title: Snyder_DPL-1_GFP_L4_rep1_TGCT

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

tag: strain

value: OP105(official name :OP105 genotype :unc119(ed3);wgIs105(dpl-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.  The DPL-1::EGFP fusion protein has broad expression pattern description :but silence in germline cells.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by :Bob Waterston's lab from UW )

value: Hermaphrodite


title: Mutant total RNA-seq

status: Public on Feb 04 2013

type: SRA

city: New Haven

last: Liu

state: CT

address: 10 Amistad st

country: USA

institute: Yale University

library_source: transcriptomic

data_processing:
TotalMT_mapped.txt; genome build: UCSC dm3
We removed the linker from the sequences by using in-house program. And sequences that perfectly match the Drosophila melanogaster release 5 genome (excluding Uextra) were collected by bowtie-0.10.0.

molecule: total RNA

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: All Drosophila melanogaster strains were reared between 18 and 25 0C on yeast/molasses agar medium. The Piwi null strain used, piwi1, has been previously described (Lin and Spradling, 1997)

extract_protocol: RNA with low weight was isolated from the adult ovaries of wild type and mutant flies, using miRNA isolation kit (Ambion). Small RNAs ranging in size below 2.5S rRNA was gel purified, and small RNA libraries were prepared using small RNA sample prep kit (Illumina) according to the alternative v1.5 protocol. The clones were sequenced using Genome Analyzer II.

tag: tissue

value: ovary

tag: genotype/variation

value: Piwi null (piwi1)

tag: antibody


title: WT

status: Public on Feb 02 2013

city: Durham

first: Teresa

middle: R

last: O'Meara

state: NC

address: DUMC 3355

institute: Duke University

data_processing:
All reads were mapped to the C. neoformans reference genome provided by the Broad Institute by using TopHat v1.3.0
The aligned reads were then analyzed for the number of fragments per kilobase of transcript per million mapped reads by using Cufflinks v.1.0.3. Statistically significant differences between strains was determined by CuffDiff
Genome_build: Broad Institute C. neoformans grubii h99
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample. Columns: test_id, locus, sample_1, sample_2, status, h99_fpkm, rim101_fpkm, ln(fold_change), test_stat, p_value, significant

organism: Cryptococcus neoformans

source_name: h99 wild type

growth_protocol: Strains were incubated in YPD to mid-log phase, washed twice, and then incubated in DMEM at 37°C with 5% CO2 or YPD for 3 h. Cells were then washed twice, frozen on dry ice, and lyophilized for 3 h.

extract_protocol:
Total RNA was extracted by using the Qiagen RNeasy Plant Minikit
Library preparation and RNA sequencing were performed by the Duke Sequencing Core Facility. Total RNA samples were purified and prepared according to the manufacturer’s protocols (Illumina, San Diego, CA)

tag: genotype

value: wild type


title: rim101

source_name: rim101 mutant


title: Transgenic fly line of Hsp70 wild type promoter [PRO-seq]

status: Public on Feb 01 2013

city: Ithaca

first: Hojoong

last: Kwak

state: NY

address: 516 Campus Rd Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

description: Tru-Seq Small RNA Preparation

data_processing:
filtering; fastx_trimmer
reverse complement; fastx_reverse_complement
alignment; bowtie
abundance measurement
The processed data is strand specific, and .pl. is an abbreviated extension for plus strand (sense) and .mn. is for minus strand (antisense) of the reference genome.
Genome_build: dm5.22
Supplementary_files_format_and_content: bedgraph; normalized or non-normalized read counts

molecule: nuclear RNA

source_name: whole body

extract_protocol:
Nuclei isolation by douncing and/or sucrose gradient ultracentrifuge (Love, Minton 1985)
Illumina Small RNA Sample Preparation v1.5 or Tru-seq Small RNA Sample Preparation with the following modifications;Biotin-NTP run on, Streptavidin affinity purifications (3 total), base hydrolysis, 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, PCR amplification

tag: cell line

tag: protocol

value: PRO-seq


title: Drosophila S2 cell line [PRO-cap_01]

description: Illumina Small RNA Preparation v1.5

source_name: embryo

value: PRO-cap


title: 11B_adult-dko

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

description: Strategy: hMeDIP, Barcode: ATTCCG

library_source: genomic

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
Mapping: bowtie
computation of coverage values: wiggles
Genome_build: mm9
Supplementary_files_format_and_content: Format: bedgraph, Content: genomic coverage

molecule: genomic DNA

organism: Mus musculus

source_name: cerebrum

extract_protocol:
Homogenized mouse tissues were incubated overnight in 100mM Tris-HCl pH 8 containing 5mM EDTA, 0.2% SDS, 200 mM NaCl and 400 µg/ml proteinase K, and DNA was then isolated using a standard protocol with phenol:chloroform:isoamyl alcohol and Phase Lock Gel™ separation tubes. Genomic DNA was finally treated with RNAse A (20 µg/ml) for 30 minutes at 37°C.
Thirty µg of genomic DNA for each sample was sonicated to 300bp fragments using a Covaris S220 (Covaris). Sheared DNA was ethanol precipitated, washed with 70% ethanol, and dissolved in TE buffer (pH8.0). Illumina adapters were ligated using the End-It DNA End-repair kit (Epicentre). DNA was purified with the QiaQuick PCR purification kit (Qiagen) and diluted to 122.5µl with ddH2O. After the addition of 15µl NEB buffer 2, 3.5µl of 10mM ATP and 9µl of 5U/µl Klenow exo- (NEB), reactions were incubated at 37°C for 50min. DNA was subsequently purified with the QiaQuick PCR purification kit, diluted to 24µl with ddH2O, and mixed with 50µl of 2x NEB quick ligation buffer, 20 µl of barcoded Illumina adapter and 6µl of quick T4 DNA ligase (NEB). After 20 minutes incubation at room temperature, DNA was purified again with QiaQuick PCR purification kit. Ligation efficiency was analyzed by PCR on 10ng of final ligated DNA with Illumina sequencing primers. Finally, five µg of adapter ligated DNA was used for the immunoprecipitation, as described above. Immunoprecipitated DNA was resolved in 20µl of water and all (h)MeDIP samples were pooled to create the MeDIP and hMeDIP libraries, respectively. Both libraries were purified on e-Gel (Invitrogen) and the 300bp bands (containing roughly 200bp fragments of adapter-ligated immunopurified DNA) were extracted. Libraries were amplified using Illumina-Enrichment Primers for 12 cycles and purified using Agencourt AMPure XP beads (Beckman Coulter). DNA concentrations were measured using a Agilent High Sensitivity DNA Assay (Agilent Technologies) and 7 pmol were used for cluster PCR and substantial 100bp paired-end sequencing on a HiSeq2000 (Illumina).

value: cerebrum

tag: developmental stage

value: adult

value: mixed 129|C57BL/6

tag: tet1/tet2 treatment

value: TET1 and TET2 knocked out

tag: vendor/catalog/lot

value: polyclonal, Active Motif, 39791


title: Drosophila S2 cell line [PRO-seq_01N]

description: Illumina Small RNA Preparation v1.5


title: Oriental_Frill_heart

status: Public on Feb 03 2013

city: Shenzhen

first: tan

last: hao

state: Guangdong

address: Building No.11,Beishan Industrial Zone,Yantian District

department: Department of Science & Technology

country: China

institute: BGI-Shenzhen

data_processing:
Using the rock pigeon genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -p 4 -r 20 --mate-std-dev 10 -m 2 -I 100000 --solexa1.3-quals
Genome_build: BioProject PRJNA167554
WGS/SRA: SRA052637

organism: Columba livia

source_name: Oriental Frill heart

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

tag: breed

value: Oriental Frill

value: heart


title: 15_neonate-dehet

description: Strategy: MeDIP, Barcode: AGCGCT

source_name: tail

value: tail

value: neonate

value: Heterozygous / TET1 and TET2 knocked out on one chromosome

value: monoclonal, Active Motif, 39649


title: 11A_adult-dko

description: Strategy: MeDIP, Barcode: ATTCCG


title: 10A_embryo-wt

description: Strategy: MeDIP, Barcode: AAGTGC

source_name: brain

value: brain

value: embryo

value: WT


title: 12B_adult-wt

description: Strategy: hMeDIP, Barcode: GCGTGG


title: pif3-RNA-3

city: Albany

first: Yu

last: Zhang

state: California

address: 800 Buchanan Street

department: Plant and Microbial Biology

institute: UC Berkeley

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
pif3.xlsx

data_processing:
Base-callling was performed using Illumina pipeline CASAVA-1.7.0.
For consistency, 50-nt reads were trimmed from 3’-end by 14 nt before alignment.
Reads that have no unrecognized nucleotides (Ns) and passed quality filtering were aligned to the TAIR10 transcriptome assembly using Bowtie-0.12.7 with the following settings: -v 0 --norc -a --best.
Only reads mapped uniquely to the 3’-end 500-bp region of the single locus were counted for gene expression.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tabular files containing raw reads counts of every locus in each of biological triplicates

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Stratified seeds were irradiated with WL at 21 ºC for 3 h to induce germination, followed by a FR pulse for 15 min to suppress pseudo dark effects, and grown in darkness at 21 ºC for 2 d before harvest.

extract_protocol: The sequencing library construction was adapted from Illumina’s directional mRNA-seq sample preparation protocol. The mRNA was fractionated from 20 µg of total RNA using Dynabeads Oligo (dT)25 (Invitrogen), and fragmented using Fragmentation Reagents (Ambion) at 70 ºC for 2.5 min in 20 µl of reaction. The polyA-tailed 3’-end fragments were captured by another run of mRNA purification as described above, and then treated by Antarctic Phosphatase and T4 Polynucleotide Kinase (NEB) at 37 ºC for 1 h and 2 h, respectively. The sample was purified using RNeasy MinElute Cleanup Kit (Qiagen) according to Illumina’s protocol. The eluted mRNA fragments were ligated with 2.5 µM of Illumina’s SRA 5’ adaptor by T4 RNA Ligase 1 (NEB) at 20 ºC for 4 h. The 3’ cDNA adapter derived from Illumina’s v1.5 sRNA 3’ adapter was conjugated with the anchored oligo (dT)20 primer, and introduced through reverse transcription using the SuperScript III First-Strand Synthesis System (Invitrogen). The first-strand cDNA was purified using the Agencourt AMPure XP system (Beckman Coulter Genomics), and then amplified by PCR reaction using Phusion High-Fidelity DNA Polymerase (NEB) with Illumina’s sRNA PCR primer set. The size of purified library DNA was validated by Bioanalyzer 2000 (Agilent).

