 % dinucleosomal DNA (Supplemental Fig. S3) was deemed “light digest”. This is in accordance with previous recommendations for an adequate level of MNase digestion in nucleosome mapping studies (Zhang and Pugh 2011). Separately, the sample exhibiting almost exclusively mononucleosomal DNA with a significant smear in the subnucleosomal region (Supplemental Fig. S3) was deemed “heavy digest”. Light and heavy-digest samples were run on a 2 % agarose-TAE gel, and the mononucleosome-sized fragment was excised and purified using a QIAquick gel extraction kit (Qiagen). Illumina libraries were prepared from mononucleosomal DNA according to manufacturer’s instructions, and subject to paired-read sequencing.
Reconstituted chromatin was adjusted to 5 mM MgCl2, 5 mM CaCl2, 70 mM KCl, and 10 mM HEPES pH 7.9. For in vitro experiments #1, the chromatin was digested with 22 Kunitz units of MNase (NEB), at 25 oC for 12 min. The digestion reaction was stopped by the addition of 21.6 μl buffer E (33 mM Tris pH 8, 100mM EDTA, 0.67 % (w/v) SDS, 16.7 % (v/v) glycerol) and 8.4 μl 20 mg/ml proteinase K. For in vitro experiments #2, all of the reagent volumes were tripled. The amount of MNase was doubled further, for the heavy digest sample. Samples were incubated at 50 oC at 1 hr. and then loaded on a 2 % agarose-TAE gel. The mononucleosome-sized fragment was gel-purified using a QIAquick gel extraction kit (Qiagen). Illumina libraries were then prepared from mononucleosomal DNA according to manufacturer’s instructions.
12.9 μg macronuclear gDNA was made up to 200 ul with TMS, and then digested with 1.79 Kunitz units of MNase (NEB) for 7 min at 25 oC. The reaction was terminated by adding 112 μl stop buffer (300 mM NaCl, 30 mM Tris pH8, 75 mM EDTA, 1.5 % [w/v] SDS, 1.5 mg/ml Proteinase K), and subsequently purified through phenol-chloroform extraction and ethanol precipitation. MNase-digested gDNA was resuspended in 25 μl buffer EB (Qiagen) and loaded on a 2 % agarose-TAE gel, and the mononucleosome-sized fragment was gel-purified using a QIAquick gel extraction kit (Qiagen).
Standard TruSeq Illumina library construction protocol

tag: nutritional state

tag: formaldehyade fixation

value: No

tag: extent of mnase digestion


title: 9_2


title: 8_2


title: 7_2


title: 11.5_2


title: Sample 17: control (samples 1,2,3,4,15)

description:
Covaris-sheared genomic DNA from log-phase cells
Tetrahymena genomic DNA, sheared in a sonicator
Used in normalize chromosome copy number in samples 1,2,3,4,15 to obtain processed data file


title: Intra-macrophage RNA-seq Replicate 1


title: Sample 15: gDNA_MNaseDigest

description:
MNase-digested genomic DNA
Naked gDNA, digested by MNase and size-selected for mononucleosome-sized DNA fragments

value: Light


title: 4_2


title: 6_2


title: 5_2


title: Sample 14: invitro2_3ugOctamer_heavydig_Rep2

description:
Mononucleosomal DNA
150ul in vitro reconstitution reaction, 4:10 histone:DNA ratio, Replicate B

source_name: in vitro reconstituted chromatin

value: in vitro

value: Heavy


title: 3_2


title: Sample 10: invitro1_5ugOctamer

description:
Mononucleosomal DNA
50ul in vitro reconstitution reaction, 7:10 histone:DNA ratio


title: Sample 12: invitro2_3ugOctamer_lightdig_Rep2

description:
Mononucleosomal DNA
150ul in vitro reconstitution reaction, 4:10 histone:DNA ratio, Replicate A


title: Sample 9: invitro1_3ugOctamer

description:
Mononucleosomal DNA
50ul in vitro reconstitution reaction, 4:10 histone:DNA ratio


title: Sample 11: invitro2_3ugOctamer_lightdig_Rep1


title: 2_2


title: Wild-type Sample_mouse_polyASeq_3

description:
processed data file: WT_3BRs_polyAseq_FCx_a.bedGraph available in polyASeq.bedGraph.tar
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
PolyA-seq on wild-type mouse frontal cortex
Mouse brain
Oligo(dT) reverse transcribed RNA

data_processing:
For polyA-seq, the raw sequencing reads were mapped to the reference genome (hg19 and mm10) using OLego (Wu et al., 2014) and processed as previously described (Derti et al., 2012; Batra et al., 2014) with modifications.  Mapping used a 13 nt seed sequence and allowed a max of 2 mismatches while specifying antisense orientation.  The potential polyA sites were recorded as the 3’end of the reverse complement read.  BedGraph files were generated and three biological replicates were pooled.  Internal priming sites representing mis-aligning of oligo(dT) were removed by filtration step that analyzed nucleotide sequence downstream of potential polyA sites.  After filtration, polyA sites were filtered by robustness and number of reads (≤ 10 reads), nearby reads were clustered (within ≤ 25 nt), and polyA sites were assigned to genes, including extended 3’ UTRs (1 kb).  The usage of each site was then quantified and the relative usage of different sites within each gene was analyzed by pairing of sites.  Differential usage between groups was identified by statistical analysis (Fisher’s exact test followed by Benjamini correction) and significant changes were reported (FDR ≤ 0.05, dI ≥ I0.15I).
genome build: mm10
processed data files format and content: PolyA-seq data are represented in bedgraph file format representing computationally combined samples per group after filtration and data processing (available on series record).

organism: Mus musculus

tag: tissue

value: Brain

value: frontal cortex

value: wildtype


title: Wild-type Sample_mouse_polyASeq_2


title: Sample 13: invitro2_3ugOctamer_heavydig_Rep1


title: Mbnl Nestin-Cre double knockout Sample_mouse_polyASeq_1

description:
processed data file: Mbnl_DKO_3BRs_polyAseq_FCx_b.bedGraph available in polyASeq.bedGraph.tar
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
PolyA-seq on Mbnl double knockout (Mbnl1-/-; Mbnl2c/c; Nestin-Cre+/-) mouse frontal cortex
Mouse brain
Oligo(dT) reverse transcribed RNA


title: Mbnl Nestin-Cre double knockout Sample_mouse_polyASeq_2

value: Mbnl double knockout (Mbnl1-/-; Mbnl2c/c; Nestin-Cre+/-)


