title: Liver LCMRRBS Fresh Frozen 20mm

source_name: Liver LCMRRBS Fresh Frozen 20mm


title: iPSS1

status: Public on Mar 21 2013

type: SRA

city: Atlanta

first: Tao

last: Wang

state: GA

address: 615 Michael Street

department: Human Genetics

country: USA

institute: Emory University

library_source: genomic

data_processing:
Bowtie aligned
remove duplicate reads
MACS peak calling
Genome_build: hg18/NCBI36
Supplementary_files_format_and_content: bed files with 5hmC enrichment peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: hiPSCs

growth_protocol: The fibroblasts were cultured in DMEM medium containing 10% FBS, 1× Non-Essential amino acids, 1× glutamine, and 1× Pen/Strep.  The stem cells were maintained in hESC/hiPSC standard medium (DMEM/F12, 20% KnockOut Serum Replacement, 1× MEM Non-Essential Amino Acids, 1× glutamine, 0.11 mM 2-mercaptoethanol, 10 ng/ml bFGF) on irradiated MEF feeders.

extract_protocol:
Genomic DNA was extracted and purified with the DNeasy Kit (Qiagen). Genomic DNA (20ug-30ug) from each cell line was sonicated to an average size of 200bp by the Covaris sonicator.  5hmC labeling reactions were performed according to the previous protocol (Song et al., 2011) with some modifications. Briefly, the UDPG-N3 transfer was carried out with 1X reaction buffer containing 50 mM HEPES (pH 7.9) and 25 mM MgCl2, 100 uM of UDP-6-N3-Glu, and 2 uM of wild-type beta-glucose transferase for 1 h at 37° C. The labeled DNA was purified by the QIAquick PCR purification kit (Qiagen). The click chemistry was performed with the addition of 150 uM of disulfide-biotin linker, and the mixture was incubated for 2 h at 37° C.  The DNA samples were then purified by the Pierce Monomeric Avidin Kit (Thermo) following the manufacturerâ€™s recommendations. Subsequently, the 5hmC enriched DNA was concentrated by 10 K Amicon Ultra-0.5 mL Centrifugal Filters (Millipore), then purified and eluted with 12ul H2O by the MinElute PCR Purification Kit (Qiagen).
Approximately 50ng (5ul) of each 5hmC enriched DNA was used for Illumina SR library preparation by NEBNext ChIP-Seq Sample Prep Reagent Set 1(NEB) according to the manufacturer's standard protocol.

tag: cell line

tag: cell type

value: hiPSCs

tag: modification

value: 5hmC-chemical label pull down


title: Adrenal Normal Mouse 3

city: St. Louis

first: Maximiliaan

last: Schillebeeckx

state: MO

address: 4444 Forest Parkway

department: Genetics

institute: Washington University in St. Louis

data_processing:
Basecalls performed using CASAVA version 1.4
All analysis was performed using the February 2009 (GrCh37/hg19) build of the human genome and the July 2007 (NCBI37/mm9) build of the mouse genome. On average 25 million single-end 42-bp raw high quality reads per sample were either aligned to the cytosine-poor strand reference using the bisulfite mode of MAQ (41) or aligned to the reduced reference using RRBSMAP (42) filtering against reads that contain adapter sequence. Reads that showed less than 90% bisulfite conversion (~1 unconverted non-CpG cytosine per read) were filtered to remove those that resulted from incomplete bisulfite converted molecules. Aligned reads with a mapping quality of zero were also discarded. The resulting high quality uniquely mapped reads were used for methylation calling. We identified the genomic coordinates of all CpGs in the reference sequence and assessed percent DNA methylation by calculating the fraction of reads that had an unconverted cytosine at the CpG position relative to the total reads. We required that each read have either a “TG” or “CG” dinucleotide at the expected CpG coordinate to be considered for analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bed tab-delimited txt files containing methylation calls for all CpGs

organism: Mus musculus

source_name: Adrenal Normal Mouse 3

extract_protocol:
Full details can be found in Schillebeeckx et al. (2013). Briefly, human tumor specimens were collected under an Institutional Review Board (IRB)-approved protocol. Immediately after surgery, a human endometrial tumor was divided in half. One half was fresh frozen while the other was formalin-fixed and paraffin-embedded (FFPE). 50 mg of fresh frozen endometrial tumor was cut into small pieces with a sterile scalpel blade and DNA extracted using the Maxwell 16 Tissue DNA Purification Kit (AS1030, Promega). The formalin-fixed paraffin-embedded preserved portion was cut into 6-µm sections onto microscope slides. Four 4 mm2 slices were scratched off the slide with a sterile scalpel blade, combined in 80 µl buffer and proteinase K (740901.50, Clontech), and incubated overnight at 65°C. Liver tissue was harvested from C57BL/6J mice and divided in half. One half was preserved in Tissue-tek optimal cutting temperature (O.C.T.) compound (25608-930, VWR) and snap frozen, while the other half was formalin-fixed and paraffin-embedded for downstream bulk DNA extraction and LCM. Fresh frozen, FFPE, and LCM samples were purified using NucleoSpin Tissue XS columns (740901.5, Clontech) following the protocol for laser-microdissected tissue and eluted in 20 μl of nuclease-free water.
Full details can be found in Schillebeeckx et al. (2013). For RRBS, genomic DNA was digested with MspI, size selected, end-repaired, 3'-terminal A extended and ligated to Illumina adapters containing methylated cytosines, bilsufite converted using the EZ DNA Methylation Gold Kit (ZYMO), PCR amplified with 18-24 cycles and sequenced. For LCM-RRBS , genomic DNA was digested with MspI, size selected, end-repaired, 3'-terminal A extended and ligated to Illumina adapters containing methylated cytosines, bilsufite converted using the EZ DNA Methylation Gold Kit (ZYMO), PCR amplified with 12 cycles and indexed primers, pooled, gel extracted, PCR amplifed with universal primers and 14 cycles, and sequenced

tag: method

value: LCM-RRBS

tag: strain

tag: tissue

value: Adrenal gland


title: Adrenal Neoplasia Mouse 2

source_name: Adrenal Neoplasia Mouse 2


title: Adrenal Neoplasia Mouse 3

source_name: Adrenal Neoplasia Mouse 3


title: SUMO-1 depleted (repeat 2)

city: Columbus

first: Jeffrey

last: Parvin

state: OH

address: 904 Biomedical Research Tower

department: Biomedical Informatics

institute: the Ohio State University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, sorted according to index barcode, then mapped to hg18 whole genome using TopHat v1.1.2
Reads Per Kilobase of gene per Megabase of library size (RPKM) were obtained by Cufflinks1.0.3
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: HeLa cell

extract_protocol:
Total RNA was isolated using Trizol reagent. 0.8 ug total RNA was then subjected to cDNA library preparation using the Illumina TruSeq RNA sample preparation kit (low-throughput protocol).
Illumina TruSeqTM RNA sample preparation kit (low-throughput protocol)
The double-stranded cDNA (0.8 µg total RNA input) was subjected to library preparation using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol.

value: HeLa cell

tag: genotype/variation

value: SUMO-1 depleted

tag: index

value: Index 7


title: Liver LCMRRBS Fresh Frozen 2mm2

source_name: Liver LCMRRBS Fresh Frozen 2mm2

value: Liver


title: Liver LCMRRBS FFPE 20mm2

source_name: Liver LCMRRBS FFPE 20mm2


title: Liver LCMRRBS 1 ng Replicate 2

source_name: Liver LCMRRBS 1 ng Replicate 2


title: Liver LCMRRBS 1 ng Replicate 1

source_name: Liver LCMRRBS 1 ng Replicate 1


title: Adrenal Normal Mouse 1

source_name: Adrenal Normal Mouse 1


title: Liver LCMRRBS 1 ng Replicate 3

source_name: Liver LCMRRBS 1 ng Replicate 3


title: Adrenal Normal Mouse 2

source_name: Adrenal Normal Mouse 2


title: PV4 MM

city: Berkeley

first: Wenjun

last: Shao

state: CA

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

description: Indexed and sequenced on Illumina HiSeq sharing with seven other samples in one lane

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to Shewanella loihica PV-4 genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella loihica PV-4/ASM1606v1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand

organism: Shewanella loihica PV-4

source_name: Shewanella loihica PV-4 grown in D,L-lactate medium till mid-log-phase

growth_protocol: Aerobic growth to mid-log phase at 30C with shaking at 200 rpm

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyze.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor. 6-mer index GTGGCC was incorporated into the reverse PCR primer. We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).

tag: treatment

value: 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7


title: Control GL2-depleted (repeat 3)

value: Control GL2-depleted

value: Index 2


title: Adrenal Neoplasia Mouse 1

source_name: Adrenal Neoplasia Mouse 1


title: SUMO-1 depleted (repeat 3)

value: Index 12


title: SUMO-1 depleted (repeat 1)

value: Index 5


title: Control GL2-depleted (repeat 2)

value: Index 6


title: Stationary phase cells with RiboZero treatment

status: Public on Mar 20 2013

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

description: STAT RIBOZERO

data_processing:
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper
Genome_build: MGAS5005 genome (NC_007297.1)
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates.

organism: Streptococcus pyogenes

growth_protocol: MGAS2221 was grown in Todd-Hewitt broth with 0.2% yeast extract to mid-exponential phase (corresponding to an O.D.600 of 0.5) and to stationary phase (3h after reaching an O.D.600 of 0.5)

extract_protocol:
Cultures and two volumes of RNAprotect (Qiagen) added upon reaching the correct growth phase and, following a 5 min room temperature incubation, centrifuged at 4,000g for 10 mins.  Bacterial cell pellets were lysed via mechanical lysis (FastPrep machine) and RNA isolated using the miRNeasy kit (Qiagen).  Isolated RNA was DNase-treated using TURBO-DNA free (Ambion).
rRNAs were removed from the RNA samples using either the RiboZero kit (Epicenter) or TEX.  The rRNA-depleted RNAs were used in conjuncation with the ScriptSeq RNA-seq library prep kit (Epicenter).  Barcodes were added to allow the four libaries to be multiplexed on a single lane of the illumina instrument.  Barcode primers were purchased from Epicenter.

tag: growth phase

value: Stationary phase

tag: rrna removal method

value: RibozZero


title: H9RPE.ksr.060311

city: New Haven

first: Mei

last: Zhong

address: 10 Amistad Street

department: Stem Cell Center

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.7.0 and 1.8.1
Sequenced reads from the sequencing run were imported into the public Galaxy platform, a free online bioinformatics interface available at http://main.g2.bx.psu.edu. The sequences were aligned against the hg19 reference genome using the Tophat for Illumina (version 1.5.0) with default parameters.
Transcripts were assembled using Cufflinks (version 0.0.5) with quartile normalization and bias correction.
Fold change in transcript expression were analyzed using  Cuffdiff (version 0.0.5) with false discovery rate of 0.05, minimum alignment count of 100, quartile normalization, and bias correction.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for RPKM values of each sample and tab-delimited text files for fold changes between two compared cell types

source_name: Retinal Pigment Epithelium

growth_protocol: RPE was differentiated and isolated from human embryonic stem cell lines H1 and H9 (three independent isolates from each strain) and compared to RPE that was isolated from 16-week gestation human fetuses (two fetuses) and expanded in primary culture. The RPE was cultured on Transwell filters and adapted to a serum-free medium (Peng et al., Invest. Ophthalmol. Vis. Sci. 52:1392-1403, 2011).  When the transepithelial electrical resistance became stable,  total RNA was isolated for making sequencing library.