tag: developmental satge

tag: growth conditions

value: true dark


title: pif145-RNA-2

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
pif145.xlsx

value: pif1pif4pif5 (pif145)


title: pifq-RNA-3

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
pifq.xlsx

value: pif1pif3pif4pif5 (pifq)


title: pifq-RNA-2


title: pif145-RNA-3


title: pif3-RNA-2


title: 9A_embryo-dko

description: Strategy: MeDIP, Barcode: CGAAAC


title: 8A_embryo-dko

description: Strategy: MeDIP, Barcode: GAATGA


title: WT-RNA-3

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
WT.xlsx


title: 4_neonate-dko

description: Strategy: MeDIP, Barcode: GCCTAA


title: Transgenic fly line of Hsp70 10 bp insert promoter [PRO-seq]

description: Tru-Seq Small RNA Preparation

value: PRO-seq


title: Drosophila S2 cell line [PRO-seq_01A]

description: Illumina Small RNA Preparation v1.5


title: 3_neonate-dko

description: Strategy: MeDIP, Barcode: GCCTAA


title: 2_neonate-wt

description: Strategy: MeDIP, Barcode: GAGAGT


title: 1_neonate-dko

description: Strategy: MeDIP, Barcode: GAGAGT


title: 16_neonate-dehet

description: Strategy: MeDIP, Barcode: AGCGCT


title: Input for H3K9me2 (d7)

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Base-calling and alignment performed by Illumina Analysis Pipeline
Conversion to BED format by bed tools v2.16
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: bed format containing the genomic coordinates of each mapped read

source_name: 3T3-L1 preadipocytes

growth_protocol: 3T3-L1 preadipocytes were routinely cultured in DMEM plus 10% BS.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For ChIP antibodies, Anti-H3K9me2 antibody from Millipore (17-648) was used for ChIP and ChIP-Seq; for H3K27me3, Millipore (07-499); for H3K4me3,   Millipore 07-473. ChIP was performed by following a protocol from R. Myers’ lab (http://www.hudsonalpha.org/myers-lab/protocols). The sequencing libraries were constructed with ChIP-Seq DNA Sample Prep kit (Illumina) and were sequenced on Illumina HiSeq 2000 system. The ChIP-enriched regions were identified using SICER (Zang et al, 2009), an algorithm designed to capture domains of diffuse signals.

treatment_protocol: adipogenesis inducing cocktails

value: mixed C57/BL6-129

tag: cell type

value: 3T3-L1 preadipocytes


title: RNA-Seq(d0)

extract_protocol: Total RNA was extracted using Trizol and the sequencing libraries were constructed with ChIP-Seq DNA Sample Prep kit (Illumina) and were sequenced on Illumina HiSeq 2000 system.


title: Input for H3K9me2


title: H3K9me2_ChIPSeq (d7)


title: H3K9me2_ChIPSeq


title: H3K27me3_ChIPSeq


title: blood draw 1 from healthy human donor 10 processed by IgG CTC chip

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description:
Sample ID: row15.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

data_processing:
Helicos Digital Gene Expression pipeline. Pubmed ID 19581875
Genome_build: hg18
Supplementary_files_format_and_content: The processed_data.txt file is a tab-delimited text file of aligned read counts.  Rownames are UCSC knownGene transcript IDs or gene symbols, column names are sample IDs. The processed_data.txt file is linked to the Series record as a supplementary file.

organism: Homo sapiens

source_name: blood

extract_protocol:
CTC capture using microfluidic chip.
Qiagen RNeasy MinElute kit followed by Helicos single molecule sequencing: Pubmed ID 18388294, 20133332

tag: donor

value: healthy human donor 10

value: blood

tag: blood draw

tag: blood processed by

value: IgG CTC chip


title: blood draw 1 from healthy human donor 10 processed by EPCAM CTC chip

description:
Sample ID: row15.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: EPCAM CTC chip


title: blood draw 1 from healthy human donor 9 processed by IgG CTC chip

description:
Sample ID: row14.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 9


title: blood draw 1 from healthy human donor 8 processed by IgG CTC chip

description:
Sample ID: row13.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 8


title: blood draw 1 from healthy human donor 8 processed by EPCAM CTC chip

description:
Sample ID: row13.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 1 from healthy human donor 6 processed by EPCAM CTC chip

description:
Sample ID: row11.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 6


title: H3K4me3_ChIPSeq

tag: strain


title: blood draw 1 from healthy human donor 7 processed by IgG CTC chip

description:
Sample ID: row12.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 7

tag: tissue


title: blood draw 1 from healthy human donor 5 processed by IgG CTC chip

description:
Sample ID: row10.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 5


title: blood draw 1 from healthy human donor 9 processed by EPCAM CTC chip

description:
Sample ID: row14.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 1 from healthy human donor 5 processed by EPCAM CTC chip

description:
Sample ID: row10.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 1 from healthy human donor 4 processed by IgG CTC chip

description:
Sample ID: row9.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 4


title: blood draw 1 from healthy human donor 4 processed by EPCAM CTC chip

description:
Sample ID: row9.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 1 from healthy human donor 3 processed by IgG CTC chip

description:
Sample ID: row8.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 3


title: blood draw 1 from healthy human donor 3 processed by EPCAM CTC chip

description:
Sample ID: row8.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 1 from healthy human donor 1 processed by IgG CTC chip

description:
Sample ID: row6.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 1


title: Input for H3K4me3 and H3K27me3


title: blood draw 1 from healthy human donor 1 processed by EPCAM CTC chip

description:
Sample ID: row6.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 5 from human breast cancer patient 1 processed by EPCAM CTC chip

description:
Sample ID: row5.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: human breast cancer patient 1


title: blood draw 4 from human breast cancer patient 1 processed by IgG CTC chip

description:
Sample ID: row4.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 1 from healthy human donor 2 processed by EPCAM CTC chip

description:
Sample ID: row7.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 2


title: blood draw 2 from human breast cancer patient 1 processed by EPCAM CTC chip

description:
Sample ID: row2.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 2 from human breast cancer patient 1 processed by IgG CTC chip

description:
Sample ID: row2.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 1 from healthy human donor 2 processed by IgG CTC chip

description:
Sample ID: row7.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: blood draw 1 from healthy human donor 7 processed by EPCAM CTC chip

description:
Sample ID: row12.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: pifq-RNA-1

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
pifq.xlsx

value: true dark

value: pif1pif3pif4pif5 (pifq)


title: WT-RNA-1

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
WT.xlsx

value: WT


title: blood draw 1 from human breast cancer patient 1 processed by EPCAM CTC chip

description:
Sample ID: row1.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: pif3-RNA-1

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
pif3.xlsx


title: blood draw 3 from human breast cancer patient 1 processed by EPCAM CTC chip

description:
Sample ID: row3.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: Transgenic fly line of Hsp70 5 bp insert promoter [PRO-seq]

description: Tru-Seq Small RNA Preparation

value: PRO-seq


title: 12_CTTGTAA

status: Public on Jan 31 2013

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Sample 12

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
Reads were aligned to the human genome, GRCh37, using TopHat (version 1.4.0) and Bowtie (version 0.12.7), using default settings and a model annotation file (GTF version 66).
Supplementary_files_format_and_content: absolute_genecounts.txt: readcounts per gene, generated by htseq-count

growth_protocol: The cell lines were cultured in DMEM 1X (Gibco) supplemented with 10% Fetal Bovine Serum (Thermo Scientific HyClone) and 1% Pen 1% Strep.

extract_protocol: Total RNA was extracted using Trizol. Sequencing libraries were constructed using Illumina TruSeq RNA PART# 15008136 REVISION A.

treatment_protocol: The samples 1/4/7/10 were grown for 4 days in the presence of 50ng/ml Doxycycline. The samples 2/5/8/11 were grown for 3 days in the presence of Doxycycline, and 24hr prior to the RNA isolation, without doxycycline to induce the expression of the m6A-Tracer or m6A-Tracer-VP16. The samples 3/6/9/12 were grown for 3 days in the presence of Doxycycline, and 24hr prior to the RNA isolation, without doxycycline and in the presence of 500nM Shield1 to induce Dam-LMNB1.

tag: clone

tag: treatment protocol

value: Doxycycline -/ Shield +


title: 11_CAGATCA

description: Sample 11

value: Doxycycline -/ Shield -


title: input_RUNX1_ChIPSeq

city: Oxford

first: Erica

last: Ballabio

address: headley way

department: The Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: Univeristy of Oxford

description: paired with the MLL ChIP-seq

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline RTA version 1.12.4. All 50-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner with the default parameters (Li and Durbin, Bioinformatics 2009, 25:1754-60). Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: hg18

source_name: Acute lymphoblastic leukemia cells with MLL/AF4 translocation

growth_protocol: The human SEM ALL cells were maintained in Iscove's Modified Dulbecco's medium (IMDM, Invitrogen, CA) with 10% fetal bovine serum (FBS).

extract_protocol:
SEM cells were double fixed with 2mM Disuccinimidyl Glutarate and then 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated. The ChIP protocol in SEM cells was followed as previously outlined  (Milne et al., Methods Mol Biol 2009, 538: 409-423), using  a 45 minute, 2mM DSG and a 45 minute 1% double fixation protocol.
Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

value: SEM

tag: chip antibody


title: RUNX1_ChIPSeq

tag: chip antibody host, amount, catelog number and provider

value: Rabbit, 2ug, ab23980, Abcam


title: blood draw 3 from human breast cancer patient 1 processed by IgG CTC chip

description:
Sample ID: row3.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: blood

value: IgG CTC chip


title: 7_CGATGTA

description: Sample 7

tag: cell line

value: Doxycycline +/ Shield -


title: pif145-RNA-1

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
pif145.xlsx

tag: genotype

value: pif1pif4pif5 (pif145)


title: 6_CTTGTAA

description: Sample 6


title: blood draw 4 from human breast cancer patient 1 processed by EPCAM CTC chip

description:
Sample ID: row4.EPCAM
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: EPCAM CTC chip


title: blood draw 1 from human breast cancer patient 1 processed by IgG CTC chip

description:
Sample ID: row1.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: 4_GCCAATA

description: Sample 4


title: 3_ACAGTGA

description: Sample 3


title: 2_TGACCAA

description: Sample 2


title: 1_CGATGTA

description: Sample 1


title: blood draw 5 from human breast cancer patient 1 processed by IgG CTC chip

description:
Sample ID: row5.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875


title: RNAP2_DHT_Polyamide_input

city: Pasadena

first: Fei

last: Yang

state: CA

address: 1200 E. California Blvd.

institute: California Institute of Technology

data_processing:
Sequencing reads were trimmed down to 36bp and then mapped against the male set of human chromosomes (excluding all random chromosomes and haplotypes) using the hg19 version of the human genome as a reference
Bowtie 0.12.7 was used for aligning reads, with the following settings: "-v 2 -t --best --strata".
ChIP-seq peaks were called using MACS2 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files: Signal profiles over genomic locations were generated using custom written python scripts; the refSeq annotation was used for gene coordinates.

source_name: LNCaP cells

extract_protocol:
Lysates were clarified from sonicated nuclei and RNAP2-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample preparation kit (Part# PE-940-2005).

