title: cBF SpliceLeader replicate_1

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

description: library strategy: Splice Leader RNA-Seq

data_processing:
RNAseq reads were aligned to the Tb927 genome TriTrypDB V5.0 using bowtie2 version 2.2.2 in local alignment mode with the following configurations -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
Read counts for each of these regions of all genes were generated using HTSeq {ref} package. Any read overlapping the CDS or 5’ UTR region either partially or fully was assigned to that region. Both unique and multipmapping reads were considered for further analyses.
Raw read counts are analyzed using statistical package edgeR and DESeq from bioconductor project.
Genome_build: Tb927 genome from TriTrypDB V5.0
Supplementary_files_format_and_content: Tab delimited files with raw read count data corresponding to the CDSregion (+46th base until stop codon).

organism: Trypanosoma brucei

source_name: Tb427 grown in vitro in HMI-9 medium

growth_protocol: In vivo T brucei TREU927 were grown in irradiated Wistar rats infected with 107-108 parasites.  The parasites were harvested on day 3 at a parasitemia of 4´107-1.2´108 cells/ml.  In vitro procyclic TREU927 cell were grown in SDM-79 to a cell density of 5´106-1.2´107 cells/ml.  In vitro bloodform Lister427 was grown in HMI-9 to a density of 8´105 to 1.5´106 cells/ml.

extract_protocol:
For in vivo blood form parasites, the blood from 2-3 infects rats was pooled and centrifuged and the buffy coat extracted and placed into 20 ml HMI-9 without serum pre-warmed to 37°C.  To arrest translation, cycloheximide was added to 100 μg/ml and incubated for 2 minutes at 37°.  To rapidly chill the cells, 300 ml of ice-cold phosphate buffered saline with glucose (PSG) was added and the cells were pelleted at 4°.  Only parasite populations with greater than 99% slender cells were used.  In vitro grown parasites were pelleted at 5000g and resuspended in 50 mls of media lacking serum.  Cycloheximide was added to 100 mg/ml at the cell incubated for 2min at room temperature (procyclic cells) or 37° (bloodform cells). Following cycloheximide treatment the cells were rapidly chilled with PSG and pelleted at 5000g.  Lysates from both type of parasite pellets were then prepared as following. Cell pellets were resuspended in Buffer A (10 mM Tris pH 7.4, 300 mM KCl, 10 mM MgCl2 plus protease inhibitors to approximately 1.3x109/ml.  Approximately one-third of the sample was placed into TRIzol (Life Technologies) for RNA extraction following manufacturer’s suggested protocol.  To the remainder, one-sixth volume of buffer A containing 0.2M sucrose and 1.2% Triton N-101 was added and the samples were dounced (30 strokes in a chilled homogenizer). After transfer to a prechilled microfuge tube, the samples were clarified by centrifugation in a microfuge at 15000 rpm for one minute.  The supernatant was withdrawn, pooled if needed, and then aliquots flash frozen in liquid nitrogen for storage at -70°C.
After thawing on ice, RNase I (Ambion) was added at 30 units/OD260 of lysate.  Samples were then incubated for 1 hour at room temperature.  RNase digestion was stopped by adding 400 units RNasin (Promega).  Samples were them layered over a 1 ml 1M sucrose cushion prepared in buffer A and ribosomes were pelleted by centrifuging for 4 hours at 70,000g in an SW55 rotor.  After removing the supernatant, the ribosomal pellet was resuspended in 500 μl buffer A with the MgCl2 replaced with 10 mM EDTA to dissociate the ribosomes and deplete larger rRNA fragments.  The protected fragments were then separated from contaminating ribosomal RNA by passage through an Amicon Ultra-4 or YM-100 column with 100,000 MW cutoff. After more than 400 μl had flowed through the membrane the RNA in the flow-through was extracted with phenol:CHCl3:iAA and the RNA precipitated.  Poly(A)+ RNA was isolated using Dynabeads mRNA Direct (Life Technologies).  RNA was fragmented as described Ingolia et all 2011.  Ribosomal protected fragments between 28 and 31 nucleotides and fragmented Poly(A)+ RNA between 30 and 70 nucleotides was isolated from 15% accrylimide gels and libraries prepared for sequencing.  For detailed protocol on generating sequencing libraries for both the ribosome protected and fragmented mRNA library see Ingolia et a 2011.  Briefly, following dephosphorylation the adapter Linker-1 (IDT) was ligated to the 3’ end of the fragment and the ligated product gel purified.  The adapter was used for priming reverse.  Following gel purification the cDNA was circularized with Circ Ligase (Epicenter Biotechnologies).  Circles containing ribosomal RNA were subtracted using biotinylated primers .  The final library was generated by PCR..To map the 5’ end of the transcripts, libraries enriched for the 5’ ends of mRNAs were constructed from three biological samples of strain 927 (2 PCF and 1 slBF selected from the biological samples above).  SL libraries were constructed as described Mittra B et al 2013.  In brief, RNA was prepared and cDNA synthesized using primer ending in a random 6 bases.  Second strand synthesis was primed using a primer that matches the T. brucei SL sequence.  The sequencing library was generated by PCR. Duplexed libraries were sequenced using Illumina GA II machines at the High Throughput Genomics Unit at the University of Washington to generate ~36 nt reads.

treatment_protocol: Cells were treated with 100 µg/ml cycloheximide for 2 min at either room temperature (procylic cells) or 37° (bloodform cells) to arrest elongating ribosomes.

tag: developmental stage

value: cultrured bloodstream Form


title: Soybean Early Maturation Cotyledon Adaxial Epidermis- biological replicate 3

status: Public on May 24 2014

type: SRA

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

country: USA

institute: University of California

description: Compartments collected from seeds ranging 6.0-7.0mm in length

library_source: transcriptomic

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max gene models (v1.1) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 4 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. Normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: Glycine max V1.1
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for each sample.

molecule: total RNA

organism: Glycine max

growth_protocol: Soybean plants were grown at the UC Davis Greenhouses with a 16:8 day:night cycle at 22°C-30°C. Seeds were germinated in Modified UC Mix (equal parts of ground canadian sphagnum, horticultural grade sand, white pumice, redwood compost) for 10 days.  Individual seedlings were transfered to 1 gallon pots where they were grown for an additional 3 weeks before being transplanted to 3 gallon pots.  Plants were watered as needed with water containing 190 ppm Nitrogen, 40 ppm Phosphorus and 140 ppm Potassium and micronutrients.

extract_protocol:
Soybean seeds (Williams 82) were fixed in 3:1 ethanol:acetic acid for 16-20 hours at 4°C, then dehydrated with 75% ethanol, 85% ethanol, 95% ethanol, and three times with 100% ethanol, each wash in one hour intervals. Then they were infiltrated with 3:1 ethanol-xylenes, 1:1 ethanol-xylenes, 1:3 ethanol-xylenes, and three times with 100% xylenes, dilution in two hour intervals. They were then infiltrated with molten paraffin at 60 deg  C for 1-4 days, depending on the size of the tissue. Laser capture microdissection was used to isolate specific compartments of the seed after tissues were sectioned in 5-10um sections. Total RNA was isolated with Ambion RNaqueous-Micro kit (Grand Island, NY) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300.
Amplification was performed using NuGen Ovation Pico WTA V1 (San Carlos, CA), starting with 15ng total RNA. Double-stranded cDNA was generated using the NuGen WT-Ovation Exon-Module (San Carlos, CA). Illumina-complatible libraries were made starting with one microgram of double-stranded cDNA using Illumina TruSeq DNA Sample prep kit (Hayward, CA), according to manufacturer's instructions except for the PCR enrichment step where Agilent Pfu Turbo Cx hotstart DNA polymerase was used for 15 cycles of amplification.  Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

tag: seed compartments/tissue


title: Soybean Early Maturation Cotyledon Abaxial Parenchyma- biological replicate 5


title: slBF SpliceLeader replicate_1

description: library strategy: Splice Leader RNA-Seq

source_name: Tb927 BF grown in irradiated Wistar rat

tag: strain

value: Slender bloodstream Form


title: cBF mRNA replicate_2

description:
mRNA control for cBF2r
library strategy: RNA-Seq

molecule: polyA RNA


title: PCF SpliceLeader replicate_1

description: library strategy: Splice Leader RNA-Seq

source_name: Tb927 PCF in SDM79 medium

value: Procyclic Form


title: cBF mRNA replicate_3

description:
mRNA control for cBF3r
library strategy: RNA-Seq


title: PCF SpliceLeader replicate_2

description: library strategy: Splice Leader RNA-Seq


title: Soybean Early Maturation Cotyledon Abaxial Parenchyma- biological replicate 4


title: Soybean Early Maturation Cotyledon Abaxial Parenchyma- biological replicate 2


title: Soybean Early Maturation Axis Stele- biological replicate 4

source_name: Soybean Early Maturation Axis Stele

value: Soybean Early Maturation Axis Stele


title: slBF mRNA replicate_2

description:
mRNA control for slBF2r
library strategy: RNA-Seq


title: cBF mRNA replicate_1

description:
mRNA control for cBF1r
library strategy: RNA-Seq


title: slBF mRNA replicate_1

description:
mRNA control for slBF1r
library strategy: RNA-Seq


title: slBF mRNA replicate_3

description:
mRNA control for slBF3r
library strategy: RNA-Seq


title: Soybean Early Maturation Axis Stele- biological replicate 1


title: Soybean Early Maturation Axis Stele- biological replicate 2


title: Soybean Early Maturation Axis Shoot Apical Meristem- biological replicate 4


title: Soybean Early Maturation Axis Shoot Apical Meristem- biological replicate 3


title: PCF mRNA replicate_2

description:
mRNA control for PCF2r
library strategy: RNA-Seq


title: PCF mRNA replicate_3

description:
mRNA control for PCF3r
library strategy: RNA-Seq


title: cBF RiboProf replicate_3

description:
Pairs with cBF3m
library strategy: ribosome profiling


title: cBF RiboProf replicate_2

description:
Pairs with cBF2m
library strategy: ribosome profiling


title: Soybean Early Maturation Axis Plumules- biological replicate 2

source_name: Soybean Early Maturation Axis Plumules

value: Soybean Early Maturation Axis Plumules


title: cBF RiboProf replicate_1

description:
Pairs with cBF1m
library strategy: ribosome profiling


title: Soybean Early Maturation Axis Root Tip- biological replicate 1

source_name: Soybean Early Maturation Axis Root Tip

value: Soybean Early Maturation Axis Root Tip


title: slBF RiboProf replicate_1

description:
Pairs with slBF1m
library strategy: ribosome profiling


title: Soybean Early Maturation Axis Plumules- biological replicate 1


title: slBF RiboProf replicate_2

description:
Pairs with slBF2m
library strategy: ribosome profiling


title: Soybean Early Maturation Axis Shoot Apical Meristem- biological replicate 2


title: PCF RiboProf replicate_3

description:
Pairs with PCF3m
library strategy: ribosome profiling


title: Soybean Early Maturation Axis Epidermis- biological replicate 3

source_name: Soybean Early Maturation Stage-Axis Epidermis


title: PCF RiboProf replicate_1

description:
Pairs with PCF1m
library strategy: ribosome profiling


title: Soybean Early Maturation Axis Epidermis- biological replicate 2

value: Soybean Early Maturation Stage-Axis Epidermis


title: PCF RiboProf replicate_2

description:
Pairs with PCF2m
library strategy: ribosome profiling


title: slBF RiboProf replicate_3

description:
Pairs with slBF3m
library strategy: ribosome profiling


title: 73_GMP_MDS 38

status: Public on May 23 2014

city: Oxford

first: Petter

last: Woll

address: Weatherall Institute of Mol Med

country: United Kingdom

institute: University of Oxford

data_processing:
RNA-Seq: Alignment by Bowtie (version 0.12.7, option –best) to genome and exon-exon junctions.
RNA-Seq: Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
RNA-Seq: Gene expression levels for Refseq transcripts were summarized as reads per kilobase of exon model per million mapped reads (RPKM) and read counts using Rpkmforgenes (Ramskold et al., 2012)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values from RNA sequencing

