title: M. pusilla CCMP1545 MNase sequencing

city: Berkeley

first: Jason

middle: T

last: Huff

address: 211 Koshland Hall

department: Plant & Microbial Biology

institute: University of California, Berkeley

data_processing:
genome build: JGI build v3.0
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

organism: Micromonas pusilla

growth_protocol: Marine algae (CCMP strains) were grown at the Provasoli-Guillard National Center for Marine Algae and Microbiota. A live culture of Cyanidioschyzon merolae (NIES-1332) was obtained from the Microbial Culture Collection at the National Institute for Environmental Studies, Japan. Cryptococcus neoformans dnmt5Δ (D632) and control (WT47; sxi1Δ) strains were obtained from the Fungal Genetic Stock Center. Strains D632 and WT47 were grown overnight at 23 °C in the dark to saturation in liquid Difco YM Broth (Becton, Dickinson and Company) and 10 μl was patched on autoclaved cellophane overlaid on Difco YM Agar (Becton, Dickinson and Company) and grown for 3 days at 23 °C in the dark. The cells and cellophane were placed in tubes with 0.5 mm Zirconia-Silica beads (BioSpec) and frozen in liquid nitrogen. The tubes were bead-beaten 4 × 1 min. with replacement in liquid nitrogen in between and pulverized material was stored at -80 °C.

extract_protocol:
The Provasoli-Guillard National Center for Marine Algae and Microbiota prepared genomic DNA and total RNA from marine algae (CCMP strains) and also provided frozen cells. Live Cyanidioschyzon merolae cells were collected by centrifugation and genomic DNA was isolated with a DNeasy Plant Mini Kit (QIAGEN). Purified wild-type Cryptococcus neoformans var. grubii H99 DNA (208821D) and Leishmania major strain Seidman DNA (PRA-309D) were obtained from ATCC. Pulverized Cryptococcus neoformans material from strains D632 and WT47 was partially thawed and genomic DNA was extracted with a DNeasy Plant Mini Kit by starting at the step with addition of AP1 and RNase, and total RNA was extracted with TRIzol (Life Technologies) using Phase Lock Gel Heavy 1.5 ml tubes (5 PRIME).
Assaying cytosine methylation by bisulfite sequencing of genomic DNA was performed as described previously (Ibarra et al., Science 2012). Briefly, genomic DNA was quantified with Qubit dsDNA Assay Kits (Life Technologies) and 50 to 250 ng were sonicated, end-repaired and ligated to methylated adapters. We performed 3 PCR reactions and combined the products before sequencing.
For RNA sequencing, total RNA was digested with RNase-free DNase I (QIAGEN) and concentrated with a RNeasy MinElute Cleanup Kit (QIAGEN). Purified total RNA was quantified by a Qubit RNA Assay Kit (Life Technologies), and between 67 and 125 ng was used to prepare a strand-specific library with the Encore Complete RNA-Seq Library System I (NuGEN).
Assaying nucleosomes by micrococcal nuclease (MNase) sequencing was performed as described previously (Teves and Henikoff, Methods Mol Biol 2012) with modification. Briefly, frozen Ostreococcus lucimarinus or Micromonas pusilla cells from 5 L of culture were thawed on ice and resuspended in 500 μl of cold 1× TM2 (10 mM Tris-HCl, pH 8, 2 mM MgCl2, supplemented with 1:200 EDTA-free plant protease inhibitors (Sigma)) per 50 mg wet-pellet mass by pipetting with a 5-ml pipet up and down 100 times. The slurry was filtered through a 40 μm-pore cell strainer (BD Falcon) by gravity. Triplicate reactions from the same cells were performed: five hundred μl of the cell suspension per reaction were collected by gentle, refrigerated centrifugation and washed once with 1 ml of 1× TM2. Cells were centrifuged again, resuspended in 200 μl of 1× TM2, and warmed to 37 °C for 5 min. Two hundred μl of 1× buffer (50 mM Tris-Hcl, pH 7.9, 5 mM CaCl2), supplemented with 100 μg ml-1 BSA and 125 gel units ml-1 for O. lucimarinus or 250 gel units ml-1 for M. pusilla (~12.5 and 25 Kunitz units ml-1, respectively, which we previously determined to yield mostly mononucleosomes) of micrococcal nuclease (NEB) were pre-heated to 37 °C and added to the 200 μl of resuspended cells, and the 400-μl mixture was further incubated at 37 °C for 10 min. with occasional vortexing. Reactions were stopped with 5 mM final EGTA. Then 100 mM final NaCl, 0.625% final SDS, 20 μg DNase-free RNase A and 50 μg proteinase K were added, and the mixture was incubated at 75 °C for 10 min. Genomic DNA was purified first by extraction with buffer-saturated phenol-chloroform-isoamyl alcohol using Phase Lock Gel Heavy 1.5 ml tubes, and then with 2 volumes of Agencourt AMPure XP beads (Beckman Coulter). For sequencing in vivo nucleosome positions, 66.7 ng from each of the triplicate reactions was combined (200 ng total) and made into a library without PCR by using the Encore Rapid Library System (NuGEN).
For in vitro nucleosome position analyses, we first generated an unmethylated equivalent of O. lucimarinus genomic DNA in vitro by isothermal multiple strand displacement amplification, using either Bst 2.0 (NEB) or an illustra Ready-To-Go GenomiPhi v3 Kit (GE Healthcare). For Bst 2.0, 15 replicate 50-μl reactions containing 10 ng O. lucimarinus genomic DNA each in 1× NEB Isothermal Amplification Buffer with 12.5 μM random hexamers, 400 μM dNTPs (with the deoxycytidine triphosphate unmethylated) and 8 units of Bst 2.0 DNA polymerase (New England Biolabs) were incubated at 50 °C for 8 hr. The DNA was amplified more than 20-fold in these reactions, so that approximately 95% of the amplified DNA molecules contain entirely unmethylated cytosines. The resulting amplified DNA and natively methylated genomic DNA were incubated separately at 75 °C for 10 min at a concentration of 4 μg ml-1 each with 0.62% SDS, 38 ng ml-1 DNase-free RNase A and 100 ng ml-1 proteinase K. DNA was purified by extracting twice with buffer saturated phenol-chloroform-isoamyl alcohol using Phase Lock Gel Heavy 1.5 ml tubes. The DNA was further purified and concentrated using 0.7 volumes of Agencourt AMPure XP beads. The purified natively methylated O. lucimarinus genomic DNA or unmethylated equivalent was assembled with purified recombinant human histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs) at a 1:2:1 molar ratio of DNA:histone H2A/H2B dimer:histone H3.1/H4 tetramer (assuming 1 nucleosome per 184 bp DNA for O. lucimarinus). The assembly began at 640 nM of 184-bp DNA in 2 M NaCl and was completed when the final concentration of 184-bp DNA was 80 nM and NaCl was 250 mM. The assembly was heated to 37 °C for 5 min and then mixed with an equal volume (80 μl) of prewarmed 1× buffer (50 mM Tris-Hcl, pH 7.9, 5 mM CaCl2), supplemented with 100 μg ml-1 BSA and 250 gel units ml-1 micrococcal nuclease (25 Kunitz units ml-1, which we previously determined to yield mostly mononucleosomes for assembly on either methylated or unmethylated DNA) and incubated at 37 °C for 10 min. Reactions were stopped with 5 mM final EGTA. Then 100 mM final NaCl, 0.625% final SDS and 20 μg proteinase K were added, and the mixture was incubated at 75 °C for 10 min. Nucleosomal fragments were purified first by extraction with buffer-saturated phenol-chloroform-isoamyl alcohol using Phase Lock Gel Heavy 1.5 ml tubes, then with 2 volumes of Agencourt AMPure XP beads, and 90 ng of each sample was made into a library without PCR by using the Encore Rapid Library System.