value: LNCaP prostate cancer cells

tag: treatment

value: DHT with Py-Im polyamide

value: none (input)


title: RNAP2_DHT_input

value: DHT


title: blood draw 1 from healthy human donor 6 processed by IgG CTC chip

description:
Sample ID: row11.IgG
mRNA
Helicos Digital Gene Expression pipeline. See pubmed ID 19581875

value: healthy human donor 6


title: adult uterus small RNAs

city: Beijing

first: Qi

last: Chen

address: 1 Beichen West Road, Chaoyang District

department: State Key Laboratory of Reproductive Biology

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

data_processing:
Data cleaning and length distribution: 1) Getting rid of low quality reads 2) Getting rid of reads with 5' primer contaminants 3) Getting rid of reads without 3' primer 4) Getting rid of reads without the insert tag 5) Getting rid of reads with poly A 6) Getting rid of reads shorter than 18nt 7) Summarize the length distribution of the clean reads
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome (build mm9).
Genome_build: mm9
Supplementary_files_format_and_content: text files containing the reads number of each sequence

source_name: adult uterus

extract_protocol: small RNA was ligated sequentially to 5'- and 3'-adapters, followed by RT-PCR to producethe sequencing library. The PCR products were purified and sequenced.

treatment_protocol: sperm was treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H 2 O) for 20 min on ice to eliminate somatic cell contamination.

value: uterus


title: RNAP2_DHT_BR2

value: 4H8 (Abcam, catalog# ab5408)


title: adult testis small RNAs

source_name: adult testis

value: testis


title: mature sperm small RNAs

source_name: mature sperm

value: mature sperm released from cauda epididymis


title: RNAP2_NT_BR2

value: nontreated


title: Elongated spermatids

data_processing:
Data cleaning and length distribution: 1) Getting rid of low quality reads 2) Getting rid of reads with 5' primer contaminants 3) Getting rid of reads without 3' primer 4) Getting rid of reads without the insert tag 5) Getting rid of reads with poly A 6) Getting rid of reads shorter than 18nt 7) Summarize the length distribution of the clean reads
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome (build mm9).
Supplementary_files_format_and_content: text files containing the reads number of each sequence

source_name: male germ cell

extract_protocol: small RNA was ligated sequentially to 5'- and 3'-adapters, followed by RT-PCR to produce the sequencing library. The PCR products were purified and sequenced.

treatment_protocol: Total RNAs were extraced from Elongated spermatid using Trizol reagent.

value: elongated spermatids


title: 5_CAGATCA

description: Sample 5

value: Doxycycline -/ Shield -


title: RNAP2_DHT_BR1


title: 10_GCCAATA

description: Sample 10


title: Senescent shRB H3K4me3 Rep1+2

city: Cold Spring Harbor

first: Agustin

last: Chicas

address: One Bungtown Road

institute: Memorial Sloan Kettering

description:
S_shRB_H3K4me3A
S_shRB_H3K4me3B
H3K4me3 ChIP-seq in Ras-induced senescent cells with RB knockdown.
This Sample represents 2 replicates.

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and were mapped to the unmasked human reference genome (NCBI v36, hg18) using the Illumina Eland program. The reads that could not be mapped to the genome were shortened by removing 3' terminal base pairs and were realigned using Eland, to a minimum read length of 20 bp. Only the tags uniquely mapped to the genome with at most one mismatch were kept.
Sequencing data from two replicates (Rep1 and Rep2) were combined to achieve higher coverage for further analysis.
ChIP-seq peak regions were determined using MACS (Zhang et al. 2008) to find ChIP-enriched regions compared with the input control with default parameter settings and a significance threshold (P<1e-5).
The control mock data (ChIP-seq using anti-mouse IgG antibody) is in GEO Sample GSM497500 (GSE19898; Chicas A et al., Cancer Cell, 2010 (20385362)).
Genome_build: NCBI36
Supplementary_files_format_and_content: Bed files; Peak.txt files: ChIP-enriched regions.

source_name: IMR90 human fetal lung fibroblast cells, Rb shRNA, senescent, H3K4me3 ChIP

extract_protocol: The ChIP experiments were done as previously described (Chicas et al. 2010 (PMID 20385362)) using anti-H3K4me3 antibody (Millipore #05–745; 1:500). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: IMR90 cells were infected with Ras vector and the indicated hairpins. The cells were collected 7 days after puromycin selection.

value: human fetal lung fibroblast cell line

tag: shRNA

value: shRb

tag: growth state

value: senescent


title: Growing H3K4me3 Rep1+2

description:
G_H3K4me3A
G_H3K4me3B
H3K4me3 ChIP-seq in growing cells.
This Sample represents 2 replicates.

source_name: IMR90 human fetal lung fibroblast cells, growing, H3K4me3 ChIP

value: growing


title: Senescent H3K4me3 Rep1+2

description:
S_H3K4me3A
S_H3K4me3B
H3K4me3 ChIP-seq in Ras-induced senescent cells.
This Sample represents 2 replicates.

source_name: IMR90 human fetal lung fibroblast cells, senescent, H3K4me3 ChIP


title: 9_ACAGTGA

description: Sample 9

value: Doxycycline -/ Shield +


title: RNAP2_DHT_Polyamide_BR2

value: LNCaP prostate cancer cells


title: Hairpin B-treated mESCs D3

status: Public on Jan 30 2013

city: Cambridge

first: Laurie

middle: A

last: Boyer

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Sequence reads were mapped to mm9 whole genome using Tophat 1.14/ Bowtie 0.12.7 with the following parameters --min-anchor-length 6 --splice-mismatches 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --max-multihits 50 --no-novel-juncs --library-type fr-unstranded
Gene expression was calculated Reads per Kilobase of modeled exon per Million mapped reads (RPKM) using Cufflinks 1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file that includes RPKM values for each Sample, and fold-changes (with an added pseudo-count of 1) for matched hairpin/scrambled samples at each time-point.

source_name: mESC E14

growth_protocol: Embryoid body (EB) formation: ESCs were pre-plated to remove feeders, diluted to 100,000 cells/ml in complete growth medium lacking LIF and plated on low-attachment cell culture plates (Corning) to induce aggregation. Cardiomyocyte differentiation: Mouse ESCs were cultured in feeder-free conditions using standard techniques.  For directed differentiations (Kattman et al., 2011), mouse ES cells were aggregated into embryoid bodies (EB) and cultured at 75,000 cells/ml for two days in serum free media (3 parts IMDM: 1 part Ham’s F12  0.05% BSA, 2 mM GlutaMax, B27 supplement, N2 supplement) supplemented with 50 ug/ml ascorbic acid and 4.5 x 10-4 M monothioglycerol.  Embryoid bodies were dissociated and reaggregated for 40 hours in the presence of 5 ng/mL human VEGF and human Activin A and human BMP4 at concentrations empirically determined depending on lot.  EBs were dissociated and plated at 470,000 cells/cm2 in StemPro-34 supplemented with 5 ng/mL VEGF, 10 ng/mL human basic FGF and 25 ng/mL FGF10.

extract_protocol: Total RNA was isolated using TRIzol® Reagent according the manufacturer’s instructions. Sequencing libraries were prepared according to Illumina RNA-Seq library kit with minor modifications. Briefly, mRNA was isolated using Dynabeads® mRNA Purification Kit (Invitrogen) followed by fragmentation (Ambion) and ethanol precipitation. First and second strand synthesis were performed followed by end repair, A-tailing, paired end adapter ligation and size selection on a Beckman Coulter SPRI TE nucleic acid extractor. 200-400 bp dsDNA was enriched by 15 cycles of PCR with Phusion® High-Fidelity DNA Polymerase (NEB) followed by gel purification of ~250 bp fragments from the amplified material. Amplified libraries were sequenced on an Illumina GAIIx or HiSeq2000 sequencer, alternatively.

treatment_protocol: shRNAs directed against Braveheart, AK143260, and control hairpins including AK085506 were cloned into pLKO.1 vector. Lentiviral particles were produced in 293 cells using standard protocols. ESCs were transduced with viral supernatant containing 8ug/ml of polybrene and selected after 24 hours using 1.5 ug/ml of Puromycin.

value: mESC

tag: age

value: embryonic

value: Hairpin B-treated

tag: time


title: Hairpin B-treated mESCs D9

tag: cell type


title: Hairpin A-treated mESCs D9

value: Hairpin A-treated


title: Hairpin B-treated mESCs D6


title: Hairpin B-treated mESCs D0


title: not2 RNA-seq

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: high-throughput profiling of transcriptome in not2 (mutant)

data_processing:
Arabidopsis genome sequences and annotated gene models were downloaded from TAIR10. The single end reads with strand direction were aligned to TAIR10 genome sequence using TopHat (Trapnell et al., 2009). Splice junction sequences required at least four bases on each side of the junction.  Reads mapped to only uniquely mapped reads were used for subsequent analysis. The gene expression levels were measured in reads per kilobase of exon model per million mapped reads (RPKM), (Mortazavi et al., 2008). The differential expressed genes were identified using DEGseq (Wang et al., 2010).
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using MACS program

source_name: not2_12DAG seedlings

growth_protocol: All of the Arabidopsis thaliana lines used in this study were Columbia ecotype (Col). Plants were grown under long photoperiod conditions (16 hours light/8 hours dark) at 23℃. Seedlings were grown on Murashige and Skoog (MS) plates containing 3% sucrose and 0.8% agar.

extract_protocol:
Total RNAs were extracted from seedlings of wild type and not2 with TRIzol Reagent (15596–026; Invitrogen).
Total RNAs were extracted from seedling using TRIzol Reagent (15596–026; Invitrogen). Polyadenylated RNAs were isolated using Dynabeads® mRNA Purification Kit (Invitrogen). The RNA-Seq libraries were prepared using Illumina Directional mRNA-Seq Library Prep. v1.5 protocol and sequenced on Illumina GAII to generate high-quality single-end reads.

tag: ecotype

value: col

tag: genotype/variation

value: not2 mutant

value: 12DAG seedlings


title: Hairpin A-treated mESCs D6


title: Hairpin A-treated mESCs D0


title: Hairpin A-treated mESCs D3


title: 8_TGACCAA

description: Sample 8


title: RNAP2_DHT_Polyamide_BR1

value: DHT with Py-Im polyamide

value: 4H8 (Abcam, catalog# ab5408)


title: v6.5 mouse ESC replicate 1

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Sequence reads were mapped to mm9 whole genome using Tophat 1.3 with the following parameters --min-anchor-length 6 --splice-mismatches 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --max-multihits 50 --no-novel-juncs --no-novel-indels --library-type fr-unstranded
Gene expression was calculated as Reads per Kilobase of modeled exon per Million mapped reads (RPKM) using rsem
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file that includes RPKM values for each Sample.

source_name: mESC v6.5

growth_protocol: Mouse ESCs and iPS cells were cultured on irradiated MEFs using standard techniques. Cell were pre-plated for 30 minutes prior to harvesting to remove MEFs. 11.3 and 11.5 cells were cultured in feeder-free conditions.