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: MDS 38

extract_protocol:
cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".
For RNA-Seq NEBNext® DNA Library Prep Reagent Set for Illumina®

treatment_protocol: Cell populations isolated by FACS sorting from human bone marrow mononuclear cells and peripheral blood

tag: tissue

value: Bone marrow GMP

tag: phenotype

value: MDS

tag: cell phenotype


title: 72_MEP_MDS 67

source_name: MDS 67

value: Bone marrow MEP


title: 71_GMP_MDS 67


title: 70_HSC_MDS 67

value: Bone marrow HSC


title: Soybean Early Maturation Axis Vasculature- biological replicate 4

description: Compartments collected from seeds ranging 6.0-7.0mm in length


title: 69_GMP_MDS 71

source_name: MDS 71


title: 68_HSC_MDS 71


title: 67_GMP_MDS 68

source_name: MDS 68


title: 66_HSC_MDS 68


title: PCF mRNA replicate_1

description:
mRNA control for PCF1r
library strategy: RNA-Seq


title: 65_MEP_MDS 71


title: 64_MEP_MDS 68


title: 63_MEP_MDS 38


title: 62_HSC_MDS 38


title: Soybean Early Maturation Axis Plumules- biological replicate 3


title: 61_MEP_MDS 2_30 months

source_name: MDS 2_30 months


title: 58_MEP_MDS 3_0 months

source_name: MDS 3_0 months


title: 57_GMP_MDS 3_0 months


title: 56_HSC_MDS 39_32 months

source_name: MDS 39_32 months


title: 54_MEP_MDS 39_32 months


title: 55_HSC_MDS 3_0 months


title: Soybean Early Maturation Axis Epidermis- biological replicate 4


title: 51_GMP_Age-matched normal BM 7

source_name: Age-matched normal BM 7

value: Age-matched normal control


title: 52_MEP_Age-matched normal BM 7


title: 53_GMP_MDS 39_32 months


title: 50_HSC_Age-matched normal BM 7


title: 49_GMP_Age-matched normal BM 5

source_name: Age-matched normal BM 5


title: modified iPAR-CLIP control (replicate 2)

city: Berlin

first: Nikolaus

last: Rajewsky

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
ALG-1 crosslinked RNA fragments
protocols specific to this sample: immuno-purified complexes were treated with PNK phospathase minus, no T4 RNA ligase was added, subsequently phosphorylated with PNK

data_processing:
removal of 3'adapter sequence with FLEXBAR (see supplementary methods)
collapsing distinct read-sequences with custom script
searching anchors of the left part of reads in mirbase ce6 mature sequences with custom script
alignment of the right part of reads with BOWTIE2 2.1.0 to ce6 AGL-1 PAR-CLIP clusters
miRNA:targets identification and quality filtering to limit false-discovery rate with custom scripts
Genome_build: ce6
Supplementary_files_format_and_content: GFF file with genomic regions of target parts of miRNA:targets

organism: Caenorhabditis elegans

source_name: L3-staged whole worms

extract_protocol:
in vivo PAR-CLIP (Jungkamp et al. 2011)
Hafner et al. 2010

tag: expression

value: whole worms

tag: 3' adapter


title: 48_MEP_Age-matched normal BM 6

source_name: Age-matched normal BM 6


title: modified iPAR-CLIP control (replicate 1)


title: early maturation-stage axis vascular

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Axis vascular compartment was captured from ten micron paraffin sections using the Leica LMD6000 system

library_source: genomic

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: Tab-delimited text file including methylation level of each sampled cytosine. Column definitions are included in the supplementary README.txt file that is linked to the Series record.

molecule: genomic DNA

source_name: Laser captured vascular compartment from early-maturation stage embryo axis

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).  Seeds with length between 6.0 and 7.0 mm containing early maturation-stage embryos were harvested.

extract_protocol: Harvested seeds were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from ten-micron sections using a Leica LMD6000.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).  Approximately 300 nanogram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications.  We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion.  Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

value: early maturation stage

value: axis vascular


title: modified iPAR-CLIP ligation (replicate 2)

description:
ALG-1 crosslinked RNA fragments
protocols specific to this sample: immuno-purified complexes were treated with PNK phospathase minus, subjected to ligation with T4 RNA ligase and subsequently phosphorylated with PNK


title: 47_GMP_Age-matched normal BM 6


title: 46_HSC_Age-matched normal BM 6


title: standard iPAR-CLIP (replicate 1)

description: ALG-1 crosslinked RNA fragments


title: early maturation-stage axis plumule

description: Axis plumule compartment was captured from ten micron paraffin sections using the Leica LMD6000 system

source_name: Laser captured plumule compartment from early-maturation stage embryo axis

value: axis plumule


title: early maturation-stage axis root tip

description: Axis root tip compartment was captured from ten micron paraffin sections using the Leica LMD6000 system

source_name: Laser captured root tip compartment from early-maturation stage  embryo axis

value: axis root tip


title: 45_MEP_Age-matched normal BM 5


title: 59_HSC_MDS 2_30 months


title: modified iPAR-CLIP ligation (replicate 1a)


title: liver_ko_lacz

city: Irvine

first: Eddie

last: Park

address: 2300 Biological Sciences 3

department: DevCell

institute: UCI

description: liver.bed

data_processing:
RNA-seq reads for each genotype were mapped to the mouse reference genome (NCBI37/mm9) and SNVs. Reads from each sample were mapped with Bowtie version 0.12.8, with at most three mismatches, suppressing all alignments for a particular read if more than one reportable alignment exist for it, and using only those alignments that fell into the best stratum The alignment files were sorted and indexed using Samtools version 0.1.18 41. Variants were called using the mpileup command. We called an SNV when at least three independent reads support a non-reference variant, and the variant is present at a minimum frequency of 10% with minimum coverage of 10 reads and is supported by at least one read per strand. Sites were removed if they had three or more different observed nucleotide variants and a minimum frequency greater than 1.5%. Editing candidate sites were required to have no more than a 5% variant frequency in Apobec1 knockout genotypes. Known SNPs from dbSNP128 that were not annotated as based on cDNA and sites lying outside of the 5’ and 3’ gene boundaries were set aside, and the remaining sites were corrected for strand sense. These sites were then annotated using ANNOVAR with a splicing threshold of 5.
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing RNA editing sites

organism: Mus musculus

source_name: liver

growth_protocol: All studies were performed using C57BL/6 from JAX (C57BL/6J) or  Apobec-1-/-  mice (both genders) backcrossed for >12 generations onto a C57BL/6 background. Apobec-1 Int/O  mice and intestinal apobec-1 transgenic mice were on a mixed background (C57BL/6 and 6xCBA). Apobec-1-/- mice were injected with 6x10^8 plaque-forming units of recombinant adenovirus encoding either ≤-galactosidase (Lac-Z) or rat Apobec-1 (ad-Apobec-1) resulting in hepatic Apobec-1 overexpression. Mice were 8-10 weeks old and fed ad libitum chow diet.

extract_protocol:
Total RNA was extracted from intestinal mucosa from wild-type, Apobec-1-/- and Apobec-1 Int/O mice and from livers isolated from wild-type, Apobec-1-/-, Apobec-1-/- + ad-LacZ and  Apobec-1-/- + ad-Apobec-1 mice (3 mice per genotype), using TRIZol reagent (Invitrogen, Grand Island, NY).
DNAse-free-RNAs were used for cDNA preparation. Ten ug of pooled RNA were subjected to oligo(dT) selection.  After chemical fragmentation RNA was reverse transcribed using random hexamer and sequencing adapters (Illumina) ligated to each end of double stranded cDNA. The fragments were then PCR-amplified using linker-specific primers (Illumina). All libraries were diluted to 10nM and an equal volume of each sample was combined to form the final sequencing pool that was run on an Illumina HiSeq2000.

value: liver

tag: genotype

value: Apobec-1-/- + ad-LacZ


title: liver_wt

description: liver.bed

value: wild type


title: 60_GMP_MDS 2_30 months


title: early maturation-stage axis parenchyma

description: Axis parenchyma compartment was captured from ten micron paraffin sections using the Leica LMD6000 system

source_name: Laser captured parenchyma compartment from early-maturation stage   embryo axis

value: Williams 82

value: axis parenchyma


title: liver_ko

description: liver.bed


title: 43_MEP_MDS 39_0 months

source_name: MDS 39_0 months


title: Soybean Early Maturation Stage Seed Coat Parenchyma-Biological replicate 1

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file.  The sequence data are in the fastq format.
Sequential filtering and processing was performed on quality-filtered reads. First, reads were trimmed to remove adapter sequences. Trimmed sequences with length greater than 15 nucleotides were kept for further analysis. Second, trimmed reads were mapped against the soybean reference genome (Glyma version 1.0) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net) using Bowtie [Langmead et al., Genome Research, (2009)].  Sequences that mapped perfectly to the genome were kept and filtered further by mapping against a reference containing soybean ribosomal RNA (rRNA) and transfer RNA (tRNA) using Bowtie. Sequences that did not map were kept. Third, the remaining filtered sequences 18 to 26 nucleotides long were collapsed and counted. The final count for each unique remaining filtered sequence is reported in a text format.
Genome_build: Glycine max v1.1
Supplementary_files_format_and_content: tab-delimited text file including the counts for each sequence.