title: Mbnl Nestin-Cre double knockout Sample_mouse_polyASeq_3


title: 20_1

value: Replicate 1

value: dark


title: Sample 8: Starve_native_heavydig_Rep2

description:
Mononucleosomal DNA
Biological replicate B

source_name: macronucleus


title: 1_2

value: Replicate 2


title: 23_1


title: Sample 7: Starve_nofix_heavydig_Rep1

description:
Mononucleosomal DNA
Biological replicate A


title: Sample 1: LogPhase_fix_lightdig_Rep1

value: log-phase

value: Yes


title: 19_1


title: Sample 6: Starve_fix_lightdig_Rep2


title: polyA+ RNA from the chromatin fraction-E2, rep 1

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Chromatin_Untreated_PlusStrand.bw, Chromatin_Untreated_MinusStrand.bw

data_processing:
RNA-seq reads were aligned to the human genome (NCBI 37, hg19) using the spliced read aligner TopHat version ver. 2.0.4
The transcriptome for each subcellular fraction and each treatment condition was then assembled by Cufflinks ver. 2.0.2
Any transcripts from the cytoplasmic and nuclear sets that have an exon overlapping protein-coding transcripts annotated in RefSeq or in GENCODE ver. 12 were eliminated
All transcripts with a PhyloCSF score greater than 150 were excluded from our lncRNA catalog
A FPKM threshold of 1 was applied to all lncRNAs for most of the bioinformatics analysis described herein to limit our focus to those transcripts that are reasonably expressed in MCF-7 cells under the experimental conditions used
Genome_build: hg19
Supplementary_files_format_and_content: txt, gtf, bigWig

growth_protocol: MCF-7 cells were kindly provided by Benita Katzenellenbogen (University of Illinois, Urbana-Champaign and maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum.

extract_protocol:
RNA-seq libraries were generated from two biological replicates for each condition.  The total RNA was extracted using the PARIS kit (Ambion).  After purification, 4000 ng of Total RNA was subjected to enrichment of polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen) as described previously (Zhong et al., 2011).
Strand-specific RNA-seq libraries were prepared from the polyA+ RNA according to the “deoxyuridine triphosphate (dUTP)” method as described previously (Zhong et al., 2011). The RNA-seq libraries were sequenced using an Illumina HiSeq 2000 as follows: (1) the polyA+ RNA-seq libraries from E2- or control-treated fractionated RNA were sequenced using paired-end methodology with a length of 100 nt (PE100) (two replicates each) and (2) the polyA+ RNA-seq library from untreated unfractionated RNA was sequenced using single-end methodology with a length of 50 nt (SE100) (one replicate).

treatment_protocol: Prior to all treatments, the cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum.  Cell fractionation - all treatments were performed for 180 min with 100 nM 17β-estradiol. Adherent cells were trypsinized, collected, and subsequently lysed in buffer A. The nuclei were collected by gentle centrifugation at 4°C and the resulting supernatant was collected as the cytoplasmic fraction. The nuclear pellet was washed twice with buffer A, each time accompanied by 10 strokes of douncing, to obtain clean and intact nuclei.  The nuclei were then extracted with the sequential addition of low salt buffer and high salt buffer. The soluble extract was collected as the nuclear fraction.  The remaining pellet was then resuspended in cell disruption buffer (PARIS kit, Ambion; AM1921), digested with DNase I (Roche), and centrifuged to remove any remaining insoluble material.  The resulting supernatant was collected as the chromatin fraction.   For lncRNA knockdown RNA-seq, transient RNAi-mediated knockdown of lncRNAs was performed by transfection of (1) siRNAs targeting selected lncRNAs  and (2) commercially available control siRNA.

tag: cell type

value: Breast adenocarcinoma epithelial cells

tag: treatment

value: Untreated


title: polyA+ RNA from the chromatin fraction-E2, rep 2


title: Sample 4: LogPhase_native_heavydig_Rep2


title: Sample 5: Starve_fix_lightdig_Rep1


title: SA877

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

data_processing:
Sequencing and base calling: Illumina HiSeq 2500, SR 50bp, bcl2fastq version 1.8.3.
Trimming and filtering: position 51st was removed with the FASTX package (v0.0.14), the 5' and 3' ends were quality trimmed with a threshold of 32 over a silding window of 5 bases and a step size of 1 (in house perl scripts), adapter sequences were removed with Trim Galore (version 0.3.7), using TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC<index>ATCTCGTATGCCGTCTTCTGCTTG as the adapter sequence (index changes for each sample) and discarding reads that became shorter than 15 bases, remaining reads were filtered with the FASTX package (v0.0.14), using a quality threshold of 20 over at least 90 percent of the read.
Alignment and counting: miRExpress (v1.0.0). Reads were mapped to the human pre-miRNAs in the miRBase database (release 21), with alignment identity threshold of 93 percect, assignment to a mature miRNA was done with an overlap of at least half the length, allowing a shift in position relative to the pre-miRNA of up to 11 bases, giving raw counts for each mature miRNA.
Differential expression: DESeq (v1.18.0)
Genome_build: miRBase, release 21
Supplementary_files_format_and_content: Tab-delimited, first row is a header line, contains 3 columns, first column is the miRNA name in the format “pre-miRNA,mature-miRNA”, second column is raw counts, third column is normalized counts.

source_name: WM3682 melanoma cell line on Control plate

growth_protocol: WM3682 melanoma cells were routinely  grown in DMEN mediom.

extract_protocol:
Total RNA was extracted using TRIZOL according to manufacturer's instructions
TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer's instructions

treatment_protocol: WM3682 melanoma cells were cultured on DLL coated plates for 5 days.

value: Melanoma

tag: cell line


title: 22_1


title: Wild-type Sample_mouse_polyASeq_1


title: 16_1


title: lane3_barcode6Pig_Rongchang_B_mRNA

city: Chongqing

first: Ling

last: Gan

address: 160#Xue Yuan Road,RongchangCounty

department: 1The Department of Veterinary Medicine

institute: Southwest University

data_processing:
Raw reads were discarded if containing more than 2 unknown (N) bases or if too short (less than 20 nt), with the remaining reads processed by clipping the adaptors and removing low quality bases. FASTX-Tool kit (Version 0.0.13) was used to get clean reads.
clean reads were aligned to the reference genome (http://hgdownload.soe.ucsc.edu/downloads.html#pig) by TopHat(Trapnell,2009). Based on gene annotation, aligned reads with more than one genomic location were discarded to eliminate location ambiguity. Uniquely localized reads were used to calculate read number and RPKM value for each gene
Genome_build: SGSC Sscrofa10.2/susScr3
Supplementary_files_format_and_content: Table containing expressed_gene_reads and expressed_gene_RPKM

source_name: liver

extract_protocol:
Brains and livers from Rongchang pig (Sus Scrofa)  were collected, and immediately frozen in liquid nitrogen, and stored in -80°C until use. The total RNA of brain and liver tissues was extracted using RNAiso plus in accordance with the manufacturers’ instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Rongchang

