title: GCB 2

data_processing:
genome build: hg18
Illumina Casava1.8 software used for basecalling.
RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml)

source_name: Tonsillar Germinal Center B cells

extract_protocol:
RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturer’s protocol.
ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

value: Tonsillar Germinal Center B cells

tag: purification

value: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker CD77


title: GCB 3

status: Public on May 13 2013

type: SRA

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

country: USA

institute: Weill Cornell Medical College

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: GCB 1


title: GCB 4


title: NB 3

source_name: Tonsillar Naïve B cells

value: Tonsillar naive B cells

value: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker IgD


title: NB 2


title: NB 4


title: GCB H3K27me3

library_source: genomic

molecule: genomic DNA

extract_protocol:
ChIP was performed as previously described (Ci et al., Blood, 2009). Briefly, 108 cells were fixed with 1% formaldehyde, lysed, and sonicated (Branson Sonicator; Branson) leading to a DNA average size of 200 bp. Five µg of antibodies were added to the precleared sample and incubated overnight at 4°C. The complexes were purified using protein-A beads (Roche) followed by elution from the beads and decrosslinking. DNA was purified using PCR purification columns (QIAGEN).
ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

tag: chip antibody

value: anti-H3K27me3 (Millipore, 07-449)


title: NB 1


title: GCB Input 1


title: WSUDLCL2 scrambled

data_processing:
genome build: hg19
Illumina Casava1.8 software used for basecalling.
RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml)

source_name: WSUDLCL2 cell line

value: WSUDLCL2 cell line

value: transuced with control scrambled shRNA for 7 days


title: NB H3K27me3


title: GCB H3K4me3 2

value: anti-H3K4me3 (Abcam, ab8580)


title: shh1_65_point_mutant  BSseqs - complementation replicate

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

description: genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane

data_processing:
ChIPseq reads were filtered for full-length (50bp) reads.  Reads containing adapter were discarded.  Small RNA reads were demultiplexed (perfect matches to each index were required) and then filtered for average QC score > 30. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 0 mismatches and retaining only uniquely mapping reads. For samples 1 and 2 the NuGen IR kit necesitates using the first 4 bp of a reads for demultiplexing purposes, therefore these reads were mapped with the first four bp trimmed (effective read length = 46bp). For samples 3-5 the NuGen DR kit has a separate dedicated read allowing the full 50bp reads to be mapped.
Genome_build: TAIR8
Supplementary_files_format_and_content: Fixed step (50bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 50bp bins / total unique mapping reads)
Small RNA reads were demultiplexed (perfect matches to each index were required) and then filtered for average QC score > 30.  Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >18 nt and <28 nt in length after trimming were retained.  Reads with no identifiable adapter were discarded.  Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 0 mismatches and retaining only uniquely mapping reads. As Samples 6 and 7 are technical replicates (resequencing of same libraries in a different flow cell).
Genome_build: TAIR8
Supplementary_files_format_and_content: Fixed step (50bp) UCSC Genome Browser wiggle format files for each chromosome for each size class of small RNAs (18 nt through 28 nt) with each bin given a value corresponding to the relative read density at that location for the corresponding size class (reads in 50bp bins / total mapping small RNA reads of all size classes)
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads. Only cytosines covered with at least 5 reads in all libraries (samples 19-21 + previously published Col and nrpe1 || samples 22-29 ) were considered. Samples 27 and 28 are technical replicates carried out to ensure comparable coverage to other libraries - reads from both lanes were merged for subsequent analysis
Genome_build: TAIR8
Supplementary_files_format_and_content: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).

organism: Arabidopsis thaliana

source_name: seedling tissue (10-day)

extract_protocol: converted and fragmented genomic DNA library as described in Stroud et al., Cell 2012

tag: tissue

value: seedling tissue (10-day)

tag: genotype

value: shh1-1 w/ shh1-3XMYC (D141A point mutant)

tag: ecotype

value: Columbia


title: shh1_240_WT  BSseqs - complementation replicate

value: shh1-1 w/ shh1-3XMYC (wild-type protein)


title: shh1_16_point_mutant  BSseqs - complementation replicate

value: shh1-1 w/ shh1-3XMYC (Y140A point mutant)


title: shh1_32_point_mutant  BSseqs - complementation replicate

value: shh1-1 w/ shh1-3XMYC (F162AF165A point mutant)


title: shh1_109_point_mutant  BSseqs - complementation replicate - A and B

value: shh1-1 w/ shh1-3XMYCC (Y212A point mutant)


title: OCI-Ly1 shEZH2 3

source_name: OCI-Ly1 cell line

value: OCI-Ly1 cell line

value: transduced with anti-EZH2 shRNA #3 for EZH2 for 7 days


title: OCI-Ly1 scrambled


title: OCI-Ly1 EZH2

value: anti-EZH2 (Millipore, 07-689, lot DAM1834941)


title: NB H3K4me3 2


title: shh1 BSseqs - complementation replicate


title: Col BSseqs - complementation replicate

value: Wild type


title: drm2 BSseq

value: drm2-2 mutant


title: SUDHL5 shEZH2 3

source_name: SUDHL5 cell line

value: SUDHL5 cell line


title: SUDHL5 scrambled


title: WSUDLCL2 shEZH2 2

value: transduced with anti-EZH2 shRNA #2 for EZH2 for 7 days


title: GCB Input 2

value: Tonsillar Germinal Center B cells

value: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker CD77


title: NB Input 1

value: Tonsillar naive B cells

value: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker IgD


title: WSUDLCL2 shEZH2 3

value: WSUDLCL2 cell line


title: NB H3K4me3 1

value: anti-H3K4me3 (Abcam, ab8580)


title: GCB H3K4me3 1


title: SUDHL5 shEZH2 2


title: shh1 BSseq

value: seedling tissue (10-day)

value: shh1-1 mutant

value: Columbia


title: Farage scrambled

source_name: Farage cell line

value: Farage cell line

value: transduced with control scrambled shRNA for 7 days


title: Farage shEZH2 3

value: transduced with anti-EZH2 shRNA #3 for EZH2 for 7 days


title: IgG_Control_Cdk9

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: The Weatherall Institute of Molecular Medicine

data_processing:
36 bp raw reads were mapped against mm9/NCBI build 37.1 of the mouse genome with ELAND (Illumina).
Uniquely mapped reads were extended to 200 bp and then transformed into the genome-wide reads density (coverage) with the ShortRead Bioconductor package.
The coverage from ChIP and IgG control was then normalized to have equal levels of background signal.
The method used to normalize was modified from Peakseq (Rozowsky et al. 2009).
After normalization, tracks of coverage profiles for all factors and IgG control were uploaded and visualized by the UCSC genome browser.
The coverage from all factors was subtracted from the normalized coverage from the corresponding IgG controls.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BigWig files

organism: Mus musculus

source_name: Murine erythroleukemia (MEL) cells

growth_protocol: MEL cell lines were maintained in DMEM supplemented with 10% fetal calf serum and penicillin/streptomycin.

extract_protocol:
10 ng of ChIPped DNA was end-repaired, ligated to adapters, size selected on gel (200±25 bp range) and PCR amplified using Phusion polymerase. Cluster generation was performed using the Illumina Cluster Reagents preparation.
ChIP-Seq library was prepared according to the Illumina protocol (www.illumina.com).

tag: cell line

value: non-induced C88 MEL cells

value: anti-IgG


title: Farage shEZH2 2


title: OCI-Ly1 shEZH2 2

value: OCI-Ly1 cell line


title: NB Input 2


title: RNAPII_ChIPSeq

value: RNA Pol II antibody (Santa Cruz Biotechnology, N20, sc899)


title: Cdk9_ChIPSeq

value: CDK9 C20 antibody (Santa Cruz Biotechnology, C20, sc-484)


title: OCI-Ly7 scrambled

source_name: OCI-Ly7 cell line

value: OCI-Ly7 cell line

value: transuced with control scrambled shRNA for 7 days


title: shh1_65_point_mutant  small RNAs - complementation replicate

description: 15-30nt isolated small RNAs from total RNA Trizol preparation; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/9 lane

source_name: floral tissue

extract_protocol:
Trizol extraction followed by PEG and then urea-PAGE fractionation
Illumina TruSeq small RNA

value: floral

value: shh1-1 w/ shh1-3XMYC (D141A point mutant)


title: OCI-Ly7 shEZH2 3


title: BCL1 Y641F H3K27me3

data_processing:
genome build: mm9
Illumina Casava1.8 software used for basecalling.
RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml)

source_name: BCL1 cell line transduced with Y641F EZH2


title: BCL1 Y641N H3K27me3

source_name: BCL1 cell line transduced with Y641N EZH2


title: shh1_109_point_mutant  small RNAs - complementation replicate

value: shh1-1 w/ shh1-3XMYC (Y212A point mutant)


title: shh1_32_point_mutant  small RNAs - complementation replicate

value: shh1-1 w/ shh1-3XMYC (F162AF165A point mutant)


title: shh1_16_point_mutant  small RNAs - complementation replicate

value: shh1-1 w/ shh1-3XMYC (Y140A point mutant)


title: IgG_Control_RNAPII


title: nrpd1 BSseq

value: seedling tissue (10-day)

value: nrpd1-4 mutant


title: BCL1 WT EZH2 H3K27me3

source_name: BCL1 cell line transduced with WT EZH2

value: BCL1 cell line transduced with WT EZH2


title: shh1 small RNAs - complementation replicate

value: Columbia


title: BCL1 Y641N GSK669

value: BCL1 cell line transduced with Y641N EZH2

value: treated with 0.5uM GSK669 for 3 days


title: WSUDLCL2 GSK669

value: WSUDLCL2 cell line

value: treated with 2uM GSK669 for 7 days


title: BCL1 Y641N GSK343

value: treated with 0.5uM GSK343 for 3 days


title: OCI-Ly7 shEZH2 2

value: transduced with anti-EZH2 shRNA #2 for EZH2 for 7 days


title: Col small RNAs - complementation replicate

value: Wild type


title: drm2 small RNAs

description: 15-30nt isolated small RNAs from total RNA Trizol preparation; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane


title: BCL1 Y641F GSK669

value: BCL1 cell line transduced with Y641F EZH2


title: Pfeiffer GSK343

source_name: Pfeiffer cell line

value: Pfeiffer cell line

value: treated with 2uM GSK343 for 7 days


title: BCL1 Y641F GSK343


title: shh1_240_WT  small RNAs - complementation replicate

value: floral

value: shh1-1 w/ shh1-3XMYC (wild-type protein)


