title: PAR-iCLIP replicate 2

description: Cytoplamic RNA

extract_protocol:
5 x 107 S2 cells were treated to 100uM 4-thiouridine 16hours prior to UV-crosslink with 250 mJ at 365nm. 0,05U/µl  ribonuclease T1 was used to trim RNA prior to IP with anti-Imp. The RNA purification and library generation was performed as described in (Konig et al. 2011, Journal of visualized experiments :JoVE). 21 cycles of PCR was used to create the library.
See individual experiment


title: STAT3_WT_nc_1685

status: Public on May 27 2015

type: SRA

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

country: USA

institute: NIH

description: for exp ID: 140609_SN923_0253_s02

library_source: genomic

data_processing:
alignment, ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
peaks, ChIP-seq: Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0E-05.
alignment, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to the  genome using TopHat 2.0.8
RPKM, RNA-seq: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek GS.
Genome_build: mm9 for mouse data, hg18 for human data
Supplementary_files_format_and_content: bw for ChIP-seq peak files, excel for a RPKM file

molecule: genomic DNA

organism: Mus musculus

source_name: mouse primary CD4+ T cells

growth_protocol:
mouse Th0: CD4+ T cells from spleens and lymph nodes of 6-8 week-old mice were purified by negative selection and magnetic separation (Miltenyi Biotec) followed by sorting of naïve CD4+CD62L+CD44-CD25- population using FACSAria III (BD). All cells were activated by plate-bound anti-CD3 (10 μg ml-1; eBioscience) and anti-CD28 (10 μg ml-1; eBioscience)  in RPMI medium with 10% (vol/vol) FCS, 2 mM glutamine, 100 IU ml-1 of penicillin, 0.1 mg ml-1 of streptomycin and 20mM HEPES buffer, pH 7.2-7.5 (all from Invitrogen) and 2 mM β–mercaptoethanol (Sigma-Aldrich) for indicated duration of time (6h, 24h, 3d).
human Th0: Peripheral blood mononuclear cells were prepared from venous blood by Ficoll-gradient centrifugation. Naïve CD4+CD45RAhighCD45ROlow population was purified by the flow cytometry using FACSAria IIi (BD) and were activated by plate-bound anti-CD3 (5 μg ml-1; eBioscience) and anti-CD28 (5 μg ml-1; eBioscience) in media (the same as protocol1) for 3 days.

extract_protocol:
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
RNA-Seq: Total RNA was prepared from approximately 1 million cells by using mirVana miRNA Isolation Kit (AM1560, ABI).
RNA-Seq: 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.
RNA-Seq. The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.

treatment_protocol:
For mouse cells, mIL6 (20 ng ml-1; R&D Systems) was added. For human cells, hIL6 (50 ng ml-1; R&D Systems) was added.
For mouse cells, mIL27 (20 ng ml-1; R&D Systems) was added. For human cells, hIL27 (50 ng ml-1; R&D Systems) was added.

tag: strain

tag: culture condition

value: 3 day in vitro culture for Th0

tag: genotype

value: wild type

tag: chip antibody

tag: lab data id


title: iCLIP replicate 2

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

country: Germany

institute: MDC-Berlin

description: Cytoplamic RNA

library_source: transcriptomic

data_processing:
Base-calling was performed with CASAVA-1.8.2
Reads were demultiplexed using their fixed barcodes
Reads were trimmed at the 3'end to remove adapter sequences and low-quality sequences using custom python scripts. Reads shorter than 18nt were discarded.
Duplicated reads were collapsed using random barcodes to discriminate between identical sequences.
Reads were mapped to the Drosophila genome (dm3) + exon junction index (ensembl72) using BWA-PSSM with parameters -n 0.04 -l 1024-m 400 -P 0.99. PAR-iCLIP experiments were mapped modeling C>T conversions that arise due to the use of 4SU assuming a 12.5% conversion rate.
Confidently mapped reads with a posterior probability > 0.99 were further clustered according to their genomic positions.
Genome_build: dm3
Supplementary_files_format_and_content: Bedgraph files containing the read clusters
Supplementary_files_format_and_content: Plain text file containing the counts per gene, fold changes and p-values as calculated by DESeq

molecule: total RNA

organism: Drosophila melanogaster

source_name: Schneider 2  (S2) cells

growth_protocol: S2 cells were growth at 26C in Schneider's Drosophila Medium containing 10% heat inactivated fetal bovine serum, 100U/ml Penicillin and 100ug/ml Streptomycin

extract_protocol:
5 x 107 S2 cells were crosslinked  250mJ/cm2 at 254nm. 0,005U/µl  ribonuclease T1 was used to trim RNA prior to IP with anti-Imp antibody.  The RNA purification and library generation was performed as described in (Konig et al. 2011, Journal of visualized experiments :JoVE). 21 cycles of PCR was used to create the library.
See individual experiment

tag: rt primer with random barcode / index

tag: random barcode

value: NNNNN Random Barcode at the read beginning


title: PAR-iCLIP replicate 1

description: Cytoplamic RNA

extract_protocol:
5 x 107 S2 cells were treated to 100uM 4-thiouridine 16hours prior to UV-crosslink with 250 mJ at 365nm. 0,05U/µl  ribonuclease T1 was used to trim RNA prior to IP with anti-Imp. The RNA purification and library generation was performed as described in (Konig et al. 2011, Journal of visualized experiments :JoVE). 34 cycles of PCR was used to create the library.
See individual experiment


title: RNA-seq WT-ProB cultured 1 day on OP9, rep1

city: Linkoping

first: Rajesh

last: Somasundaram

address: Dept of Clinical and Experimental Medicine (IKE)

department: Microbiology and Molecular Medicine

country: Sweden

institute: Linkoping University

data_processing:
For RNA-Seq samples, data analysis was performed with Arraystar (DNA STAR). The reads were aligned to mouse reference genome (mm9, NCBI 37) and RPKM normalized. Statistical analysis in Arraystar was performed with Student´s t-test with correction for multiple testing (Benjamini Hochberg). A p-value > 0.05 was considered as statistically significant.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Processed data files include BED files. All genomic coordinates are relative to the mm9 mouse assembly.

source_name: WT ProB, 1 day culture on OP9 stromal cells

growth_protocol: ProB-cell isolation / culture protocol: For sorting of Pro B cells, CD16/CD32 (FC) -blocked (93, eBioscience) cells were stained with antibodies against lineage markers CD11b/Mac1 (M1/70), Gr1 (RB6-8C5), TER119 (Ter119), CD3 (17A2, BD Pharmingen), CD11c (N418) and NK1.1 (PK136) and further stained with CD19 (ID3), CD45R/B220 (RA3-6B2), CD43 (S7), IgM (RMM-1) and IgD (11-26. eBioscience, San Diego, CA). Cell sorting was performed on a BD FACSAriaTM (BD Biosciences, San Jose, California) using propidium iodide (PI, Invitrogen, Paisly, UK) as viability marker. For  expansion, Pro-B cells were cultured on OP9 stromal cells supplemented with 10ng/mL KIT ligand, 10ng/mL Fms-like tyrosine kinase 3 ligand (FLT3L), and 10ng/mL Interleukin-7 in Optimem supplemented with 10% FCS, Beta-mercaptoethanol, HEPES and Penstrep.

extract_protocol:
RNA-Seq: RNA was extracted with the Qiagen RNeasy Micro Kit.
RNA-seq 1 day on OP9DL1 and OP9: Libraries were constructed using Nugen's Ovation Ultralow Library systems. Detailed protocol is available on their website. In short, input DNA were fragmented using sonication, end repaired, followed by ligation of adapters, amplification and finally bead purification. The samples were run on NextSeq 500.

treatment_protocol: See above.

tag: strain/background

tag: genotype/variation

value: WT

tag: cell type

value: ProB

tag: treatment

value: 1 day culture on OP9 stromal cells


title: STAT1_WT_IL27_1689

description: for exp ID: 140609_SN923_0253_s06

value: 3 day in vitro culture for Th0, treatment (IL27)

value: STAT1 (Santa Cruz Biotechnology, sc-592)(Lot #E1209)


title: RNA-seq WT-ProB cultured 1 day on OP9, rep2


title: STAT3_S1KO_IL6_1697

description: for exp ID: 140609_SN923_0253_s14

value: 3 day in vitro culture for Th0, treatment (IL6)

value: STAT1 KO


title: iCLIP replicate 1

description: Cytoplamic RNA


title: RNA-seq WT-ProB cultured 1 day on OP9DL1, rep2

source_name: WT ProB, 1 day culture on OP9DL1 stromal cells

value: 1 day culture on OP9DL1 stromal cells


title: input_WT_IL27_1694

description: for exp ID: 140609_SN923_0253_s11

value: none, input_


title: RNA-seq WT-ProB cultured 1 day on OP9DL1, rep3


title: Soybean Heart Stage Hilum-Biological replicate 2

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

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

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

organism: Glycine max

source_name: Soybean Heart Stage Hilum

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

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

tag: cultivar

value: Williams 82

tag: subregion

value: Soybean Heart Stage Hilum

tag: total rna input amount


title: RNA-seq replicate 4 (Control for RIP-seq rep2)

description: Cytoplamic mRNA

extract_protocol:
4 x 107 S2 cells were lyzed, and total RNA was purified using TriReagent. Poly(A) RNA was enriched from 40ug total RNA using Poly(A)Purist MAG kit (Ambion) according to manufacturer’s specifications. Library was performed as described in (Kielpinski et al. 2013, Deep Sequencing Data Analysis). 28 cycles of PCR was used to create the final library
See individual experiment


title: RNA-seq WT-ProB cultured 1 day on OP9DL1, rep1


title: RNA-seq replicate 3 (Control for RIP-seq rep1)

description: Cytoplamic mRNA


title: RNA-seq TH-ProB cultured 1 day on OP9, rep4

source_name: Ebf1+/- Pax5+/- ProB, 1 day culture on OP9 stromal cells


title: RNA-seq WT-ProB cultured 1 day on OP9, rep4


title: RNA-seq replicate 2 (Control for iCLIP rep2)

description: Cytoplamic mRNA

extract_protocol:
Total RNA was isolated from 5x107 S2 cells using the standard TRI Reagent protocol (Sigma Aldrich). Poly(A) RNA was enriched from 100ug total RNA using Poly(A)Purist MAG kit (Ambion) according to manufacturer’s specifications. Poly(A) RNA was fragmented using MgCl2. The rest of the library preparation was performed as described in (Konig et al, 2011) with PCR amplification using 17 cycles.
See individual experiment


title: Tomato_PSTVd-I

city: Sherbrooke

first: Charith Raj

last: Adkar-Purushothama

state: Quebec

address: 3201 rue Jean-Mignault

department: Biochemistry

country: Canada

institute: Université de Sherbrooke

description: RNA extracted from the plants inoculated with PSTVd-I

data_processing:
CASAVA version 1.4 was used for base-calling.
The primers were trimmed
21- to 24-nt long small RNAs were filtered
Obtained small RNA reads were mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm.
Genome_build: Filtered 21- to 24-nt small RNA sequence obtained from the PSTVd-M inoculated plants were mapped against the genomic and anti-genomic strands of the PSTVd-M (GenBank Acc. No. AB623143) while, the small RNA sequence obtained from PSTVd-I inoculated plants were mapped against the genomic and anti-genomic strands of the PSTVd-I (GenBank Acc. No. AY937179).
Supplementary_files_format_and_content: tab-delimited text files include the 21 to 24-nt long sRNA used for the analysis. The files were used to plot the graph on the PSTVd genome which will be presented in the manuscript as a figure.