value: liver


title: Sample 3: LogPhase_nofix_heavydig_Rep1

value: No


title: polyA+ RNA from the chromatin fraction+E2, rep 2

description: Chromatin_E2treated_PlusStrand.bw, Chromatin_E2treated_MinusStrand.bw

value: E2 treated


title: 21_1


title: 24_1


title: polyA+ RNA from the chromatin fraction+E2, rep 1


title: 14.5_1


title: SA878


title: polyA+ RNA from the nuclear fraction-E2, rep 1

description: Nuclear_Untreated_PlusStrand.bw, Nuclear_Untreated_MinusStrand.bw


title: polyA+ RNA from the cytoplasmic fraction+E2, rep 2

description: Cytoplasm_E2treated_PlusStrand.bw, Cytoplasm_E2treated_MinusStrand.bw


title: Sample 2: LogPhase_fix_lightdig_Rep2

value: Light


title: 14_1


title: Control Sample_frontalcortex_HITS_CLIP_1

description:
more processed data files available on series record: dCLIP.frontalcortex.bedgraph.tar, Control_3BRs_MBNL2_CLIP_FCx_hg19c_wiggle.bedgraph.gz
Supplementary tables are available on the series and include content as follows: Table 1) MBNL2 HITS-CLIP from human brain, significant peaks and repeat binding, Table 2) dCLIP, list of differential MBNL2 binding events in DM brain, Table 3) RNA-seq, list of differential splicing events in DM brain, and Table 4) PolyA-seq, list of differential alternative polyadenylation events in human DM and Mbnl DKO brain
HITS-CLIP of MBNL2 from control human frontal cortex
Human brain autopsy
Immunoprecipitated RNA

tag: disease status

value: control

value: Brain

tag: tissue compartment


title: 17_1

tag: strain

tag: replicate time course


title: 13.5_1

tag: protocol

tag: time (zeitgeber)


title: 18_1


title: polyA+ RNA from the nuclear fraction+E2, rep 2

description: Nuclear_E2treated_PlusStrand.bw, Nuclear_E2treated_MinusStrand.bw


title: Ler - sample 3 -short fraction

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

data_processing:
Adapter clipping and poly(A)-filtering.
rRNA filtering using RiboPicker (Schmieder et al., 2012).
TopHat2 (Kim et al., 2013) mapping with reference annotation.
Quantifying gene expression using cufflinks (Trapnell et al., 2010).
Genome_build: TAIR10 + spiked-in controls
Supplementary_files_format_and_content: text files containing gene IDs and fpkm values.

organism: Arabidopsis thaliana

source_name: Ler_seedling_short fraction

extract_protocol:
Total RNA were obtained using Phenol:Chloroform extraction. RNA concentrations were measured with the Picodrop and a mix of all RNAs with a concentration of 1 ng/µl was made.  1 µl of this mix was added to each RNA sample before fractionation. The mRNA fractionation was carried out with the Promega PolyATract® System 1000 and the protocol modified as follows:The GTC, DIL, ß-mercaptoethanol (BME), biotinylated oligod(T), 0.5x SSC and H2O were allowed  to reach room temperature. Forty-one microliter of BME were added per ml of GTC (GTC/BME) and 20.5 µl BME were added per ml of DIL and preheated to 70 °C. The SSC buffer was diluted to a concentration of 0.085x. In a 2 ml tube, 80 µg of total RNA (in a maximum of 40 µl) were mixed with 400 µl GTC/BME, 15 µl biotinylated oligo d(T) (Promega) and 816 µl DIL/BME and heated to 70 °C for 5 min. Afterwards the samples were spun at 13 000 rpm for 10 minutes at room temperature. In the meantime the paramagnetic beads were washed. Afterwards the beads were resuspended in 600 µl 0.5x SSC. The supernatant of the spun samples was added to the washed beads and the biotinylated oligod(T) was allowed to bind the beads by rotation at room temperature for 15 min. In the following step, the beads were captured and the supernatant transferred to a new tube (unbound fraction). The beads were washed three times with rotation for at least 5 min between each wash step. Afterwards, the beads were resuspended in 400 µl of 0.085 x SSC and rotated for 10 min at room temperature. The beads were capture and the eluate transferred to a new tube (short fraction). This step was repeated once (total of 800 µL). The beads were then washed with 400 µl nuclease free water (rotation for 10 min) twice and the eluates transferred to a new tube (800 µl, long fraction). All collected samples where centrifuged for 10 min at 13000 rpm, 4 °C to remove any transferred beads. Then 0.1 vol of Co-precipitant Pink buffer (BioLine) were added and the samples mixed well. Afterwards 30 µg of Co-precipitant pink (BioLine) were added, mixed well, and 1 vol 100 % ethanol was added. The samples were incubated overnight (15 - 16 hours) at -20 °C. In the next step, the samples were centrifuged at 13000 rpm, 4 °C for 30 min. The supernatant was removed, the pellet washed with 500 µl 80 % ethanol, dried, and dissolved in 15 µl DEPC treated water.
Libraries were prepared using the Illumina TruSeq protocol.

tag: line background

value: Ler

tag: genotype/variation

value: wild type

value: seedling


title: 13_1

value: Replicate 1

value: dark


title: lane3_barcode6Pig_Rongchang_A_mRNA

source_name: brain

value: brain


title: polyA+ RNA from the nuclear fraction+E2, rep 1


title: SA876

source_name: WM3682 melanoma cell line on DLL1 coated plate


title: Ler - sample 3 - long fraction

source_name: Ler_seedling_long fraction


title: polyA+ RNA from the nuclear fraction-E2, rep 2


title: 15_1


title: SA875


title: Ler - sample 2 - long fraction


title: 12_1

value: light


title: Ler - sample 4 -short fraction


title: 12.5_1


title: Ler - sample 4 - long fraction


title: 11.5_1


title: si-lncRNA67-2, rep 1

description: Cufflinks_output_genes_fpkm_tracking_for_lnc67KD.txt

tag: transfection

value: Breast adenocarcinoma epithelial cells


title: polyA+ RNA from the cytoplasmic fraction+E2, rep 1


title: polyA+ RNA from the cytoplasmic fraction-E2, rep 1

description: Cytoplasm_Untreated_PlusStrand.bw, Cytoplasm_Untreated_MinusStrand.bw

