title: SA NS

city: Worcester

first: Michael

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
Images were analyzed using OLB 1.9 and CASAVA_v1.8.2
TopHat v2.0.6 was used to map the sequences to human genome hg19
cuffdiff v2.0.1 was used to generate the differetially spliced isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff fpmk results as txt format

source_name: cell line

growth_protocol: SA cells are grown in BEGM medium

extract_protocol:
RNA were extracted using TriPure
library constructed following Illumina TruSeq  Stranded mRNA Sample Prep guide.

treatment_protocol: SA cells are infected with shRNA targeting SFRS9 or non-silencing control

tag: treatment

value: Non-silencing shRNA

value: SA


title: SA SFRS9 KD

status: Public on May 20 2014

type: SRA

state: MA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: SFRS9 knock down

tag: cell line


title: H3K27me3_UM-SCC-4

city: Ann Arbor

first: Maureen

middle: A

last: Sartor

state: MI

address: 2017 Palmer Commons Bldg., 100 Washtenaw Ave

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

description: HPV-

library_source: genomic

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly using BWA from raw fastq files with default settings
samtools and bedtools were then used to convert the SAM files to BED files
Our custom peak caller, PePr, was used to determine peaks specific to HPV(-) or HPV(+) samples
Genome_build: hg19
Supplementary_files_format_and_content: BED format files with chromosome, start, end, sequence id, quality score from BWA and strand

molecule: genomic DNA

source_name: UM-SCC-4 cell line

growth_protocol: Squamous cell carcinoma derived cell lines were propagated in DMEM supplememnted with 10% fetal bovine serum, 100nM Non-essential amino acids, and profilactic panicillin and streptomycin until 80% confluence

extract_protocol: H3K27me3 ChIP Seq Library was constructed by GenPathway, Inc., San Diego, CA using a commercial quality antibody against H3K27 trimethylation for the first four samples. DNA was amplified according to the Illumina ChIP-Seq library construction protocol, and a region of 250-350 bp was excised from the preparative Agarose gel. QC of the final libraries by Agarose gel showed the expected broad bands of the same size range.

treatment_protocol: At 80% confluence, cells were fixed in their growth media for 15 minutes with 1% (final) buffered formaldehyde solution. Fixation was terminated with glycine. Adherent cells were scraped from the culture flask and washed with ice cold PBS containing Igepal and PMSF after which the cell pellet was flash frozen.

tag: hpv-status

value: HPV-negative

tag: age

tag: Sex

value: female

tag: tumor site

value: Base of tongue

tag: antibody

tag: antibody vendor

value: Millipore cat# 07-449, lot# JBC1854858, Rab pAb


title: H3K27me3_UM-SCC-47

description: HPV+

source_name: UM-SCC-47 cell line

value: HPV-positive

value: male


title: input_UM-SCC-47

description: HPV+


title: H3K27me3_UM-SCC-74A

description: HPV-

source_name: UM-SCC-74A cell line


title: H3K27me3_Caski

description: HPV+

source_name: CaSki (ATCC) cell line

value: Cervix


title: input_UM-SCC-4

description: HPV-


title: LS174T, GATA6 ChIP-seq 3

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

data_processing:
Image analysis and per-cycle basecalling was 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 BWA version 0.5.9-r16 allowing 0-1 mismatches
Unique aligned reads were converted to BED format
GATA6 ChIP-seq replicates & Input DNA aligment files were normalized to the same number of reads randomly.
Peaks were called using macs version 2.0.9 with the following setting: format (BED), effective genome size (2.70e+09), band width (300), model fold (10,30),  qvalue cutoff (5.00e-02)
Reproducibility of replicates was assessed ranking the peaks of each by q-value. For each replicate, top 40% of peaks were evaluated to be present in the list of identified peaks for the other replicates with the method described by Chikina et al. (Chikina, MD. And Troyanskaya, OG. Ann effective statistical evaluation of ChIPseq dataset similarity. Bioinformatics 28, 607-613. (2012))
Such as for all replicates more of the 85% of top 40% significant peaks were present in the others and the number of peaks identified for each replicate don't differ by more than a factor of 2, reads from replicates were combined to repeat the peak finding analysis as described above, significant peaks obtained following this strategy were used for further analysis
The reads after merge the replicates of the ChIP-seq and normalize with the input were directionally extended to 300 bp, and for each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window to create a wig file to visualize the data in the University of California Santa Cruz genome browser
Genome_build: GRCh37
Supplementary_files_format_and_content: peak file was generated with macs version 2.0.9

source_name: LS174T, GATA6 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.
20ng 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 Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

tag: cell type

value: colorectal carcinoma

value: anti-hGATA6 (R&D AF1700)


title: LS174T, GATA6 ChIP-seq 1


title: LS174T, GATA6 ChIP-seq 2


title: Spermatozoa

city: Madrid

first: Jesus

last: Garcia Lopez

address: C/Ramiro de Maeztu 9

department: Cellular and Molecular Biology

institute: Cib (CSIC)

data_processing:
Illumina sequence reads were clustered and collapsed into unique_reads files that contain both the sequences and their counts
Sequences were aligned (bowtie release 0.12.9) to the RNAdb (http://jsm-research.imb.uq.edu.au/rnadb/) against the sequences previously annotated as piRNAs.
Sequences that were not aligned with RNAdb were aligned (bowtie release 0.12.9) against the sequences contained in deepBase (http://deepbase.sysu.edu.cn/)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited *.txt files include the expression analysis performed using DeSeq (Bioconductor version: 2.11) normalized by TMM: trimmed mean of M values method. Size factors obtained for each sample were: 1.2293392 (oocyte sample)/ 0.8735805 (sperm. sample)/ 0.8945942 (Zygote sample)
Supplementary_files_format_and_content: tab-delimited *.csv files contain the result of ping-pong pairing quests: piRNAs are a type of small non-coding RNAs and have been related to the down-regulation of TEs conferring a means to safeguard genome integrity. The binding between each piRNA and their TE target RNA takes place at the 5´ end of the piRNA sequence. Upon binding, poorly characterized proteins participate in the cleavage of TE transcripts after nucleotide position 10 at the 5´end of the piRNA binding site. Cleavages generate new piRNAs derived from the RNA of TEs. The piRNAs derived from TEs can bind to new TE transcripts generating new piRNAs in a cyclic mechanism that is known as the "ping-pong model" or "ping-pong cycle". The ping-pong cycle generates characteristic cleavage specific piRNA sequence signatures. In this manner, piRNAs whose targets are the TE transcripts show a bias for uridine at the 5´ end (5U), whereas the piRNA sequences generated from TE cleavage show a bias for nucleotide adenosine at position 10 (10A). But also exists, sequences that enclose both features: uridine at the 5´ end, and adenine at position 10 (5U10A), and sequences that contain none of the above features (Other). Ping-pong signatures were searched in all sequences classified as piRNAs in oocytes, sperm and zygotes. We searched for overlapping regions between the sequences that corresponded to the 5U piRNA group and the 10A piRNA group. The same type of search was also performed with sequences clustered in groups 5U10A and Other. The "PING-PONG ANALYSIS" folder contains the sequences that potentially overlap, and the name of the piRNAs to which these sequences belong.

organism: Mus musculus

source_name: Mouse spermatozoa

growth_protocol: Fully-grown oocytes and zygotes were collected from the oviducts of mice. Briefly, superovulation was induced in 4-5 week old C57BL6 mouse female mice by intraperitoneal injection of 5 IU pregnant mare serum (PMSG), followed 48 hours later by 5 IU human chorionic gonadotropin (HCG). Female mice were mated with DBA/6J males after HCG administration. Fully-grown oocytes and zygotes were treated with hyaluronidase (300 µg/ml, Sigma H3884) to remove the cumulus cells and they were washed by passing through several drops of M2 medium (Sigma M7167).

extract_protocol:
Total RNA from 15,200 metaphase II oocytes, 500 million of spermatozoa and 15,400 zygotes was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina sequencing reported sequences 18-32 nucleotides long.

treatment_protocol: For high-throughput sequencing 15210 fully-grown oocytes and 15416 zygotes were collected. In all cases, the zona pellucida was removed by incubation in 30 ml of prewarmed acidic Tyrode solution under mineral oil for approximately 15 seconds, followed by careful washing in three drops of M2 medium under a stereomicroscope.