extract_protocol: Libraries were prepared according to Illumina’s mRNA Sequencing Sample Preparation Guide for mRNA-Seq 8 Sample Prep Kit (Cat# RS-100-0801) for illumina Genome Analyzer II and TruSeq RNA Sample Preparation Guide for TruSeq RNA Sample Prep Kit v2 (Cat RS-122-2001) for HiSeq 2000. Briefly, poly-A containing mRNA molecules were purified from 10ug of total RNA using poly-T oligo-attached magnetic beads then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process 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 (3’ to 5’ 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. These products are then purified and enriched with 15 cycles of PCR to create the final cDNA library. Library fragments of 150 to 350 bp (insert plus adaptor and PCR primer sequences) were isolated from 2% E-Gel EX Gel (Invirotgen #G4020-02). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: origen of cultured cells

value: hESC H9 line - derived RPE

tag: transepithelial electrical resistance

value: 49± 4 ohm*cm^2

tag: peak transepitheilal electrical resistance (ksr only)

value: 55±4 ohm*cm^2


title: Stationary phase cells with TEX treatment

description: STAT TEX

value: TEX


title: PV4 LB

source_name: Shewanella loihica PV-4 grown in LB till mid-log-phase

value: Luria-Bertani broth (LB)


title: H1RPE.sfm.051311

data_processing:
Basecalls performed using CASAVA version 1.7.0
Sequenced reads from the sequencing run were imported into the public Galaxy platform, a free online bioinformatics interface available at http://main.g2.bx.psu.edu. The sequences were aligned against the hg19 reference genome using the Tophat for Illumina (version 1.5.0) with default parameters.
Transcripts were assembled using Cufflinks (version 0.0.5) with quartile normalization and bias correction.
Fold change in transcript expression were analyzed using  Cuffdiff (version 0.0.5) with false discovery rate of 0.05, minimum alignment count of 1000, quartile normalization, and bias correction.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for RPKM values of each sample and tab-delimited text files for fold changes between two compared cell types

extract_protocol: Libraries were prepared according to Illumina’s mRNA Sequencing Sample Preparation Guide for mRNA-Seq 8 Sample Prep Kit (Part# RS-100-0801). Briefly, poly-A containing mRNA molecules were purified from 10ug of total RNA using poly-T oligo-attached magnetic beads then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process 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 (3’ to 5’ 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. These products are then purified and enriched with 15 cycles of PCR to create the final cDNA library. Library fragments of 150 to 350 bp (insert plus adaptor and PCR primer sequences) were isolated from 2% E-Gel EX Gel (Invirotgen #G4020-02). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: hESC H1 line - derived RPE


title: H1RPE.sfm.022311


title: hfRPESeq012611

value: RPE isolated from 16 weeks gestation human fetus


title: Liver LCMRRBS Fresh Frozen 10mm2

source_name: Liver LCMRRBS Fresh Frozen 10mm2

value: LCM-RRBS


title: H1RPE.sfm.042011


title: hfRPESeq090910


title: H9RPE.ksr.041511

value: 37± 4 ohm*cm^2


title: H9RPE.sfm.042011


title: H1RPE.ksr.061511

value: 41±1 ohm*cm^2


title: Exponential phase cells with RiboZero treatment

description: EXPO RIBOZERO

value: Exponential phase

value: RiboZero


title: Control GL2-depleted (repeat 1)

value: HeLa cell

value: Control GL2-depleted

value: Index 4


title: MCF-7 input DNA

city: bethesda

first: Lijun

last: Di

address: 41 center dr

institute: NCI

data_processing:
ChIP-seq reads were aligned to the HG19 genome.
The sequencing data from matching input samples are used for the processing  of ChIP data, as a measure of background signal which might be significant. After normalizing the input data to match the number of tags in the ChIP data, the number of input tags is subtracted from the number of ChIP tags in the target window before calculating its z-score. In addition, ChIP hotspots were refined into 150 bp peaks using a peak-finding procedure. For each hotspot, a new z-score ‘peak z’ was computed similarly as for hotspot detection, but instead using a 150 bp window within the hotspot and the hotspot as the target window and local background window, respectively. The peak z score was computed scanning through the hotspot with bp resolution for all possible 150 bp windows. A putative peak is defined as a 150 bp window whose peak z score is above 30.
Genome_build: HG19
Supplementary_files_format_and_content: bedgraph files are generated based on z score

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were maintained in regular DMEM supplemented with 10% (v/v) FBS, penicillin-streptomycin (Invitrogen) and insulin.

extract_protocol: Lysates were clarified from sonicated nuclei and CtBP-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit . 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 Genome Analyzer following the manufacturer's protocols.

value: Immortalized breast cancer cells

tag: passages

tag: chip antibody


title: H9RPE.sfm.041511


title: Exponential phase cells with TEX treatment

description: EXPO TEX


title: smRNA-seq_Mo17_root

status: Public on Mar 19 2013

city: Beijing

first: Xuncheng

address: 5 Yiheyuan Road

country: China

institute: Peiking University

description: small RNA gel isolated

data_processing:
Raw sequencing reads from all libraries were mapped to the reference genome of the maize inbred line B73 (version 2; ZmB73_RefGen_v2) (http://ftp.maizesequence.org/current/assembly/) (Schnable et al., 2009) using Bowtie software (Langmead et al., 2009). Sequencing reads from mRNA-seq were also mapped to Mo17 whole-genome shotgun sequences (ftp://ftp.jgi-psf.org/pub/JGI_data/Zea_mays_Mo17/) using the same software. For the data of mRNAs, histone modifications and DNA methylation, up to two mismatches per read were allowed during the alignment procedure. For small RNA data, the 3’ adapter sequences were removed by a custom Perl script before alignment, and adapter-trimmed small RNA reads which were perfectly matched to the reference genome were retained. Small RNA sequencing reads matched to tRNAs, rRNAs, small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) were also excluded from further analysis. For all sequencing data, the reads mapped equally well to multiple locations in the genome without mismatch or with identical mismatches were assigned to one position at random.
Genome_build: B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mRNA seq samples,  read counts for ChIP and McrBC seq peaks, and read counts for small RNA seq clusters.

organism: Zea mays

growth_protocol: Maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrids (B73 x Mo17 and Mo17 x B73) were used in this study. Seeds were grown in soil under controlled environmental conditions (15 hours light at 25oC, and 9 hours dark at 20oC) in a growth chamber. After 14 days, seedling shoots and roots were harvested, respectively, frozen in liquid nitrogen and stored at -80oC for DNA and total RNA isolations, or processed directly for ChIP assays after harvesting.

extract_protocol: mRNA-seq, smRNA-seq, McrBC-seq and ChIP-seq libraries were all prepared for sequencing using standard Illumina protocols. Total RNAs were isolated using TRIzol reagent (Invitrogen) and treated with RNase-free DNase I (New England Biolabs) to remove any contaminating genomic DNA. mRNA extraction was performed using Dynabeads oligo(dT) (Invitrogen Dynal). Double-stranded cDNAs were synthesized using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. The cDNAs were then fragmented by nebulization, and the standard Illumina protocol was followed thereafter to create the mRNA-seq libraries. Genomic DNAs were isolated using a DNeasy plant maxi kit (Qiagen). Isolated gDNAs were then digested with McrBC (New England Biolabs) followed by gel purification to enrich methylated genomic DNAs. The McrBC-seq libraries were generated following the standard Illumina protocol. The ChIP-seq libraries were generated by immunoprecipitating chromatin with antibodies against H3K4me3 (Abcam), H3K9ac (Upstate), or H3K36me3 (Abcam), as described previously (Gendrel et al., 2005). The eluted ChIP DNAs from the three ChIP reactions were pooled to generate ChIP-seq libraries for Illumina sequencing following the manufacturer’s protocol. sRNAs were gel-purified from total RNAs and were subsequently ligated with 3′ and 5′ adapters, followed by reverse transcription using 3′ RT primer. The cDNAs were then amplified by PCRs using primers specific to sRNAs (Mi et al., 2008). After gel purification, the sRNA-seq libraries were subjected to Illumina sequencing following the manufacturer’s protocol.

tag: line

value: root

tag: developmental stage

value: 14 day old seedling


title: smRNA-seq_Mo17/B73_root

description: small RNA gel isolated

value: Mo17 x B73


title: smRNA-seq_B73/Mo17_shoot

description: small RNA gel isolated

value: B73 x Mo17

value: shoot


title: CtBP_ChIPSeq

tag: cell type

value: CtBP

tag: catalog#

tag: vendor

value: Santa Cruz


title: H9RPE.sfm.060311

value: hESC H9 line - derived RPE


title: smRNA-seq_Mo17_shoot

description: small RNA gel isolated


title: smRNA-seq_B73_root

description: small RNA gel isolated


title: H3K36me3_ChIP-seq_Mo17/B73_root

description: Chromatin IP against H3K36me3 (Abcam)


title: H3K36me3_ChIP-seq_B73/Mo17_root

description: Chromatin IP against H3K36me3 (Abcam)


title: H3K36me3_ChIP-seq_Mo17_shoot

description: Chromatin IP against H3K36me3 (Abcam)


title: H3K36me3_ChIP-seq_B73_root

description: Chromatin IP against H3K36me3 (Abcam)


title: H3K36me3_ChIP-seq_Mo17_root

description: Chromatin IP against H3K36me3 (Abcam)


title: H3K36me3_ChIP-seq_B73/Mo17_shoot

description: Chromatin IP against H3K36me3 (Abcam)


title: H3K9ac_ChIP-seq_Mo17/B73_root

description: Chromatin IP against H3K9ac (Upstate)


title: H3K9ac_ChIP-seq_Mo17/B73_shoot

description: Chromatin IP against H3K9ac (Upstate)


title: H3K9ac_ChIP-seq_B73/Mo17_root

description: Chromatin IP against H3K9ac (Upstate)


title: H3K9ac_ChIP-seq_B73_root

description: Chromatin IP against H3K9ac (Upstate)


title: H3K9ac_ChIP-seq_Mo17_shoot

description: Chromatin IP against H3K9ac (Upstate)


title: H3K36me3_ChIP-seq_B73_shoot

description: Chromatin IP against H3K36me3 (Abcam)


title: H3K9ac_ChIP-seq_B73/Mo17_shoot

description: Chromatin IP against H3K9ac (Upstate)


title: H3K9ac_ChIP-seq_Mo17_root

description: Chromatin IP against H3K9ac (Upstate)


title: hfRPESeq072611

value: RPE isolated from 16 weeks gestation human fetus


title: H3K9ac_ChIP-seq_B73_shoot

description: Chromatin IP against H3K9ac (Upstate)


title: H3K4me3_ChIP-seq_Mo17/B73_root

description: Chromatin IP against H3K4me3 (Abcam)


title: H3K4me3_ChIP-seq_Mo17/B73_shoot

description: Chromatin IP against H3K4me3 (Abcam)


title: H3K4me3_ChIP-seq_B73/Mo17_root

description: Chromatin IP against H3K4me3 (Abcam)


title: smRNA-seq_B73_shoot

description: small RNA gel isolated


title: H3K4me3_ChIP-seq_Mo17_shoot

description: Chromatin IP against H3K4me3 (Abcam)


title: H3K4me3_ChIP-seq_B73/Mo17_shoot

description: Chromatin IP against H3K4me3 (Abcam)


title: H3K4me3_ChIP-seq_Mo17_root

description: Chromatin IP against H3K4me3 (Abcam)


title: H3K4me3_ChIP-seq_B73_root

description: Chromatin IP against H3K4me3 (Abcam)


title: DNAmethyl_McrBC-seq_B73/Mo17_root

description: McrBC digestion

data_processing:
Library strategy: McrBC-Seq
Raw sequencing reads from all libraries were mapped to the reference genome of the maize inbred line B73 (version 2; ZmB73_RefGen_v2) (http://ftp.maizesequence.org/current/assembly/) (Schnable et al., 2009) using Bowtie software (Langmead et al., 2009). Sequencing reads from mRNA-seq were also mapped to Mo17 whole-genome shotgun sequences (ftp://ftp.jgi-psf.org/pub/JGI_data/Zea_mays_Mo17/) using the same software. For the data of mRNAs, histone modifications and DNA methylation, up to two mismatches per read were allowed during the alignment procedure. For small RNA data, the 3’ adapter sequences were removed by a custom Perl script before alignment, and adapter-trimmed small RNA reads which were perfectly matched to the reference genome were retained. Small RNA sequencing reads matched to tRNAs, rRNAs, small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) were also excluded from further analysis. For all sequencing data, the reads mapped equally well to multiple locations in the genome without mismatch or with identical mismatches were assigned to one position at random.
Genome_build: B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mRNA seq samples,  read counts for ChIP and McrBC seq peaks, and read counts for small RNA seq clusters.