tag: library strategy

value: MNase sequencing


title: M. pusilla CCMP1545 bisulfite sequencing

status: Public on Mar 13 2014

type: SRA

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

source_name: Whole cells

tag: strain

value: Bisulfite sequencing


title: E. huxleyi RNA sequencing

library_source: transcriptomic

data_processing:
genome build: JGI build v1.0
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

molecule: total RNA

organism: Emiliania huxleyi

value: RNA sequencing


title: C. merolae bisulfite sequencing

data_processing:
genome build: 100% complete chromosomes
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

organism: Cyanidioschyzon merolae


title: WT_1_130611

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

data_processing:
Custom software was used to process raw reads and are summarized by sequence identity (observations). Details of processing are described in the manuscript.
Supplementary_files_format_and_content: obs.txt file with sequence and number of observations for sequence on each row

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential  Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo  Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential  amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β-  mercaptoethanol

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen). RNA between 18-75 nt was size selected via 15% denaturing polyacrylamide gels.
5’-phosphate independent cloning was accomplished using a circularization based protocol adapted from  (Churchman and Weissman, 2011).  5’-phosphate dependent cloning was performed using the NEBNext Small RNA Library  Prep Set for Illumina (New England Biolabs). (3' adapter sequence: AGATCGGAAGAGCGGTTCAGCAGGAATGCCGA)

treatment_protocol: TT-FHAgo2 and TT-Ago2 clonal cell lines were propagated in 0.1  μg/mL doxycycline (Sigma). Induced to 2.5 μg/mLfor wildtype Ago2 levels.

tag: cell type

value: mouse embryonic stem cells

tag: cell line name

value: wildtype

tag: treatment

value: No Dox

tag: protocol

value: 5'-phosphate dependent


title: KO_2_130611

value: Dicer null


title: B. prasinos bisulfite sequencing

data_processing:
Genome build: Bioinformatics Gent 15072011 build
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

organism: Bathycoccus prasinos

tag: molecule subtype

value: Genomic DNA


title: M. pusilla CCMP1545 RNA sequencing


title: FHAgo2_Total_input_121116

value: 2.5 μg/mL  Dox

value: 5'-end independent

tag: antibody


title: Ago2_Total_input_121116


title: FHAgo2_Total_IP_130109

value: FLAG-IP


title: Ago2_Total_input_130109


title: Ago2_Total_IP_130109


title: Dox2.5_1_130611


title: FHAgo2_Total_input_130109


title: FHAgo2_Total_IP_121116


title: GA4741-85-EtOH-ILC2-WT1

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: RNA-Seq

data_processing:
Basecalls performed using CASAVA 1.0
Sequence reads were mapped to the mouse (mm9) genomes with bowtie (0.12.7).Uniquely mapped reads were kept for each lane. The last 20 bps of each reads were discarded (due to low sequencing quality) to increase maping rate when running bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: BED

source_name: type 2 Innate lympoid cells (ILC2s)

growth_protocol: Gata3fl/fl-CreERT2 mice were injected with IL-25 for 3 days. Cells from mesenteric lymph nodes were stained with a cocktail of antibodies to various lineage markers, including antibodies to CD3, CD5, CD45R, CD11b, CD11c, NK1.1, Gr-1, TER119, FcεRI and TCRγ/δ to identify lineage negative (Lin-) cells. Lin- cells were sorted using a FACS Aria and then cultured with IL-7 (10 ng/ml), IL-33 (10 ng/ml) and IL-25 (10 ng/ml) for 5 days. Cells were either treated with 4-OHT or ethanol as a control for 2 days in the presence of IL-7/IL-25/IL-33. Gata3-sufficient (wild type, WT) ILC2s were sorted from ethanol treated samples. Gata3-deficient (Gata3 KO) cells were sorted from 4-OHT treated samples excluding residual T1/ST2-expressing cells.

extract_protocol:
RNA-Seq experiments were performed using total RNAs isolated from Gata3-deficient and sufficient ILC2s in duplicate.
100 ng of total RNA was amplified using the Ovation RNA-Seq system V2 kit (NuGEN).  The resulting dsDNA was sonicated to 200-400 bp.  250 ng of sonicated DNA was used to prepare sequencing libraries for multiplex sequencing (Illumina).

value: type 2 Innate lympoid cells (ILC2s)

value: C57BL/6 Gata3fl/fl-CreERT2

tag: in vivo treatment

value: three IL-25 injections

tag: in vitro treatment

value: IL-7/IL-25/IL-33 5 days+ EtoH 2 days


title: GA4744-86-EtOH-ILC2-WT2

description: RNA-Seq


title: GA4743-85-4-OHT-Low-ILC2-Gata3KO1

description: RNA-Seq

source_name: type 2 Innate lympoid cells (ILC2s) lacking Gata3

value: IL-7/IL-25/IL-33 5 days+ 4-hydroxytamoxifen (4-OHT) 2 days


title: E. huxleyi bisulfite sequencing


title: ZL1-Root [miRNA]

status: Public on Mar 14 2014

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

description: C.annuum Zunla 1

data_processing: Genome_build: Pepper Ref_v1.0 (ASJU00000000)

organism: Capsicum annuum

extract_protocol:
Total RNA for different tissues was isolated from the frozen root samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions
Five libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) as previously described, then sequenced on an Illumina HiSeq2000 system.

tag: inbred line

value: Zunla 1

tag: tissue

value: Roots

tag: developmental stage

value: developing roots


title: NoDox_1_130611

value: mouse embryonic stem cells


title: S7A 2

city: London

first: Danny

middle: Asher

last: Bitton

address: Darwin Building, Gower Street

department: Department of Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

description: S7A_2 (Name in expression table)

data_processing:
Paired-end reads of length 51 bases (each part) originating from each sample were aligned using Bowtie 0.12.7 to the S. pombe genome sequence (Ensembl S. pombe, Build EF1) as well as to its corresponding exon-exon junctions database (only thesecond part of the paired-end reads was considered). Up to 3 mismatches were allowed. Reads that matched multiple loci were removed from further analysis and the resultant alignment files were processed to generate ‘pile-ups’ against each chromosome.
Searches were performed against the genome sequence combined with a dataset of known exon-exon junctions as defined by Ensembl S. pombe release-13. To ensure that a 51-base read mapped to a splice junction, only the last 45 bases of the first exon and the first 45 bases of the second exon were considered (if the exon length exceeded 45 nucleotides). In this way, reads that overlapped a junction by less than 6 nucleotides were excluded. Reads that matched to more than one junction or elsewhere in the genome were also discarded.
Genome_build: Ensembl S. pombe, Build EF1, version 58.1a
Supplementary_files_format_and_content: Expression table and RPKM summary for all samples tab-delimited

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: Two biological replicates of the WT, Y1F, S2A, T4A, S7A,Y1F-S7A, S2A-S7A and T4A-S7A cultures were grown in YES (yeast extracts plus supplements) media at 30°C till they reached OD600 0.4 -0.7.