tag: strain

tag: developmental stage

value: Cauda epididymis Spermatozoa


title: Sperm_smallRNAseq_Donor1

status: Public on May 19 2014

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

description: processed data file: D1D2_SPERM_RPKM_miRNA.txt

data_processing:
Basecalls performed using CASAVA
Reads were aligned to hg18 using Novoalign V2.07.09 allowing up to 10 alignments per read, using these parameters for mRNA-seq alignments: -FILMFQ -o SAM -m -l17 -t60 -rA 10 -a and these settings for smRNA-seq alignments: -FILMFQ -o SAM -m -l17 -h90 -t30 -rA 10 -a.
The novoalign index was made by combining hg18 fasta files (UCSC), Illumina adapter sequences, and splice junction fasta files made using MakeSpliceJunctionFasta (USeq version 6.0) with -s 34 as input radius and merged ensGene and knownGene table (from genome.ucsc.edu) as annotation.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit (Cat # 80004), ribosomal RNA was depleted using RiboZero kit.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

tag: donor

value: adult donor 1

tag: tissue

value: sperm


title: Oocytes

source_name: Mouse oocytes

value: Metaphase II Oocytes


title: livers group f

city: London

first: Gioia

last: Altobelli

address: 5 University Street

country: United Kingdom

institute: UCL

description: dna methylation profile from livers of 6 animals in group f

data_processing:
base calling was performed by the genomic facility, presumably using CASAVA
1st: normalization using Medips, rpm, , R-Bioconductor package
1st bis: quality control using fastq, inhouse software and genome browser
2nd: alignment to the genome using Bowtie
2nd bis: quality control (aligned reads count,visualization)
3rd: peak calling using MACS
4th: genomic annotation (ENSEMBL API,GREAT)
5th: biological annotation (GSEA,GREAT)
Genome_build: rn4
Supplementary_files_format_and_content: wig, normalized methylation profiles (step 1)
Supplementary_files_format_and_content: peaks.bed:  peak calling using MACS

organism: Rattus norvegicus

source_name: livers group f

extract_protocol:
genomic DNA was isolated and fragmented by sonication; MBD fusion protein was incubated with fragmented DNA.
Genomic DNA from rat livers was subjected to selection according to the methyl-CpG binding domain-based (MBD) protein protocol (DNA pooled from 6 individuals per group) and the resulting fragments sequenced in high throughput. Methylated DNA was captured with MethylCap kit (Diagenode). Approximately 10 ng of captured DNA was used for library preparation (ChIP-seq DNA sample Prep Kit, Illumina).

tag: diet

value: low protein+folate

value: Wistar

tag: gender

value: 1 day


title: livers group p

description: dna methylation profile from livers of 6 animals in group p

source_name: livers group p

value: low protein


title: Sperm_smallRNAseq_Donor2

value: adult donor 2


title: Zygotes

source_name: Mouse zygotes

value: C57BL/6 females mated with DBA/6J males

value: 15-18h post-fertillization Zygotes


title: Sperm_RNAseq_Donor2

description: processed data file: D1D2_SPERM_RPKM_mRNA.txt


title: H3K27ac_ChIPseq_Human_rep2

description: processed data file: H3K27ac_EnrichedRegions.txt

data_processing:
ChIP-seq data processing and analysis was performed as previously described in Hammoud et al., 2009.  Briefly, differential enrichment between histone ChIP-seq dataset and mononucleosomal control datasets (from GSE15690) were determined with ScanSeqs (USeq), and statistically enriched peaks were called with EnrichedRegionMaker (USeq).
Genome_build: hg18
Supplementary_files_format_and_content: Enrichment were determined with ScanSeqs (USeq), and statistically enriched peaks were called with EnrichedRegionMaker (USeq). Useq files were generated as part of the USeq software collection ChIPseq pipeline.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

tag: donor age

value: adult

tag: chip antibody

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #


title: livers group c

description: dna methylation profile from livers of 6 animals in group c

source_name: livers group c

value: normal diet

value: male


title: H3K27ac_ChIPseq_Human_rep1


title: Sperm_RNAseq_Donor1


title: input_UM-SCC-74A

description: HPV-

tag: hpv-status

value: HPV-negative

value: Base of tongue


title: H3K4me1_ChIPseq_Human_rep2

description: processed data file: H3K4me1_EnrichedRegions.txt

value: Abcam


title: M_RNASeq

description: Sample 12

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 whole genome using tophat version 1.4.1 with parameters : -p 8 --splice-mismatches 1  --segment-mismatches 2 --solexa1.3-quals
FPKM and differential expression were calculated using the Cufflinks suite version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include abundance measurements (FPKM) values for each Sample

source_name: Mature Sperm_RNA-seq

tag: age

value: postnatal week 8

value: Testis

value: Mature Sperm


title: LS174T, input

source_name: LS174T, input

tag: cell line

value: colorectal carcinoma

value: none (input)


title: H3K4me1_ChIPseq_Human_rep1

value: sperm


title: Input_ChIPSeq_SC

description: Sample 20

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet --solexa1.3-quals
Peak calling was done using MACS 2.0.9 with the following configurations: -q 1e-5 --llocal=10000 --bw 300 -m 5,30  --slocal=1000  -B  --keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were automatically generated as an output of MACS 2.0.9; useq files were generated as part of the USeq software collection ChIPseq pipeline. Values in useq represent the Log2Ratio of the ChIP signal.

value: Spermatocytes


title: Input_ChIPSeq_ST

description: Sample 21

value: Spermatids


title: H3K27ac_ChIPSeq_ST

description: Sample 11

value: Histone H3K27ac antibody

tag: chip antibody cat.#


title: H3K4me1_ChIPSeq_SC

description: Sample 7

value: Anti-Histone H3 (mono methyl K4) antibody


title: H27me3_ChIPSeq_ST

description: Sample 6

value: Anti-trimethyl-Histone H3 (Lys27) Antibody

value: Upstate


title: H3K27ac_ChIPSeq_SC

description: Sample 10

value: Active Motif


title: H27me3_ChIPSeq_SC

description: Sample 5


title: H3K4me3_ChIPSeq_ST

description: Sample 3

value: Histone H3K4me3 antibody


title: input_Caski

description: HPV+

value: HPV-positive

tag: Sex

value: female

tag: tumor site

value: Cervix

tag: antibody


title: H3K4me3_ChIPSeq_SC

description: Sample 2

tag: strain

value: postnatal week 8

tag: cell type


title: M_BiSeq_Rep4

description:
processed_data_file: MATURE_BaseFractionNonConverted.useq
Sample 16

data_processing:
Basecalls performed using CASAVA
Bisulfite reads were aligned using Novocraft novoalign in bisulfite mode with the following parameters: [-o SAM -rRandom -t240 -h120 -b2]
All downstream analysis and file manipulation were done using the USeq (http://useq.sourceforge.net/) suite.
Genome_build: mm9
Supplementary_files_format_and_content: Point methylation data files generated by useq viewable on IGB browser

source_name: Mature Sperm_Bisulfite-Seq

extract_protocol:
DNA was extracted using Gentra PUREGENE DNA Isolation Kit and sheared on COVARIS to a median 400 bp fragment.
For all samples unmethylated lambda DNA was added to 1% final concentration (Promega Madison, WI 53711). Methylated paired-end adapters were ligated to sheared DNA according to the Illumina library preparation protocol. Sodium bisulfite conversion was performed using the EpiTect Bisulfite Kit (Qiagen, Valencia, CA 91355) with an additional incubation step at 60C for 120 min to increase conversion rate. Bisulfite treated DNA was then PCR amplified with 16 cycles and sequenced. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

value: Testis


title: Eic2-GFP ChipSeq

city: Edinburgh

first: Nicholas

last: Toda

state: Midlothian

address: 6.34 Michael Swann Building

department: Institute of Cell Biology

institute: University of Edinburgh

description: GTGTTCTA

data_processing:
Reads were aligned to the S. pombe EF2 genome using Bowtie2 with parameters  --non-deterministic --no-mixed -X 300 -5 20 -3 20
Sorted bam files were generated using samtools
Coverage was calculated using MACS with parameters  -w -S -g 12570000 --keep-dup=1000000 --space=1
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: wig files

organism: Schizosaccharomyces pombe

source_name: Eic2-GFP ChipSeq

growth_protocol: Cells were grown in an asynchronous culture of YES media to a density of 1x10^7 cells/ml

extract_protocol:
Cells were fixed for 15 min in 1% formaldehyde (Sigma) and lysed with 0.4 mg/ml Zymolase (AMS Biotechnology Europe) in PEMS for 1 hour at 36°C. Samples were sonicated for 20 minutes in a Bioruptor (Diagenode). The samples were incubated overnight with 7.5 µl αGFP antibody and 125 µl Protein G dynabeads. The samples were washed and incubated with 1% SDS for 4 hours at 65°C. The DNA was purified with a Qiagen PCR purification kit and centromeric enrichment was verified by qPCR.
Illumina libraries were  prepared following the TruSeq Nano DNA kit guidelines (Illumina) using NEXTflex (Bioo Scientific) adapters with internal barcodes. Multiplexed libraries were sequenced on an Illumina HiSeq2000 (Ark Genomics, Edinburgh, UK).