value: Untreated


title: polyA+ RNA from the cytoplasmic fraction-E2, rep 2


title: Ler - sample 2 -short fraction


title: si-lncRNA67-2, rep 2


title: 10_1


title: paps1 - sample 4 - long fraction

source_name: paps1_seedling_long fraction


title: Ler - sample 1 - long fraction


title: paps1 - sample 3 -short fraction

source_name: paps1_seedling_short fraction


title: 11_1


title: si-lncRNA67-1, rep 2


title: si-lncRNA67-1, rep 1


title: paps1 - sample 4 -short fraction


title: si-lncRNA152-2, rep 1

description: Cufflinks_output_genes_fpkm_tracking_for_lnc152KD.txt


title: 9_1


title: 5_1


title: si-lncRNA152-2, rep 2


title: paps1 - sample 3 - long fraction


title: Ctrl siRNA(67), rep 1

value: Control


title: 4_1


title: Ctrl siRNA(67), rep 2


title: 3_1


title: 8_1


title: Ctrl siRNA(152), rep 2


title: 7_1


title: 1_1


title: 6_1


title: si-lncRNA152-1, rep 2


title: paps1 - sample 2 - long fraction


title: Ler - sample 1 -short fraction


title: polyA+ RNA from total RNA

description: Cufflinks_output_genes_fpkm_tracking_for_Unfractionated_polyA_RNAseq.txt


title: paps1 - sample 2 -short fraction


title: paps1 - sample 1 -short fraction


title: si-lncRNA152-1, rep 1


title: paps1 - sample 1 - long fraction


title: 2_1


title: Ctrl siRNA(152), rep 1


title: MML_P2

status: Public on Jul 29 2015

city: Dunedin

first: Peter

middle: Kenneth

last: Dearden

address: 710 Cumberland St

department: Department of Biochemistry

country: New Zealand

institute: University of Otago

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_MML_P2_GTGAAA

data_processing:
Paired-end reads were mapped to the Ovis aries genome (Oar_v3.1) using CLC Genomics Workbench (CLC Bio). Data were subjected to quantile normalization and a reads-per-kilobase per million mapped reads (RPKM) statistic was generated for each gene annotated. A Baggerly test was used to analyze differences in gene expression between the nutritional programming treatment groups. A false discovery rate (FDR) P value <0.05 and RPKM expression fold change >1.2 were used as cutoffs to determine potentially meaningful differences in gene expression in our dataset.
Genome_build: Oar_v3.1

organism: Ovis aries

source_name: maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during lactation. Pool 2.

extract_protocol:
Total RNA was isolated from mammary tissue samples using Trizol (Invitrogen) and purified using RNeasy mini kit (Qiagen). Genomic DNA contamination was eliminated via on-column digestion with DNase (Qiagen), as per the manufacturer’s protocol. The concentration and quality of RNA was measured using a Nanodrop ND-1000 spectrophotometer (Nanodrop) and integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
TruSeq RNA sample prep kit – V2

treatment_protocol: Romney ewes (G0 dams) were fed a sub-maintenance (Sm[L], P21-50), maintenance (M, P21-50) or ad-libitum (Ad, P21-50) pasture allowance during early gestation (P21-50), and reallocated to either a maintenance (M,P50-140) or ad libitum (Ad[H], P50-140) pasture allowance during mid-to-late gestation (P50-140). The ewe offspring generated were utilised as the experimental animals of the present study, and were therefore from one of six dam nutritional treatment groups: SmM, SmAd, MM, MAd, AdM, and AdAd. All ewe offspring (G1 offspring) were managed under the same New Zealand commercial pastoral farming conditions and received the same level of nutrition (average intakes). Mammary parenchymal tissue (30 - 50 mg) was sampled from 10 ewes per treatment (n=60) via needle biopsy (Bard® Magnum® reusable core biopsy gun and 12G, 10cm core biopsy needles, Bard Biopsy Systems) during late pregnancy (135 ± 2.4 SD days of gestation) and again during lactation (15 ± 1.27 SD days post partum). Tissue samples were immediately frozen in liquid nitrogen, then stored at -80°C until RNA extraction.

tag: physiological status

value: lactation

value: mammary gland


title: LMLP_P3

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_LMLP_P3_CCGTCC

source_name: sub maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 3.

value: late pregnancy


title: MML_P1

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_MML_P1_GTCCGC

source_name: maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during lactation. Pool 1.


title: MMLP_P2

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_MMLP_P2_TTAGGC

source_name: maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 2.


title: MMLP_P3

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_MMLP_P3_ACTTGA

source_name: maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 3.


title: HML_P1

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_HML_P1_CGATGT

source_name: ad libitium maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during lactation. Pool 1.


title: LML_P1

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_LML_P1_CTTGTA

source_name: sub maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during lactation. Pool 1.


title: LMLP_P2

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_LMLP_P2_ATGTCA

source_name: sub maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 2.


title: LMLP_P1

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_LMLP_P1_AGTTCC

source_name: sub maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 1.


title: HMLP_P1

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_HMLP_P1_ACAGTG

source_name: ad libitium maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 1.


title: HML_P2

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_HML_P2_TGACCA

source_name: ad libitium maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during lactation. Pool 2.


title: WES_diagnostic

city: Boston

first: Eric

middle: A

last: Severson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description: ETP-ALLpt1_diagnostic.maf - variant calls

data_processing:
Sequencing data were aligned to the human reference genome hg19 using Picard tools (http://broadinstitute.github.io/picard/). Mutation calls were made on the WES samples with the mutation calling workflow in Firehose (https://www.broadinstitute.org/cancer/cga/Firehose) using Mutect with default parameters and enabled to run without matched normal DNA
Genome_build: hg19

source_name: bone marrow

growth_protocol: Mononuclear cells were isolated from marrow using Ficoll gradients, washed, and resuspended in WIT medium in the presence of MS5 feeder cells expressing the Notch ligand DLL-1 for short-term culture assays

extract_protocol:
WES was performed using DNA extracted from peripheral blood mononuclear cell pellets.
Genomic DNA (250ng) was subjected to shearing, barcoded sequencing library preparation, and hybrid capture as described in Fisher et al. 2011.

treatment_protocol: Cell cultures were treated with the GSI DBZ (dibenzazepine, 1mM) or DMSO vehicle (control) for 3 days.

value: bone marrow


title: 61N

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

data_processing:
Reads were aligned to human genome hg19 by Bowtie, with parameters  -a -m 1 --best --strata. The mapped reads were then analyzed by the Dregion function in  danpos 2.2.3, with command line: python danpos.py dregion aligned_reads.bowtie --smooth_width 0 -c 25000000 --frsz 200 --extend 200 --extend_dis 3000 --pheight 1e-8 -ep 1e-5
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq reads density

source_name: Lung normal tissue

growth_protocol: The cells were maintained in 10% fetal calf serum (FCS)-supplemented DMEM medium prior to extract preparation.