organism: Solanum lycopersicum

source_name: leaf tissue

growth_protocol: Grown at a temperature of 25 ºC with 16 h of light and 8 h of darkness.

extract_protocol:
Total RNA from the leaf samples (at 21-days of post inoculation) was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA), with modifications. Briefly, 100 mg of leaf sample was ground with 800 µl of Lysis/Binding buffer. Then, 80 µl of miRNA homogenate was added and the resulting solution was mixed by vortexing, and then placed on ice for 10 minutes. Acid phenol-chloroform extraction was then performed. Samples were treated with the DNAse RQ1 (Promega, MA) for 1 h at 37 ºC and then the chloroform extraction was performed. RNA integrity was examined in a 2100 Bioanalyzer (Agilent Technologies, California, USA).
The small RNA of 15- to 50-nt was purified from the total RNA samples and then subjected to small RNA library preparation using NEBNext Multiplex Small RNA Library Prep Set for Illumina according to manufacturers instructions (New England Biolabs).
RNA libraries obtained for the RNA extracted from the control plants, PSTVd-M inoculated plants and PSTVd-I inoculated products were processed simultaneously in the Illumina Hi-Seq platform using the multiplex strategy.

treatment_protocol: After the development of primary leaves, plants were inoculated with the 1 µg of the RNA transcripts of the respective viroid variants, while control plants were inoculated with inoculation buffer.

tag: agent

value: PSTVd-I

value: Rutgers


title: Nucleosome-gDNA_control_1

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTAATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Adaptor sequences were trimmed from the sequence reads. Adaptor sequences is for TrueSeq-3.
Naked and nucleosome reads were mapped to the genome through Bowtie with options (-m 1 -X 1000; otherwise with default) . To focus on the analysis of mono-nucleosome protected sequences, MNase-seq reads from nucleosome-protected or naked gDNA were further analyzed if the fragment size (distance between PE reads) was between 140-170 bp. The mapped reads from 2 replicates of nuclesome gDNAs were combined for the downstream analyses. For each nucleotide in the genome, the degree of nucleosome occupancy was represented by the Nucleosome Occupancy (NOC) score that is the number of reads mapped to the position in question divided by the total mapped reads per million for each sample.
genome_build: Reference genome dataset was retrieved from The Arabidopsis Information Resources (TAIR10; http://www.arabidopsis.org).
processed_data_files_format_and_content: The "Processed data_nucleosome_occupancy" is bed file that contains the Nucleosome Occupancy (NOC) score of each nucleotide in the genome for 3 samples (Nucleosome-gDNA_control,Nucleosome-gDNA_COR and Naked-gDNA_control).

organism: Arabidopsis thaliana

source_name: Replicate#1:nucleosome-protected gDNAs from water-treated rosette leaves

growth_protocol: Arabidopsis thaliana Col-0 seeds were imbibed in water at 40C in darkness for 4 days for stratification, grown on soil (Arabidopsis mix) under long-day conditions (16 h of light/8 h of dark) at a fluence rate of 100 μmol/m2/s1 and watered with ½ strength Hoagland nutrient solution once per week (otherwise with deionized water).

extract_protocol:
To assess the effect of environmental stimuli on nucleosome occupancy, plants were treated with coronatine (COR) (Sigma, St. Louis, MO) or water (control) for 1 hr. The harvested samples were ground with liquid nitrogen and divided into 3 aliquots for nucleosome genomic DNA (gDNA), naked gDNA, and RNA isolation. For isolating nucleosome gDNA, the nuclei were purified from one aliquot with nuclei extraction buffer (10 mM Hepes (pH 7.6), 5mM potassium chloride, 5 mM magnesium chloride, 1 M sucrose, 14 mM β-mercaptoethanol, 0.6% Triton-X 100, 0.4 mM phenylmethanesulfonyl fluoride, 1x ethylenediaminetetraacetic acid-free protease inhibitor (Roche, Mannheim, Germany)), digested with 0.4 U/μl micrococcal nuclease (MNase) (NEB, MA, USA) for 9 min, and purified with phenol/chloroform. To generate the naked gDNA sample, the gDNA was isolated without the nucleus isolation step as described previously (Dellaporta et al. 1983), purified with phenol/chloroform to strip off proteins, and digested with 0.25 U/μl MNase (NEB, MA, USA) for 1.75 or 3 min. Total RNA was purified with the E.Z.N.A. Plant RNA kit (Omega Bio-Tek, GA, USA)
The purified nucleosome and naked gDNA was used to construct a library for 50-bp paired-end sequencing following the Illumina protocol. The purified total RNA was used to construct a library for 50-bp single-end sequencing following the Illumina protocol.

treatment_protocol: 4-week-old plants (before bolting) wre treated with 5 μM coronatine (COR) or water (control) for 1 hr

tag: tissue

value: rosette leaves


title: Soybean Globular Stage Embryo Proper-Biological replicate 4

description: Compartments collected from seeds 1 mm in length

source_name: Soybean Globular Stage Embryo Proper

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

value: Embryo


title: RNA-seq_COR_1

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Adaptor sequences were trimmed from the sequence reads. Adaptor sequences is for TrueSeq-3.
The RNA-seq reads to the genome through TopHat with the options (-I 500 -g 1; otherwise with default). Transcript levels of annotated genes were determined and shown as FPKM (Fragments Per Kilobase per Million fragments mapped) calculated with Cufflinks
genome_build: Reference genome dataset was retrieved from The Arabidopsis Information Resources (TAIR10; http://www.arabidopsis.org).
processed_data_files_format_and_content: The "Processed data_RNA-expression" contains the RNA expression (FPKM value) of annotated genes in 4 RNA samples (RNA-seq_control#1, RNA-seq_control#2, RNA-seq_COR#1, RNA-seq_COR#1).

source_name: Replicate#1:total RNA from coronatine-treated rosette leaves


title: STAT1_WT_nc_1684

description: for exp ID: 140609_SN923_0253_s01

value: 3 day in vitro culture for Th0

value: wild type


title: Naked-gDNA_control_1

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG

source_name: Replicate#1:naked gDNAs from control-treated rosette leaves


title: STAT1_WT_IL6_1686

description: for exp ID: 140609_SN923_0253_s03


title: Nucleosome-gDNA_COR_2

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG

source_name: Replicate#2:nucleosome-protected gDNAs from coronatine-treated rosette leaves


title: Nucleosome-gDNA_COR_1

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTTATCTCGTATGCCGTCTTCTGCTTG

source_name: Replicate#1:nucleosome-protected gDNAs from coronatine-treated rosette leaves


title: DKO

city: Dalian

first: Zhiguang

last: Li

state: Liaoning

address: 9 Lvshun Road South

department: Institute of Cancer Stem Cell, Cancer Center

country: China

institute: Dalian Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
For detailed mapping, mouse reference genome (UCSC mm9) was applied to two types of nucleotide replacement by changing C to T (C2T genome) or G to A (G2A genome) and indexes were made using bowtie-build. Reads also underwent nucleotide replacement by changing cytosine in read1 of pair-end sequencing to thymine and guanine in read2 to adenine. Mapping was done using bowtie (version 0.12.7) by allowing three mismatches in the leading 40 bases with up to 140 of phred score at mismatched positions. Twenty multiple alignments were allowed at most for each read, i.e. using k=20 when running bowtie program.
Monoclones were chosen by selecting only one pair of alignments with the maximum phred score from the pairs that have the same mapping positions for both ends.
The methylation statuses of cytosine were determined by considering read end types, DNA strand that the reads align against, nucleotide on reference genome, and nucleotide on reads.
Genome_build: mm9
Supplementary_files_format_and_content: Space-delimited text files include methylation scores for each C/G base. We use the following formula: S = rC / (rC + rT)  where rC is the number of reads that C still remains as C after bisulfite treatment, rT is the number of reads that C becomes T after bisulfite treatment.

source_name: ES cells

growth_protocol: Mouse ES Cells were maintained without feeder cells on 0.1% gelatin coated Petri dish in DMEM medium supplemented with 15% FBS (ES cell grade), 2mM glutamine, 10uM mercapto-ethanol, 100U/ml LIF, Penicillin/Streptomycin mixture 100ug/ml, 1X non-essential amino acid.

extract_protocol:
DNA was havest using DNeasy Blood & Tissue Kit(Qiagen, Germany)
One to five microgram of genomic DNA was fragmentized to 200~500bp by Covaris S2 sonicator (Covaris, USA). End repairing was then performed following manufacturer’s instruction (End-It DNA end repair kit, Epicentre, USA).  After Ampure XP (Sigma USA) purification, adenine was added to 3’ end with 3ml DNA Taq polymerase (M0267S, NEB) and 1mM dATP in 50ml reaction solution incubated at 70°C for 30 mins. After Ampure XP purification, 1ml of Illumina Trueseq adaptors were ligated with 4ml T4 DNA ligase (M0202L, NEB) in 40ml reaction solution and incubated at 16°C overnight. Fragments at 300-600 bp from adaptor-ligated DNA were collected from 2% agarose gel, and then bisulfite-treated using Imprint DNA modification Kit (MOD50-1 KIT, Sigma USA) as manufacturer instructed.  PCR enrichment was performed to amplify the libraries, which were then collected from 2% agarose gel electrophoresis at size 300-600bp.

value: embryonic stem cells


title: TKO


title: Soybean Globular Stage Seed Coat Epidermis-Biological replicate 2

value: seed coat epidermis


title: 1KO


title: WT


title: Soybean Heart Stage Hilum-Biological replicate 1


title: Nucleosome-gDNA_control_2

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATATCTCGTATGCCGTCTTCTGCTTG

source_name: Replicate#2:nucleosome-protected gDNAs from water-treated rosette leaves


title: Soybean Globular Stage Seed Coat Epidermis-Biological replicate 1


title: RNA-seq_COR_2

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG

source_name: Replicate#2:total RNA from coronatine-treated rosette leaves


title: RNA-seq_control_2

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG

source_name: Replicate#2:total RNA from water-treated rosette leaves


title: Soybean Globular Stage Embryo Proper-Biological replicate 1


title: haematopoietic stem cell [HSC1_90]

status: Public on May 26 2015

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-seq reads aligned to mm10 using STAR (version 2.3.0) with parameters --outFilterMultimapScoreRange 1 --outSAMstrandField intronMotif --genomeLoad NoSharedMemory --outStd SAM.
SAM files converted to BAM format and then sorted using samtools (version 0.1.18).
Read counts for features were calculated using HTSeq (version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts/spreadsheet.