tag: genotype/variation

value: expressing GFP-tagged Eic2

value: asynchronous haploid cells

value: GFP

value: Molecular Probes


title: Mis18-GFP Input ChipSeq

description: CATCAAGT

source_name: Mis18-GFP Input ChipSeq

value: expressing GFP-tagged Mis18


title: Mis18-GFP ChipSeq

description: GTCGTAGA

source_name: Mis18-GFP ChipSeq


title: Eic1-GFP ChipSeq

description: TAGGATGA

source_name: Eic1-GFP ChipSeq

value: expressing GFP-tagged Eic1


title: Eic1-GFP Input ChipSeq

description: CTGTAGCC

source_name: Eic1-GFP Input ChipSeq


title: M_BiSeq_Rep3

description:
processed_data_file: MATURE_BaseFractionNonConverted.useq
Sample 15

tag: tissue

value: Mature Sperm


title: M_BiSeq_Rep2

description:
processed_data_file: MATURE_BaseFractionNonConverted.useq
Sample 14


title: ST_BiSeq_Rep4

description:
processed_data_file: SPERMATID_BaseFractionNonConverted.useq
Sample 12

value: Spermatids


title: M_BiSeq_Rep1

description:
processed_data_file: MATURE_BaseFractionNonConverted.useq
Sample 13


title: ST_BiSeq_Rep2

description:
processed_data_file: SPERMATID_BaseFractionNonConverted.useq
Sample 10


title: ST_BiSeq_Rep1

description:
processed_data_file: SPERMATID_BaseFractionNonConverted.useq
Sample 9


title: SC_BiSeq_Rep4

description:
processed_data_file: SPERMATOCYTE_BaseFractionNonConverted.useq
Sample 8

value: Spermatocytes


title: atf21del_180_r3

city: Manchester

first: Hui Sun

last: Leong

address: Wilmslow Road

department: The University of Manchester

institute: Cancer Research UK Manchester Institute

description: strand-specific RNA-seq

data_processing:
Sequencing reads were aligned to the fission yeast genome (PomBase database release 11) using SHRiMP2 aligner with default parameters. Total number of reads that can be aligned to the genome at exactly one locus per sample range from 7.5 to 20.1 millions. These uniquely mapped reads were used to identify stretches of unambiguous transcription. Reads that aligned to more than one locus (generally paralogous regions in the genome) were discarded. Adjacent unambiguous transcription regions with minimum peak height of two and located within 50 bases of each other were merged to yield an extensive transcription map of S. pombe. These regions were then positioned relative to known annotation and labelled according to the gene(s) they overlapped with using the Bioconductor package annmap.
The expression of a locus was measured by the Reads Per Kilobase Per Million Mapped (RPKM) score, which was calculated by counting the number of uniquely mapped reads in a given locus and normalizing for by transcript length and for the total read count in the library prep.
Genome_build: PomBase database release 11
Supplementary_files_format_and_content: Tab-delimited text file of RPKM values for all samples

source_name: fission yeast cells

extract_protocol:
Total RNA was extracted from the fission yeast cells as follows: cells were treated with hot acidic phenol-chloroform, followed by phenol-chloroform extraction and RNA precipitation. Then RNA was column purified using QIAGEN RNeasy Kit 74104 according to the manufacturers instructions. RNA quality was determined using an Agilent 2100 Bioanalyser. Ribosomal reduction of total RNA (8μg) was performed using the Ribominus Eukaryote Kit for RNA-Seq (Invitrogen A10837-08) and the Ribominus Concentration Module (Invitrogen K155005). Greater than 90% ribosomal reduction was achieved for all samples when assessed on the Agilent 2100 Bioanalyzer.
Libraries were prepared with 350ng of ‘ribosomally-reduced’ total RNA using the SOLiD Total RNA-Seq Kit (Life Technologies 4445374). We used the chemical hydrolysis method to fragment the RNA and performed size selection on Novex 6% TBE-Urea Gels (Invitrogen EC6865). Samples were multiplexed by barcoding with the SOLiD Transcriptome Multiplexing Kit (Life Technologies 4427046). Library quantitation was carried out with the Quant-IT DSDNA HS Assay Kit (Invitrogen Q32851) on the Qubit Fluorometer (Invitrogen Q3287). Molarities were determined using a High Sensitivity DNA Assay (Agilent Technologies 5067-1504) before pooling the libraries in equimolar quantities. Emulsion PCR was carried out on the pooled libraries using an input of 0.5pM in the EZ Bead System to prepare template beads following the manufacturer’s instructions  (Life Technologies PN 4448417). Templated beads were then sequenced on a 5500XL Genetic Analyser (Life Technologies 4460730) according to manufacturer’s instructions to generate 50 bases strand-specific reads.

treatment_protocol: Cells were cultured in yeast extract (YE) medium and harvested immediately before and at 15, 30, 60, 120 and 180 min after addition of 1M sorbitol (Sigma S6021) to the culture.

value: atf21 deletion mutant

tag: treatment

value: sorbitol

tag: time  (min)

tag: replicate


title: atf21del_180_r2

description: strand-specific RNA-seq


title: SC_BiSeq_Rep2

description:
processed_data_file: SPERMATOCYTE_BaseFractionNonConverted.useq
Sample 6


title: atf21del_180_r1

description: strand-specific RNA-seq


title: SC_BiSeq_Rep3

description:
processed_data_file: SPERMATOCYTE_BaseFractionNonConverted.useq
Sample 7


title: H3K4me1_ChIPSeq_ST

description: Sample 8

tag: chip antibody

value: Anti-Histone H3 (mono methyl K4) antibody

value: Abcam


title: Scm3-GFP Input ChipSeq

description: AGTGGTCA

source_name: Scm3-GFP Input ChipSeq

value: expressing GFP-tagged Scm3


title: atf21del_120_r3

description: strand-specific RNA-seq


title: Eic2-GFP Input ChipSeq

description: ACAAGCTA

source_name: Eic2-GFP Input ChipSeq


title: AGSC_Kit_BiSeq_Rep4

description:
processed_data_file: AGSC_BaseFractionNonConverted.useq
Sample 4

value: Spermatogonia


title: AGSC_Kit_BiSeq_Rep3

description:
processed_data_file: AGSC_BaseFractionNonConverted.useq
Sample 3

value: postnatal week 8


title: atf21del_120_r2

description: strand-specific RNA-seq


title: AGSC_Kit_BiSeq_Rep2

description:
processed_data_file: AGSC_BaseFractionNonConverted.useq
Sample 2

value: Testis


title: atf21del_60_r3

description: strand-specific RNA-seq


title: AGSC_Kit_BiSeq_Rep1

description:
processed_data_file: AGSC_BaseFractionNonConverted.useq
Sample 1


title: ST_RNASeq_Rep5

description: Sample 11


title: atf21del_120_r1

description: strand-specific RNA-seq


title: atf21del_60_r1

description: strand-specific RNA-seq


title: ST_RNASeq_Rep4

description: Sample 10


title: atf21del_60_r2

description: strand-specific RNA-seq


title: atf21del_30_r3

description: strand-specific RNA-seq


title: ST_BiSeq_Rep3

description:
processed_data_file: SPERMATID_BaseFractionNonConverted.useq
Sample 11


title: ST_RNASeq_Rep3

description: Sample 9


title: SC_BiSeq_Rep1

description:
processed_data_file: SPERMATOCYTE_BaseFractionNonConverted.useq
Sample 5


title: atf21del_30_r1

description: strand-specific RNA-seq


title: ST_RNASeq_Rep2

description: Sample 8


title: ST_RNASeq_Rep1

description: Sample 7


title: SC_RNASeq_Rep5

description: Sample 6


title: atf21del_15_r2

description: strand-specific RNA-seq


title: SC_RNASeq_Rep4

description: Sample 5


title: atf21del_15_r3

description: strand-specific RNA-seq


title: atf21del_15_r1

description: strand-specific RNA-seq


title: SC_RNASeq_Rep2

description: Sample 3


title: atf21del_0_r3

description: strand-specific RNA-seq


title: SC_RNASeq_Rep1

description: Sample 2


title: H2AZ_ChIPSeq_ST

description: Sample 18

value: Anti-Histone H2A.Z antibody

tag: chip antibody vendor


title: Input_ChIPSeq_AGSC

description: Sample 19


title: WT_180_r2

description: strand-specific RNA-seq

value: wild type


title: Pol2_ChIPSeq_ST

description: Sample 16

value: RNA Pol2 antibody

value: Active Motif


title: atf21del_0_r1

description: strand-specific RNA-seq


title: WT_180_r3

description: strand-specific RNA-seq


title: H3K9ac_ChIPSeq_ST

description: Sample 17

value: Anti-acetyl-Histone H3 (Lys9) Antibody

value: Upstate


title: atf21del_30_r2

description: strand-specific RNA-seq


title: WT_120_r3

description: strand-specific RNA-seq


title: 5hMC_M

description: Sample 15

value: postnatal week 9

value: Mature Sperm


title: Scm3-GFP ChipSeq

description: GCTCGGTA

source_name: Scm3-GFP ChipSeq

value: asynchronous haploid cells

value: GFP

value: Molecular Probes


title: WT_120_r2

description: strand-specific RNA-seq

value: sorbitol


title: 5hMC_ST

description: Sample 14

value: Spermatids


title: 5hMC_SC

description: Sample 13

value: Spermatocytes


title: H3K27ac_ChIPSeq_AGSC

description: Sample 9

value: Spermatogonia

value: Histone H3K27ac antibody


title: H3K4me3_ChIPSeq_AGSC

description: Sample 1

value: postnatal week 8

value: Testis

value: Histone H3K4me3 antibody


title: WT_60_r2

description: strand-specific RNA-seq

value: wild type


title: WT_60_r3

description: strand-specific RNA-seq


title: SC_RNASeq_Rep3

description: Sample 4


title: WT_30_r3

description: strand-specific RNA-seq


title: WT_30_r2

description: strand-specific RNA-seq


title: WT_30_r1

description: strand-specific RNA-seq


title: WT_15_r3

description: strand-specific RNA-seq


title: WT_15_r2

description: strand-specific RNA-seq


title: IVT only replicate 2

status: Public on May 21 2014

city: Philadelphia

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: WT_0_r1

description: strand-specific RNA-seq


title: WT_0_r2

description: strand-specific RNA-seq


title: atf21del_0_r2

description: strand-specific RNA-seq

value: atf21 deletion mutant


title: WT_0_r3

description: strand-specific RNA-seq


title: WT_15_r1

description: strand-specific RNA-seq


title: FA123_8_H3K4

first: Nuria

last: Montserrat

address: Baldiri Reixac, 10-12

institute: Institute for Bioengineering of Catalonia (IBEC)

description: 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.