extract_protocol:
Soybean seeds (Williams 82) were fixed in 3:1 ethanol:acetic acid for 16-20 hours at 4°C, then dehydrated with 75% ethanol, 85% ethanol, 95% ethanol, and three times with 100% ethanol, each wash in one hour intervals. Then they were infiltrated with 3:1 ethanol-xylenes, 1:1 ethanol-xylenes, 1:3 ethanol-xylenes, and three times with 100% xylenes, dilution in two hour intervals. They were then infiltrated with molten paraffin at 60 deg  C for 1-4 days, depending on the size of the tissue. Laser capture microdissection was used to isolate specific subregions of the seed after tissues were sectioned in 5-10um sections. Total RNA was isolated with Ambion RNaqueous-Micro kit (Grand Island, NY) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300.
Sequencing libraries were prepared using 250 nanograms of total RNA (unless otherwise noted), using the Illumina TruSeq Small RNA Sample Preparation Kit (cat no RS-200-0012 & RS-200-0024). Briefly, total RNA was ligated with 3’ and 5’ RNA adapter using T4 RNA ligase. Adapter-ligated small RNA was converted to complementary DNA (cDNA) and amplified by PCR for 15 cycles.  Libraries were size-selected on a polyacrylamide gel for the desired size of 147-160 bp and purified. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument (Thermo Scientific, Waltham, MA).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

value: Stage Seed Coat Parenchyma

tag: rna input amount


title: intestine_ko

description: intestine.bed

source_name: intestine

value: intestine


title: 42_GMP_MDS 39_0 months

value: Bone marrow GMP


title: Soybean Early Maturation Stage Seed Coat Parenchyma-Biological replicate 2


title: liver_ko_ad_apobec

description: liver.bed

value: Apobec-1-/- + ad-Apobec-1


title: intestine_io_low

description: intestine.bed

value: C57BL/6J and 6xCBA

value: Apobec-1 Int/O


title: standard iPAR-CLIP (replicate 2)

description: ALG-1 crosslinked RNA fragments


title: 41_GMP_Age-matched normal BM 4

source_name: Age-matched normal BM 4

value: Age-matched normal control


title: Soybean Early Maturation Stage Seed Coat Palisade-Biological replicate 2

value: Stage Seed Coat Palisade


title: Soybean Early Maturation Stage Seed Coat Hilum-Biological replicate 2

value: Stage Seed Coat Hilum


title: 38_HSC_MDS 72

source_name: MDS 72

value: Bone marrow HSC

value: MDS


title: Soybean Early Maturation Stage Seed Coat Palisade-Biological replicate 1

value: 50 ng


title: 39_HSC_Age-matched normal BM 4


title: 40_MEP_Age-matched normal BM 8

source_name: Age-matched normal BM 8

value: Bone marrow MEP


title: intestine_io_high

description: intestine.bed


title: Soybean Early Maturation Stage Seed Coat Hourglass-Biological replicate 2

value: Stage Seed Coat Hourglass


title: Soybean Early Maturation Stage Seed Coat Hourglass-Biological replicate 1


title: 36_MEP_Age-matched normal BM 4


title: 44_HSC_Age-matched normal BM 5


title: 35_GMP_MDS 72


title: 34_HSC_MDS 39_0 months


title: modified iPAR-CLIP ligation (replicate 1b)

value: whole worms


title: intestine_tg88

description: intestine.bed

value: Apobec-1 transgenic


title: Soybean Early Maturation Stage Endosperm-Biological replicate 1

value: Stage Endosperm

value: Williams 82


title: Soybean Early Maturation Stage Endosperm-Biological replicate 2


title: 32_GMP_MDS 2_0 months

source_name: MDS 2_0 months


title: 31_HSC_MDS 2_0 months


title: 30_MEP_MDS 2_0 months


title: Soybean Early Maturation Stage Cotyledon Adaxial Parenchyma-Biological replicate 1

value: Stage Axis Cotyledon Abaxial Parenchyma


title: Soybean Early Maturation Stage Cotyledon Adaxial Parenchyma-Biological replicate 2


title: Soybean Early Maturation Stage Cotyledon Vasculature-Biological replicate 1

value: Stage Axis Cotyledon Vasculature


title: 29_HSC_Age-matched normal BM 3

source_name: Age-matched normal BM 3


title: Soybean Early Maturation Stage Cotyledon Adaxial Epidermis-Biological replicate 1

value: Stage Axis Cotyledon Abaxial Epidermis


title: 28_GMP_MDS 56

source_name: MDS 56

value: Bone marrow GMP


title: 26_HSC_MDS 54

source_name: MDS 54


title: 27_GMP_MDS 54


title: Soybean Early Maturation Stage Seed Coat Hilum-Biological replicate 1


title: Soybean Early Maturation Stage Cotyledon Adaxial Epidermis-Biological replicate 2


title: Soybean Early Maturation Stage Cotyledon Abaxial Parenchyma-Biological replicate 1


title: Soybean Early Maturation Stage Cotyledon Abaxial Epidermis-Biological replicate 1


title: 24_GMP_Age-matched normal BM 1

source_name: Age-matched normal BM 1


title: 23_MEP_Age-matched normal BM 1


title: Soybean Early Maturation Stage Axis Vasculature-Biological replicate 2

value: Stage Axis Vasculature


title: 37_MEP_MDS 14

source_name: MDS 14


title: 21_MEP_MDS 37

source_name: MDS 37


title: Soybean Early Maturation Stage Axis Stele-Biological replicate 2

value: Stage Axis Stele


title: Soybean Early Maturation Stage Cotyledon Vasculature-Biological replicate 2


title: intestine_wt

description: intestine.bed

value: intestine

value: wild type


title: 22_HSC_MDS 19_120 months

source_name: MDS 19_120 months

value: Bone marrow HSC


title: 20_MEP_MDS 19_120 months

value: MDS


title: Soybean Early Maturation Stage Axis Shoot Apical Meristem-Biological replicate 2

value: Stage Axis Shoot Apical Meristem

value: 50 ng


title: 18_GMP_MDS 1

source_name: MDS 1


title: Soybean Early Maturation Stage Axis Shoot Apical Meristem-Biological replicate 1


title: Soybean Early Maturation Stage Cotyledon Abaxial Parenchyma-Biological replicate 2


title: 17_HSC_MDS 1


title: Soybean Early Maturation Stage Axis Root Tip-Biological replicate 1

value: Stage Axis Root Tip


title: Soybean Early Maturation Stage Cotyledon Abaxial Epidermis-Biological replicate 2


title: 25_MEP_Age-matched normal BM 3

value: Bone marrow MEP

value: Age-matched normal control


title: 15_HSC_Age-matched normal BM 1


title: 16_MEP_MDS 1


title: 14_GMP_Age-matched normal BM 2

source_name: Age-matched normal BM 2


title: Soybean Early Maturation Stage Axis Parenchyma-Biological replicate 1

value: Stage Axis Parenchyma


title: Soybean Early Maturation Stage Axis Plumule-Biological replicate 2

value: Stage Axis Plumule

value: Williams 82


title: 19_HSC_MDS 37


title: 13_MEP_Age-matched normal BM 2


title: Soybean Early Maturation Stage Axis Plumule-Biological replicate 1


title: 11_GMP_MDS 37


title: 12_HSC_Age-matched normal BM 2


title: 10_MEP_MDS 70

source_name: MDS 70


title: 9_GMP_MDS 19_120 months


title: Soybean Early Maturation Stage Axis Epidermis-Biological replicate 1

value: Stage Axis Epidermis


title: Soybean Early Maturation Stage Axis Epidermis-Biological replicate 2


title: 33_MEP_MDS 72


title: 7_GMP_MDS 20

source_name: MDS 20


title: 8_GMP_MDS 70


title: 5_HSC_MDS 20


title: 6_HSC_MDS 70


title: Soybean Early Maturation Stage Axis Root Tip-Biological replicate 2


title: 2_HSC_MDS 56


title: 3_MEP_MDS 54


title: 1_GMP_Age-matched normal BM 3


title: 4_MEP_MDS 56


title: Th9_IN_VIVO

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

description: PolyA purified mRNA

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm9 reference genome
Cufflink was applied
Genome_build: mm9
Supplementary_files_format_and_content: fpmk

source_name: Th9 CD4+ T cells harvested after in vivo injection

growth_protocol: CD4 T naive cells were isolated from C57/Bl6 WT mice. Differentiation was induced in RPMI culture medium complemented with 10% FBS,1% antibiotics in CD3/CD28 coating plates

extract_protocol:
Total RNA was extracted from 300,000 Th9 or Th9+Il-1b cells with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq or polyA purified thanks to the NEBNext Poly(A) mRNA magentic isolation module
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

treatment_protocol: Differentiation was induced with 20 ng/ml IL-4 and 2 ng/ml TGFb with or without 10 ng/ml IL-1b in presence of IFNgamma blocking antibody for 1 hour or 3 days. For in vivo experiments, CD45.2 cells were injected 3 days after differentiation in CD45.1 mice and sorted 1 week later

tag: age

value: 7 weeks

value: Wild-type

tag: cell type


title: Th9+il1b_IN_VITRO_Day_3

description: PolyA purified mRNA

source_name: Naive T cells from spleen and nodes

value: Naive T cells from spleen and nodes


title: Soybean Early Maturation Stage Axis Stele-Biological replicate 1

value: Stage Axis Stele


title: Th9_IN_VITRO_Day_3

description: PolyA purified mRNA


title: Th9+Il1b_IN_VITRO_1hour

description: rRNA depleted RNA


title: Th9+il1b_IN_VIVO

description: PolyA purified mRNA

source_name: Th9+Il-1b CD4+ T cells harvested after in vivo injection


title: Soybean Early Maturation Stage Axis Parenchyma-Biological replicate 2


title: Th9_IN_VITRO_1hour

description: rRNA depleted RNA


title: K12_HTF2

status: Public on May 22 2014

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description:
RIP-Seq
E. coli K12 hfq::HTF 2

data_processing:
barcodes3.pl M=0 barcode_list.txt input.fq.  Custom script to demultiplex fastq file.
fastq_preprpcessing.sh -Q 33 -L TGGAATTCTC -M 15 NNNbarcode_input.txt. Custom script to clip linkers and apply quality filters. Based on fastx toolkit
novoalign -f NNNbarcode_input.fq -d Saki.novoindex -h 150 -F STDFQ (or ILFMQ) -r Random. Map reads to E. coli O157:H7 genome using novoalign
pyReadCounters.py -f input.novo --gtf Sakai_UCSC_1.0.gtf.  Custom program used to generate hit tables and plots of read density. From the pyCRAC software package (sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html).
novo2pws.awk input.novo.  Mapped reads were alternatively analysed by converting to PWS format (tab-delimited file with chromosome, position, strand, read, substitution and deletion information at each nucleotide position)
Genome_build: The reads generated from E. coli O157:H7 str. Sakai were mapped against UCSC microbial genome Escherichia coli O157H7 29/3/2000 assembly
Genome_build: The reads generated from E. coli K12 str. MG1655 were mapped against E. coli K12 str. MG1655 genome (NC000913.2)
Supplementary_files_format_and_content: GTF. Hashed header contains overall information including input files and processing commands. Number of mapped reads are given in column 6. The final semi-colon seperated column of "attributes" gives the position of deletions (D) and substitutions (S).

