title: CS-B (6-4)PP 4h XR-seq Rep2

status: Public on Mar 15 2016

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

institute: Hebrew University of Jerusalem

description: Excised oligomer released in Nucleotide Excision Repair (XR-seq)

data_processing:
Library strategy: XR-seq
Base calling using Casava v1.8.2. Demultiplexing performed allowing 1 mismtach in the index
Flanking adapter sequences were removed from the reads using trimmomatic (Bolger et al. 2014).
Reads were aligned to the hg19 human genome using bowtie (Langmead et al. 2009) with the command options  -q --nomaqround --phred33-quals -m 4 -n 2 -e 70 -l 20 --best –S
Aligned readsfor each biological replicate were split into “PLUS” and “MINUS” strands, transformed to bed format, and sorted to remove duplicate reads.
Wiggle base counts files of 25bp fixed step windows were created for each of the replicates from the bed files. The count data was normalized for total sequencing depth on each chromosome. Wiggle files were d transferred to bigWig format for viewing on the UCSC browser.
Genome_build: hg19
Supplementary_files_format_and_content: For XR-seq performed for either CPD or (6-4)PP repair, in NHF1 and CS-B cells there are bigWig files of normalized 25bp fixedStep count data for both biological replicates, split into plus and minus strands

growth_protocol: CS-B Mutant cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum at 37 °C in a 5% CO2 humidified chamber. The NHF1 cells were maintained under the same conditions with the addition of 2 mM glutamine.

extract_protocol:
Cell pellets from one 150mm tissue culture dish were resuspended in 400 µl of ice cold Buffer A (25 mM Hepes pH 7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 0.5% NP-40) and incubated for 10 min on ice. Resuspended cells were transferred to an ice-cold Dounce homogenizer/tissue grinder and lysed on ice with 15 strokes using a tight plunger. The chromatin fraction was then pelleted by centrifugation for 30 min at 16, 873 x g at 4oC.
The supernatants were collected, 2 µg anti-p89 (XPB, Santa Cruz sc293 lot L1514), 1 µg anti-p62 (Santa Cruz sc292  lot F2113) and 200 µg RNaseA (Sigma R4642) were added. The reactions were rotated for 3-5 hrs at 4oC and then incubated overnight with 15 µL of recombinant protein A/G PLUS-agarose (Santa Cruz sc2003). After washing three times with 1 ml of buffer A and once with 1ml of buffer B (25 mM Hepes pH 7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 1% NP-40), DNA was eluted from immunoprecipitates with 100 µl of buffer C (10 mM Tris-Cl pH 7.5, 1 mM EDTA, and 1% SDS) at 65oC for 15 min. The eluted DNA was then isolated by phenol/chloroform extraction followed by ethanol precipitation. DNA pellets were resuspended in 45 µl water, and then incubated with 5 µL of RNaseA/T1 mixture (Thermo EN0551) for 1 hr at 37oC. After phenol-chloroform extraction, purification through G50 filtration columns (GE Healthcare) and ethanol precipitation, the DNA was then used for ligation.  To add double-stranded adaptors to both ends, purified excised oligomers were incubated with 40 pmol 5′ adaptor and  100 pmol 3′ adaptor in 10 µL 2x Hybridization Buffer (20mM Tris-HCl pH7.5, 200mM NaCl, 0.2mM EDTA) at 60oC for 10min, then 16oC for 5min in a thermal cycler. To perform ligation, 4 µL 5x ligase buffer, 1 µL T4 DNA ligase HC (Life 15224-041), 1 µL 50% PEG8000 (NEB) and 4 µL H2O were added to each reaction. The reactions were incubated at 16oC overnight. After phenol-chloroform extraction and ethanol precipitation, ligation products were subjected to immunoprecipitation with anti-CPD (For the 16h sample - Cosmo NM-DND-001 lot TM-C-08, for all the rest, Kamiya cat MC-062, lot 11569062) or anti-(6-4)PP (Cosmo cat NM-DND-002, lot TM-P-04) antibodies.Purified DNA were repaired by (6-4)PP photolyase or CPD photolyase. DNA containing (6-4)PP or CPD were incubated with 1.25pmol E.coli (6-4)PP photolyase or 20pmol D.melanogaster CPD photolyase in 50 µL PLR buffer for 2hr on ice and irradiated with 18mW/cm2 of 366 nm light. 1% of unrepaired or repaired samples were used for quality check. After phenol-chloroform extraction and ethanol precipitation, repaired DNA were PCR amplified by Kapa Hifi HotStart ReadyMix with RP1 and RPIn (n means different index sequences, compatible with Illumina TrueSeq Small RNA Kit.) The PCR products were extracted with phenol-chloroform, precipitated with ethanol and subjected to electrophoresis in a 10% native polyacrylamide gel in 1xTBE. Gel slices corresponding to 130 to 155-nt fragments were excised. The DNA was eluted for 6 hrs in 0.3 M NaCl at room temperature, precipitated with ethanol and resuspended in buffer EB (10mM Tris-HCl pH8.5).

treatment_protocol: UV irradiation was performed as described previously (Gaddameedhi et al. 2010). Briefly, cells were grown to ~80% confluence before UV irradiation. Culture medium was removed, and then cells were placed under a GE germicidal lamp emitting primarily 254-nm UV light (1J/m2/s) connected with a digital timer for 10s or 20s (10 or 20J/m2 in total). Following irradiation, fresh culture medium was added to the cells, which were further incubated for the indicated time. Cells were washed with ice-cold PBS, harvested with a cell scraper in PBS and collected by centrifugation at 2500rpm for 4min.

value: Coriell GM16095 (CS1ANps3g2)

tag: cell line source

value: Cockayne Syndrome patient (CS-B mutant)

value: skin fibroblast

tag: uv exposure

tag: time after irradiation

tag: type of uv-induced dna damage

value: (6-4) pyrimidine-pyrimidone photoproduct ((6-4)PP)


title: CS-B (6-4)PP 1h XR-seq Rep1

type: SRA

city: Jerusalem

country: Israel

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: CS-B (6-4)PP 1h XR-seq Rep2


title: CS-B (6-4)PP 4h XR-seq Rep1


title: CS-B (6-4)PP 2h XR-seq Rep1


title: CS-B (6-4)PP 2h XR-seq Rep2


title: CS-B (6-4)PP 5min XR-seq Rep1


title: NHF1 (6-4)PP 4h XR-seq Rep2

description:
Source of NHF1 cell line: W.K. Kaufmann, UNC, Chapel Hill (Heffernan et al. 2002).
Excised oligomer released in Nucleotide Excision Repair (XR-seq)

value: normal newborn

value: foreskin fibroblast


title: V2A.t24

status: Public on Mar 16 2016

city: Freiburg

first: Emanuel

last: Clauss-Lendzian

address: Hugstetter Straße 55

country: Germany

institute: University Medical Center

library_source: transcriptomic

data_processing:
Raw sequencing reads were aligned to the reference genome of E. faecalis 12030 using Bowtie2 (version 2.2.3).
Post-processing of the SAM files into sorted BAM files was performed with SAMtools (version 1.2-207).
Length normalized confidence interval Fragments Per Kilobase of exon per Million fragments mapped (FPKM) values were obtained with Cufflinks using optimized settings for the Ion ProtonTM Sequencer.
Statistical analysis was carried out with the recently developed T-REx RNA sequencing expression analysis pipeline (de Jong et al., BMC Genomics, 2015) using the differential expression method of EdgeR.
A gene was considered significantly differentially expressed when the expression ratio was ≥|2.0| and the false discovery rate (FDR) adjusted p-value ≤ 0.05.
Genome_build: Enterococcus faecalis 12030
Supplementary_files_format_and_content: Tab-delimited txt files with GeneID, logFC, logCPM, LR, pvalue, adj_pvalue and Fold value for each contrast (= comparison of sample X versus sample Y).
Supplementary_files_format_and_content: Tab-delimited txt file with FPKM for all samples.

molecule: total RNA

organism: Enterococcus faecalis

source_name: Cell

growth_protocol: Enterococcus faecalis 12030 was pre-cultured overnight at 37°C in Brain Heart Infusion (BHI, Oxoid Deutschland GmbH, Wesel, Germany) medium with constant agitation at 150 rpm and diluted in BHI medium to an OD600 of 0.05.

extract_protocol:
Cells from 30 ml culture were harvested by centrifugation for 1 min at 10 000 rpm and 4°C in a Sorvall RC6+ centrifuge (Thermo Scientific GmbH, Langenselbold, Germany). Cell pellets were immediately frozen in liquid nitrogen and stored at -80°C or directly used for RNA isolation. RNA was isolated using the ZR Fungal/Bacterial RNA MiniPrepTM Kit (Zymo Research, Freiburg, Germany) following the manufacturer's instructions. To recover total RNA including small RNAs, 1.5 volumes of absolute ethanol were added in step 5. Finally, total RNA was eluted with 50 µl DNase-/RNase-free water and stored at -80°C. RNA quantity and quality were assessed with Agilent RNA 6000 Nano and Pico Kits using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA). Residual contaminating DNA was digested with DNA-freeTM DNase (Ambion, Carlsbad, USA).
To remove rRNAs and tRNAs from the total RNA, MICROBExpressTM and MEGAclearTM Kits were applied. After purification, 500 ng of the enriched (m)RNA was fragmented with RNase III. Fragmented (m)RNA (50-100 ng) was used for the preparation of barcoded whole transcriptome cDNA libraries using the Ion Total RNA-Seq Kit v2 and Ion XpressTM RNA-Seq Barcode 1-16 Kits. Finally, strand-specific, multiplexed RNA sequencing was carried out on Ion PITM chips in an Ion ProtonTM Sequencer. All kits and devices for RNA sequencing were from Ambion, Carlsbad, USA and used according to the manufacturer's instructions.

treatment_protocol: E. faecalis 12030 cultures in mid-exponential growth phase (OD600 ≈ 0.6) were either subjected to metal stress by exposure to an AGXX®- or Ag-coated V2A steel mesh or exposed to an uncoated V2A steel mesh (12 cm2 each in 30 ml BHI medium to obtain a mesh-surface : medium-volume ratio of 0.4) followed by further incubation for 3, 6, 12, 24, 60 and 90 min at 37°C with constant agitation at 150 rpm. As control, no metal mesh was added.

tag: strain

tag: growth in the presence of steel mesh

tag: exposure time [min]


title: NHF1 (6-4)PP 2h XR-seq Rep1


title: NHF1 (6-4)PP 4h XR-seq Rep1


title: NHF1 (6-4)PP 2h XR-seq Rep2


title: Ag.t03

value: Ag


title: NHF1 (6-4)PP 1h XR-seq Rep1


title: NHF1 (6-4)PP 1h XR-seq Rep2


title: NHF1 (6-4)PP 20min XR-seq Rep2


title: totalRNA4-1

city: Pohang

first: Hee Jung

last: Koo

address: Hyojadong San 31

country: South Korea

institute: Pohang University of Science and Technology

description: total RNA set1

data_processing:
Illumina Casava1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to TAIR10 whole genome using TopHat v1.4.0 (Trapnell et al., 2009)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks (Trapnell et al., 2009)
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each sample