extract_protocol:
Cell or Chopped tissue pellets were homogenized in PBS containing proteinase inhibitor. The nuclei were checked by phase-contrast microscopy to maximize the yield of nuclei (~5x107). With sufficient lysis in 25% sucrose, 0.2% NP-40/TBS, the pellets were layered on 50% [w/v] sucrose/TBS, and then centrifuged at 21,000 g, 30 min, 4°C. The nuclei pellets were resuspended in digestion buffer (0.32 M sucrose, 50 mM Tris-HCl (pH 7.5), 4 mM MgCl2, 1 mM CaCl2), and digested with MNase for ~10 min to generate mainly mononucleosomes that were immunoprecipitated with anti-H3K4me3 antibody (ab8580, Abcam). After incubation over night, Protein A Dynal magnetic beads were washed 6 times using modified RIPA buffer (50 mM Tris-HCL pH 7.8, 1 mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5 M LiCl). The DNA was eluted in 1% SDS and 0.1M NaHCO3 and reversed cross-linking at 65°C, over night.
The library was generated using NEBNext ChIP-Seq Library Prep Master Mix Set, and amplified with 10 PCR cycles. The library was prepared by size selection for mononucleosome fragments.

treatment_protocol: The frozen tissues (50-100 mg), purchased from Cureline, were trimmed and chopped into small pieces on ice, and then washed with ice cold PBS twice.

value: Lung normal

tag: antibody


title: 185T

source_name: Liver tumor tissue

value: Liver tumor


title: A549_F1

source_name: cell line treated with flavopiridol


title: ChIP-seq H3K27Ac_GSI

description: H3K27Ac_GSI.bedgraph, H3K27Ac.GSI_peaks.broadPeak.txt, H3K27Ac.GSI_peaks.xls generated by macs2.

data_processing:
ChIP-seq sequence reads were aligned to the hg19 genome using bowtie2 with default parameters.  Peak calls were generated with macs2 with an fdr=0.01.
Genome_build: hg19

source_name: Cultured Leukemic Blasts

extract_protocol:
Chromatin from formaldehyde-fixed cells (5 × 106 cells per histone mark) was fragmented to a size range of 200–700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with an antibody against H3K27ac (2.5 μl; ActiveMotif, ab4729), and enrichment for H3K27ac was confirmed by dot blot as described (Ernst et al. 2011). Antibody-chromatin complexes were pulled down with protein G magnetic beads (Dynabead, 10003D), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was treated with RNase and purified with Agencourt AMPure XP (Beckman Coulter A63880).
Libraries were prepared according to Illumina's instructions.

tag: chip antibody

value: H3K27ac (ActiveMotif, ab4729)

value: Cultured Leukemic Blasts

tag: treatment compound


title: RNA-seq_GSI

description: RNA-Seq_log2(fpkm).csv - log2(fpkm) values for all expressed genes.

data_processing:
RNA-seq alignment and transcript quantitation were performed with tophat2/cufflinks.  Data was quantile normalized using the R package preprocessCore v 1.28.0.  R was used to transform data into log2(fpkm) values.
Genome_build: hg19

extract_protocol:
RNA-seq was performed on poly-A selected RNA extracted from 1x106 cultured leukemic cells
Libraries were prepared according to Illumina's instructions.

tag: tissue


title: RNA_seq_DMSO

value: DMSO


title: HMLP_P3

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_HMLP_P3_CAGATC

source_name: ad libitium maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 3.


title: ChIP-seq H3K27Ac_DMSO

description: H3K27Ac_DMSO.bedgraph, H3K27Ac.DMSO_peaks.broadPeak.txt, H3K27Ac.DMSO_peaks.xls generated by macs2.


title: MMLP_P1

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_MMLP_P1_ATCACG

source_name: maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 1.


title: A549_V1

source_name: cell line not treated with flavopiridol


title: HMLP_P2

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_HMLP_P2_GCCAAT

source_name: ad libitium maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during late pregnancy. Pool 2.


title: WES_remission

description: ETP-ALLpt1_remission.maf - variant calls


title: 61T

source_name: Lung tumor tissue

value: Lung tumor


title: 155N

source_name: Liver normal tissue

value: Liver normal


title: Cauda_epididymis_rep3

city: Callaghan

first: Bettina

middle: P

last: Mihalas

state: NSW

address: Level 4 Life Science Building, University Drive

department: Life Sciences

country: Australia

institute: University of Newcastle

description:
cauda9
processed_data_file: Epididymis_counts.txt

data_processing:
Basecalls were dones using CASAVA pipeline version 1.8.2.
Reads were screened and trimmed based on matches to Illumina smallRNA adaptors, PhiX, ChrM and rRNAs using flicker script with Illumina smallRNA kit with default settings
Cleaned reads were aligned using the bowtie ver 1.1.1 against human genome and miRNA database version 21
miRNA gene counts were summarised with custom shell scripts
Differential expression analysis was performed using the R-bioconductor libraies: limma and voom
Genome_build: miRNA database version 21
Supplementary_files_format_and_content: miRNA gene counts

source_name: Epididymis

extract_protocol:
Total RNA was extracted from purified epididymal epithelial cells and total epididymis  (caput, corpus and cauda) using a Direct-zol™ RNA MiniPrep Kit (Zymo Research Corporation, Irvine, CA, USA) according to manufacturer’s instructions before being incubated with 1% DNase (Promega) to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Swiss

tag: age

value: 8 weeks

tag: Sex

value: Male

value: Epididymis

value: Cauda


title: 185N


title: Cauda_epididymis_rep2

description:
cauda8
processed_data_file: Epididymis_counts.txt


title: Cauda_epididymis_rep1

description:
cauda7
processed_data_file: Epididymis_counts.txt


title: LML_P2

description:
The samples were run across two lanes of the illumina and the data were combined prior to processing so that there are four fastq files for each sample in the processed data file (two lanes, paired end reads).
D146FACXX_NZGL00260_LML_P2_AGTCAA

source_name: sub maintainence maternal nutrition during early pregnancy (P20-50) maintenance nutrition during late pregnancy (P51-140), biopsies taken during lactation. Pool 2.