title: BCL1 WT EZH2 GSK669


title: OCI-Ly1 GSK343

value: OCI-Ly1 cell line


title: nrpe1 small RNAs


title: OCI-Ly1 GSK669


title: WSUDLCL2 GSK343


title: SUDHL5 GSK669

value: SUDHL5 cell line


title: Col small RNAs - technical replicate


title: BCL1 WT EZH2 GSK343


title: nrpd1 small RNAs


title: SUDHL5 GSK343


title: ChIP_H3K4me3_C2C12_6hDAPT_repl1

city: Nijmegen

first: Arjen

last: Brinkman

address: NCMLS #274, Geert Grooteplein Zuid 30

department: Molecular Biology

country: Netherlands

institute: Radboud University, Nijmegen Center for Molecular Life Sciences

description: Sample 33

data_processing:
ChIP-seq. Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the mouse (mm9) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. Duplicated reads were discarded to obtain a non-redundant set. Further analysis was performed using the 36 bp sequence reads. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Mus Musculus mm9 genome assembly.
Strand-specific RNA-seq. Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the mouse (mm9) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. Further analysis was performed using the 36 bp sequence reads. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Mus Musculus mm9 genome assembly.
Genome_build: mm9
Supplementary_files_format_and_content: bed, wig, RPKMs, peaks

growth_protocol: C2C12 cells were cultured in DMEM medium supplemented with 20% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen) at 37 °C in 5% CO2 atmosphere

extract_protocol:
Cells were trypsinized according to standard procedures. A cell suspension with cell density of 5 million/ml was made in cell medium. Cells were subsequently cross-linked for 30 min at RT in medium plus 1% formaldehyde and 1/14 volume of buffer A (0.1M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM HEPES pH7.6), quenched with 0.125 M glycine and washed at 4°C with the following buffers: (i) PBS, (ii) buffer B: 0.25% Triton-X-100, 10mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, (iii) buffer C: 0.15M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50 mM HEPES pH7.6. During each washing step cells were rotated for 10 min at 4°C and subsequently centrifuged for 7 min at 500g 4°C. Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton-X-100, 0.15M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, 1x protease inhibitor cocktail complete (Roche)) at 20 million/ml and sheared using a Bioruptor (Diagenode) with the following settings: high power, 30s on/off, 18 cycles. Sonicated chromatin was centrifuged for 5 min at 13000 rpm in eppendorf tubes, supernatant was snap-freezed in liquid nitrogen and stored at -80 °C or directly used in ChIPs. For one ChIP, 100 µl chromatin was incubated with 2 µg antibody, 20 µl 50% protein A/G bead (Santa Cruz), in 1x ChIP incubation buffer with 0.1% BSA in a total volume of 300 µl o/n at 4°C. Beads were then washed with the following buffers: twice with buffer1: 0.1% SDS, 0.1% NaDOC, 1% Triton-X-100, 0.15M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, once with buffer2: 0.1% SDS, 0.1% NaDOC, 1% Triton-X-100, 0.5M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, once with buffer3: 0.25M LiCl, 0.5% NaDOC, 0.5% NP-40, 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, and twice with buffer4: 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6. During each washing step beads were rotated for 5 min at 4°C and subsequently centrifuged for 2 min at 4000 rpm 4°C. Precipitated chromatin was then eluted from beads in 200 µl elution buffer (1% SDS, 0.1M NaHCO3) for 40 min at RT. Materials (precipitated chromatin or input chromatin in elution buffer) were decross-linked for 5h at 65 °C with addition of 200 mM NaCl. DNA was purified on QIAquick spin columns according to QIAGEN protocols. For sequencing, 6-8 ChIPs were pooled.
Strand-specific RNA-seq using RiboZero. Total RNA was extracted using RNeasy Mini and Micro kit (Qiagen) following the manufacturer instruction. Ribosomal RNA was removed from 200 ng total RNA using the Ribo-Zero rRNA Removal Kit Low Input for Human/Mouse/Rat (Epicentre Biotechnologies), according to the manufacturer’s protocol. RNA was subsequently fragmented in fragmentation buffer (40 mM Tris-Ac pH8.2, 100 mM KAc, 30 mM MgAc) for 90 s at 95 ºC and purified by ethanol purification. cDNA was synthesized using random hexamers by Superscript III Reverse Transcriptase (Invitrogen), in presence of 6 ng/µl ActinomycinD. cDNA was purified (MinElute Reaction Cleanup Kit, QIAGEN) and subjected to second strand synthesis by E.Coli DNA Polymerase I (Invitrogen) and E.Coli DNA Ligase (New England Biolabs) in the presence of RNaseH (Ambion). For second strand synthesis dUNTPs were used, containing dUTP instead of dTTP. After second strand synthesis, ds-cDNA was purified (MinElute Reaction Cleanup Kit, QIAGEN) and prepared for Illumina sequencing according to standard procedures using the DNA sample Prep Kit (Illumina, cat# IP-102–1001) and starting from the A-tailing step. After ligation of adapters, a 200 bp band is excised using the E-Gel system (Invitrogen). Before final PCR amplification uracil containing second strand DNA was removed by USER enzyme (New England Biolabs) for 15 min at 37 ºC followed by 10 min at 95 ºC in 1x Phusion Buffer (Finnzymes).
1 to 20 ng was used for library preparation using the ChIP-seq DNA sample Prep Kit (Illumina, cat# IP-102–1001) using the recommended protocol. After ligation of adapters, a 300 bp band is excised using the E-Gel system (Invitrogen), which correspond to a 234 bp fragment of genomic DNA. PCR enrichment of adapter-ligated DNA was done using 14 cycles of PCR.

treatment_protocol:
DAPT treatments: DAPT dissolved in DMSO (Calbiochem) was added to Fc only dishes at a final concentration of 20µM for 6h or 24h.
Delta treatments: For ligand-dependant activation of Notch signaling, cells were grown in the presence of the extracellular domain of Delta-like 1 fused to the Fc fragment of human IgG (Hicks et al., 2002) (kindly provided by N.Gupta upon permission from G.Weinmaster). Culture dishes were first coated with 10 µg/ml anti-Fc antibody for 1h at RT. Dishes were then incubated with conditioned medium from transfected 293T cells expressing the fusion proteins, for 1h at RT. C2C12 cells were plated in fresh medium and grown for 6h or 24h on the immobilized-ligand containing dishes.
GFP or NICDGFP protein induction: the cells were induced for 8h with 2ug/ml Doxycyclin.

value: Mouse myoblast cell line (established from thigh muscle from an adult C3H strain female)

tag: technique

value: ChIP-sequencing

tag: chip antibody vendor

value: Diagenode


title: ChIP_H3K4me3_C2C12_6hDelta_repl1

description: Sample 34


title: Col small RNAs

value: Columbia


title: shh1 PolIV ChIP replicate 2

description: immunoprecipitated formaldehyde-crosslinked leaf tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/3 lane

extract_protocol:
extracted by ChIP followed by phenol-chloroform exctract as described
NuGen Ovation Ultralow DR sample prep kit

value: shh1-1; nrpd1-4 with NRPD1-3XFLAG transgene

tag: antibody

value: FLAG antibody


title: Farage GSK669

value: Farage cell line

value: treated with 2uM GSK669 for 7 days


title: Farage GSK343


title: PolIV ChIP replicate 2

value: nrpd1-4 with NRPD1-3XFLAG transgene


title: ChIP_H3K4me1_C2C12_6hDelta_repl1

description: Sample 32


title: OCI-Ly7 GSK669

value: OCI-Ly7 cell line


title: Columbia ChIP replicate 2

value: Wild type


title: ChIP_H3K4me1_C2C12_6hDAPT_repl1

description: Sample 31


title: ChIP_H3K27ac_C2C12_6hDelta_repl1

description: Sample 30


title: Columbia ChIP

description: immunoprecipitated formaldehyde-crosslinked leaf tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/8 lane

extract_protocol:
extracted by ChIP followed by phenol-chloroform exctract as described
NuGen Ovation Ultralow IR sample prep kit


title: OCI-Ly7 GSK343


title: ChIP_H3K27ac_C2C12_6hDAPT_repl1

description: Sample 29


title: LSY-2 GFP L4 v2 C.elegans Input Rep2

status: Public on May 11 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

organism: Caenorhabditis elegans

source_name: LSY-2 L4 v2 InputRep2

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

tag: strain

value: OP240(official name :OP240 genotype :unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by :Unknown )

tag: developmental stage

tag: Sex

value: Hermaphrodite


title: LSY-2 GFP L4 v2 C.elegans ChIP Rep1

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

source_name: LSY-2 L4 v2 ChIPRep1


title: LSY-2 GFP L2 v2 C.elegans ChIP Rep1

description: input DNA

source_name: LSY-2 L2 v2 ChIPRep1


title: LSY-2 GFP L2 v2 C.elegans ChIP Rep2

description: input DNA

source_name: LSY-2 L2 v2 ChIPRep2


title: LSY-2 GFP L4 v2 C.elegans Input Rep1

description: input DNA

source_name: LSY-2 L4 v2 InputRep1


title: LSY-2 GFP L2 v2 C.elegans Input Rep1

source_name: LSY-2 L2 v2 InputRep1


title: CEH-28 GFP L3 C.elegans ChIP Rep2

source_name: CEH-28 L3 ChIPRep2

value: OP241(official name :OP241 genotype :unc119(ed3);wgIs241(ceh-38::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-38::EGFP fusion protein is expressed in the correct ceh-38 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-38 transcription factor. made_by :Unknwon )


title: CEH-28 GFP L3 C.elegans ChIP Rep1

source_name: CEH-28 L3 ChIPRep1


title: CEH-28 GFP L3 C.elegans Input Rep1

description: input DNA

source_name: CEH-28 L3 InputRep1


title: Pfeiffer GSK669

value: Pfeiffer cell line


title: CEH-28 GFP L4 C.elegans Input Rep2

source_name: CEH-28 L4 InputRep2


title: CEH-28 GFP L4 C.elegans Input Rep1

source_name: CEH-28 L4 InputRep1


title: CEH-28 GFP L4 C.elegans ChIP Rep2

description: input DNA

source_name: CEH-28 L4 ChIPRep2


title: CEH-28 GFP L4 C.elegans ChIP Rep1

description: input DNA

source_name: CEH-28 L4 ChIPRep1


title: PolIV ChIP

source_name: floral tissue

value: floral


title: NHR-10 GFP L4 C.elegans Input Rep2

source_name: NHR-10 L4 InputRep2

value: OP239(official name :OP239 genotype :unc119(ed3);wgIs239(nhr-10::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-10::EGFP fusion protein is expressed in the correct nhr-10 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-10 transcription factor. made_by :Unknown )