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf

extract_protocol:
RNA was isolated using WelPrepTM (WelGENE, Korea). Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value greater than 8.5
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: leaf

tag: days after emergence


title: NHF1 (6-4)PP 5min XR-seq Rep2


title: NHF1 (6-4)PP 20min XR-seq Rep1


title: NHF1 CPD 48h XR-seq Rep1

source_name: NHF1, CPD, 48h

value: cyclobutane pyrimidine dimer (CPD)


title: NHF1 CPD 48h XR-seq Rep2


title: 750T input DNA

city: Los Angeles

first: Gangning

last: Liang

state: CA

address: 1441 Eastlake Ave, NOR 7344

department: Urology

country: USA

institute: University of Southern California

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were aligned to hg19 using BWA-0.6.2
Data were filtered by removing nonuniquely mapping reads and PCR duplicates
ChIP-seq reads were extended to sequencing library’s mean fragment size, estimated using the default setting of HOMER v.4.3’s makeTaqDirectory command
Each data set was normalized into a single value for each genomic position using the Wiggler tool with default settings and “globalmap_k20tok54” as the mappability parameter
Mean Wiggler values were calculated in 10-bp bins, and Z-score transformation by subtracting the mean Wiggler value across the genome and dividing by the standard deviation of the genome-wide Wiggler subtraction value
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigwig files were generated using the Wiggler tool; values represent Z-scores for each 10bp bin

source_name: Patient x750 ccRCC Tumor Tissue

extract_protocol:
Flash-frozen minced tissue was thawed in cell culture medium (Gibco® Keratinocyte-SFM (1X) Catalog #17005-042) with 1% formaldehyde for 10 minutes under rotation for cross-linking, which was then quenched with 2M Glycine (final concentration of 100mM). Minced tissue was then washed twice with ice-cold PBS with Protease Inhibitor Cocktail (PIC) and resuspended in 1mL ChIP Lysis Buffer (1% SDS, 50mM Tris HCl pH 8.1, 10mM EDTA) with PIC. The suspension was ground in a dounce homogenizer 10-15 times and then passed through a 40µM filter and checked for lysis with Trypan Blue under a microscope. The nuclei were then sonicated using a probe sonicator (Branson Sonifier® Cell Disruptor 185, 4.5 Output Control, 12 cycles, 10 seconds ON/30 seconds OFF) and centrifuged at 12,000rpm for 10 minutes at 4°C.
Libraries were constructed using the KAPA DNA library preparation kit (KK8230)

tag: chip antibody

value: Clear cell renal cell carcinoma tumor


title: 753T input DNA

source_name: Patient x753 ccRCC Tumor Tissue


title: NHF1 CPD 1h XR-seq Rep1

source_name: NHF1, CPD, 1h


title: NHF1 CPD 4h XR-seq Rep1

source_name: NHF1, CPD, 4h


title: NHF1 CPD 1h XR-seq Rep2


title: CS-B (6-4)PP 5min XR-seq Rep2


title: 750N input DNA

source_name: Patient x750 Adjacent Normal Tissue

value: Normal Kidney adjacent to tumor


title: NHF1 (6-4)PP 5min XR-seq Rep1


title: 753T H3K27ac_ChIPSeq

value: H3K27ac (Active Motif, 39135)


title: 753T H3K27me3_ChIPSeq

value: H3K27me3 (Active Motif, 39155)


title: 753N input DNA

source_name: Patient x753 Adjacent Normal Tissue


title: 753N H3K27me3_ChIPSeq


title: 750T H3K27ac_ChIPSeq


title: 750T H3K27me3_ChIPSeq


title: 750N H3K27ac_ChIPSeq


title: NHF1 CPD 4h XR-seq Rep2


title: 753N H3K4me3_ChIPSeq

value: H3K4me3 (Active Motif, 39160)


title: 750N H3K27me3_ChIPSeq


title: RWPE-1 hMeSeal-Seq Input DNA

city: Toronto

first: Shivani

middle: Nainesh

last: Kamdar

state: Ontario

address: 60 Murray Street, L6-304B

department: Cancer Biology

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
processed_data_file: RWPE1_DiffBind_hmC.txt
RWPE1_MACSDataAll.txt - contains reads compared to input for RWPE1 for hMeSeal-seq and MBD-seq
input for hydroxymethylation profiling

data_processing:
Library strategy: hMeSeal-Seq
hMeSeal-Seq: Base calling was performed using CASAVA v1.8.2. Sequenced reads were mapped to the reference human genome (GRCh37, hg19) using Bowtie (v0.12.7). Repitools package was used as an enrichment diagnostic screen of sequenced samples, enriched and input. Significantly enriched regions/peaks of hydroxymethylation were determined using model-based analysis of ChIP-seq (MACS) algorithm, by comparing bound, enriched samples to input, non-enriched samples.  Annotation was performed using ChIPpeakAnno R package (v.1.12.0) and a customized version of Annovar program with RefSeq genes to determine specific genomic features: promoter, genic, exons, introns, and intergenic (previously described for MBD-seq). UCSC CpG island definitions were used to define CpG islands. RWPE-1 DNase-seq data from The Encyclopedia of DNA Elements (ENCODE) project (GEO accession: GSM1008595) was correlated to MACS peak sets in both RWPE-1 and 22Rv1 cells. The genomic feature, RWPE-1 UCSC DNAseI peaks, was defined as: within 5 kb of a DNase peak. MACS data was further analyzed using DiffBind R package (v.1.12.0) to determine two consensus peak sets by requiring one or both MACS peaks to be present for a consensus peak to be called. The first consensus peak set was subsequently defined as differentially hydroxymethylated regions (DHMRs) between RWPE-1 and 22Rv1 cells (fold change >1).
genome build: hg19
processed data files format and content: diffBind output

source_name: Normal prostate epithelium cells

extract_protocol:
80% confluent cells were harvested from flasks, and genomic DNA was extracted using the QIAamp DNA Mini Kit (Cat No. 51306).
Libraries were prepared for sequencing as per the standard Illumina protocol for genomic DNA.

value: Normal prostate epithelium

tag: passage

tag: enrichment

value: none (input)


title: 750T H3K4me3_ChIPSeq


title: 750N H3K4me3_ChIPSeq


title: MEF_kap1_TI

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description: Total Input

data_processing:
Illumina Casava1.82 for basecalling
Alignement for ChIP-seqs: bowtie2 v2.2.1 with --sensitive-local parameter.
Peak calling for ChIP-seqs were done using MACS v.1.4.2.1 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq, a bed file containing the output of the peak called by MACS is provided.

organism: Mus musculus

source_name: MEF

growth_protocol: Cells were cultured with Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum, and 1x penicillin/streptomycin solution. KAP1 KO was induced with overnight treatment with 1µM of tamoxifen (Cre-mediated excision), and KO cells were stably cultured and cloned. KO cells were transduced with pSicoR-KAP1-HA for HA-tagged KAP1 expression.

extract_protocol:
Cells were harvested, washed with Episerf, fixed in 12mL per 1x107 cells (10 min in 1% formaldehyde), quenched with glycine in 10mL (at 125 mM final), washed three times with PBS, and pelleted. Each pellet containing 1x107 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 30 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65oC, RNAse A at 1µg/µL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 1x107, with Dynabeads (Protein G, ThermoFisher) in IP buffer (16.25 mM  Tris at pH 8.1, 137.5 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1.25% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65oC, Proteinase K at 400ng/µL, overnight) and DNA was extracted.
Single-end libraries were prepared and sequenced in 100bp reads runs according to Illumina instructions.

value: Mouse embryonic fibroblasts

tag: genotype/variation

value: KAP1 KO, overexpressing HA-tagged KAP1

value: none, input


title: RWPE-1 hMeDIP-Seq Input DNA

description:
processed_data_file: RWPE1_hMeDIP.txt
RWPE1_MACSDataAll.txt - contains reads compared to input for RWPE1 for hMeSeal-seq and MBD-seq
hydroxymethylation profiling

data_processing:
hMeDIP-Seq: Sequencing image analyses and base calling were performed using Off-Line Basecaller software (OLB V1.8).  After passing Solexa CHASTITY quality filter, sequenced reads were mapped to the reference human genome (GRCh37, hg19) using Bowtie (V2.1.0) [44]. Significantly enriched regions/peaks of hydroxymethylation were determined using model-based analysis of ChIP-seq (MACS, V2) algorithm [45], by comparing immunoprecipitated, enriched  samples to input, non-enriched samples (p-val <10-4). Annotation was performed using the UCSC RefSeq database, where peaks were mapped to the nearest gene and specific genomic features were determined: promoter (2kb upstream and downstream from the TSS), gene body (2kb downstream of the TSS to the TTS), intergenic (remaining regions not defined as ‘promoter’ or ‘gene body’).
genome build: hg19
processed data files format and content: MACS output


title: 22Rv1 hMeSeal-Seq Input DNA

description:
processed_data_file: 22Rv1_DiffBind_hmC.txt
22Rv1_MACSDataAll.txt  - contains reads compared to input for 22Rv1 for hMeSeal-seq and MBD-seq)
input for hydroxymethylation profiling

source_name: Prostate adenocarcinoma cells

value: prostate adenocarcinoma


title: RWPE-1 hMeDIP-Seq Rep 1

value: hMeDIP-Seq


title: MEF_kap1_chip_2

description: replicate 2

value: HA


title: Glomus cell 1

city: Durham

first: Hiroaki

last: Matsunami

state: NC

address: CARL Building room 264 Research Drive

institute: Duke University

data_processing:
Reads were aligned to mouse genome mm10 by bowtie -m 1 to keep the uniquely mapped reads
Generated sam files from bowtie were modified and subjected to Annovar for annotation
Only exonic reads were kept for calculating the RPM (reads per million) for each gene
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts and RPM values

source_name: Carotid body

extract_protocol:
Single cells were lysed in lysis buffer and subjected to RT-PCR. Amplified cDNA were used for library construction
Illumina DNA Sample Preparation Kit, Illumina Nextera DNA Sample Preparation Kit

value: carotid body

value: glomus cell

tag: age

value: post natal day 4-5

tag: genotype

value: wild type


title: MEF_kap1_chip_1

description: replicate 1


title: Glomus cell 4


title: Glomus cell 5


title: Glomus cell 7


title: Glomus cell 8


title: Glomus cell 3


title: 753N H3K27ac_ChIPSeq


title: 516 ILW backfat, mRNA

city: Bologna

first: Roberta

last: Davoli

state: Bologna

address: Viale G. Fanin, 46

department: DISTAL

country: Italy

institute: Bologna University

data_processing:
Raw read fragments with quality Phred score lower than 30 were trimmed using the DynamicTrim script of the SolexaQA v2.1. Reads shorter than 50nt were discarded along with their mate. Clean read were mapped to the Sscrofa10.2 genome using Tophat v2.0.8, which used Bowtie v2.1.0.0, with default parameters and transcriptome inference from annotation enabled Ensembl Sscrofa10.2 v70.
Gene annotation for the reference genome was retrieved from Ensembl (BioMart) using the biomaRt R package. Read alignments were processed by Cufflinks v2.1.1 to identify and discover expressed genes and transcripts, and to quantify their expression. Expression data were indicated as Fragments per Kilobase of transcript per Million mapped reads (FPKM). Differential expression was assessed for genes and transcripts resulting from the filtered Cufflinks predictions. Two different methods, Cuffdiff2 and DESeq2, were used for the genes. For transcript DE test only Cuffdiff2 was used as long as the DESeq2 model is not suitable for the analysis of transcript predictions.
Genome_build: Sscrofa10.2

organism: Sus scrofa

source_name: backfat

growth_protocol: All animals were housed in the same environment and fed the same diet.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) according to the manufacturer's instruction. Results of the extraction were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and the quality of the extracted RNA was assayed using an Agilent 2100 BioAnalyzer (Agilent Technologies). The mRNA library was prepared using the TruSeq RNA sample preparation kit (Illumina) and version 3 of the reagents, following the manufacturer's suggested protocol (oligo-dT selection). The library was sequenced on an Illumina HiSeq 2000 as 100 bp long paired-end reads using half lane per sample.