title: p300-0hours-ChIPseq

city: Barcelona

first: Chris

last: van Oevelen

state: Catalunya

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files, which were subsequently aligned to the mouse genome (mm9) using either the Illumina Eland alignment tool or Bowtie (cmd: bowtie -n 0 -l 28 -m 1 mm9 INPUT OUTPUT, Langmead et al, 2009, PMID: 19261174) without mismatches. Aligned sequences were further filtered to remove identical sequence tags and sequence tags that do not align uniquely to the mouse genome
To detect regions enriched for factor  binding relative to background, we used HOMER (http://biowhat.ucsd.edu/homer/ngs/index.html) (Heinz et al, 2010, PMID: 23064439) with the peak localization/shape option set to region and the style option set to factor.
Genome_build: mm9
Supplementary_files_format_and_content: USCS bed format: chr start end strand

source_name: Haftl pre-B cells

growth_protocol: C10 cells were grown in RPMI 1640 without phenol red (Lonza) supplemented with 10% charcoal/dextran-treated FBS (Hyclone) and 50 μM 2-mercaptoethanol (GIBCO), incubated at 37°C in 5% CO2

extract_protocol: ChIP experiments were performed as described previously (van Oevelen et al, 2008, PMID:20956564). DNA libraries of C/EBPa and C/EBPb enriched chromatin fragments were prepared using Illumina's reagents and instructions. All other libraries were prepared according to manufacturer’s instructions with some modifications (Asp et al, 2011, PMID: 21551099). All libraries were sequenced on the Illumina 2AAIIx sequencer except C/EBPa and PU.1 libraries generated 10, 30 and 60 minutes post induction and pax5 (0 hours) and Foxo1 (0 hours) that were sequenced using the Illumina Hiseq2000 sequencer.

treatment_protocol: C10 cells were induced by the addition 100 nM of β-estradiol (Calbiochem) and grown with 10 nM of IL-3 and CSF-1 (Peprotech). Control cells were treated with 0.1% ethanol (solvent)

tag: cell type

value: haftl derived C10 cells

tag: time after induction

value: 0 hours


title: Corpus_epididymis_rep1

description:
corpus5
processed_data_file: Epididymis_counts.txt

tag: tissue compartment

value: Corpus


title: 14724N


title: Caput_epididymis_rep2

description:
caput2
processed_data_file: Epididymis_counts.txt

tag: strain

value: Caput


title: p300-24hours-ChIPseq

value: 24 hours


title: p300-3hours-ChIPseq

value: 3 hours


title: Ebf1-48hours-ChIPseq

value: 48 hours

value: abnova 1879-mol clone 1c12


title: Ebf1-3hours-ChIPseq


title: Caput_epididymis_rep1

description:
caput1
processed_data_file: Epididymis_counts.txt


title: p300-12hours-ChIPseq

value: 12 hours


title: Cauda_epithelium_rep2

description:
12_GGTAGC
processed_data_file: Epithelial_counts.txt

source_name: Epididymal epithelial cells

value: Epididymal epithelial cells


title: Ebf1-24hours-ChIPseq


title: Cauda_epithelium_rep1

description:
9_GTTTCG
processed_data_file: Epithelial_counts.txt


title: Caput_epithelium_rep2

description:
10_CGTACG
processed_data_file: Epithelial_counts.txt


title: PU.1-48hours-ChIPseq

value: PU.1 (sc-352, Santa Cruz)


title: Ebf1-12hours-ChIPseq


title: Ebf1-0hours-ChIPseq


title: PU.1-24hours-ChIPseq


title: Corpus_epithelium_rep2

description:
11_GAGTGG
processed_data_file: Epithelial_counts.txt


title: 155T

value: Liver tumor


title: 14724T

value: Lung tumor


title: PU.1-12hours-ChIPseq


title: Caput_epithelium_rep1

description:
7_GTGAAA
processed_data_file: Epithelial_counts.txt

value: Swiss

value: 8 weeks


title: PU.1-3hours-ChIPseq


title: Corpus_epididymis_rep2

description:
corpus6
processed_data_file: Epididymis_counts.txt

value: Male

value: Epididymis


title: PU.1-0hours-ChIPseq

value: haftl derived C10 cells


title: Caput_epididymis_rep3

description:
caput3
processed_data_file: Epididymis_counts.txt


title: Tumor_Brg1_null

city: San Francisco

first: Shivani

last: Malik

address: 1450 3rd street

department: Hematology

institute: UCSF

data_processing:
Sequenced reads were processed using Galaxy public server and the tools installed therein. Reads were checked for quality using QC tool.
Reads were mapped using Tophat-2 to mm9
Transcript assembly and differential expression analysis was performed using Cufflinks and Cuffdiff using default parameters (Ref: Trapnell C, et al, Nat Biotechnol. 2010)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text.  The All genes_duct_seq file is the cufflink-cuffdiff output and represents FPKM values of the genes in WT(value 1), Kras(value2) and Kras,Brg1f/f(Value3) of duct cells. The 2134e_wt file is the cufflink-cuffdiff output of Brg1_null tumor cell(empty) compared to Brg1 put back(WT) cells. The values represent FPKM .

source_name: Cell line

growth_protocol: Duct cells were isolated according to the protocol described in the text of the publication. For Brg1 put backs, cells were grown to 70% confluence.

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit v2 (Cat#FC-122-1001) was used with 800 ug of total RNA to prepare libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transduction

value: +pBabe-Empty


title: Duct_Kras_Brg1f/f_3

source_name: Duct cell


title: Duct_Kras_Brg1f/f_2


title: C/EBPb-12hours-ChIPseq

value: C/EBPb (sc-150, Santa Cruz)


title: C/EBPb-24hours-ChIPseq


title: Duct_Kras_Brg1f/f_1


title: C/EBPb-48hours-ChIPseq


title: Duct_Kras_3


title: C/EBPb-3hours-ChIPseq


title: Tumor_Brg1_putback


title: Duct_Kras_2


title: Duct_Kras_1


title: Duct_WT_3

value: WT


title: C/EBPa-24hours-ChIPseq

value: 24 hours

value: C/EBPa (sc-61, Santa Cruz)


title: C/EBPa-48hours-ChIPseq

value: 48 hours


title: Duct_WT_2


title: C/EBPa-0hours-ChIPseq

value: 0 hours


title: Duct_WT_1


title: Mnase-48hours-Mnaseseq

description: Sample 51

data_processing:
Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files, which were subsequently aligned to the mouse genome (mm9) using either the Illumina Eland alignment tool or Bowtie (cmd: bowtie -n 0 -l 28 -m 1 mm9 INPUT OUTPUT, Langmead et al, 2009, PMID: 19261174) without mismatches. Aligned sequences were further filtered to remove identical sequence tags and sequence tags that do not align uniquely to the mouse genome
Genome_build: mm9
Supplementary_files_format_and_content: USCS bed format: chr start end strand

extract_protocol: Nucleosome positioning was determined by a modification of published method (Cappabianca et al, 1999, PMID: 10804530) .DNA libraries mononucleosomes were prepared using Illumina's reagents and instructions. All libraries were sequenced on the Illumina Hiseq2000 sequencer.