title: NHR-10 GFP L4 C.elegans ChIP Rep1

description: input DNA

source_name: NHR-10 L4 ChIPRep1


title: ZTF-4 GFP L1 C.elegans ChIP Rep1

description: input DNA

source_name: ZTF-4 L1 ChIPRep1

value: OP322(official name :OP322 genotype :unc-119(ed3); wgIs322(ztf-4::TY1 EGFP FLAG; unc119(+)) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by :Bob Waterston's lab from UW )

value: L1 26dC


title: NHR-10 GFP L4 C.elegans ChIP Rep2

description: input DNA

source_name: NHR-10 L4 ChIPRep2


title: ZTF-4 GFP L1 C.elegans ChIP Rep2

description: input DNA

source_name: ZTF-4 L1 ChIPRep2

value: unc-119(ed3); wgIs322(ztf-4::TY1 EGFP FLAG; unc119(+))


title: ZTF-4 GFP L1 C.elegans Input Rep2

source_name: ZTF-4 L1 InputRep2


title: NHR-10 GFP L4 C.elegans Input Rep1

source_name: NHR-10 L4 InputRep1


title: LSY-2 GFP L2 v2 C.elegans Input Rep2

source_name: LSY-2 L2 v2 InputRep2


title: ZTF-4 GFP L1 C.elegans Input Rep1

source_name: ZTF-4 L1 InputRep1


title: LSY-2 GFP L4 v2 C.elegans ChIP Rep2

source_name: LSY-2 L4 v2 ChIPRep2


title: NHR-21 GFP L2 C.elegans ChIP Rep2

description: input DNA

source_name: NHR-21 L2 ChIPRep2

value: OP361(official name :OP361 genotype :unc119(ed3);wgIs361(nhr-21::TY1-GFP-3xFLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-21::EGFP fusion protein is expressed in the correct nhr-21 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-21 transcription factor. made_by :Unknown )


title: CEH-28 GFP L3 C.elegans Input Rep2

description: input DNA

source_name: CEH-28 L3 InputRep2


title: NHR-21 GFP L2 C.elegans Input Rep2

source_name: NHR-21 L2 InputRep2


title: NHR-21 GFP L2 C.elegans ChIP Rep1

description: input DNA

source_name: NHR-21 L2 ChIPRep1


title: ZTF-4 GFP L2 C.elegans ChIP Rep2

source_name: ZTF-4 L2 ChIPRep2


title: NHR-21 GFP L2 C.elegans Input Rep1

source_name: NHR-21 L2 InputRep1


title: ZTF-4 GFP L2 C.elegans ChIP Rep1

source_name: ZTF-4 L2 ChIPRep1


title: ZTF-4 GFP L2 C.elegans Input Rep1

description: input DNA

source_name: ZTF-4 L2 InputRep1


title: LIN-13 GFP L4 C.elegans ChIP Rep2

description: input DNA

source_name: LIN-13 L4 ChIPRep2

value: OP49(official name :OP49 genotype :unc119(ed3);wgIs49(lin-13::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by :Unknown )


title: LIN-13 GFP L4 C.elegans Input Rep2

source_name: LIN-13 L4 InputRep2


title: LIN-13 GFP L2 C.elegans ChIP Rep2

description: input DNA

source_name: LIN-13 L2 ChIPRep2


title: LIN-13 GFP L4 C.elegans Input Rep1

source_name: LIN-13 L4 InputRep1


title: LIN-13 GFP L2 C.elegans Input Rep1

source_name: LIN-13 L2 InputRep1


title: LIN-13 GFP L2 C.elegans ChIP Rep1

description: input DNA

source_name: LIN-13 L2 ChIPRep1


title: LIN-13 GFP L2 C.elegans Input Rep2

source_name: LIN-13 L2 InputRep2


title: LIN-13 GFP L1 C.elegans ChIP Rep2

description: input DNA

source_name: LIN-13 L1 ChIPRep2


title: LIN-13 GFP L1 C.elegans ChIP Rep1

description: input DNA

source_name: LIN-13 L1 ChIPRep1


title: NHR-12 GFP EMB C.elegans ChIP Rep2

description: input DNA

source_name: NHR-12 EMB ChIPRep2

value: OP318(official name :OP318 genotype :unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross :3 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by :Bob Waterston's lab from UW )

value: embryo

tag: sex type

value: mixed Male and Hermaphrodite population


title: LIN-13 GFP L1 C.elegans Input Rep1

source_name: LIN-13 L1 InputRep1


title: NHR-12 GFP EMB C.elegans Input Rep2

source_name: NHR-12 EMB InputRep2


title: NHR-12 GFP EMB C.elegans Input Rep1

source_name: NHR-12 EMB InputRep1


title: NHR-12 GFP L3 C.elegans ChIP Rep2

description: input DNA

source_name: NHR-12 L3 ChIPRep2


title: NHR-12 GFP EMB C.elegans ChIP Rep1

description: input DNA

source_name: NHR-12 EMB ChIPRep1


title: NHR-12 GFP L3 C.elegans ChIP Rep1

description: input DNA

source_name: NHR-12 L3 ChIPRep1


title: NHR-12 GFP L3 C.elegans Input Rep2

source_name: NHR-12 L3 InputRep2


title: NHR-12 GFP L3 C.elegans Input Rep1

source_name: NHR-12 L3 InputRep1


title: ELT-3 GFP EMB C.elegans ChIP Rep2

description: input DNA

source_name: ELT-3 EMB ChIPRep2

value: OP75(official name :OP75 genotype :unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. made_by :R Waterston )


title: ZTF-4 GFP L2 C.elegans Input Rep2

description: input DNA

source_name: ZTF-4 L2 InputRep2


title: ELT-3 GFP EMB C.elegans Input Rep2

source_name: ELT-3 EMB InputRep2


title: ELT-3 GFP EMB C.elegans ChIP Rep1

description: input DNA

source_name: ELT-3 EMB ChIPRep1


title: LIN-13 GFP L4 C.elegans ChIP Rep1

description: input DNA

source_name: LIN-13 L4 ChIPRep1


title: UNC-39 GFP L2 C.elegans Input Rep2

description: input DNA

source_name: UNC-39 L2 InputRep2

value: OP186(official name :OP186 genotype :unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The UNC-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by :Unknown )


title: UNC-39 GFP L2 C.elegans ChIP Rep2

source_name: UNC-39 L2 ChIPRep2

value: unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;unc119)


title: ELT-3 GFP EMB C.elegans Input Rep1

source_name: ELT-3 EMB InputRep1


title: UNC-39 GFP L2 C.elegans ChIP Rep1

source_name: UNC-39 L2 ChIPRep1


title: UNC-39 GFP L2 C.elegans Input Rep1

description: input DNA

source_name: UNC-39 L2 InputRep1


title: UNC-39 GFP EMB C.elegans ChIP Rep2

description: input DNA

source_name: UNC-39 EMB ChIPRep2


title: shh1 small RNAs

source_name: floral tissue

value: Columbia


title: LIN-13 GFP L1 C.elegans Input Rep2

source_name: LIN-13 L1 InputRep2

value: Hermaphrodite


title: UNC-39 GFP EMB C.elegans Input Rep2

source_name: UNC-39 EMB InputRep2


title: nhr-23 GFP L2 C.elegans Input Rep1

description: input DNA

source_name: nhr-23 L2 InputRep1

value: OP43(official name :OP43 genotype :unc-119(ed3); wgIs43(nhr-23::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The NHR-23::EGFP fusion protein is expressed in the correct nhr-23 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-223 transcription factor. made_by :Bob Waterston's lab from UW )


title: nhr-23 GFP L2 C.elegans ChIP Rep2

source_name: nhr-23 L2 ChIPRep2

value: unc-119(ed3); wgIs43(nhr-23::TY1 EGFP FLAG; unc-119)


title: ELT-1 GFP L2 C.elegans ChIP Rep2

description: input DNA

source_name: ELT-1 L2 ChIPRep2

value: OP354(official name :OP354 genotype :unc119(ed3);wgIs354(elt-1::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by :Bob Waterston's lab from UW )


title: ELT-1 GFP L2 C.elegans Input Rep2

source_name: ELT-1 L2 InputRep2


title: ELT-1 GFP L2 C.elegans ChIP Rep1

description: input DNA

source_name: ELT-1 L2 ChIPRep1


title: JUN-1 GFP L3 C.elegans ChIP Rep2

description: input DNA

source_name: JUN-1 L3 ChIPRep2

value: OP234(official name :OP234 genotype :unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by :Unknown )


title: SKN-1 GFP L4 C.elegans Input Rep2

description: input DNA

source_name: SKN-1 L4 InputRep2

value: OP342(official name :OP342 genotype :unc119(ed3);wgIs341(skn-1::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by :Bob Waterston's lab from UW )