extract_protocol:
Cells were harvested and RNA was isolated using the Qiagen RNeasy kit. RNA quality was assessed on a Bioanalyzer instrument (Agilent) and 1µg of total RNA was used to prepare polyA+ RNA using the Illumina TruSeq RNA sample kit .
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded total RNA Sample Prep Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled (8 samples per lane) for paired-end sequencing performed using an Illumina HiSeq 2000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: genetic markers

value: h- ade6 ura4-D18 leu1–32


title: T4A 2

description: T4A_2 (Name in expression table)


title: S2A 2

description: S2A-2 (Name in expression table)

value: h+ ade6 ura4-D18 leu1–32


title: Y1F-S7A 2

description: Y1F-S7A_2 (Name in expression table)


title: T4A-S7A 2

description: T4A-S7A_2 (Name in expression table)


title: Y1F 2

description: Y1F_2 (Name in expression table)


title: S2A-S7A 2

description: S2A-S7A_2 (Name in expression table)


title: T4A-S7A 1

description: T4A-S7A_1 (Name in expression table)


title: S7A 1

description: S7A_1 (Name in expression table)


title: Ago2_Total_IP_121116


title: T4A 1

description: T4A_1 (Name in expression table)


title: S2A 1

description: S2A_1 (Name in expression table)


title: Y1F 1

description: Y1F_ 1 (Name in expression table)


title: GA4746-86-4-OHT-Low-ILC2-Gata3KO2

description: RNA-Seq


title: O. lucimarinus RNA sequencing

data_processing:
genome build: JGI build v2.0
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

organism: Ostreococcus sp. 'lucimarinus'

value: RNA sequencing


title: P. tricornutum bisulfite sequencing

data_processing:
genome build: JGI build Phatr2 and Phatr2_bd
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

organism: Phaeodactylum tricornutum

value: Bisulfite sequencing


title: P. tricornutum RNA sequencing


title: T. pseudonana bisulfite sequencing

data_processing:
genome build: JGI build Thaps3 and Thaps3_bd
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

organism: Thalassiosira pseudonana


city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
Basecalls performed using RTA 1.8.70.0
The strand specific paired-end reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). Non matching reads were considerd downstream.
The rRNA subtracted paired-end reads were aligned with TopHat (v1.4.1) against the Drosophila melanogaster genome (FlyBase r5.44) and a maxiumum of 6 missmatches.  Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r5.44).
Aligned reads in valid pairs are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with FlyBase annotation (r5.44) were allowed and counted towards the number of mapped hits used in the FPKM denominator.  snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked.
The aligned reads were counted with HTSeq. The polyA containing transcripts were subjected to differential expression analysis with DESeq (v1.8.3). DESeq parameters were chosen to match the DESeq publication (Anders S, Huber W., 2010). Additionally, DESeq was instructed to ignore the condition labels and estimate the variance by treating all the samples as if they were replicates of the same condition (method=“blind”).
Genome_build: FlyBase dmel_r5.44
Supplementary_files_format_and_content: The tab-delimited text file reporting FPKM values for each Sample (Standard output cufflinks) is linked below; tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq) is linked as a supplementary file on the Series record.

organism: Drosophila melanogaster

source_name: larval brain, wild type type II lineages (NB and INP/GMC, neurons excluded)

growth_protocol: Flies expressing UAS-CD8::GFP (for wild type) or UAS-CD8::GFP and osa RNAi (VDRC TID:7810) under worniu-Gal4, ase-Gal80 were flipped on fresh food, left to lay for 24 h, flipped into fresh vials and then kept at 25 degree for five days, before dissection of larval brains.

extract_protocol: Type II lineages (GFPhigh population) were FACS sorted from wild type (w1118 strain) or osa RNAi , and RNA was isolated using Trizol reagent. Total RNA(~1µg) was enriched for polyA mRNA, fragmented and first strand and second strand (dUTP, instead dTTP was used) was generated. Library preparation was done using a modified protocol from Illumina with NEBNext DNA sample Prep Reagent kits (NEB), and UGDase treatment was done to confer strand specificity.

value: brain

value: type II NBs/INPs/GMCs (no neurons)

value: late third instar

tag: marker

value: cells express membrane-bound GFP marker UAS-CD8::GFP (for wild type)

tag: genotype/variation

value: wild type


title: osa RNAi type II lineages

source_name: larval brain, osa RNAi type II lineages

value: type II NBs/NB-like revertant cells/INPs

value: cells express membrane-bound GFP marker UAS-CD8::GFP and osa RNAi (VDRC TID:7810)

value: osa RNAi


title: T. pseudonana RNA sequencing


title: F. cylindrus RNA sequencing

organism: Fragilariopsis cylindrus


title: F. cylindrus bisulfite sequencing


title: O. lucimarinus bisulfite sequencing


title: S2A-S7A 1

description: S2A-S7A_1 (Name in expression table)


title: C. neoformans WT47 RNA sequencing

data_processing:
genome build: Broad Institute build, JGI copy
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

organism: Cryptococcus neoformans


title: C. neoformans WT47 bisulfite sequencing


title: C. neoformans dnmt5Δ bisulfite sequencing


title: C. neoformans WT bisulfite sequencing


title: Dmel_fne_Male_Biorep1_Techrep2

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
Basecalls performed using Illumina pipeline version 1.6.47.1 for runs on Illumina GAIIx, or CASAVA version 1.7 for runs on Illumina HiSeq 2000 instrument.
Reads that passed Illumina pipeline quality filtering criteria (those output to s_x_x_sequence.txt fastq files) were mapped to a reference genome.
Reads that passed Illumina pipeline quality filtering criteria (those output to s_x_x_sequence.txt fastq files) were mapped to a reference genome
Mapping was then performed using Tophat v1.4.1 (Trapnell et al., 2010), with Bowtie v0.12.7 (Langmead et al., 2010), and samtools 0.1.12a (Li et al., 2009), and parameters “-g 1  –solexa1.3-quals, -i 42.”  A reference annotation (ENSEMBL release 62) was supplied in gtf format with the -G option.
The reference sequence for mapping was the dm3 assembly from the UCSC Genome Browser which corresponds to the April 2006 Drosophila melanogaster draft assembly from the Berkeley Drosophila Genome Project (Release 5), with sequence identified as “chrUextra” removed, and with sequence for ERCC exogenous controls (Jiang et al., 2011) added.  See GSE20555 for control reference sequences.
BAM files were used to generate base level coverage in bedgraph format using Bedtools (Quinlan et al.), with the genomeCoverageBed command and the -bg option.
Genome_build: dm3
Supplementary_files_format_and_content: BEDGRAPH contain base-level coverage

growth_protocol: Drosophila were raised at 25o C under constant lighting (internal and room lighting) to ablate their circadian rhythm. Cultures were raised at low density during a minimum of 3 generations to minimize competition among larvae during development. Specifically, 4-5 males and 4-5 females were placed on fresh vials of standard corn-meal/yeast/agar medium and kept for two days before being changed to new vials. Adults for RNA isolation were collected once every 24 hours  as soon as the first emergents were detected and placed on new vials with 50-100 flies/vial. Animals were aged for 7-8 days.     7-8 day old flies were flash frozen in dry-ice and stored at -80o C. Once significant quantities were available, frozen flies were sex-sorted on aluminum blocks kept on dry ice, and heads hand-dissected, collected and stored at -80 until homogenization for RNA preparation.

extract_protocol: Solexa library preparation was as follows: We fragmented mRNA using alkaline hydrolysis. First, 9 µl of 100 ng of mRNA, 1 ng of ERCC spike-in controls (Jiang et al., 2011) and 1 µl of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70°C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 µl 3 M NaOAC (pH 5.2), 2 µl glycogen (5 µg/µl , Ambion, Austin, Texas), and 30 µl 100% EtOH and then incubated for 30 minutes at -80 °C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 µl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3µg/µl, Invitrogen, Carlsbad, California) was placed with 10.5 µl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 µl 100 mM DTT, 1 µl dNTP, and 0.5 µl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/µl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61µl H2O to the first strand mix, 10 µl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 µl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 µl RNaseH (2U/µl, Invitrogen, Carlsbad, California) and 5 µl DNA Pol I (10 U/µl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 µl. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 µl of DNA, 45 µl H2O, 10 µl T4 DNA ligase buffer with 10 mM ATP, 4 µl dNTP mix (10 mM), 5 µl T4 DNA polymerase (3 U/µl), 1 µl Klenow DNA polymerase (5U/µl), and 5 µl T4 PNK(10 U/µl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 µl of Buffer EB. A single “A” base was added to the ends of cDNA by using 5 µl Klenow buffer, 10 µl dATP (1 mM) and 3 µl Klenow 3’ to 5’ exonuclease (5 U/µl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19µl of EB solution. Paired-end adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 µl DNA ligase buffer, 1 µl adaptor olio mix, and 5 µl DNA ligase (1U/µl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 µl of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo-specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 200 (+/- 25) bp region, purified with a QIAquick gel extraction kit, and eluted with 30 µl buffer EB. Purified cDNA was amplified in a 50 µl reaction using 25 µl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 µl PE primer 1.1, 1 µl PE primer 2.1, and 23 µl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 µl buffer EB.