tag: antibody

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

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

tag: genotype correction status

value: not-corrected


title: Dcr23

city: Lasuanne

first: David

last: Gatfield

address: UNIL CIG

department: CIG

country: Switzerland

institute: University of Lausanne

description: rRNA-depleted total RNA

data_processing:
Base-calling: Casava 1.8.2
QC: Sequencing runs were only further processed, if their quality related statistics were within three standard deviations of the mean of all runs. The five quality related statistics used were the percentage of clusters passed filtering (%PF clusters), mean quality score (PF clusters), percentage of reads aligned, mean alignment score and percentage of alignment error.
QC: Presence of adapter sequences in the datasets were checked with cutadapt utility. It was not necessary to trim reads to remove the adapter sequences.
Pre-alignment: Sequences were first mapped to local databases of mouse rRNA (Ensembl and NCBI) and rodent-specific repeat sequences (RepBase Update version 18.10) using bowtie2 version 2.1.0 with default alignment parameters. Mapped reads were tagged to be filtered in later steps of the analysis.
Alignment: All reads were mapped to Genome Reference Consortium GRCm38 (mm10) version of mouse reference genome sequence using tophat version 1.4.1 with known mm10 transcripts provided via the –transcriptome-index option.
Filtering: Only non-rRNA, non-repeat reads that mapped uniquely to the mouse genome were selected for further analysis.
Abundance measurement: Expression levels for mRNA and pre-mRNA were estimated per locus. An in-house Python script was used to count the reads mapped within each annotation feature in a similar way as implemented in htseq-count utility software against modified gene models (filtered, flattened, provided as processed data file: Mmusculus_v1.1_flatten.gtf). Only reads which can be unambiguously identified as either exonic (continuous or spliced) or intronic for a single locus were counted towards the mRNA or pre-mRNA counts of that locus, respectively.
Pre-normalization: Mappable and countable mRNA and pre-mRNA lengths (in bps) for each locus were calculated by means of generating all possible 100-bp long reads in silico (faux reads) for each transcript type and counting the faux reads through identical mapping and counting work flow used for real experimental reads. These lengths were later used in RPKM calculations.
Normalization: Based the extend of differential expression and the presence of highly-expressed genes, read counts of mRNA and pre-mRNA datasets were normalized with upper quantile and TMM normalization methods, respectively. Prior to normalization, transcripts which did not have at least 10 counts in at least one third of the samples were removed from the datasets.
Normalization: RPKM values were calculated as the number of counted reads per 1000 mappable and countable bases per geometric mean of normalized read counts per million.
Genome_build: Genome Reference Consortium GRCm38 (mm10)
Supplementary_files_format_and_content: rpkm files were generated with R; gene IDs are ENSEMBL-IDS
Supplementary_files_format_and_content: GTF file were generated with a series of in-house Python scripts; briefly unexpressed transcript models were filtered out, some new models were constructed with Cufflinks 2.0.2 and all models were flattened per gene.

source_name: liver

extract_protocol:
Total RNA was prepared as in Gatfield et al., (Genes Dev., 23:1313, 2009)
Dnase-treated total RNAs were subjected to rRNA depletion using Ribo-Zero Magnetic Kit (Human/Mouse/Rat, Epicentre). The resulting rRNA-depleted RNA samples were then used to prepare random-primed cDNA libraries using the Illumina Tru-Seq RNA Sample Preparation Kit (Illumina) according to the manufacturer's recommendations

treatment_protocol: Mice were i.p. injected with tamoxifen for 5 consecutive days (total 2 mg), then entrained to light-dark cycles for one month with free access to food/water and sacrificed at 4-hour intervals around-the-clock

tag: genotype

value: Dicer knockout

value: liver

tag: timepoint

tag: age

value: 3-6 months

tag: genetic background

value: C57BL/6 x 129SvEv x 129S2/SvPas


title: Dcr24

description: rRNA-depleted total RNA

tag: tissue


title: Dcr22

description: rRNA-depleted total RNA


title: Dcr21

description: rRNA-depleted total RNA


title: H27me3_ChIPSeq_AGSC

description: Sample 4

tag: strain

tag: cell type

value: Anti-trimethyl-Histone H3 (Lys27) Antibody

value: Upstate

tag: chip antibody cat.#


title: WT_180_r1

description: strand-specific RNA-seq

tag: treatment

value: sorbitol

tag: time  (min)

tag: replicate


title: EHEC_HTF5

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
EHEC hfq::HTF5

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 O157:H7 str. Sakai

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: 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: Dcr18

description: rRNA-depleted total RNA

value: control littermate


title: Dcr16

description: rRNA-depleted total RNA


title: Dcr19

description: rRNA-depleted total RNA


title: Dcr15

description: rRNA-depleted total RNA


title: Dcr13

description: rRNA-depleted total RNA


title: Dcr14

description: rRNA-depleted total RNA


title: Dcr11

description: rRNA-depleted total RNA


title: Dcr12

description: rRNA-depleted total RNA


title: Dcr10

description: rRNA-depleted total RNA


title: Dcr7

description: rRNA-depleted total RNA


title: Dcr9

description: rRNA-depleted total RNA


title: WT_120_r1

description: strand-specific RNA-seq

value: wild type


title: Dcr6

description: rRNA-depleted total RNA


title: Human_Biseq_Donor2_Rep9

description: processed data file: D1D2_HyperHypo_Loci.bed

data_processing:
Basecalls performed using CASAVA
Bisulfite reads were aligned using Novocraft novoalign in bisulfite mode with the following parameters: [-o SAM -rRandom -t240 -h120 -b2]
All downstream analysis and file manipulation were done using the USeq (http://useq.sourceforge.net/) suite.
Genome_build: hg18
Supplementary_files_format_and_content: Point methylation data files generated by useq viewable on IGB browser

tag: donor age

value: adult

value: testis

value: sperm


title: WT_60_r1

description: strand-specific RNA-seq


title: Dcr20

description: rRNA-depleted total RNA


title: Dcr4

description: rRNA-depleted total RNA


title: Human_Biseq_Donor2_Rep6


title: Human_Biseq_Donor2_Rep7


title: Dcr1

description: rRNA-depleted total RNA


title: Dcr3

description: rRNA-depleted total RNA


title: Human_Biseq_Donor2_Rep5


title: Human_Biseq_Donor2_Rep8


title: Dcr5

description: rRNA-depleted total RNA


title: Human_Biseq_Donor2_Rep4


title: Human_Biseq_Donor2_Rep3


title: Human_Biseq_Donor2_Rep2


title: Dcr17

description: rRNA-depleted total RNA


title: Human_Biseq_Donor1_Rep8


title: Human_Biseq_Donor1_Rep7


title: Human_Biseq_Donor1_Rep6


title: Human_Biseq_Donor2_Rep1


title: Human_Biseq_Donor1_Rep5


title: Human_Biseq_Donor1_Rep4


title: Human_Biseq_Donor1_Rep2


title: RNA-Seq: 48h Hypox

city: Chicago

first: Christopher

last: Mariani

state: IL

institute: University of Chicago

description: RNA-Seq

data_processing:
hMe-Seal: DNA reads were aligned using BWA aligner
hMe-SEAL: Peaks called using MACS1.4
RNA-Seq: Reads aligned with tophat2 and bowtie2
RNA-Seq: Cufflinks (cufflinks, cuffcompare, cuffdiff) for expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: wig for DNA data; tab-delimited output of FPKM for RNA

growth_protocol: DMEM with 10% FBS

extract_protocol:
hMe-SEAL followed previously described methods(Song et al., Nature Biotechnology, 2011). RNA extracted with Trizol reagent.
Standard Illumina protocols