title: SKN-1 GFP L4 C.elegans Input Rep1

description: input DNA

source_name: SKN-1 L4 InputRep1


title: SKN-1 GFP L4 C.elegans ChIP Rep1

source_name: SKN-1 L4 ChIPRep1


title: ELT-1 GFP L2 C.elegans Input Rep1

source_name: ELT-1 L2 InputRep1


title: SKN-1 GFP L4 C.elegans ChIP Rep2

source_name: SKN-1 L4 ChIPRep2


title: JUN-1 GFP L3 C.elegans ChIP Rep1

description: input DNA

source_name: JUN-1 L3 ChIPRep1


title: UNC-39 GFP EMB C.elegans ChIP Rep1

description: input DNA

source_name: UNC-39 EMB ChIPRep1


title: [E-MTAB-1310] polyA+_testis_7060321

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

description: Performer: University of Lausanne, Lausanne, Switzerland

data_processing: processed data not provided

extract_protocol:
extraction | Human polyA+ RNAs were purchased from Clontech. The RNAs were isolated from tissue samples using a modified guanidium thiocynate extraction method followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns.
specified_biomaterial_action | We experimentally assessed three categories of gene models: (1) spliced models in which one primer could be placed within 75 nt of a junction and that will result in about half of the sequencing reads covering the junction (â€œMulti-spanâ€); (2) spliced models in which this was unfeasible (â€œMultiâ€); and (3) monoexonic genes (â€œMonoâ€). In the case of â€œMulti-spanâ€ primers, the â€œjunction primerâ€ is positioned within an exon not more than 65 bp away from the targeted junction to ensure that sequencing reads will cross the junctions with a minimum of 10 nt, while the second primer maps within an adjacent exon. To increase the fraction of junctions we could possibly test, we then designed primer pairs further away from the junction (â€œMultiâ€ primers). Primers were designed using Primer3. We used parameters minimizing the formation of primer dimers and maximizing primers â€œstickinessâ€. Primer pairs were further filtered for mapping within repeat-regions and alternative priming within 30 kb in duplications and paralogous sequences (maximum of two tolerated mismatches).
specified_biomaterial_action | First-strand cDNA samples were prepared from human poly(A)+ RNAs (BD-Clontech) with the SuperScript III kit (Invitrogen). Amplifications were performed in a final volume of 12.5 Î¼L with JumpStart REDTaq ReadyMix (Sigma-Aldrich) and a primer concentration of 0.4 Î¼M in 384-well plates format on an automatized Evoware platform (TECAN) combined with a Tetrad2 thermocycler (Bio-Rad) that allows processing four plates in parallel. Because monoexonic amplification is sensitive to genomic DNA contaminations, monoexonic models were assessed by amplification of cDNA in which a dNTP analog was incorporated using the mRNA Selective PCR Kit (TAKARA).
sequencing | Aliquots of up to 5000 RT-PCRs reactions were pooled together and the sequencing library was prepared with no fragmentation using the TruSeq DNA protocol. DNA fragments were sequenced on a Illumina HiSeq2000 sequencer and 2 multiplexed libraries were loaded per lane. The sequencing was performed at the University of Lausanne, Lausanne, Switzerland.
data acquisition | Illumina pipeline export files were transformed into fastq format by applying this Unix command: awk '{print @$1_$2:$3:$4:$5:$6#$7/$8\n$9\n+\n$10}' file_export.txt > file.fastq

tag: material type

value: organism part

tag: organismpart

value: testis

value: male

tag: biosourcetype

value: frozen sample

tag: biosourceprovider

value: Clontech


title: JUN-1 GFP L3 C.elegans Input Rep2

source_name: JUN-1 L3 InputRep2


title: [E-MTAB-1310] polyA+_spleen_6090097

value: spleen

value: mixed sex


title: [E-MTAB-1310] polyA+_muscle_7040106

value: muscle


title: JUN-1 GFP L3 C.elegans Input Rep1

source_name: JUN-1 L3 InputRep1


title: JUN-1 GFP L1 C.elegans ChIP Rep2

source_name: JUN-1 L1 ChIPRep2

value: L1 26dC


title: [E-MTAB-1310] polyA+_liver_6100188

value: liver


title: [E-MTAB-1310] polyA+_lung_1100350

value: lung


title: JUN-1 GFP L1 C.elegans ChIP Rep1

source_name: JUN-1 L1 ChIPRep1

value: Hermaphrodite


title: UNC-39 GFP EMB C.elegans Input Rep1

source_name: UNC-39 EMB InputRep1

value: OP186(official name :OP186 genotype :unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The UNC-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by :Unknown )

value: embryo

value: mixed Male and Hermaphrodite population


title: [E-MTAB-1310] polyA+_heart_7082801A

value: heart


title: nhr-23 GFP L2 C.elegans Input Rep2

description: input DNA

source_name: nhr-23 L2 InputRep2

value: OP43(official name :OP43 genotype :unc-119(ed3); wgIs43(nhr-23::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The NHR-23::EGFP fusion protein is expressed in the correct nhr-23 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-223 transcription factor. made_by :Bob Waterston's lab from UW )


title: JUN-1 GFP L1 C.elegans Input Rep1

description: input DNA

source_name: JUN-1 L1 InputRep1

value: OP234(official name :OP234 genotype :unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by :Unknown )


title: nhr-23 GFP L2 C.elegans ChIP Rep1

source_name: nhr-23 L2 ChIPRep1

value: unc-119(ed3); wgIs43(nhr-23::TY1 EGFP FLAG; unc-119)


title: [E-MTAB-1310] polyA+_brain_6120217

value: organism part

value: brain

value: male


title: [E-MTAB-1505] polyA+_testis_7060321

extract_protocol:
extraction | Human polyA+ RNAs were purchased from Clontech. The RNAs were isolated from tissue samples using a modified guanidium thiocynate extraction method followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns.
specified_biomaterial_action | We experimentally assessed three categories of gene models: (1) spliced models in which one primer could be placed within 75 nt of a junction and that will result in about half of the sequencing reads covering the junction ('Multi-span'); (2) spliced models in which this was unfeasible ('Multi'); and (3) monoexonic genes ('Mono'). In the case of 'Multi-span' primers, the 'junction primer' is positioned within an exon not more than 65 bp away from the targeted junction to ensure that sequencing reads will cross the junctions with a minimum of 10 nt, while the second primer maps within an adjacent exon. To increase the fraction of junctions we could possibly test, we then designed primer pairs further away from the junction ('Multi' primers). Primers were designed using Primer3. We used parameters minimizing the formation of primer dimers and maximizing primers 'stickiness'. Primer pairs were further filtered for mapping within repeat-regions and alternative priming within 30 kb in duplications and paralogous sequences (maximum of two tolerated mismatches).
specified_biomaterial_action | First-strand cDNA samples were prepared from human poly(A)+ RNAs (BD-Clontech) with the SuperScript III kit (Invitrogen). Amplifications were performed in a final volume of 12.5 uL with JumpStart REDTaq ReadyMix (Sigma-Aldrich) and a primer concentration of 0.4 uM in 384-well plates format on an automatized Evoware platform (TECAN) combined with a Tetrad2 thermocycler (Bio-Rad) that allows processing four plates in parallel. Because monoexonic amplification is sensitive to genomic DNA contaminations, monoexonic models were assessed by amplification of cDNA in which a dNTP analog was incorporated using the mRNA Selective PCR Kit (TAKARA).
sequencing | Aliquots of up to 5000 RT-PCRs reactions were pooled together and the sequencing library was prepared with no fragmentation using the TruSeq DNA protocol. DNA fragments were sequenced on a Illumina HiSeq2000 sequencer and 2 multiplexed libraries were loaded per lane. The sequencing was performed at the University of Lausanne, Lausanne, Switzerland.
data acquisition | Illumina pipeline export files were transformed into fastq format by applying this Unix command: awk '{print @$1_$2:$3:$4:$5:$6#$7/$8\n$9\n+\n$10}' file_export.txt > file.fastq

value: testis

value: frozen sample

value: Clontech


title: NHR-76 GFP L4 C.elegans ChIP Rep2

description: input DNA

source_name: NHR-76 L4 ChIPRep2

value: OP203(official name :OP203 genotype :unc-119(ed3); wgIs203(nhr-76::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-76::EGFP fusion protein is expressed in the correct nhr-76 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-76 transcription factor. made_by :R. Waterston )


title: NHR-76 GFP L4 C.elegans ChIP Rep1

description: input DNA

source_name: NHR-76 L4 ChIPRep1

value: unc-119(ed3); wgIs203(nhr-76::TY1 EGFP FLAG; unc-119)


title: [E-MTAB-1505] polyA+_lung_1100350

value: lung

value: mixed sex


title: [E-MTAB-1505] polyA+_muscle_7040106

value: muscle


title: NHR-76 GFP L4 C.elegans Input Rep2

source_name: NHR-76 L4 InputRep2

value: Hermaphrodite


title: NHR-76 GFP L4 C.elegans Input Rep1

source_name: NHR-76 L4 InputRep1


title: ZTF-11 GFP L4 C.elegans ChIP Rep1

description: input DNA

source_name: ZTF-11 L4 ChIPRep1

value: OP236(official name :OP236 genotype :unc119(ed3);wgIs236(elk-2::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by :Unknown )


title: [E-MTAB-1505] polyA+_spleen_6090097

value: spleen


title: [E-MTAB-1505] polyA+_kidney_7110096

value: kidney


title: ZTF-11 GFP L4 C.elegans ChIP Rep2

description: input DNA

source_name: ZTF-11 L4 ChIPRep2


title: JUN-1 GFP L1 C.elegans Input Rep2

description: input DNA

source_name: JUN-1 L1 InputRep2

value: OP234(official name :OP234 genotype :unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by :Unknown )

value: L1 26dC


title: [E-MTAB-1505] polyA+_heart_7082801A

value: organism part

value: heart


title: ZTF-11 GFP L4 C.elegans Input Rep2

source_name: ZTF-11 L4 InputRep2


title: ZTF-11 GFP L4 C.elegans Input Rep1

source_name: ZTF-11 L4 InputRep1


title: ZTF-11 GFP L3 C.elegans ChIP Rep2

description: input DNA

source_name: ZTF-11 L3 ChIPRep2


title: [E-MTAB-1505] polyA+_brain_6120217

value: brain

value: male


title: [E-MTAB-1310] polyA+_kidney_7110096

value: frozen sample


title: [E-MTAB-1309] polyA+_testis_7060321

value: testis

value: Clontech


title: ZTF-11 GFP L3 C.elegans Input Rep2

source_name: ZTF-11 L3 InputRep2


title: ZTF-11 GFP L3 C.elegans ChIP Rep1

description: input DNA

source_name: ZTF-11 L3 ChIPRep1


title: JUN-1 GFP L4 C.elJUN-1 GFP L4 C.elegans ChIP Rep2

description: input DNA

source_name: JUN-1 L4 ChIPRep2


title: JUN-1 GFP L4 C.elJUN-1 GFP L4 C.elegans ChIP Rep1

description: input DNA

source_name: JUN-1 L4 ChIPRep1


title: ZTF-11 GFP L3 C.elegans Input Rep1

source_name: ZTF-11 L3 InputRep1


title: [E-MTAB-1309] polyA+_muscle_7040106


title: JUN-1 GFP L4 C.elJUN-1 GFP L4 C.elegans Input Rep2

source_name: JUN-1 L4 InputRep2


title: JUN-1 GFP L4 C.elJUN-1 GFP L4 C.elegans Input Rep1

source_name: JUN-1 L4 InputRep1


title: [E-MTAB-1226] polyA+_brain_6120217

description: Performer: Centre for Genomic Regulation (CRG), Barcelona, Spain

extract_protocol:
nucleic_acid_extraction | RNA from tissues was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns.
PCR_amplification | 5' and 3' RACE reactions were performed in 12.5 ul volume independently with brain and testis polyA+ RNA with the SMART RACE amplification kit (Clontech) using manufacturer's instructions. 7.5ul of each of the 400 lncRNA targets were pooled respecting tissues and directionality of the RACE reaction (5' and 3' RACE) and purified with the QIAquick kit (Quiagene) as described for RT-PCR-seq experiments (Howald et al, 2012). A set of 25 control reactions targeting full-length annotated transcripts were RACEd in parallel as positive controls. 1.5ul of these controls were pooled with the other reactions prior to library preparation.
sequencing | The RACE samples were fragmented to approximately 800-900bp and libraries were prepared following the Rapid Library Preparation Method Manual for GS FLX+ Series / XL+ Kit with minor mofications. The emulsion PCRs (emPCRs) for the library titrations and the sequencing reactions were prepared according to the emPCR Method Manual ??? Lib-L LV for GS FLX Titanium Series. The ratios of DNA molecules per bead were 0.1 (brain) and 0.12 (testis). From each emulsion-based clonal amplified library 900.000 enriched DNA beads were sequenced using the 200 nucleotide cycles option following the Sequencing Method Manual for GS FLX+ Series / XLR70 Kit on a GS FLX+ Instrument.