treatment_protocol: The Doa and fne mutant lines were backcrossed through 10 generations to the "Canton-S" line, in order to isogenize their genetic backgrounds. The mutant allele was selected at each generation based on phenotype (w+ in the case of fne; for Doa, whiteapricot was co-selected during backcrossing in order to allow selection of the Doa mutation at each generation). A TM6B balancer chromosome stock was also isogenized in the same way. This was crossed after the ten generations to the three Doa alleles (HD, DEM and EMS2) to re-create stable balanced stocks.

value: Adult

tag: gender

value: Male

value: Heads

value: FNE


title: Dmel_Canton-S_Female_Biorep1_Techrep2

value: Female

value: WT


title: Dmel_fne_Female_Biorep1_Techrep2


title: O. lucimarinus MNase sequencing

tag: library strategy

value: MNase sequencing


title: Dmel_fne_Male_Biorep1_Techrep1

tag: strain


title: Dmel_Canton-S_Male_Biorep1_Techrep1


title: Dmel_doaEMS_Female_Biorep1_Techrep2

value: doaEMS


title: Dmel_doaHD_Male_Biorep1_Techrep2

value: doaHD


title: Dmel_doaEMS_Male_Biorep1_Techrep2


title: Dmel_Canton-S_Female_Biorep1_Techrep1


title: Dmel_doaEMS_Male_Biorep1_Techrep1


title: L. major bisulfite sequencing

data_processing:
Genome build: Wellcome Trust Sanger Institute build v5.2
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

organism: Leishmania major

value: Seidman

value: Bisulfite sequencing

value: Genomic DNA


title: Dmel_doaHD_Female_Biorep1_Techrep3


title: Dmel_doaEMS_Female_Biorep1_Techrep1


title: Y1F-S7A 1

description: Y1F-S7A_1 (Name in expression table)

value: h- ade6 ura4-D18 leu1–32


title: Dmel_fne_Male_Biorep2_Techrep1


title: Dmel_doaHD_Male_Biorep1_Techrep1


title: Dmel_doaHD_Female_Biorep1_Techrep1


title: Dmel_fne_Female_Biorep2_Techrep1


title: Dmel_Canton-S_Male_Biorep2_Techrep1


title: Dmel_Canton-S_Male_Biorep1_Techrep2


title: Dmel_Canton-S_Female_Biorep2_Techrep1


title: Dmel_fne_Female_Biorep1_Techrep1


title: A. anophagefferens RNA sequencing

organism: Aureococcus anophagefferens

value: RNA sequencing


title: O. lucimarinus unmethylated in vitro assembled nucleosomes MNase sequencing

data_processing:
Genome build: JGI build v2.0
Analyses were performed with Perl scripts from dzlab-tools (http://dzlab.pmb.berkeley.edu/tools/) and custom scripts written in AWK and R (http://www.r-project.org/). bs-sequel from dzlab-tools was used to map bisulfite sequencing reads with Bowtie v0.12.7 (Langmead et al., Genome Biol 2009) and quantify fractional methylation in CG, CHG, and CHH sequence contexts. Paired micrococcal nuclease sequencing reads were mapped with Bowtie 2 beta 5 (Langmead and Salzberg, Nat Methods 2012), and only nucleosomal (or similarly sized naked DNA) fragments of length 125 to 171 bp (inclusive) were analyzed. Genomic maps per base of nucleosomal fragment centers and coverage were generated with genomeCoverageBed from bedtools (http://bedtools.googlecode.com/). RNA sequencing reads were mapped with Bowtie v0.12.7 / Tophat v1.4.1 (Trapnell, Pachter, and Salzberg, Bioinformatics 2009) and FPKMs (fragments per kilobase transcript per million mapped reads) were calculated with Cufflinks v1.3.0 using bias correction (Roberts et al., Genome Biol 2011).
Supplementary files format and content: Bisulfite sequencing GFF files contain fractional methylation data for individual cytosines in either the CG, CHG, or CHH sequence context. RNA sequencing GTF files contain transcripts quantified by Cufflinks. MNase sequencing "centers" GFF files contain the number of nucleosomal fragment centers at each position and "coverage" GFF files contain the number of nucleosomal fragments covering each genomic position.

source_name: In vitro replicated genomic DNA

value: Digested in vitro replicated DNA


title: Dmel_doaEMS_Female_Biorep2_Techrep1


title: O. lucimarinus natively methylated in vitro assembled nucleosomes MNase sequencing

source_name: Purified genomic DNA

value: Digested genomic DNA


title: A. anophagefferens bisulfite sequencing


title: Dmel_doaHD_Male_Biorep2_Techrep1


title: FVB_F_8wk_smallRNA_2

status: Public on Mar 12 2014

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores, while all 42 nt reads use phred64 quality scores.
Indexes have been removed from the supplied raw data files. However, raw reads still contain Illumina sequencing adapters 3' to the termination of small RNAs. Thus, pre-processing of raw reads needs to involve sequence removal including, and 3' to, the Illumina adapter sequence.
The E-miR software package (Buermans et al 2010, see below) was used to map trimmed sequencing reads to the mouse genome and quantitate mapped reads.  Mouse noncoding RNA and miR-3p/5p annotation was current as of 3/7/14.
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, t Hoen PA. New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 2010;11:716. PubMed PMID: 21171994; PubMed Central PMCID: PMC3022920.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include microRNA names, Ensembl transcript information, chromosomal location, and counts.
basecalling quality score phred33 and phred64 (9 week samples only)

source_name: Heart

extract_protocol:
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq small RNA preparation kits (version C) were used for all library construction.  3' and 5' adapters capable of recognizing non-mRNA species were sequentially ligated to 1 microgram of total cardiac RNA, followed by reverse transcription, limited PCR amplification to add indexes, and size-selection.

value: FVB/NJ

value: Whole-heart tissue

tag: age (weeks)

tag: Sex

value: F


title: FVB_F_9wk_smallRNA_2


title: FVB_F_8wk_smallRNA_1


title: FVB_F_7wk_smallRNA_1


title: FVB_F_9wk_smallRNA_3


title: Dmel_doaHD_Female_Biorep1_Techrep2

value: Adult

value: Heads


title: FVB_F_9wk_smallRNA_4


title: FVB_F_9wk_smallRNA_1


title: FVB_F_7wk_smallRNA_3


title: FVB_F_9wk_smallRNA_5


title: FVB_F_6wk_smallRNA_5


title: FVB_M_16wk_smallRNA_1

value: M


title: FVB_F_6wk_smallRNA_2


title: FVB_F_6wk_smallRNA_1


title: FVB_F_6wk_smallRNA_6


title: FVB_M_7wk_smallRNA_1


title: FVB_F_7wk_smallRNA_2


title: FVB_M_6wk_smallRNA_9


title: Dmel_doaEMS_Male_Biorep2_Techrep1

value: Male


title: FVB_M_6wk_smallRNA_12


title: FVB_M_8wk_smallRNA_3


title: FVB_M_6wk_smallRNA_11


title: FVB_M_8wk_smallRNA_1


title: FVB_M_8wk_smallRNA_2


title: FVB_M_8wk_smallRNA_4


title: FVB_M_6wk_smallRNA_10


title: O. lucimarinus naked DNA control mock assembly MNase sequencing

value: MNase sequencing


title: FVB_M_6wk_smallRNA_8


title: FVB_M_6wk_smallRNA_7


title: FVB_F_6wk_smallRNA_3


title: FVB_M_6wk_smallRNA_3


title: FVB_M_6wk_smallRNA_2


title: FVB_M_6wk_smallRNA_4


title: FVB_F_6wk_smallRNA_4


title: FVB_M_6wk_smallRNA_6


title: FVB_M_6wk_smallRNA_5


title: FVB_M_5wk_smallRNA_2


title: FVB_M_4wk_smallRNA_2


title: FVB_M_6wk_smallRNA_1


title: FVB_M_4wk_smallRNA_1


title: FVB_M_5wk_smallRNA_3


title: FVB_M_5wk_smallRNA_1


title: FVB_F_9wk_mRNA_4

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores, while all 42 nt reads use phred64 quality scores.
Sequence reads were mapped to the transcriptome, defined by the UCSC genes.gtf, for the mm10 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10 .
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the UCSC mm10 genes.gtf.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
basecalling quality score phred33 and phred64 (9 week samples only)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each gene