title: DNAmethyl_McrBC-seq_Mo17/B73_shoot

description: McrBC digestion


title: DNAmethyl_McrBC-seq_Mo17_root

description: McrBC digestion


title: DNAmethyl_McrBC-seq_B73/Mo17_shoot

description: McrBC digestion


title: H3K4me3_ChIP-seq_B73_shoot

description: Chromatin IP against H3K4me3 (Abcam)


title: DNAmethyl_McrBC-seq_Mo17/B73_root

description: McrBC digestion


title: DNAmethyl_McrBC-seq_Mo17_shoot

description: McrBC digestion


title: H3K36me3_ChIP-seq_Mo17/B73_shoot

description: Chromatin IP against H3K36me3 (Abcam)


title: DNAmethyl_McrBC-seq_B73_root

description: McrBC digestion


title: mRNA-seq_Mo17/B73_root

description: polyA RNA isolated


title: DNAmethyl_McrBC-seq_B73_shoot

description: McrBC digestion


title: mRNA-seq_B73_shoot

description: polyA RNA isolated


title: mRNA-seq_Mo17_root

description: polyA RNA isolated


title: mRNA-seq_B73/Mo17_shoot

description: polyA RNA isolated


title: mRNA-seq_B73/Mo17_root

description: polyA RNA isolated


title: mRNA-seq_B73_root

description: polyA RNA isolated


title: mRNA-seq_Mo17/B73_shoot

description: polyA RNA isolated


title: R63_400-500mgCOT_BR2

status: Public on Mar 18 2013

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Standard Illumina pipeline including CASSAVA
Sequenced reads were aligned to 78,773 Glyma1 cDNA soybean gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Genome_build: Glyma1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Glycine max

source_name: cotyledon

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated days after flowering or mg fresh weight. Whole seeds were divided by hand into cotyledons and seed coats for some samples.

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina Genome Analyzer II or an Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Williams 43

tag: Stage

value: 400-500mg fresh weight

tag: preservation

value: lyophilized

tag: purification

value: Qiagen Rneasy Midi kit


title: R50_5-6mgCOT

value: 5-6mg fresh weight

value: fresh frozen


title: R49_5-6mgSC

source_name: seed coat


title: R103_DrySeed_BR2

source_name: whole seed

value: dry mature seed

value: room temperature


title: R36_22-24DAF_BR1

value: 22-24 days after flowering


title: R60_22-24DAF_BR2


title: R61_5-6mgWS_BR2


title: R83_4DAF_BR2

value: 4 days after flowering


title: R14_DrySeed_BR1


title: R59_12-14DAF_BR2

value: 12-14 days after flowering


title: R13_400-500mgCOT_BR1


title: R12_100-200mgCOT_BR1

value: 100-200mg fresh weight


title: R09_12-14DAF_BR1


title: R11_5-6mgWS_BR1


title: R08_4DAF_BR1


title: HIF2α #17-56 kidney 1

city: New York

first: Leiping

last: Fu

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

data_processing:
Reads were aligned to the genome using the Burrows-Wheeler Aligner in Goby web software (goby_1.9.8.3 (20120216154520)), using default parameters.
Differential Expression Analysis were done with Differential Expression Analysis with Goby in Goby web software (goby_1.9.8.3 (20120216154520)), using default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Goby Web software.
Genome_build: NCBI37.55/MM9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: kidney cortex

growth_protocol: Animals were kept at standard conditions in Research Animal Resource Center of WCMC

extract_protocol:
Thin outer slice of kidney cortex was immediately removed from the animals. mRNA was extracted from the kidney cortex slice using mini-RNAeasy columns (Qiagen, Valencia, CA).
illumina TruSeq RNA Sample Preparation kit

treatment_protocol: No treatment

tag: strain

tag: gender

value: male

tag: genotype

value: gamma-HIF2alphaM3 TG+

tag: tissue

value: kidney cortex


title: HIF2α #17-56 kidney 2


title: HIF2α #17-53 kidney 1


title: HIF2α #17-53 kidney 2


title: mRNA-seq_Mo17_shoot

description: polyA RNA isolated

value: shoot

value: 14 day old seedling


title: HIF2α #17-51 kidney 2


title: WT #3 kidney 2

value: wild type


title: WT #2 kidney 2


title: WT #1 kidney 1


title: eWAT_PPARg

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequencing: High throughput sequencing was done by the Functional Genomics Core of the Penn Diabetes Research Center using the Illumina Genome Analyzer IIx or HiSeq 2000, and the reads were aligned to the mm8 genome assembly genome using Bowtie. In each ChIP-seq sample, all the duplicate reads were removed except for one before downstream analysis.
Peak Calling: To identify depot-specific Pparg peaks, we performed peak calling for one depot sample as foreground and the other sample as background, and vice versa. All the peak calling were performed using Homer with options, peak size 200bp and minimum distance 200bp (-size 200 -minDist 200), then 1 rpm cutoff was applied. Common Pparg peaks were defined as follows. First, Pparg peaks were called for each depot using a matching input sample, then all the peaks were pooled and overlapping peaks were merged. Among these peaks, any peak that overlaps with the depot-specific Pparg peaks were eliminated, and the remaining peaks were defined as common Pparg peaks. It should be noted that our definition of common peak here is naïve in the sense that some peaks might show different peak height between different depots. However, this should not be a problem in this work because our primary target is to identify depot-specific (especially BAT-specific) Pparg binding sites.
Genome_build: mm9
Supplementary_files_format_and_content: Peak calling results for each tissue-specific PPARg binding sites in bed format

source_name: Epididymal White Adipose Tissue

growth_protocol: 8-10 week old male Sv129 mice has been housed in regular 12h light/12h dark cycles on normal chow diet.

extract_protocol: Nuclei were lysed and sonicated. Protein-DNA complexes were isolated from lysates using antibodies, and DNA were extracted. For each condition, ChIP was performed on lysates from 4 different mice, and ChIPed DNA or input DNA samples were pooled for sequencing. ChIPed DNA or input DNA samples were pooled for sequencing.

treatment_protocol: Mice were euthanized and BAT/eWAT were removed at ZT10, 5pm. BAT and eWAT samples were cross-linked with 1% formaldehyde, and used for ChIP with PPARg antibody.

value: Epididymal White Adipose Tissue

value: PPARg

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: R62_100-200mgCOT_BR2

value: Williams 43

value: lyophilized

value: Qiagen Rneasy Midi kit


title: TSKM-3D cell 5mC

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute Of Biological Sciences, Beijing (NIBS)

data_processing:
The reads generated by Illumina standard pipeline (CASAVA version 1.8) were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. Only unique mapped reads were extracted for the following analysis.
The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA modification enriched regions (peaks). The MACS parameters were referred to the literature (default parameters with addition of "--nolambda   --nomodel  -g mm")
To adjust the library size variance and facilitate the data exhibition, the total 30 million mapped reads were randomly selected from each sample.
Genome_build: mouse reference genome (mm9/NCBI37)
Supplementary_files_format_and_content: Bed files were generated using MACS (v1.4.1), it contained the genomic coordinates of identified peaks

source_name: TSKM-3D cells(intermediate stage)

growth_protocol: The iPS cells were cultured on mitomycin C treated MEFs in ES medium containing DMEM medium (Gibco Invitrogen, Carlsbad, CA) supplemented with 15% (v/v) fetal bovine serum (FBS), 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF. The TSKM 2nd induction cells were deriven from TSKM iPS mice and cultured with Feeder Medium for 3 passages. On passages 4 the culture were changed to ES Medium with doxycycline for 3 days.

extract_protocol: In brief, the sonicated genomic DNA was treated using NEBNext master Mix to repair the ends of DNA fragments and ligate the paired-end sequencing specific adaptors (Illumina), the DNA product was then immunoprecipitated and purified. Here we used 500ng ligation product for each IP reaction. Fragments were amplified with 14–16 cycles using adaptor specific primers (Illumina). The final product (300-500bp) was gel-purified (Qiagen) before cluster generation and sequencing.

treatment_protocol: The cells were cultured until the appropriate stage. The culture medium were threw out and washed with PBS. The cells were  centrifuge dissociated by 0.05% trypsin EDTA.The ESCs were added 2-folds-volume ESM and dissociated to single cells. The cell suspension were plated in new dished for 0.5hr(37℃) to clear away the feeder cells. The supernatant supension were further collected carefully and centrifuged for RNA extraction. The fibroblasts were centrifuged to collect the cells and treated with centrifuge centrifuged and treated with Trizol (Invirtrogen).

value: TSKM-iPS mouse derived fibroblast cells (3-days induced)

tag: stage or passages

value: p4  supply with doxycycline for 3 days

value: 5mC mAb

value: Calbiochem


title: TSKM-3D cell 5hmC

tag: chip antibody

value: 5hmC pAb

value: Active Motif


title: BAT_PPARg

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: iPS cell line 5hmC

source_name: iPS cell line

value: tet1 sox2 klf4 and c-Myc inducted iPS cells (derived driven from TSKM 2nd reprogramming system with full pluripotency)


title: iPS cell line 5mc


title: fibroblast 5mC

source_name: fibroblast cell line

value: TSKM-iPS mouse derived fibroblast


title: fibroblast 5hmC


title: TCF7L2 ChIP-seq vehicle treatment

status: Public on Mar 16 2013

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

description: ChIP-seq data

data_processing:
Basecalls performed using CASAVA version 1.9
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie-0.12.7
peaks were called using MACS2
Genome_build: hg18
Supplementary_files_format_and_content: peak files represent the boundary of each ChIP-enriched region are in the BED format

source_name: TCF7L2 ChIP-seq vehicle treatment

growth_protocol: The MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovine serum at 37oC incubator

extract_protocol:
Lysates were clarified from sonicated cells and the transcription factor-bound complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions with 10 ng of ChIP-DNA.