source_name: Bone marrow

extract_protocol:
Bone marrow cells were isolated from the bones (femurs and tibiae) of 9–12-week-old C57BL/6 mice. Cells were stained with antibodies to permit the separation of the individual populations. A FACS Influx (BD Biosciences) was used for all single-cell sorting, unstained populations and single-stains were used as gate-setting controls. Single cells were sorted by FACS directly into individual wells of a 96-well plate containing lysis buffer. Single cell RNA-Seq analysis was performed as described previously (Picelli et al., 2014). Pooled libraries were then run on the Illumina Hi-Seq 2500.
single cell RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

tag: age

value: 9-12 weeks old

value: haematopoietic stem cell


title: haematopoietic stem cell [HSC1_91]

tag: strain


title: haematopoietic stem cell [HSC1_86]


title: haematopoietic stem cell [HSC1_85]


title: haematopoietic stem cell [HSC1_79]


title: Tomato_PSTVd-M

description: RNA extracted from the plants inoculated with PSTVd-M

value: PSTVd-M


title: Tomato_control

description: RNA extracted from mock inoculated plant was used as control

value: mock, control


title: RNA-seq_control_1

description: Adaptor sequence: 5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG

source_name: Replicate#1: total RNA from water-treated rosette leaves


title: Hnrnpu mutant rep2

city: New York

first: Sean

last: O'Keeffe

address: 701 West 168th Street

institute: Columbia University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and then mapped to the mm9 whole genome using Bowtie v0.12.9 with parameters -X 20000 -k 2 -m 2 -q -p
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. Differential gene expression was calculated using the R statistical package DESeq.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: hnrnpu-heart-P14.xlsx: Tab-delimited text file includes RPKM values for each Sample.

source_name: Heart, Hnrnpu mutant

extract_protocol:
Whole hearts were dissected from P14 mice of distinct genotypes, atria were removed. Total RNAs were extracted from ventricles by Trizol extraction protocol.
Libraries were prepared for sequencing using standard Illumina protocols.

value: hnrnpu mutant

value: ventricle

value: postnatal day 14

tag: gender

value: female


title: Hnrnpu mutant rep1

value: male


title: haematopoietic stem cell [HSC1_83]


title: Wild type rep2

source_name: Heart, wild type


title: haematopoietic stem cell [HSC1_96]


title: haematopoietic stem cell [HSC1_94]


title: haematopoietic stem cell [HSC1_95]


title: Wild type rep1


title: haematopoietic stem cell [HSC1_93]


title: haematopoietic stem cell [HSC1_76]


title: ES2_H3K27me3

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 2 v2.1.0 with default configuration.
Coverage across the genome was calculated using genomeCoverageBed from Bedtools v2.17.0 and converted to BigWig format using bedGraphToBigWig downloaded from the UCSC website.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files representing read coverage

source_name: ES Cell(2i)

extract_protocol:
Chromatin was isolated from 2i mouse ES cells (2 male, 2 female; C57BL/6J background) and sonicated to produce 100 to 700 bp frgments. Immunoprecipitation was performed with the following antibodies; anti-H3K27me3 (07-449, Millipore), anti-H3K4me3 (39159, Active Motif) and anti-H3K9me3 (ab8898, Abcam).
ChIP-seq libraries were prepared using the Illumina TruSeq ChIP sample prep kit.

value: M

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


title: haematopoietic stem cell [HSC1_87]


title: haematopoietic stem cell [HSC1_82]


title: haematopoietic stem cell [HSC1_81]


title: haematopoietic stem cell [HSC1_84]


title: haematopoietic stem cell [HSC1_89]


title: haematopoietic stem cell [HSC1_88]


title: haematopoietic stem cell [HSC1_72]


title: haematopoietic stem cell [HSC1_80]


title: ES1_H3K27me3


title: haematopoietic stem cell [HSC1_78]


title: haematopoietic stem cell [HSC1_71]


title: haematopoietic stem cell [HSC1_92]


title: haematopoietic stem cell [HSC1_75]


title: haematopoietic stem cell [HSC1_68]


title: haematopoietic stem cell [HSC1_74]


title: ES3_H3K27me3

value: F


title: haematopoietic stem cell [HSC1_77]


title: haematopoietic stem cell [HSC1_73]


title: ES4_H3K27me3


title: haematopoietic stem cell [HSC1_67]


title: haematopoietic stem cell [HSC1_70]


title: haematopoietic stem cell [HSC1_66]


title: ES3_H3K9me3

value: anti-H3K9me3 (ab8898, Abcam)


title: haematopoietic stem cell [HSC1_64]


title: ES1_H3K9me3


title: haematopoietic stem cell [HSC1_63]


title: ES4_H3K4me3

value: anti-H3K4me3 (39159, Active Motif)


title: haematopoietic stem cell [HSC1_59]


title: haematopoietic stem cell [HSC1_69]


title: haematopoietic stem cell [HSC1_58]


title: haematopoietic stem cell [HSC1_62]


title: ES4_H3K9me3


title: ES1_H3K4me3


title: ES2_H3K4me3


title: haematopoietic stem cell [HSC1_61]


title: haematopoietic stem cell [HSC1_60]


title: haematopoietic stem cell [HSC1_53]


title: haematopoietic stem cell [HSC1_54]


title: haematopoietic stem cell [HSC1_55]


title: haematopoietic stem cell [HSC1_52]


title: haematopoietic stem cell [HSC1_51]


title: haematopoietic stem cell [HSC1_65]


title: haematopoietic stem cell [HSC1_56]


title: Adult Liver24

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using Tophat v2.0.4 with Bowtie 2 v2.1.0 and samtools v0.1.18 with default settings
Duplicates were filtered using Picard Tools and reads were assigned to a gene using HTSeq
Gene annotation file was downloaded from Tophat website (downloaded on September 25th 2013)
Genome_build: mm10
Supplementary_files_format_and_content: RAW counts per gene

source_name: Adult Liver

extract_protocol:
RNA-seq libraries from embryonic stem cells, fetal and adult liver samples were constructed using the Illumina TruSeq Stranded Total RNA Kit, with 1 mg of Total RNA extracted with Qiagen miRNeasy Micro Kit.
The eight-cell embryo RNA-seq libraries were generated using a single-cell protocol adapted from: Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535. All other RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: adult liver


title: ES2_H3K9me3

tag: chip antibody


title: Adult Liver23


title: haematopoietic stem cell [HSC1_50]


title: haematopoietic stem cell [HSC1_49]


title: Adult Liver22


title: haematopoietic stem cell [HSC1_48]


title: ES3_H3K4me3


title: Adult Liver21


title: haematopoietic stem cell [HSC1_46]


title: haematopoietic stem cell [HSC1_57]


title: Adult Liver20


title: haematopoietic stem cell [HSC1_45]


title: Adult Liver19


title: haematopoietic stem cell [HSC1_43]


title: haematopoietic stem cell [HSC1_42]


title: Adult Liver18


title: haematopoietic stem cell [HSC1_40]


title: haematopoietic stem cell [HSC1_41]


title: haematopoietic stem cell [HSC1_39]


title: haematopoietic stem cell [HSC1_37]


title: haematopoietic stem cell [HSC1_36]


title: Adult Liver15


title: haematopoietic stem cell [HSC1_34]


title: haematopoietic stem cell [HSC1_35]


title: haematopoietic stem cell [HSC1_32]


title: haematopoietic stem cell [HSC1_33]


title: Adult Liver14


title: Adult Liver13


title: haematopoietic stem cell [HSC1_31]


title: haematopoietic stem cell [HSC1_30]


title: haematopoietic stem cell [HSC1_28]


title: haematopoietic stem cell [HSC1_29]


title: haematopoietic stem cell [HSC1_47]


title: haematopoietic stem cell [HSC1_27]


title: Adult Liver11


title: haematopoietic stem cell [HSC1_44]


title: haematopoietic stem cell [HSC1_26]


title: haematopoietic stem cell [HSC1_25]


title: haematopoietic stem cell [HSC1_24]


title: haematopoietic stem cell [HSC1_38]


title: Adult Liver16


title: haematopoietic stem cell [HSC1_23]


title: Adult Liver17


title: Adult Liver9


title: haematopoietic stem cell [HSC1_21]


title: Adult Liver7


title: Adult Liver12


title: haematopoietic stem cell [HSC1_20]


title: Adult Liver6


title: haematopoietic stem cell [HSC1_18]


title: haematopoietic stem cell [HSC1_15]


title: haematopoietic stem cell [HSC1_17]


title: haematopoietic stem cell [HSC1_14]


title: haematopoietic stem cell [HSC1_16]


title: haematopoietic stem cell [HSC1_19]


title: Adult Liver5


title: Adult Liver4


title: Adult Liver10


title: haematopoietic stem cell [HSC1_11]


title: haematopoietic stem cell [HSC1_13]


title: haematopoietic stem cell [HSC1_12]


title: haematopoietic stem cell [HSC1_9]


title: Adult Liver3


title: haematopoietic stem cell [HSC1_22]


title: haematopoietic stem cell [HSC1_10]


title: Adult Liver8


title: Adult Liver2


title: haematopoietic stem cell [HSC1_8]


title: haematopoietic stem cell [HSC1_7]


title: Adult Liver1


title: Fetal Liver24

source_name: Fetal Liver

value: fetal liver


title: haematopoietic stem cell [HSC1_4]


title: haematopoietic stem cell [HSC1_3]


title: Fetal Liver22


title: Fetal Liver23


title: LARP4B_PARCLIP

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrück-Center for Molecular Medicine

description:
PARCLIP RNA
binding sites

data_processing:
Adapters were removed with FAR 1.81 (the flexible adapter remover: http://sourceforge.net/projects/theflexibleadap/; for LARP4B_4SU_2.fastq the first to bases were removed due to cloning with OR5-NN), and aligned to hg18 with BWA 0.5.8c. Mapped reads were converted to read clusters scored for characteristic conversions by PAR-CLIP data analysis piplene (Lebedeva et al. 2010 Mol Cell). After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340–352 for details.
PAR-CLIP cDNA sequencing data was analyzed basically as described in Lebedeva et al. Molecular Cell 43, 340-352
Genome_build: hg18
Supplementary_files_format_and_content: bed8

organism: Homo sapiens

source_name: HEK293 cell culture

growth_protocol: Flp-In 293 T-REx cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 10,000 U/ml penicillin 10,000 µg/ml streptomycin.

extract_protocol:
PAR-CLIP cDNA and small RNA cDNA preparation were prepared basically as described in Hafner et al. Cell 141, 129–141. Briefly, PAR-CLIP was performed as described (Hafner et al., 2010). UV-irradiated cells were lysed in NP-40 lysis buffer (50 mM HEPES-KOH pH 7.4, 150 mM KCl, 2 mM EDTA, 0.5% (v/v) NP40, 0.5 mM DTT, complete EDTA-free protease inhibitor cocktail (Roche)). After treatment with RNaseT1 (Fermentas) at a final concentration of 2 U/ul for 7 min, immunoprecipitation was carried out with Anti-Flag Magnetic beads (SIGMA) for 1 h at 4ºC. Following an additional RNaseT1 treatment (final concentration 2 U/ul) for 7 min the beads were incubated with calf intestinal phosphatase (NEB) and RNA fragments were radioactively end-labeled using T4 polynucleotide kinase (Fermentas) and γ-(32P)-ATP. The crosslinked protein-RNA complexes were resolved on a 4-12% NuPAGE gel (Invitrogen). The SDS-PAGE gel was transferred to a nitrocellulose membrane (Whatman) and the protein-RNA complex migrating at an expected molecular weight was excised. RNA was isolated by Proteinase K (Roche) treatment and phenol-chloroform extraction. In subsequent steps barcoded 3’ adapters (NBC6 AppTCTCCATTCGTATGCCGTCTTCTGCTTG-InvdT for LARP4B_4SU_1, NBC8 AppTCTCTGCTCGTATGCCGTCTTCTGCTTG-InvdT for LARP4B_4SU_2) and 5’ adapters (OR5 GUUCAGAGUUCUACAGUCCGACGAUC for LARP4B_4SU_1, OR5-NN GUUCAGAGUUCUACAGUCCGACGAUCNN for LARP4B_4SU_2)  were ligated to the isolated RNA. Adapter-ligated RNA was reverse transcribed and PCR-amplified. The amplified cDNA was sequenced on a HighSeq2000 (Illumina) with a 1x51 nt cycle.
PAR-CLIP

treatment_protocol: A tetracycline-inducible HEK293 cell line was used for inducible expression of N-terminally FLAG/HA-tagged LARP4B (Schaffler et al. 2010). Cells were cultivated overnight in medium containing 100 µM 4SU and expression of FLAG/HA-LARP4B was induced with 0.5 µg/ml tetracycline for 5 h. After labeling the cells, PAR-CLIP was performed as described in (Hafner et al. 2010 Cell 141, 129–141) .