title: [E-MTAB-1226] polyA+_testis_7060321


title: [E-MTAB-1309] polyA+_lung_1100350


title: [E-MTAB-1505] polyA+_liver_6100188

value: liver


title: [E-MTAB-1222] polyA+_testis_7060321

description: Performer: Andalusian Human Genome Sequencing Centre

extract_protocol:
nucleic_acid_extraction | RNA from tissues was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns.
PCR_amplification | 5' and 3' RACE reactions were performed in 12.5 ul volume independently with brain and testis polyA+ RNA with the SMART RACE amplification kit (Clontech) using manufacturer's instructions. 7.5ul of each of the 400 lncRNA targets were pooled respecting tissues and directionality of the RACE reaction (5' and 3' RACE) and purified with the QIAquick kit (Quiagene) as described for RT-PCR-seq experiments (Howald et al. 2012). A set of 25 control reactions targeting full-length annotated transcripts were RACEd in parallel as positive controls. 1.5ul of these controls were pooled with the other reactions prior to library preparation.
sequencing | Libraries were prepared following the Rapid Library Preparation Method Manual for GS FLX+ Series / XL+ Kit. The emulsion PCRs (emPCRs) for the library titrations and the sequencing reactions were prepared according to the emPCR Method Manual Ã¢ Lib-L LV for GS FLX+ Series - XL+. Sequencing was performed on a GS FLX+ Instrument following the Sequencing Method Manual for GS FLX+ Series / XL+ Kit. Sequencing images were analyzed with the Roche 454 Shotgun-pipeline and Amplicons-pipeline programs. Two FastQ files were generated, one per lane.


title: [E-MTAB-1309] polyA+_kidney_7110096


title: [E-MTAB-1222] polyA+_brain_6120217


title: [E-MTAB-1309] polyA+_brain_6120217


title: [E-MTAB-1309] polyA+_heart_7082801A


title: FAIRE_Seq_rep1

status: Public on May 10 2013

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Basecalls performed using Illumina Casava1.7 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to hg19 whole genome using tophat with default parameters.
Peaks were called using findPeaks from HOMER (http://biowhat.ucsd.edu/homer), using a triangle-based distribution with a median length of 150bp with an alpha value of 0.01 (99.0% confidence interval)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using makeTagDirectory B84and makeUCSCfile from homer with following -o auto -res 1 -fsize 5e7; Peak files were generated using following settings (-alpha 0.01 -subpeaks 0.6) and score represents number of tags found clustered together.

source_name: Human Mammary Epithelial Cells

growth_protocol: HMEC cells were obtained from Lonza (Lonza, Walkersville, MD) and cultured under recommended conditions.

extract_protocol:
Nuclei were extracted after the crosslinking step (1% formaldehyde in PBS) of intact cells, followed by re-suspension in SDS lysis buffer before sonication. FAIRE DNA samples were purified by phenol/chloroform extraction. Input DNA was also purified by phenol/chloroform extraction after the crosslinking was reversed.
Libraries were prepared according to Illumina's instructions (refer to http://epigenome.usc.edu/services/nextgen/making_libraries.html)

tag: cell type

value: Mammary epithelial cells

tag: sample type

value: crosslinked

tag: passages

value: second or third


title: FAIRE_Seq_rep2


title: With downshift - Culture 2

city: Leeds

first: David

last: Romero A.

state: West Yorkshire

address: Woodhouse lane

institute: University of Leeds

description:
Enriched for mRNA
RNA-seq (differential)

data_processing:
The sample source of a read was determined by the barcoding. The barcodes for minus and plus TAP treatment respectively are GATCAG and TTAGGC for Culture 1 without downshift; TAGCTT and TGACCA for Culture 1 with downshift; GGCTAC and ACAGTG for Culture 2 without downshift; CTTGTA and GCCAAT for Culture 2 with downshift.
For each of the 8 libraries (2 cultures x 2 conditions x 2 treatments), we counted the number of times each nucleotide position was the first in a sequence read using a simple script (unpubl resource). The forward and reverse strands were processed seperately.

organism: Cutibacterium acnes KPA171202

source_name: Batch subculture with potassium downshift - Culture 2

growth_protocol: Propionibacterium acnes strain KPA171202 (Bruggemann et al. 2004. Science 305: 671) was cultivated in an anaerobic workstation (MACS-MG-1000, Don Whitely Scientific) at 34°C under 80% [v/v] N2, 10% [v/v] CO2, and 10% [v/v] H2. All analyses were done using cells cultivated without shaking in 100 mL of modified Holland Synthetic Medium (HSM) (Holland et al. 1979. J Appl Bacteriol 47: 383-394). Inocula were prepared in two stages. First a single colony isolated from the surface of reinforced clostridial agar (Hirsch and Grinstead 1954. J Dairy Res 21: 101) was used to inoculate 10 mL of tryptone-yeast extract-glucose (TYG) broth (Kim and Naylor 1966. Appl Microbiol 14: 690). After growing to stationary phase, an aliquot was used to inoculate 100 mL of TYG broth to an O.D.600nm of 0.2. The culture was then incubated to an O.D.600nm of 1.0, after which cells were harvested by centrifugation (3,000 x g for 20 min) and washed by first resuspending in 10 mL of HSM (pre-warmed to 34oC) and then repeating the harvesting step. Finally, the cells were resuspended in 10 mL of pre-warmed HSM and an appropriate aliquot was used to inoculate 100 mL of pre-warmed HSM to an O.D.600nm of 0.2.

extract_protocol:
Cell pellets of P. acnes were resuspended in Kirby mix (Kieser et al. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich.), 100 µL per 1 O.D.600nm unit, and transferred to Lysing Matrix B tubes containing fine silica beads (MP Biomedical). Tubes were then placed in a high-speed benchtop homogenizer (Fastprep-24, MP Biomedical; set at 6.5 M/s). Cells were lysed by three cycles of homogenisation for 1 min with cooling between each cycle in an ice-water bath for 1 min. Lysates were extracted using an equal volume of acidic phenol: chloroform: isoamyl alcohol (50: 50: 1) and then chloroform: isoamyl alcohol (49: 1). Nucleic acid in the aqueous phase was precipitated by adding NaCl to 150 mM and 2.5 x volumes of 100% [v/v] ethanol, chilling at -20°C for 1 h, and then harvested by centrifugation (13,000 x g for 30 min at 4°C) . Nucleic acid pellets were washed twice with 700 µL of 70% [v/v] ethanol, air dried for 5 min and resuspended in RNase-free water. To remove contaminating DNA, samples were treated with DNase I using conditions described by the vendor (Ambion) and extracted with phenol: chloroform as described above. The concentration and integrity of RNA samples were determined using a NanoDropTM 1000 spectrophotometer (Thermo Fisher Scientific) and agarose gel electrophoresis (Kime et al. 2008. In RNA Turnover in Bacteria, Archaea and Organelles, Vol 447 (ed. LE Maquat, CM Arraiano), pp. 215), respectively. Samples were enriched for mRNA using MICROBExpress-Bacteria beads, as described by the manufacturer (Ambion),
Libraries were constructed by vertis Biotechnologie AG, Germany  (www.vertis-biotech.com) as a service that included treating an aliquot of each RNA sample with TAP. The 5’-sequencing adaptor was ligated to transcripts prior to fragmentation, thereby allowing the 5’ ends of both long and short transcripts to be detected. Each of the 8 libraries was constructed using a different barcode.

treatment_protocol: Potassium downshift (depletion from growth media) was performed by growing a 100 mL culture of P. acnes in HSM to an O.D.600nm of 1.0, after which the culture was separated into two equal halves and cells harvested by centrifugation. One half was washed using standard HSM, then used to inoculate 100 mL of fresh HSM and reincubated. The other half was processed in the same way, except the HSM lacked potassium (KH2PO4 and K2HPO4). After 1 h of reincubation, 12.5 mL of stop solution (95% [v/v] ethanol; 5% [v/v] phenol) was added to inhibit cell metabolism (Kime et al. 2008. In RNA Turnover in Bacteria, Archaea and Organelles, Vol 447 (ed. LE Maquat, CM Arraiano), pp. 215), and the cells were harvested by centrifugation. When necessary, cell pellets were stored frozen at -80C.