treatment_protocol: The MDA-MB-453 cells were grown in the phenol red-free medium supplemented with 5% charcoal/dextran-treated fetal bovine serum for 3 days, followed by treatment of vehicle or 10 nM DHT for the indicated time.

tag: cell line

value: breast cancer

value: sc-8631 Santa Cruz


title: Chromatin input-seq

description: Input-seq data

source_name: MDA-MB-453 chromatin input-seq


title: MDA-MB-453 siCtrl-veh

description: RNA-seq

data_processing:
Basecalls performed using CASAVA version 1.9
RNA-seq reads were aligned to hg19 using TopHat v2.0.4
Differential expression was characterized using Cuffdiff (version 0.0.5).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each condition

molecule: polyA RNA

source_name: MDA-MB-453 cells transfected with control siRNA followed by vehicle treatment

growth_protocol: The MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37oC incubator

extract_protocol:
Total RNA was prepared using RNeasy Mini Kit (Qiagen) according to the manufacturer's instruction. The polyadenylated mRNA was purified using oligo d(T)25 beads (NEB).
1 ng of mRNA was used for library preparation using Encore Complete RNA-seq kit (NuGEN) according to the manufacturer's instruction.

treatment_protocol: The MDA-MB-453 cells were transfected with siRNA and then grown in the phenol red-free medium supplemented with 5% charcoal/dextran-treated fetal bovine serum for 48 h, followed by treatment of vehicle or 10 nM DHT for 6 h.


title: MDA-MB-453 siCtrl-DHT

description: RNA-seq

source_name: MDA-MB-453 cells transfected with control siRNA followed by DHT treatment


title: MDA-MB-453 siMYC-DHT

description: RNA-seq

source_name: MDA-MB-453 cells transfected with MYC siRNA followed by DHT treatment


title: TCF7L2 ChIP-seq, 16h DHT treatment

description: ChIP-seq data

source_name: TCF7L2 ChIP-seq, 16h DHT treatment


title: FOXA1 ChIP-seq, 16h DHT treatment

description: ChIP-seq data

source_name: FOXA1 ChIP-seq, 16h DHT treatment

value: ab23738 Abcam


title: K562_mRNA_Rep1

status: Public on Mar 15 2013

city: Cambridge

first: Tarjei

middle: S

last: Mikkelsen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: Motif-centered mutagenesis of ENCODE enhancer predictions, reporter mRNA, replicate 1

data_processing: To infer the tag copy numbers in each Tag-Seq library, all sequence reads were examined, regardless of their quality scores. If the first ten nucleotides of a read perfectly matched one of the 55,000 designed tags and the remaining nucleotides matched the expected upstream MPRA construct sequence, this was counted as one occurrence of that tag. All reads that did not meet this criterion were discarded.

source_name: K562 cells

extract_protocol: Total RNA was isolated from cell lysates using RNeasy kits (Qiagen). mRNA was extracted from total RNA using MicroPoly(A)Purist™ kits (Ambion) and treated with DNase I using the Turbo DNA-free™ kit (Ambion). First-strand cDNA was synthesized from 400-700 ng mRNA using High Capacity RNA-to-cDNA kits (Applied Biosystems). Tag-Seq sequencing libraries were generated directly from 12% of a cDNA reaction or 50 ng plasmid DNA by 26 cycle PCR using Pfu Ultra HS DNA polymerase 2x master mix (Agilent) and primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG (where XXXXXXXX is a library-specific index sequence). The resultant PCR products were size-selected using 2% agarose E-Gel EX (Invitrogen).


title: MYC ChIP-seq, 6h DHT treatment

description: ChIP-seq data

source_name: MYC ChIP-seq, 6h DHT treatment

value: sc-764 Santa Cruz


title: AR ChIP-seq, 16h DHT treatment

description: ChIP-seq data

source_name: AR ChIP-seq, 16h DHT treatment

value: sc-816 Santa Cruz


title: HepG2_mRNA_Rep1

source_name: HepG2 cells


title: HIF2α #17-51 kidney 1

source_name: kidney cortex

value: male

value: gamma-HIF2alphaM3 TG+

value: kidney cortex


title: HepG2_mRNA_Rep2

description: Motif-centered mutagenesis of ENCODE enhancer predictions, reporter mRNA, replicate 2


title: WT #3 kidney 1

value: wild type


title: MPRA_Plasmid_Rep2

description: Motif-centered mutagenesis of ENCODE enhancer predictions, MPRA plasmid pool, replicate 2

organism: Escherichia coli

source_name: Plasmid pool

tag: source

value: plasmid


title: MPRA_Plasmid_Rep1

description: Motif-centered mutagenesis of ENCODE enhancer predictions, MPRA plasmid pool, replicate 1


title: WT #2 kidney 1


title: Methylome of CFSAN001992

city: College Park

first: Justin

middle: St. Giles

last: Payne

state: Maryland

address: 5100 Paint Branch Parkway

department: DM

institute: FDA/CFSAN

data_processing:
Base calling, assembly, mapping, and inter-pulse duration/base modification analysis performed by Pacific Biosciences SMRT Analysis Suite 1.4.0
Supplementary_files_format_and_content: base modifications in GFF, base modification table in CSV, motif summary in CSV - methylome data

organism: Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992

source_name: cultured isolate

extract_protocol:
Qiagen DNeasy Blood and Tissue Kit
PacBio 10kb SMRTBell

tag: subspecies

value: enterica

tag: serovar

value: Javiana

tag: pathogen

value: foodborne pathogen


title: chronic myeloid leukemia blood from human s1, in early disease

city: Jiangyin

first: JianBo

last: Zhou

state: Jiangsu

address: Shou Road No. 163

institute: People's Hospital of Jiangyin City

data_processing:
We used TopHat 1.33 software to align the sequence reads to reference genome (hg19). Then we used the cufflink program of Cufflinks 1.2.1 to call the expression values (FPKM, Fragments Per Kilobase of exon model per Million mapped fragments) of mapped human genes.
Genome Build:
exp.txt: hg19

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit. The RNA extraction is Trizol.Briefly, 10 ug of each total RNA sample was used for polyA mRNA selection using streptavidin-coated magnetic beads, followed by thermal mRNA fragmentation. The fragmented mRNA was subjected to cDNA synthesis using reverse transcriptase (Super- Script II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase) and 3-'A' add process (Klenow exo- fragment), was finally ligated to Illumina Truseq adaptors. Size selection was performed using a 2% agarose gel, generating cDNA libraries ranging in size 380 bp. Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 11 pM on one Genome Analyzer (GAII) lane using 115 bp sequencing. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: chronic myeloid leukemia blood


title: WT #1 kidney 2


title: PQBP1_knockdown_rep2

first: Qingqing

address: 161 Koshland Hall, UC Berkeley

institute: University of California, Berkeley

data_processing:
Sequencing data were mapped to the mouse genome by Tophat (2.0.4)
Perl scripts were written to call out all alternatively spliced splicing junctions and read counts to each junctions were calculated
We modified the algorithm of DEXseq and used it to perform diffrerential analysis on alternative splicing between the mock and PQBP1 knockdown samples
Genome_build: mm10
Supplementary_files_format_and_content: Excel file. The following data are enclosed: Gene name that the AS event belongs to; the AS event ID; sub-AS-junction IDs in this AS event; the corresponding genome coordinates for the sub-AS-junctions; p-values of differential usage of the corresponding sub-AS-junction between control and PQBP1 KD samples; fold changes of usage (on log2 scale) for the sub-AS-junction between control and PQBP1 KD samples.

source_name: cortical neurons dissected from E16.5 mouse embryo cortices

extract_protocol:
Cellular RNA was extracted by RNeasy Mini Kit (Qiagen).
We used the PrepX mRNA IntegenX kit to prepare library constructions. The detailed protocol can be tracked through the link provided below:  http://www.genome.med.harvard.edu/documents/illumina/IntegenX_Apollo324_mRNA_Seq_Protocol_10012012.pdf

tag: neuron age

value: day 5 in vitro

tag: treated with

value: lentivirus from a PQBP1-targeting shRNA


title: mock_knockdown_rep3

value: lentivirus from a non-targeting control shRNA


title: mock_knockdown_rep1


title: mock_knockdown_rep2


title: K562_mRNA_Rep2


title: PQBP1_knockdown_rep1


title: Ring1-delta-Rnf2+_E11.5_male_rep2

status: Public on Mar 14 2013

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

data_processing:
Basecalling was carried out with Illuina RTA software (version 1.13.48) and TruSeq libraries were de-multiplexed with the script configureBclToFastq.pl and CASAVA_v1.8.0
Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the Refseq transcripts (downloaded Aug 13, 2012) were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. Reads mapping to several locations were fractionated and distributed equally among all mapping sites.
Genome_build: mm9 and Refseq Transcripts downloaded on Aug 13, 2012
Supplementary_files_format_and_content: tabular file with read counts per transcript for all Refseq transcripts

source_name: Primordial germ cells

extract_protocol:
RNA was extracted from 500 PGCs per embryo using RNeasy Micro Kit (QIAGEN). The RNA amplification and cDNA generation were performed using NuGEN Ovation RNA-seq System V2 (Part No. 7102)
sequencing libraries were prepared using Truseq DNA Sample Preparation Kit (low-throughput protocol) (Part# 15005180 Rev. C)

tag: developmental stage

tag: cell type

value: primordial germ cells

tag: genetic background

value: 129/Sv and C57BL6J


title: Hu HITS-CLIP from age P13 mouse brain polysomes, IPed with anti-Hu antisera

first: Jennifer

last: Darnell

address: 1230 York Ave.