treatment_protocol: Backfat sample was collected in a commercial slaughterhouse. The sample was immediately frozen in liquid nitrogen and stored at -80C in a deep freezer until RNA isolation.

tag: breed

value: Italian Large White

tag: gender

value: female

value: backfat

value: 250 days

tag: weight


title: 753T H3K4me3_ChIPSeq

value: H3K4me3 (Active Motif, 39160)

value: Clear cell renal cell carcinoma tumor


title: MEF_WT_R2

description: replicate 2

data_processing:
Illumina Casava1.82 for basecalling
Alignment for ChIP-seqs: bowtie2 v2.2.1 with --sensitive-local parameter. For RNA-seq: tophat2 v. 2.0.11 with -g 1 --no-novel-juncs --no-novel-indels --b2-sensitive and --library-type fr-firststrand in case of stranded
Peak calling for ChIP-seqs were done using MACS v.1.4.2.1 with default parameters
Counts of reads on genes were computed using HTseq-count v0.6.1 with default parameters
Counts of read on TEs were generated using bedtools multicov with options: -split.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq, a bed file containing the output of the peak called by MACS is provided.  Genome-wide signal is provided in the .bw files. For RNA-seq, the .pileup.txt files contain reads count for genes and the .txt files contain read counts for TEs

growth_protocol: Cells were cultured with Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum, and 1x penicillin/streptomycin solution. For KAP1 KO, cells were treated with 1µM of tamoxifen overnight in order to induce Cre-mediated excision.

extract_protocol:
Total RNA was extracted and DNAse-I treated using a spin column-based RNA purification kit (Macherey-Nagel).
Single-end 100bp RNA-seq libraries were prepared using 200ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina).

value: Mouse embryonic fibroblasts WT

value: WT Kap1 loxP/loxP


title: MEF_KAP1KO_R1

description: replicate 1

value: Mouse embryonic fibroblasts KAP1 KO

value: KAP1 KO Kap1 loxP/loxP Cre


title: 517 ILW backfat, mRNA

value: male

tag: phenotype

value: castrated

value: 241 days


title: 490 ILW backfat, mRNA

value: 235 days


title: 489 ILW backfat, mRNA


title: MEF_KAP1KO_R2

description: replicate 2


title: MEF_WT_R1

description: replicate 1


title: 488 ILW backfat, mRNA

value: 244 days


title: Liver_female_KAP1KO_d670

description: replicate 3

source_name: Liver

growth_protocol: Mice were housed in standard conditions with water and chow diet provided ad libitum and were sacrificed at 8 weeks of age.

extract_protocol:
Mice underwent a short term food starvation period of 4 hours before sacrifice. Liver samples were collected in Trizol and processed for RNA isolation using the miRNeasy kit (Qiagen).
Single-end 100bp RNA-seq libraries were prepared using 200ng of total RNA and the Illumina TruSeq mRNA reagents (Illumina).

value: Liver

value: Alb-Cre Kap1fl/fl


title: Liver_female_KAP1KO_d680

description: replicate 4


title: Liver_male_KAP1KO_e073

description: replicate 2


title: 485 ILW backfat, mRNA

value: Italian Large White

value: 249 days


title: 486 ILW backfat, mRNA

value: female

value: backfat


title: 484 ILW backfat, mRNA


title: 483 ILW backfat, mRNA

value: 250 days


title: Glomus cell 6

value: carotid body

value: glomus cell

value: post natal day 4-5

value: wild type


title: Liver_female_WT_d644

description: replicate 4

value: WT Kap1fl/fl


title: Liver_male_WT_d439

description: replicate 2


title: 482 ILW backfat, mRNA

value: 237 days


title: Liver_female_WT_d643

description: replicate 3


title: 481 ILW backfat, mRNA

value: male

value: castrated


title: 480 ILW backfat, mRNA

value: 243 days


title: Liver_male_KAP1KO_e040

description: replicate 1


title: Liver_male_WT_d437

description: replicate 1


title: 477 ILW backfat, mRNA


title: 476 ILW backfat, mRNA

value: 235 days


title: 479 ILW backfat, mRNA


title: ES_WT_mRNAseq_R1

description: replicate 1

source_name: Embryonic stem cell (ES3)

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium with 1mM sodium pyruvate, 1x MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1x penicillin/streptomycin, ES cell tested FBS, and leukaemia inhibitory factor (LIF). Cells were grown on 0.1% gelatin-coated plates and split every two days. For KAP1 KO, cells were treated with 1µM of tamoxifen overnight in order to induce Cre-mediated excision and harvested 4 days later.

value: Embryonic stem cells (ES3)

value: WT Kap1 loxP/loxP


title: 478 ILW backfat, mRNA

value: Italian Large White

value: 239 days


title: ES_WT_mRNAseq_R3

description: replicate 3


title: ES_KAP1KO_mRNAseq_R2

description: replicate 2

value: KAP1 KO Kap1 loxP/loxP Cre


title: ES_KAP1KO_mRNAseq_R1

description: replicate 1


title: ES_ZFP932/Gm15446KO_mRNAseq_clone2

description: replicate 2

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium with 1mM sodium pyruvate, 1x MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1x penicillin/streptomycin, ES cell tested FBS, and leukaemia inhibitory factor (LIF). Cells were grown on 0.1% gelatin-coated plates and split every two days. For KRAB-ZFPs KO, cells were transduced with an integrase defective lentiviral vector containing the pLentiCRISPR with an sgRNA for Zfp932 and Gm15446 or a control sgRNA against luciferase. Cells were selected for puromycin, cloned from single cells, and genotyped.

value: ZFP932/Gm15446 KO, clone 2


title: 475 ILW backfat, mRNA

value: backfat

value: 233 days


title: ES_control_mRNAseq_clone1

description: replicate 1

value: WT, clone 1


title: ES_ZFP932/Gm15446KO_mRNAseq_clone1

description: replicate 1

value: ZFP932/Gm15446 KO, clone 1


title: ES_WT_mRNAseq_R2

description: replicate 2


title: ES_control_mRNAseq_clone2

description: replicate 2

value: WT, clone 2


title: 473 ILW backfat, mRNA

value: female

value: 247 days


title: CTRL, rep3 (Paired-end)

first: Yi

last: Xing

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

description: CTRL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl mouse transcript (release 72) then mm10 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-firststrand -initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample …

source_name: Mouse embryo blastocyst

extract_protocol:
Total RNA were extrated from cells using TRIzol reagent (ThermoFisher 15596) according to the protocol.
cDNA libraries for sequencing were prepared using the Illumina True-seq Stranded mRNA kit and protocol.

value: embryo

value: CTRL


title: C2C12_Gm15446_input_R1

description: replicate 1

source_name: C2C12 cells

growth_protocol: Cells were cultured with Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum, and 1x penicillin/streptomycin solution. Cells were transduced with lentiviral vectors containing the KRAB-ZFP of interest, selected with 1µg/mL puromycin, and expression was induced by addition of 1 µg/mL of doxycline 48h prior harvesting.

extract_protocol:
Cells were harvested, washed with Episerf, fixed in 2mL per 1x107 cells (10 min in 1% formaldehyde), quenched with glycine in 10mL (at 125 mM final), washed three times with PBS, and pelleted. Each pellet containing 1x107 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 1 mM EDTA, 0.1% SDS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65oC, RNAse A at 1µg/µL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 4x107, with Dynabeads (Protein G, ThermoFisher) in IP buffer (10 mM Tris at pH 8, 1 mM EDTA, 0.1% SDS, 150 mM NaCl, 10% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65oC, Proteinase K at 400ng/µL, overnight) and DNA was extracted.
Single-end libraries were prepared and sequenced in 100bp reads runs according to Illumina instructions.

tag: cell line

value: muscle

value: overexpressing HA-tagged Gm15446

value: none (input)


title: C2C12_ZFP932_input_R2

description: replicate 2

tag: cell type

value: overexpressing HA-tagged ZFP932


title: C2C12_Gm15446_input_R2

description: replicate 2

tag: strain


title: C2C12_ZFP932_input_R1

description: replicate 1


title: ESRP DKO, rep3 (Paired-end)

description: ESRP DKO

value: ESRP DKO


title: C2C12_Gm15446_ChIPseq_R2

description: replicate 2

value: HA (Covance, MMS-101P)


title: 487 ILW backfat, mRNA

value: Italian Large White

value: male

value: castrated

value: 241 days


title: C2C12_ZFP932_ChIPseq_R2

description: replicate 2


title: ES_KAP1KO_mRNAseq_R3

description: replicate 3

value: Embryonic stem cells (ES3)

value: KAP1 KO Kap1 loxP/loxP Cre


title: 474 ILW backfat, mRNA

value: backfat

value: 237 days


title: ESRP DKO, rep1 (Paired-end)

description: ESRP DKO


title: ES_Gm15446_input_R2

description: replicate 2

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium with 1mM sodium pyruvate, 1x MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1x penicillin/streptomycin, ES cell tested FBS, and leukaemia inhibitory factor (LIF). Cells were grown on 0.1% gelatin-coated plates and split every two days. Cells were transduced with lentiviral vectors containing the KRAB-ZFP of interest, selected with 1µg/mL puromycin, and expression was induced by addition of 1 µg/mL of doxycline 48h prior harvesting.


title: ES_Gm15446_input_R1

description: replicate 1


title: C2C12_ZFP932_ChIPseq_R1

description: replicate 1


title: ES_ZFP932_input_R2

description: replicate 2


title: CTRL, rep2 (Paired-end)

description: CTRL


title: ES_Gm15446_ChIPseq_R1

description: replicate 1


title: CTRL, rep1 (Paired-end)

description: CTRL


title: Clone, rep2 (Paired-end)

description:
Clone
IPSC-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl mouse transcript (release 72) then mm10 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-firststrand -initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample.

source_name: Mouse embryo fibroblasts

extract_protocol:
Cell lysates for RNA extraction were harvested using Trizol reagent (Life Technologies) followed by chloroform extraction, isopropanol precipitation and resuspension in Tris-HCL pH 8.0. cDNA libraries for RNA-sequencing were prepared with poly-A purified mRNAs and the TruSeq™ Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturers protocol . We generated ~734 million 101x2 bp paired-end and ~335 million 101 bp single-end RNA-seq reads on a HiSeq 2000 sequencer.
cDNA libraries for sequencing were prepared using the Illumina True-seq Stranded mRNA kit and protocol.