tag: cell line source

value: HAFTL (pre-B cells)

tag: molecule subtype

value: mononucleosomal genomic DNA


title: C/EBPa-3hours-ChIPseq

value: 3 hours


title: C/EBPa-12hours-ChIPseq

value: 12 hours


title: H3K27Ac-48hours-ChIPseq

data_processing:
Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files, which were subsequently aligned to the mouse genome (mm9) using either the Illumina Eland alignment tool or Bowtie (cmd: bowtie -n 0 -l 28 -m 1 mm9 INPUT OUTPUT, Langmead et al, 2009, PMID: 19261174) without mismatches. Aligned sequences were further filtered to remove identical sequence tags and sequence tags that do not align uniquely to the mouse genome
Genome_build: mm9
Supplementary_files_format_and_content: USCS bed format: chr start end

extract_protocol: ChIP experiments were performed as described previously (van Oevelen et al, 2008, PMID:20956564). Libraries were prepared according to manufacturer’s instructions with some modifications (Asp et al, 2011, PMID: 21551099). All libraries were sequenced on the Illumina 2AAIIx sequencer

value: H3K27Ac (ab4729, Abcam)


title: C/EBPb-0hours-ChIPseq


title: C/EBPa-30minutes-ChIPseq

value: 30 minutes


title: C/EBPa-10minutes-ChIPseq

value: 10 minutes


title: H3K27Ac-12hours-ChIPseq


title: Mnase-0hours-Mnaseseq

description: Sample 47


title: H3K27Ac-0hours-ChIPseq


title: H3K27Me3-12hours-ChIPseq

value: H3K27Me3 (17-622, Millipore)


title: H3K27Me3-48hours-ChIPseq


title: H3K27Me3-3hours-ChIPseq


title: H3K27Me3-0hours-ChIPseq


title: H3K4Me1-48hours-ChIPseq

value: H3K4Me1 (037-050, Diagenode)


title: H3K27Me3-24hours-ChIPseq

value: haftl derived C10 cells


title: H3K4Me1-24hours-ChIPseq


title: H3K4Me1-0hours-ChIPseq


title: H3K4me2-ChIPSeq-NMVM

status: Public on Jul 28 2015

city: Aurora

first: Rebecca

middle: L

last: O'Rourke

state: CO

address: 12801 East 17th Ave

institute: University of Denver

data_processing:
ChiP-Seq reads were aligned to the mm9 genome using GSNAP version 20120720 with the following configurations: --gunzip -d mm9 -v mm9_total.snp128_strict --use splicing=mm9_total.ensembl.splicesites --max-mismatches=0.04 -i2 -n1 -Q --nofails -B5 -t12 with read-group-id,name&library=sample name and read-group platform=illumina
Unmaped reads were removed from the sam file and the results written to a bam file using samtools view -bS -F4, then sorted and indexed using samtools sort and samtools index
The sorted bam files were used to create Tag Directories using HOMER v4.6 makeTagDirectories command
The bedGraph files were generated using HOMER v4.6 makeUCSCfile command
The ChiP-Seq peaks were determined using HOMER v4.6 findPeaks command with the following configurations: -size 1000 -minDist 2500 -fragLength x -inputFragLength 250 -i input_DNA (x= MEF:250; D3:275; D5:297; D7:295; NMVM:278)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph.gz are gzipped UCSC bedGraph files, text files contain peak coordinates.

source_name: cardiomyocytes

growth_protocol: MEFs were plated and cultured in growth medium (DMEM/Hi glucose (Hyclone),10% FBS (Gemini), 1.1% Penicillin-Streptomycin (Gibco) and 1.1% GlutaMAX supplement (Gibco)) at 370C with 5% CO2 at day 0. Fibroblasts were transduced with retroviruses at day 1 and day2. At day 3, viral media were be replaced with induction medium composed of DMEM/199 (4:1) (Gibco),  10% FBS (Gemini) , 5% horse serum(Gemini), antibiotics (Gibco), 1 × non-essential amino acids (Gibco), 1 × essential amino acids (Gibco), 1 × B-27(Gibco), 1 × insulin-selenium-transferin (Gibco), 1 × vitamin mixture (Gibco), and 1 × sodium pyruvate (Gibco).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody anti-H3K4me2.
Libraries were prepared using Nugen Ovation Ultralow System Cat No  0344.  Briefly, DNA was end-repaired, A-tailed, adapter ligated and amplified with 10 cycles of PCR.  DNA libraries were purified using Agencourt XP Beads, quantified with the Qubit, run on a bioanalzyer tape station and clustered to an Illumina HiSEQ 2500 High Throughput Flow Cell.

value: heart

tag: developmental stage

value: H3K4me2 (Abcam, Ab7766)


title: C/EBPa-60minutes-ChIPseq

value: 60 minutes


title: H3K4Me1-12hours-ChIPseq


title: H3K27Ac-24hours-ChIPseq

value: 24 hours


title: H3K4me2-ChIPSeq_GHMTd5

source_name: fibroblasts

value: embryo


title: H3K4me2-ChIPSeq_GHMTd3


title: Input DNA_GHMTd7


title: Arap_LIV_CpG_WT

city: Oakland

first: David

middle: B

last: West

state: California

address: 5700 Martin Luther King Jr way

institute: CHORI

data_processing:
Bowtie2  and Bismark were used for base calling and alignment
Sequenced reads were trimmed for adaptor sequence, reference chromosomes were converted to bisulfite treated and indexed using Bismark,  then reads were mapped to specific chromosomes of mm9 genome assembly using bismark and bowtie2 with default parameters
Methylation calling with Bismark methylation extractor using merge non-CpG option
Genome_build: MM9
Supplementary_files_format_and_content: text files contain counts of methylated and unmethylated C's at each CpG site
Supplementary_files_format_and_content: column headers: Seq-ID, start position, end position, methylation %, methylated calls, non-methylated calls

source_name: Liver

extract_protocol:
Tissues were removed, flash frozen in LN2, and DNA was isolated using Tri-reagent.
Illumina TruSeq RNA Sample Prep Kit (Illumina RS-122-2001/2) was used to construct sequencing libraries from double stranded amplicons of Bisulfite treated DNA. Illumina protocol

treatment_protocol: Genomic DNA was treated with bisulfite using the MethylEasy Xceed kit (Human Genetic Signature, Australia) according to the manufacture’s protocol.