institute: The Rockefeller University

description: very detailed desscription is published in PMID 21784246

data_processing:
standard 454 GS20 base caller
454 reads collected from five different FMRP CLIP experiments were mapped to the mouse genome (NCBI37/mm9, July 2007) by BLAT (Kent, 2002), using the parameters stepSize=5 and minScore=15. A read whose best score was higher than the second best was considered to be unambiguously mappable. Reads without unambiguous mapping were excluded from further analysis. For each of the five protocol 1 CLIP experiments in which the fulllength of the RNA tag was sequenced, reads with the same start and stop positions were considered to be duplicates potentially resulting from RT-PCR amplification, and collapsed to identify unique reads used for further analysis.
Two additional FMRP CLIP experiments and two Hu CLIP experiments sequenced by the Illumina Genome Analyzer are 76-nucleotide (nt) reads, including a 5-nt degenerate “barcoded” linker sequence read-able from the 5´ end of each CLIP tag to distinguish potential PCR duplicates from genuinely unique reads mapped to the same locations. Therefore, the sequence of actual RNA tags was determined up to 71 nt in length, and the relatively long reads maximized the chance of detecting the full length RNA fragments (modal size ~50 nt) pulled down by immunoprecipitation. To minimize sequencing errors resulting from the ultrahigh-throughput sequencing and hence alignment errors in downstream analysis, we first filtered the raw reads based on the quality scores. We required a minimum quality score " 20 in the first five nucleotides (the degenerate region), and an average score " 20 in the next 25 nucleotides (i.e., the first 25 nucleotides of each actual RNA tag). The filtered reads were then subject to the removal of the 5´ degenerate “barcode” (whose identity was however recorded) and the 3´ linker to get the actual RNA tag sequences. Since RNA CLIP tags differ in size, 3´ linkers were detected and trimmed by aligning each read to the linker sequence using the needle program (parameters: gapopen: 100, gapext 10 for alignment; #matches-#mismatches>=4 nt, %mismatches<=15%, and #indels <1 nt for detection of the linker (Rice et al., 2000)). The linker-trimmed reads were then mapped to the mouse genome (NCBI37/mm9, July 2007) by the program Novoalign (http://www.novocraft.com), requiring $2 mismatches (substitutions or indels) in " 28 nt. Only reads with unambiguous mapping were kept. Mappable reads for all four experiments were then pooled together, so that PCR duplicates and potential contaminations (e.g., between neighboring lanes in the flow cells during Illumina sequencing) were eliminated to identify unique reads, using an expectation-maximization (EM)-based algorithm, which modeled the starting coordinates of mappable tags, and the identity and copy number of their degenerate “barcode” sequences.  More detailed description is published in PMID 21784250.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with unique CLIP tags after removal of PCR duplicates

source_name: whole brain minus white matter tracts

extract_protocol:
The brain was removed and placed in ice-cold dissection buffer (1X Hank’s balanced salt solution (Gibco) containing 10 mM HEPES, pH 7.3 (USB) (HHBSS) and 0.1 mg/ml cycloheximide (Sigma C-7698, made fresh in methanol). Cortex and cerebellum were dissected free of underlying white matter, homogenized in 1 ml lysis buffer (10mM HEPES-KOH, pH 7.4, 150mM KCl or NaCl, 5mM MgCl2, 0.5mM dithiothreitol, 0.1 mg/ml cycloheximide, 1X Complete EDTA-free protease inhibitor cocktail (Roche), 40U/ml rRNAsin (Promega)) per brain, with 10-12 strokes at 900rpm in a motor-driven Teflon-5 ml glass homogenizer. NP-40 was added to a final concentration of 1% from a 10% stock (Calbiochem) and allowed to sit on ice 10 minutes. The homogenate was spun at 2,000xg for 10min at 4C. The supernatant (S1) was respun at 20,000xg for 10min at 4C. The resulting supernatant (S2) was loaded onto a 20-50% w/w linear density gradient of sucrose in gradient buffer (10mM HEPES-KOH pH 7.4, 150mM KCl, and 5mM MgCl2) prepared using a Gradient Master 107 (BioComp), in 14 x 89 mm polyallomer ultracentrifuge tubes (Beckman 331372). Gradients were centrifuged at 40,000 rpm for 2hrs at 4C in a Beckman SW41 rotor and sixteen fractions of 0.75ml volume were collected with continuous monitoring at 260nm using an ISCO UA-6 UV detector
Crosslinking-IP (HITS-CLIP) Protocol 1: Polyribosome gradients were prepared from P14, P15 and P25 male FVB wild type and Fmr1Tm1Cgr littermate mice as described above. The S2 supernatants were UV-crosslinked in a 3.5 cm tissue culture dish on a bed of ice- slush three times at 400 mJ/square cm (254nm UV light) with swirling between each irradiation, using a Stratalinker 2400. Fractions containing polyribosome-associated FMRP were pooled, diluted 1:1 with gradient buffer and polyribosomes were pelleted by centrifugation for 2hr at 300,000xg in polycarbonate centrifuge tubes (Beckman 362305) in a TLA110 rotor (Beckman) using a tabletop ultracentrifuge (Optima MAX, Beckman) at 4C. (2) Dissociation of RNPs, RNAse treatment and IP-- Polyribosome pellets were dissociated in 1% SDS containing buffer based on a published protocol (Hinck et al., 1994) with modifications. The polyribosomal pellet was resuspended in 100 ul SDS-IP buffer (15 mM Tris, pH 7.5, 5 mM EDTA, 2.5 mM EGTA, and 1% SDS), heated to 90 degrees for 10 minutes with vigorous shaking to dissociate RNP complexes, and diluted with 9V of CSK buffer (20 mM Tris, pH 7.0, 50 mM NaCl, 3 mM MgCl2, 0.5% Triton X- 100, 300 mM sucrose) and stored on ice. Lysates were treated with 200 units/ml RNAse T1 (Applied Biosystems/Ambion AM2280) in CSK buffer for 10 minutes at 37C and stopped with the addition of 1320 units of SuperAse-In (Applied Biosystems/Ambion) so that RNAs crosslinked to FMRP were reduced to a modal size of about 60-100 nts. FMRP was IPed from these samples using Protein A Dynabeads (Invitrogen) bound to either rabbit polyclonal anti-FMRP (ab17722, Abcam) or mouse mixed monoclonal antibodies to 2 different epitopes on FMRP (7G1-1; (Brown et al., 2001) and 2F5; (Gabel et al., 2004)) described below.  Following IP (described below) the beads were washed sequentially (1 ml washes) with high stringency buffer (15 mM Tris-HCl, pH 7.5, 5 mM EDTA, 2.5 mM EGTA, 1% Tx-100, 1% Na-DOC, 0.1% SDS, 120 mM NaCl, 25 mM KCl), high salt buffer (15 mM Tris-HCl, pH 7.5, 5 mM EDTA, 2.5 mM EGTA, 1% Triton X-100, 1% Na-DOC, 0.1% SDS, 1 M NaCl) and twice with low salt buffer (15 mM Tris-HCl, pH 7.5, 5 mM EDTA) followed by one wash with NT-2 buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM MgCl2, and 0.05% NP-40). (3) Dephosphorylation of RNA, 3’ linker ligation and SDS-PAGE separation of RNABP:RNA complexes-- Immunoprecipitations were treated with calf intestinal phosphatase to remove the 5’ phosphate from RNA crosslinked to FMRP (“RNA tags”). Beads were resuspended in 0.08 ml of 1X dephosphorylation buffer and 3 units of calf intestinal alkaline phosphatase (CIAP, Roche) was added, incubated in the Thermomixer R at 37C for 20 min, programmed to shake at 1000rpm for 15 sec every 4 min, followed by 3X 1ml washes with NT-2, 2X PXL, and 2X NT-2 with one tube change during washing. To ligate a 32P-labelled RNA linker to the 3’ end of the RNA, the puromycin- blocked linker (L32, 5’-OH-GUGUCAGUCACUUCCAGCGG-3’-puromycin) was first labeled using T4 phosphonucleotide kinase (PNK, New England Biolabs, NEB). 50 pmol of L32 RNA, 0.015 ml 32P-γ-ATP, and 2 ul of T4 PNK in 1X PNK buffer were incubated at 37C for 30min, an additional 0.02 ml 10 mM ATP was added and the reaction incubated 5 min. Radiolabeled linker was spun through a G-25 column (Amersham) to remove free ATP. 30 pmol of the labeled 3’ RNA linker was added to a 0.08 ml T4 RNA ligase reaction (Fermentas), according to kit instructions, and on-bead ligation reactions were incubated at 16C for 1 hr in the Thermomixer R programmed 1000rpm for 15 sec every 4 min. After 1 hr, 80 pmol of L32 RNA linker WITH 5’ phosphate was added to each tube of reaction and incubated overnight followed by 3X wash with NT-2 buffer. To rephosphorylate the 5’ end of the RNA for 5’ linker ligation, 80 ul of PNK mix (6 ul of 1 mM ATP, 4 ul T4 PNK enzyme (NEB), 1 ul RNasin in 1X PNK buffer (NEB), total volume 80ul) was added to each tube and incubated for 20 min at 1000rpm shaking for 15 sec every 4 min and washed 1X with PXL and 2X with NT-2 buffers. Each tube of beads was resuspended in 40 ul NuPAGE loading buffer (LDS, Invitrogen), containing reducing agent, and incubated at 70C for 10min at 1000rpm. Supernatants were taken off the beads and run on Novex NuPAGE 10% Bis-Tris gels (Invitrogen) in MOPS running buffer (Invitrogen) for 3 hr at 175V and transferred to Protran nitrocellulose (S&S) using a Novex wet transfer apparatus (Invitrogen). After transfer, the nitrocellulose was quickly rinsed with RNAse-free PBS, blotted with Kimwipes, wrapped in plastic wrap and exposed to Biomax MR film (Kodak). (4) Recovery of complexes, protease digestion and 5’linker ligation--Nitrocellulose membranes were aligned carefully with the exposed film and filter excised with a scalpel from 105-140 kDa kDa (the size of FMRP crosslinked to RNA of approx. 100+ nucleotides). Each band of nitrocellulose membrane was further cut into smaller pieces and proteinase K treated (0.2 ml of a 1:5 dilution of proteinase K (4mg/ml, Roche) in PK buffer (100mM Tris-Cl pH 7.5, 50mM NaCl, 10mM EDTA)) at 37C, 1100rpm for 20min. Then 0.2 ml of PK+7M urea solution was added and incubated for another 20min at 37C at 1100rpm. Finally, 0.4 ml of RNA phenol (pH 6.8, Applied Biosystems/Ambion) and 0.13 ml of 49:1 CHCl3:isoamyl alcohol were added and incubated at 37C, 1100rpm for additional 20 min. Tubes were spun at 20,000xg in a microcentrifuge. Glycogen (0.5 ul, Applied Biosystems/Ambion), 50ul 3M NaOAc pH 5.2, and 1 ml of 1:1 ethanol:isopropanol were added to the aqueous phase in a fresh tube and RNA was precipitated overnight at -20C. RNA was pelleted, washed with 75% ethanol, the pellet dried and dissolved in 6 ul RNAse-free H2O. RNA ligation to add the 5’ linker (L51 (RNA linker 51), 5’-OH- AGGGAGGACGAUGCGG-3’) was performed with 1ul 10X T4 RNA ligase buffer (Fermentas), 1ul BSA (0.2ug/ul), 1ul ATP (10mM), 0.1ul T4 RNA ligase (3U, Fermentas), and 20 pmol of each L51 RNA linker in a total volume of 10 ul at 16C overnight. To the ligation reaction, 77ul H2O, 11ul 10X RQ1 DNase buffer, 5ul RQ1 DNase (Promega) and 5ul RNasin (Promega) were added and incubated at 37C for 20min. 0.3 ml H2O, 0.3 ml RNA phenol (Ambion) and 0.1 ml CHCl3 were added, vortexed, spun and the aqueous layer taken. RNA was precipitated with 50ul 3M NaOAc pH 5.2, 1ul glycogen (Ambion) and 1 ml 1:1 ethanol:isopropanol overnight at -20C. (5) RT-PCR and high-throughput sequencing of PCR products--RNA was pelleted, washed, dried, and resuspended in 8 ul of RNAse-free H2O. The RNA was mixed with 2ul of primer P32 (3’ DNA primer 32, 5’- CTTCACTCACCTCG

treatment_protocol: Mice of the indicated genotypes and ages were sacrificed by isoflurane anaesthesia and decapitation.