extract_protocol:
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.


title: FVB_F_9wk_mRNA_5


title: FVB_F_9wk_mRNA_1


title: FVB_F_9wk_mRNA_3


title: FVB_F_8wk_mRNA_1


title: FVB_F_7wk_mRNA_1


title: FVB_F_7wk_mRNA_3


title: FVB_F_6wk_mRNA_6


title: FVB_F_6wk_mRNA_4


title: FVB_F_6wk_mRNA_5


title: Gba708

city: Menlo Park

first: Tyson

middle: A

last: Clark

address: 1380 Willow Rd.

institute: Pacific Biosciences

data_processing:
Sequencing reads were processed and mapped to the respective reference sequences using the BLASR mapper (http://www.pacbiodevnet.com/SMRT-Analysis/Algorithms/BLASR) and the Pacific Biosciences' SMRT Analysis pipeline (http://www.pacbiodevnet.com/SMRT-Analysis/Software/SMRT-Pipe) using the standard mapping protocol.
To identify modified positions, we used Pacific Biosciences' SMRTPortal analysis platform, v. 2.1.1, which uses an in silico kinetic reference, and a t-test based kinetic score detection of modified base positions (details are available at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf)
Supplementary_files_format_and_content: modifications.gff files are comma separated text files that contain data for genome positions with Qmod scores greater than 20; Data includes Qmod scores, IPD ratios, coverage, and sequence contexts for a +/- 20 nt window surrounding the modified position
Supplementary_files_format_and_content: modifications.csv files are comma separated text files that contain data for all positions (both strands) in the reference sequence; data includes Qmod score, IPD ratio, and coverage

organism: Gemmatirosa kalamazoonensis

source_name: Bacterial gDNA

growth_protocol: Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411) was grown for 5 days on VL55 minimal media with 0.025% peptone.

extract_protocol:
Genomic DNA was extracted using an UltraClean Microbial DNA Isolation kit (MoBio Laboratories).
Native gDNA was randomly sheared to an average size of approximately 10 kb, end repaired, and ligated to blunt end hairpin adapters for form standard SMRTbell templates.  Linear TdT libraries were also generated by adding polyA tails to the 10 kb fragments using TdT.  Both libraries were sequenced with the XL/C2 polymerase


title: FVB_F_8wk_mRNA_2


title: FVB_F_7wk_mRNA_2


title: FVB_F_6wk_mRNA_2


title: FVB_F_6wk_mRNA_1


title: FVB_M_16wk_mRNA_1


title: FVB_F_6wk_mRNA_3


title: FVB_M_8wk_mRNA_4


title: FVB_M_8wk_mRNA_2


title: FVB_M_8wk_mRNA_3


title: FVB_M_8wk_mRNA_1


title: FVB_M_7wk_mRNA_1


title: Halo-Sox2D (Sox2 1 - 120aa)

city: Ashburn

first: Zhe

last: Liu

state: Virginia

address: 19700 Helix Dr.

department: Janelia Farm Research Campus

institute: Howard Hughes Medical Institute

description:
Sample 4
ChIP-exo enriched genomic DNA

data_processing:
Reads Mapping: Bowtie 2
Strand seperation: Customized
Strand sensitive peak calling: GeneTrack
Peak pairing: Customized
Thresholding
Genome_build: mm10
Supplementary_files_format_and_content: Bed files containing the genomic localizations of ChIP-exo mapped peak-pairs

source_name: Embryonic Stem Cells

growth_protocol: Regular mouse ES cell culturing protocol

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody or HaloLink Resin.
Libraries were prepared according to "Rhee, H.S., and Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419." with custom-made illumina adapters

tag: cell line

value: D3 Embryonic Stem Cells

tag: targeted protein

value: Halo-Sox2 mutant (Halo-Sox2D; Sox2 1 - 120aa)

tag: purification of halotag fusion protein

value: Halo-Link Resin (Promega, Cat. # G1913, Lot # 31905004)


title: Halo-Sox2

description:
Sample 2
ChIP-exo enriched genomic DNA


title: Halo-Sox2M (M47G:F50:M51G)

description:
Sample 3
ChIP-exo enriched genomic DNA

value: Halo-Sox2 mutant (Halo-Sox2M; M47G:F50:M51G)


title: FVB_M_6wk_mRNA_12


title: FVB_M_6wk_mRNA_13


title: Mx1cre-JAK2V617F 6wks post-induction (n=3)

city: Madrid

first: Simón

last: Méndez-Ferrer

address: Calle Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: Mx

data_processing:
Fastq files obtained and demultiplexed with CASAVA1.8.
Illumina adaptors were trimmed with cutadapt v1.2.1.
First 15 nucleotides were trimmed with fastx_timmer to remove signatures left by ovation protocol.
PolyGC stretches at the beginning of the reads were also removed.
Reads shorter than 30nt were discarded for posterior analysis.
Reads were mapped with tophat v2.0.7 and bowtie 2.0.6.
Gene FPKM were quantified using Cufflinks.
Gene build: Ensembl v70
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKMs

source_name: Bone marrow nestin+ cells, Mx1-cre;JAK2-V617F

extract_protocol:
RNA was obtained using Picopure RNA isolation kit (Arcturus).
cDNA Amplification: Amplified cDNAs were prepared from RNA samples (2-3 ng) using Ovation RNA-SeqSystem v2 (Nugen).
Library preparation: 1 ug of amplified cDNAs were fragmented by sonication to an average size of 300 pb aprox. Libraries for high-throughput sequencing were prepared from fragmented cDNAs using the Truseq DNA Sample Prep Kit (Illumina).
Sequencing: Libraries were sequenced in a Genome Analyzer IIx using standard procedures.

treatment_protocol: pIpC

tag: strain/background

tag: cell type

value: bone marrow CD45- CD31- Ter119- Nes-GFP+ cells

value: adult


title: FVB_F_9wk_mRNA_2


title: Control littermates (n=3)

description: Control

source_name: Bone marrow nestin+ cells, control

value: Nes-gfp


title: FVB_M_6wk_mRNA_11


title: H9_SOX2_AF2018

city: Boston

first: Shouyong

last: Peng

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: IP

data_processing:
Bowtie alignment
read counts normalization in 100kb window size
Peak calling (MACS 1.4.1)
Genome_build: hg18
Supplementary_files_format_and_content: MACS_peak files

organism: Homo sapiens

extract_protocol: Crosslinked with 1% formaldehyde, washed with PBS, lysed in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), sonicated with Covaris E210 to shear DNA to 200-1500bp. After immunoprecipitation or without immunoprecipitation for input, beads were washed, RNase A and Proteinase K treated and reverse crosslinked in elution buffer (1% SDS, 0.1M NaHCO3). DNAs were column purified and subjected to standard Illumina library construction.