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

source_name: whole cells_His-FLAG tagged Hfq

growth_protocol: Strains were intially grown in LB for 16hrs and then diluted (1/100) into appropriate media and grown to and OD600 of ~0.8 at 37 degrees C.

extract_protocol:
Cells were lyzed by vortexing with zirconia beads in lysis buffer. Hfq.RNA complexes were purified over M2 anti-FLAG resin, trimmed with RNase A/T1 and repurified under denaturing conditions using Ni-NTA resin. RNA.Hfq complexes were seperated by SDS-PAGE, transferred to a nitrocelluose membrane and extracted. Protein was removed by Prrteinase K digestion and RNAs purified by phenol:chloroform extraction.
Extracted RNAs were converted to cDNA and PCR amplified. PCR products between ~150 and 250 bp were gel extracted and submitted for Solexa sequencing.

treatment_protocol: Cells were crosslinked with 1800mJ of UV-C and collected by centrifugation. Cell were pelleted, resuspended in PBS, and divided into 1g aliquots that were snap frozen in liquid nitrogen.

tag: media

value: LB

tag: rna chaperone hfq

value: His-FLAG tagged

tag: purification strategy

value: ANTI-FLAG M2 affinity gel (Sigma-Aldrich, cat# A2220); Ni-NTA resin


title: K12_control1

description:
RIP-Seq
E. coli K12 control 1

source_name: whole cells_untagged control

value: untagged control


title: K12_control2

description:
RIP-Seq
E. coli K12 control 2


title: K12_HTF1

description:
RIP-Seq
E. coli K12 hfq::HTF 1


title: KO_Doxo_r3

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

description:
Sample 12
processed data file: edgeRWTKODox_noYX_summary_131113_expf2_CAP_exprData.txt

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation.
Read mapping was performed with TopHat version 2.0.6 using default options.
Counts per gene were calculated with htseq-count with Ensembl annotation.
Abundance counts and differential analysis were performed with EdgeR.
Only genes on autosomal chromosomes with counts > 2 in all doxorubicin treated samples were used in analysis.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Tab delimited files with normalized counts per million for each sample without doxorubicin (edgeRWTKONODOX*.txt) or with doxorubicin treatment (edgeRWTKODox*.txt).

source_name: lincRNA-p21-/- murine MEF RNA-seq with Doxorubicin

growth_protocol: MEFs were maintained as primary cultures in DMEM supplemented with 15% FBS, pen/strep, L-glutamine, non-essential amino acids, and beta-mercaptoethanol.

extract_protocol:
Total RNA was extracted using the RNeasy MIDI kit Qiagen.
RNA libraries were prepared for sequencing using standard Illumina  protocols for the Tru-seq stranded mRNA CT prep kit.

treatment_protocol: To induce DNA damage, cells were treated with 0.5 mM doxorubicin for 24hrs.

tag: strain background

value: hybrid 129/B6

tag: genotype/variation

value: lincRNA-p21 KO; lincRNA-p21-/-

value: mouse embryonic fibroblast (MEF)

tag: treatment

value: 0.5 mM doxorubicin for 24hrs


title: KO_NoDoxo_r1

description:
Sample 7
processed data file: edgeRWTKONODOX_noYX_summary_131113_expf2_CAP_exprData.txt

source_name: lincRNA-p21-/- murine MEF RNA-seq without Doxorubicin

value: Mock


title: KO_NoDoxo_r2

description:
Sample 8
processed data file: edgeRWTKONODOX_noYX_summary_131113_expf2_CAP_exprData.txt


title: KO_Doxo_r1

description:
Sample 10
processed data file: edgeRWTKODox_noYX_summary_131113_expf2_CAP_exprData.txt


title: KO_Doxo_r2

description:
Sample 11
processed data file: edgeRWTKODox_noYX_summary_131113_expf2_CAP_exprData.txt


title: KO_NoDoxo_r3

description:
Sample 9
processed data file: edgeRWTKONODOX_noYX_summary_131113_expf2_CAP_exprData.txt


title: WT_Doxo_r2

description:
Sample 5
processed data file: edgeRWTKODox_noYX_summary_131113_expf2_CAP_exprData.txt

source_name: lincRNA-p21+/+ murine MEF RNA-seq with Doxorubicin

value: wild type; lincRNA-p21+/+


title: MGE_WT_6hrsKCl

city: Boston

first: Ivo

last: Spiegel

state: MA

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

data_processing:
Target sequences for alignment of 35-bp reads included (1) 21 mm9 autosomal and sex chromosomes plus (2) a single pseudochromosome containing a read-length-dependent splice library (~2.2M sequences, each 35-68bp).  The latter comprised all possible minimal intragenic sequences of two or more exons (based on the RefSeq annotation) for which one or more exon-exon junctions could be crossed by reads of the required length.
SOLiD raw reads were aligned using Corona with 0-3 colorspace (cs) mismatches for 35-bp reads.  Uniquely mapped reads output to SOLiD-format "unique.csfasta.gz.ma" files served as input for further processing.    SOLiD quality scores are in the .qual.gz files.
Aligned reads were minimally filtered for QC, removing any reads with uncalled bases or with unmapped or nonuniquely mapped sequences.
Employing "MAPtoFeatures" perl scripts, the loci of uniquely mapped reads were compared to the loci of all genic features (exons, introns, UTRs, CDSs, etc., and all junctions between them) of all genes based on the RefSeq annotation.  Every overlap of an individual read with genic features, including exon-exon splice junctions, was counted towards the features' "nrds" while the number of bases overlapped was added to their "rdbp".  For every genic feature the average Density (read coverage per bp) was calculated, equal to rdbp per feature length.  Each sample's Densities were renormalized to a standard total of 10M reads (with the standard read length of 35bp), and further corrected for mappability as described below.  With these conventions, units of Density always equal RPKM times 0.35.  Normalized Densities were treated as expression levels comparable among all samples.  Also note that in analyses using the MAPtoFeatures code, a "gene" is a construct based on the Refseq annotation of transcripts:  all exons from all transcripts assigned to a given gene are unioned together; the resulting discontinuous pieces are labeled as individual exons ("EXN"); and the gaps between them are defined as the gene's introns ("INT").
Exonic features (EXN), for each gene's whole exonic region and for individual exons, were corrected for mappability as follows.  A collection of fake reads was constructed from 35-bp sequences beginning at every single base of the mapping targets, i.e., the mm9 reference genome and its accompanying 35-bp splice library pseudochromosome.  These were aligned as for any other set of reads, allowing up to 3 mismatches, and only uniquely mapped ones were considered further.  The mappability index of an exon or an exonic region was defined in such a way that perfect coverage -- unique mapping of every fake read -- yields an index of unity; without correcting for normalization, this case would correspond to Density = 35.  The mappability index "i" for a genomic region is thus i = <unnormalized Density of fake reads>/<read length>.  Densities for a region are corrected for mappability by dividing the uncorrected (but normalized) Density for that region by its index i.  (Occasionally, double-counting of splice library members in multiple transcripts for the same gene lead to indices slightly greater than one.)
Genome_build: Mouse mm9 (NCBI reference assembly C57BL/6J, build 37, version 1, July 2007).
Supplementary_files_format_and_content: The "Genes-FEATURES-READS" .tsv files are spreadsheets output by MAPtoFeatures.  Each row has data for one gene (with NCBI Entrez Gene IDs).  A 1-line header labels 14 columns containing genomic information, followed by blocks of columns labeled "num" (number of each feature type per gene), "bp" (total length of each feature type per gene, followed by data columns.  Data in the remaining blocks are distinguished by reads that mapped S[ense] or A[ntisense] to each gene:  "nrds" (number of overlapping reads wholly contained within each feature type per gene), "rdbp" (total number of bases of reads that overlap each feature type at all, including reads crossing feature junctions), "Density" (expression levels, equal to normalized, mappability-corrected coverage as described above).  Some columns labeled "-ALL" give concatenated values for all individual features, listed 5' to 3', within each gene.  Exon-exon junctions, labeled "SPL", are notated as <count>(<exons>) with "^" between adjoining exons; e.g., "2(5^6)" indicates 2 reads crossing the junctions between exons 5 and 6, and "1(3^5^6)" for 1 read crossing from exon 3 to 5, through all of 5, and crossing to exon 6.  Exon-intron junctions, labeled "JXN", are notated as, e.g., "1(8>8<)" for 1 read crossing from exon 8 into intron 8 or "3(8<9>)" for 3 reads crossing intron 8 and exon 9.  Exonic mappability indices are listed (column "S_mappability", applicable to both strands) where appropriate as "EXN=<i0>[<i1>|<i2>|...]", where <i1>, <i2>, ... are the indices for individual exons, and <i0> is the index calculated over all exonic bases.  (Owing to a glitch that was later corrected, the 3'-most exon's index is missing from the output, though not from the exonic Density calculation, for genes with multiple exons.)
Supplementary_files_format_and_content: The "cross_reads_and_features__LOG" .txt files document each MAPtoFeatures analysis, including total reads used for normalization, totals per feature across the genome, and other statistics.

source_name: MGE 10 DIV

growth_protocol: Mouse E14 MGE- and CTX-derived neurons were cultured for 10 days

extract_protocol:
Total RNA was extracted with Trizol according to the manufacturer's instructions
Whole Transcriptome sequencing (WT-Seq, RNA-Seq: sequencing of total RNA): WT-Seq was performed according to a protocol/kit now available from Life Technologies, with minor modifications that are included below. Briefly, 5ug of total RNA isolated from DIV10 mouse MGE-cultures cultures was depleted of ribosomal RNAs using two rounds of Human/Mouse RiboMinus treatment (Life Technologies) with overnight ethanol precipitations for sample re-concentration. The removal of ribosomal RNAs was confirmed on a Bioanalyzer Nano Chip (Agilent). 500–1000ng of riboRNA-depleted total RNA was fragmented by heating for 18 minutes at 95°. Fragmentation was followed by size selection of ~50 to ~150bp fragments using the flashPAGE denaturing PAGE-fractionator (Life Technologies) and ethanol precipitation overnight. The resulting RNA was directionally ligated, reverse-transcribed, and RNAseH treated. After trial PCR to assess library quality and quantity, 30ul cDNA was run on a native 6% PAGE gel. The 90–120bp size window (corresponding to 50–80bp RNA insert size) was cut from the gel, shredded, and inserted directly into a 400ul PCR reaction using standard WT-Seq kit components and submitted to 11–15 cycles of PCR. The PCR product was phenol-chloroform extracted, ethanol precipitated, and resuspended in 20ul WT-Seq gel loading buffer. The resulting sample was run on a 6% native PAGE gel, and the 150–175bp size range (corresponding to 60–85bp) was cut from the gel, shredded, and extracted overnight in WT-Seq PAGE elution buffer. The resulting library was filtered through 0.45um spin filters (Life Technologies) to remove gel pieces and ethanol precipitated. We note that WT-Seq can detect neither the 5'-most fragment from transcripts with 5'-modified ends (such as mRNA 5' 7-methyl-guanosine caps) nor the 3'-most fragment from transcripts with 3'-modified ends. However, for transcripts long enough to produce multiple 50+ bp fragments, WT-Seq should detect the remaining fragments.

treatment_protocol: At DIV 9, the cells were quieted O.N. with TTX and AP-5 and membrane-depolarized on DIV 10 for 0, 1 and 6 hours with 55 mM extracellular KCl

value: E14 MGE derived neurons, 10 DIV

value: 55mM KCL

tag: time

value: 6 h

tag: genetic background


title: MGE_WT_1hrsKCl

value: 1 h


title: WT_NoDoxo_r3

description:
Sample 3
processed data file: edgeRWTKONODOX_noYX_summary_131113_expf2_CAP_exprData.txt

source_name: lincRNA-p21+/+ murine MEF RNA-seq without Doxorubicin


title: WT_NoDoxo_r1

description:
Sample 1
processed data file: edgeRWTKONODOX_noYX_summary_131113_expf2_CAP_exprData.txt


title: WT_NoDoxo_r2

description:
Sample 2
processed data file: edgeRWTKONODOX_noYX_summary_131113_expf2_CAP_exprData.txt


title: NoDoxo_WT_H3K27me3_ChIPSeq

description: lincRNA-p21+/+ murine MEF H3K27me3 ChIP-seq without Doxorubicin.