tag: strain

value: FVB

value: brain

tag: age

tag: ip antibody

value: anti-Hu

tag: dissociation protocol and sequencing platform

value: 2% SDS, Illumina


title: FMRP HITS-CLIP from age P15 mouse brain polysomes, IPed with mixed monoclonal antibodies

tag: tissue

value: 7G1-1 and 2F5, mixed


title: FMRP HITS-CLIP from age P25 mouse brain polysomes, IPed with mixed monoclonal antibodies


title: Ring1-delta-Rnf2+_E11.5_male_rep1

tag: genotype

tag: gender

value: male


title: FMRP HITS-CLIP from age P13 mouse brain polysomes, IPed with a polyclonal antibody


title: MeCP2-G273X_ChIP-Seq

status: Public on Mar 12 2013

first: Peng

last: Yu

address: 1 Baylor Plaza

institute: BCM

data_processing: The reference genome is mm9. CASAVA-1.7.0

source_name: Whole Brain

extract_protocol: Lysates were clarified from sonicated/micrococcal nuclease treated nuclei and MeCP2-DNA complexes were isolated with antibody. Libraries were prepared from 10 ng of ChIPed DNA and sequenced on the Illumina Solexa HiSeq according to manufacturer protocols.

value: Adult whole brain

tag: genotype/variation

value: Mecp2 -/y; MECP2-G273X TG

tag: background mouse strain

tag: antibody

value: anti-GFP

tag: vendor

value: Abcam

tag: catalog#


title: MeCP2-R270X_ChIP-Seq

value: Mecp2 -/y; MECP2-R270X TG


title: FMRP HITS-CLIP from age P14 mouse brain polysomes, IPed with a polyclonal antibody


title: FMRP HITS-CLIP from age P11 mouse brain polysomes, IPed with a polyclonal antibody


title: Te_PAm[SP]

status: Public on Mar 11 2013

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

description: RNA-seq/SPIA (Nugen) library prep

data_processing:
Illumina Firecrest and Bustard modules were used to obtain basecalls and quality scores for each read.  FASTQ files are contain paired end reads .
1st 4 bases of R1 were used for demultiplexing (4 samples/lane).  Demultiplexing was performed with fastq_multx script.
Reads were aligned with Novoalign (V2.07.09) to Human Genome hg19 with addition of 18S and 28S ribosomal sequences
Genome_build: hg19
Supplementary_files_format_and_content: Aligned reads (Novoalign) in bed file format

source_name: Testes Ambion

extract_protocol:
Spermatozoal RNAs were isolated from ejaculates from three fertile donors following selection by 50% percoll gradient centrifugation. RNA was extracted from purified sperm using the RNEasy system. Total testis RNAs were obtained from two commercial libraries. Following removal of genomic DNA, RNA size and quality were assayed using the 2100 bioanalyzer with a RNA Pico chip. Separate RNA-seq libraries were constructed for each sample using the Illumina mRNA-Seq kit. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Libraries for each sample were sequenced in 2 lanes - each lane was 2x36.
Nugen Ovation kit (Nugen Inc., San Carlos, CA U.S.A.) for cDNA and initial linear amplification. The Nugen Encore system was used for adaptor ligation, end-repair, and amplification.

value: testes

tag: size

tag: sequencing library

value: paired-end, 1st 4 bases of Read 1 used for multiplexing


title: AS066

data_processing:
Illumina Firecrest and Bustard modules were used to obtain basecalls and quality scores for each read.  QSEQ files are contain paired end reads .  Most samples were run in 2 lanes - paired reads from each lane ("A" and "B") are bundled in separate tar.gz files.
Reads from both lanes of each of samples 1,2,3,4 and single lane of samples 7,8 were aligned (Novoalign) to 18S and 28S human ribosomal RNA sequences in order to examine population of ribosomal RNA in sperm and testis. Results are presented in .wig files for 18S and 28S, showing read counts at each transcript position.

source_name: Donor 3 Sperm

extract_protocol: Spermatozoal RNAs were isolated from ejaculates from three fertile donors following selection by 50% percoll gradient centrifugation. RNA was extracted from purified sperm using the RNEasy system. Total testis RNAs were obtained from two commercial libraries. Following removal of genomic DNA, RNA size and quality were assayed using the 2100 bioanalyzer with a RNA Pico chip. Separate RNA-seq libraries were constructed for each sample using the Illumina mRNA-Seq kit. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Libraries for each sample were sequenced in 2 lanes - each lane was 2x36.

tag: sample type

value: proven fertile

tag: lane#

value: 2x36 - 2 lanes

value: sperm


title: AS064

source_name: Donor 2 Sperm


title: Sp_P2[SP]

description: RNA-seq/SPIA (Nugen) library prep

source_name: Pooled Donors Sperm

tag: cell type

tag: fertility status


title: Testis_Clonetech

source_name: Testis

value: 2x36 - 1 lane

value: testis


title: Testis_Ambion


title: Sp_D66[SP]

description: RNA-seq/SPIA (Nugen) library prep


title: Sp_D64[SP]

description: RNA-seq/SPIA (Nugen) library prep


title: Hu HITS-CLIP from age P11 mouse brain polysomes, IPed with anti-Hu antisera

tag: strain

value: FVB

value: brain

tag: age


title: FMRP HITS-CLIP from age P25 mouse brain polysomes, IPed with a polyclonal antibody

tag: ip antibody

tag: dissociation protocol and sequencing platform


title: Ring1-delta-Rnf2-delta-_E11.5_male_rep1

tag: genotype

tag: developmental stage

value: primordial germ cells

tag: genetic background

value: 129/Sv and C57BL6J


title: Fb_BS-seq_II

status: Public on Mar 08 2013

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

data_processing:
Illumina RTA 1.7.45 and Casava 1.8 were used for base calling
Novoalign Bisulfite module was used for mapping to the mouse assembly mm9
The base calls per reference position on each strand were used to identify methylated cytosines in the context of CpG, CHG and CHH.
genome build: mm9
processed data files format and content: tab-delimited text files include methylation percent for dermal fibroblasts
processed data file (Percent_Fb_onlyCpG.bed) is available on the Series record

source_name: Mouse primary dermal fibroblasts

growth_protocol: Primary dermal fibroblasts were cultured for 8 days in DMEM/F12: GlutaMAX medium (Invitrogen) with 10% FBS.

extract_protocol:
Primary mouse dermal fibroblasts were cultured for 8 days. DNA was extractes using Qiagen DNA purification kit from the primary cells. .
Methylome libraries were prepared for sequencing using standard Illumina protocols

value: Primary dermal fibroblasts

tag: Sex

value: Female

value: FVB/N

tag: treatment

value: Bisulfite treated Genomic DNA


title: ATF4_ChIP-seq

data_processing:
Illumina RTA 1.7.45 were used for base calling
ChIP-seq reads were aligned to mm9 assembly using using Casava 1.7/1.8 or BWA with default parameters (Illumina; Li et al. Bioinformatics (2009) 25:1754-60).
Data were filtered by removing the PCR duplicates using SAMTOOLS (Li et al.  Bioinformatics (2009) 25, 2078-9)
Peaks were called using MACS with default parameters
genome build: mm9
processed data file format: bed files were generated using MACS with default parameter (Zhang et al. Genome Biol (2008) 9 (9))

extract_protocol:
Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dermal fibroblasts were either treated with thapsigargin to induce ER stress and ATF4 expression for 3hrs or left untereated before harvesting the cross-linked cells.

tag: chip antibody

value: Thapsigargin treatment for 3 hrs


title: Fb_BS-seq_I


title: CEBPB_Tg_ChIP-seq


title: small RNA-H

status: Public on Mar 09 2013

city: Roanoke

first: Aboozar

last: Monavarfeshani

state: VA

address: 2 Riverside Circle

department: Biological Science

institute: Virginia Tech

data_processing:
Image analysis and base calling were performed according to Illumina Pipeline.
Remove adaptors, low-quality tags, as well as contaminants to generate clean reads
Clean sequence tags were then annotated as belonging to different categories (rRNA, snRNA, siRNA, snoRNA, tRNA, miRNA) by performing BLASTn (version 2.2.24+) search against relevant databases (Rfam, miRBase)
The remaining unannotated reads were aligned with non-coding unigenes of in-house C. aurantifolia Transcriptome database (deposited in SRA database with Accession no. SRA058604) using Mireap
The normalized miRNA expression level (The actual count of miRNA/Total count of clean reads*1000000) was used to compare the differential expression of miRNAs in healthy and infected trees
Supplementary_files_format_and_content: Clean-H.fa: FASTA file of all clean reads in Healthy sample. , Format:Each sequence with a unique Id
Supplementary_files_format_and_content: Clean-I.fa: FASTA file of all clean reads in Phytoplasma-infected sample. , Format:Each sequence with a unique Id
Supplementary_files_format_and_content: Match miRBase-H.txt: This file contains Healthy sample small RNAs whose sequences are similar with miRNAs deposited at miRBase, Format:1. small RNA sequnece Id2. length of small RNA sequence3. count of small RNA sequence4. small RNA sequnce5. homolog (best one)6. homolog length7. homolog sequence8. family9. match number 10. mismatch number11. gap number12. score
Supplementary_files_format_and_content: Match miRBase-I.txt: This file contains Phytoplasma-infected sample small RNAs whose sequences are similar with miRNAs deposited at miRBase, Format:1. small RNA sequnece Id2. length of small RNA sequence3. count of small RNA sequence4. small RNA sequnce5. homolog (best one)6. homolog length7. homolog sequence8. family9. match number 10. mismatch number11. gap number12. score
Supplementary_files_format_and_content: Match Rfam-H.txt: This file contains Healthy sample small RNAs matching rRNA, tRNA, snRNA, snoRNA deposited at Rfam datbase, Format:1. small RNA sequnece Id2. length of small RNA sequence3. count of small RNA sequence4. small RNA sequnce5. type6. Rfam sequence Id
Supplementary_files_format_and_content: Match Rfam-I.txt: This file contains Phytoplasma-infected sample small RNAs matching rRNA, tRNA, snRNA, snoRNA deposited at Rfam datbase, Format:1. small RNA sequnece Id2. length of small RNA sequence3. count of small RNA sequence4. small RNA sequnce5. type6. Rfam sequence Id
Supplementary_files_format_and_content: siRNA-H.txt: This file contains Healthy sample small RNAs matching siRNAs., Format:1. small RNA sequnece Id2. type3. count of small RNA sequence4. small RNA sequnce5. length of small RNA sequence
Supplementary_files_format_and_content: siRNA-I.txt: This file contains Phytoplasma-infected sample small RNAs matching siRNAs., Format:1. small RNA sequnece Id2. type3. count of small RNA sequence4. small RNA sequnce5. length of small RNA sequence
Supplementary_files_format_and_content: Match repeat-H.txt: This file contains Healthy sample small RNAs matching repeat deposited at hg18 database., Format:1. small RNA sequence Id2. repeat type and 0 for antisense,1 for sense3. start position4. end position6. small RNA sequence
Supplementary_files_format_and_content: Match repeat-I.txt: This file contains Phytoplasma-infected sample small RNAs matching repeat deposited at hg18 database., Format:1. small RNA sequence Id2. repeat type and 0 for antisense,1 for sense3. start position4. end position6. small RNA sequence

organism: Citrus x aurantiifolia

source_name: Healthy leaves

growth_protocol: One-year-old Mexican lime trees were prepared by growing healthy seedlings in a greenhouse at 25°C–28°C.

extract_protocol:
The RNA from 100-mg samples of leaves from six infected trees and six healthy trees was isolated using the High Pure miRNA Isolation Kit (Roche, Germany) in accordance with the manufacturer's instructions, and quantified using an ND-1000 spectrophotometer (NanoDrop Thermo Scientific, USA)
Libraries were prepared using the Small RNA Sample Preparation Kit

treatment_protocol: Obtained healthy trees were grafted using cuttings from either healthy or “Ca. Phytoplasma aurantifolia”-infected Mexican lime trees. .All of the grafted plants were arranged randomly in the greenhouse and covered with plastic bags for 1 month to increase the humidity in their immediate environment. Twenty weeks after inoculation, the branches of six healthy and six infected plants were harvested, frozen immediately in liquid nitrogen, and stored at –80°C until further use. Phytoplasma infection was detected by nested PCR.

value: Wild type

value: Healthy

tag: tissue

value: Leaves


title: small RNA-I

source_name: Phytoplasma-infected leaves


title: Tet2CD_hMeDIP-seq

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

description: extracting genomic DNA at D1 after infection

data_processing:
Illumina Casava1.8 software used for basecalling.
hMeDIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 2.1.0 with the parameters（ --end-to-end --sensitive)
peaks were called using MACS (1.4.2) with the following parameters ( --nomodel -p 1e-5 )
genome build: mm9
files format: bed files were generated using MACS, showing the results of peaks calling.

source_name: mouse embryonic fibroblasts (MEFs)

extract_protocol:
Genomic DNA was extracted by Wizard@ Genomic DNA Purification Kit (Promega, A1125). Genome DNA was sonicated to 100-500 base pairs (bp) for library construction.
Illumina adaptors were ligated before hmeDIP following NEBNext® DNA Library Prep Reagent Set for Illumina® instruction manual, and then the adaptor-ligated DNA was denatured and DIP using hmC-antibody. After hmeDIP, DNA was purified and amplified.