value: Clinical isolate

tag: potassium downshift

value: with


title: With downshift - Culture 1

source_name: Batch subculture with potassium downshift - Culture 1


title: Without downshift - Culture 2

source_name: Batch subculture without potassium downshift - Culture 2

value: without


title: [E-MTAB-1309] polyA+_spleen_6090097

value: spleen

value: mixed sex


title: ribosomal RNA-depleted total RNA wt OSCs - rep1

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
N-containing reads were discarded
reads were trimmed to high-quality bases 6-50 using HomerTools, version 3.9 and mapped to genome and transcriptome using in-house developed pipeline
Reads were mapped to the dm3 genome (Release 5) and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) and bfast reconciling the outputs. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from a all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths.
Genome_build: Release 5 (dm3)

organism: Drosophila melanogaster

growth_protocol: OSC were grown at 27 degrees on M3 medium

extract_protocol:
total RNA was isolated with Trizol
mRNA from wildtype OSCs was  selected with Dynabeads Oligo(dT) (Invitrogen) from total RNA, fragmented and reverse transcribed with random hexamers. Strand-specific libraries were prepared using the UDG-digestion-based strategy and cloned with NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB)

tag: tissue

value: Ovarian Somatic Cells (OSC)

tag: genotype

value: wild-type

tag: Stage


title: RNAseq nos::KD-Yb

city: Cold Spring Harbor

first: Benjamin

last: Czech

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: mRNA seq

data_processing:
Basecalling with Illumina CASAVA version 1.3+.  Pooled libraries were de-multiplexed according to the barcode sequence used during ScriptSeq library generation.
Sequenced reads were trimmed for adaptor sequence and iteratively mapped to the genome of Drosophila melanogaster (dm3) using Bowtie. Reads were mapped allowing 0 mismatches, and remaining reads were remapped with 1 and 2 mismatches in subsequent steps to produce a total pool of 0-, 1-, and 2- mismatch mapped reads.
Unmapped reads were mapped to annotated Drosophila melanogaster transcripts (dm3) in the refSeq database (release 48 [September 13, 2011]) using Tophat to detect reads overlapping known splice junctions using the parameters --no-novel-juncs -g 1
Bowtie and Tophat outputs were catenated and processed by Cufflinks to produce mRNAs quantified in fragments per kilobase per million reads (FPKM)
In parallel, all trimmed reads were mapped using the same bowtie parametsr to the consensus sequences of Drosophila transposons, using Flybase transposon sequences version 9.42.
Genome_build: dm3
Supplementary_files_format_and_content: For gene expression profiling of Drosophila tissues: tab-delimted text file in the standard Cufflinks FPKM Tracking Format
Supplementary_files_format_and_content: For quantification of transposable element expression in nos-driven knockdown ovaries:  tab-delimited text file with column listing transposable element name and column 2 displaying reads_per_million_genomic_mappers rounded to the nearest integer.  The first row contains the total number of genomic mappers in that library.

source_name: Drosophila melanogaster ovary

growth_protocol: OSS cells were grown in M3 media supplemented with 10% FBS, 5% Fly extract, 1X insulin and 1X glutathione and kept in a 25C incubator.  Flies were raised at 25°C on standard cornmeal-molasses agar medium.

extract_protocol: RNA was extracted from cells or tissues using TRIzol reagent (Invitrogen).  RNA-seq libraries were prepared using the ScriptSeq V2 kit from Epicentre.  5ug total RNA was depleted of ribosomal RNA using the RiboZero Gold (Human/Mouse/Rat) kit from Epicentre and used as input for the ScriptSeq protocol, as per the manufacturer's instructions.

treatment_protocol: Flies were fed with yeast paste.

value: Whole dissected ovaries


title: RNAseq nos::KD-w_rep2

description: mRNA seq


title: RNAseq nos::KD-vasa

description: mRNA seq


title: RNAseq nos::KD-zuc

description: mRNA seq


title: RNAseq nos::KD-w_rep1

description: mRNA seq


title: RNAseq nos::KD-tej

description: mRNA seq


title: Hst2  ChIP-seq

city: Charlottesville

first: Kunal

last: Poorey

state: VA

address: 1340 Jefferson Park Avenue

department: Biomedical Sciences: Biochemistry, Molecular Biology & Genetics

institute: University of Virginia Health System

data_processing:
Basecalls performed using CASAVA version 1.7.0
ChIP-seq reads were aligned to the sacCer2 genome assembly using BWA version 0.5.7.
Data were filtered on basis of quality score and repeats were allowed only on rDNA locus on chrXII
peaks were called using BayesPeak version 1.2.3.
Genome_build: sacCer2
Supplementary_files_format_and_content: BedGraph files were generated where Scores represent tag counts

organism: Saccharomyces cerevisiae

source_name: Genomic DNA

growth_protocol: Yeast strains were grown in YPD medium containing 2% glucose as the carbon source. All yeast growth was performed at 30°C.

extract_protocol:
Log-phase cultures were cross-linked with 1% formaldehyde for 20 min at 30°C.Cells were pelleted by centrifugation and washed 2 times with cold Tris-buffered saline. The cells, in 0.6 ml of FA-140 lysis buffer were lysed with glass beads and a Mini-BeadBeater (Biospec Products). The cell lysate was drawn off the beads, sonicated for 60 cycles (30 s “on” at high level and 30 s “off” per cycle) in a Bioruptor (Diagenode) and spun for 10 min at 16,000x g in a microcentrifuge. Equivalent amounts of lysate (2.5 mg protein)  were incubated overnight at 4°C with 5 µg of anti-Myc antibody (9E10) and 20 µl of protein G magnetic beads (Millipore). The immunoprecipitated chromatin was then recovered and the DNA purified using a Magna ChIPTM G Chromatin Immunoprecipitation Kit (Millipore).
The ChIP-sequencing libraries were made using an Illumina ChIP-Seq DNA Sample Prep Kit (cat. # IP-102-1001), starting with 0.5 µg of DNA isolated from the immunoprecipitation step.

value: Myc tagged Hst2

tag: chip antibody

value: Anti-myc (9E10)

tag: chip antibody manufacturer

value: Hybridoma core facility at UVA


title: Hst1  ChIP-seq

value: Myc tagged Hst1

tag: strain


title: Input ChIP-seq


title: RNAseq nos::KD-squ

description: mRNA seq


title: Hst4  ChIP-seq

value: Myc tagged Hst4


title: Hst3  ChIP-seq

value: Myc tagged Hst3


title: Sum1 ChIP-seq

value: Myc tagged Sum1


title: [E-MTAB-1309] polyA+_liver_6100188

value: organism part

value: liver

value: male

value: frozen sample

value: Clontech


title: RNAseq nos::KD-spn-E

description: mRNA seq


title: Input DNA

value: Mammary epithelial cells

value: crosslink was reversed

value: second or third


title: Sir2 ChIP-seq

value: Myc tagged Sir2


title: RNAseq nos::KD-shu

description: mRNA seq

value: Whole dissected ovaries


title: Without downshift - Culture 1

source_name: Batch subculture without potassium downshift - Culture 1

value: Clinical isolate

value: without


title: RNAseq nos::KD-rhi

description: mRNA seq


title: RNAseq nos::KD-mael

description: mRNA seq


title: Non-smoker female, NSCLC, MeDIP-Seq [P8T]

city: Daejeon

first: Sanghyuk

last: Lee

address: 125 Gwahak-ro

department: KOBIC

country: South Korea

institute: KRIBB

description: 62 years;  female; a non-smoker

data_processing:
Basecalls performed using Illumina Genome AnalyzerIIx
DNA methylation density is calculated by counting reads after binning with bin size 200bp
Genome_build: hg19
Supplementary_files_format_and_content: text

source_name: Non-smoker female, NSCLC

extract_protocol: Methylated CpG island-associated DNA was prepared using methylation specific antibody. This ChIPed DNA was processed for high throughput sequencing using Illumina ChIP-Seq Sample Prep Kit. For sequencing, 200bp insert sized library was selected from agarose gel. Sequencing was performed at Illumina Genome Analyzer IIx, single read sequencing.

treatment_protocol: Standard protocol by phenol extraction

tag: disease

value: Adenocarcinoma, NSCLC

tag: patient

tag: tissue type

value: tumor

value: IA

tag: gender

value: female

tag: age

value: 62 years

tag: smoker

value: non-smoker


title: RNAseq nos::KD-piwi

description: mRNA seq


title: Non-smoker female, NSCLC, MeDIP-Seq [P6N]

description: 70 years;  female; a non-smoker

value: normal

value: IB

value: 70 years


title: Non-smoker female, NSCLC, MeDIP-Seq [P8N]

description: 62 years;  female; a non-smoker


title: Non-smoker female, NSCLC, MeDIP-Seq [P6T]

description: 70 years;  female; a non-smoker

value: IIB


title: Non-smoker female, NSCLC, MeDIP-Seq [P5T]

description: 44 years;  female; a non-smoker

value: IIA

value: 44 years


title: RNAseq nos::KD-del

description: mRNA seq


title: RNAseq nos::KD-gasz

description: mRNA seq


title: Non-smoker female, NSCLC, MeDIP-Seq [P5N]

description: 44 years;  female; a non-smoker


title: Non-smoker female, NSCLC, MeDIP-Seq [P4N]

description: 60 years;  female; a non-smoker

value: 60 years


title: Non-smoker female, NSCLC, MeDIP-Seq [P4T]

description: 60 years;  female; a non-smoker


title: RNAseq nos::KD-aub

description: mRNA seq


title: RNAseq nos::KD-CG3893

description: mRNA seq


title: RNAseq nos::KD-cuff

description: mRNA seq


title: Non-smoker female, NSCLC, MeDIP-Seq [P3T]

description: 53 years;  female; a non-smoker

value: 53 years


title: RNAseq nos::KD-ars2

description: mRNA seq

value: Whole dissected ovaries


title: Non-smoker female, NSCLC, MeDIP-Seq [P1T]

description: 44 years;  female; a non-smoker


title: Non-smoker female, NSCLC, MeDIP-Seq [P3N]

description: 53 years;  female; a non-smoker


title: embryo replicate 1

description: mRNA seq

source_name: 0-2 hour embryo

value: 0-2 hour embryo


title: embryo replciate 2

description: mRNA seq


title: Non-smoker female, NSCLC, smRNA-Seq [P8N]

description: 62 years;  female; a non-smoker

data_processing:
Basecalls performed using Illumina Genome AnalyzerIIx
Mapped to hg19 whole genome using bowtie v0.12.7 with parameters -a -v 0
Expression level is calculated by counting reads
Supplementary_files_format_and_content: text

extract_protocol: Purified total RNA was processed by illumina small RNA sample preparation kit. Before sequencing, small RNA library, from 22nt and 30nt small RNA fragment, was selected from PAGE gel. Sequencing was performed at Illumina Genome Analyzer IIx, 36bp single read sequencing.