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation.
Reads were aligned to the mouse genome (genome build mm9) with Bowtie version 0.12.7 for uniquely mapping reads with up to 2 mismatches.
Peaks were called using MACS version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: BED files for peaks were generated using MACS version 1.4.2. Score column represents: -10log10(pvalue) compared to input control. Peaks were filtered for those with -10log10(pvalue) > 80

growth_protocol: MEFs were maintained as primary cultures in DMEM supplemented with 15% FBS, pen/strep, L-glutamine, non-essential amino acids, and -mercaptoethanol.

extract_protocol:
Lysates were clarified from sonicated nuclei and bound DNA fragments were isolated with antibody.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce DNA damage, cells were treated with 0.5 mM doxorubicin for 24hrs. MEF cells were harvested by trypsinization, counted, washed once in PBS and cross-linked in 1% formaldehyde diluted in PBS for 10 min at room temperature.  5-10x106 nuclei were isolated and chromatin was sonicated to 300-500 bp in an ice-water slurry for 2x10 min cycles using a Bioruptor sonicator (Diagenode). The sonicated chromatin was used to set up chromatin immunoprecipitations with antibody overnight at 40C on a rotator. Beads were washed once in each of the following washes for 5 min at 40C on the rotator: Low salt wash (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8.0, 150 mM NaCl supplemented with protease inhibitors), High salt wash (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.0, 500 mM NaCl), LiCl wash (0.25 M LiCl, 1% NP-40, 1% Na deoxycholate, 1 mM EDTA, 20 mM Tris-HCl, pH 8.), and TE wash (10 mM Tris-HCl, pH 8.0, 1 mM EDTA).

value: wild type:lincRNA-p21+/+

tag: chip antibody

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: Doxo_WT_H3K27me3_ChIPSeq

description: lincRNA-p21+/+ murine MEF H3K27me3 ChIP-seq with Doxorubicin


title: Doxo_KO_H3K27me3_ChIPSeq

description: lincRNA-p21-/- murine MEF H3K27me3 ChIP-seq with Doxorubicin


title: Doxo_WT_H3K4me3_ChIPSeq

description: lincRNA-p21+/+ murine MEF H3K4me3 ChIP-seq with Doxorubicin


title: NoDoxo_KO_H3K27me3_ChIPSeq

description: lincRNA-p21-/- murine MEF H3K27me3 ChIP-seq without Doxorubicin.


title: NoDoxo_KO_H3K4me3_ChIPSeq

description: lincRNA-p21-/- murine MEF H3K4me3 ChIP-seq without Doxorubicin.


title: Doxo_WT_input_ChIPSeq

description: lincRNA-p21+/+ murine MEF  WCE input with Doxorubicin

value: none (input)


title: NoDoxo_WT_H3K4me3_ChIPSeq

description: lincRNA-p21+/+ murine MEF H3K4me3 ChIP-seq without Doxorubicin.


title: NoDoxo_KO_input_ChIPSeq

description: lincRNA-p21-/- murine MEF WCE input without Doxorubicin.


title: Doxo_KO_input_ChIPSeq

description: lincRNA-p21-/- murine MEF WCE input with Doxorubicin


title: EHEC_control1

description:
RIP-Seq
EHEC control 1

organism: Escherichia coli O157:H7 str. Sakai

value: MEM-HEPES

tag: strain

value: Sakai


title: MGE_WT_0hrsKCl

value: unstimulated

value: control


title: NoDoxo_WT_input_ChIPSeq

description: lincRNA-p21+/+ murine MEF  WCE input without Doxorubicin.

value: hybrid 129/B6


title: Soybean Early Maturation Stage Axis Vasculature-Biological replicate 1

description: Compartments collected from seeds ranging 6.0-7.0mm in length

tag: tissue

value: Stage Axis Vasculature

tag: cultivar

value: Williams 82


title: WT_Doxo_r3

description:
Sample 6
processed data file: edgeRWTKODox_noYX_summary_131113_expf2_CAP_exprData.txt

value: mouse embryonic fibroblast (MEF)

value: 0.5 mM doxorubicin for 24hrs


title: EHEC_HTF2

description:
RIP-Seq
EHEC hfq::HTF2

value: His-FLAG tagged

value: ANTI-FLAG M2 affinity gel (Sigma-Aldrich, cat# A2220); Ni-NTA resin


title: EHEC_HTF1

description:
RIP-Seq
EHEC hfq::HTF1


title: GFP IP 3

city: New York

first: Jeffrey

middle: M

last: Friedman

state: NY

address: 1230 York Avenue

department: Molecular Genetics

institute: The Rockefeller University

description: Translated mRNAs present on ribosomes in neurons that project to the nucleus accumbens.

data_processing:
Tophat2 (v2.0.3) was used to align the reads using the --bowtie1 (v0.12.7) option. Segment size was 25bp allowing for 2 mismatches, anchor size for splices was set to 10bp allowing for 0 mismatches.
The gene annotation was from Ensembl (NCBIM37).
For transcript abundance estimation and differential expression testing, the cufflinks (v2.1.1) package was used.
Genome_build: mm9

source_name: Midbrain and hypothalamus

growth_protocol: SYN-NBL10 mice were injected into the nucleus accumbens (NAc) with the retrogradely transported virus CAV-GFP. The virus will express GFP in neurons that project to the injection site (NAc). Fourteen days after injections, mice were sacrificed and the ventral midbrain and posterior hypothalamus were rapidly dissected on ice. Briefly, a 3 mm slice was made approximately covering the region 1-4 mm posterior to bregma. Lateral and dorsal parts were removed to isolate hypothalamus and the ventral midbrain.

extract_protocol:
The Input and GFP IP RNA samples were purified using the Absolutely RNA Nanoprep Kit (Agilent)
SMARTer Ultra Low Input RNA Kit for Illumina Sequencing

treatment_protocol: Brains were pooled into 3 groups of 6 mice per group, homogenized and centrifuged to clarify. Total RNA (Input) samples were saved and GFP Immunoprecipitation was performed on the remaining lysate with two mouse monoclonal antibodies (19C8, 19F7; Doyle et al., 2008).

tag: antibody

value: GFP IP


title: GFP IP 1


title: WT_Doxo_r1

description:
Sample 4
processed data file: edgeRWTKODox_noYX_summary_131113_expf2_CAP_exprData.txt

value: wild type; lincRNA-p21+/+

tag: cell type


title: Input 3

description: All RNA in the dissected piece


title: Input 2

description: All RNA in the dissected piece


title: GFP IP 2


title: Input 1

description: All RNA in the dissected piece


title: Soybean Cotyledon Stage Seed Coat Outer Integument-biological replicate 2

description: Compartments collected from seeds ranging 3.0-3.5mm in length

extract_protocol: Sequencing libraries were prepared using 250 nanograms of total RNA, using the Illumina TruSeq Small RNA Sample Preparation Kit (cat no RS-200-0012 & RS-200-0024). Briefly, total RNA was ligated with 3’ and 5’ RNA adapter using T4 RNA ligase. Adapter-ligated small RNA was converted to complementary DNA (cDNA) and amplified by PCR for 15 cycles.  Libraries were size-selected on a polyacrylamide gel for the desired size of 147-160 bp and purified. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument (Thermo Scientific, Waltham, MA).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: subregion

value: seed coat outer integument


title: Doxo_KO_H3K4me3_ChIPSeq

description: lincRNA-p21-/- murine MEF H3K4me3 ChIP-seq with Doxorubicin

value: lincRNA-p21 KO; lincRNA-p21-/-


title: Soybean Cotyledon Stage Seed Coat Inner Integument-biological replicate 1

value: seed coat inner integument


title: Soybean Cotyledon Stage Seed Coat Outer Integument-biological replicate 1


title: Soybean Cotyledon Stage Seed Coat Inner Integument-biological replicate 2


title: Soybean Cotyledon Stage Seed Coat Hilum-biological replicate 1

source_name: Soybean Cotyledon Stage Seed Coat Hilum

value: seed coat hilum


title: Soybean Cotyledon Stage Seed Coat Hilum-biological replicate 2


title: Soybean Cotyledon Stage Endosperm-biological replicate 2

source_name: Soybean Cotyledon Stage Endosperm

value: endosperm


title: Soybean Cotyledon Stage Seed Coat Epidermis-biological replicate 1

value: seed coat epidermis


title: Control_IgG, replicate2

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: Sample 3

data_processing:
Basecalls performed using Casava 1.4
Fastq files were split by barcode.
Reads were aligned to the human genome (hg19) using BWA 0.5.0
peaks were called by two different approaches, MACS 1.4 and Homer , using default settings. Regions that were detected by both methods were considered as the binding regions
Genome_build: hg19

growth_protocol: The isolation procedure and culture/differentiation conditions have been described previously (PMID:23393180; 15492368).

extract_protocol:
Cells were harvested and nuclear fractions were enriched by a brief sonication in lysis buffer . Then protein-DNA complexes were isolated with antibody.
ChIP-sequencing libraries were prepared using NEBnext chip-seq library Prep master mix set (New England Biolabs, USA)   from 5 ng of anti-EBF1 and anti-IgG ChIP DNA according to manufacturer's protocol.The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane.samples were indexed with DNA barcodes and 3 different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads).  Barcode for IgG sample is ATTT and for EBF1 sample is GCCT in replicate 1 In replicate2, barcode for IgG sample is ACAT and for EBF1 sample is TAAT .

value: Adipose stromal cell (ASC) adipocyte

tag: time (relative to induction)

value: 12 days

value: rabbit IgG

value: Santa Cruz Biotechnology

tag: chip antibody cat.#


title: Soybean Cotyledon Stage Seed Coat Epidermis-biological replicate 2

value: Williams 82


title: Soybean Cotyledon Stage Endosperm-biological replicate 1


title: anti_EBF1, replicate 2

description: Sample 4

value: custom-made EBF1 antibody (rabbit)

value: Abmart, P.R.China


title: Control_IgG, replicate1

description: Sample 1


title: anti_EBF1, replicate 1

description: Sample 2


title: Soybean Cotyledon Stage Embryo Proper Cotyledon-biological replicate 2

value: embryo proper cotyledon


title: Soybean Cotyledon Stage Embryo Proper Cotyledon-biological replicate 1


title: Soybean Cotyledon Stage Embryo Proper Axis-biological replicate 2

value: embryo proper axis


title: Soybean Cotyledon Stage Embryo Proper Axis-biological replicate 1


title: Soybean Cotyledon Stage Embryo Proper-biological replicate 1

source_name: Soybean Cotyledon Stage Embryo Proper

value: embryo proper


title: Soybean Heart Stage Suspensor-biological replicate 2

description: Compartments collected from seeds 1.7-2.5 mm in length

source_name: Soybean Heart Stage Suspensor

extract_protocol: Sequencing libraries were prepared using 250 nanograms of total RNA (unless otherwise noted), using the Illumina TruSeq Small RNA Sample Preparation Kit (cat no RS-200-0012 & RS-200-0024). Briefly, total RNA was ligated with 3’ and 5’ RNA adapter using T4 RNA ligase. Adapter-ligated small RNA was converted to complementary DNA (cDNA) and amplified by PCR for 15 cycles.  Libraries were size-selected on a polyacrylamide gel for the desired size of 147-160 bp and purified. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument (Thermo Scientific, Waltham, MA).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