treatment_protocol: 1% O2 or 20% O2 for 48 hours

tag: cell line

value: hypoxia


title: Dcr8

description: rRNA-depleted total RNA

value: Dicer knockout


title: Dcr2

description: rRNA-depleted total RNA

value: liver


title: Human_Biseq_Donor1_Rep1


title: hMe-SEAL: input

description: hMe-SEAL

value: input control


title: H3_ChIPSeq_Human

description: processed data file: H3.3_EnrichedRegions.txt

tag: chip antibody

tag: chip antibody vendor

value: Abnova


title: hMe-SEAL: 48 Hypoxia_Rep1

description: hMe-SEAL


title: mutant_Input DNA

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

data_processing:
Basecalls performed using CASAVA version 1.8.2
FASTQ preprocessing was done in Galaxy (https://usegalaxy.org/) using tools "Remove sequencing artifacts (version 1.0.0)" and "Flexbar (v. 2.4).  The settings for Flexbar were - (2nd read set (paired) off; Max uncalled 1; Trimming of ends off; Phred-trimming on, Threshold 39; Barcode detection off; Adapter removal on, Adapter source data adapters.fa; Trim-end mode Any; Change tail length no; Removal for single read set No; Min-overlap 1; Threshold 1; Modify alignment scores no; Trimming to length off; Minimum read length 18;)
The numbers of reads per sample vary from app. 14 million for H3K4me2 precipitate to 3 million for input samples. FASTQ files were assembled to reference (Drosophila melanogaster genome Release 5, dm3) in CLC Genomics workbench application using its assembly algorithm. Inspection of resulting contigs reveals a high degree of similarity between two biological replicas, so we pooled sequencing data from two repeats for each sample type (HP1a, H3K4me2, H3K9me3 and input) and assembled to the reference dm3 genome. Mapping was performed either by mapping only uniquely positioned reads (single mapping, discarding non-specific matches function of CLC Genomics) or mapping all the reads by assigning non-uniquely positioned reads to a random position in the genome (multi-mapping, random distribution function of CLC Genomics). The parameters of the assembler were: mismatch cost = 2, insertion cost = 3, deletion cost = 3, limit = 8. Ambiguity nucleotides were replaced by FASTA codes. Final genome coverage (in both genotypes is app. the same) was: HP1a sample – 5x, H3K4me2 – 7.4x, H3K9me3 – 5.7x, input – 3.5x. Coverage data for different regions were exported from CLC Genomics workbench into CSV files (chromosome position-coverage) and used for subsequent analysis. Consensus sequences of transposable elements were obtained from Flybase (http://flybase.org/static_pages/downloads/FB2013_06/transposons/transposon_sequence_set.embl.txt.gz). piRNA cluster coordinates were taken from the piRNA bank http://pirnabank.ibab.ac.in and converted to Release 5 of D. melanogaster genome for subsequent analysis. For the analysis of dual-strand clusters we took the clusters, producing nearly equal amounts of piRNAs homologous to two complementary strands.
Genome_build: Drosophila melanogaster genome Release 5, dm3
Supplementary_files_format_and_content: UCSC bedGraph files representing genome reads coverage calculated from ChipSeq(s) to reference genome (Drosophila R5/dm3) assembly

organism: Drosophila melanogaster

source_name: mutant_mutant_Input DNA

growth_protocol: Ovaries of 1-5 day old transheterozygous piwiNt/piwi2 flies and their heterozygous siblings (piwi/+) were used.

extract_protocol:
Antibodies were used to perform ChIP and resulting chromatin fragments were used to prepare deep sequencing libraries. Please see treatment protocol for antibodies used.
Libraries were prepared with NEBNext ChIP-Seq Sample Prep Master Mix Set 1 (NEB# E6240S) which provides in-line barcodes and libraries were sequenced with Illumina HiSeq 2000. Single-end sequencing of reads were up to 50 bases.

treatment_protocol: Two replicates of each ChIP-seq experiment were done. Сhromatin IP assay was performed as described previously (7), using polyclonal rabbit anti-HP1 (PRB-291C Covance innovative) and polyclonal rabbit antibodies (Upstate): Anti-H3K4me2 (#07-030) and Anti-H3K9me3 (#07-523). The quality of DNA precipitates was checked by real-time quantitative PCR before sequencing. For this we amplified intergenic 60D region, rp49 gene and HeT-A transposon using primers indicated previously (10). Samples containing 10-30 ng of precipitated DNA were used for sequencing. Input IP samples for each genotype were prepared and sequenced in parallel and the obtained data were used further for the normalization and calculation of enrichment levels. Illumina HiSeq platform was used for sequencing.

value: piwiNt/piwi2 (mutant)

tag: age of animals

value: 1-5 day old

value: Ovaries

tag: sample type

value: Input chromatin


title: mutant_Anti-H3K9me3- replicate#2

value: Upstate

tag: chip antibody cat. #


title: MCF7_No_Treat_PolII

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

data_processing:
The data was processed using the genomatix mining station (GMS). Align and convert to bed files
Genome_build: hg19

source_name: Breast cancer cells

growth_protocol: MCF-7 cells were cultured in DMEM with 10% FCS at 37 °C. Cells were maintained in DMEM w/o phenol red and 5% charcoal stripped FCS for 72 hours before induction

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
End repair was performed using the precipitated DNA of ∼6 million cells using Klenow and T4 PNK. A 3′ protruding A base was generated using Taq polymerase and adapters were ligated. The DNA was loaded on gel and a band corresponding to ∼200 bp (ChIP fragment + adapters) was excised. The DNA was isolated, amplified by PCR, and used for cluster generation on the Illumina 1G genome analyzer. The 32 bp tags were mapped to the human genome hg19 using the eland program allowing one mismatch. The 32 bp sequence reads were directionally extended to 133 bp, corresponding to the length of the original fragments used for sequencing. For each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window and visualized in the University of California Santa Cruz genome browser (http://genome.ucsc.edu).

treatment_protocol: MCF-7 cells were mock treated or with 10nM 17b-E2 to nine time points (5', 10', 20', 40', 80', 160', 320')

tag: time point

value: Pleural effusion

tag: passages

value: Homemade Anti-Pol II Monoclonal


title: mutant_Anti-H3K4me2- replicate#2

tag: strain

tag: tissue


title: MCF7_E2_80min_PolII_rep

data_processing:
The data was processed using the genomatix mining station (GMS). Align and convert to bed files.
Genome_build: hg19

value: 80 min

tag: cell type


title: MCF7_E2_20min_PolII_rep

value: 20 min


title: MCF7_E2_40min_PolII_rep

value: 40 min


title: Human_Biseq_Donor1_Rep3

value: adult

value: testis


title: MCF7_E2_10min_PolII_rep

value: 10 min


title: mutant_Anti-H3K4me2- replicate#1


title: MCF7_E2_160min_PolII_rep

value: 160 min


title: MCF7_E2_320min_PolII_rep

value: 320 min


title: MCF7_E2_5min_PolII_rep

value: 5 min


title: mutant_anti-HP1- replicate#1

value: Covance innovative


title: mutant_anti-HP1- replicate#2

value: piwiNt/piwi2 (mutant)


title: WT_PAS preincubation

source_name: WT_WT_PAS preincubation

value: piwi/+ (wildtype)

value: 1-5 day old

value: Chromatin bound to Protein-A-sepharose without antibody


title: mutant_Anti-H3K9me3 - replicate#1

value: Ovaries

value: Upstate


title: WT_Input DNA

source_name: WT_WT_Input DNA

value: Input chromatin


title: WT_Anti-H3K4me2- replicate#2


title: WT_Anti-H3K4me2- replicate#1


title: WT_Anti-H3K9me3- replicate#2


title: hMe-SEAL: 48 Normoxia_Rep1

description: hMe-SEAL

tag: treatment

value: normoxia


title: WT_Anti-H3K9me3 - replicate#1


title: WT_anti-HP1- replicate#2


title: RNA-Seq: 48h Normox

description: RNA-Seq


title: WT_anti-HP1- replicate#1


title: bat_TK167834_smallRNA_fraction

city: Mississippi State

first: neal

last: platt

address: 32 Creelman St.

institute: Mississippi State Univeristy

data_processing:
Adapters were trimmed and reads quality filtered using the FastX toolkit
Reads outside of a 17-25 bp range were excluded

organism: Eptesicus fuscus

source_name: Testes

extract_protocol:
Testes were snap frozen from dog, horse, and a bat (Eptesicus fuscus).  Total RNA was extracted from ground tissue using standard TRIzol protocols.
The small RNA fraction was isolated and prepped for Illumina sequencing (50 bp, single-end).

value: Testes

tag: age


title: mutant_PAS preincubation

source_name: mutant_mutant_PAS preincubation


title: horse_smallRNA_fraction

data_processing:
Adapters were trimmed and reads quality filtered using the FastX toolkit
miRNAs haiprin structure predicted using miRanalyzer
Genome_build: equCab2 (GCA_000002305.1)
Genome_build: canFam3.1 (GCF_000002285.3)
Genome_build: Ept.fus.01 (GCA_000308155.1)
Supplementary_files_format_and_content: Tab delimted text files output from miRanalyzer. The header/content information of each column is provided in 'readme.txt' file.

organism: Equus caballus


title: bat_smallRNA_fraction


title: dog_smallRNA_fraction

organism: Canis lupus familiaris


title: WT Cas9 only

status: Public on May 18 2014

city: Charlottesville

first: Mazhar

last: Adli

state: VA

address: 1340 Jefferson Park Ave

department: Mol.Bio and Genetics

institute: Uni

description: PCR amplicons

data_processing:
Illlumina MiSeq Sequencer was used for base calling.
Sequence reads were aligned to hg19 reference genome using Bowtie for HA-Chip data and Bowtie2 for deep sequencing data.
Two re-sequenced files : sgRNA2_1_Replicate1 and sgRNA3_1_Replicate1 were merged with sgRNA2_Replicate1 and sgRNA3_Replicate1 respectively
Peaks were called by using MACS14 tool for HA-ChIP (-c=Control_dCas9only -p=1e-6)
Further data processing steps have been described in the method sections.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig and Bed files containing peaks.

source_name: Human Embryonic Kidney

growth_protocol: HEK293T cells were culture in DMEM(high glucose) with 10% FBS.