treatment_protocol: Qiagen miRNeasy kit (Cat. 217004)


title: Non-smoker female, NSCLC, smRNA-Seq [P8T]

description: 62 years;  female; a non-smoker


title: carcass replicate 2

description: mRNA seq

source_name: ovariectomized carcass

value: ovariectomized carcass


title: RNAseq nos::KD-armi

description: mRNA seq


title: Non-smoker female, NSCLC, smRNA-Seq [P6T]

description: 70 years;  female; a non-smoker

value: Adenocarcinoma, NSCLC


title: Non-smoker female, NSCLC, smRNA-Seq [P5T]

description: 44 years;  female; a non-smoker

value: tumor


title: ovary replicate 1

description: mRNA seq


title: Non-smoker female, NSCLC, smRNA-Seq [P5N]

description: 44 years;  female; a non-smoker


title: OSS replicate 1

description: mRNA seq

source_name: Ovarian Somatic Sheet (OSS) cells

value: Ovarian Somatic Sheet cells (OSS)


title: ovary replicate 2

description: mRNA seq


title: Non-smoker female, NSCLC, smRNA-Seq [P4T]

description: 60 years;  female; a non-smoker

value: IA

value: female


title: OSS replicate 2

description: mRNA seq


title: Non-smoker female, NSCLC, smRNA-Seq [P4N]

description: 60 years;  female; a non-smoker

value: non-smoker


title: Non-smoker female, NSCLC, smRNA-Seq [P3T]

description: 53 years;  female; a non-smoker


title: tj-spnE

description: small RNA sequencing

data_processing:
Demultiplexed, concatenated files with the 50nt or 36nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome (dm3) using nexalign. Only reads that met these conditions were subjected to further analyses.
For annotations we used a combination of UCSC [dm3], miRBase [release 14], and Flybase [r5.26] tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request). For comparison of small RNA counts between samples, libraries of dsRNA-white samples were set to one million reads. Next, all libraries were normalized based on unique mappers to the flamenco (for nos-GAL4 knockdowns) or 42AB (for tj-GAL4 knockdowns) piRNA clusters.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimted text files contain genome-matching small RNA sequences, read lengths, annotation names and read counts. Format: SEQ = the sequence of the small RNA. LENGTH = the length of the small RNA. NAME = annotation name of the small RNA. READS = read count in respective library. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

source_name: tj-spnE

growth_protocol: Flies were raised at 25°C on standard cornmeal-molasses agar medium.

extract_protocol: Total RNA from ovaries of 2-3 day old females of the indicated knockdowns was isolated using TRIzol (Invitrogen). 19- to 28-nt small RNAs were cloned as described (Brennecke et al., 2007), with slightly modified adapters that enabled multiplexed sequencing.

value: ovaries

tag: rna subtype

value: small RNA


title: Non-smoker female, NSCLC, smRNA-Seq [P3N]

description: 53 years;  female; a non-smoker

value: normal

value: IB


title: tj-gasz

description: small RNA sequencing

source_name: tj-gasz


title: tj-zuc

description: small RNA sequencing

source_name: tj-zuc


title: Non-smoker female, NSCLC, smRNA-Seq [P1T]

description: 44 years;  female; a non-smoker

value: IIA


title: tj-armi

description: small RNA sequencing

source_name: tj-armi


title: tj-yb

description: small RNA sequencing

source_name: tj-yb


title: nos-del

description: small RNA sequencing

source_name: nos-del


title: tj-w

description: small RNA sequencing

source_name: tj-w


title: Non-smoker female, NSCLC, RNA-seq [P6N]

description: 70 years;  female; a non-smoker

data_processing:
Mapped to hg19 whole genome using bowtie v0.12.7 with parameters -a -v 0; expression levels: NEUMA v1.1.4 and edgeR normalization
Genome_build: hg19
Supplementary_files_format_and_content: text

extract_protocol: Total RNA was prepared in accordance with Illumina's sample preparation protocol for PE sequencing of mRNA. mRNA from total RNA was isolated using poly-T oligo-attached magnetic beads and fragmented with fragmentation buffer in mRNA Sequencing Sample Prep Kit (Illumina). Following steps were identical with exome sequencing, except that purified fragments size from agarose gel was 300bp, bigger than exome sequencing.

treatment_protocol: Qiagen miRNeasy kit (Cat. 217004)

value: 70 years


title: Non-smoker female, NSCLC, smRNA-Seq [P1N]

description: 44 years;  female; a non-smoker

value: 44 years


title: Non-smoker female, NSCLC, RNA-seq [P6T]

description: 70 years;  female; a non-smoker

value: IIB


title: carcass replicate 1

description: mRNA seq

tag: cell type


title: nos-spnE

description: small RNA sequencing

source_name: nos-spnE


title: Non-smoker female, NSCLC, RNA-seq [P8N]

description: 62 years;  female; a non-smoker

value: 62 years


title: Non-smoker female, NSCLC, RNA-seq [P8T]

description: 62 years;  female; a non-smoker


title: nos-aub

description: small RNA sequencing

source_name: nos-aub


title: Non-smoker female, NSCLC, smRNA-Seq [P6N]

description: 70 years;  female; a non-smoker


title: nos-gasz

description: small RNA sequencing

source_name: nos-gasz


title: Non-smoker female, NSCLC, RNA-seq [P5T]

description: 44 years;  female; a non-smoker


title: Non-smoker female, NSCLC, RNA-seq [P5N]

description: 44 years;  female; a non-smoker


title: nos-yb

description: small RNA sequencing

source_name: nos-yb


title: nos-armi

description: small RNA sequencing

source_name: nos-armi


title: Non-smoker female, NSCLC, RNA-seq [P4T]

description: 60 years;  female; a non-smoker

value: 60 years


title: Non-smoker female, NSCLC, RNA-seq [P3T]

description: 53 years;  female; a non-smoker

value: 53 years


title: nos-w

description: small RNA sequencing

source_name: nos-w


title: Non-smoker female, NSCLC, RNA-seq [P4N]

description: 60 years;  female; a non-smoker

source_name: Non-smoker female, NSCLC

value: Adenocarcinoma, NSCLC


title: Non-smoker female, NSCLC, RNA-seq [P3N]

description: 53 years;  female; a non-smoker


title: smallRNAs (18-29nt) from UAS-Dcr-2;NGT;nanosGAL4>w-

description: small RNA

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings
after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9
reads matching the release5 genome sequence of D. melanogaster were the basis for the processed data file
Genome_build: Release 5 (dm3)

growth_protocol: flies were grown at 25 degrees; OSC were grown at 27 degrees on M3 medium

extract_protocol:
total RNA was isolated with Trizol
small-RNAs were cloned as described in Brennecke et al. 2009

treatment_protocol: OSC were transfected twice with siRNAs and analyzed after 4 days

value: fly ovaries

value: from 5-6 days old flies


title: smallRNAs (18-29nt) from CG2183 RNAi

description: small RNA

source_name: smallRNAs (18-29nt) from CG2183 RNAi

extract_protocol:
total RNA was isolated with Trizol
small-RNAs were cloned as described in Brennecke et al. 2008

value: Ovarian Somatic Cells (OSC)

value: RNAi CG2183

value: 96h after transfection


title: Non-smoker female, NSCLC, RNA-seq [P1T]

description: 44 years;  female; a non-smoker

value: tumor

value: female

value: non-smoker


title: smallRNAs (18-29nt) from GFP RNAi

description: small RNA

source_name: smallRNAs (18-29nt) from GFP RNAi

extract_protocol:
total RNA was isolated with Trizol
small-RNAs were cloned as described in Brennecke et al. 2007

value: RNAi gfp


title: Non-smoker female, NSCLC, RNA-seq [P1N]

description: 44 years;  female; a non-smoker

value: normal

value: IB


title: ribosomal RNA-depleted total RNA wt OSCs - rep2

value: wild-type


title: ChIP-seq CDK9

status: Public on May 09 2013

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

data_processing:
All sequenced tags were trimmed and mapped to the mouse genome (mm9) by using Bowtie (version 0.12.2-0.12.7). Generally, two mismatches were allowed in the first 25nt region and only those tags with one unique hit in the mouse genome were kept. Multiple tags mapped to the same genomic position were collapsed into one or up to 4 tags to remove potential PCR amplicons.
Density files were generated by using bedItemOverlapCount and wigToBigWig programs from UCSC kent source package. Different density files in group of experiments such as WT and KO were normalized to same number of total mapped reads for comparision.
Genome_build: mm9

growth_protocol: DMEM plus 10% FBS

extract_protocol:
For genomic DNA extraction, we used QIAquick PCR purification kit. For RNA extraction, we used Trizol kit by following manufacturer's instructions.
For HA, SRSF1, SRSF2, RNAPII, CDK9, and HEXIM1 ChIP-seq, MEF cells were fixed with 1% Formaldehyde or 1% glutaraldehyde at room temperature for 10 min. After the treatment, cross linking was quenched with 0.125 M glycine for 5 min;10-50 million cells were used per ChIP. For GRO-Seq, ~20 million cell nuclei from wildtype or SR protein depleted cells were extracted and harvested, then We carried out the global nuclear run-on assay and then analyzed by deep sequencing using a published protocol (Wang et al., 2011). RNA-seq was performed after SR proteins depletion. Trizol-isolated RNA was enriched  for Poly(A+) RNA with paramagnetic oligo(dT), fragmented into ~200 nt in length, converted to cDNA with Superscript III (Invitrogen), and subjected to deep sequencing to detect counts at the 3’ end of individual transcripts (Fox-Walsh et al., 2011).