value: suspensor

tag: total rna input amount

value: 50 ng


title: Soybean Cotyledon Stage Embryo Proper-biological replicate 2


title: Soybean Heart Stage Seed Coat Outer Integument-biological replicate 1

value: seed coat outer integument


title: Soybean Heart Stage Seed Coat Outer Integument-biological replicate 2


title: Soybean Heart Stage Suspensor-biological replicate 1


title: Soybean Heart Stage Seed Coat Inner Integument-biological replicate 2

value: seed coat inner integument


title: Soybean Heart Stage Seed Coat Inner Integument-biological replicate 1


title: Soybean Heart Stage Seed Coat Epidermis-biological replicate 2

source_name: Soybean Heart Stage Seed Coat Epidermis


title: Soybean Heart Stage Endothelium-biological replicate 2

source_name: Soybean Heart Stage Endothelium

value: endothelium


title: Soybean Heart Stage Embryo Proper-biological replicate 1

source_name: Soybean Heart Stage Embryo Proper


title: Soybean Heart Stage Embryo Proper-biological replicate 2


title: Soybean Heart Stage Endosperm-biological replicate 2

source_name: Soybean Heart Stage Endosperm

value: endosperm


title: Soybean Heart Stage Endosperm-biological replicate 1


title: Soybean Heart Stage Endothelium-biological replicate 1


title: EHEC_HTF4

description:
RIP-Seq
EHEC hfq::HTF4

tag: media

value: MEM-HEPES

tag: rna chaperone hfq

value: His-FLAG tagged

tag: purification strategy

value: ANTI-FLAG M2 affinity gel (Sigma-Aldrich, cat# A2220); Ni-NTA resin

value: Sakai


title: EHEC_HTF3

description:
RIP-Seq
EHEC hfq::HTF3


title: FAGC_Input

status: Public on May 21 2014

city: Barcelona

first: Nuria

last: Montserrat

address: Baldiri Reixac, 10-12

country: Spain

institute: Institute for Bioengineering of Catalonia (IBEC)

description: Gene corrected Induced pluripotent Stem cells from human fibroblasts from patients with FA disease

data_processing:
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 with the default parameters
peaks were called by using MACS version 1.4.2
Genome_build: hg19
Supplementary_files_format_and_content: tab separated text file containing peak coordinates and FDR score

growth_protocol: Induced pluripotent stem cells were grown in mTSER media and

extract_protocol:
Immunocomplexes were incubated with 1:1 mix of protein A and G Dynabeads (Invitrogen, Carlsbad, CA) for 2 hours at 4°C, with rotation. Beads were immobilised on magnetic racks and the supernatants discarded, after which the beads were washed with low salt buffer, high salt buffer and LiCl buffer. All washes were carried out for 5 minutes at 4°C on a rotating wheel in the presence of protease inhibitors. Beads were then resuspended in 100 μl of elution buffer and DNA complexes were decrosslinked at 65 °C for 3 hour with shaking. DNA was then eluted in 50 μl of water using the PCR purification kit (QIAGEN).
Libraries were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® kit (ref. E6200S) according to the manufacturer's protocol. Briefly, 10 ng of input and ChIP enriched DNA were subjected to end repair, addition of “A” bases to 3′ ends and ligation of PE adapters. All purification steps were performed using Qiagen PCR purification columns (refs. 50928106 and 50928006). Library size selection was done with 2% low-range agarose gels and DNA was extracted using QIAquick Gel extraction kit (ref. 50928706, Qiagen) and eluted in 36 µl EB. Library amplification was performed by PCR on the size selected fragments. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot.   Sequencing was done on the HiSeq2000, Single Reads, 50nts.

treatment_protocol: Cells were trypsinized and crosslinked in 1% formaldehyde for 10 min at room temperature (RT). Crosslinking was quenched with 0.125 M glycine for 5 minutes at RT. Pelleted cells were lysed in 1,3 ml ChIP buffer and sonicated for 6 min in a Bioruptor sonicator (Diagenode, Liège, Belgium). Soluble material was quantified by Bradford assays and the 100 μg of total protein amount were used for immunoprecipitation with H3K4me3 antibody overnight with rotation.

value: none (input)

value: Induced pluripotent stem cells from human fibroblasts from patients with FA disease

tag: genotype correction status

value: corrected


title: FA123_5Fancas5_Input


title: FA123_5_Input

description: Induced pluripotent Stem cells from human fibroblasts from patients with FA disease

value: not-corrected


title: FA123_5_H3K4

value: Anti-trimethyl-histoneH3(lys4) Polyclonal Antibody Cat. #07-473 Millipore


title: EHEC_control2

description:
RIP-Seq
EHEC control 2

value: untagged control


title: FA123_5Fancas5_H3K4


title: Soybean Heart Stage Seed Coat Epidermis-biological replicate 1

value: seed coat epidermis

value: Williams 82


title: FA123_8

data_processing:
Reads were aligned to the reference genome by using tophat2 by using the following parameters:
tophat --library-type=fr-firststrand -M -G and annotations from iGenomes (Ensembl / GRCh37)
Resulting alignments were analyzed by cuffdiff (v2.1.1) by using the following parameters
cuffdiff --library-type=fr-firststrand -b -u and annotations from iGenomes (Ensembl / GRCh37)
Genome_build: GRCh37
Supplementary_files_format_and_content: cuffdiff output (tab separated file) containing information about genes FPKM.

growth_protocol: Induced pluripotent stem cells were grown in mTSER media in plastic dishes coated with mTSER matrigel. Cells were weekly amplified with dispase

extract_protocol:
Total RNA from each cell line was isolated using Trizol following the manufacturer's guidelines. All RNA samples were treated with TURBO DNase inhibitor (Ambion) to remove any residual genomic DNA
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 (ref. RS-122-2101/2) according to the manufacturer's protocol. Briefly, 1.5 µg of total RNA were used for poly(A)-mRNA selection using streptavidin-coated magnetic beads and were subsequently fragmented to approximately 300bp. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and random primers. The second strand of the cDNA incorporated dUTP in place of dTTP. Double-stranded DNA was further used for library preparation. dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. All purification steps were performed using Qiagen PCR purification columns (refs. 50928106 and 50928006). Library size selection was done with 2% low-range agarose gels. Fragments with insert sizes of 200 to 400 bp were cut from the gel, and DNA was extracted using QIAquick Gel extraction kit (ref. 50928706, Qiagen) and eluted in 20 µl EB. Library amplification was performed by PCR on the size selected fragments using the primer cocktail supplied in the kit for 15 cycles. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot.   Libraries were sequenced Paired End, 50nts on Illumina’s HiSeq 2000

value: not corrected


title: FA123_FANCA5


title: FA123_5


title: Jurkat GABPa 1 Input

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description: Jurkat GABPa input

data_processing:
Single-end 36 bp reads generated by the Illumina HiSeq 2000 were aligned against the Human Reference Genome (assemby hg18, NCBI Build 36) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15 as well as duplicate reads.
Enriched regions of the genome were identified by comparing ChIP samples to input samples using MACS and SWEMBL. Only peaks that were identified by both MACS and SWEMBL were used for further analyses.
Genome_build: hg18
Supplementary_files_format_and_content: MACS peaks in .bed file format

source_name: Jurkat cell line

growth_protocol: cells were grown in RPMI medium supplemented with 10% Foetal Bovine Serum and passage was performed at 80% confluence using 0.05% Trypsin EDTA.

extract_protocol: Briefly, 54 ul of ChIP DNA or 50 ng of total input control DNA were subjected to end-repair using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase, before purification using the DNA Clean and concentrator-5 kit (Zymo Research). Adenine overhangs were added using Klenow 5¡¦-3¡¦exo-minus, Illumina Solexa sequencing adapters were ligated using T4 DNA ligase and amplified with 18 PCR cycles using Phusion DNA polymerase (Finnzymes) and Illumina Solexa sequencing primers 1.1 and 2.1. Libraries were size selected by electrophoresis, excising the DNA smear between 200-300 bp on a Dark Reader non-UV transilluminator, purified using a Qiagen gelextraction mini-elute kit and quantified using an Agilent Bioanalyser.

treatment_protocol: cells were grown to 75-80% confluence and then transferred to media supplemented with charcoal-stripped serum for 48 hrs. Cells were then either treated with 1 nM methyltrienolone (R1881), a synthetic androgen, or an equal volume of ethanol. ChIP was performed using ERG (Santa Cruz SC-816X) or GABPa (Santa Cruz SC-22810) antibodies.

tag: cell line

value: Jurkat

tag: chip antibody

value: Input


title: Jurkat ERG 1 Input

description: Jurkat ERG input


title: V ERG VCaP Input

description: VCaP ERG input

source_name: VCaP cell line

value: VCaP

tag: treatment

value: vehicle


title: Soybean Globular Stage Seed Coat Outer Integument-biological replicate 1

description: Compartments collected from seeds 1 mm in length

value: seed coat outer integument


title: t0 ERG VCaP Input

description: VCaP ERG input


title: Soybean Globular Stage Seed Coat Outer Integument-biological replicate 2


title: V GABPa VCaP Input

description: VCaP GABPa input


title: IVT only replicate 1

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

description: rRNA-depleted RNA

data_processing:
Raw reads from all sequencing samples were aligned to the human genome (GRCh37/hg19) using the RNA-seq Unified Mapper (v2.0.4) with default parameters. RUM also generated coverage bedgraph files and calculated RPKM values using the annotations from the MGC genes track in the UCSC genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain RPKM values for each exon, intron, and transcript contained in the IVT sequences
Supplementary_files_format_and_content: bigwig files contain coverage plots for uniquely-aligned reads.

source_name: Mammalian gene collection

growth_protocol: cDNAs from the Mammalian Gene Collection, cloned into pCMV-Sprot 6 plasmid, were collected from three 384-well plates (total of human 1062 transcripts) as follows: 10 µl sterile dH2O was added to each well and incubated at 37oC for 10 min to resuspend plasmid DNA in water. Plasmid DNAs were collected and combined in 1.5 mL tube with aid of multichannel pipette and concentrated by ethanol precipitation. To amplify the library 10 ng of plasmid library was transferred into E.coli DH5α (Invitrogen catalog no. 18258-012) with heat shock method. Cells were incubated with plasmid library for 5 min on ice and were subjected to 42oC for 30 sec. Then cells were transferred back to ice and incubated for 2 min. Next, 0.95 mL SOC medium was added to the cells and incubated at 37 oC for 1 h by shaking at 225 rpm. Cells were plated on LB-agar plates containing 100 µg/ml ampicilin. Plates were incubated for 16h at 37oC to grow the colonies and 3500 (approx 3-fold of library size) colonies were collected with liquid LB. Cells were transferred into 100 mL liquid LB and incubated at 37oC for 2 h. Plasmids were purified using Qiagen maxiperep kit (catalog no. 12163), according to the manufacturer's protocol.