tag: cell lines

tag: antibody

tag: antibody vendor

tag: antibody lot#


title: HCC95_p63_4A4

description: IP

value: Santa-Cruz (sc-8431)


title: H9_input

description: Input


title: FVB_M_6wk_mRNA_10

tag: tissue


title: FVB_M_6wk_mRNA_9


title: HCC95_input

description: Input


title: TT_p63_4A4

description: IP

value: TT


title: TT_input

description: Input


title: FVB_M_6wk_mRNA_7

value: FVB/NJ


title: TT_SOX2_AF2018

description: IP


title: KYSE70_p63_4A4

description: IP


title: KYSE70_input

description: Input


title: HCC95_SOX2_AF2018

description: IP


title: FVB_M_6wk_mRNA_5

value: Whole-heart tissue


title: Sox2

description:
Sample 1
ChIP-exo enriched genomic DNA

tag: chip antibody

value: Anti-Sox2 (R&D Systems, Cat. # AF2018, Lot # KOY0112011)


title: KYSE70_SOX2_AF2018

description: IP


title: FVB_M_6wk_mRNA_3


title: FVB_M_6wk_mRNA_2


title: FVB_M_6wk_mRNA_6


title: FVB_M_6wk_mRNA_1


title: FVB_M_5wk_mRNA_2


title: FVB_M_6wk_mRNA_8


title: FVB_M_5wk_mRNA_3


title: FVB_M_6wk_mRNA_4


title: FVB_M_4wk_mRNA_2


title: FVB_M_4wk_mRNA_1


title: FVB_M_5wk_mRNA_1


title: C57_M_18wk_smallRNA_6

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores, while all 42 nt reads use phred64 quality scores.
Indexes have been removed from the supplied raw data files. However, raw reads still contain Illumina sequencing adapters 3' to the termination of small RNAs. Thus, pre-processing of raw reads needs to involve sequence removal including, and 3' to, the Illumina adapter sequence.
The E-miR software package (Buermans et al 2010, see below) was used to map trimmed sequencing reads to the mouse genome and quantitate mapped reads.  Mouse noncoding RNA and miR-3p/5p annotation was current as of 3/7/14.
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, t Hoen PA. New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 2010;11:716. PubMed PMID: 21171994; PubMed Central PMCID: PMC3022920.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include microRNA names, Ensembl transcript information, chromosomal location, and counts.
basecalling quality score phred33


title: C57_M_18wk_smallRNA_3


title: C57_M_18wk_smallRNA_5


title: C57_M_18wk_smallRNA_2


title: C57_M_12wk_mRNA_3

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores, while all 42 nt reads use phred64 quality scores.
Sequence reads were mapped to the transcriptome, defined by the UCSC genes.gtf, for the mm10 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10 .
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the UCSC mm10 genes.gtf.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
basecalling quality score phred33
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each gene


title: C57_M_12wk_mRNA_4


title: IgG Control

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

description: ChIP-seq data with an immunoprecipitated sample using a control IgG

data_processing:
Alignment with bowtie/0.12.8 using hg19 as reference genome and default parameters
Peak calling with macs/1.4.2 using mfold:10,30, pvalue cutoff: 1.00e-05, bandwidth: 300 to generate peak calling model
samtools/0.1.18 and  bedtools/2.15.0 used to interconvert between file formats
Genome_build: hg19 reference assembly
Supplementary_files_format_and_content: bed and wiggle files

growth_protocol: SW480 cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
After cross-linking, cells were scraped and sonicated utilizing Diagenode Bioruptor at High setting and cycling 30 seconds ON, 30 seconds OFF. Beta-catenin-DNA complexes were isolated with lab generated anti-beta-catenin antibody .
ChIP DNA fragment ends were repaired and phosphorylated using Klenow, T4 DNA Polymerase and T4 Polynucleotide Kinase.  Next, an ‘A’ base was added to the 3’ end of the blunted fragments, followed by ligation of Illumina adapters via T-A mediated ligation.  The ligated products were size selected by gel purification and then PCR amplified using Illumina primers.  The library size and concentration were determined using an Agilent Bioanalyzer.

value: Colon cancer

tag: passage

value: Control IgG

value: Santa Cruz/sc-2027


title: beta-catenin ChIP

description: ChIP-seq data with an immunoprecipitated sample using an antibody against beta-catenin

value: Anti-beta catenin(H102)

value: Santa Cruz/sc-7199


title: C57_M_12wk_mRNA_2

value: M


title: C57_M_12wk_mRNA_1


title: WT rep1

status: Public on Mar 11 2014

city: Köln

first: Corinna

last: Klein

address: Joseph-Stelzmann-Straße 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

description: Sample A

data_processing:
trimming at both ends with the FASTA/Q Trimmer of the FASTX-Toolkit
Mapping reads to the genome with tophat2 (v2.0.7) allowing only unique mapping
Differential gene expression was performed with cuffdiff - which is part of the cufflinks package (v2.0.2)
Genes with a FPKM value >0.5 in at least one of the N2 and blmp1 samples were considered expressed. Those with a q-value < 0.05 and fold change > +/- 1.5 were classified as differentially expressed.
Genome_build: Caenorhabditis_elegans.WBcel215.70.gtf

organism: Caenorhabditis elegans

source_name: L3 larvae

growth_protocol: Animals were synchronized by bleach treatment and grown on regular NGM plates to the mid-L3 stage

extract_protocol:
mRNA was extracted using Qiazol and the RNeasy Mini kit (Qiagen)
Illumina TruSeq RNA and DNA Sample Preparation Kit v2

value: N2 Bristol

tag: developmental stage

value: L3 larvae


title: WT rep2

description: Sample G


title: blmp-1(tm548) rep3

description: Sample J


title: blmp-1(tm548) rep2

description: Sample I


title: WT rep3

description: Sample H


title: blmp-1(tm548) rep1

description: Sample B


title: Ath_Bc_48hpi

city: Riverside

first: Hailing

last: Jin

address: 3447 Boyce Hall

department: Department of Plant Pathology and Microbiology

institute: University of California, Riverside

data_processing:
Sequenced reads were trimmed for adaptor sequence using fastx_clipper v0.0.13.2 with parameters -Q 33 -l 18 -a CTGTAGGCACCATCAATC.
Sequenced reads were masked low-quality sequence using fastq_quality_filter v0.0.13.2 with parameters -Q 33 -q 30 -p 70 and masked low-complexity sequence using fastx_artifacts_filter v0.0.13.2 with default parameters.
Sequenced reads were mereged using fastx_collapser v0.0.13.2 with default parameters.
Supplementary_files_format_and_content: Each row of tab-delimited text are sequence and small RNA count.