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)

tag: passage


title: AS062PLUS

source_name: Donor 1 Sperm (PolyA+)

value: proven fertile

value: 2x36 - 2 lanes


title: FMRP HITS-CLIP from age P14 mouse brain polysomes, IPed with mixed monoclonal antibodies

value: 7G1-1 and 2F5, mixed


title: Tet1CD_hMeDIP-seq


title: NPC_5hmC

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

description:
IP against hydroxymethylated gDNA using 5hmC mouse polyclonal antibody (Active Motif, catalog #39769)
hMeDIP-seq

data_processing:
The image analysis and base calling were performed with the Illumina package OLB (v1.8).
We used SolexaQA(v1.9) to assess the quality of data and then used DynamicTrim.pl to cut off the low-quality part .
Sequence reads were mapped onto the reference mouse genome (NCBI Build UCSC mm9) using Bowtie (v0.12.7) algorithm (Langmead et al. 2009).
Extend 350bp from 5' end of read as end site of fragment due to our library fragment length was ~200-500bp, center at about 350 bp.
Genome_build: mm9
Supplementary_files_format_and_content: [bed format] chrom: The name of the chromosome scaffold.chromStart: The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.chromEnd: The ending position of the feature in the chromosome or scaffold.name: Defines the name of the BED line. score: A score between 0 and 1000.strand - Defines the strand - either '+' or '-'.

source_name: NPCs

growth_protocol: 46C mouse ES cells (gifts from Dr. Qi-Long Ying, USC) were cultured in standard ES culture conditions (DMEM supplemented with 10% fetal bovine serum, non-essential amino acid, beta-mercaptoethanol, and 1000U/ml leukemia inhibitory factor).

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen; Germany).
Genomic DNA was sonicated to <500 bp by Bioruptor sonicator (Diagenode; Belgium) and quantified using Quant-iTdsDNA HS assay kit (Q32851, Invitrogen; USA) according to the manufacturer’s manual. The sonicated DNA fragments (4 ug of each sample) were end-repaired using the End-It DNA End Repair Kit (ER0720, EPICENTRE Biotechnologies) according to the manufacturer’s instructions, followed by treatment with Klenow fragment 3’–5’exo and dATP to generate a protruding 3’A for ligation with the adaptor containing specific barcode sequence. The barcode sequence (four-base index: CCAG and TAGC) within adaptor was designed as described previously (Cronn et al. 2008) with a little modification.Equal amount (~4 μg) of bar-code tagged gDNA from ESCs and NPCs were pooled together in one tube. The mixed DNA was denatured and diluted by IP buffer (10% input were taken off at this step). The denatured DNA was incubated with 4 μg 5hmC antibody (Active Motif) at 4℃ overnight. Antibody-DNA complexes were captured by protein A/G beads and the enriched 5hmC-containing DNA fragments (hMeDIP product) were purified and recycled.The hMeDIP products, as well as input DNA, were amplified for 10-12 cycles and the PCR products were recycled by Qiagen Mini Gel Purification Kit.

treatment_protocol: ES-derived NPCs (neural progenitor cells) were differentiated from 46C ES cells according to the monolayer N2B27 neural differentiation protocol (Ying and Smith 2003; Ying et al. 2003). Rosette-like Sox1-GFP+ NPCs at day 9 upon neural differentiation were used in our experiments.

tag: cell line

value: ES-derived neural progenitor cells

tag: sequencing type

value: hMeDIP

tag: sirna or shrna treatment

value: No

tag: antibody


title: mES_Input

description:
input
hMeDIP-seq

source_name: ESCs

value: input


title: AS062

source_name: Donor 1 Sperm

tag: sample type

tag: lane#

value: sperm


title: Tet2CDmut_RNAseq

description: extracting RNA at D3 after infection

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
genome build: mm9
files format: TXT files including tau values for each RNA-seq samples, and TPM values are generated for all the samples.

extract_protocol:
Total RNA was extracted by Trizol-based protocol.
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

tag: cell type

tag: strain


title: Tet2CD_RNAseq

description: extracting RNA at D3 after infection


title: DR_RNAseq

description: extracting RNA at D3 after infection


title: Tet1CDmut_RNAseq

description: extracting RNA at D3 after infection


title: Sp_D62[SP]

description: RNA-seq/SPIA (Nugen) library prep

tag: fertility status

tag: size

tag: sequencing library

value: paired-end, 1st 4 bases of Read 1 used for multiplexing


title: Tet1CD_RNAseq

description: extracting RNA at D3 after infection


title: mES_5hmC

value: 5hmC mouse polyclonal antibody (Active Motif, catalog #39769)


title: ys-1 degradome

city: Wuhan

first: Xiyan

last: Yang

state: Hubei

address: Shizishan 1, Hongshan

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, abandon seqences small than 18 nt, and masked for low-complexity or low-quality sequence, then mapped to ref2 database using soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap
Genome_build: genome unavailable, use assemble cotton EST sequences for reads alignment
Supplementary_files_format_and_content: abundance: length abundance sequence

organism: Gossypium hirsutum

source_name: seedlings

growth_protocol: Seeds of G. hirsutum YZ1 were decoated, surface-sterilized and germinated on half MS medium (1/2 macro salts plus 15 g glucose, pH 6.0) at 28℃ in the dark for 5–7 days. The hypocotyls of the seedling were cut into 5-7  mm sections, some of which were immediately  sampled as control (CK).Then the explants were cultured on MSB (MS medium plus B5 vitamins) medium supplemented with the combination of 1.0 mg/L IBA plus 0.1 mg/L kinetin. After 40 d culturing, all explants were transferred to fresh MSB medium for embryogenic calli (ECs) induction.

extract_protocol:
Total RNA was isolated from each sample by using a modified guanidine thiocyanate method from Zhu et al., Acta Agron Sin, 2005
For the small RNA sequencing, the small RNAs (~18-30 nt) were purified from 10μg of total RNA by polyacrylamide gel electrophoresis, and ligated first to a 5′ RNA adapter and then a 3′ RNA adapter. A reverse transcription reaction was followed by several cycles of PCR to obtain sufficient product which was gel-purified for Sequencing by Synthesis (SBS) sequencing via Solexa technology. For degradome sequencing, poly (A+) RNA molecules were isolated from 200 μg of total RNA using the Oligotex mRNA kit (Qiagen), and then a 5′ RNA oligonucleotide adapter containing a MmeI recognition site was ligated to the 5′-phosphate of the poly(A+) RNA by T4 RNA ligase. This was followed by purification of the ligated products using the Oligotex kit. Subsequently, five PCR cycles was performed on the products of a reverse transcription reaction which were then digested with MmeI and ligated to a 3′ double DNA adapter. Finally, the ligation products were amplified with 20 PCR cycles, gel-purified and subjected to SBS sequencing by the Solexa/Illumina analyzer.

value: polyA RNA

tag: cultivar

value: hypocotyls

tag: developmental stage

value: 7 days seedlings

tag: condition of culture

value: 28'C in dark


title: ys-3 small RNA

source_name: hypocotyls

value: small RNA

value: embryogenic calli

value: 2 months after inducement

value: 28'C in light


title: Zdr_1

status: Public on Mar 07 2013

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations.
Approximately one to three micrograms of genomic DNA was sonicated to ~100 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using Qiagen DNeasy minielute columns (Qiagen). Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using Pfu Cx Turbo (Agilent, Santa Clara, CA) using the following PCR conditions (2 minutes at 95C, 4 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).

value: leaf

tag: ecotype id


title: Wt_5

tag: tissue


title: ys-3 degradome


title: Zdr_1_bud

source_name: mixed stage inflorescence

value: mixed stage inflorescence


title: ys-1 small RNA


title: Fb_RNA-seq

data_processing:
Illumina RTA 1.7.45 were used for base calling
Illumina CASAVA 1.8.2/bowtie  used for mapping
Transcript abundances were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cufflink software with default parametrs (Trapnel et al, 2010 Nature Biotechnology).
genome build: mm9
processed data file format: tab-delimited text files include FPKM values for dermal fibroblasts with and without thapsigargin treatment

extract_protocol:
Primary mouse dermal fibroblasts were cultured for 8 days. Either cell were treated with Thapsigargin to induce ER stress and induces ATF4 expression for 3 hours or left untreated. RNA was harvested using Trizol reagent from the primary cells. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dermal fibroblasts were either treated with thapsigargin to induce ER stress and ATF4 expression for 3hrs or left untereated before harvesting the cells.