extract_protocol:
For IVT RNA:  Plasmids were linearized by NotI-HF enzyme so that the SP6 polymerase promoter site will be upstream of the sequences to be transcribed. Reactions consists of 5 U NotI-HF (NEB catalog no. R3189L), 5 µg library plasmid DNA, 1 X NEBuffer 4 (supplied with enzyme) and 90 µl of dH2O. Reaction was incubated at 37oC for 2 h to achieve complete digestion. The complete digestion of plasmid DNA was assessed by DNA gel electrophoresis. To eliminate NotI-HF and possible RNase in reaction mixture, samples was subjected to Proteinase K treatment. SDS and Proteinase K were added to the reaction mixture to a final concentration of 0.5% and 100 µg/mL, respectively. Sample was incubated at 37oC for 30 min. After Proteinase K treatment, sample was subjected to the phenol/chlororform extraction, followed by ethanol precipitation. Pellet was dissolved in 50 µl of RNase-free water. Next in vitro transcription was carried out using MAXIscript® SP6 Kit (Ambion catalog no: AM1308). Reaction composed of 1 µg of library plasmid, 1X transcription buffer, 0.5 mM of NTPs (GTP,ATP, CTP, and UTP),  40 U of SP6 RNA polymerase and 10 µl of RNase-free water. Reaction was incubated at 37oC for 30 min. Next, samples were treated with TURBO DNase to remove the plasmid templates. Briefly, 10 U of TURBO DNase (included with MAXIscript SP6 kit) were added to reaction mixture and incubated at 37oC for 15 min. To stop the reaction 1 μL of 0.5 M EDTA was added. To remove unincorporated NTPs and other impurities sample was precipitated with ammonium acetate/ethanol. The following reagents were added to the DNase -treated reaction mixture: 30 μL RNase-free water to bring the volume to 50 μL,  5 μL 5 M Ammonium Acetate, and 3 volumes 100% ethanol. Sample was chilled at -20oC for 30 min and then centrifuged at maximum speed in a 4oC table-top microfuge. The supernatant was discarded and pellet was washed with ice-cold, 70% ethanol. Pellet was dissolved in 50 μL RNase-free water and quality of RNA was assessed by agrose gel electrophoresis. In addition, PCR was carried out with in vitro transcribed RNA to confirm total depletion of plasmid DNA as well.  For mouse RNA:  WT 6-week old male C57/BL6 mice were acquired from Jackson Labs. Mice were sacrificed and liver samples were quickly dissected and snap-frozen in liquid nitrogen. RNA was isolated from frozen mouse liver samples by TRIzol reagent according to manufacturer’s protocol (Invitrogen catalog no. 15596-026). All animal experiments were performed in accordance with the approval of the Institutional Animal Care and Use Committee.
IVT RNA (2500 ng, 150ng, 75ng, 15 ng, and 0 ng) was pooled with mouse liver RNA (0 ng, 2350 ng, 2425 ng, 2485 ng, and 2500 ng respectively) to a final quantity of 2.5 µg. Each pool was split into two replicate samples of 1 µg each. RNA pools were treated with Ribo-Zero Gold kit (Epicentre catalog no. RZHM11106) and converted into Illumina RNA-seq libraries with the TruSeq RNA sample prep kit (Ilumina catalog no. FC-122-1001). Briefly, rRNA was removed from 1 ug of pooled RNA using Ribo-Zero Gold kit and purified via ethanol/sodium acetate precipitation according to manufacturer’s protocol. After drying, the RNA pellet was dissolved in 18 μL of Elute, Prime, Fragment mix (provided with TruSeq RNA sample prep kit). RNA was fragmented for 8 minutes and 17 uL of this fragmented RNA was used to make the RNA-seq library according to Illumina TruSeq RNA sample prep kit protocol. After fragmentation/ priming, first strand cDNA synthesis with SuperScript II (Invitrogen catalog no. 18064014), second-strand synthesis, end-repair, a-tailing, and adapter ligation, the library fragments were enriched with 15 cycles of PCR. Quality and size of library was assessed using Agilent 2100 BioAnalyzer. The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2000 (paired 100 bp reads).

tag: bc accession ids

tag: rna selection method

value: rRNA-depletion (Ribo-zero gold)

tag: mouse strain

tag: mouse tissue

tag: plasmid backbone

tag: ivt rna input quantity

tag: mouse rna input quantity

value: 0 ng


title: Soybean Globular Stage Seed Coat Inner Integument-biological replicate 2

tag: subregion

value: seed coat inner integument

tag: cultivar


title: Jurkat ERG 2

description: Jurkat ERG

value: ERG

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog#


title: FA123_8_Input

tag: antibody

value: none (input)

tag: cell type

value: Induced pluripotent stem cells from human fibroblasts from patients with FA disease


title: Mouse only replicate 2

description: rRNA-depleted RNA

source_name: Mouse liver

value: Liver


title: Soybean Globular Stage Seed Coat Inner Integument-biological replicate 1


title: FAGC_H3K4

value: Anti-trimethyl-histoneH3(lys4) Polyclonal Antibody Cat. #07-473 Millipore

tag: genotype correction status

value: corrected


title: Jurkat ERG 1

description: Jurkat ERG

tag: cell line


title: Soybean Globular Stage Seed Coat Hilum-biological replicate 2

source_name: Soybean Globular Stage Seed Coat Hilum

value: seed coat hilum

value: Williams 82


title: Soybean Globular Stage Endosperm-biological replicate 4

source_name: Soybean Globular Stage Endosperm

value: endosperm


title: Soybean Globular Stage Seed Coat Hilum-biological replicate 1


title: Jurkat GABPa 2

description: Jurkat GABPa

value: Jurkat

tag: chip antibody

value: GABPa


title: Jurkat GABPa 1

description: Jurkat GABPa


title: Soybean Globular Stage Endosperm-biological replicate 3


title: FAGC16neo


title: EWS CLIP-Seq replicate 2

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

data_processing:
Basecalling was performed using Illumina pipeline versions 1.5.0 within within SCS 2.5.
Reads were mapped to the human genome using GEM (Marco-Sola et al. 2013), allowing for up to 2 mismatches and retaining only sequences that mapped uniquely to the genome.
All the unmapped reads were then trimmed 1 base from the 3’ end and remapped. This sequential trimming and mapping was continued up to 21nt length reads (15 bases of trimming).
All EWS CLIP-Seq replicate 1 reads were extended to 30nt and all EWS CLIP-Seq replicate 2 andontrol reads were extended to 60 nt.
Additional filtered datasets and analysis description can be found here: http://regulatorygenomics.upf.edu/Data/EWS/
Genome_build: hg18
Supplementary_files_format_and_content: BED files containing all mapped reads.

source_name: HeLa cells

growth_protocol: HeLa cells (purchased from ATCC) were maintained in Dulbecco’s modified Eagles medium (DMEM; Gibco BRL) supplemented with 10% fetal bovine serum (FBS) (Gibco), penicillin and streptomycin.

extract_protocol:
HeLa cells were grown in 150mm plates, rinsed once with ice-cold PBS and placed in a Stratalinker without the cover plate and irradiated once with an energy of 400mJ/cm. Cells were then scraped off the palte and centrifuged at 2500rpm for 5 min at 4°C and the pellet re-suspended in 3x the cells volume of PBS and distributed in two separate eppendorf tubes. Each tube of crosslinked lysate was resuspended in 700 μl of 1X PXL (PBS (tissue culture grade without Mg++ or Ca++) 0.1% SDS 0.5% deoxycholate 0.5% NP-40, supplemented with protease inhibitors and with 15 μl RNAsin (Promega)) and kept on ice for 10 min. 30 μl of RQ1 DNAse (Promega, M6101) were added to each tube and extracts were incubated at 37° for 5 min, centrifuged at 1000 rpm, followed by an incubation at 37° for 5 minutes with RNAse I. Extracts were the centrifuged at 12000 rpm for 10’ and then clarified on protein A Dynabeads  for 2 hours at 4°C,  before immunoprecipitation using protein A pre-adsorbed with either rabbit IgGs or EWS antibody (5μg) at 4 °C under constant rotation. After incubation for 3 hours, stringent washes were performed with ice-cold buffers as follows: 2 washes with 1X PXL, 2 washes with 5X PXL (High-salt Wash Buffer) and 2 washes with PNK Buffer (50 mM Tris-Cl pH 7.4 10 mM MgCl2 0.5% NP-40). Alkaline phosphatase (Roche) treatment (3μl) was performed at 37°C for 20’ in Thermomixer, followed by 4 washes in PNK buffer (one wash including 20mM EGTA). 3’ RNA linker ligation was carried out overnight at 16°C on beads using T4 RNA ligase (Fermentas) and radioactively-labeled linkers. Beads were extensively washed (1x PXL buffer, 1x 5XPXL buffer, 3x PNK buffer), before and after PNK treatment (T4, NEB, [40 units]) for 20’ at 37°C.  Finally, beads were resuspended in 30ml of PNK buffer, supplemeted with Novex loading buffer and loaded on a Novex NuPAGE 10% Bis-Tris gel. The gel was run at 175V in the cold room and subsequently transfered to nitrocellulose using the Novex wet transfer apparatus, for 1 h at 30V in NuPAGE Transfer Buffer with 10% methanol. After transfer, the nitrocellulose filter was rinsed in 1X PBS, and exposed to autoradiogram. The radioactively labeled RNA-protein complexes were excised and proteinase K treatment was performed (20’ at 37°C) before RNA extraction with Phenol-Chloroform and preciiptation overnight with 3M NaOAc pH 5.2, glycogen (Ambion, 9510) and 1:1 EtOH:isopropanol.
The RNA was resuspended in RNase free water and 5’ end linker ligation (containing also barcode sequences) was carried out with T4 RNA ligase at 16°C for 5 hours. RNAs were reverse-transcribed, PCR amplified with barcoded primers and sequenced using Solexa (Illumina) technology.

value: HeLa

value: EWS antibody


title: R GABPa VCaP

description: VCaP GABPa

value: VCaP

tag: treatment

value: methyltrienolone


title: EWS CLIP-Seq replicate 1


title: t0 GABPa VCaP Input

description: VCaP GABPa input

value: Input


title: Mouse only replicate 1

description: rRNA-depleted RNA

tag: bc accession ids

value: rRNA-depletion (Ribo-zero gold)

value: 0 ng


title: t0 GABPa VCaP

description: VCaP GABPa

value: Santa Cruz


title: Control IgG CLIP-Seq

value: Non-specific rabbit IgG antibody


title: R ERG VCaP

description: VCaP ERG

value: ERG


title: V ERG VCaP

description: VCaP ERG

value: vehicle


title: 1 IVT : 10 mouse replicate 2

description: rRNA-depleted RNA

organism: mixed libraries

source_name: Mammalian gene collection / mouse liver

tag: rna selection method

value: Liver


title: IVT polyA selected

description:
polyA RNA
As with the other RNA-seq libraries, these libraries were prepared using the TruSeq RNA sample prep kit (Illumina catalog no. FC-122-1001). For the polyA sample, 1 µg of IVT RNA was treated with polyA selection reagents included with the TruSeq RNA sample prep kit according to manufacturer's protocol. RNA was fragmented for 8 minutes and 17 uL of this fragmented RNA was used to make the RNA-seq library according to Illumina TruSeq RNA sample prep kit protocol. After fragmentation/ priming, first strand cDNA synthesis with SuperScript II (Invitrogen catalog no. 18064014), second-strand synthesis, end-repair, a-tailing, and adapter ligation, the library fragments were enriched with 15 cycles of PCR. Quality and size of library was assessed using Agilent 2100 BioAnalyzer. The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2500 (paired 100 bp reads).

value: polyA selection (included with TruSeq library prep kit)

tag: mouse strain


title: 1 IVT : 2 mouse replicate 1

description: rRNA-depleted RNA

tag: mouse tissue


title: t0 ERG VCaP

description: VCaP ERG


title: OsNMD3ΔNLSL2

city: Beijing

first: Baocai

last: Zhang

state: Beijng

address: Beichen west road

department: Center for Genome Biology

country: China

institute: Institute of Genetics and Developmental Biology, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oryza sative whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Oryza sative reference cDNAs, MSU version 6.1
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample ...