tag: strain background

value: 7 weeks

tag: genotype/variation

value: Wild Type

value: Liver

tag: accession # for mapping


title: Input DNA_GHMTd3


title: H3K4me2-ChIPSeq_MEF


title: H3K27Ac-3hours-ChIPseq


title: Arap_BRN_CpG_WT

source_name: Brain

value: Brain


title: Input DNA-NMVM


title: Arap_LNG_CpG_WT

source_name: Lung

value: Lung


title: Arap_KID_CpG_WT

source_name: Kidney

value: Kidney


title: H3K4me2-ChIPSeq_GHMTd7


title: Arap_LNG_LacZ_KO

value: Arap -/-

value: LacZ reference


title: H3K4Me1-3hours-ChIPseq

value: 3 hours


title: Arap_HRT_CpG_WT

source_name: Heart

value: Heart


title: Input DNA_GHMTd5


title: Arap_HRT_LacZ_KO


title: Arap_LIV_LacZ_KO


title: Arap_LNG_CpG_KO


title: Arap_KID_LacZ_KO


title: Arap_LIV_CpG_KO


title: Input DNA_MEF


title: PSR1 Input (Peptide B, Sulfur starvation 6 hr)

city: Walnut Creek

first: Chia-Lin

last: Wei

address: 2800 Mitchell Drive

department: Genomic Technologies

institute: DOE Joint Genome Institute

data_processing:
Raw reads were mapped as single-end read to C. reinhardtii genome (v5.3.1) by BWA v0.6.2 with default parameters
Enriched regions in the non-redundant mapped reads were identified by MACS2 v2.0.10 (effective genome size=107270392, FDR< 5%)
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz
Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations

growth_protocol: C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium.

extract_protocol:
ChIP-seq was performed as previously described (Chen et al., 2008). Briefly, cross-linked cells were lysed with Lysis Buffer (50 mM Tris-HCl pH8, 5 mM EDTA, 1% SDS) and chromatin was then sheared. 5-50 ug of chromatin was used in each immuno-precipitation.  Chromatin was first pre-cleared and then mixed with beads pre-bound with antibody. Beads were washed and eluted at 37ºC. The eluate was then de-crosslinked and DNA was purified by phenol/ chloroform extraction, followed by ethanol precipitation (Chen et al. 2008). Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117.
5-10 ng of purified DNA was used in ChIP-seq library preparation using Truseq DNA Sample Preparation Kit (Illumina)

treatment_protocol: N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780).

tag: time

value: 0 hr


title: Arap_BRN_LacZ_KO


title: Arap_BRN_CpG_KO


title: PSR1 Input (Peptide B, Sulfur starvation 2 hr)

tag: chip antibody


title: PSR1 Input (Peptide B, Nitrogen starvation 1 hr)


title: PSR1 ChIP-Seq (Peptide B, Sulfur starvation 1 hr)

value: polyclonal antibodies against PSR1 peptide sequences aa465-48 (peptide B:C-LQHQPQLLQPQGSLPA)


title: PSR1 Input (Peptide B, Sulfur starvation 1 hr)


title: PSR1 ChIP-Seq (Peptide B, Sulfur starvation 6 hr)


title: PSR1 ChIP-Seq (Peptide B, Nitrogen starvation 1 hr)


title: PSR1 ChIP-Seq (Peptide B, Sulfur starvation 2 hr)


title: PSR1 Input (Peptide B, Nitrogen starvation 30 min)


title: Arap_HRT_CpG_KO


title: Arap_KID_CpG_KO


title: PSR1 Input (Peptide A, Sulfur starvation 6 hr)


title: PSR1 ChIP-Seq (Peptide A, Sulfur starvation 6 hr)

value: polyclonal antibodies against PSR1 peptide sequences aa54-69 (peptide A:C-QQQGLALGGYGLTQQP)


title: PSR1 Input (Peptide A, Sulfur starvation 2 hr)


title: PSR1 ChIP-Seq (Peptide B, Nitrogen starvation 30 min)


title: PSR1 ChIP-Seq (Peptide A, Sulfur starvation 2 hr)


title: PSR1 ChIP-Seq (Peptide A, Sulfur starvation 1 hr)


title: PSR1 Input (Peptide A, Nitrogen starvation 1 hr)


title: RNA Pol2 Input (Sulfur starvation 1 hr)

data_processing:
Raw reads were mapped to C. reinhardtii genome (v5.3.1) by BWA v0.6.2 with default parameters
Enriched regions in the non-redundant mapped reads were identified by MACS2 v2.0.10 (effective genome size=107270392, FDR< 5%)
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz
Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations

source_name: RNA Pol2 Input (Sulfur starvation 1 hr)

value: 1 hr


title: PSR1 ChIP-Seq (Peptide A, Nitrogen starvation 1 hr)


title: PSR1 Input (Peptide A, Nitrogen starvation 30 min)


title: H3K27me3 Input (Sulfur starvation 1 hr)

source_name: H3K27me3 Input (Sulfur starvation 1 hr)


title: H3K4me3 ChIP-Seq (Sulfur starvation 1 hr)

description:
H3K4m3SD1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Sulfur_starvation_1hr_16states_genome_segmentation.bed.gz

data_processing:
Raw reads were mapped to C. reinhardtii genome (v5.3.1) by BWA v0.6.2 with default parameters
Enriched regions in the non-redundant mapped reads were identified by MACS2 v2.0.10 (effective genome size=107270392, FDR< 5%)
ChromHMM v1.0.6 (Ernst and Kellis, 2010) was used to perform unsupervised segmentation of the genome into 16 states initialized by information initialization strategy based on the combination of chromatin modifications from baseline (0 hr), nitrogen starvation (1hr) and sulfur starvation (1 hr).   * Ernst and Kellis. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature biotechnology 28, 817-825.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz
Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations

value: H3K4me3 (Abcam ab8580)


title: H3K4me3 Input (Sulfur starvation 1 hr)

description:
H3K4m3SD1hrInputR1
Please note that the raw data associated with this sample was also used as 'H3K36me3 Input replicate 2 (Sulfur starvation 1 hr)'

source_name: H3K4me3 Input (Sulfur starvation 1 hr)


title: H3K27me3 ChIP-Seq (Sulfur starvation 1 hr)

description:
H3K27m3SD1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Sulfur_starvation_1hr_16states_genome_segmentation.bed.gz

value: H3K27me3 (Abcam ab6002)


title: H3K27ac ChIP-Seq (Sulfur starvation 1 hr)

description:
H3K27acSD1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Sulfur_starvation_1hr_16states_genome_segmentation.bed.gz

value: H3K27ac (Abcam ab4729)


title: H3K36me3 ChIP-Seq replicate 1 (Sulfur starvation 1 hr)

description:
H3K36m3SD1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Sulfur_starvation_1hr_16states_genome_segmentation.bed.gz

source_name: H3K36me3 ChIP-Seq (Sulfur starvation 1 hr)

value: H3K36me3 (Abcam ab9050)


title: H3K9me3 ChIP-Seq (Sulfur starvation 1 hr)

description:
H3K9m3SD1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Sulfur_starvation_1hr_16states_genome_segmentation.bed.gz

value: H3K9me3 (Abcam ab8898)


title: RNA Pol2 Input (Nitrogen starvation 1 hr)