tag: antibody

value: FLAG

tag: culture medium

value: DMEM

tag: barcoded adapters

value: TCTCCATTCGTATGCCGTCT


title: haematopoietic stem cell [HSC1_5]

value: 9-12 weeks old

value: haematopoietic stem cell


title: Fetal Liver21


title: haematopoietic stem cell [HSC1_6]


title: Fetal Liver20


title: haematopoietic stem cell [HSC1_1]


title: Fetal Liver18


title: HUVEC_RNAseq_AdSlit2+AdVammin_rep2

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the hg19 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (RPKM) and UCSC Bedgraphs are provided

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich).

extract_protocol:
RNA was purified using RNeasy Mini Kit and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit.
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 10 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: Confluent cultures of HUVECs were washed with PBS, followed by transduction with AdCMV, AdSlit2, AdCMV+AdVammin or AdSlit2+AdVammin. After 24 hrs, starvation of cells was started with EGM medium supplemented with 0.5 % FBS and continued for 24 hrs .

tag: cell collection details

value: Sample from 1 individual

tag: passage

value: passage 5

tag: replicate

value: biological replicate #2

tag: protocol

value: AdSlit2+AdVammin 48h


title: HUVEC_RNAseq_AdCMV+AdVammin_rep2

value: AdCMV+AdVammin 48h


title: HUVEC_RNAseq_AdSlit2+AdVammin_rep1

value: biological replicate #1


title: HUVEC_RNAseq_AdCMV+AdVammin_rep1


title: haematopoietic stem cell [HSC1_2]

tag: cell type


title: Fetal Liver17


title: Fetal Liver16


title: HUVEC_RNAseq_AdSlit2_rep2

value: AdSlit2 48h


title: Fetal Liver14

value: F


title: HUVEC_RNAseq_AdSlit2_rep1


title: HUVEC_RNAseq_AdCMV_rep1

value: AdCMV 48h


title: HUVEC_RNAseq_AdCMV_rep2


title: RP 6 h p.i. - Rep 2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

description:
Ribosome protected RNA fragments (29-30nt)
Library sequenced three times.

data_processing:
3' sequencing adapter sequence were removed from the 50 nt long reads by computing a prefix-suffix sequence alignment
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use.
Bowtie 0.12.7 was used to align all reads to the human genome, Ensembl transcripts (v75), ribosomal rRNA, the HSV1 genome (JN555585, terminal repeats masked), the HSV1 transcripts as well as novel junctions identified in the 4sU data by ContextMap. Only reads aligning to at most 3 distinct genome positions with at most 2 mismatches were kept for further analyses.
At each alignment position a greedy algorithm successively discarded alignments such that no read sequence remained that has hamming distance 1 to any other read. The total number of unique sequences was taken as the conservative fragment count.
Alignments were clustered, assembled to ORF DAGs. Longest paths were extracted and classified as described.
RPKM values were calculated based on the total number of reads mapping to the human and viral genome using the longest ORF identified for each gene.
Genome_build: hg19, JN555585

source_name: Ribosome profiling

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 13 were infected at 60% confluency 24h after the last split.

extract_protocol:
Cells were snap frozen followed by cell lysis in presence of cycloheximide. Following removal of cell nuclei by centrifugation and stringent RNAse digest, ribosomes were pelleted through a sucrose cushion. Translated RNA fragments were recovered by size selection.
Translated RNA fragments were cloned following the protocol described by Stern-Ginossar N et al. Science 2012. rRNA depletion involved additional biotinylated oligos to improve depletion. To efficiently remove all biotinylated oligos complementary to specific rRNA sequences, two rounds of streptavidin depletion were performed. cDNA libraries were amplified by PCR and sequenced (HiSeq 50nt reads).
50 nt single end reads:    Solexa P5, 9 nt barcode, ribosome protected mRNA fragment, Solexa P3 adaptor

treatment_protocol: Cells were infected for 10 min with HSV-1 strain 17 at an MOI of 10 followed by PBS wash and media replacement. 500µM 4-thiouridine was added to the cell culture at the indicated time points.

value: human foreskin fibroblasts

tag: time post infection

value: 6 h p.i.

tag: infection with

value: Herpes simplex virus 1, strain 17

tag: barcode

value: NNNTGGCNN


title: RP 4 h p.i. - Rep 2

value: 4 h p.i.

value: NNNCCGGNN


title: Fetal Liver15

value: fetal liver


title: RP 8 h p.i. - Rep 2

value: 8 h p.i.

value: NNNCCACNN


title: Fetal Liver13


title: RP mock - Rep 2

value: mock

value: NNNTTGTNN


title: Fetal Liver19


title: RP 1 h p.i. - Rep 2

value: 1 h p.i.

value: NNNCAATNN


title: RP 8 h p.i. - Rep 1


title: Fetal Liver12

value: M


title: Fetal Liver11


title: RP 4 h p.i. - Rep 1


title: Fetal Liver10


title: RP 1 h p.i. - Rep 1


title: RP 2 h p.i. - Rep 1

value: 2 h p.i.

value: NNNGGCGNN


title: Fetal Liver8


title: Fetal Liver7


title: Fetal Liver9


title: Fetal Liver6


title: p300

city: Worcester

first: Troy

middle: W.

last: Whitfield

address: 55 Lake Ave. N.

institute: University of Massachusetts Medical School

data_processing:
Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6, Illumina).
Reads were mapped to the human genome (GRCh37, hg19) using bowtie (version 0.12.8) with up to two mismatches allowed.
Peak calling was performed on pooled replicates using MACS (version 2.0.10.20131216) with default settings and retaining peaks with a p < 10^{-20} threshold.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files correspond to summits (+/- 50 bp) for peaks with p < 10^{-20}.

growth_protocol: Kasumi-1 cells were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and maintained in RPMI-1640 media supplemented with 20% FBS. Cells were expanded every 3-4 days in T75 tissue culture flasks. Kasumi-1 cells growing in log phase (1-1.5 million cells/ml) were fixed with 1% formaldehyde for 10 minutes at room temperature and subsequently quenched with 0.25 M glycine. Approximately 30 million cells were used for each ChIP-Seq library.

extract_protocol:
Kasumi-1 cells growing in log phase were fixed with 1% formaldehyde for 10 minutes at room temperature and subsequently quenched with 0.25 M glycine. After washes in PBS, cells were flash frozen in liquid nitrogen. Thawed pellets were resuspended in Buffer A (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and rotated at 4ºC for 10 minutes. Following centrifugation, pellets were resuspended in Buffer B (10 mM Tris-HCl, 200 mM NaCl, 1 mM EDTA, 1 mM EGTA) and rotated at 4ºC for 10 minutes. Pellets from centrifuged samples were resuspended in Buffer C (10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Samples were aliquoted, 3 ml per tube, and sonicated to a fragment size of 100-500 base pairs using a 3.2 mm sonication probe (QSonica, Newtown, CT). Sheared chromatin (from approximately 30 million cells) was immunoprecipitated with antibodies overnight. All ChIP experiments included either normal goat or rabbit IgG (EMD Millipore, Billerica, MA) as controls. Antibody-lysate complexes were mixed with Protein G Dynabeads (Life Technologies, Grand Island, NY) for 2 hours. For AML1, ETO, H3K4me3, and H3K27me3 immunoprecipitations, beads were washed once with IP buffer, 3 times with RIPA buffer (50 mM HEPES, 500 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.25% sodium deoxycholate), once with PBS, and once with TE buffer. For N-CoR and p300 pulldowns, beads were washed once with IP buffer, once with high salt buffer (2 mM EDTA, 20 mM Tris-HCl, 500 mM NaCl), 1 time with RIPA buffer (50 mM HEPES, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.25% sodium deoxycholate), once with PBS, and once with TE buffer. Protein-DNA complexes were extracted from beads at 37ºC in elution buffer (10 mM EDTA, 50 mM Tris-HCl, 1% SDS). For reverse crosslinking, supernatants from centrifuged samples were rotated overnight at 60ºC. RNAse and proteinase K treated samples were extracted with phenol:chloroform:isoamyl alcohol. Precipitated DNA was resuspended in 10 mM Tris-HCl, quantified with a Qubit fluorometer (Life Technologies, Grand Island, NY).
The Illumina protocol (Illumina, Inc., San Diego, CA) for ChIP-seq library generation was used with slight modifications. Approximately 5-10 ng chromatin was end-repaired (EpiCentre Biotechnologies, Madison, WI). Material was then A-tailed and ligated with adapters for single end deep sequencing (Illumina, Inc., San Diego, CA). Adapter modified DNA was size-selected, 300-400 base pair (bp) range, and then amplified using the Phusion polymerase (New England Biolabs, Ipswich, MA). Amplified ChIP libraries were size selected and sequenced on an Illumina GAIIx Genome Analyzer (Illumina, Inc., San Diego, CA) at the UMass Medical School Deep Sequencing Core Facility (Worcester, MA).

tag: cell line

tag: tissue origin

value: peripheral blood

value: myeloblast

tag: passages

tag: chip antibody vendor

value: Santa Cruz Biotechnology, Inc

tag: chip antibody cat. #

tag: chip antibody lot #


title: N-CoR

tag: chip antibody

value: N-CoR


title: AML1-ETO

value: ETO

value: EMD Millipore


title: Fetal Liver5

tag: gender

tag: strain

tag: Stage


title: Fetal Liver3


title: Fetal Liver4


title: AML1

value: Active Motif


title: 4sU-RNA - 7-8 hpi Rep 2

description: Purified from total RNA using 4sU-tagging

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.3.0
RPKM values were calculated based on the total number of reads mapping to the human genome.
Genome_build: hg19, JN555585
Supplementary_files_format_and_content: text files with RPKM values

extract_protocol:
Total RNA was prepared using Trizol. Newly transcribed RNA was purified as described in Rädle et al., JoVE 2013.
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat (only for total RNA). No rRNA depletion was performed for the 4sU-RNA samples!

tag: tissue

value: foreskin

value: fibroblasts

value: 60 min 500 µM 4sU at 7-8 h p.i.