value: fibroblasts

tag: developmental stage at isolation

tag: day of dox treatment

value: Clone


title: Clone, rep3 (Paired-end)

description:
Clone
IPSC-3

tag: tissue

value: embryo


title: Day20, rep3 (Paired-end)

description:
Day20
IPS20-3

value: homozygous for a TET-OP-OKSM polycistronic transgene targeted to the collagen 1A locus and homozygous for rtTA targeted to the Rosa26 locus


title: Clone, rep1 (Paired-end)

description:
Clone
IPSC-1


title: ESRP DKO, rep2 (Paired-end)

description: ESRP DKO


title: C2C12_Gm15446_ChIPseq_R1

description: replicate 1

value: muscle

value: overexpressing HA-tagged Gm15446


title: ES_ZFP932_ChIPseq_R1

description: replicate 1

value: overexpressing HA-tagged ZFP932


title: Day15, rep3 (Paired-end)

description:
Day15
IPS15-3


title: Day15, rep1 (Paired-end)

description:
Day15
IPS15-1


title: Day20, rep1 (Paired-end)

description:
Day20
IPS20-1


title: Day10, rep3 (Paired-end)

description:
Day10
IPS10-3


title: Day20, rep2 (Paired-end)

description:
Day20
IPS20-2


title: Day10, rep1 (Paired-end)

description:
Day10
IPS10-1


title: Day15, rep2 (Paired-end)

description:
Day15
IPS15-2


title: ES_ZFP932_input_R1

description: replicate 1

value: none (input)


title: Day7, rep2 (Paired-end)

description:
Day7
IPS7-2


title: ES_ZFP932_ChIPseq_R2

description: replicate 2

value: HA (Covance, MMS-101P)


title: Day7, rep1 (Paired-end)

description:
Day7
IPS7-1


title: Day7, rep3 (Paired-end)

description:
Day7
IPS7-3


title: Time Point 12 - RNA_Seq

city: New York

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

data_processing:
alignment - bowtie2
nucleosome peak calling - iNPS_V1.1.2
RPKM values were generated using in house created software. RPKM = (ReadsWithinORF) / ( ORFLength/1000 x TotalNumReads/1,000,000 )
Genome_build: R64-1-1
Supplementary_files_format_and_content: wig files for nucleosome data were generated with iNPS

organism: Saccharomyces cerevisiae

growth_protocol: Yeast Metabolic Cycle (Minimal Media)

extract_protocol:
RNA was extracted using the hot phenol method
RNA from each time-point was extracted by utilizing the hot phenol method, and libraries were generated with the NEBNext Ultra RNA Library Prep Kit for Illumina as per manufacturer’s instructions (Catalog #E7530L)

tag: time

value: 260 minutes


title: ES_Gm15446_ChIPseq_R2

description: replicate 2

tag: chip antibody


title: Day4, rep2 (Paired-end)

description:
Day4
IPS4-2


title: Day4, rep3 (Paired-end)

description:
Day4
IPS4-3


title: Time Point 10 - RNA_Seq

value: 230 minutes


title: Time Point 11 - RNA_Seq

value: 240 minutes


title: Time Point 9 - RNA_Seq

value: 220 minutes


title: Day0, rep3 (Paired-end)

description:
Day0 (no DOX treatment)
IPS0-3


title: Time Point 8 - RNA_Seq

value: 210 minutes


title: Time Point 7 - RNA_Seq

value: 200 minutes


title: Day4, rep1 (Paired-end)

description:
Day4
IPS4-1


title: Glomus cell 2

organism: Mus musculus x Mus spretus

value: carotid body

value: glomus cell

value: C57BL/6 X SPRET/EiJ

value: post natal day 4-5

value: wild type


title: Time Point 6 - RNA_Seq

value: 180 minutes


title: Day10, rep2 (Paired-end)

description:
Day10
IPS10-2

value: homozygous for a TET-OP-OKSM polycistronic transgene targeted to the collagen 1A locus and homozygous for rtTA targeted to the Rosa26 locus

value: embryo

value: fibroblasts


title: Time Point 4 - RNA_Seq

value: 110 minutes


title: Day0, rep2 (Paired-end)

description:
Day0 (no DOX treatment)
IPS0-2


title: Day0, rep1 (Paired-end)

description:
Day0 (no DOX treatment)
IPS0-1


title: Time Point 1 - RNA_Seq

value: 0 minutes


title: Time Point 5 - RNA_Seq

value: 140 minutes


title: Day20, rep1 (Single-end)

description:
Day20
IPS20-1


title: Clone, rep3 (Single-end)

description:
Clone
IPSC-3

value: Clone


title: Clone, rep2 (Single-end)

description:
Clone
IPSC-2


title: Clone, rep1 (Single-end)

description:
Clone
IPSC-1


title: Day15, rep3 (Single-end)

description:
Day15
IPS15-3


title: Time Point 11 - MNaseSeq

description: nucleosomal DNA

extract_protocol:
chromatin was formaldehyde crosslinked prior to nuclease digestion (1% formaldehyde with gentle shaking at room temp for 10 minutes)
500ng from each sample was incubated with 10U of PNK in a reaction containing 1X T4 Ligase Buffer, and 1mM dNTPs for 30 minutes at 37˚C (Total volume = 20ul).. 3U of T4 Pol was then added to each sample and incubation was allowed to proceed for 15 minutes at 12˚C. Subsequently, 1ul of 0.5M EDTA was added to inhibit the activity of T4 Polymerase and the reaction was killed by incubation at 75˚C for 20 minutes. 1.8 volumes of Ampure beads was added to each reaction to purify the nucleosomal DNA and remove the PNK and T4 Pol. DNA was resuspended in 15ul of TE (pH 8). dA tailing reactions of end cleaned DNA included 1X Taq Buffer, 1mM dNTPs, and 5U of Taq Polymerase (Total volume = 20ul), and were incubated at 72˚C for 30 minutes. Reactions were then again cleaned with 1.8 volumes of Ampure beads and resuspended in 17.5ul TE. To the dA tailed products we then ligated dT tailed hairpin adaptors purchased from NEB (Catalog #E7500L). Ligation reactions included the 17.5ul of nucleosomal DNA, 1X T4 Ligase Buffer, and 400U of T4 DNA Ligase (Total volume = 25ul), and were allowed to proceed at room temperature for 1 hour. To remove unligated adaptors and clean up the reaction, 1.8 volumes of Ampure beads were added and the adaptor ligated nucleosomal DNA was subsequently resuspended in 25ul of TE. Half of this product was then used in a reaction which served to both amplify and barcode each sample. PCR reactions included the adaptor ligated substrates, 1uM Universal Oligo, 1mM Barcode Addition Oligo, 3U of NEB USER enzyme, and 1X KAPA Hot Start Polymerase Mix (Final volume = 50ul). Libraries were amplified for 10 cycles of PCR. PCR reactions were purified with 1.8 volumes of Ampure beads and resuspended in 20ul of TE. Products were then run on a 1.4% agarose gel and monosomal bands were excised and gel purified.  The MNase digested samples were sequenced on the Illumina HiSeq platform, and the paired-end reads were mapped back to the S. cerevisiae genome using the Bowtie 2 software.

value: 240 minutes


title: Time Point 12 - MNaseSeq

description: nucleosomal DNA

value: 260 minutes


title: Day15, rep2 (Single-end)

description:
Day15
IPS15-2


title: Time Point 10 - MNaseSeq

description: nucleosomal DNA

value: 230 minutes


title: Day20, rep3 (Single-end)

description:
Day20
IPS20-3


title: Time Point 9 - MNaseSeq

description: nucleosomal DNA

value: 220 minutes


title: Time Point 8 - MNaseSeq

description: nucleosomal DNA

value: 210 minutes


title: Time Point 2 - RNA_Seq

value: 20 minutes


title: Time Point 3 - RNA_Seq

value: 60 minutes


title: Day10, rep2 (Single-end)

description:
Day10
IPS10-2


title: Day10, rep3 (Single-end)

description:
Day10
IPS10-3


title: Time Point 7 - MNaseSeq

description: nucleosomal DNA

value: 200 minutes


title: Day7, rep1 (Single-end)

description:
Day7
IPS7-1


title: Day10, rep1 (Single-end)

description:
Day10
IPS10-1


title: Day7, rep3 (Single-end)

description:
Day7
IPS7-3


title: Day7, rep2 (Single-end)

description:
Day7
IPS7-2


title: Time Point 5 - MNaseSeq

description: nucleosomal DNA


title: Day15, rep1 (Single-end)

description:
Day15
IPS15-1


title: Time Point 4 - MNaseSeq

description: nucleosomal DNA


title: Time Point 6 - MNaseSeq

description: nucleosomal DNA


title: Time Point 3 - MNaseSeq

description: nucleosomal DNA


title: Day0, rep3 (Single-end)

description:
Day0 (no DOX treatment)
IPS0-3


title: Day4, rep2 (Single-end)

description:
Day4
IPS4-2


title: Time Point 2 - MNaseSeq

description: nucleosomal DNA


title: Day4, rep1 (Single-end)

description:
Day4
IPS4-1


title: Day4, rep3 (Single-end)

description:
Day4
IPS4-3


title: Day20, rep2 (Single-end)

description:
Day20
IPS20-2


title: Time Point 1 - MNaseSeq

description: nucleosomal DNA


title: Day0, rep1 (Single-end)

description:
Day0 (no DOX treatment)
IPS0-1


title: BMPR2 kinase domain mutant rep1

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
quality trimming with Trimmomatic v0.33, resulting in read length of 25-51bp
alignment with STAR v 2.4.0, controlling for unannotated, non-canonical and rare junctions
read counting with HTSeq-Count v0.6.1p1, in the intersection nonempty mode, using same gtf as used in alignment step
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: txt files, raw read counts output from HTSeq-Count

molecule: polyA RNA

organism: Rattus norvegicus

extract_protocol:
RNA was extracted from H9C2 cells with a Qiagen RNEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: BMPR2 kinase domain mutant rep2


title: BMPR2 tail domain mutant rep2


title: BMPR2 tail domain mutant rep1


title: Empty Vector rep2


title: 22Rv1 MBD-Seq Input DNA

description:
processed_data_file: 22Rv1_DiffBind_mC.txt
22Rv1_MACSDataAll.txt  - contains reads compared to input for 22Rv1 for hMeSeal-seq and MBD-seq)

data_processing:
MBD-Seq: Base calling was performed using CASAVA v1.8.2. Sequenced reads were mapped to the reference human genome (GRCh37, hg19) using Bowtie (v0.12.7). Significantly enriched regions/peaks of methylation were determined using model-based analysis of ChIP-seq (MACS) algorithm, by comparing bound, enriched samples to input, non-enriched samples. Annotation was performed using ChIPpeakAnno R package (v.1.12.0) and a customized version of Annovar program with RefSeq genes to determine specific genomic features: promoter regions (2.5 kb upstream and 500 bp downstream from the nearest TSS), genic (further defined as 500 bp downstream from the nearest TSS), exons, introns, and intergenic (defined as greater than 100 kb up/downstream from the nearest TSS). UCSC CpG island definitions were used to define CpG islands.  RWPE-1 DNase-seq data from The Encyclopedia of DNA Elements (ENCODE) project (GEO accession: GSM1008595) was correlated to MACS peak sets in both RWPE-1 and 22Rv1 cells. The genomic feature, RWPE-1 UCSC DNAseI peaks, was defined as: within 5 kb of a DNase peak.The following options for ChiPpeakAnno were used:  PeakLocForDistance=”middle”, FeatureLocForDistance=”middle” for DNase I HS and CpG data, and FeatureLocForDistance=”TSS” for RefSeq gene annotations. MACS data was further analyzed using DiffBind R package (v.1.12.0) to determine three consensus peak sets by requiring that peaks from one, two, or all three replicates be present at the same location. The third consensus peak set was subsequently defined as differentially methylated regions (DMRs) between RWPE-1 and 22Rv1 cells (fold change >1, FDR <0.1).
genome build: hg19
processed data files format and content: diffBind output

value: prostate adenocarcinoma

tag: passage

value: none (input)