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Arabidopsis was grown under long day light conditions. B. cinerea was grown on malt agar.

extract_protocol:
Total RNA was extracted using hot phenol method. Small RNAs were size-separated on a 15% PAGE for library cloning
Small RNA libaries were generated using miRCAT cloning kit

treatment_protocol: Arabidopsis was inculated with 2x10exp5 per ml B. cinerea spores

tag: infection

value: B. cinerea

tag: time

value: 48 hpi

value: rosette leaves

tag: age

value: 5 weeks

tag: ecotype


title: Ath_Bc_72hpi

value: 72 hpi


title: OAXA

city: Irvine

first: Maria Concepcion

last: Munoz Diez

state: California

address: 321 Steinhaus Hall

department: Ecology and Evolutionary Biology

institute: UC-Irvine

data_processing:
After sequencing siRNA, we trimmed adapters and 3’-end low quality nucleotides to ensure every read had three or more successive nucleotides with a quality score ≥ 20 at the 3’-end. Subsequently, we selected reads of 22 and 24 nt using CutAdapt-0.9.5
These reads were filtered to eliminate rRNAs, rRNAs, miRNAs and snoRNAs and then mapped to the TE exemplar database (TEdb) of maize (Baucom et al. 2009) with bwa-0.5.9, using default settings. Uniquely and multiple mapped reads without mismatches were retained for further analyses.
The number of hits and the RPKM value for each TE exemplar were estimated. To do so, we divided the expression (abundance) of reads with multiple targets by their number of targets.
Genome_build: n/a
Supplementary_files_format_and_content: Tab-delimited text files include the identification name (ID), the abundance in the original library, and the sequence of the siRNAs (22 and 24 nt) that matched the TE exemplar database (TEdb)
Supplementary_files_format_and_content: Excel files report the siRNA (22 and 24 nt) hits and RPKM values for each TE exemplar as well as  their class, length and group (defined by Diez et al. Plos Genetics, in press)

organism: Zea mays

source_name: Zea mays ssp. mays cv. Olote Colorado, leaf

growth_protocol: Ten seeds per cultivar were planted in individual pots and grown in a growth chamber under controlled conditions of 12 h light at 26 C, 12 h dark at 20 C, a relative humidity of 70%, and 500-600 cal/cm2 of radiation per day

extract_protocol:
For each maize cultivar, total RNA was isolated from 1 g of pooled tissue (3rd and 4th leaves from 10 plants) using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. siRNA was extracted by running total RNA on a 15% PAGE gel and selecting bands in the 20 to 30 nt size range.
Libraries for siRNAs were prepared from 100 ng of siRNA using the Illumina Truseq Small RNA Sample Prep Kit, according to the manufacturer’s protocol. siRNA sequencing was performed in one lane, on an IlluminaHiSeq 2000 sequencer per genotype using the Truseq SR cluster kit v. 2 for B73 and v.3 for PT and OAXA libraries

tag: cultivar

value: Olote Colorado (OAXA522)

tag: inbred/open pollinated

value: open pollinated

value: 3rd and 4th leaves


title: PT

source_name: Zea mays ssp. mays cv. Palomero Toluqueno, leaf

value: Palomero Toluqueno (MEXI05)


title: Ath_Bc_0hpi

value: 0 hpi


title: B73

source_name: Zea mays ssp. mays cv. B73, leaf

value: inbred


title: Ath_Bc_24hpi

value: 24 hpi


title: Sly_leaf_bc_24hpi

data_processing:
Sequenced reads were trimmed for adaptor sequence using fastx_clipper v0.0.13.2 with parameters -Q 33 -l 18 -a CUGUAGGCACCAUCAAUC.
Sequenced reads were masked low-quality sequence using fastq_quality_filter v0.0.13.2 with parameters -Q 33 -q 30 -p 70 and masked low-complexity sequence using fastx_artifacts_filter v0.0.13.2 with default parameters.
Sequenced reads were mereged using fastx_collapser v0.0.13.2 with default parameters.
Supplementary_files_format_and_content: Each row of tab-delimited text are sequence and small RNA count.

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: Tomato was grown under long day light conditions. B. cinerea was grown on malt agar.

treatment_protocol: Tomato was inoculated with 1x10exp4 per ml B. cinerea spores

value: leaf

value: 6 weeks

tag: strain

value: MoneyMaker


title: Sly_leaf_bc_72hpi


title: Sly_fruit_bc_24hpi

source_name: fruit

value: fruit


title: Sly_fruit_bc_72hpi


title: Sly_fruit_0hpi


title: Sly_leaf_0hpi


title: C57_M_18wk_smallRNA_1

organism: Mus musculus

value: Whole-heart tissue

tag: age (weeks)

tag: Sex

value: M


title: C57_M_18wk_smallRNA_4


title: PTCL-NOS-2

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

data_processing:
RNA-seq reads were obtained using Bustard (Illumina Pipeline version 1.3)
Reads were quality–filtered using standard Illumina process and a 0 (no) or 1 (yes) was used to define whether a read passed filtering or not
The fastq files were mapped to the reference human genome using the gene model Ensembl (release 68). The mapping was performed with the software ArrayStudio, version 6.0 (Hu et al.) using the default parameters, allowing detection of insersions/deletions (indels
The mapped reads were used to calculated the expression values per gene, transcript, exon and exon junction. The expression values were initially obtained in FPKM (fragment per kilobase of exon model per million of mapped read
Genome_build: Human.B37.3
Supplementary_files_format_and_content: naive read count for all samples

source_name: PTCL-NOS_Lymph node

extract_protocol:
TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA) was used for a total RNA extraction. cDNA was synthesized from 1 μg of total RNA using reverse transcriptase Superscript II ( Invitrogen, 30 5   Carlsbad, CA, USA) and random primer (Invitrogen, Carlsbad, CA, USA).
The Illumina standard kit (Illumina ® TruSeq™ RNA Sample Preparation Kit, San Diego, CA, USA) was used for the mRNA-sequencing sample preparation according to the manufacturer’s protocol. The quality of the libraries was checked by Agilent Technologies 2100 Bioanalyzer, using the Chip (Agilent 7 DNA 1000 Kit)

tag: diagnosis

value: Peripheral T-cell lymphoma not otherwise specified (PTCL-NOS)

tag: karyotype

value: Lymph node


title: PTCL-NOS-3

value: Spleen


title: DERL2

value: Hepatosplenic T-cell lymphoma (HSTL)

value: culture


title: normal-spleen

source_name: normal tissue_Spleen

value: normal tissue


title: case 7


title: Bc_spore

data_processing:
Sequenced reads of Bc_total were trimmed for adaptor sequence using fastx_clipper v0.0.13.2 with parameters -Q 33 -l 18 -a CTGTAGGCACCATCAATC. Sequenced readsof Bc_myc and Bc_spore were trimmed for adaptor sequence using fastx_clipper v0.0.13.2 with parameters -Q 33 -l 18 -a CACTCGGGCACCAAGGAC.
Sequenced reads were masked low-quality sequence using fastq_quality_filter v0.0.13.2 with parameters -Q 33 -q 30 -p 70 and masked low-complexity sequence using fastx_artifacts_filter v0.0.13.2 with default parameters.
Sequenced reads were mereged using fastx_collapser v0.0.13.2 with default parameters.
Supplementary_files_format_and_content: Each row of tab-delimited text are sequence and small RNA count.

organism: Botrytis cinerea

source_name: conidiospores

growth_protocol: B. cinerea was grown on malt agar for 10 days at 23 degree celsius.

treatment_protocol: B. cinerea mycelium and conidiospores were separated using miracloth as filter

value: 10 days

tag: sample type

value: conidiospores


title: case 5


title: case 4


title: Bc_myc

source_name: mycelium

value: mycelium


title: Bc_total

source_name: mycelium and conidiospores

value: mycelium and conidiospores


title: HEF

status: Public on Mar 10 2014

city: Beijing

first: Jinlin

last: Wang

state: - If in U.S, Select a State -

address: Yiheyuan Road 5#,Haidian district

institute: Peking University

data_processing:
We used TopHat 2.0.9 to align the clean reads to hg19 Refseq.
FPKM values were analyzed according to this protocol (Cole Trapnell et al. Nature Protocols.doi:10.1038/nprot.2012.016).
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values,sample title and gene symbols.

source_name: human fibroblasts

growth_protocol: iHep was cultured in modified William's E medium. HEF and HepG2 was cultured in DMEM with 10% FBS. ES-Hep was cultured in HCM (Lonza).