tag: infection reagent

value: Herpes simplex virus 1, strain 17


title: 8 Cell12

source_name: 8 Cell

value: F

value: 8 cell


title: 8 Cell11


title: Fetal Liver1

value: fetal liver


title: Fetal Liver2

value: M


title: RP 6 h p.i. - Rep 1

value: human foreskin fibroblasts

value: 6 h p.i.

value: NNNTGGCNN


title: 4sU-RNA - 6-7 hpi Rep 2

value: 60 min 500 µM 4sU at 6-7 h p.i.


title: 8 Cell10


title: RP mock - Rep 1

value: mock

value: NNNTTGTNN


title: 4sU-RNA - 5-6 hpi Rep 2

value: 60 min 500 µM 4sU at 5-6 h p.i.


title: 4sU-RNA - 2-3 hpi Rep 2

value: 60 min 500 µM 4sU at 2-3 h p.i.


title: 8 Cell8


title: 8 Cell6


title: 8 Cell7


title: 4sU-RNA - 3-4 hpi Rep 2

value: 60 min 500 µM 4sU at 3-4 h p.i.


title: 8 Cell9


title: 4sU-RNA - 1-2 hpi Rep 2

value: foreskin

value: 60 min 500 µM 4sU at 1-2 h p.i.


title: 4sU-RNA - 0-1 hpi Rep 2

value: fibroblasts

value: 60 min 500 µM 4sU at 0-1 h p.i.


title: 8 Cell5


title: RP 2 h p.i. - Rep 2

value: 2 h p.i.

value: Herpes simplex virus 1, strain 17

value: NNNGGCGNN


title: 8 Cell4

value: M

value: 8 cell


title: 8 Cell3


title: 8 Cell2


title: Total RNA - 8hpi Rep 2

description: Total RNA prepared using Trizol

source_name: Total RNA

value: 8 h p.i.


title: 8 Cell1


title: Total RNA - 6hpi Rep 2

description: Total RNA prepared using Trizol

value: 6 h p.i.


title: ES4

source_name: ES Cell (2i)

value: F

value: ES


title: Total RNA - 4hpi Rep 2

description: Total RNA prepared using Trizol

value: 4 h p.i.


title: 4sU-RNA - 4-5 hpi Rep 2

value: 60 min 500 µM 4sU at 4-5 h p.i.


title: Total RNA - mock Rep 2

description: Total RNA prepared using Trizol

value: mock


title: 4sU-RNA - 7-8 hpi Rep 1

value: 60 min 500 µM 4sU at 7-8 h p.i.


title: 4sU-RNA - 6-7 hpi Rep 1

value: foreskin

value: 60 min 500 µM 4sU at 6-7 h p.i.


title: ES2


title: ES1


title: ES3


title: Total RNA - 2hpi Rep 2

description: Total RNA prepared using Trizol

value: fibroblasts


title: 4sU-RNA - 4-5 hpi Rep 1


title: 4sU-RNA - 3-4 hpi Rep 1

value: 60 min 500 µM 4sU at 3-4 h p.i.


title: Chip-seq_CHD8_45_EtOH

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using ELANDv2 allowing up to 2 mismatches in the first 32 bases
ChIP-seq peak calling, genomic annotation of peaks and comparison between ChIP-seq and ENCODE datasets were performed using ChIPseeqer (v.2.1), using default parameters. Minimum peak width 100bp. Mininum distance between peaks 100bp. Significance negative log p-value, t = 10^-10
Genome_build: hg19
Supplementary_files_format_and_content: Format: wig files generated using Chipseeqer  (v.2.1). Content: read density track for the UCSC Genome Browser.

growth_protocol: Cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin

extract_protocol:
After  treatment, the medium was replaced by medium containing 1% formaldehyde and incubated 10 min at 37ºC for cross-linking. The reaction was stop by adding 125 mM glycine and incubated 5 min at room temperature. Cells were washed twice with cold PBS, and collected. Preparation of chromatin and ChIP experiments were performed as previously described (Strutt et al, Methods Mol Biol. 1999; 119:455-567). Immunoprecipitated DNA was purified by phenol:chloroform followed by ethanol precipitation
Libraries were prepared according to Illumina's instructions.

treatment_protocol: For R5020 treatments, cells were subjected to serum-free conditions in RPMI medium without phenol red during 48 h. After serum starvation, cells were incubated with 10 nM R5020 or vehicle (ethanol; EtOH) for 5 or 45 min.

tag: treatment

value: EtOH

tag: time

value: 45 min

value: Cell line derived from T47D that contain one copy of MMTV promoter

value: anti-CHD8 (A301-224A, Bethyl Laboratories)


title: Chip-seq_CHD8_5_R5020

value: 5 min


title: Chip-seq_IgG

value: Rabbit IgG SIGMA


title: 4sU-RNA - 2-3 hpi Rep 1

tag: cell type

tag: time post infection

value: 60 min 500 µM 4sU at 2-3 h p.i.

value: Herpes simplex virus 1, strain 17


title: Chip-seq_CHD8_45_R5020


title: 4sU-RNA - 5-6 hpi Rep 1

value: 60 min 500 µM 4sU at 5-6 h p.i.


title: 4sU-RNA - 1-2 hpi Rep 1

value: 60 min 500 µM 4sU at 1-2 h p.i.


title: Chip-seq_CHD8_exp


title: 4sU-RNA - mock Rep 1

value: 60 min 500 µM 4sU prior to infection


title: Total RNA - 8hpi Rep 1

description: Total RNA prepared using Trizol

value: 8 h p.i.


title: 4sU-RNA - mock Rep 2

value: mock


title: Total RNA - 4hpi Rep 1

description: Total RNA prepared using Trizol

value: foreskin

value: 4 h p.i.


title: Total RNA - 2hpi Rep 1

description: Total RNA prepared using Trizol

value: fibroblasts

value: 2 h p.i.


title: Total RNA - 6hpi Rep 1

description: Total RNA prepared using Trizol

value: 6 h p.i.


title: Total RNA - mock Rep 1

description: Total RNA prepared using Trizol


title: mex-5 (RNAi) rep2

status: Public on May 25 2015

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description: Illumina index 11

data_processing:
Library strategy: PAT-seq
All analysis was carried out using Tail Tools version 0.29 available from http://www.vicbioinformatics.com/software.tail-tools.shtml
Reads were first clipped of poly(A) and adaptor sequence: The read was searched for a run of "A"s extending to the end of the read, or a run of "A"s extending into the adaptor sequence. An error rate of one base in five was allowed, and read bases with quality below 10 were ignored.
Clipped reads were then aligned to the reference genome using Bowtie version 2.2.2. Where a read had several equal best alignments, one was chosen at random.
Alignments which were followed by As in the reference genome were extended to cover these As if they were also seen in the original read. We refer to the number of non-templated As in a read as its tail length. Reads with tail length of at least 4 are referred to as poly(A) reads below.
Reads were assigned to genes if their alignment overlapped the region from the 5' end of the gene to 1000 bases 3' of the 3' end of the gene. If this would assign a read to multiple genes, the gene minimizing the distance between the 3' end of the alignment and the 3' end of the gene was chosen.
From this a count of reads per gene is obtained. Where a gene has at least 10 poly(A) reads, the average tail length of poly(A) reads is also calculated for that gene. This statistic provides information about the poly(A) tail length of transcripts. It is expected to be an underestimate as the whole poly(A) tail is not always read, except in the case of poly(A) tails shorter than 12 bases, in which case it may be an overestimate.
Polyadenylation sites were called where the 3' end of the alignments of at least 50 poly(A) reads occurred within 10 bases of each other. Where multiple candidate sites existed within 50 bases of each other, only the site with the greatest number of poly(A) reads was called.
Reads were assigned to polyadenylation sites if their alignmnet overlapped a region from 100 bases 5' of the site to the site itself. Again, if a read could be assigned to multiple polyadenylation sites the site minimizing the distance to the 3' end of the alignment was chosen.
As with genes, read counts and average tail lengths were calculated for each called polyadenylation site.
Genome_build: ce10
Supplementary_files_format_and_content: genes.gff contains the genome region used for each gene.
Supplementary_files_format_and_content: genewise-counts.csv contains counts of reads aligning to these regions or up to 1000 bases downstrand.
Supplementary_files_format_and_content: genewise-tails.csv contains average poly(A) read tail lengths for each gene.
Supplementary_files_format_and_content: peaks.gff contains the called polyadenylation sites. The polyadenylation site is the 3' end of each of these features.
Supplementary_files_format_and_content: peakwise-counts.csv contains counts of reads aligning to each polyadenylation site.
Supplementary_files_format_and_content: peakwise-tails.csv contains average poly(A) real tail lengths for each polyadenylation site.

organism: Caenorhabditis elegans

source_name: N2 (mex-5 RNAi)

growth_protocol: C. elegans N2 (wildtype) worms were grown on 15 cm plates with Agar Nematode Growth Medium spotted with concetrated E. coli OP50

extract_protocol:
Total RNA was extracted from snap frozen cell pellets Trizol extraction. 1 microgram of this was input into the library preperation.
Library construction was by the PAT-seq approach. Breifly this involves a modified the ePAT approach to tagging adenylated RNA to generate libraries suitable for deep sequencing.  Briefly, adenylated RNA is sequence specifically extended by dNTPs using Klenow polymerase and an annealed DNA anchor oligonucleotide. This takes advantage of the native function of DNA polymerase to extend an RNA primer from a DNA template in second strand synthesis. Importantly, any unwanted priming to internal poly(A)-tracts in RNA is avoided by a requirement for 3’ extension in subsequent fragment selection and reverse transcription. No ribosome depletion is necessary. Here, the anchor sequence was compatible with the Illumina index primers and included a 5’ biotin moiety to facilitate handling. In a second step, the 3’ tagged RNA was subject to limited fragmentation by RNase T1. This cleaves RNA after G-residues and ensures that cleavage is only possible within the body of the RNA, not the poly(A)-tract or the DNA sequence of the extended tag. The fragmented RNA was 5’ phosphorylated to allow RNA Ligase 2 mediated ligation of an Illumina compatible splinted-linker to the RNA fragments. Reverse transcription was primed from the anchor sequence. Note: All manipulations after limited fragmentation were performed in association with streptavidin magnetic beads. The cDNA PAT-seq libraries was eluted from beads, size-selected by Urea PAGE and amplified with primers that introduce the features for directional Illumina sequencing and indexing. In samples analysed here, the window of selection was between 120-300 bases. This size range was selected to allow for ≥ 25 bases of 3’UTR sequence to map reads to the genome, the an average yeast poly(A)-tail of ~25 bases (maximum ~90 bases), the majority of reads would contain heterogeneous 5’ sequence of sufficient length to map uniquely to the yeast genome. Note: all reads run in 5’ to 3’ direction from unique sequence into a variable length of poly(A) homopolymers. This means that color balance is preserved and that any low fidelity within the homopolymers is limited to the end of the read.
Cluster Generation: 9pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012
Sequencing chemistry: 1 x 150bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012

treatment_protocol: To induce RNAi, C. elegans N2 (wildtype) worms were grown on 15 cm plates with Agar Nematode Growth Medium spotted with concetrated E. coli HT115(DE3) expressing dsRNA of interest, cultured in terrific broth and induced with IPTG for 6 hours in the culturing liquid media

tag: strain backround

value: N2 (mex-5 RNAi)

tag: developmental stage

value: Early embryos (> 90% zygote to 24 cell stage)


title: gld-2 (RNAi) rep2

description: Illumina index 10

source_name: N2 (gld-2 RNAi)

value: N2 (gld-2 RNAi)


title: mex-6(pk440) rep2

description: Illumina index 12


title: gld-3 (RNAi) rep2

description: Illumina index 9

source_name: N2 (gld-3 RNAi)

value: N2 (gld-3 RNAi)


title: N2 Rep2

description: Illumina index 7

source_name: N2 genetic background

value: N2 genetic background


title: pos-1 (RNAi) rep2

description: Illumina index 8

source_name: N2 (pos-1 RNAi)

value: N2 (pos-1 RNAi)


title: Chip-seq_CHD8_5_EtOH

value: EtOH

value: 5 min

tag: cell line

value: Cell line derived from T47D that contain one copy of MMTV promoter

value: anti-CHD8 (A301-224A, Bethyl Laboratories)


title: mex-5 (RNAi) rep1

description: Illumina index 5


title: gld-2 (RNAi) rep1

description: Illumina index 4


title: gld-3 (RNAi) rep1

description: Illumina index 3


title: mex-6(pk440) rep1

description: Illumina index 6


title: N2 Rep1

description: Illumina index 1


title: 4sU-RNA - 0-1 hpi Rep 1

value: 60 min 500 µM 4sU at 0-1 h p.i.