title: Empty Vector rep1


title: RWPE-1 MBD-Seq Input DNA

description:
processed_data_file: RWPE1_DiffBind_mC.txt
RWPE1_MACSDataAll.txt - contains reads compared to input for RWPE1 for hMeSeal-seq and MBD-seq

value: Normal prostate epithelium

tag: enrichment


title: 22Rv1 hMeSeal-Seq Rep 1

description:
processed_data_file: 22Rv1_DiffBind_hmC.txt
22Rv1_MACSDataAll.txt  - contains reads compared to input for 22Rv1 for hMeSeal-seq and MBD-seq)
hydroxymethylation profiling

value: hMeSeal-Seq


title: 22Rv1 MBD-Seq Rep 3

value: MBD-Seq


title: RWPE-1 hMeSeal-Seq Rep 1

description:
processed_data_file: RWPE1_DiffBind_hmC.txt
RWPE1_MACSDataAll.txt - contains reads compared to input for RWPE1 for hMeSeal-seq and MBD-seq
hydroxymethylation profiling


title: Day0, rep2 (Single-end)

description:
Day0 (no DOX treatment)
IPS0-2

value: homozygous for a TET-OP-OKSM polycistronic transgene targeted to the collagen 1A locus and homozygous for rtTA targeted to the Rosa26 locus

value: embryo

value: fibroblasts


title: RWPE-1 MBD-Seq Rep 3


title: 22Rv1 MBD-Seq Rep 2


title: RWPE-1 MBD-Seq Rep 2


title: liver_pooled 6 pigs control diet (L)

city: Magdalenka

first: Agnieszka

last: Szostak

address: Postępu, Jastrzębiec

country: Poland

institute: Institute of Genetics and Animal Breeding PAS

data_processing:
Illumina pipeline were used for image acquisition and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sus scrofa v.10.2 whole genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Alignment and filtering were performed using ArrayStar aplication from DNASTAR Lasergene Genomics Suite software
Genome_build: Genome_build: Sus scrofa v.10.2
Supplementary_files_format_and_content: Supplementary files format and content: tab-delimited text files include RPKM values and counts for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted from the liver samples using RNeasy Fibrous Tissue Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: dietary group

value: standard diet (control)


title: liver_pooled 6 pigs enriched diet (H)

value: enriched with PUFA


title: Wild-type rep 2

status: Public on Mar 14 2016

city: Irvine

first: Klemens

last: Hertel

address: 19182 Jamboree Rd. 811 Med Sci I, C270

department: MMG

institute: UCI

data_processing:
Illumina Casava base-calling
Sequenced reads were trimmed for adaptor sequence, then were trimmed by 10 bases at the 5' end. Trimmed 40 bp long reads were then mapped to the human genome hg19 using TopHat (version 2.0.4) with default parameters.
Replicate samples were combined and only uniquely mapped reads were kept.
MISO was used to determine splicing variance between Wild-type and CstF64KD. Results were filtered with the following parameters --delta-psi 0.15 --bayes-factor 10
In-house Perl script assigned gene name based on splicing event information.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files, with the splicing event name, psi-values for each sample, the delta-psi, bayes factor and associated gene name among other identifiers.

source_name: HeLa cell line

extract_protocol:
HeLa cell lines were stably transfected with shRNA plasmids targeting CstF64 and maintained by culturing in the presence of 1 mg/ml puromycin. Total RNA was isolated from CstF64 KD and wild-type control cells using Trizol reagent.
Total RNA isolated from two biological replicates was used to generate independent libraries using the Illumina TruSeq RNA sample preparation kit according to manufacturer’s protocols. Each library was diluted to approximately 10 pM prior to loading and sequencing on the Illumina GA IIx instrument.

value: HeLa

value: Wild-type


title: CstF64 KD rep 2

value: CstF64 knockdown


title: CstF64 KD rep 1


title: Wild-type rep 1


title: FUSKIwt2

city: Charlestown

first: Clotilde

last: Lagier-Tourenne

state: MA

address: Bldg. 114 16th Street, Room 3125

department: Neurology

institute: Massachusetts General Hospital

description: RASL-Seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to mm9 whole genome using tophat-2.0.8b.Linux_x86_64 with parameters --no-coverage-search -G genes.gtf --transcriptome-index=transcriptome_data/known --prefilter-multihits --max-multihits 1 --library-type fr-firststrand -o *_thout genome *.fastq.bz2
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks version v2.1.1 with parameters -N -F 0 -G genes.gtf -o *_clout *_thout/accepted_hits.bam
Significant gene expression change between groups has been detected using cuffdiff
For RASL-seq data, the reads were mapped to targetd exon-exon junctions with Bowtie1 by allowing up to two mismatches, then the number of reads for each isoform was counted.
Genome_build: mm9
Supplementary_files_format_and_content: excel files include count values of short isoform (*_s) and long isoform (*_l) from FUS KI and KO for each sample
Supplementary_files_format_and_content: excel files include FPKM values from FUS KI and KO for each sample

extract_protocol:
Total RNA from E18.5 mouse brains was extracted with Trizol.
Illumina TruSeq Stranded mRNA Sample Preparation Kit
RASL library was constructed according to Li H, et al protocol published Current Protocols in Molecular Biology.

value: Brain

value: Non-Tg


title: FUSKIwt3

description: RASL-Seq


title: FUSKIwt1

description: RASL-Seq


title: FUSKIhet4

description: RASL-Seq

value: FUS deltaNLS/-


title: FUSKIhet1

description: RASL-Seq


title: PDPN KD LEC rep2

city: Boston

first: Noorjahan

last: Panjwani

address: 136 Harrison Ave

department: Ophthalmology

institute: Tufts University

data_processing:
Illumina Bcl2Fastq software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using tophat2 with additional parameter -p 8, with accepted_hits.bam for each individual sample as output.
Differential gene expression analysis was performed using Cuffdiff with parameters -p 8 -L CTRL,PDPNKD -u, with the accepted_hits.bam for each sample from the tophat as input.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample from cuffdiff, in a single file "genes.fpkm_tracking"

source_name: lymphatic endothelial cell

extract_protocol:
Primary LECs were transfected with AllStar Negative siRNA and PDPN siRNA. (N=2 for each group). After 48 hr, total RNA was isolated using RNeasy Mini Kit and  the  resulted  RNA  samples  were  treated  with  DNase  I  to  eliminate  DNA  contamination (Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA transfection with RNAiMax

value: 48 hr post-transfection

tag: sirna

value: podoplanin siRNA


title: FUSKIhet2

description: RASL-Seq

tag: genotype


title: PDPN KD LEC rep1


title: FUSKIhet3

description: RASL-Seq


title: ZLW01

city: Hefei

first: chaoling

last: Wei

state: Anhui

address: 130 West Changjiang Road

country: China

institute: Anhui Agricultural University

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18-25 nucleotide were mapped to specific species precursors in miRBase 21 by BLAST search to identify known miRNAs and novel 3p - and 5p - derived miRNAs. Length variation at both 3’ and 5’- ends and one mismatch inside of the sequence were allowed in the alignment.
Supplementary_files_format_and_content: miRNAs and counts

organism: Camellia sinensis

source_name: Leaves and roots

growth_protocol: Three-year-old tea plant clone cuttings were cultured in pots (30-cm diameter, 35-cm height), and grown under natural daylight conditions at the tea plantation in Anhui Agricultural University, Hefei, China.

extract_protocol:
Total RNA was prepared from leaves and roots using the Total RNA Purification kit (Norgen Biotek Corporation, Canada), following the manufacturer’s instructions using the on-column DNA contamination removal protocol. A portion of the RNA samples for all tissue samples were mixed into a single RNA pool by equal fraction ratio. The quality and integrity of the total RNA were examined by using the Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA)
The small RNA fragments (16-30 bases) were isolated from the 200 l total RNA pool using a 15% polyacrylamide denaturing gel. After purification, the small RNAs were ligated sequentially to RNA 5’ adapters and 3’ adapters, reversely transcribed to cDNA, and amplified by PCR. Finally, the purified and validated sRNA-derived cDNA library was sequenced by Solexa sequencing technology using an Illumina GAIIX system provided by LC Sciences (Houston, Texas, USA)

value: tender leaves and young lateral roots

tag: cultivar

value: Shuchazao


title: Control LEC rep2

value: control siRNA


title: FUSKIhom4

description: RASL-Seq

value: FUS deltaNLS/ deltaNLS


title: FUSKIhom3

description: RASL-Seq


title: MCF7

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: nanoCAGE in MCF7 cells

data_processing:
Clustered using onboard clustering and sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64). Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite. The quality scale is Sanger /  phred33 / Illumina 1.8+.
nanoCAGE reads corresponding to transcription start sites (TSS) were extracted, de-multiplexed and reads aligning to ribosomal RNA were removed using TagDust 2.13.
The resulting reads were aligned to hg19 using Bowtie 1.0.1 (Langmead et al. 2009) allowing 2 mismatches (default parameters). Uniquely aligned reads (using “m” and “best” parameter in bowtie) and reads that failed to align to hg19 were then aligned to RefSeq 5’ UTRs plus 78 bases of upstream genomic sequence and 78 bases of downstream sequence using bowtie as above but without the “m” parameter to allow reads to map to multiple isoforms. The alignments were then trimmed to remove sequence mismatches within the first two bases. Reads originating from strand invasion were removed as described (Tang et al. 2013) with the “-e” parameter set to 2 and sequences from the same set of 5’ UTRs with 78 bases upstream genomic and 78 bases downstream sequence.
All high confident RefSeqs (>50 reads) and peaks (>5 reads at the exact same position) where then collected and 5’ UTR lengths were calculated either by determining the length suggested by the position that obtained the largest number of reads (mean if 2 or more positions had the same number of reads) or by determining the mean length suggested by all reads.
Genome_build: hg19
Supplementary_files_format_and_content: This is a tab-delimited text file with the following columns: geneID - entrez gene identifier; geneSymb - entrez gene symbol; nReads - number of mapped reads. wUtrL indicates weighted UTR length; peakUtrL indicated UTR length suggested by majority of reads; refseq 5'UTR indicates the RefSeq to which the reads map; UTRseq indicates the suggested sequence using the peak approach. Notice: Some genes have alternative 5'UTRs. For these data for all UTRs are shown and separated by ";" in each column.

growth_protocol: MCF7 cells (ATCC) were maintained in Dulbecco modified Eagle medium (DMEM; Wisent, St-Bruno, Quebec, Canada), supplemented with 10% fetal bovine serum (Wisent), 1% penicillin/streptomycin (Wisent) and 1% L-Glutamine (Wisent).

extract_protocol: Total RNA was extracted using Trizol


title: RWPE-1 MBD-Seq Rep 1

extract_protocol:
80% confluent cells were harvested from flasks, and genomic DNA was extracted using the QIAamp DNA Mini Kit (Cat No. 51306).
Libraries were prepared for sequencing as per the standard Illumina protocol for genomic DNA.