extract_protocol: Total RNA was isolated using TRIzol® Reagent according the manufacturer’s instructions. Sequencing libraries were prepared according to Illumina RNA-Seq library kit with minor modifications. Briefly, mRNA was isolated using Dynabeads® mRNA Purification Kit (Invitrogen) followed by fragmentation (Ambion) and ethanol precipitation. First and second strand synthesis were performed followed by end repair, A-tailing, paired end adapter ligation and size selection on agarose gels. 200-400 bp dsDNA was enriched by 15 cycles of PCR with Phusion® High-Fidelity DNA Polymerase (NEB) followed by gel purification of ~250 bp fragments from the amplified material. Amplified libraries were sequenced on an Illumina GAII or GAIIx sequencer, alternatively.

treatment_protocol: No treatment was applied to the cell lines used to identify candidate lincRNAs.

value: 129/svJae x C57BL/6

value: wild type


title: 11.3/ MCV6, partially reprogrammed MEF

description: Described in http://www.ncbi.nlm.nih.gov/pubmed/18509334; subclone 6 generated in http://www.ncbi.nlm.nih.gov/pubmed/17724450

value: partially reprogrammed mouse embryonic fibroblast

value: Oct4-GFP, retrovirally-transduced with Oct4, Sox2, c-myc and Klf4


title: miPS MCV8.1, fully reprogrammed MEF (iPS)

description: Generated as described in http://www.ncbi.nlm.nih.gov/pubmed/18509334

value: induced pluripotent stem cell

value: reprogrammed cell


title: Scrambled Hairpin-treated mESCs D9

value: Scrambled Hairpin-treated


title: Scrambled Hairpin-treated mESCs D3


title: Scrambled Hairpin-treated mESCs D0


title: E14 mouse ESC replicate 1


title: E14 mouse ESC replicate 2


title: 11.5/ MCV8, partially reprogrammed MEF

description: Described in http://www.ncbi.nlm.nih.gov/pubmed/18509334; subclone 12 generated in http://www.ncbi.nlm.nih.gov/pubmed/17724450


title: RNAP2_NT_BR1

value: LNCaP prostate cancer cells

value: nontreated


title: WT  RNA-seq

description: high-throughput profiling of transcriptome in WT (wild type)

source_name: WT_12DAG seedlings


title: Quiescent H3K4me3 Rep1+2

description:
Q_H3K4me3A
Q_H3K4me3B
H3K4me3 ChIP-seq in quiescent cells.
This Sample represents 2 replicates.

source_name: IMR90 human fetal lung fibroblast cells, quiescent, H3K4me3 ChIP

value: human fetal lung fibroblast cell line

value: quiescent


title: v6.5 mouse ESC replicate 2

value: mESC

value: embryonic


title: mouse_p0_cortex_p300

status: Public on Jan 29 2013

city: Berkeley

first: Matthew

middle: James

last: Blow

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

description: Tissue from a single individual. Chromatin IP against acCBP/p300 (rabbit polyclonal, Cell Signaling Technology, catalog number = 4771,  lot number = 2)

data_processing:
Peaks: Sequence data in the file mouse_e11.5_forebrain_p300.fastq was supplemented with reads from a previously described forebrain p300 ChIP‐seq dataset (Visel et al, Nature 2009).  P300 enriched regions were were identified using CCAT (Xu et al, bioinformatics 2010), using a previously described forebrain control sample (Visel et al, Nature 2009). CCAT was run using default parameters for ‘histone’ ChIP-Seq, except for minscore = 2. Enriched regions were filtered to remove those with: i)mapping to an unassembled genomic fragment, ii) an FDR < 0.2, iii) a CCAT enrichment score of <6.5, iv) a sample/control read depth ratio of <2, v) overlap with another CCAT peak with a higher-score region, and v) length >7kb. Finally, peaks within 5kb of the nearest transcript start site were excluded as likely promoters
Peaks: AcCBP/p300 enriched regions in mouse p0 cortex, and human fetal cortex p300 ChIP samples were identified from the intersection of peaks identified by MACS11 (version 1.4, with default settings except: bw = 300; P = 1 × 10−5; mfold = 10,30; local = 20,000; off-auto–shift size = 100) and a modified Grizzly Peak fitting algorithm. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.
Alignment: Sequence data in the file mouse_e11.5_forebrain_p300.fastq was supplemented with reads from a previously described forebrain p300 ChIP‐seq dataset (Visel et al, Nature 2009) prior to alignment. Reads were mapped to the mouse genome (mm9) or human genome (hg18) using the Burrows‐ Wheeler Alignment (BWA) tool. Repetitively mapped reads (mapping to multiple sites) and likely PCR artifacts (multiple reads mapping with identical start sites) were removed.
Wig: Aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
Genome_build: mm9
Genome_build: hg18

source_name: mouse postnatal (P0) cortex

extract_protocol: Tissue samples were cross linked and cells were dissociated and subject to  chromatin isolation, sonication and immunoprecipitation using an anti-P300 or anti-acCBP/p300 antibody.  ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters.  Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the  Illumina  GAII or Illumina HiSeq 2000 platforms

value: mouse cortex

tag: developmental stage


title: rrp6_s3_ribominus_bio-rep2_tech-rep1 [RNA-Seq]

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description:
RiboMinus_rRNA depleted RNA sample
processed data file: rrp6-s3-ribominus.csv

data_processing:
Base-calling performed on GAII (pipeline v 1.7.0) or HiSeq machines (pipeline v 1.7.0, CASAVA 1.8)
Adapters were trimmed from raw fastq reads with cutadapt v1.0
Reads were aligned to Drosophila dm3 (excluding chrUextra) using TopHat v1.4.1 with parameters –butterfly-search -X
Reads were counted in annotated genes from FlyBase r5.33 using htseq-count v0.5.3p9
Counts from technical replicates were summed
Differential expression was evaluated using Bioconductor/R (v2.15.2) and DESeq v1.9.11, using method=”per-condition” where biological replicates were available, or “blind” otherwise, sharingMode=”fit-only” and fitType=”local”
Genome_build: Release 5
Supplementary_files_format_and_content: CSV files of DESeq output (see http://www.bioconductor.org/packages/release/bioc/html/DESeq.html for details), with gene identifiers from FlyBase r5.33.  Headers of processed data files indicate configuration and parameters used for DESeq (in YAML format); nested lists of sample IDs in the configuration indicate technical replicates whose counts were summed prior to running DESeq

source_name: S3 cells

growth_protocol: cells maintained at 2.0 x 10e6 cells/mL - 1.0 x 10e7 cells/mL

extract_protocol: Total RNA was isolated from S2 and S3 cells using Trizol Reagent (Invitrogen) using the recommended protocol.  Polyadenylated RNA and rRNA depleted RNA was purified from total RNA using the Poly(A)Purist MAG or MicroPoly(A)Purist Kits (Ambion) and the RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen) respectively.  Depletion of rRNA was approximately 99% by qPCR measurement of 5S rRNA.  Sequencing libraries were prepared from Poly(A)+ and rRNA depleted RNA samples according to the manufacturer’s protocol (Illumina)

treatment_protocol: Amplicons used for dsRNA knockdowns were designed based on recommendations from the Drosophila RNAi Screening Center.  Templates were PCR amplified from genomic DNA using primers containing the T7 promoter sequence.  DsRNAs were produced by in vitro transcription of PCR templates using the MEGAscript T7 kit (Ambion) and purified using NucAway Spin Columns (Ambion).  S2 and S3 cells were grown at 25C in Shields and Sang M3 Insect medium (Sigma) supplemented with 0.1% yeast extract, 0.25% bactopeptone, and 10% fetal bovine serum (HyClone).  Transfections of 1 x 107 cells using 2 ug of dsRNA were performed using Cell Line Nucleofector Kit V (Amaxa Biosystems) transfection reagent using the G-30 protocol.  On day 2, cells were diluted with normal media approximately 1:5.  Five days after transfection, cells were collected, and knockdown efficiency was confirmed by Western blotting.

tag: knockdown

tag: post-trizol, rna enrichment protocol

tag: qualscores


title: rrp6_s3_ribominus_bio-rep2_tech-rep2 [RNA-Seq]

value: RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen)


title: rrp6_s3_polya_bio-rep3 [RNA-Seq]

description:
Poly(A)+ RNA sample
processed data file: rrp6-s3-polyA.csv

value: Poly(A)Purist MAG or MicroPoly(A)Purist Kit (Ambion)


title: rrp6_s2_ribominus_bio-rep3 [RNA-Seq]

description:
RiboMinus_rRNA depleted RNA sample
processed data file: rrp6-s2-ribominus.csv

source_name: S2 cells


title: MEF, used for reprogramming to MCV6/MCV8/MCV8.1

description: Generated as described in http://www.ncbi.nlm.nih.gov/pubmed/18159219

source_name: MEF

tag: strain

tag: tissue

value: fibroblast


title: SD-nitrogen mRNA-seq Replicate 2

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

data_processing:
Base calling was performed according to Illumina's protocols.
Low-quality reads were removed if they met any of the following criteria: <18 nt, only homopolymer As, missing 3’ adapter, 5’-3’ adapter ligation products, 5’-5’ adapter ligation products, low quality (more than 4 bases with quality scores below 10 or more than 6 bases with a quality score below 13).
High-quality reads were aligned to S. cerevisiae genome version sacCer3 using Bowtie v0.12.7 with the parameters -k 275 -v 3 --best --strata.
Read counts in each library were normalized to the total number of mapped reads in millions (RPM).
For mRNA-seq: Reads mapping uniquely to the genome with zero mismatches were were used to calculate RPM per kilobase of transcript (RPKM) for each gene.
For gPAR-CLIP and Puf3p PAR-CLIP: Reads mapping uniquely to the genome with 1 or 2 T-to-C mismatches were used to generate read clusters defined as a continuous stretch of nucleotides covered by at least 1 read. Clusters were fitted with a Gaussian curve based on the aggregate RPM of each position in the cluster.
A false discovery rate was calculated for each gPAR-CLIP and Puf3p PAR-CLIP clusters based on clusters derived from mRNA-seq reads with 1 or 2 T-to-C mismatches.
Genome_build: SGD/sacCer3 (April 2011) from S288C strain
Supplementary_files_format_and_content: Normalized read coverage for each binding site in each gPAR-CLIP library and Puf3p PAR-CLIP library is presented.
Supplementary_files_format_and_content: Normalized transcript abundance (RPKM) is presented for each transcript in each mRNA-seq library.

organism: Saccharomyces cerevisiae

source_name: Whole cell

growth_protocol: For gPAR-CLIP, mRNA-seq, and Puf3p PAR-CLIP, strains were grown at 30°C with rigorous shaking in synthetic defined (SD) media supplemented with 200 µM 4-thiouracil (when indicated) to OD600 = 0.7-0.8.