value: Primary dermal fibroblasts

tag: Sex

value: Female

value: FVB/N


title: Ws_2_bud


title: Wl_0_bud


title: Fb+Tg_RNA-seq


title: CEBPB_ChIP-seq

tag: chip antibody

tag: treatment

value: No treatment


title: Yo_0


title: NPC_Input

description:
input
hMeDIP-seq

tag: cell line

value: ES-derived neural progenitor cells

tag: sequencing type

value: input

tag: sirna or shrna treatment

value: No


title: Utrecth_bud


title: Uod_1_bud


title: Wa_1


title: Ty_0_bud


title: Van_0_bud


title: Ta_0_bud


title: Westkar_4


title: Uk_1


title: Uk_1_bud


title: Sus_1_bud


title: Tscha_1_bud


title: Vind_1


title: Tol_0_bud


title: Si_0


title: Tamm_2_bud


title: Tu_0_bud


title: Sg_1


title: Sei_0_bud


title: Seattle_0


title: Sp_0_bud


title: Se_0_bud


title: Rubezhnoe_1_bud


title: RRS_7


title: Su_0


title: Sq_8_bud


title: Sorbo_bud


title: Stw_0


title: Rd_0


title: Rome_1_bud


title: Rld_1_bud


title: Rmx_A02_bud


title: Rennes_1_bud


title: Pu2_23_bud


title: Pt_0


title: Ragl_1_bud


title: Pro_0_bud


title: Ragl_1


title: Ra_0


title: Pu2_7_bud


title: Ove_0_bud


title: Old_1_bud


title: Ob_0_bud


title: Pi_0


title: Pna_17_bud


title: Pu2_23


title: Pog_0_bud


title: Pla_0_bud


title: Mz_0_bud


title: Mh_0_bud


title: Mc_0


title: Ms_0_bud


title: Per_1


title: Litva_bud


title: Li_2_1_bud


title: Nw_0_bud


title: Np_0_bud


title: Nok_3_bud


title: La_0


title: Lan_0


title: Ler_1


title: Nc_1_bud


title: Neo_6_bud


title: Lp2_2


title: Kyoto

value: Kyoto


title: Litva

value: Litva


title: Kondara

value: Kondara


title: Kz_9


title: Kro_0


title: Lm_2


title: Krot_0


title: Kin_0


title: Kin_0_bud


title: Kl_5


title: Knox_18


title: Kil_0


title: Kas_1


title: Kelsterbach_4


title: TSC22D3

city: Berkeley

first: Nir

last: Yosef

address: Berkeley

department: EECS

institute: UC Berkeley

data_processing:
ChIP-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using Bowtie (Langmead et al., 2009). Duplicated reads were filtered (allowing no more than 2 reads at the same location).
Genome_build: mm9
Supplementary_files_format_and_content: TDF format; generated with igvtools count program

source_name: Th17 cells

growth_protocol: C57BL/6 mice were purchased from The Jackson Laboratory. All animals were housed and maintained in a conventional pathogen-free facility at the Harvard Institute of Medicine in Boston, MA.  All experiments were performed in accordance to the guidelines outlined by the Harvard Medical Area Standing Committee on Animals at the Harvard Medical School (Boston, MA).

extract_protocol:
CD4+CD62LhighCD25− naive CD4+ T cells were purified by FACS sorting following a MACS bead isolation of CD4+ cells as previously described (Xiao et al., 2008).
ChIP was carried out as described previously (Marson et al., 2007). Briefly, ~50-100 x 106 cells for each ChIP were crosslinked with formaldehyde, lysed, and fragmented with a Misonix Sonicator 3000. Following immunoprecipitation with anti-TSC22D3 (ABCAM), the protein-DNA crosslinks were reversed and DNA was purified and used for the preparation of Illumina sequencing libraries.  Purified ChIP DNA was used to prepare ChIP-seq libraries using the Illumina TruSeq DNA Sample Preparation v2 kit.

treatment_protocol: Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter.  Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.  For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). Cells were cultured for 48 hours.

value: Th17 cells

tag: chip antibody manufacturer

value: Abcam


title: PROCR Knockdown 4_18_12__48h_procr__2

description: PROCR Knockdown

data_processing:
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using Bowtie
We ran RSEM v1.1138 with default parameters on these alignments to estimate expression levels
Genome_build: mm9
Supplementary_files_format_and_content: text files produced by RSEM; data is in transcirpts per million (TPM)

extract_protocol:
48h post-activation, culture media was removed from each well and samples were gently washed with 100 μL of PBS before being lysed in 20 μL of buffer TCL (Qiagen) supplemented with 2-mercaptoethanol (1:100 by volume).  After mRNA was harvested in Turbocapture plates (Qiagen) and converted to cDNA using Sensiscript RT enzyme (Qiagen), qRT-PCR was used to validate both knockdown levels and phenotypic changes relative to 8-12 non-targeting siRNA control samples.  A 60% reduction in target mRNA was used as the knockdown threshold.
Validated single stranded cDNAs from the NW-mediated knockdowns were converted to double stranded DNA using the NEBNext mRNA Second Strand Synthesis Module (New England BioLabs) according to the manufacturer’s recommendations. The samples were then cleaned using 0.9x SPRI beads (Beckman Coulter). Libraries were prepared using the Nextera XT DNA Sample Prep Kit (Illumina), quantified, pooled, and then sequenced on the HiSeq 2500 (Illumnia) to an average depth 20M reads.

treatment_protocol: Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. 4 x 4 mm silicon nanowire (NW) substrates were prepared and coated with 3 μL of a 50 μM pool of four siGENOME siRNAs (Dharmcon) in 96 well tissue culture plates.  Briefly, 150,000 sorted naïve T cells were seeded on siRNA-laced NWs in 10 μL of complete media and placed in a cell culture incubator (370C, 5% CO2) to settle for 45 minutes before full media addition. These samples were left undisturbed for 24 hours to allow target transcript knockdown. Afterward, siRNA-transfected T cells were activated with αCd3/Cd28 dynabeads (Invitrogen), according to the manufacturer’s recommendations, under Th17 polarization conditions (2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec)).

tag: cell type

tag: batch

value: PROCR Knockdown


title: Non-targeting control 4_18_12__48h_nt__2_2

description: Non-targeting control

tag: strain

value: Non-targeting control


title: Je_0


title: Non-targeting control 4_18_12__48h_nt__1_4

description: Non-targeting control


title: Non-targeting control 4_18_12__48h_nt__1_3

description: Non-targeting control


title: Is_0_bud


title: Is_0


title: In_0


title: Non-targeting control 3_9_12__48h_NT__12

description: Non-targeting control


title: Hs_0


title: HR_5_bud


title: Hey_1


title: Non-targeting control 3_9_12__48h_NT__11

description: Non-targeting control


title: Ha_0


title: FAS Knockdown 3_9_12__48h_Fas__1

description: FAS Knockdown

value: FAS Knockdown


title: WCE

description: WCE


title: Gy_0

value: leaf


title: IKZF4 Knockdown 3_9_12__48h_IKZF4__1

description: IKZF4 Knockdown

value: IKZF4 Knockdown


title: Gre_0


title: Gu_0


title: ZEB1 Knockdown 3_2_12__48h_Zeb1__4

description: ZEB1 Knockdown

value: ZEB1 Knockdown


title: SMARCA4 Knockdown 3_2_12__48h_SMARCA4__3

description: SMARCA4 Knockdown

value: SMARCA4 Knockdown


title: EGR2 Knockdown 3_9_12__48h_EGR2__4

description: EGR2 Knockdown

value: EGR2 Knockdown


title: Gr_1


title: Non-targeting control 3_2_12__48h_NT__2_4

description: Non-targeting control


title: Non-targeting control 3_2_12__48h_NT__1_4

description: Non-targeting control


title: Jm_0


title: Got_7


title: Non-targeting control 4_18_12__48h_nt__1_2

description: Non-targeting control


title: Gel_1


title: ETV6 Knockdown 3_2_12__48h_ETV6__3

description: ETV6 Knockdown

value: ETV6 Knockdown


title: Non-targeting control 2_16_nt_3_1

description: Non-targeting control


title: Gie_0


title: IRF8 Knockdown 3_2_12__48h_IRF8__2

description: IRF8 Knockdown

value: IRF8 Knockdown


title: Non-targeting control 3_9_12__48h_NT__13

description: Non-targeting control


title: Non-targeting control 2_16_nt_2_3

description: Non-targeting control


title: Non-targeting control 2_16_nt_2_2

description: Non-targeting control


title: MINA Knockdown 2_16_mina_6

description: MINA Knockdown

value: MINA Knockdown


title: Et_0


title: Ga_0


title: Fr_2_bud

value: mixed stage inflorescence


title: Fr_2


title: Fi_0


title: Est

value: Est


title: Es_0


title: Ema_1_bud


title: Ema_1


title: Non-targeting control 2_16_nt_2_4

description: Non-targeting control


title: Non-targeting control 12_21_11__48h_NT__1_2

description: Non-targeting control


title: Ei_2


title: Non-targeting control 12_21_11__48h_NT__1_1

description: Non-targeting control


title: Dja_1


title: El_0


title: Gifu_2


title: Di_G


title: Non-targeting control 1_26_12__48h_NT__1_2

description: Non-targeting control


title: Non-targeting control 12_21_11__48h_NT__1_7

description: Non-targeting control


title: Non-targeting control 12_9_11__48h_NT__1_2

description: Non-targeting control


title: Non-targeting control 1_26_12__48h_NT__2_2

description: Non-targeting control


title: SP4 Knockdown 1_26_12__48h_SP4__1

description: SP4 Knockdown

value: SP4 Knockdown


title: Non-targeting control 12_9_11__48h_NT__2_4

description: Non-targeting control


title: POU2Af1 Knockdown 12_21_11__48h_pou2f1a__8

description: POU2Af1 Knockdown

value: POU2Af1 Knockdown


title: Zdr-1

data_processing:
Bioscope version 1.3 was used to align .csfasta and .qual files to SNP-substituted reference genomes for each accession using default parameters which allows up to 10 locations per sequenced read.
Cufflinks version 1.1 was used to quantify gene expression values using the following parameters: -F 0 –b –N –library-type fr-secondstrand –G TAIR10.gtf.
Genome_build: TAIR10
Supplementary_files_format_and_content: Expression values for all genes in the TAIR10 reference annotation as defined by Cufflinks version 1.1

extract_protocol:
RNA was isolated using the Qiagen Plant RNeasy kit (Qiagen) following the manufacturer’s instructions.
RNA-Seq libraries were prepared according to the described methods in Li, L. et al. Linking photoreceptor excitation to changes in plant architecture. Genes Dev 26, 785-790 (2012).


title: TSC22D3 Knockdown 12_9_11__48h_TSC22d3__2

description: TSC22D3 Knockdown

value: Th17 cells

value: TSC22D3 Knockdown


title: Db_1


title: Com_1


title: Da_1_12


title: Wt-5


title: Ws-2


title: Yo-0


title: Wl-0


title: En_D


title: Co_1_bud


title: Wc-1


title: Wa-1


title: Vind-1


title: Cnt_1


title: Chi_0


title: Ven-1


title: Cal_0


title: Chat_1


title: Van-0


title: Cvi_0


title: Uk-1


title: Ty-0


title: Ultrecht

value: Ultrecht


title: Tul-0


title: Col_0


title: Tu-0


title: Bu_0


title: Ca_0


title: Ts-1


title: Bs_1


title: Tol-0


title: Bsch_0


title: Ting-1


title: Ta-0


title: Tamm-2


title: Uod-1


title: Sus-1


title: Su-0


title: Stw-0


title: Sq-8


title: Sp-0


title: Tscha-1


title: Si-0


title: Ann_1


title: Ba_1


title: Bla_1


title: Bik_1


title: Bl_1


title: Appt_1


title: Anholt_1


title: Baa_1


title: Bor_4_bud


title: Benk_1


title: Bor_4


title: Anz_0


title: Br_0_bud


title: Sg-1


title: Amel_1


title: Sei-0


title: Boot_1


title: Altai_5


title: An_1


title: Ag_0


title: Se-0


title: Ag_0_bud


title: Ak_1


title: RRs-10


title: RRs-7


title: Abd_0


title: Rmx-A02


title: Rld-1


title: Seattle-0


title: Pu2-23


title: Pla-0


title: Per-1


title: Ob-0


title: Pu2-7


title: Pog-0


title: Ove-0


title: Aa_0


title: Pna-17


title: Np-0


title: Rhen-1


title: Neo-6


title: Nw-0


title: Nc-1


title: Old-1


title: Nok-3