treatment_protocol: We treated SRSF1-MEFs with Dox for 4 days and SRSF2-MEFs with Dox for 2 days to deplete respective SR protein to ~90%. For DRB treated cells, treat MEFs with 100μM DRB for 3 hours

value: MEF cell line

tag: molecule type

value: genomic DNA


title: smallRNAs (18-29nt) from UAS-Dcr-2;NGT;nanosGAL4>CG2183 RNAi

description: small RNA

extract_protocol:
total RNA was isolated with Trizol
small-RNAs were cloned as described in Brennecke et al. 2010

value: UAS-Dcr-2;NGT;nanosGAL4>CG2183 RNAi


title: 3'-end RNA-seq SRSF2 control

data_processing:
Library strategy: 3' end RNA-Seq (MAPS)
All sequenced tags were trimmed and mapped to the mouse genome (mm9) by using Bowtie (version 0.12.2-0.12.7). Generally, two mismatches were allowed in the first 25nt region and only those tags with one unique hit in the mouse genome were kept. Multiple tags mapped to the same genomic position were collapsed into one or up to 4 tags to remove potential PCR amplicons.
Density files were generated by using bedItemOverlapCount and wigToBigWig programs from UCSC kent source package. Different density files in group of experiments such as WT and KO were normalized to same number of total mapped reads for comparision.
Genome_build: mm9

molecule: polyA RNA

tag: passages

value: polyA RNA


title: 3'-end RNA-seq SRSF1 control


title: Gro-seq No-DRB

data_processing:
Library strategy: GRO-Seq
All sequenced tags were trimmed and mapped to the mouse genome (mm9) by using Bowtie (version 0.12.2-0.12.7). Generally, two mismatches were allowed in the first 25nt region and only those tags with one unique hit in the mouse genome were kept. Multiple tags mapped to the same genomic position were collapsed into one or up to 4 tags to remove potential PCR amplicons.
Density files were generated by using bedItemOverlapCount and wigToBigWig programs from UCSC kent source package. Different density files in group of experiments such as WT and KO were normalized to same number of total mapped reads for comparision.
Genome_build: mm9

value: nascent RNA


title: ChIP-seq HEXIM1


title: 3'-end RNA-seq SRSF1 KO


title: ChIP-seq IgG

value: Rabbit normal IgG


title: Gro-seq SRSF1 control


title: Pol II ChIP-seq siRNA hnRNPB1


title: Gro-seq SRSF1 KO


title: Gro-seq SRSF2 KO


title: Gro-seq SRSF2 control


title: Pol II ChIP-seq siRNA NC


title: Gro-seq DRB-3h


title: Pol II ChIP-seq SRSF2 wildtype


title: Pol II ChIP-seq SRSF1 KO


title: Pol II ChIP-seq 2-o-methyl antisense-7SK control


title: SRSF2 ChIP-seq SRSF1 KO

value: anti-HA (ab9110)


title: Pol II ChIP-seq SRSF1 wildtype


title: Pol II ChIP-seq SRSF2 KO


title: SRSF2 ChIP-seq SRSF1 wildtype


title: 3'-end RNA-seq SRSF2 KO


title: SRSF1 ChIP-seq SRSF2 wildtype


title: SRSF2 native ChIP-seq

value: (Fu and Maniatis, 1990)


title: Pol II ChIP-seq siRNA hnRNPA1


title: Pol II ChIP-seq 2-o-methyl antisense-7SK


title: 10 min post-deflagellation

city: Saint Louis

first: Huawen

last: Lin

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

data_processing:
Tophat (v2.0.5) was used to align all reads from individual samples to Chlamydomonas v5.3 genome, parameters are the following: splice-mismatches 1; max-multihits 100; segment-mismatches 1; no coverage search; segment length 18.
Cufflinks (v2.0.2) with default setting was used to calculate transcript abundance using bam files generated by Tophat with gene annotation from Chlamydomonas v5.3 genome
Genome_build: Chlamydomonas v5.3 genome
Supplementary_files_format_and_content: They are in txt format and it results from cufflinks reports of transcript abundance. It contains the gene id name, position, FPKM, FPKM confidence level, and FPKM status.

molecule: cytoplasmic RNA

organism: Chlamydomonas reinhardtii

source_name: cells

growth_protocol: 25C constant light, rich (R) medium

extract_protocol:
RNA was extracted with Qiagen RNAeasy mini kit followed by DNaseI treatment
cDNA libraries were made with Illumina RNA-Seq prep kit

treatment_protocol: for post-deflagellation samples, pH lowered to 4.0 for 45 sec then raised to 7.1

tag: growth condition

value: vegetative

value: 10 min post-deflagellation


title: 30 min post-deflagellation

value: 30 min post-deflagellation


title: SRSF1 native ChIP-seq


title: RNAseq_tj-aub_GD30125_rep1

first: Felix

last: Muerdter

state: New York

institute: Cold Spring Harbor Laboratories

description: total RNA (rRNA depleted with ribo-zero)

data_processing:
RNA-seq libraries were prepared using the Illumina Script Seq v2 RNA-Seq library preparation kit and were sequenced on an Illumina HiSeq platform for 36 cycles in a single end run. After collapsing all reads into a non-redundant list (cloning counts were preserved) using the FASTX Toolkit 0.0.14 by A. Gordon (gordon@cshl.edu), they were mapped to Drosophila viral, tRNA and miscRNA (rRNA, snoRNA etc) sequences using the short read aligner Bowtie (Langmead et al., 2009). Only sequences in each library that did not map to either of these contaminants were then mapped to the Drosophila genome with up to two mismatches. Additionally, only uniquely mapping sequences were considered for further analysis. The same reads were mapped to a custom index of transposon consensus sequences with up to 2 mismatches (Kaminker et al., 2002). Reads mapping to up to 2 locations were considered for further analysis. For differential expression analysis of transposons we aggregated read counts mapping to these consensus sequences in sense orientation. For differential expression analysis of genes, we used htseq-counts (Part of the 'HTSeq' framework, version 0.5.3p3) to assess read counts per gene. In both cases we used the R package DESeq to call differential expression at a FDR cutoff of 0.05 based on two biological replicates.
Genome_build: dm3
Supplementary_files_format_and_content: H3K9me3 peaks in heterozygous 204406 flies identified with Homer are provided as BED files. Tag counts over these regions in heterozygous and homozygous 204406 flies calculated with Homer (annotatePeaks) are provided as text files.

source_name: Drosophila melanogaster ovary

extract_protocol:
Trizol extraction followed by isopropanol precipitation
ScriptSeq v2 RNA-Seq Library Preparation Kit after rRNA depletion with Ribo-zero of 2.5-5 ug total RNA

tag: tissue

value: ovaries

value: VDRC GD30125

tag: sample type

value: tj driven knockdown of aub (negative control for Samples 19, 20)


title: RNAseq_tj-aub_GD30125_rep2


title: 60 min post-deflagellation

tag: Stage

value: 60 min post-deflagellation


title: sRNAseq_tj-white_GD30033

description: small RNA (2s rRNA depleted, no size selection)

data_processing:
Small RNA -seq libraries were sequenced on  a Illumina HiSeq single-end 36 run, the TruSeq adapter (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) was clipped from the 3’ end of the read and sequences shorter than 15 nt were discarded from further analysis. The remaining sequences were collapsed into a non-redundant list and mapped to Drosophila viral, tRNA and miscRNA (rRNA, snoRNA etc) sequences using the short read aligner Bowtie (Langmead et al., 2009). Clipping and collapsing was done using the FASTX Toolkit 0.0.14 by A. Gordon (gordon@cshl.edu). Only non-mapping reads were consequently mapped to the D. melanogaster genome (D. melanogaster Apr. 2006 [BDGP R5/dm3]). Up to two mismatches were allowed.
Genome_build: dm3
Supplementary_files_format_and_content: H3K9me3 peaks in heterozygous 204406 flies identified with Homer are provided as BED files. Tag counts over these regions in heterozygous and homozygous 204406 flies calculated with Homer (annotatePeaks) are provided as text files.

extract_protocol:
Trizol extraction followed by isopropanol precipitation
TruSeq Small RNA Sample Preparation Kit after 2s rRNA depletion of 2.5ug total RNA

value: VDRC GD30033

value: tj driven knockdown of white (negative control for Sample 7)


title: sRNAseq_tj-lin52_KK108404

value: VDRC KK108404

value: tj driven knockdown of lin52


title: sRNAseq_tj-aub_KK101252_rep2

value: VDRC KK101252

value: tj driven knockdown of aub (negative control for Samples 11,13)


title: RNAseq_tj-wde_KK105719_rep1

value: VDRC KK105719

value: tj driven knockdown of wde


title: RNAseq_tj-nxt1_KK103146_rep2

value: VDRC KK103146

value: tj driven knockdown of nxt1


title: SRSF1 ChIP-seq SRSF2 KO

value: MEF cell line

tag: chip antibody

value: anti-HA (ab9110)

value: genomic DNA


title: RNAseq_tj-wde_KK105719_rep2

value: ovaries


title: sRNAseq_tj-nxt1_KK103146


title: RNAseq_tj-uba2_KK110173_rep1

value: VDRC KK110173

value: tj driven knockdown of uba2


title: RNAseq_tj-nxt1_KK103146_rep1


title: RNAseq_tj-lin52_KK108404_rep2


title: sRNAseq_tj-CG3893_GD40480

value: VDRC GD40480

value: tj driven knockdown of CG3893


title: RNAseq_tj-mael_KK100907_rep2

value: VDRC KK100907

value: tj driven knockdown of mael


title: RNAseq_tj-mael_KK100907_rep1


title: RNAseq_tj-lin52_KK108404_rep1

value: VDRC KK108404

value: tj driven knockdown of lin52


title: 3 min post-deflagellation

value: vegetative

value: 3 min post-deflagellation


title: RNAseq_tj-aub_KK101252_techrep

value: VDRC KK101252

value: tj driven knockdown of aub


title: RNAseq_tj-aub_KK101252_rep2

value: tj driven knockdown of aub (negative control for Samples 28-37)


title: pre-deflagellation

value: pre-deflagellation


title: RNAseq_Kyoto_DGRC204406_het

value: DGRC 204406 heterozygous

value: total RNA (rRNA depleted with ribo-zero)


title: RNAseq_tj-aub_KK101252_rep1

value: ovaries


title: RNAseq_Kyoto_DGRC204406_hom

value: DGRC 204406 homozygous


title: RNAseq_tj-armi_KK103589_rep2

value: VDRC KK103589

value: tj driven knockdown of armi


title: RNAseq_tj-uba2_KK110173_rep2

value: VDRC KK110173

value: tj driven knockdown of uba2


title: RNAseq_tj-CG3893_GD40480_rep1

value: VDRC GD40480

value: tj driven knockdown of CG3893


title: RNAseq_tj-CG3893_GD40480_rep2


title: sRNAseq_tj-aub_KK101252_rep1

value: tj driven knockdown of aub (negative control for Samples 8,12,14,15)


title: sRNAseq_Kyoto_DGRC204406_het

value: small RNA (2s rRNA depleted, no size selection)


title: sRNAseq_tj-wde_KK105719

value: VDRC KK105719

value: tj driven knockdown of wde


title: sRNAseq_tj-armi_KK103589


title: sRNAseq_tj-mael_KK100907

value: VDRC KK100907

value: tj driven knockdown of mael


title: sRNAseq_Kyoto_DGRC204406_hom