organism: Oryza sativa

source_name: the 2nd internodes

growth_protocol: The plants were cultivated in experimental fields during natural growing seasons.

extract_protocol:
Total RNA was extracted from the 2nd internodes of development-matched wild-type and transgenic plants using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: the 2nd internodes

tag: development stage

value: elongation stage

tag: genotype

value: overexpression of OsNMD3ΔNLS


title: 1 IVT : 10 mouse replicate 1

description: rRNA-depleted RNA

tag: plasmid backbone

tag: ivt rna input quantity

tag: mouse rna input quantity


title: 1 IVT : 2 mouse replicate 2

description: rRNA-depleted RNA


title: OsNMD3ΔNLSL1


title: IVT no selection

description:
Total RNA
For the no selection sample, 100 ng of IVT RNA at a concentration of 100 ng/µL was diluted with 17 μL of Elute, Prime, Fragment mix (provided with TruSeq RNA sample prep kit).  RNA was fragmented for 8 minutes and 17 uL of this fragmented RNA was used to make the RNA-seq library according to Illumina TruSeq RNA sample prep kit protocol. After fragmentation/ priming, first strand cDNA synthesis with SuperScript II (Invitrogen catalog no. 18064014), second-strand synthesis, end-repair, a-tailing, and adapter ligation, the library fragments were enriched with 15 cycles of PCR. Quality and size of library was assessed using Agilent 2100 BioAnalyzer. The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2500 (paired 100 bp reads).


title: 1 IVT : 1 mouse replicate 2

description: rRNA-depleted RNA

value: 75 ng


title: 1 IVT : 1 mouse replicate 1

description: rRNA-depleted RNA


title: WT

value: wild type


title: IVT plasmid templates

description:
cDNA
MGC plasmids were linearized by NotI-HF enzyme as before. These linearized plasmids were then fragmented using a Covaris S220 Focused-ultrasonicator. Briefly, 1.2 µg of linearized plasmid in a final volume of 60 uL of H2O was loaded into a microTUBE (Covaris catalog no. 520045). The ultrasonicator was de-gassed and prepared according to manufacturer’s protocol. Linearized plasmids were sonicated using the following conditions: intensity 5, duty factor 10%, cycles per burst 200, time 120s, and water bath temperature 7ºC. Fragmented plasmids were gel-purified using a 1% agarose gel (BioRad catalog no. 161-3107) and TAE running buffer (BioRad catalog no. 161-0743). Gel slice between 100 bp and 700 bp was excised and DNA was purified using MinElute gel extraction kit (Qiagen catalog no. 28606) according to manufacturer’s protocol. Fragmented DNA was converted into a sequencing library using TruSeq DNA sample prep kit (Illumina catalog no. FC-121-2001). End repair, adenylation, adapter ligation, gel size-selection, and PCR enrichment were performed according to manufacturer’s protocol. During the gel size-selection, a band between 300 bp and 500 bp was excised. Quality and size of library was assessed using Agilent 2100 BioAnalyzer. This library was sequenced using an Illumina MiSeq (paired 100 bp reads).


title: Sample 3 (d9)

status: Public on May 20 2014

city: Yangzhou

first: Zhenguo

last: Liu

address: 88 South University Ave.

institute: Yangzhou University

data_processing:
Illumina GA Pipeline v1.5 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence,and filtered for reads with more than 10% unknown bases, then aligned to The DFCI Apis mellifera Gene Index (AMGI) by  SOAP2 aligner,no more than 2 mismatches are allowed in the alignment
Sequencing saturation analys, distribution of reads on reference genes, and coverage analysis were employed for the qulity control prupose.
The level of gene expression was calculated as RPKM (reads per kilobase transcriptome per million mapped reads), differentially expressed Genes (DEGs) were identified using an FDR≤0.001 (false discovery rate no greater than 0.05)
Cluster v3.0 and javaTreeview v1.1.1 were used forExpression pattern analysis of DEGs. Gene Ontology functional analysis was based on GO::TermFinder. KEGG (major public pathway-related database) is used in our pipeline to perform pathway enrichment analysis of DEGs for  further understand genes biological functions.
Genome_build: The DFCI Apis mellifera Gene Index (AMGI)
Supplementary_files_format_and_content: Excel files include RPKM values, discription, GO function, and Blastnr for each Sample

organism: Apis mellifera

source_name: Hypopharyngeal glands tissue

growth_protocol: Full-sister honey bees (Apis mellifera carnica Pollmann) produced by sexually mature virgin queens were artificially fertilized with sperm collected from an isolated, sexually mature drone using an artificial insemination instrument to minimize noise in the genetic background. Bees were left to develop age-matched adults after emergence from the comb in the apiaries of Yangzhou University, China.

extract_protocol:
Total RNA was extracted from the HGs of the samples (each pooled from 30 honey bees) using TRIzol reagent (Invitrogen, USA). A Qubit fluorometer (Invitrogen, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., USA) were used to determine the quality and quantity of the RNA. The mRNA was enriched using oligo (dT) magnetic beads, then fragmented into short fragments (approximately 200-700 nt) using fragmentation buffer (Invitrogen, USA). Double-stranded cDNA product was synthetized and purified .
sequencing adapters were ligated to the fragments, and the fragments were purified by agarose gel electrophoresis (AGE) and enriched by PCR amplification. The library products were sequenced using the Illumina HiSeqTM 2000 system.

value: Hypopharyngeal glands tissue

tag: age

value: day 9 after emergence from the comb

tag: strain

value: Apis mellifera carnica Pollmann


title: Sample 5 (d16)

value: day 16 after emergence from the comb


title: Sample 4 (d12)

value: day 12 after emergence from the comb


title: Sample 2 (d6)

value: day 6 after emergence from the comb


title: RNA from anaerobic culture

city: Austin

first: Seung Hee

last: Cho

state: Texas

address: 200 E Dean Keeton St. Stop C0400

department: iCMB

institute: University of Texas at Austin

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to genome using bwa-0.7.0 with default parameters
Mapped reads visialized with IGV were compared between two samples only expressed within intergenic regions.
The number of reads falling in the region of each small RNA transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: Zymomonas mobilis ZM4 complete genome(NC_006526)
Supplementary_files_format_and_content: tab-delimited text files include normalized reads counts per verified small RNAs by Northern blot analysis under aerobic and anaerobic conditions

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: cells

growth_protocol: Zymomonas mobilis ZM4 (ATCC 31821) was cultured in RM media at 30°C (pH 6.0). A single colony was inoculated into 5 ml RM media (Glucose, 20.0 g/L; Yeast Extract, 10.0 g/L; KH2PO4, 2.0 g/L; pH 6.0) (4, 31) and cultured aerobically at 30°C overnight. A 1/100 of initial culture was added to 1 L of pre-warmed RM broth and then cultured overnight at 30°C with shaking at 150 rpm. The inoculum was added to each culture so that the initial OD 600nm was around 0.17. Each culture was grown aerobically or anaerobically and then collected at 13hrs (late exponential/early stationary phase) or 26hrs (late stationary phase) post-inoculation as pH was adjusted every 4 hr.

extract_protocol:
cells were grown aerobically or anaerobically and collected at 16 hrs after inoculation for Deep Sequencing. All centrifugation was performed at 4°C. Cells were pelleted and resuspended in 1 ml TRIzol reagent (Invitrogen). Following pelleting, cells were transferred to screw cap tubes containing glass beads (Sigma) and incubated at 25°C for 5 min. Cells were lysed using a mini-beadbeater (BIOSPEC), with 100-s pulses three times. Cells were kept on ice for 10 min between each 100-s treatment. The beads and cellular debris were centrifuged at 4°C for 2 min. The supernatant was transferred to a clean siliconized 2 ml tube. After addition of 300 µl of chloroform: isoamyl alcohol mix (v/v 24:1), the samples were inverted for 15 s, and then incubated at 25°C for 3 min. Then, tubes were centrifuged at 13,000 rpm for 10 min, and the aqueous top phase transferred to a clean siliconized 1.5 ml tube.  Following this step, 270 µl of isopropanol and 270 µl of a mixture of 0.8 M sodium citrate and 1.2 M sodium chloride was added. The samples were mixed well, and then incubated on ice for 10 min. The RNA was pelleted by centrifugation at 13,000 rpm for 15 min. The pellet was washed with 1 ml 95% cold ethanol and centrifuged for 5 min. The pelleted RNA was allowed to air-dry for ∼5 min, and was resuspended in 30 µl RNase-free water (Ambion).
RNA libraries were prepared for sequencing using NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs Inc.) according to manufacturer's protocol.

tag: culture condition

value: Anaerobic


title: Sample 1 (d3)

value: day 3 after emergence from the comb


title: V GABPa VCaP

description: VCaP GABPa

value: VCaP

value: GABPa

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog#


title: RNA from aerobic culture

value: Aerobic


title: LS174T, H3K4me1 ChIP-seq

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

data_processing:
Image analysis and per-cycle basecalling were performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie 0.12.5, rejecting reads aligning to more than one genomic location, allowing up to 2 mismatches in the first 28 bases of the reads and no gapped alignments.
Aligned reads were filtered with the htSeqTools R package. PCR artifacts were detected and removed with the filterDuplicateReads function using a FDR of 1%. Strand shift bias was removed using the alignPeaks function with the default options.
A first step for peak calling was done using the enrichedRegions function from the htSeqTools package to find genomic regions with coverage above 10 reads, comparing the proportion of reads inside/outside of each region between each IP sample and the Input with a logistic regression likelihood-ratio test. Enriched regions were defined as those with a Benjamini-Hochberg adjusted P-value below 0.05.
In a second step, we used the function enrichedPeaks from htSeqTools to define peaks (i.e., putative binding sites) as locations within the enriched regions with a coverage difference between IP and Input above 10 reads.
Genome_build: GRCh37
Supplementary_files_format_and_content: Peak file was generated with htSeqTools R package. Bedgraph files contain coordinates of peaks and corresponding p-value of chi-square test.

source_name: LS174T, H3K4me1 ChIP

growth_protocol: LS174T cells were grown in DMEM plus 10% FBS. When cells were at 70-80% confluence, proteins were cross-linked to DNA with formaldehyde 1% 15 minutes.

extract_protocol:
Cells were lysed in 0.5% SDS, lysates were sonicated and clarified. Chromatin was diluted 5 fold and incubated with beads for pre-clearing. After pre-clearing, chromatin was incubated o/n with anti-GATA6, anti-H3K4me3, anti-H3K4me1, or anti-H3K27ac antibodies.
10ng of DNA, as quantitated by fluorometry, was resolved by electrophoresis and fractions of 50-250bp were extracted. Fractions were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Illumina PE primers (12 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Illumina Hi-Seq 2000 with SBS TruSeq v5 reagents by following manufacturer's protocols.

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: antibody

value: anti-H3K4me1 (Abcam, ab8895, lot:GR46388-1)


title: LS174T, H3K4me3 ChIP-seq

source_name: LS174T, H3K4me3 ChIP

value: anti-H3K4me3 (Diagenode, pab003050, lot:A5051-001P)


title: LS174T, H3K27ac ChIP-seq

source_name: LS174T, H3K27ac ChIP