value: Normal prostate epithelium

value: MBD-Seq


title: 22Rv1 MBD-Seq Rep 1

value: prostate adenocarcinoma


title: FUSKIhom2

description: RASL-Seq


title: FUSKIhom1

description: RASL-Seq


title: FUSKIwt4

description: RASL-Seq


title: wt5886

description: RASL-Seq


title: wt5884

description: RASL-Seq


title: wt5734

description: RASL-Seq


title: wt5813

description: RASL-Seq


title: ko7301

description: RASL-Seq

value: FUS -/-


title: SZ2_A  NPC

first: Kristen

last: Brennand

state: NY

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: 1792#1 NPC#A

data_processing:
The Illumina TruSeq RNA kit was used for 100nt/paired end reads, 4 samples were run per lane using the standard Truseq indices.  Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at both the geneic and exonic levels for UCSC and ensemble annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the read count for each gene

source_name: hiPSC forebrain NPCs

growth_protocol: hiPSC forebrain NPCs were derived as described previously (Brennand et al., 2011). Forebrain NPCs were maintained at high density, grown on either Matrigel-coated plates in NPC media (DMEM/F12, 1x N2, 1x B27-RA (Invitrogen), 1 μg/ml Laminin (Invitrogen) and 20 ng/ml FGF2 (Invitrogen) and split approximately 1:3-1:4 every week with Accutase (Millipore).

extract_protocol:
Cells were lysed in RNA BEE (Tel-test, Inc). RNA was chloroform extracted, pelleted with isopropanol, washed with 70% ethanol and resuspended in water. RNA was treated with RQ1 RNAse-free DNAse (Promega) for 30 minutes at 37C and then the reaction was inactivated by incubation with EGTA Stop buffer at 65C for 10 minutes.
RNA libraries were prepared for sequencing using standard Illumina protocols
Hi-Seq, 100nt, Paired-End Read, 4 samples per lane

tag: diagnosis

value: Schizophrenia

tag: gender

value: male

tag: repository source fibroblast id

value: GM01792 (Coriell)


title: SZ1_B  NPC

description: 2038#1 NPC#B

value: GM02038 (Coriell)


title: SZ3 NPC

description: 1835#1 NPC#3

value: female

value: GM01835 (Coriell)


title: SZ4 NPC

description: 2497#1 NPC#B

value: GM02497 (Coriell)


title: C6 NPC

description: 9429#3 NPC#A

value: Control

value: AG09429 (Coriell)


title: SZ2_E  NPC

description: 1792#1 NPC#E


title: ko5867

description: RASL-Seq

value: Brain


title: ko5881

description: RASL-Seq


title: C4 NPC

description: 4506#B NPC#A

value: GM04506 (Coriell)


title: C5 NPC

description: 9319#2 NPC#A

value: AG09319 (Coriell)


title: C3 NPC

description: 3651#A NPC #A

value: GM03651 (Coriell)


title: wt5715

description: RASL-Seq

value: Non-Tg


title: ko5862

description: RASL-Seq


title: C2 NPC

description: 3440#5 NPC#A

value: GM03440 (Coriell)


title: Control LEC rep1

value: 48 hr post-transfection

value: control siRNA


title: ko5732

description: RASL-Seq

value: FUS -/-


title: KO10

description: RNA-seq


title: KO9

description: RNA-seq


title: KO7

description: RNA-seq


title: C1 NPC

description: BJ#2 NPC#A

value: male

value: BJ


title: KO5

description: RNA-seq


title: KO8

description: RNA-seq


title: KO4

description: RNA-seq


title: SZ1_A  NPC

description: 2038#1 NPC#A

value: Schizophrenia

value: GM02038 (Coriell)


title: KO2

description: RNA-seq


title: KO1

description: RNA-seq


title: Br375

description: RNA-seq


title: Br374

description: RNA-seq


title: Br378

description: RNA-seq

value: FUS deltaNLS/ deltaNLS


title: Br377

description: RNA-seq


title: Br370

description: RNA-seq


title: Br379

description: RNA-seq


title: Br371

description: RNA-seq


title: Br367

description: RNA-seq


title: Br372

description: RNA-seq


title: KO6

description: RNA-seq


title: Cluster 16

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

data_processing:
RNA-seq reads were mapped to mm9 using Stampy with default parameters.
Read pairs with the same outer coordinates were filtered out using samtools rmdup.
Reads were assigned to Ensembl transcripts using htseq-count.
TMM normalization was performed using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file containing Ensembl gene IDs and gene names in the first two columns, followed by normalized gene expression values (tags per million) for each individual sample in the subsequent 78 columns.

source_name: Placenta

extract_protocol:
Cells were digested from dissected E9.5 placenta using Liberase TM and cells of interest enriched by FACS.  Single cells were picked by mouth pipette and cDNA prepared exactly as in Tang et al., Nature Protocols 5, - 516 - 535 (2010).
Sequencing libraries were prepared using the Illumina ChIP-seq DNA Sample Prep Kit. Libraries were size selected at ~200bp, multiplexed and sequenced using a HiSeq 2500.

value: Primary placental cells

tag: develpomental stage


title: Cluster 14

tag: cell type


title: Cluster 13

tag: strain


title: Cluster 12


title: Cluster 10


title: Cluster 11


title: Grain_184_spleen

city: College Park

first: Jose

middle: Adrian

last: Carrillo

state: MD

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

institute: University of Maryland

data_processing:
Illumina HiSeq 2000 sequencer for basecalling
Alignment to the reference genome (Bos_taurus_UMD3.1/bosTau6) obtained from the UCSC (http://genome.ucsc.edu/) was performed employing Bowtie (Ultrafast, memory-efficient short read aligner). During this step, the first 15 bases of each read (50 bp) were trimmed to avoid low Phred quality scores, resulting in 35 bp tags
Counting of reads per gene was executed by the summarizeOverlaps function implemented in R
The identification of differentially expressed genes was achieved employing the edgeR software package and the included generalized linear model (GLM) approach, which requires a design matrix to describe the treatment conditions (grass-fed and grain-fed).
Genome_build: Bos_taurus_UMD3.1/bosTau6
Supplementary_files_format_and_content:
SpleenCountRaw.txt: Raw count per gene
SpleenCountNormalizededgeR.txt: Normalized reads count per gene using edgeR
SpleenSigensembl_edgeRGLM.txt: Differentially expressed genes, with statistical measurement obtained from edgeR using GLM measurement obtained from edgeR using GLM approach

organism: Bos taurus

growth_protocol: The animals were born, raised and maintained at the Wye Angus farm. All animals received the same diet until weaning

extract_protocol:
Total RNA was extracted individually (two animals per group) using Trizol (Invitrogen, Carlsbad, CA, USA) followed by DNase digestion and Qiagen RNeasy column purification (Invitrogen, Carlsbad, CA, USA). The RNA sample was dissolved in RNAse-free H2O; the integrity and quality of RNA were then checked by a NanoDrop 1000 spectrophotometer and by resolution on a 1.5% non-denaturing agarose gel
Each library was identified by adding 6-bp adaptors and sequenced at 50 bp/sequence read using an Illumina HiSeq 2000 sequencer

treatment_protocol: After weaning, the calves were randomly assigned to one diet and exclusively received that regimen until termination. The grain group received conventional diet consisting of corn silage, shelled corn, soy bean and trace minerals. The grass fed steers consumed normally grazed alfalfa; during wintertime, bailage was utilized. The alfalfa has been harvested from land without any fertilizers, pesticides or other chemicals. The steers ate no animal, agricultural or industrial byproducts and never receive any type of grain

tag: breed

value: Aberdeen Angus

tag: treatment group

value: Grain-fed

value: spleen


title: Grain_224_spleen

tag: tissue


title: Grass_104_spleen

data_processing:
Illumina HiSeq 2000 sequencer for basecalling
Alignment to the reference genome (Bos_taurus_UMD3.1/bosTau6) obtained from the UCSC (http://genome.ucsc.edu/) was performed employing Bowtie (Ultrafast, memory-efficient short read aligner). During this step, the first 15 bases of each read (50 bp) were trimmed to avoid low Phred quality scores, resulting in 35 bp tags
Counting of reads per gene was executed by the summarizeOverlaps function implemented in R
The identification of differentially expressed genes was achieved employing the edgeR software package and the included generalized linear model (GLM) approach, which requires a design matrix to describe the treatment conditions (grass-fed and grain-fed).
Genome_build: Bos_taurus_UMD3.1/bosTau6
Supplementary_files_format_and_content:
SpleenCountNormalizededgeR.txt: Normalized reads count per gene using edgeR
SpleenSigensembl_edgeRGLM.txt: Differentially expressed genes, with statistical measurement obtained from edgeR using GLM !Sample_data_processing = SpleenSigensembl_edgeRGLM.txt: Differentially expressed genes, with statistical measurement obtained from edgeR using GLM approach

value: Grass-fed


title: Grass_222_spleen


title: Cluster 15


title: KO3

description: RNA-seq

value: Brain


title: Cluster 6


title: Cluster 7


title: Cluster 8


title: Cluster 5


title: Cluster 4


title: Cluster 3


title: Cluster 2


title: Cluster 1


title: Cell 60


title: Cell 61


title: Cluster 17


title: Cell 58


title: Cell 56


title: Cell 59


title: Cell 57


title: Cell 55


title: Cluster 9


title: Cell 54


title: Cell 53


title: Cell 52


title: Cell 50


title: Cell 51


title: Cell 45


title: Cell 43


title: Cell 39


title: Cell 46


title: Cell 37


title: Cell 40


title: Cell 35


title: Cell 36


title: Cell 47


title: Cell 38


title: Cell 42


title: Cell 48


title: Cell 49


title: Cell 41


title: Cell 32


title: Cell 34


title: Cell 26


title: Cell 31


title: Cell 23


title: Cell 33


title: Cell 30


title: Cell 24


title: Cell 29


title: Cell 25


title: Cell 44


title: Cell 21


title: Cell 27


title: Cell 19


title: Cell 22


title: Cell 18


title: Cell 15


title: Cell 28


title: Cell 9


title: Cell 6


title: Cell 17


title: Cell 16


title: Cell 10


title: Cell 14


title: Cell 12


title: Cell 8


title: Cell 7


title: Cell 5


title: Cell 4


title: Cell 3


title: Cell 1


title: Cell 2


title: Cell 20


title: Control Input for Flag-Glis3

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Input DNA

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Binding sites as defined by SISSRs [PMID: 18684996]
Genome_build: mm9
Supplementary_files_format_and_content: TEXT file containing the list of binding sites

source_name: pancreatic alpha cells aTC1-9 expressing 3xFlag-Glis3-mcherry

growth_protocol: αTC1-9 cells were maintained in DMEM medium (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
αTC1-9 cells in culture dishes were cross-linked with 1% formaldehyde for 10 minutes, processed for chromatin lysate preparation and chromatin immunoprecipitation (ChIP). Chromatin lysate was sonicated with a Bioruptor system (Diagenode) to yield a DNA smear averaging ~200-500 bp. Sonicated chromatin lysate from 5 million ES cells was used for each ChIP with ANTI-FLAG® M2 Affinity Gel.
Input and ChIP DNA were size-selected (~200-500nt). Libraries were prepared from size-selected Input and ChIP DNA according to the standard Illimina library preparation protocol

value: pancreatic alpha cells

tag: cell line

value: none (input)


title: ChIP-Seq Flag-Glis3

description: ChIP DNA

tag: chip antibody

value: Antibody: ANTI-FLAG® M2 Affinity Gel A2220 (Sigma-Aldrich)


title: E15.5 input

status: Public on Mar 12 2016

city: san francisco

first: olga

last: golonzhka

address: 1550 4th street

department: psychiatry

institute: UCSF

data_processing:
Samples were sequenced on Illumina HiSeq 2000 platform (50bp single-end reads). Base calls were performed using RTA 1.13.48 software.
All reads were mapped to the mouse genome (mm9) using the Burrows-Wheeler Alignment (BWA).
Peaks were filtered to remove regions where the majority of supporting reads originated in repeat sequence and annotated to genomic features.
Peaks were called using MACS1.4 with default settings.
We used the union of peaks called against input control and negative blocking peptide control.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: bigWig files