extract_protocol: For gPAR-CLIP, crosslinked cells were resuspended in polysome lysis buffer (20 mM HEPES pH 7.5, 140 mM KCl, 1.5 mM MgCl2, 1% Triton X-100, 1X Complete Mini Protease Inhibitor EDTA-free (Roche 1 836 170), 0.2 U/µL SUPERase·In (Invitrogen AM2696)), mixed with ½ volume of acid-washed glass beads, and lysed by vortexing four times at 4°C, 1 min each with 1 min incubation on ice in between. Cell debris was removed by centrifugation for 5 min at 1,300Xg at 4°C. Supernatant was cleared by 20,000Xg spin for 10 min at 4°C. 15-50% (w/v) sucrose density gradients were prepared in Beckman polycarbonate centrifugation tubes (11 X 34 mm) by sequentially layering and freezing 0.24 mL of 50%, 41.25%, 32.5%, 23.75% and 15% sucrose dissolved in polysome gradient buffer (20 mM HEPES pH 7.5, 140 mM KCl, 5 mM MgCl2). Gradients were thawed overnight at 4°C before use. 100 µL of clarified lysate was loaded on top of a gradient, centrifuged for 1 hr at 54,000 rpm at 4°C using a TLS-55 rotor in an Optima MAX-E ultracentrifuge (Beckman Coulter). The top 600 µL of the gradient was recovered and supplemented with 2 µL of SUPERase·In (20 U/µL). 60 µL of freshly prepared 10mM EZ-Link NHS-SS-Biotin (Pierce 21441) dissolved in dimethylformamide was added to the recovered lysate and incubated on a Nutator for 2 hr at 4°C. 50 µL of 5 M NaCl was added to increase the total salt concentration to 0.5 M. Biotinylated lysate was mixed with 1 mg of oligo(dT)25 magnetic beads (NEB S1419S), then incubated on a Nutator for 30 min at 4°C. Beads were washed 4 times with ice-cold hybridization buffer (10 mM HEPES pH 7.5, 0.5 M NaCl, 1 mM EDTA). RNAs were eluted by incubating beads with 500 µL of elution buffer (10 mM HEPES pH 7.5, 1 mM EDTA) and heating at 65°C for 3 min. Eluted sample was transferred to a new tube and mixed with 55 µL of 10XPBS. PolyA-selected samples were mixed with 1 mg of streptavidin M280 Dynabeads (Invitrogen 112-05D) and incubated on a Nutator for 30 min at 4°C. Beads were washed 3 times with 1XPBS, then incubated with 20 µL of 50 U/µL RNase T1 (Fermentas EN0541, 1:20 dilution in 1XPBS) at 22°C for 15 min on an Eppendorf Thermomixer (15 sec shaking at 1,000 rpm followed by a 2 min rest interval), followed by 5 min incubation on ice. Beads were washed twice with wash buffer (1XPBS, 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40), twice with high-salt wash buffer (5XPBS, 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40), and twice with 1XPNK buffer (50 mM Tris pH 7.4,10 mM MgCl2, 0.5% NP-40). Beads were incubated with 20 µL of CIP mix (50 mM Tris pH 7.9, 100 mM NaCl, 10 mM MgCl2, 0.5 U/µL CIP (NEB M0290S)) at 37°C for 15 min, with 15 sec shaking at 1,000 rpm followed by a 2 min rest interval on a Thermomixer. After CIP treatment, beads were washed twice with 1XPNK+EGTA buffer (50 mM Tris pH 7.4, 20 mM EGTA, 0.5% NP-40) and twice with 1XPNK buffer. Beads were incubated with 20 µL of ligation mix (50 mM Tris pH 7.4, 10 mM MgCl2, 0.5 mM DTT, 2 µM Pre-adenylated 3’ DNA linker, 25% PEG-8000, 10 U/µL T4 RNA ligase 2, truncated K227Q (NEB M0351S)) at 16°C overnight (≥16 hr), with 15 sec shaking at 1,000 rpm followed by a 2 min interval on a Thermomixer. After linker ligation, beads were washed 3 times with 1XPNK+EGTA buffer. Beads were mixed with 12 µL of 1XPNK+EGTA buffer, 3 µL of freshly made 1M DTT and 15 µL of 4X NuPAGE LDS sample buffer (Invitrogen NP0007), and incubated at 70°C for 10 min. Beads were removed, and the supernatant was loaded onto NuPAGE 4-12% Bis-Tris gel (Invitrogen NP0335BOX) and run at 150 V for 35 min. Gel was transferred to Protran BA 85 nitrocellulose membrane (pore size 0.45 µm, Whatman 10402594) using Novex wet transfer at 30 V for 1 hr. A broad band from 31 kDa up to the top of the gel was excised, cut into small pieces, and transfered into a microfuge tube. Excised membranes were incubated with 500 µL of 4 mg/mL Proteinase K prepared in 1X PK buffer (100 mM Tris pH 7.5, 50 mM NaCl, 10 mM EDTA) for 20 min at 37°C on a Thermomixer. 500 µL of 7M urea prepared in 1X PK buffer were added to the tube followed by another 20 min incubation at 37°C. Proteinase K digestion reaction was mixed with 1 mL of Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma-Aldrich P2069) by vortexing and spun for 5 min at 20,000Xg. Liquid phase was transferred to a new tube, mixed with 125 µL of 3 M NaOAc, 2.5 mL of 100% ethanol and 1 µL of 15 mg/mL glycoblue (Invitrogen AM9516), and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature followed by 2 washes with cold 75% ethanol. RNA pellets were air-dried briefly, resuspended in 10 µL of PNK mix (70 mM Tris pH 7.6, 10 mM MgCl2, 5 mM DTT, 1 mM ATP, 1 U/µL T4 polynucleotide kinase (NEB M0201S), 1 U/µL SUPERase·In), and incubated at 37°C for 30 min. The reaction was combined with 90 µL of H2O and 100 µL of Phenol:Chloroform:Isoamyl Alcohol 25:24:1, mixed well, and spun for 5 min at 20,000Xg. The liquid phase was mixed with 12.5 µL of 3 M NaOAc, 250 µL of 100% ethanol, 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by 2 washes with cold 75% ethanol. RNA pellets were resuspended in 10 µL of ligation mix (50 mM Tris pH 7.5, 10 mM MgCl2, 10 mM DTT, 1mM ATP, 0.1 mg/mL BSA, 2 µM 5’ RNA linker, 1 U/µL T4 RNA ligase (Fermentas EL0021), 1 U/µL SUPERase•In, 10% DMSO) and incubated at 15°C for 2 hr. Ligation reaction was terminated by adding 10 µL of 2X formamide gel loading buffer (Invitrogen AM8546G), heated for 2 min at 70°C, and then quickly chilled on ice. Samples were loaded onto a 6% TBE UREA gel (Invitrogen EC6865BOX) and run at 150 V for 45 min. After staining with 1X Sybr Gold Stain (Invitrogen S-11494), a gel piece corresponding to 70-90 nt RNA (80-100 nt ssDNA) was excised, crushed, and soaked in 400 µL of 0.3 M NaOAc overnight at room temperature. After removing gel pieces, the solution was combined with 1 mL of 100% EtOH and 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by two washes with cold 75% ethanol. After brief drying, RNAs were resuspended in 15 µL of H2O. 10 μL of ligated RNA was combined with 2 μL of 5 µM RT primer, heated at 65°C for 5 min, and then quickly chilled on ice, followed by the addition of 1 µL of 10 mM dNTP, 1 μL of 0.1 M DTT, 4 μL of 5X First strand buffer, 1 μL of SUPERase•In (20 U/µL) and 1 µL of SuperScript III Reverse transcriptase (Invitrogen 18080-093, 200 U/µL). RT reaction was kept at 50°C for 45 min, 55°C for 15 min and 90°C for 5 min. A test PCR was performed with 2.5 µL of RT product in 50 µL PCR mix: 1X AccuPrime PCR buffer I, 0.5 µM P5 long primer, 0.5 µM P7 primer, 0.2 µL AccuPirme Taq High Fidelity (Invitrogen 12346-086, 5 U/µL). PCR was carried out with an initial 3 min denaturation at 98°C, followed by 14-22 cycles of 80 sec denaturation at 98°C, 90 sec annealing and extension at 65°C, and termination with a final 5 min extension at 65°C. 15 µL PCR product was collected after 14, 18, and 22 cycles and analyzed on a 10% TBE gel (Invitrogen EC6275BOX) at 150 V for 1 hr to determine the optimal amplification cycles (the lowest cycle number required to generate 96-116 bp amplicons detected by Sybr Gold staining). A 50 µL PCR reaction was carried out with the determined cycle number. Amplicons were purified using DNA clean and concentrator-5 (Zymo D4013), run on 10% TBE gels at 150 V for 1 hr and stained with Sybr Gold. A gel piece corresponding to 96-116 bp DNA was excised, crushed, and soaked overnight in 400 µL 0.3 M NaOAc at room temperature. After removing gel pieces, the solution was combined with 1 mL of 100% EtOH and 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. DNAs were collected by centrifugation for 20 min at

treatment_protocol: For gPAR-CLIP and mRNA-seq, glucose and nitrogen starvation was performed by pelleting cells, discarding media, rinsing once with H2O, and re-suspending cells in SD without glucose or nitrogen. Cells were returned to 30°C with rigorous shaking for 2 hr. For gPAR-CLIP and PAR-CLIP procedure, 50 mL of mid-log phase cultures (OD600 of 0.7-0.8) were pelleted for 5 min at 3,000Xg at room temperature, resuspended in 2 mL of 1XHBSS (Invitrogen 14025), transferred to 60 mm cell culture dish (BD Biosciences 353002), placed on ice, and irradiated with 365nm UV at 150 mJ/cm2 4 times using a UVP CL-1000L UV crosslinker. Cells were then pelleted for 2 min at 5,000Xg at 4°C. After removing 1X HBSS, the cells were frozen in liquid nitrogen.