value: Herpes simplex virus 1, strain 17


title: SPF5

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: polyA+ RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
alignment: tophat with deafult parameters
Expression table done using ESAT http://garberlab.umassmed.edu/software/esat/
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited

source_name: Brain

growth_protocol: Mice were housed under SPF or germ-free condiotions. Animals were 6-8 weeks old.

extract_protocol:
Adult microglia were harvested using density gradient separation. CD11b+CD45lo microglial cell populations were FACS-sorted and collected directly in cell lysis buffer.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: no prior treatment

value: Microglia

value: C57BL/6 (SPF)

tag: age

value: 6-8 weeks


title: SPF7

description: polyA+ RNA


title: GF3

description: polyA+ RNA

value: C57BL/6 (germ-free)


title: SPF6

description: polyA+ RNA


title: GF5

description: polyA+ RNA


title: GF7

description: polyA+ RNA


title: GF1

description: polyA+ RNA


title: SPF4

description: polyA+ RNA


title: AIP rep3

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

data_processing:
The raw data containing adaptor sequences, reads with low quality sequences and unknown nucleotides N were filtered to obtain clean reads with 50 nt in length
All clean reads were mapped to the transcripts sequence of by bowtie, only 1 bp mismatch is allowe
For monitoring the mapping events on both strands, both of the sense and the complementary antisense sequences were included in the data collection
The number of perfect clean reads corresponding to each gene was calculated and normalized to the number of Reads Per Kilobase of exon model per Million mapped reads (RPKM)
Based on the expression levels, the significant DEGs (Difierentially expressed genes) among different samples were identified with p-value ≤0.05 and log2fold-change｜log 2 FC∣ ≥1.The cluster of the DEGs was performed by using the common perl and R scripts.
Genome_build: ensemble Sus_scrofa.Sscrofa10.2
Supplementary_files_format_and_content: gene expression data and differential analysis result

organism: Sus scrofa

source_name: longissimus dorsi muscle

extract_protocol:
Total RNA was extracted from longissimus dorsi using TRIzol (Invitrogen, CA, USA) and further purified with RNeasy column (Qiagen, USA) according to the manufacturer’s protocol
Approximately 10 ug of total RNA representing a muscle tissue was sub-jected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Thermo-fisher). Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were constructed into the final cDNA library in accordance with the protocol for the Illumina RNA ligation based method (Illumina, San Diego, USA). In brief, the fragmented RNA has been dephosphorylated at the 3' end by the phosphatase and been phosphorylated at the 5' end by the PNK. The treated RNA has been cleaned up with the RNeasy MinElute Kit (Qiagen) following the instructions of the manufacturer. The purified RNA was ligated with a pre-adenylated 3' adapter, which enables the subsequent ligation of the 5' adapter. Based on the adapter sequence, a reverse transcription followed by PCR used to create cDNA constructs. The average insert size for the single-end libraries was 300 bp (±50 bp). And then we performed the single end sequencing on an Illumina Hiseq2000 at the (LC Sciences,USA) following the vendor's recommended protocol.

tag: development satge

value: After inflection point (post natal day 243)

value: longissimus dorsi muscle

tag: breed

value: Liangshan

tag: Sex

value: female


title: GF6

description: polyA+ RNA


title: GF4

description: polyA+ RNA


title: SPF1

description: polyA+ RNA


title: AIP rep2


title: SPF3

description: polyA+ RNA


title: UIP rep2

value: Under inflection point (post natal day 193)


title: pos-1 (RNAi) rep1

description: Illumina index 2

value: Early embryos (> 90% zygote to 24 cell stage)


title: UIP rep3


title: SPF2

description: polyA+ RNA


title: UIP rep1


title: BIP rep3

value: Before inflection point (post natal day 143)


title: BIP rep1


title: BIP rep2


title: GF2

description: polyA+ RNA


title: EE_Infected_whole_rep3

status: Public on May 23 2015

city: Utrecht

first: Devanjali

last: Dutta

state: Netherlands

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Amplified mRNA

data_processing:
Tophat, phred+33 was used as a quality score measurement
Raw fastqc reads were mapped to the Drosophila genome (Drosophila_melanogaster.BDGP5.70.dna.toplevel.fa) using Tophat 2.0.9 at default (using boost_1_54_0, bowtie2-2.1.0, samtools-0.1.19).
IGV was used to visualize mapped reads. Unmapped reads were discarded. All mapped reads were then counted to generate raw count for each genomic feature using HTSeq-0.5.4p5 (used with option -a 10).
For differential expression analysis, DESeq (p-value adjustment 0.05 by method Benjamini-Hochberg) was used. The reads were normalized also to Reads per kilobase of transcript per million mapped reads (RPKM).
Genome_build: Drosophila_melanogaster.BDGP5.70.dna.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Female Midgut whole

extract_protocol:
Midguts were removed, dissociated and cells were FACS Sorted. RNA was harvested using Arcturus Pico Pure RNA extraction kit and amplified with RiiboAmp HS plus amplification kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type marker

tag: fluorescent cell marker

value: YFP

value: FACS Sorted midgut cells

tag: genotype

value: Pseudomonas entomophila Infected


title: ESG_Infected_whole_ rep1

description: Amplified mRNA

value: ESG

value: GFP

tag: gender


title: EE_Infected_whole_rep2

description: Amplified mRNA

tag: tissue


title: ESG_Infected_whole_ rep2

description: Amplified mRNA


title: ESG_Infected_whole_ rep3

description: Amplified mRNA


title: EE_Infected_whole_rep1

description: Amplified mRNA


title: VM_physiological_regions_ R5_rep2

description: Amplified mRNA

source_name: Female Midgut regions

value: How

value: wild type How Gal4-UAS GFP


title: EB_Infected_whole_rep1

description: Amplified mRNA

value: Su(H)


title: VM_physiological_regions_ R4_rep2

description: Amplified mRNA


title: EC_Infected_whole_rep2

description: Amplified mRNA


title: EB_Infected_whole_rep2

description: Amplified mRNA


title: PIWI -immunoprecipitated RNAs in wild type fly testis

city: New Haven

state: CT

address: 10 Amistad st

institute: Yale University

description: piRNA

data_processing:
After being trimmed off the adaptor sequence, 18-42nt sequences were collected and mapped to Drosophila melanogaster release 5 genome with bowtie0.12.7
Genome_build: drosophila melanogaster release 5
Supplementary_files_format_and_content: text file format, contain the sequence and their sequence read count

source_name: adult fly testis

growth_protocol: Flies were maintained on standard cornmeal-molasses agar

extract_protocol:
Small RNAs ranging in size between ~16-to-28 nucleotides (nt) (below 2S rRNA) were gel-purified
library was constructed with Illumina TruSeq small RNA kit

treatment_protocol: immunoprecipited RNAs by using mouse anti-Piwi (P3G11) were isolated from the immunopurified complexes with phenol:chloroform and precipitated with ethanol. RNAs were dephosphorylated with calf intestinal phosphatase (NEB) and labeled with [γ-32P]ATP with T4 polynucleotide kinase (NEB) for visualization.

value: testis

value: adult

tag: strain = P{PZ}Hsp83 08445


title: EC_Infected_whole_rep1

description: Amplified mRNA


title: ISC_Infected_whole _rep2

description: Amplified mRNA

value: Delta


title: AIP rep1

value: After inflection point (post natal day 243)

value: longissimus dorsi muscle


title: ISC_Infected_whole _rep1

description: Amplified mRNA

value: female


title: VM_physiological_regions_ R3_rep1

description: Amplified mRNA


title: ESG_ physiological_whole_ rep2

description: Amplified mRNA

value: wild type ESG Gal4-UAS GFP


title: VM_physiological_regions_ R2_rep1

description: Amplified mRNA


title: ESG_ physiological_whole_ rep1

description: Amplified mRNA


title: EE_ physiological_whole_ rep2

description: Amplified mRNA

value: wild type Rab3-YFP


title: VM_physiological_regions_ R2_rep2

description: Amplified mRNA


title: VM_physiological_regions_ R1_rep2

description: Amplified mRNA


title: VM_physiological_regions_ R1_rep1

description: Amplified mRNA


title: ESG_ physiological_whole_ rep3

description: Amplified mRNA


title: EE_ physiological_whole_ rep1

description: Amplified mRNA


title: EC_ physiological_whole_ rep2

description: Amplified mRNA

value: wild type Myo1A Gal4-UAS GFP


title: EB_ physiological_whole_ rep3

description: Amplified mRNA

value: wild type Su(H) Gal4-UAS GFP


title: ESG_physiological_regions_ R4_rep2

description: Amplified mRNA

value: FACS Sorted midgut cells


title: VM_physiological_regions_ R5_rep1

description: Amplified mRNA


title: ESG_physiological_regions_ R5_rep2

description: Amplified mRNA


title: ESG_physiological_regions_ R5_rep1

description: Amplified mRNA


title: EC_ physiological_whole_ rep1

description: Amplified mRNA


title: VM_physiological_regions_ R4_rep1

description: Amplified mRNA


title: ESG_physiological_regions_ R3_rep2

description: Amplified mRNA


title: VM_physiological_regions_ R3_rep2

description: Amplified mRNA


title: ESG_physiological_regions_ R4_rep1

description: Amplified mRNA


title: ISC_physiological_whole_rep3

description: Amplified mRNA

value: wild type Delta Gal4-UAS GFP


title: ESG_physiological_regions_ R3_rep1

description: Amplified mRNA

value: ESG


title: EB_ physiological_whole_ rep2

description: Amplified mRNA

value: GFP


title: EB_ physiological_whole_ rep1

description: Amplified mRNA


title: ISC_physiological_whole_rep2

description: Amplified mRNA


title: ESG_physiological_regions_ R2_rep1

description: Amplified mRNA


title: ESG_physiological_regions_ R1_rep2

description: Amplified mRNA


title: ESG_physiological_regions_ R2_rep2

description: Amplified mRNA


title: ISC_physiological_whole_rep1

description: Amplified mRNA


title: EE_physiological_regions_ R4_rep2

description: Amplified mRNA

value: Pros

value: wild type Pros Gal4-UAS GFP


title: EE_physiological_regions_ R5_rep1

description: Amplified mRNA


title: EE_physiological_regions_ R5_rep2

description: Amplified mRNA


title: EE _physiological_regions_R4_rep1

description: Amplified mRNA


title: EE_physiological_regions_ R3_rep2

description: Amplified mRNA


title: EE_physiological_regions_ R1_rep2

description: Amplified mRNA


title: EE_physiological_regions_ R2_rep1

description: Amplified mRNA


title: EE_physiological_regions_ R1_rep1

description: Amplified mRNA


title: EE_physiological_regions_ R3_rep1

description: Amplified mRNA


title: EC_physiological_regions_ R5_rep2

description: Amplified mRNA


title: EC_physiological_regions_ R4_rep2

description: Amplified mRNA


title: EC_physiological_regions_ R4_rep1

description: Amplified mRNA


title: EC _physiological_regions_R5_rep1

description: Amplified mRNA


title: ESG_physiological_regions_ R1_rep1

description: Amplified mRNA


title: EC _physiological_regions_R3_rep2

description: Amplified mRNA


title: EC_physiological_regions_ R2_rep1

description: Amplified mRNA


title: EC _physiological_regions_R1_rep2

description: Amplified mRNA


title: EB _physiological_regions_R4_rep2

description: Amplified mRNA

value: Su(H)