source_name: E15.5 cortex, input

extract_protocol:
WT cortices (one litter of E15.5) were dissected, triturated in 1% formaldehyde in PBS and fixed for total of 10min at room temperature. Fixed cells were pelleted and washed with cold PBS. Pellets were lysed in 500ul of lysis buffer (1% SDS, 10mM EDTA and 50mM Tris, pH 8.1) on ice for 10min and lysates were sonicated using Bioruptor (Diagenode) on High Settings for 15 cycles (7.5 min of total sonication time). Resulting average chromatin size was 200-500 bp as verified by the Bioanalyzer. Cleared Chromatin was diluted 10 times with Dilution buffer (0.01% SDS, 1.1% Triton X- 100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl) and was incubated overnight at 4C with 3ug of appropriate antibody. Mixture of protein A and G magnetic beads (Life Technologies) was preblocked overnight with BSA and tRNA and was added to the chromatin next day for 3 hours. Immune complexes were washed once with Low Salt buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), High Salt buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP-40, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris, pH 8.1) and TE buffer. Complexes were eluted in 1% SDS, 10mM Sodium bicarbonate buffer at 65C for 10min. Crosslinks were reversed at 65C overnight, proteins were digested using proteinase K and DNA was purified using Zymo Chip DNA Clean and Concentrator kit (Zymo research). Immunoprecipitation was performed using the following antibody: Pbx1/2/3/ (sc-888, Santa Cruz). As a negative control in PBX ChIP experiments, the PBX antibody was incubated with PBX blocking peptide (sc-888P, Santa Cruz) at 1:400 molar ratio, and added to the chromatin lysates.
ChIP-Seq libraries were prepared using NEBNext library Prep kit (New England Biolabs) and Illumina standard adaptors. 50bp single end.

tag: strain/background

value: mixed

tag: genotype/variation

value: wild type

value: cerebral cortex

tag: developmental stage


title: 46c_H3K122ac_rep1

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

description:
processed data file:
46C_H3K122acmerged.10bpres.bed, 46C_H3K122acmerged.10bpres.bedGraph.gz

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-0.12.8 (options bowtie -e 40 -m 1 -v 2)
Bedgraph tracks were generated from the aligned reads by the program makeUCSC file from HOMER software suite (version 4.3) at a resolution of 10bp and the total number of tags is normalized to 10 million.
bed peak files were generated using SICER (v1.1) (Zang et al, 2009), using GSM1156619 UD46c input as control library, a window size of 200bp, gap size of 600bp and and FDR of 0.01
column headers for islands-summary-FDR0.01.bed files;
chrom,start,end,ChIP_island_read_count,CONTROL_island_read_count,p_value,fold_change,FDR_threshold
Genome_build: 46c data: NCBI37/mm9; K562 data: GRCh37/hg19

growth_protocol: 46c (Sox1-GFP) ESCs (Ying et al. Nature biotechnology 2003) were cultivated without feeders in GMEM media containing With L-Glutamine media containing 10% fetal bovine serum (FBS), L-glutamine, Sodium Pyruvate, Lif,  beta-Mercaptoethanol, Nonessential aminoacids, penicillin and streptomycin.  Human erythro-myeloblastoid leukemia cells (K562) were cultured in RPMI 1640 With L-Glutamine media containing 10% fetal bovine serum (FBS), L-glutamine, penicillin and streptomycin.

extract_protocol:
Chromatin was digested with MNase and released at 4C overnight, then histone-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Undifferentiated ESCs and K562 cells

value: 46c (sox1-GFP)

value: mouse embryonic stem cells

tag: passages

value: anti-H3K122ac (Tropberger et al 2013, PMID:23415232)


title: E15.5 minus

description: Immunoprecipitated genomic DNA (with antibody preblocked with blocking peptide).

source_name: E15.5 cortex, negative control

value: Pbx1/2/3 (Santa Cruz, sc-888) mixed with the PBX blocking peptide (Santa Cruz, sc-888P) at 1:400 molar ratio


title: 46c_H3K64ac_rep1

description:
processed data file:
46C_H3K64acmerged.10bpres.bed, 46C_H3K64acmerged.10bpres.bedGraph.gz

value: anti-H3K64ac (Di Cerbo et al 2014, PMID:24668167)


title: Cell 13

value: Primary placental cells


title: Cell 11


title: E15.5 plus

description: Immunoprecipitated genomic DNA. Antibody recognizes three Pbx isoforms: Pbx1, Pbx2 and Pbx3.

source_name: E15.5 cortex, Pbx1/2/3 ChIP

value: Pbx1/2/3 (Santa Cruz, sc-888)


title: RNA-Seq of rrp6 deletion (with Chd1-Ume6)- 2

city: Eugene

first: Jeffrey

middle: N

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) appended with ERCC Spike-in Control reads (https://tools.lifetechnologies.com/content/sfs/manuals/ERCC92.zip) using TopHat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Differential transcript analysis was performed using CuffDiff (cufflinks 2.2.1) with a maskfile for rRNA and tRNA
Independent isolates were merged
Genome_build: Saccharomyces_cerevisia.EF4.65

growth_protocol: cells were grown to OD600 0.4 to 0.6

extract_protocol:
RNA was extracted with hot acid phenol, treated with Dnase I, and depleted of rRNA
Strand-specific libraries were prepared according to dUTP method and TruSeq (Illumina) Sample Prep Kit

tag: strain background

value: rrp6 deletion with Chd1-Ume6

tag: isolate number

value: isolate 2

tag: presence of chd1-ume6 fusion

value: yes


title: RNA-Seq of wild type cells (with Chd1-Ume6) - 2

value: wild type (with Chd1-Ume6)


title: RNA-Seq of ume6 deletion (with Chd1-Ume6) - 2

value: ume6 deletion (with Chd1-Ume6)


title: RNA-Seq of rrp6 deletion - 2

value: rrp6 deletion

value: no


title: RNA-Seq of ume6 deletion - 2

value: ume6 deletion


title: RNA-Seq of rrp6 deletion - 1

value: isolate 1


title: PL45 IGF2BP3 RIP-seq 3

city: Santa Cruz

first: Jonathan

middle: Michael

last: Howard

address: 1154 High Street

department: Molecular, Cell, and Developmental Biology

institute: University of California-Santa Cruz

description:
total RNA
PL45_RIP.txt

data_processing:
The following steps were applied to the PL45 RIPseq samples and controls (pu001-pu006).
RIPseq 1:  Constructed a version of the hg19 genome where regionsoutside of genes were masked out
RIPseq 2: transcriptome used was RefSeq
RIPseq 3: RMAP was used for read mapping.
RIPseq 4: Per-gene read counts were constructed by counting the number of reads partially or fully overlapping one or more transcripts of a particular gene.
RIPseq 5: Target identification from per-gene read-counts of RIP-seq data was performed using Piranha.
hg19
PL45_RIP.txt; contains chomosome number, start and stop coordinates, Gene symbols, p-values for each replicate, average p-value across replicates, putative target? (1 = yes; 0=no)

source_name: PL45 cells

growth_protocol: For iCLIP, RIP-seq, and small RNA-seq protocols, PL45 and/or Panc1 cells were grown in 10 cm2 cell culture plates reaching 70-80% confluency. For RNA-seq protocol, PL45 and Panc1 control and IGF2BP3 KD cell lines were grown to 60-70% confluency in 6-well plates.

extract_protocol:
For iCLIP protocol, cytosolic extracts (detergent lysis) were prepared from PL45 and Panc1 cell lines prior to immunoprecipitation.  For RNA-seq, cytosolic extracts (detergent lysis) were prepared from control and IGF2BP3 shRNA Pl45 and Panc1 cell lines, and RNA isolation from these extracts was performed with TRIreagentLS. For PL45 and Panc1 RIP-seq, cells where lysed in polysomal lysis buffer buffer (10 HEPES pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP40, 2 mM dithiothreitol) containing proteinase and RNA inhibitors.
For iCLIP, libraries were constructed as previously described (Huppertz, I., et al. Methods. 2014) with minor changes. 3' Adenylated adapter, AIR ligase, and PCR primers used from NEXTflex™  Illumina Small RNA-Seq Library Prep Kit (Bioo Scientific) and RT primers were adapted for kit reagent use. For RNA-seq, and Panc1 RIP-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ Kit was used (Bioo Scientific). For small RNA-seq library prepartation, NEXTflex™ Small RNA-Seq Kit v2 was used.
For iCLIP, RNA purification was performed as previously described (Huppertz, I., et al. Methods. 2014). For RNA-seq, PolyA+ selection was performed. For small RNA-seq. For Panc1 RIP-seq samples, RNA was eluted from IP using Proteinase K digestion of protein, followed by isolation using acid Phenol-chloroform extraction. For small RNA-seq, total RNA from TRIreagentLS prep was used.

treatment_protocol: PL45 and Panc1 control and IGF2BP3 shRNA cells were selected with puromycin treatment at 5µg/mL for 3 days and later used for RNA isolation and library construction.

value: Epithelial

tag: disease

value: Pancreatic ductal adenocarcinoma

tag: knockdown


title: PL45 IGF2BP3 RIP-seq 2

description:
total RNA
PL45_RIP.txt


title: PL45 IGF2BP3 RIP-seq 1

description:
total RNA
PL45_RIP.txt


title: PL45 IgG RIP-seq 1

description:
total RNA
PL45_RIP.txt


title: PL45 IgG RIP-seq 2

description:
total RNA
PL45_RIP.txt


title: PL45 IgG RIP-seq 3

description:
total RNA
PL45_RIP.txt


title: miRNA-seq 3

description:
total RNA/small RNA
miRNA_Expression.txt

data_processing:
miRseq 1: each read was searched for the presence of adaptor sequence TGGAATTC and trimmed from that point on. Reads without the adaptor were discarded. Reads shorter than 18bp after trimming were discarded.
miRseq 2: based on 8 random bases of internal barcode at the first 4 and last 4 positions of each read after adaptor trimming, the readIDs were divided into classes (for later use in duplicate removal).
miRseq 3: 4bp were trimmed from the 5' end and 4bp were trimmed from the 3' end of each read before mapping
miRseq 4: reads mapping (by bowtie2) to human repeatMasker elements were discarded
miRseq 5: reads were mapped by STAR to hg19 with an additional set of junctions derived from Gencode V19 basic with 100bp overlap
miRseq 6: for each class of internal random barcode bases from step (2), duplicate read mappings of the same start and end position were discarded
miRseq 7: bam files were converted to coverage using bedtools
miRseq 8: for each preMicroRNA (type=miRNA in UCSC hg19 table of sno/miRNA), the total coverage was calculated over all its positions.
hg19
miRNA_Expression.txt; contains information on microRNA ID Expresssion values from three replicates, average expression value, Average Overlap (yes/no)

source_name: Panc1 cells

value: Pancreatic epithelioid carcinoma


title: ume6_Chd1Ume6_MNase_2

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Tophat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Between-strain comparisons were done using best-matched MNase digests. For isw2-related parent strains, wild-type 2 is best-matched. For ume6-related strains, wild-type 1 is best-matched. For WT +Chd1Ume6, wild-type 1 is best-matched.
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts

source_name: W303 auxotroph

growth_protocol: log cells were grown to OD600 0.4 to 0.6

extract_protocol:
DNA was purified by phenol/chloroform and mononucleosome size fragments were purified from an agarose gel for library construction
TruSeq protocol (Illumina) was followed

treatment_protocol: cells were treated with zymolyase and spheroplasts were treated with MNase and ExoIII to produce nucleosome ladders corresponding to roughly 80% mononucleosomes

value: W303 auxotroph

value: ume6 deletion with hybrid remodeling protein

tag: matched wild type sample


title: miRNA-seq 2

tag: cell type


title: Panc1 IGF2BP3 RIP-seq 3

description:
total RNA
PANC1_RIP.txt


title: Panc1 IGF2BP3 RIP-seq 2

description:
total RNA
PANC1_RIP.txt


title: ume6_MNase_2


title: WT_MNase_3

value: wild-type


title: Panc1 IGF2BP3 RIP-seq 1

description:
total RNA
PANC1_RIP.txt


title: RNA-Seq of wild type cells (with Chd1-Ume6)