value: WT BY4742 (MATa his3-delta-1 leu2-delta-0 lys2-delta-0 ura3-delta-0)

value: 2 hr growth without nitrogen

tag: 4-thiouracil addition

value: Yes

tag: sucrose gradient step

value: ACTTGA


title: Puf3p PAR-CLIP

value: (MATa his3-delta-1 leu2-delta-0 met15-delta-0 ura3-delta-0 PUF3-TAP::HIS5)

value: TTAGGC


title: SD-glucose mRNA-seq Replicate 2

value: 2 hr growth without glucose

value: GCCAAT


title: SD total mRNA-seq Replicate 2

value: No

value: TGACCA


title: SD total mRNA-seq Replicate 1


title: rrp6_s2_polya_bio-rep3 [RNA-Seq]

description:
Poly(A)+ RNA sample
processed data file: rrp6-s2-polyA.csv


title: SD mRNA-seq Replicate 2


title: SD-glucose mRNA-seq Replicate 1

value: ACAGTG


title: SD mRNA-seq Replicate 1


title: rrp40_s3_ribominus_bio-rep2_tech-rep2 [RNA-Seq]

description:
RiboMinus_rRNA depleted RNA sample
processed data file: rrp40-s3-ribominus.csv


title: Scrambled Hairpin-treated mESCs D6

value: mESC

value: Scrambled Hairpin-treated


title: rrp40_s3_ribominus_bio-rep2_tech-rep1 [RNA-Seq]


title: rrp6_s3_ribominus_bio-rep3 [RNA-Seq]


title: gfp_s3_ribominus_bio-rep2_tech-rep2 [RNA-Seq]

description: RiboMinus_rRNA depleted RNA sample

value: GFP


title: rrp40_s2_ribominus_bio-rep3 [RNA-Seq]

description:
RiboMinus_rRNA depleted RNA sample
processed data file: rrp40-s2-ribominus.csv

value: RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen)


title: rrp40_s3_polya_bio-rep2_tech-rep1 [RNA-Seq]

description:
Poly(A)+ RNA sample
processed data file: rrp40-s3-polyA.csv

value: Poly(A)Purist MAG or MicroPoly(A)Purist Kit (Ambion)


title: rrp40_s2_polya_bio-rep3 [RNA-Seq]

description:
Poly(A)+ RNA sample
processed data file: rrp40-s2-polyA.csv


title: gfp_s3_ribominus_bio-rep3 [RNA-Seq]

description: RiboMinus_rRNA depleted RNA sample


title: rrp40_s3_polya_bio-rep2_tech-rep2 [RNA-Seq]


title: SD-4sU mRNA-seq Replicate 2

value: CGATGT


title: rrp40_s3_polya_bio-rep3 [RNA-Seq]


title: SD-nitrogen mRNA-seq Replicate 1

value: WT BY4742 (MATa his3-delta-1 leu2-delta-0 lys2-delta-0 ura3-delta-0)

value: CAGATC


title: gfp_s3_ribominus_bio-rep2_tech-rep1 [RNA-Seq]

description: RiboMinus_rRNA depleted RNA sample


title: gfp_s3_polya_bio-rep3 [RNA-Seq]

description: Poly(A)+ RNA sample


title: rrp40_s3_ribominus_bio-rep3 [RNA-Seq]


title: gfp_s3_polya_bio-rep2_tech-rep2 [RNA-Seq]

description: Poly(A)+ RNA sample


title: WT-RNA-2

description:
3'-end fragments were captured by polyA purification after mRNA fragmentation
WT.xlsx

source_name: whole seedlings

tag: developmental satge

tag: growth conditions

value: true dark

tag: genotype

value: WT


title: gfp_s3_polya_bio-rep2_tech-rep1 [RNA-Seq]

description: Poly(A)+ RNA sample


title: gfp_s2_polya_bio-rep3 [RNA-Seq]

description: Poly(A)+ RNA sample


title: gfp_s2_ribominus_bio-rep3 [RNA-Seq]

description: RiboMinus_rRNA depleted RNA sample


title: SD-4sU mRNA-seq Replicate 1

tag: treatment

value: Yes

value: ATCACG


title: SD-glucose gPAR-CLIP Replicate 2

value: 2 hr growth without glucose


title: SD-nitrogen gPAR-CLIP Replicate 2

value: 2 hr growth without nitrogen


title: SD-nitrogen gPAR-CLIP Replicate 1

value: TTAGGC


title: tnfpre0h2

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: molecule: bru-labeled RNA

data_processing:
Library strategy: Bru-Seq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)

source_name: Foreskin fibroblasts

growth_protocol: Cells were hTERT immortalized and grown as monolayers in MEM supplied with 10% fetal bovine serum and antibiotics.

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: Bromouridine (Aldrich) was added to the media to a final concentration of 2 mM and cells were incubated at 37°C for 30 min. Cells were then washed 3 times in PBS and either collected directly (nascent RNA, Bru-Seq) or chased in conditioned media containing 20 mM uridine for 6 hours at 37°C (6-hour old RNA, BruChase-Seq). For TNF treatments, recombinant human TNF-alpha (R&D Systems, Minneapolis, MN) was used in a concentration of 10 ng/ml from a 10 μg/ml stock solution in PBS.

value: Foreskin fibroblasts

tag: extraction time

value: 0h after Bru labeling

value: TNF exposure prior to Bru labeling

tag: stranded

value: TRUE


title: SD-glucose gPAR-CLIP Replicate 1


title: SD gPAR-CLIP Replicate 2


title: 12A_adult-wt

description: Strategy: MeDIP, Barcode: GCGTGG

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
Mapping: bowtie
computation of coverage values: wiggles
Genome_build: mm9
Supplementary_files_format_and_content: Format: bedgraph, Content: genomic coverage

source_name: cerebrum

extract_protocol:
Homogenized mouse tissues were incubated overnight in 100mM Tris-HCl pH 8 containing 5mM EDTA, 0.2% SDS, 200 mM NaCl and 400 µg/ml proteinase K, and DNA was then isolated using a standard protocol with phenol:chloroform:isoamyl alcohol and Phase Lock Gel™ separation tubes. Genomic DNA was finally treated with RNAse A (20 µg/ml) for 30 minutes at 37°C.
Thirty µg of genomic DNA for each sample was sonicated to 300bp fragments using a Covaris S220 (Covaris). Sheared DNA was ethanol precipitated, washed with 70% ethanol, and dissolved in TE buffer (pH8.0). Illumina adapters were ligated using the End-It DNA End-repair kit (Epicentre). DNA was purified with the QiaQuick PCR purification kit (Qiagen) and diluted to 122.5µl with ddH2O. After the addition of 15µl NEB buffer 2, 3.5µl of 10mM ATP and 9µl of 5U/µl Klenow exo- (NEB), reactions were incubated at 37°C for 50min. DNA was subsequently purified with the QiaQuick PCR purification kit, diluted to 24µl with ddH2O, and mixed with 50µl of 2x NEB quick ligation buffer, 20 µl of barcoded Illumina adapter and 6µl of quick T4 DNA ligase (NEB). After 20 minutes incubation at room temperature, DNA was purified again with QiaQuick PCR purification kit. Ligation efficiency was analyzed by PCR on 10ng of final ligated DNA with Illumina sequencing primers. Finally, five µg of adapter ligated DNA was used for the immunoprecipitation, as described above. Immunoprecipitated DNA was resolved in 20µl of water and all (h)MeDIP samples were pooled to create the MeDIP and hMeDIP libraries, respectively. Both libraries were purified on e-Gel (Invitrogen) and the 300bp bands (containing roughly 200bp fragments of adapter-ligated immunopurified DNA) were extracted. Libraries were amplified using Illumina-Enrichment Primers for 12 cycles and purified using Agencourt AMPure XP beads (Beckman Coulter). DNA concentrations were measured using a Agilent High Sensitivity DNA Assay (Agilent Technologies) and 7 pmol were used for cluster PCR and substantial 100bp paired-end sequencing on a HiSeq2000 (Illumina).

value: cerebrum

value: adult

value: mixed 129|C57BL/6

tag: tet1/tet2 treatment

tag: antibody

tag: vendor/catalog/lot

value: monoclonal, Active Motif, 39649


title: csl4_s3_ribominus_bio-rep2_tech-rep2 [RNA-Seq]

description:
RiboMinus_rRNA depleted RNA sample
processed data file: csl4-s3-ribominus.csv

tag: cell type

value: RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen)


title: tnfpost6h1

description: molecule: bru-labeled RNA

value: 6h after Bru labeling

value: TNF exposure post Bru labeling

value: FALSE


title: csl4_s3_ribominus_bio-rep2_tech-rep1 [RNA-Seq]

tag: knockdown


title: SD gPAR-CLIP Replicate 1

value: WT BY4742 (MATa his3-delta-1 leu2-delta-0 lys2-delta-0 ura3-delta-0)

value: Yes


title: csl4_s3_polya_bio-rep3 [RNA-Seq]

description:
Poly(A)+ RNA sample
processed data file: csl4-s3-polyA.csv

tag: post-trizol, rna enrichment protocol

value: Poly(A)Purist MAG or MicroPoly(A)Purist Kit (Ambion)


title: csl4_s2_polya_bio-rep3 [RNA-Seq]

description:
Poly(A)+ RNA sample
processed data file: csl4-s2-polyA.csv

tag: qualscores


title: nf6h2

description: molecule: bru-labeled RNA

value: Control


title: nf6h3b

description: molecule: bru-labeled RNA


title: tech_rep2_input_S3 [ChIP-Seq]

data_processing:
ChIP-seq reads were aligned to Drosophila dm3 (excluding chrUextra) using bowtie 0.12.7 with parameters --best --strata -- --sam -m1 -n2 --tryhard -k1
Libraries from technical replicates were merged for peak calling
Duplicate reads were collapsed with Picard's MarkDuplicates
Peaks were called with SPP, FDR=0.01
BAM files generated using bowtie and BED files of called peaks generated using SPP
Genome_build: dm3
Supplementary_files_format_and_content: BED files (linked to Series record) of called peaks generated using SPP

extract_protocol:
Cells were fixed by addition of 1% formaldehyde to cell media for 10 min at R.T. with gentle agitation. Formaldehyde was quenched by addition of glycine to 0.125 M with gentle agitation for 5 min at R.T. Cells were pelleted at 400 rcf, washed twice in PBS, and resuspended in 1 mL ice cold cell lysis buffer (5 mM PIPES, pH 8, 85 mM KCl, 0.5% NP-40) supplemented with Complete protease inhibitors (Roche). Nuclei were released by Dounce homogenization with pestle B and pelleted by centrifugation at 9190 rcf for 5 min at 4C. Nuclei and chromatin were further processed as described previously [Moshkovich, N. and Lei, E.P. (2010). HP1 recruitment in the absence of argonaute proteins in Drosophila. PLoS Genet, 6 (3), e1000880. PMID: 20300658].
Immunoprecipitations were performed with 3 uL rabbit anti-Rrp6 [Andrulis, E.D., et al. (2002). The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature, 420 (6917), 837-841. PMID: 12490954], rabbit anti-Rrp40 [Graham, A.C., Kiss, D.L. and Andrulis, E.D. (2006). Differential distribution of exosome subunits at the nuclear lamina and in cytoplasmic foci. Mol Biol Cell, 17 (3), 1399-1409. PMID: 16407406] or guinea pig anti-Su(Hw) [Moshkovich, N. and Lei, E.P. (2010). HP1 recruitment in the absence of argonaute proteins in Drosophila. PLoS Genet, 6 (3), e1000880. PMID: 20300658] coupled to rProtein A agarose beads (GE Healthcare).
Samples for ChIP-seq from input DNA, Rrp6 ChIP, Rrp40 ChIP, and Suhw ChIP were prepared according to the manufacturer's protocol with standard or TruSeq adapters (Illumina). DNA was sequenced on an Illumina Genome Analyzer II or Hi-Seq at the NIDDK Genomics Core Facility.