title: EB_physiological_regions_ R5_rep2

description: Amplified mRNA


title: EE _physiological_regions_R2_rep2

description: Amplified mRNA


title: EC _physiological_regions_R2_rep2

description: Amplified mRNA


title: EB_physiological_regions_ R3_rep2

description: Amplified mRNA


title: EB_physiological_regions_ R5_rep1

description: Amplified mRNA


title: EC_physiological_regions_ R1_rep1

description: Amplified mRNA


title: EB _physiological_regions_R4_rep1

description: Amplified mRNA


title: EB _physiological_regions_R3_rep1

description: Amplified mRNA


title: EB_physiological_regions_ R2_rep1

description: Amplified mRNA


title: EB _physiological_regions_R1_rep2

description: Amplified mRNA


title: EB_physiological_regions_ R2_rep2

description: Amplified mRNA


title: EB_physiological_regions_ R1_rep1

description: Amplified mRNA


title: ISC_physiological_regions_ R5_rep1

description: Amplified mRNA


title: ISC_physiological_regions_ R5_rep2

description: Amplified mRNA


title: EC _physiological_regions_R3_rep1

description: Amplified mRNA


title: ISC _physiological_regions_R4_rep2

description: Amplified mRNA


title: ISC_physiological_regions_ R3_rep2

description: Amplified mRNA


title: ISC_physiological_regions_ R3_rep1

description: Amplified mRNA


title: ISC _physiological_regions_R2_rep1

description: Amplified mRNA


title: ISC_physiological_regions_ R1_rep1

description: Amplified mRNA


title: VM_ physiological_whole_ rep2

description: Amplified mRNA

value: How

value: wild type How Gal4-UAS GFP


title: ISC_physiological_regions_ R1_rep2

description: Amplified mRNA

value: Delta


title: VM_ physiological_whole_ rep1

description: Amplified mRNA


title: Hu6 RS 5'RACE 3

status: Public on May 22 2015

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

description: Global 5'RACE

data_processing:
Basecalling with Illumina Real Time Analysis
Small RNA reads were trimmed to clipped to remove 3' adaptor sequences, and then collapsed to non-redundant sequences using the FASTX toolkit. They were then mapped to mm9 or hg19 genome using Bowtie (v1.0.0), allowing up to 2 mismatches (-v 2) and maximum 100 genomic alignments (-k 100, -m 100).
RNA-seq reads were mapped to mm9 genome using STAR (v2.3.1z12) allowing up to 2 mismatches and maximum of 100 genomic alignments. HTSeq-count (v0.6.1p1) was used to quantify expression of Refseq genes in each library, and DESeq (v1.16.0) was used to calculate differential expression.
5' RACE reads were mapped to mm9 genome using STAR (v2.3.1z12) allowing up to 2 mismatches and maximum of 100 genomic alignments. The 5' position of each read is then extracted and overlapped with the 5' ends of small RNA reads from the appropriate small RNA library.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: Processed files are tab-delmited texts. sRNA processed files contain counts, number and location of genomic alignments for each non-redundant sequences. RNA-seq processed files contain read counts for each RefSeq in the library.  5' RACE processed files contain  5' site of RACE reads that overlap sRNAs.

source_name: Round spermatid

growth_protocol: Mice were grown and mated under standard conditions. Males were grown to adult age (2-6months) before having their testes extracted for cell sorting, MIWI immunoprecipitation or immediate RNA extraction. The Hu6 mouse is a C57BL/6N genetic background mouse with the human BAC, RP11-119C22 inserted into the mouse genome.

extract_protocol:
Adult mouse testes tissue or sorted spermatogenic cells were lysed in Trizol or Trizol-LS reagent and total RNA was isolated according to manufacturer’s recommendations.
Small RNA libraries: 20µg of total RNA was size selected on a 15% denaturing polyacrylamide (dPAA) gel to obtain 19-33nt RNA species. The resultant RNA was ligated at its 3’end to the Illumina RA3 using NEB truncated T4 RNA ligase 2 at 20OC for 2 hours. Ligated products were size selected on a 15% dPAA before being ligated at its 5’end to RA5 using Ambion T4 RNA ligase at 20OC for 2 hours. Ligated products were size selected on a 15% dPAA before being reverse transcribed with RTP and superscript III reverse transcriptase. Resultant cDNAs were amplified using RP1 forward primer and indexed reverse primers using NEB Phusion PCR mastermix. Amplified libraries were gel purified on a 2% low-melting agarose gel and sequenced using the Illumina Hi-seq platform. RA3: /5rApp/TGGAATTCTCGGGTGCCAAGG/3ddC/ (ddC: dideoxyC, rN: ribonucleotide, p: phosphate). RA5: rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC. RTP: GCCTTGGCACCCGAGAATTCCA. RP1: AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA. RPI: CAAGCAGAAGACGGCATACGAGATIIIIIIGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA (IIIIII: 6-mer Illumina index sequence). Global 5'RACE and Scriptseq: Total RNA from sorted pachytene spermatocytes, secondary spermatocytes or round spermatids was treated with RQ1 DNase at 37oC for 30 minutes, depleted of ribosomal RNA using the Ribo-Zero kit, and used to generate global 5’RACE libraries as described 7. Post-amplification libraries were size selected on a BluePippin 2% agarose chip using a cutoff of 180-350bp. Ribo-depleted RNA was also used for strand-specific RNA libraries, which was constructed using the Scriptseq v2 RNA-Seq library preparation kit.

treatment_protocol: MIWI immunoprecipitation of small RNAs: Both mouse testes were homogenized in 1ml lysis buffer. The lysate was then clarified on a tabletop centrifuge for 30 minutes and the supernatant was passed through a 45μm filter. The lysate was incubated with 6μg rabbit anti-MIWI-N3 polyclonal antibody (Covance Inc.; Rabbit anti-mouse-miwi polyclonal antibody (MIWI N3)) and 4ml NT2 buffer, while rotating at 4oC for 3 hours. 100μl protein A-agarose beads were pre-washed in NT2 buffer and pre-blocked with 5% BSA before being incubated with the lysateantibody mixture, while rotating at 4oC for 2 hours. Beads were then washed twice in 1.4ml NT2 buffer, twice in 1.4ml NT-2 (with additional 150mM NaCl), and twice with 1.4ml NT-2 (with additional 350mM NaCl). MIWI-immunoprecipitated small RNAs were eluted by treating beads with 400μg proteinase K and 1x proteinase K buffer at 60oC for 1 hour with light agitation. Finally, eluted RNA was extracted with phenol-chloroform. A quarter of the eluted RNA was visualized with 5’end labeling to verify the precipitation of ~30nt RNA species, and the remainder was used for small RNA cloning. Spermatogene cell isolation: Spermatogenic cell isolation: Testes were isolated from one adult mouse for each sorting experiment and the tunica was removed. Tissue was digested for 45 minutes at 37°C in dissociation buffer. Cell were resuspended at the concentration of 1x106 cells/ml in HBSS+ and stained with 5mg/ml Hoechst for 30 minutes at 37°C. Immediately before analysis, propidiumIodide (1mg/ml) was added for dead cell exclusion. Analysis was performed in a five-laser AriaII cell sorter. Hoechst was excited with a UV laser at 350nm and fluorescence was recorded with a 450/50 filter (Hoechst Blue) and 670LP filter (Hoechst Red). A 505LP filter was used to separate the emission wavelengths. PY, SS and RS were gated based on their Hoechst Blue-Red profile in scatter plots, as well as Hoechst Blue fluorescence and Forward and Side Scatter properties. After applying gates, cells were collected directly into Trizol-LS for RNA isolation.

value: Round spermatid


title: Hu6 RS 5'RACE 2

description: Global 5'RACE


title: MW+/+ RS 5'RACE 4

description: Global 5'RACE


title: MW+/+ RS 5'RACE 3

description: Global 5'RACE


title: MW-/- SS 5'RACE 2

description: Global 5'RACE

source_name: Secondary spermatocyte

value: Secondary spermatocyte


title: MW+/+ RS 5'RACE 1

description: Global 5'RACE


title: MW-/- RS 5'RACE 1

description: Global 5'RACE


title: MW+/- RS 5'RACE 1

description: Global 5'RACE


title: MW+/- RS 5'RACE 2

description: Global 5'RACE


title: ISC_physiological_regions_ R4_rep1

description: Amplified mRNA

value: female


title: MW-/- RS 5'RACE 2

description: Global 5'RACE


title: MW-/- SS 5'RACE 1

description: Global 5'RACE


title: MW+/- SS 5'RACE 1

description: Global 5'RACE


title: MW+/- SS 5'RACE 2

description: Global 5'RACE


title: MW-/- PY 5'RACE 2

description: Global 5'RACE

source_name: Pachytene spermatocyte

value: Pachytene spermatocyte


title: T47D_E2+R5020_3hr_Rep5

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description: RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 5)

data_processing:
Single-end 40 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014).
Read counts were normalised and tested for differential gene expression using the DESeq5 workflow. Multiple testing correction was applied using the Benjamini-Hochberg method. Genes were selected as differentially expressed such that FDR <0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

molecule: polyA RNA

growth_protocol: Cells grown in DMEM, supplemented with 10% FBS

extract_protocol:
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

treatment_protocol: Cells were treated with progesterone (100nM) or R5020 (10nM) for 3hr and RNA extracted

value: ER+ breast cancer cell line

tag: treated with


title: T47D_E2+Progesterone_3hr_Rep7

description: RNA-seq from T47D cells treated with E2+Progesterone_3hr (Replicate 7)