extract_protocol:
Crosslinked-cells were sonicated to get 300bp average fragments size followed by pulldown of histone-DNA complexes with HA antibody.
Sequencing libraries were prepared by using 1-5 ng of immunoprecipitated DNA via Illumina TruSeq Chip Library Kit according to the manufacturer’s protocol. DNA fragments between 300 and 650 bp were isolated from gel and PCR amplified. Each library was validated by appropriate primer pairs on intended target regions of sgRNA.

treatment_protocol: Cells were transfected with appropriate Cas9(d or WT )  and sgRNA(1-12) in the presence of Fugene6 and collocted after 3 days.

value: HEK 293T

tag: passage


title: sgRNA6

value: HA(abcam #9110)


title: SEC14_me_rep1

city: New Haven

first: Timothy

last: Nelson

state: CT

department: Department of Molecular, Cellular and Developmental Biology

institute: Yale University

description: section 14 mesophyll cells, replicate 1

data_processing:
Illumina Casava 1.3 software used for basecalling.
Reads were aligned to the maize reference genome agpv3 using the software Tophat v2.0.10
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Tophat
The cuffdiff software (v2.1.1) was used to get the read count of each gene, as reported in the genes.read_group_tracking file.
Genome_build: Maize AGPv3
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample .

molecule: polyA RNA

organism: Zea mays

source_name: section 14 mesophyll cells

growth_protocol: The seedlings were grown under an 80:20 mix of metal halide, with capsylite halogen lamps at light intensity of 550 μmol/m2/sec, 12:12 l/D, 31 °C L/22 °C D and 50% relative humidity.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, CA) following manufactory’s suggestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Maize Mo17 leaf sections were collected from synchronously grown plants and preserved in 100% ice-cold acetone.  After fixation in paraffin, BS and M cells were captured using a PixCell IIe or Veritas microdissection system (Life Technologies) and the RNA recovered with a Picopure RNA isolation kit (Life Technologies) according the to the manufacturer’s instructions.  A sample of 50 to 100 ng of total RNA was amplified through one round using the RiboAmp HS plus RNA amplification kit (Life Technologies).

tag: cultivar

value: leaf

tag: leaf section

value: mesophyll

tag: cell capture method

value: LCM


title: SEC14_bs_rep1

description: section 14 bundle sheath cells, replicate 1

source_name: section 14 bundle sheath cells

value: bundle sheath


title: SEC14_me_rep2

description: section 14 mesophyll cells, replicate 2


title: WT Cas9+sgRNA

description: PCR amplicons

tag: cell line


title: SEC14_bs_rep2

description: section 14 bundle sheath cells, replicate 2


title: Cotyledon stage whole seed

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole seeds 2.7 - 3.0 mm in length were collected.

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

organism: Glycine max

source_name: Soybean seeds containing cotyledon (COT) stage embryos

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Whole seeds containing globular (GLOB) stage, cotyledon (COT), early- (EM), mid- (MM), and late- (LM) maturation, pre-dormancy (PD1 and PD2) stage embryos were collected. Whole dry (DRY) seeds containing dormant embryos were also collected. For seedlings, seeds were sown on soil and after six days after imbibition, the whole seedlings and the cotyledons of seedling were manually collected.

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: Williams 82


title: sgRNA1-replica2

tag: chip antibody


title: sgRNA3-replica2


title: SEC9_bs_rep2

description: section 9 bundle sheath cells, replicate 2

source_name: section 9 bundle sheath cells


title: sgRNA4


title: sgRNA1-replica1


title: dCas9 only


title: SEC9_bs_rep1

description: section 9 bundle sheath cells, replicate 1


title: SEC9_me_rep1

description: section 9 mesophyll cells, replicate 1

source_name: section 9 mesophyll cells


title: sgRNA5


title: SEC4_bs_rep2

description: section 4 bundle sheath cells, replicate 2

source_name: section 4 bundle sheath cells


title: sgRNA2-replica1


title: sgRNA2-replica2


title: SEC9_me_rep2

description: section 9 mesophyll cells, replicate 2


title: SEC4_me_rep2

description: section 4 mesophyll cells, replicate 2

source_name: section 4 mesophyll cells


title: SEC4_bs_rep1

description: section 4 bundle sheath cells, replicate 1


title: sgRNA3-replica1


title: HIV infected Human CD4 T-Cells at 5 hours 3

status: Public on May 17 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
All libraries were sequenced to a 54-nucleotide (nt) read length on individual lanes of a Genome Analyzer IIx (Illumina, San Diego, CA).
Small RNA sequences were submitted to Geospiza (PerkinElmer, Seattle, WA) for initial analysis. Raw reads were trimmed to remove adapter sequence. Trimmed reads were aligned using Burrows-Wheeler Aligner (BWA) software against a filter reference containing rRNA, tRNA, snRNA, and mtRNA sequences.
The remaining reads were aligned to NCBI build 37.2 of the human genome using BWA and subsequently quantified using genomic annotations for microRNAs (miRBase 17), piRNAs, and known genes (Ref-Seq gene, build 37.2) or classified as unmapped.
MicroRNA read count data were obtained from Geospiza (available at http://viromics.washington.edu).
Genome_build: NCBI Human 37.2. For microRNAs (miRBase 17), piRNAs, and known genes (Ref-Seq gene, build 37.2) or classified as unmapped.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample at Each time point

source_name: human lymphoblastoid SUP-T1 cells

extract_protocol:
TotalRNA was extracted using the mirVana kit (Applied Biosystems/Ambion, Austin, TX), and quality and concentration of RNA were determined by an Agilent 2100 Bioanalyzer.
Small RNA libraries were prepared with a small RNA version 1.5 sample preparation kit (Illumina, San Diego, CA). Total RNA was ligated with two adaptors: a 3=RNAadaptor specifically modified to target microRNAs (5=-/5rApp/ATCTCGTATGCCGTCTTCTGCTTG/3ddC/) and a 5= RNA adaptor that included the sequencing primer (5=- GUUCAGAGUUCUACAGUCCGACGAUC). Reverse transcription (RT)-PCR amplification was performed using  he adaptors as primers. The resulting double-stranded cDNA libraries were purified by polyacrylamide gel electrophoresis using 6% Novex Tris-borate-EDTA gels (Invitrogen, Carlsbad, CA) and size selected to eliminate dimerized adaptors. The quality and concentration of libraries were determined by an Agilent 2100 Bioanalyzer and RiboGreen fluorescence on QuBit (Invitrogen, Carlsbad, CA).

tag: timepoint(hours)

value: HIV infected


title: HIV infected Human CD4 T-Cells at 5 hours 2


title: HIV infected Human CD4 T-Cells at 5 hours 1


title: HIV infected and UV treated Human CD4 T-Cells at 5 hours 3

value: HIV infected and UV treated


title: HIV infected and UV treated Human CD4 T-Cells at 5 hours 1


title: HIV infected and UV treated Human CD4 T-Cells at 5 hours 2


title: Mock treated Human CD4 T-Cells at 5 hours 2

value: Mock treated


title: Mock treated Human CD4 T-Cells at 5 hours 1


title: HIV infected Human CD4 T-Cells at 24 hours 2


title: SEC4_me_rep1

description: section 4 mesophyll cells, replicate 1


title: HIV infected Human CD4 T-Cells at 24 hours 1


title: HIV infected and UV treated Human CD4 T-Cells at 24 hours 1


title: Mock treated Human CD4 T-Cells at 24 hours 2


title: HIV infected Human CD4 T-Cells at 12 hours 2


title: HIV infected and UV treated Human CD4 T-Cells at 12 hours 3


title: HIV infected Human CD4 T-Cells at 12 hours 3


title: Mock treated Human CD4 T-Cells at 12 hours 2


title: Mock treated Human CD4 T-Cells at 24 hours 3


title: Mature green stage embryo

description:
EMB
Embryo from 13DAP seeds were collected.

data_processing:
Basecalls performed using RTA version 1.12.4.2.
Original data files from the Illumina sequencing pipeline were 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 Arabidopsis thaliana genome (TAIR10) obtained from the TAIR website (http://www.arabidopsis.org/) 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: TAIR10
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.

organism: Arabidopsis thaliana

source_name: Arabidopsis mature green stage embryo

growth_protocol: Arabidopsis thaliana (L.) Heynh, ecotype Wassilewskja (ws-0) plants were grown under standard greenhouse conditions (Belmonte et al., PNAS 2013). Siliques were staged according to criteria described in methods of Belmonte et al. Whole seeds containing mature green stage embryos were collected. The embryo and seed coat were manually separated.

extract_protocol:
Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA was isolated from the powder using the DNeasy Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer's instructions.
Approximately 500 and 250 nanogram of genomic DNA isolated from embryo and seed coat, respectively, 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.

tag: developmental stage

value: mature green seed

value: 13 DAP

value: embryo


title: HIV infected and UV treated Human CD4 T-Cells at 24 hours 2


title: HIV infected and UV treated Human CD4 T-Cells at 12 hours 1


title: HIV infected Human CD4 T-Cells at 12 hours 1


title: Mock treated Human CD4 T-Cells at 24 hours 1


title: HIV infected and UV treated Human CD4 T-Cells at 12 hours 2


title: Mock treated Human CD4 T-Cells at 12 hours 1


title: Mature green stage seed coat

description:
SC
Seed coats from 13DAP seeds were collected.