treatment_protocol: chromatin immunoprecipitation using respective antibodies

tag: chip antibody

value: S3 late embryonic cells


title: tech_rep2_Rrp6_S3 [ChIP-Seq]

description: Processed data file: Rrp6_S3.bed


title: nf0h2

description: molecule: bru-labeled RNA

value: Foreskin fibroblasts


title: tech_rep2_Rrp40_S3 [ChIP-Seq]

description: Processed data file: Rrp40_S3.bed


title: csl4_s2_ribominus_bio-rep3 [RNA-Seq]

description:
RiboMinus_rRNA depleted RNA sample
processed data file: csl4-s2-ribominus.csv


title: nf0h3a

description: molecule: bru-labeled RNA

value: 0h after Bru labeling


title: nf0h4

description: molecule: bru-labeled RNA


title: tech_rep2_input_S2 [ChIP-Seq]

value: S2 late embryonic cells


title: tech_rep2_Rrp6_S2 [ChIP-Seq]

description: Processed data file: Rrp6_S2.bed


title: nf0h1

description: molecule: bru-labeled RNA


title: csl4_s3_ribominus_bio-rep3 [RNA-Seq]


title: tnfpre0h1

description: molecule: bru-labeled RNA

value: TNF exposure prior to Bru labeling


title: gfp_s3_polya_bio-rep1 [RNA-Seq]

description: Poly(A)+ RNA sample

value: GFP


title: rrp6_s3_polya_bio-rep1 [RNA-Seq]


title: rrp6_s2_polya_bio-rep1 [RNA-Seq]


title: gfp_s2_polya_bio-rep1 [RNA-Seq]

description: Poly(A)+ RNA sample


title: tech_rep1_Rrp40_S3 [ChIP-Seq]

description: Processed data file: Rrp40_S3.bed


title: csl4_s2_polya_bio-rep1 [RNA-Seq]


title: tech_rep1_input_S2 [ChIP-Seq]


title: csl4_s3_polya_bio-rep1 [RNA-Seq]


title: tech_rep1_input_S3 [ChIP-Seq]


title: tech_rep1_Rrp6_S3 [ChIP-Seq]

description: Processed data file: Rrp6_S3.bed


title: Suhw_S2 [ChIP-Seq]

description: Processed data file: Suhw_S2.bed

value: Su(Hw)


title: tech_rep2_Rrp40_S2 [ChIP-Seq]

description: Processed data file: Rrp40_S2.bed


title: tech_rep1_Rrp6_S2 [ChIP-Seq]

description: Processed data file: Rrp6_S2.bed


title: tech_rep1_Rrp40_S2 [ChIP-Seq]

description: Processed data file: Rrp40_S2.bed


title: mouse_e11.5_forebrain_p300

description: Tissue pooled from ~200 embryos Chromatin IP against p300 (rabbit polyclonal anti‐p300 (C‐20), Santa Cruz Biotechnology, catalog number = SC-585, Lot number = L2704)

source_name: Mouse embryonic day 11.5 (e11.5) forebrain

tag: strain

tag: tissue

value: mouse forebrain

tag: developmental stage


title: Erythroid KLF1

status: Public on Jan 28 2013

city: New Haven

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

data_processing:
Basecalls were performed using CASAVA version 1.7.0
ChIP-seq reads were aligned to the hg18 genome assembly using elandv2.
The eland extended format alignments were converted to bed format using the elandextended2bed.py script.
Peaks were called against the total input sample using macs version 1.4.0rc2 with default parameters.
Quality scores in the fastq files were converted from Illumina1.3 to sanger using the fq_all2std.pl script.
Genome_build: hg18
Supplementary_files_format_and_content: The macs peaks.bed output files have a fifth field that is -10*log10(pvalue)

source_name: R3/R4 Erythroid cells

growth_protocol: Human CD34+-selected stem and progenitor cells were obtained from the Yale Center for Excellence in Molecular Hematology. To obtain primary human erythroid cells, CD34+ cells were cultured and selected as described.(Panzenbock, B., Bartunek, P., Mapara, M. Y., and Zenke, M. (1998) Blood 92, 3658-3668. Migliaccio, A. R., Migliaccio, G., Di Baldassarre, A., and Eddleman, K. (2002) Bone Marrow Transplant 30, 75-80) Briefly, Human CD34-selected stem and progenitor cells were cultured  for 9 to 14 days in StemSpan SF expansion medium which contains human transferrin (200 ng/ml) and insulin (10 ng/ml) (StemSpan 09650) and was supplemented with estradiol (1 micromolar), dexamethasone (1 micromolar),  Flt3 ligand (100 ng/ml), stem cell factor (100 ng/ml), interleukin-3 (50 ng/ml), interleukin-6 (20 ng/ml), insulin-like growth factor 1 (50 ng/ml), and erythropoietin (3 U/ml). FACS analysis was used to analyze cellular expression of CD71 (transferrin receptor) and CD235a (glycophorin A). These cells represent the R3/R4 cell population of nucleated erythroid cells defined by Zhang et al.(Zhang, J., Socolovsky, M., Gross, A. W., and Lodish, H. F. (2003) Blood 102, 3938-3946)

extract_protocol: Approximately 500ng of ChIP DNA was run on a 1.5% agarose gel to size select ChIP DNA in the 200-300-bp range. The size-selected ChIP DNA was purified using a gel extraction kit (Qiagen) and processed for sequencing as per manufacturer's protocol. Briefly, size-selected ChIP DNA was end repaired using an End-IT DNA end repair kit (ER0720; Epicenter), followed by addition of an adenine base at the 3′ end by Klenow reaction and Solexa adaptor ligation. The modified DNA was then PCR amplified with one initial heating step of 98°C for 30 s, followed by 15 cycles of amplification with a melting temperature of 98°C for 30 s, an annealing temperature of 65°C for 30 s, and a product extension at 72°C for 30 s. At the end of the amplification, a final extension at 72°C for 5 min was performed. Amplified ChIP DNA was then size selected on a 1.5% agarose gel, purified by using a gel extraction kit (Qiagen), and subjected to deep sequencing.

treatment_protocol: ChIP assays were performed as previously described with minor variations (Steiner, L. A., Maksimova, Y., Schulz, V., Wong, C., Raha, D., Mahajan, M. C., Weissman, S. M., and Gallagher, P. G. (2009) Mol Cell Biol). 1 × 107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, followed by Dounce homogenization. Cross-linked nuclei were isolated, followed by sonication with a Covaris S2 shearing device (duty cycle 10%, intensity 5, 15 minutes), to obtain chromatin-containing DNA fragments with an average size of ~200-400bp. For each ChIP, 20 µg of antibody or the appropriate control IgG species was used. Samples were immunoprecipitated with antibodies against GATA1 (sc-265; Santa Cruz), NF-E2 (sc-22827; Santa Cruz), KLF1 (ab2483; Abcam), SCL/Tal1 (sc-12984; Santa Cruz), P300 (sc-585; Santa Cruz) and nonspecific rabbit IgG (sc-2091; Santa Cruz). The antigen-antibody complex was captured on protein G beads, washed four times with radioimmunoprecipitation assay buffer, and then washed with phosphate-buffered saline. The DNA-protein complex was eluted from the protein G beads with 1% sodium dodecyl sulfate at 65°C, and cross-linking of DNA-protein adducts was reversed by 4 hours of incubation at 65°C. After proteinase K and RNase digestion of the reverse-cross-linked sample, DNA was cleaned with the QIAquick PCR Purification Kit (Qiagen) according to manufacturer instructions.

tag: cell

value: R3/R4 Erythroid cells


title: Erythroid H3K4me3


title: Brinker ChIPSeq

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: chromatin IP against Brk

data_processing:
Alignment: Sequence reads were obtained and mapped to Drosophila melanogaster (dm3, April 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.PeakSeq was used to create the signal maps as wig files.
Peak-calling: Peak detection was performed with the PeakSeq program (http://www.gersteinlab.org/proj/PeakSeq/), using the Input DNA published in GEO GSE24115 record as a control. The final peak files are provided in BED format.
Genome_build: dm3
Supplementary_files_format_and_content: Brk.aligned.wig(WIG, genome wide ChIP profile)
Supplementary_files_format_and_content: Brk.peaks.txt (BED, signal enriched regions)

source_name: Wing imaginal discs

growth_protocol: Flies were grown in standard medium.

extract_protocol:
Chromatin from Drosophila third instar larvae wing discs was immunoprecipitated with 2 ug of antibody using standard protocols.
Libraries were prepared according to Illumina instructions.

value: wt

value: third instar larvae

value: wing imaginal disc

value: Brinker

tag: chip antibody manufacturer

value: Generated in A. Teleman's lab

tag: genetic background

value: Canton S


title: KO

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

description: Embryos obtained from tatraploid complementation of embryonic stem cells in which Fendrr was knocked-out on both alleles via homologous recombination. The first run (WT) was originally started as a 2x100bp run, but the run aborted during the ~20th cycle of the second mate. The base-calling of the first 100bp was then performed manually by Illumina (because the automated MiSeq pipeline was not doing it after aborting the run), at which point it is possible that they applied a 100bp filter. For the second sample (KO) to be comparable, only a 1x100bp run was performed which finished without problems and the normal MiSeq pipeline was performing the base-calling.

data_processing:
The raw reads were aligned against the mouse genome (mm9) using Tophat (version 2.0.6) and Bowtie2 (version 2.0.2), supplying the UCSC refseq transcriptome annotation and using the following parameters: --coverage-search --library-type fr-secondstrand --b2-very-sensitive --no-novel-juncs --no-novel-indels
We used Cufflinks (version 2.0.2) to calculate transcript coverage and abundance (FPKM) across the UCSC mm9 refseq transcripts and combined all isoforms into one metagene.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-seperated file containing gene symbols and the corresponding WT and KO FPKM values.

source_name: embryonic heart ventricles

extract_protocol:
RNA was extracted from 4 pooled ventricles of each WT and KO samples using the RNAeasy Mini Kit (Qiagen). Ribosomal RNA from 500ng of total RNA was depleted using the Ribo-Zero Magnetic Kit (Epicentre) according to manufacturer’s instructions with minor modifications to accommodate for input amounts lower than 1µg. In brief, we used 90µl of beads per reaction, washed them with an equal amount of H2O and resuspended them in 35µl of resuspension solution with the addition of 0.5µl of RNase inhibitor. We added 2µl of rRNA removal solution and 2µl of reaction buffer to 16µl of the total RNA (corresponding to 500ng). The final eluate was cleaned-up using RNA MinElute columns (Qiagen) and eluted in 10µl H2O.
The complete eluate was used to prepare sequencing libraries using the Script-Seq v2 RNA-Seq Library Preparation Kit (Epicentre) according to manufacturer’s instructions. The cDNA was purified using DNA MinElute columns (Qiagen), 15 cycles of PCR were used to amplify the library using index primers and the final library was purified using AMPure XP beads (Beackman Coulter). The libraries were sequenced on two independent runs using the MiSeq v2 (Illumina) running at 1x100bp cycles.

tag: genotype

value: Fendrr KO

value: heart ventricle


title: Erythroid Total Input

value: Total Input


title: Erythroid p300


title: Erythroid H3K4me2


title: Erythroid NFE2


title: Erythroid GATA1


title: Suhw_S3 [ChIP-Seq]

description: Processed data file: Suhw_S3.bed

value: S3 late embryonic cells


title: Human Methylated Nucleosome Sample R2

city: West Lafayette

first: Clayton

middle: Kenneth

last: Collings

state: Indiana

address: 915 W. State Street

department: Biological Sciences

institute: Purdue University

description: Sample 5

data_processing:
Reads were mapped to the reference sequence with the Bioscope (bioscope-v1.3-rBS130_50843_20101020105719) software.  The human reference sequence consisted of 3 BACs: RP11-89D11 (hp53), RP11-440N18 (hmyc), and RP11-980A6 (halb).  The mouse reference sequence consisted of 3 BACs: RP23-51O13 (mp53), RP23-302D24 (mmyc), and RP23-67F18 (malb).  Information in the output SAM files was used to identify and localize the midpoints of properly-paired reads with desired insert lengths (141-155 bp).  Only properly-paired reads with the following SAM flags were utilized:  83, 99, 147, 163, 1107, 1123, 1171, and 1187. We defined the midpoint of a paired-end read by adding int((insert length - 1) / 2) to the left-most coordinate of the paired-end read (int =  integer truncation).  Therefore, if a read insert was 147 bp in length, the midpoint would be located 73 bp downstream from the left-most coordinate.  The number of properly-paired reads with desired insert lengths at midpoints was then determined at each position for each individual library, and these processed data are provided in text files for the 7 human and 7 mouse samples.