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) appended with ERCC Spike-in Control reads (https://tools.lifetechnologies.com/content/sfs/manuals/ERCC92.zip) using TopHat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Differential transcript analysis was performed using CuffDiff (cufflinks 2.2.1) with a maskfile for rRNA and tRNA
Independent isolates were merged
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: Normalized FPKM Values of all Genes for Indicated Strains. The existance of a Ume6 binding motif (WNGGCGGCWW) within 500 base pairs of the associated gene is indicated by Has_Motif = yes.


title: RNA-Seq of wild type - 2

source_name: RNA-Seq of wild type

value: wild type


title: RNA-Seq of rrp6 deletion (with Chd1-Ume6)- 1


title: IGF2BP3 shRNA RNA-seq 4

description:
polyA RNA
DESeq_Results.txt

data_processing:
RNAseq 1: the 101x101bp pairedEnd reads were trimmed to 80x80 by trimming from each read, 21bp from the 3' endend
RNAseq 2: reads mapping (by bowtie2) to human repeatMasker elements were discarded
RNAseq 3: reads were mapped to hg19 by tophat, aided by a gtf file based on UCSC Knowngenes
RNAseq 4: duplicate read mappings of the same start and end position were discarded
RNAseq 5: bam files were converted to coverage using bedtools
RNAseq 6: for each gene in UCSC KnownGenes, the total coverage was calculated over all the coding positions in all potential exons of the gene.
RNAseq 7: the coverage per gene was divided by 160 to generate an effective count of (80x80bp pairedEnd) reads per gene for input to DESeq
RNAseq 8: DESeq was run to compare the 2 control replicates to the 2 knockdown replicates for all genes with coverage in any sample
hg19
DESeq_Results.txt; contains information regarding  gene symbol, genome id, baseMean, baseMean_panc1ctrl, baseMean_panc1shrn, foldChange, log2FoldChange, p-value, adjusted p-value, and Cell Line


title: Panc1 IgG RIP-seq 2

description:
total RNA
PANC1_RIP.txt


title: Panc1 IgG RIP-seq 1

description:
total RNA
PANC1_RIP.txt


title: Panc1 IgG RIP-seq 3

description:
total RNA
PANC1_RIP.txt


title: IGF2BP3 shRNA RNA-seq 3

description:
polyA RNA
DESeq_Results.txt


title: control shRNA RNA-seq 3

description:
polyA RNA
DESeq_Results.txt

value: control


title: RNA-Seq of wild type - 1


title: control shRNA RNA-seq 4

description:
polyA RNA
DESeq_Results.txt


title: RNA-Seq of ume6 deletion

source_name: RNA-Seq of ume6 deletion


title: RNA-Seq of ume6 deletion (with dead Chd1-Ume6)

value: ume6 deletion (with control Chd1-Ume6)

value: yes, catalytically dead


title: WT_Chd1Ume6_MNase_2

value: wild-type with hybrid remodeling protein


title: miRNA-seq 1


title: 46c_H3K27ac_rep2

description:
processed data file:
46C_H3K27acmerged.10bpres.bed, 46C_H3K27acmerged.10bpres.bedGraph.gz

value: 46c (sox1-GFP)

value: mouse embryonic stem cells


title: control shRNA RNA-seq 1

description:
polyA RNA
DESeq_Results.txt


title: RNA-Seq of rpd3 deletion

source_name: RNA-Seq of rpd3 deletion

value: rpd3 deletion


title: control shRNA RNA-seq 2

description:
polyA RNA
DESeq_Results.txt


title: PL45 IGF2BP3 iCLIP 2

description:
total RNA
iCLIP.txt

data_processing:
iCLIP 1: (samples pl45xx_imp3_jh080c, panc1x_imp3_js004b) based on random bases of internal barcode positions 1-9 of each read, the readIDs were divided into classes (for later use in duplicate removal). Note: positions 4-7 comprised fixed values for each sample
iCLIP 2: (samples pl45xx_imp3_jh080c, panc1x_imp3_js004b) each read was searched for the presence of adaptor sequence TGGAATTC and trimmed from that point on. Reads without the adaptor were discarded. Reads shorter than 30bp after trimming (including internal barcode positions 1-9) were discarded.
iCLIP 3: (samples pl45xx_imp3_jh080c, panc1x_imp3_js004b) internal barcode positions 1-9 were trimmed before mapping
iCLIP 3: (samples pl45_imp3h_jh59) 25bp were trimmed from the 3' end of each read before mapping
iCLIP 4: reads mapping (by bowtie2) to human repeatMasker elements were discarded
iCLIP 5: (samples pl45xx_imp3_jh080c, pl45_imp3h_jh59) reads were mapped to hg19 by tophat, aided by a gtf file based on UCSC Knowngenes, and with parameters --no-novel-juncs, --no-coverage-search
iCLIP 5: (samples panc1x_imp3_js004b ) reads were mapped by STAR to hg19 with an additional set of junctions derived from Gencode V19 basic with 100bp overlap
iCLIP 6: for each class of internal random barcode bases from step (1), duplicate read mappings of the same length and position were discarded
iCLIP 7: peaks were called on the dup-removed bam files from step (6) by Clipper (Yeo et al) using default parameters for hg19.
hg19
iCLIP.txt; contains information on Cell Line, chromosome start and  stop, strand, IGF2BP3 Location in Nearest Intragenic Anchor,  Exon Coordinates First/Internal/Last, Gene Symbol


title: RNA-Seq of ume6 deletion (with Chd1-Ume6)

value: ume6 deletion (with Chd1-Ume6)

value: yes


title: IGF2BP3 shRNA RNA-seq 1

description:
polyA RNA
DESeq_Results.txt


title: 46c_H3K27ac_rep1


title: Panc1 IGF2BP3 iCLIP 1

description:
total RNA
iCLIP.txt


title: RNA-Seq of isw2/rpd3 double deletion

description: prototrophic

source_name: RNA-Seq of isw2/rpd3 double deletion

value: W303 Prototroph

value: isw2 rpd3 double deletion

value: isolate 1

value: no


title: 46c_H3K64ac_rep2

value: anti-H3K64ac (Di Cerbo et al 2014, PMID:24668167)


title: RNA-Seq of isw2 deletion - 2

source_name: RNA-Seq of isw2 deletion

value: isw2 deletion

value: isolate 2


title: RNA-Seq of isw2 deletion - 1


title: ume6_Chd1D513N_MNase

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Tophat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Between-strain comparisons were done using best-matched MNase digests. For isw2-related parent strains, wild-type 2 is best-matched. For ume6-related strains, wild-type 1 is best-matched. For WT +Chd1Ume6, wild-type 1 is best-matched.
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: coverage file with tab-delimited chromosome/position/normalized dyad counts

value: W303 auxotroph

value: ume6 deletion with catalytically inactive hybrid remodeling protein


title: WT_Chd1Ume6_MNase


title: ume6_Chd1Ume6_MNase

value: ume6 deletion with hybrid remodeling protein


title: ume6_MNase

value: ume6 deletion


title: isw2_Chd1Ume6_MNase

value: isw2 deletion with hybrid remodeling protein


title: WT_2_MNase

value: wild-type


title: isw2_MNase


title: WT_1_MNase


title: K562_Input

value: human erythroleukemic cell line


title: K562_H3K4me1


title: K562_H3K27ac


title: K562_H3K122ac

value: anti-H3K122ac (Tropberger et al 2013, PMID:23415232)


title: WT_rep1

status: Public on Mar 11 2016

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

description: Small RNA

data_processing:
Base calling by Illumina CASAVA-1.8.2.
Trimmed reads of 14nt to 30nt in length were selected to be mapped to TAIR10 genome using Bowtie (Langmead et al., 2009) by permitting up to 1 mismatch in the first 14 read nucleotides and no limit beyond. Reads that could map to more than 50 loci were discarded and only the best alignment(s) of each small RNA sequence was kept.
The resulting alignment was annotated using the intersectBed tool from the BEDTools suite (v2.17.5) (Quinlan and Hall, 2010), and either the Arabidopsis annotation file ath.gff with 427 mature miRNA sequences (http://www.mirbase.org/) or a custom annotation file with genome coordinates for 8 siRNA loci (siR-1: CACGGTCTTGGCTCAACCCGCC, siR-2: GAACGCTATGTTGGACTTAGGATG, siR-3: ATTATCCCCCGTGTTTTGTCC, siR-4: TGCCCGGACCCTGTCGCAC, siR-5: TTAGATTCACGCACAAACTCT, siR-6: CCTTTGCAGACGACTTAAATAC, siR-7: TCCGCTGTAGCACACAGGC, siR-8: CCTTTGTCGCTAAGATTCGA).
Tailing and trimming at the 3' end of small RNA was identified using a homemade python script. Canonical variants were first isolated by looking for reads with perfect match for miRNA and siRNA sequences. Then, miRNA and siRNA sequences were successively trimmed from 1 nt to 7 nt in order to identify trimmed variants. At each matching step, 3' tails were extracted, i.e., untemplated nucleotides at the 3’ end of sRNA reads. To minimize bias due to reads with sequencing errors, that would be considered as having 3' untemplated nucleotide, if the nucleotide after the first mismatch matched to the miRNA/siRNA sequence, the read was removed from the analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample, two processed data files are provided with either miRNA or siRNA data. Data were generated using homemade python and R scripts. For each miR loci, we indicate : 1) the name of the miRNA, 2) the canonical sequence, 3) the read sequence, 4) the number of trimmed nucleotides at the 3’ end of the miRNA, 5) the number of added nucleotides at the 3’ end of the miRNA , 6) the composition of the tail , 7) the normalized number of reads (multi-mapped reads were weighted by a factor 1/n, n being the number of identical loci where reads mapped), and 8) the tail category. For each siR loci, we indicate : 1) the name of the siRNA loci, 2) the genomic-encoded sequence, 3) the read sequence, 4) the number of added nucleotides at the 3’ end of the siRNA, 5) the composition of the tail , 6) the normalized number of reads (multi-mapped reads were weighted by a factor 1/n, n being the number of identical loci where reads mapped), and 7) the tail category.

source_name: seedlings, WT

growth_protocol: Arabidopsis thaliana plants were grown in vitro on MS with 16h light/8h darkness cycles.

extract_protocol:
RNAs were extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
Small RNA libraries were generated from 3µg of total RNA using the Illumina Small RNA TruSeq protocol.

tag: ecotype

value: WT

value: seedlings

tag: age

value: two weeks


title: WT_rep2

description: Small RNA