source_name: Arabidopsis mature green stage seed coat

value: seed coat


title: Cotyledon-stage embryonic axis

description:
COT-AXIS
Whole embryonic axis was captured from ten micron paraffin sections using Leica LMD6000 system.

data_processing:
Basecalls were performed using RTA version 1.12.4.2.
Original data files from the Illumina sequencing pipeline were 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.

source_name: Laser-captured embryonic axis part from soybean cotyledon-stage seed

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Seeds with length between 2.7 mm and 3.0 mm containing cotyledon (COT) 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 parts (seed coat, embryonic cotyledons, and embryonic axis) were captured from ten-micron longitudinal sections using a Leica LMD6000. Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).
Approximately 100, 250, and 500 nanogram of genomic DNA isolated from embryonic axis, embryonic cotyledons, and seed coat, respectively, were 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: cotyledon-stage seed

value: embryonic axis


title: Mock treated Human CD4 T-Cells at 12 hours 3


title: Cotyledon-stage embryonic cotyledons

description:
COT-COT
Whole embryonic cotyledons were captured from ten micron paraffin sections using Leica LMD6000 system.

source_name: Laser-captured embryonic cotyledons from soybean cotyledon-stage seed

value: embryonic cotyledons


title: Cotyledon-stage seed coat

description:
COT-SC
Whole seed coat was captured from ten micron paraffin sections using Leica LMD6000 system.

source_name: Laser-captured seed coat from soybean cotyledon-stage seed


title: early maturation-stage seed coat parenchyma

status: Public on May 16 2014

description:
EM-SC-PY
Seed coat parenchyma compartment was captured from ten micron paraffin sections using the Leica LMD6000 system.

data_processing:
Basecalls were performed using RTA version 1.12.4.2.
Original data files from the Illumina sequencing pipeline were in the QSEQ format. Each lane of sequencing was in an individual file.
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.

source_name: Laser-captured parenchyma compartment from early-maturation stage seed coat

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: seed coat parenchyma


title: early maturation-stage seed coat palisade

description:
EM-SC-PA
Seed coat palisade compartment was captured from ten micron paraffin sections using the Leica LMD6000 system.

source_name: Laser-captured palisade compartment from early-maturation stage seed coat

value: seed coat palisade


title: HIV infected Human CD4 T-Cells at 24 hours 3


title: R116_RNASeq_Harosoy_defective

city: Urbana

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
75 bp (from GAII) and 100bp (from HiSeq2000) reads were aligned to soybean reference genome cv. Williams 82 (phytozome v.4), using BOWTIE (Langmead et al., Genome Biology, 2009) with up to 3 mismatches and 25 alignments allowed.
RNA-Seq data was normalized in Reads per Kilobase of Gene Model Per Million Mapped Reads (RPKM) (Mortazavi et al., Nat Met 5:621-628, 2008).
Genome_build: Glycine max cv. Williams 82 (http://www.phytozome.net/soybean.php)

source_name: HD: 400-500mg seed weight stage

growth_protocol: Soybean plants (standard and defective seed coat isolines) were grown in the green house and the seeds were harvasted at different seed weight ranges. Seed coats from 50-100mg, 100-200mg and 400-500mg seed weight satges were dissected. All tissues were lyophillized and stored at -70C till further use.

extract_protocol:
Total RNA from Harosoy isolines was extracted using standard phenol-chloroform method with lithium chloride precipitation.  Extraction of RNA from seed coats with dark pigmentation required the use of a modified extraction protocol which prevents procyanidins from binding the RNA based on the procedure from Wang et al. Plant Physiology, 1994.
Library construction and high-throughput sequencing was carried out using RNA-Seq technology with Illumina GAII and HiSeq2000 at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois, Urbana-Champaign.

treatment_protocol: optimal green house growth conditions

value: Harosoy

tag: genotype/variation

value: Seed coat mutant

value: Seed coat (400-500mg seed weight stage)


title: HIV infected and UV treated Human CD4 T-Cells at 24 hours 3


title: R118_RNASeq_Clark_defective

source_name: CD: 400-500mg seed weight stage

value: Clark


title: R120_RNASeq_Clark_standard

source_name: CS: 400-500mg seed weight stage

value: Seed coat wild-type


title: R119_RNASeq_Clark_defective

source_name: CD: 50-100mg seed weight stage

value: Seed coat (50-100mg seed weight stage)


title: R121_RNASeq_Clark_standard

source_name: CS: 50-100mg seed weight stage


title: R115_RNASeq_Harosoy_standard

source_name: HS: 50-100mg seed weight stage


title: R17_RNASeq_Clark_defective

source_name: CD: 100-200mg seed weight stage

value: Seed coat (100-200mg seed weight stage)


title: R40_RNASeq_Clark_standard

source_name: CS: 100-200mg seed weight stage


title: U1-70K iCLIP-Seq, experiment 2

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

department: Biochemistry

country: Germany

institute: University of Giessen

description: U1-70K specific co-immunoprecipitated RNA after UV-crosslinking

data_processing:
Library strategy: ICLIP-Seq as described by König et al. (NSMB, 2010)
The sample- and random barcode sequence are removed from 5’ end following linker sequence trimming at the 3’ end. Trimmed sequence reads with a minimum length of 15-bp are aligned to the T. brucei 427 genomic sequence
Reads mapped to tRNAs and rRNAs are excluded and only uniquely mapped reads are selected as iCLIP tags for crosslink sites analysis. (s. König et al; Nat Struct Mol Biol 17:909-915, 2010 for details).
Due to the multi-copy array of the SL RNA locus, the sequence reads were aligned separately to the 139-nucleotide SL RNA sequence to determine the SL RNA iCLIP tags.
Random-barcode filtered crosslink site tag-counts (excluding the snRNAs sites, which are listed separately) in Tb427 genome are listed.
Genome_build: Tb427_v4
Supplementary_files_format_and_content: Tab-delimited text files with barcode-filtered crosslink site tag-counts of all five samples (U1-70K_1, U1-70K_2, U1C_1, U1C_2, U1C_3)
Supplementary_files_format_and_content: CrossLinkSite_Tb427.txt: Crosslink sites in Tb427 genome (exclude snRNA, tRNA, rRNA sites) of all five samples (U1-70K_1, U1-70K_2, U1C_1, U1C_2, U1C_3 in columns 3-7)
Supplementary_files_format_and_content: SL_CrossLinkSite.txt: Crosslink sites on SL RNA of all five samples (U1-70K_1, U1-70K_2, U1C_1, U1C_2, U1C_3 in columns 2-6)
Supplementary_files_format_and_content: U1_CrossLinkSite.txt: Crosslink sites on U1 snRNA of all five samples (U1-70K_1, U1-70K_2, U1C_1, U1C_2, U1C_3 in columns 2-6)
Supplementary_files_format_and_content: U6_CrossLinkSite.txt: Crosslink sites on U6 snRNA of all five samples (U1-70K_1, U1-70K_2, U1C_1, U1C_2, U1C_3 in columns 2-6)

organism: Trypanosoma brucei

source_name: U1-70K iCLIP

growth_protocol: T.brucei cell culture was previously described (Cross et al., Mol Cell Biol 11: 5516-5526, 1991)

extract_protocol:
Cell lysates were prepared in extraction buffer (500 mM KCl, 20 mM Tris-Cl, pH 7.7, 3 mM MgCl2, 0.5 mM DTT), using a Dounce homogenizer and sonication.
As described by König et al. (NSMB, 2010)

treatment_protocol: T.brucei cell cultures were UV-irradiated, as described for the iCLIP procedure (König et al; Nat Struct Mol Biol 17:909-915, 2010).

value: procyclic form cells


title: R20_RNASeq_Harosoy_defective

source_name: HD: 100-200mg seed weight stage


title: U1-70K iCLIP-Seq, experiment 1


title: R19_RNASeq_Harosoy_standard

source_name: HS: 100-200mg seed weight stage


title: Xieqingzao B-12 rep2

city: hangzhou

first: Rongrong

last: Zhai

address: No. 359, Tiyuchang Rd

country: China

institute: China National Rice Research Institute

data_processing:
Basecalls performed using CASAVA version 1.8
The raw reads were filtered to obtain high-quality reads by removing low-quality reads containing more than 30% Q<20 bases. Then  the low-quality bases (Q<20) at the 5’ and 3’ ends of the remaining reads were discarded.
Sequences were mapped onto the Nipponbare reference genome using Stampy (v1.0.13). Single nucleotide polymorphisms (SNPs) were called using the Samtools (v. 0.1.16) .
Supplementary_files_format_and_content: text file include SNPs for each Sample ...

organism: Oryza sativa

source_name: Root

growth_protocol: Rice seeds were surface-sterilized with 3% H2O2 for 10 min and then rinsed with distilled water several times. After soaking in distilled water at 37℃ for 2d, germinated seeds were sowed in the field of the China National Rice Research Institute, Fuyang, China, for approximately 30 d. Then 40 seedlings of each genotype were transplanted in plots on a floating foamed plastic in a pool full of nutrient solution. Roots were sampled with ten replicates at the tillering stage and heading stage to measure root traits and estimate heterosis. Meantime, for RNA-Seq analysis, two roots of every genotype at either stage were collected and stored at -80℃ before use.