The properly-paired read counts in the 3 unmethylated and 2 methylated human nucleosome libraries at each position were normalized by the average number of read midpoints per base pair, which is equal to the total number of reads in a library divided by the combined lengths of the BACs.  To account for midpoint discrepancies, the counts were converted to 3 bp sliding window sums.  After normalization and conversion to 3 bp sums, combined unmethylated and methylated libraries were produced by adding the counts at each position together and then dividing by three and two, which are the number of unmethylated and methylated libraries, respectively.  The same procedure was done for the mouse data.  These combined normalized unmethylated and methylated libraries in 3 bp sums are available in text files for both human and mouse [on Series records].

11,448 human nucleosome positions were then generated by non-specific filtering and a peak finding algorithm, using the human combined unmethylated and methylated nucleosome libraries (See Methods in Paper).  13,741 mouse nucleosome positions were also generated in the same manner, using the mouse combined unmethylated and methylated nucleosome libraries.  Additionally, for the mouse unmethylated and methylated MNase controls, 12,884 positions were derived.  For these 3 datasets, the BAC, the BAC coordinate, the numbers of unmethylated and methylated reads, the fractional difference, and the numbers of CGs in the insert (made to be 147 bp surrounding the midpoint) are given for each position in txt files. For each of these positions, the fractional difference between the unmethylated and methylated libraries was computed by dividing the absolute difference between the unmethylated and methylated peaks by the larger peak of the two and multiplying by -1 if the larger peak was from the unmethylated library.  Additionally, for the human and mouse nucleosome libraries, the adjusted p-values that were assigned by DESeq are given, and for just the human nucleosome libraries, the base mean of the five libraries as well as translational scores for each position are also provided.

For differential nucleosome positioning analysis, the statistical software package DESeq was utilized, which is implemented in R and distributed by the Bioconductor project.  DESeq fits count data to a negative binomial model and is typically used to test for differential gene expression in RNA-Seq datasets with small sample sizes.  For the human data, the number of normalized reads in 3 bp sums from the three individual unmethylated and the two individual methylated replicates at the 11,448 nucleosome midpoint positions were used as the human count dataset input into DESeq.  For the mouse data, the number of normalized reads in 3 bp sums from the two individual unmethylated and the two individual methylated replicates at the 13,741 nucleosome midpoint positions were used as the mouse count dataset input into DESeq.  These two count datasets are presented in text files.  Note that these numbers are required to be rounded to the nearest integer for analysis by DESeq and that the size factors should be set to 1 since the data are already normalized.

Genome_build: hg19, mm9

Supplementary_files_format_and_content: There are 23 text files, and their content is described in the data processing steps.

source_name: Human Methylated Nucleosome

growth_protocol: BAC clones on LB agar stabs were obtained from the BACPAC Resources Center and were grown according to instructions provided by the supplier.  BAC DNAs were isolated by standard protocols and sheared 10 times through a 26 gauge needle.  Equal molar mixtures of the BAC DNAs were then prepared.

extract_protocol: Equal molar mixtures of the BAC DNAs were reconstituted into nucleosomes under selective pressure for nucleosome-favoring sequences. The unmethylated or methylated DNA was mixed with core histones (isolated from H1/H5-stripped chicken erythrocyte nucleosomes) in 2.0 M NaCl at a DNA-histone mass ratio of 5:1 with 60 µg of DNA in a volume of 150 µl.   Nucleosome reconstitution was carried out by gradient dialysis (2.0 M NaCl to 0.01 M NaCl) over a period of 16 hours at 4°C.  Samples (30 µg DNA in 2 parallel reactions) were digested with micrococcal nuclease (MNase) using 1 Worthington unit at 37°C for 5 minutes with 1 mM CaCl2 in a volume of 200 µl.  The samples were then deproteinized, protected fragments were extracted, and mononucleosome-length DNA was isolated by gel electrophoresis on a 5% polyacrylamide gel.  For controls, naked DNA was fragmented to a length of ~150 bp with a Covaris sonicator, and naked DNA (30 µg) was digested separately with MNase using 0.3 Worthington units at 37°C for 5 minutes with 1 mM CaCl2 in a volume of 120 µl.  These controls were then size-selected on a 5% polyacrylamide gel (between 140 and 160 bp).  It is important to note that all nucleosome samples were biological, not technical, replicates and were produced on different days.  The unmethylated/methylated nucleosome and control samples for both human and mouse were submitted to the Purdue Genomics Core Facility where these 14 samples were end-repaired, barcoded, nick translated, amplified by 7 cycles of PCR, and simultaneously sequenced with the SOLiD paired-end sequencing technology in a single run on a quarter slide.

treatment_protocol: The CpGs in equal molar mixtures of  BAC DNAs were methylated by treatment with CpG Methyltransferase (M.SssI) from New England Biolabs (2 Units of Methyltransferase / µg DNA overnight at 30°C), which is claimed to methylate all cytosine residues in CpG dinucleotides.  Completion of CpG methylation was verified by resistance to digestion with methylation-specific endonucleases (BstUI & HhaI) with subsequent analysis on an agarose gel.

tag: methylation status

value: Methylated

tag: bac clone source


title: Human Unmethylated Sonicated Control Sample

description: Sample 7

source_name: Human Unmethylated Sonicated Control

value: Unmethylated


title: Human Unmethylated MNase Control Sample

description: Sample 6

source_name: Human Unmethylated MNase Control


title: human_fetal_cortex_p300

description: Tissue from a single individual. Chromatin IP against acCBP/p300 (rabbit polyclonal, Cell Signaling Technology, catalog number = 4771,  lot number = 2)

source_name: human fetal (gestational week 20) cortex

value: human cortex

value: fetal (gestational week 20)


title: WT

description: Embryos obtained from tatraploid complementation of embryonic stem cells. The first run (WT) was originally started as a 2x100bp run, but the run aborted during the ~20th cycle of the second mate. The base-calling of the first 100bp was then performed manually by Illumina (because the automated MiSeq pipeline was not doing it after aborting the run), at which point it is possible that they applied a 100bp filter. For the second sample (KO) to be comparable, only a 1x100bp run was performed which finished without problems and the normal MiSeq pipeline was performing the base-calling.

value: wild type


title: Human Unmethylated Nucleosome Sample R1

description: Sample 1

source_name: Human Unmethylated Nucleosome


title: Mouse Unmethylated Sonicated Control Sample

description: Sample 14

source_name: Mouse Unmethylated Sonicated Control


title: striated_muscle_wt_2

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

data_processing:
demultiplexing and barcode clipping
quality filtering
mapping with tophat1.2.0, USCS known genes, mm9
cuffdiff0.0.5
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_values.xls;normalized expression values used for assessment of differential gene expression, only one fpkm value is calculated per sample type

source_name: striated muscle

extract_protocol: total RNA was isolated by the TRIZOL method and purified with RNeasy kit. NUGEN ovation RNA-Seq (samples 1-6) and NUGEN complete RNA-Seq protocol (samples 7-12)

tag: sample type

value: striated muscle

tag: genotype/variation


title: myoblast_LMNA_wt

source_name: myoblast

value: myoblast


title: striated_muscle_LBR_KO_2


title: striated_muscle_LMNA_KO_2


title: nf0h3b

description: molecule: bru-labeled RNA

value: Foreskin fibroblasts

tag: extraction time

value: 0h after Bru labeling

tag: treatment

value: Control

tag: stranded

value: TRUE


title: Human Methylated Nucleosome Sample R1

description: Sample 4


title: striated_muscle_wt_1

value: wt


title: striated_muscle_LBR_KO_1


title: Mouse Methylated MNase Control Sample

description: Sample 13

source_name: Mouse Methylated MNase Control


title: Human Unmethylated Nucleosome Sample R2

description: Sample 2


title: myoblast_LMNA_KO_1


title: Mouse Unmethylated MNase Control Sample

description: Sample 12

source_name: Mouse Unmethylated MNase Control


title: Human Unmethylated Nucleosome Sample R3

description: Sample 3


title: myoblast_LMNA_KO_2


title: Mycelium  incubated  48h

city: Chengdu

first: Aiping

last: Zheng

state: Sichuan

address: 555 Dongbei Road, Wenjiang District

institute: Rice Research Institute of Sichuan Agricultural University

description: Heavy necrosis appeared on rice surface

data_processing: Tophat v1.3.1 for RNA-seq reads mapping; Cufflinks v1.0.3 for expression analysis, cuffdiff caculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM).

organism: Rhizoctonia solani AG-1 IA

source_name: Mycelium

growth_protocol: Rhizoctonia solani AG1 IA strain was inoculated to rice leaves and infected the leaves at 28°C, 80% humidity culture condition

extract_protocol: Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from samples. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis.  And rawdatas were produced using Illumina GA II. The insert size of libraries are ~180bp.

treatment_protocol: The strain were collected from the infected rice leaves,then washed with sterile H2O, frozen in liquid N2 and freeze dried

tag: age

value: 48 hour

tag: isolate

value: AG1 IA


title: Mycelium  incubated  32h

description: Middle necrosis appeared on rice surface

value: 32 hour


title: Mycelium  incubated  72h

description: Light gray sclerotia appeared on rice surface

value: 72 hour


title: Mouse Methylated Nucleosome Sample R1

description: Sample 10

source_name: Mouse Methylated Nucleosome


title: Mouse Methylated Nucleosome Sample R2

description: Sample 11


title: Mycelium  incubated  24h

description: Mycelium invaded host, light necrosis appeared on rice surface

value: 24 hour


title: myoblast_LBR_wt


title: Mycelium  incubated  18h

description: Infection cushion appeared on rice surface

value: 18 hour


title: myoblast_LBR_KO_2


title: Mouse Unmethylated Nucleosome Sample R2

description: Sample 9

source_name: Mouse Unmethylated Nucleosome

value: Unmethylated


title: Mycelium  incubated  10h

description: Mycelium grew on rice surface

value: 10 hour


title: myoblast_LBR_KO_1


title: Mouse Unmethylated Nucleosome Sample R1

description: Sample 8