title: T47D_E2+Progesterone_3hr_Rep3

description: RNA-seq from T47D cells treated with E2+Progesterone_3hr (Replicate 3)


title: ISC_physiological_regions_ R2_rep2

description: Amplified mRNA


title: MW+/- PY 5'RACE 1

description: Global 5'RACE


title: Hu6 RS RNA-seq 2

description: ScriptSeq


title: Hu6 RS RNA-seq 1

description: ScriptSeq


title: T47D_E2+R5020_3hr_Rep8

description: RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 8)


title: MW-/- RS RNA-seq 2

description: ScriptSeq


title: T47D_E2_Rep7

description: RNA-seq from T47D cells treated with E2 (Replicate 7)


title: Hu6 RS 5'RACE 1

description: Global 5'RACE


title: T47D_E2_Rep8

description: RNA-seq from T47D cells treated with E2 (Replicate 8)


title: MW-/- RS RNA-seq 1

description: ScriptSeq


title: MW+/+ RS 5'RACE 2

description: Global 5'RACE


title: T47D_E2+R5020_3hr_Rep1

description: RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 1)


title: MW+/- RS RNA-seq 2

description: ScriptSeq


title: MW+/- RS RNA-seq 1

description: ScriptSeq


title: MW+/- PY 5'RACE 2

description: Global 5'RACE


title: MW+/+ RS RNA-seq 3

description: ScriptSeq


title: T47D_E2+Progesterone_3hr_Rep8

description: RNA-seq from T47D cells treated with E2+Progesterone_3hr (Replicate 8)


title: MW-/- PY 5'RACE 1

description: Global 5'RACE


title: T47D_E2_Rep6

description: RNA-seq from T47D cells treated with E2 (Replicate 6)


title: T47D_E2+R5020_3hr_Rep3

description: RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 3)


title: MW+/+ RS RNA-seq 2

description: ScriptSeq


title: MW+/+ RS RNA-seq 1

description: ScriptSeq


title: T47D_E2_Rep4

description: RNA-seq from T47D cells treated with E2 (Replicate 4)


title: T47D_E2+R5020_3hr_Rep2

description: RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 2)


title: MW-/- SS RNA-seq 2

description: ScriptSeq


title: MW+/- SS RNA-seq 1

description: ScriptSeq


title: MW+/+ SS RNA-seq 2

description: ScriptSeq


title: MW+/+ SS RNA-seq 3

description: ScriptSeq


title: MW-/- SS RNA-seq 1

description: ScriptSeq


title: MW+/- SS RNA-seq 2

description: ScriptSeq


title: MW-/- PY RNA-seq 1

description: ScriptSeq


title: MW-/- PY RNA-seq 2

description: ScriptSeq


title: T47D_E2+Progesterone_3hr_Rep1

description: RNA-seq from T47D cells treated with E2+Progesterone_3hr (Replicate 1)


title: MW+/+ SS RNA-seq 1

description: ScriptSeq


title: T47D_E2_Rep1

description: RNA-seq from T47D cells treated with E2 (Replicate 1)


title: T47D_E2_Rep5

description: RNA-seq from T47D cells treated with E2 (Replicate 5)


title: T47D_E2+R5020_3hr_Rep6

description: RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 6)


title: T47D_E2+Progesterone_3hr_Rep5

description: RNA-seq from T47D cells treated with E2+Progesterone_3hr (Replicate 5)


title: T47D_E2+R5020_3hr_Rep7

description: RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 7)


title: MW+/- PY RNA-seq 2

description: ScriptSeq


title: T47D_E2+Progesterone_3hr_Rep6

description: RNA-seq from T47D cells treated with E2+Progesterone_3hr (Replicate 6)


title: MW+/- PY RNA-seq 1

description: ScriptSeq


title: MW+/+ PY RNA-seq 3

description: ScriptSeq


title: T47D_E2_Rep2

description: RNA-seq from T47D cells treated with E2 (Replicate 2)


title: MCF7_E2_Rep2

description: RNA-seq from MCF7 cells treated with E2 (Replicate 2)


title: MCF7_E2+Progesterone_3hr_Rep6

description: RNA-seq from MCF7 cells treated with E2+Progesterone_3hr (Replicate 6)


title: T47D_E2+Progesterone_3hr_Rep4

description: RNA-seq from T47D cells treated with E2+Progesterone_3hr (Replicate 4)


title: Hu6-delta total small RNA

description: Total testes small RNA

source_name: Total testes

value: Total testes

value: Hu6 delta


title: T47D_E2_Rep3

description: RNA-seq from T47D cells treated with E2 (Replicate 3)


title: MCF7_E2+Progesterone_3hr_Rep7

description: RNA-seq from MCF7 cells treated with E2+Progesterone_3hr (Replicate 7)


title: MCF7_E2+Progesterone_3hr_Rep8

description: RNA-seq from MCF7 cells treated with E2+Progesterone_3hr (Replicate 8)


title: Hu6 total small RNA

description: Total testes small RNA


title: MCF7_E2+R5020_3hr_Rep8

description: RNA-seq from MCF7 cells treated with E2+R5020_3hr (Replicate 8)


title: T47D_E2+Progesterone_3hr_Rep2

description: RNA-seq from T47D cells treated with E2+Progesterone_3hr (Replicate 2)


title: MW+/+ total small RNA

description: Total testes small RNA


title: MCF7_E2+R5020_3hr_Rep6

description: RNA-seq from MCF7 cells treated with E2+R5020_3hr (Replicate 6)


title: MCF7_E2_Rep4

description: RNA-seq from MCF7 cells treated with E2 (Replicate 4)


title: 9103_Ucn3null

city: Davis

first: Mark

middle: O.

last: Huising

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

data_processing:
reads were mapped to mm9 (NCBI build 37) using STAR
Bedtools was used to create count tables of the sorted bam files using reads aligning to RefSeq defined exons.
DESeq was used for statistical comparison.
Genome_build: mm9 (NCBI build 37)

source_name: isolated islets

growth_protocol: Isolated were isolated by collagenase injection through the common bile duct per common protocols and collected in Trizol.

extract_protocol:
Islets were collected in Trizol post FACS purification and isolated by a chloroform extraction, assisted by phase lock tubes. RNA was precipitated by isopropanol and cleaned up over an RNEasy microcolumn per the Qiagen's taking great care to avoid carry over of ethanol following the column washes. Elution volume was 30 microliter.
Indexed sequencing libraries were constructed using the TruSeq RNA sample prep Kit v2 per Illumina instructions.

value: islets

value: mixed

tag: Stage

value: adult, 3 months

tag: genotype/variation

value: Ucn3 null islets


title: 9104_Ucn3null

tag: cell type


title: MCF7_E2+R5020_3hr_Rep2

description: RNA-seq from MCF7 cells treated with E2+R5020_3hr (Replicate 2)


title: 9095_Ucn3wt

value: wild type


title: 9092_Ucn3wt


title: T47D_E2+R5020_3hr_Rep4

description: RNA-seq from T47D cells treated with E2+R5020_3hr (Replicate 4)


title: MW+/+ MIWI-IP small RNA 2

description: MIWI-immunoprecipitated small RNA


title: MW+/+ MIWI-IP small RNA 1

description: MIWI-immunoprecipitated small RNA


title: MW+/+ PY RNA-seq 2

description: ScriptSeq


title: MW+/+ PY RNA-seq 1

description: ScriptSeq


title: 9087_Ucn3wt


title: MCF7_E2_Rep7

description: RNA-seq from MCF7 cells treated with E2 (Replicate 7)


title: MCF7_E2+Progesterone_3hr_Rep2

description: RNA-seq from MCF7 cells treated with E2+Progesterone_3hr (Replicate 2)


title: Leo1_KO_Input

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

data_processing:
Quality trimming and adapter removal: Trimmomatic version 0.32 with parameters:  ILLUMINACLIP:adapters_illumina_genomic_w_revcomps.fasta:2:40:15 HEADCROP:5 SLIDINGWINDOW:5:20 MINLEN:30
Alignment: novoalign V2.07 with -r Random option
Filter out MT reads with bedTools
Merge replicate samples with picardTools v1.107 MergeSamFiles
Extend paired end reads and normalise to FPKM: deepTools package bamCoverage –normalizeUsingRPKM
Genome_build: S.Pombe ASM294v2.22
Supplementary_files_format_and_content: bigWig files with normalised read depth profiles for merged replicate samples

organism: Schizosaccharomyces pombe

source_name: Leo1 KO Input

extract_protocol:
DNA and proteins were crosslinked in vivo by treatment of cells with 1% PFA. Cells were lysed and sonicated, and histone-DNA complexes  isolated using anti-H3K9me2 antibody. Crosslinks were reversed using 1% SDS, proteins were removed by digestion with proteinase K, and DNA was recovered using a PCR purification kit.
Libraries were constructed using 5ng of input DNA or 16 to 20ng of immunoprecipitated DNA. Recovered DNA fragments were blunted, and ligated to adapters with internal barcodes  (NextFlex, Biooscientific). Libraries were then PCR amplified and  sequenced on an Illumina Hiseq 2000.

tag: strain

tag: chip antibody


title: Control_K9me2_ChIP

source_name: Control K9me2 ChIP

value: wild-type


title: 9083_Ucn3null


title: MCF7_E2+R5020_3hr_Rep7

description: RNA-seq from MCF7 cells treated with E2+R5020_3hr (Replicate 7)

tag: cell line


title: Control_Input

source_name: Control Input


title: MCF7_E2+R5020_3hr_Rep3

description: RNA-seq from MCF7 cells treated with E2+R5020_3hr (Replicate 3)


title: Hu6 MIWI-IP small RNA

description: MIWI-immunoprecipitated small RNA


title: MCF7_E2_Rep8

description: RNA-seq from MCF7 cells treated with E2 (Replicate 8)


title: MCF7_E2+Progesterone_3hr_Rep5

description: RNA-seq from MCF7 cells treated with E2+Progesterone_3hr (Replicate 5)


title: Leo1_KO_K9me2_ChIP

source_name: Leo1 KO K9me2 ChIP


title: MCF7_E2_Rep6

description: RNA-seq from MCF7 cells treated with E2 (Replicate 6)


title: MCF7_E2_Rep1

description: RNA-seq from MCF7 cells treated with E2 (Replicate 1)


title: MCF7_E2+Progesterone_3hr_Rep4

description: RNA-seq from MCF7 cells treated with E2+Progesterone_3hr (Replicate 4)


title: MCF7_E2+R5020_3hr_Rep1

description: RNA-seq from MCF7 cells treated with E2+R5020_3hr (Replicate 1)


title: MCF7_E2+R5020_3hr_Rep4

description: RNA-seq from MCF7 cells treated with E2+R5020_3hr (Replicate 4)


title: MCF7_E2_Rep5

description: RNA-seq from MCF7 cells treated with E2 (Replicate 5)


title: MCF7_E2+R5020_3hr_Rep5

description: RNA-seq from MCF7 cells treated with E2+R5020_3hr (Replicate 5)


title: MCF7_E2+Progesterone_3hr_Rep3

description: RNA-seq from MCF7 cells treated with E2+Progesterone_3hr (Replicate 3)


title: MCF7_E2+Progesterone_3hr_Rep1

description: RNA-seq from MCF7 cells treated with E2+Progesterone_3hr (Replicate 1)