extract_protocol:
Total RNA was extracted from roots using TRIzol regent (Invitrogen) and purified with Oligotex mRNA Midi Kit (QIAGEN). RNA quality was checked by the Bioanalyzer 2100 (Aligent) and all samples had RNA Integrity Number (RIN) value more than 8.5. The sequencing library was prepared according to manufacturer′s instructions (Illumina). The poly-A containing mRNA was isolated from total RNA using two rounds of purification with poly-T oligo-attached magnetic beads and subsequently fragmented by the RNA fragmentation kit. The first strand cDNA was generated using reverse transcriptase and random primers. After the second strand cDNA synthesis and adaptor ligation, cDNA fragments of 200 bp were isolated by gel electrophoresis and enriched by 18 cycles of PCR. The products were loaded on Illumina Hiseq2000 instrument for pair-end 100 bp×2 sequencing for 100 cycles.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cv.Xieqingzao B

value: root

value: Tillering stage


title: R9308-12 rep2


title: R9308-34 rep2

value: Heading stage


title: Xieyou 9308-34 rep1

value: cv. Xieyou9308


title: R9308-34 rep1


title: Xieyou 9308-34 rep2


title: Xieyou 9308-12 rep1


title: J1_Ino80KD_Pol 2

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description: Library was prepared by Nextera XT kit

data_processing:
Basecalls performed using CASAVA version 1.7
Raw data from the replicates were merged.
Raw data was filtered by the following steps:  reads were filtered if the average base quality score <20 and duplicate reads removed (based on identical sequences)
Reads were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bowtie (v0.12.8 using the following parameters:  -v 2 -m 1)
Mapped data was filtered to remove hits with >2 mismatches to the reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file per sample per strand showing normalized mapped read coverage; generated by BEDtools genomeCoverageBed and bedGraphToBigWig.
Supplementary_files_format_and_content: Ino80 peak bed files were generated by SICER v1.1 (redundancy threshold=1, window size=200, gap size=800, fragment size=300, FDR=1e-6)

source_name: cell line

growth_protocol: J1 cell were maintianed in ESGRO medium. Cell were cultured in M15 medium when ChIP was performed.

extract_protocol:
Cells were fixed with 1% formaldehyde, sonicated and precipitated by Ino80, Oct4, Klf4, Med1, or Pol2 antibodies. Then precipitated DNA was reverse crosslinked, extracted and quantified for library.
Library was prepared by TruSeq DNA Sample Prep kit (Illumina) or Nextera XT DNA sample prep kit (Illumina) according to the manufacturer's protocol.

tag: antibody

value: Pol 2

tag: vendor/catalog#

value: Santa Cruz, SC899x

tag: transfection

value: lentiviral mediated-shRNA against non-targeting Ino80


title: Xieqingzao B-34 rep2

tag: strain


title: R9308-12 rep1

tag: tissue


title: Xieqingzao B-34 rep1


title: Xieyou 9308-12 rep2


title: R114_RNASeq_Harosoy_standard

source_name: HS: 400-500mg seed weight stage


title: U1C iCLIP-Seq, experiment 3

description: U1C specific co-immunoprecipitated RNA after UV-crosslinking

source_name: U1C iCLIP

tag: cell type


title: J1_Ino80KD_Med1

description: Library was prepared by Nextera XT kit

value: Bethyl, A300-793A


title: R117_RNASeq_Harosoy_defective

source_name: HD: 50-100mg seed weight stage

value: Harosoy


title: J1_Ino80KD_Klf4

description: Library was prepared by Nextera XT kit


title: J1_Ino80KD_Oct4

description: Library was prepared by Nextera XT kit


title: J1_Ino80KD_input

description: Library was prepared by Nextera XT kit


title: M1 M2 M4 Brn1-PK6 ChIP DNA, replicate 3

city: Heidelberg

first: Ilaria

last: Piazza

address: 1, Meyerhofstrasse

institute: EMBL

data_processing:
Base-calling was done during processing of sequencing data with the illumina pipeline casava v1.8.2
ChIP-Seq paired-end sequencing reads were mapped to the S. cerevisiae genome  using bowtie 2, v2.1.0  with default settings.
Reads with identical boundaries were discarted as PCR duplicates, and the central position of each paired read mapping uniquely to the genome (mapq > 10) was used for computing the sequencing coverage.
Genome_build: R64-1-1 (sacCer3)
Supplementary_files_format_and_content: bedGraph files containing center positions

organism: Saccharomyces cerevisiae

growth_protocol: Asyncronous cells were grown in YPAD complete media

extract_protocol:
Anti-PK ChIP was performed and both input and IP samples were sequenced. NEBNext ChIP-Seq kit (see attachment) with an E-gel selection of desired fragment size range in the finished library.  Made by Bianka Baying (EMBL Heidelberg Genomics core facility) and Ilaria Piazza
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina

treatment_protocol: cells were treated with formaldehyde 15 minutes before harvesting pellets

tag: genotype

value: Brn1 M1 M2 M4-PK6

value: anti-V5 tag antibody (AbD Serotec, mouse IgG2a, MCA 1360, batch 1009A)


title: Xieqingzao B-12 rep1


title: J1_NT_Pol 2

description: Library was prepared by Nextera XT kit

value: lentiviral mediated-shRNA against non-targeting NT


title: U1C iCLIP-Seq, experiment 1


title: M1 M2 M4 Brn1-PK6 ChIP DNA, replicate 2


title: J1_NT_Med1

description: Library was prepared by Nextera XT kit


title: Wild type Brn1-PK6 ChIP DNA, replicate 3


title: M1 M2 M4 Brn1-PK6 ChIP DNA, replicate 1


title: R3

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

description: total RNA processed to enrich for mRNA that was subsequently used for whole transcriptome cDNA library generation using random hexameric primers

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were trimmed by removing adapter sequences and ambiguous nucleotides. Reads with quality scores less than 20 and length below 30 base pairs were all trimmed.
The resulting high-quality reads from each of the 3 replicate samples were mapped onto the N. gonorrhoeae FA1090 reference genome using CLC Genomics Workbench software.
The total number of reads mapped for each transcript was determined and then normalized to detect the reads per kilobase per million reads (RPKM) measure.
Genome_build: NCBI accession number NC_002946 (Neisseria gonorrhoeae FA 1090 genome was used as the mapping template)
Supplementary_files_format_and_content: Kandler RNASeq RPKM.xlsx contains RPKM values of all genes for six samples

organism: Neisseria gonorrhoeae

source_name: planktonic log phase cells

growth_protocol: N. gonorrhoeae FA19 WT and FA19 misR::kan were each grown in triplicate in GC broth supplemented with Kellogg's supplements I and II (see Dillard 2011 Current Protocols in Microbiology), 0.043% sodium bicarbonate, and 10 mM MgCl2 in a 37 degree water bath shaking at 150 rpm (75 mL culture volume).  Genotypes were confirmed using PCR/Western blot analysis of log phase samples from all 6 cultures.  Culture purity was confirmed by Gram stain/selective/nonselective plating of all 6 cultures following completion of the growth curve.

extract_protocol: Total RNA was isolated from RNAprotect-treated pellets using chicken egg white lysozyme (Sigma) and the RNeasy kit (Qiagen).  Turbo DNA-free enzyme (Applied Biosciences) was used to deplete total RNA of any contaminating DNA.  We further purified our samples by magnetically depleting ribosomal RNA two times using the MICROBExpress mRNA enrichment kit (Ambion).  Global cDNA was made using random hexameric primers (Invitrogen).  Agilent Bioanalyzer analysis was performed following DNA removal, mRNA enrichment, and cDNA library production to ensure sample quality.  The double-stranded, non-directional cDNA libraries representative of the transcriptomes of all three WT and all three misR::kan mutant cultures (see Passalacqua et al., 2009; Croucher and Thomson, 2010) were sent to the Emory GRA Genomics Core for library amplification and sequencing on the Hi-Seq2000 next generation sequencing platform (Illumina).

treatment_protocol: 4 mL were taken from each culture (in duplicate) at late log phase, mixed immediately with 8 mL RNAprotect reagent (Qiagen) per 4 mL culture, and vigorously vortexed for 5 seconds.  Treated cells were pelleted at 6000 rpm for 10 minutes at 20 degrees C, as per the manufacturer's instructions.  Pelleted, RNAprotect-treated cells were then stored at -70 degrees C until RNA extraction.

value: FA19 misR::kan

value: mutant derivative lacking the NGEG_00293 "misR" gene due to an insertion/deletion knockout mutation using the nonpolar aphA3 kanamycin resistance cassette


title: J1_NT_Oct4

description: Library was prepared by Nextera XT kit

value: Santa Cruz, SC8628


title: Wild type Brn1-PK6 ChIP DNA, replicate 1


title: R1


title: J1_NT_input

description: Library was prepared by Nextera XT kit


title: R2


title: Wild type Brn1-PK6 ChIP DNA, replicate 2


title: J1_Ino80_input

description: Library was prepared by Nextera XT kit

value: embryonic stem cells


title: Wild type Brn1 input DNA, replicate 1


title: WT2

value: FA19 wild type

value: WT parent strain


title: U1C iCLIP-Seq, experiment 2

value: procyclic form cells


title: M1 M2 M4 Brn1 input DNA, replicate 1


title: WT1


title: WT3


title: J1_Ino80

description: Library was prepared by Nextera XT kit