extract_protocol:
Total RNA extracted by QIAGEN Rneasy Kit following manufacturer's instructions.
RNA libraries were prepared and sequenced following Illumina protocol

tag: cell type

value: skin fibroblasts

value: embryonic


title: HepG2

source_name: hepatoma cell line

value: hepatoma cell line


title: SM10_wild_type

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

data_processing:
base calling was performed at GATC Biotech (Konstanz, Germany) with the RTA (real time analysis) software (Illumina)
reads were trimmed for low quality bases, and reads with undefined bases ("N") were removed as described in Teichert et al. 2012, BMC Genomics 13: 511
read counts and expression ratios for annotated gene models were determined as described in Teichert et al. 2012, BMC Genomics 13:511, but using DESeq instead of LOX (see processed data file for parameters)
Genome_build: Sordaria macrospora genome version 2 (acc. no. CABT02000000)
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts and expression ratios for all annotated genes calculated with two different analyses, and consensus expression analysis

organism: Sordaria macrospora

source_name: total sexual mycelium

growth_protocol: growth conditions for mycelia for total RNA and for samples for microdissection were as described in Teichert et al. 2012, BMC Genomics 13: 511, with the exception that strains were grown on cornmeal medium instead of SWG.

extract_protocol:
extraction of total RNA from mycelium undergoing development as well as RNA extraction by phenol/chloroform extraction and amplification from microdissected samples were as described in Teichert et al. 2012, BMC Genomics 13: 511.
RNA libraries were prepared for sequencing using standard Illumina protocols (TrueSeq kit) at GATC Biotech (Konstanz, Germany)

value: wild type

tag: tissue

value: total sexual mycelium

tag: genotype


title: SM15_nox1_rep2

value: delta-nox1, hph


title: iHep1

value: functional hepatocytes generated by lineage reprogramming


title: iHep2

source_name: hepatocytes generated by lineage reprogramming


title: SM16_nox1_proto_rep1

description: RNA amplification (linear)

source_name: protoperithecia

value: protoperithecia


title: F-HEP1

source_name: freshly isolated human hepatocytes

value: liver parenchyma cells

value: adult


title: F-HEP2


title: iHep3


title: ES cells

description: mRNA-seq

data_processing:
Reads Mapping: Bowtie
Differential Gene expression analysis: Cuffdiff
Significance Thresholding: R
Genome_build: mm9
Supplementary_files_format_and_content: Table containing differential gene expression information

source_name: ES cells

extract_protocol:
Total RNA was extracted with TRIzol LS Reagent (Invitrogen)
Libraries were prepared with Illumina mRNA-seq sample prep kit

tag: mouse strain of origin

value: day 0

value: Wildtype

tag: cell line


title: Polr2b (ZT22)

city: Lausanne

first: Beatrice

last: Desvergne

state: Vaud

address: Dorigny

department: CIG

country: Switzerland

institute: UNIL

description:
Points to SRX119656
Equivalent to GSM874955

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT22.bedGraph: (NCBI37/mm9)

source_name: RPB2_ZT22, liver cells

growth_protocol: C57/BL6 male, 12-14 week old (at time of sacrifice), mice were housed in a 12h Light/12h dark light regimen for 2 weeks with food and water available ad libitum during night and day.

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

treatment_protocol: They were then entrained with a 12h Light/12h dark light regimen with food access between ZT12 and ZT24 for 7 days (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off).  At each ZT02 and, as a biological replicate, ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 5 ml of PBS through the spleen and immediately collected. Up to 100 mg of liver was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The rest of the livers was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation.

tag: gender

value: male

value: liver

tag: chip antibody

tag: chip antibody manufacturer

value: Santa Cruz Biotechnology

tag: chip antibody catalog number

tag: chip antibody lot/batch


title: Polr2b (ZT14)

description:
Points to SRX119654
Equivalent to GSM874953

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT14.bedGraph: (NCBI37/mm9)

source_name: RPB2_ZT14, liver cells

tag: time


title: Polr2b (ZT06)

description:
Points to SRX119652
Equivalent to GSM874951

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT06.bedGraph: (NCBI37/mm9)

source_name: RPB2_ZT06, liver cells

tag: strain


title: Polr2b (ZT10)

description:
Points to SRX119653
Equivalent to GSM874952

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT10.bedGraph: (NCBI37/mm9)

source_name: RPB2_ZT10, liver cells


title: PTCL-NOS-1

value: Peripheral T-cell lymphoma not otherwise specified (PTCL-NOS)

value: Lymph node


title: INPUT (ZT22)

description:
Points to SRX119677
Equivalent to GSM874976

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT22.bedGraph: (NCBI37/mm9)

source_name: Input, liver cells


title: INPUT (ZT10)

description:
Points to SRX119674
Equivalent to GSM874973

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT10.bedGraph: (NCBI37/mm9)


title: INPUT (ZT18)

description:
Points to SRX119676
Equivalent to GSM874975

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT18.bedGraph: (NCBI37/mm9)


title: INPUT (ZT14)

description:
Points to SRX119675
Equivalent to GSM874974

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT14.bedGraph: (NCBI37/mm9)


title: Brachyury knockdown EBs

description: mRNA-seq

source_name: embryoid bodies

tag: developmental stage

value: day 4

value: Brachyury knockdown


title: INPUT (ZT02)

description:
Points to SRX119672
Equivalent to GSM874971

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT02.bedGraph: (NCBI37/mm9)


title: INPUT (ZT06)

description:
Points to SRX119673
Equivalent to GSM874972

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
INPUT_ZT06.bedGraph: (NCBI37/mm9)


title: SM17_nox1_proto_rep2

description: RNA amplification (linear)


title: SM12_nox1_rep1


title: ES-Hep

source_name: hepatocytes generated by human ES differentiation

value: functional hepatocytes generated by ES differentiation


title: SREBP1 (ZT22)

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome.
Duplicated reads were removed.
Enriched peaks, in bedGraph format, are available for each sample.
Additional processed data and visualization tools are available at “http://cyclix.vital-it.ch”.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were generated after peaks definition. Scores represent nucleotide counts  in the refined peaks normalized according to the total number of non redundant mapped reads

source_name: SREBP1_ZT22, liver cells

tag: genotype/variation

value: wild type

tag: chiip antibody manufacturer


title: Control EBs

description: mRNA-seq


title: Polr2b (ZT18)

description:
Points to SRX119655
Equivalent to GSM874954

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT18.bedGraph: (NCBI37/mm9)

source_name: RPB2_ZT18, liver cells


title: Tc/Tc E10

description: Directional mRNA-seq

data_processing:
Reads Mapping: Bowtie 2
Differential Gene expression analysis: Cuffdiff
Significance Thresholding: R
Genome_build: mm9
Supplementary_files_format_and_content: Table containing differential gene expression information

source_name: embryos

extract_protocol:
Total RNA was extracted with TRIzol LS Reagent (Invitrogen)
Libraries were prepared with ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre)

value: Tc/Tc

value: embryos


title: SREBP1 (ZT18)

source_name: SREBP1_ZT18, liver cells


title: Tc/Tc E8

description: Directional mRNA-seq


title: Wildtype E8

description: Directional mRNA-seq


title: Brachyury

description: ChIP-exo enriched genomic DNA

data_processing:
Reads Mapping: Bowtie
Strand seperation: Customized
Strand sensitive peak calling: GeneTrack
Peak pairing: Customized
Thresholding
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing the genomic localizations of ChIP-exo mapped peak-pairs

source_name: ES cell derived Mesoendoderm Cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody or HaloLink Resin.
Libraries were prepared according to "Rhee, H.S., and Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419." with custom-made Illumina adapters

treatment_protocol: Activin A dependent Serum free in vitro differentiation of EBs was performed to derive mesoendoderm cells.

tag: antibody

value: Anti-Brachyury antibody, Custom-made, rabbits were immunized with Brachyury residues 249-436 GST fusion proteins


title: Polr2b (ZT02)

description:
Points to SRX119651
Equivalent to GSM874950

data_processing:
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
POLR2B_ZT02.bedGraph: (NCBI37/mm9)

source_name: RPB2_ZT02, liver cells


title: Brachyury ChIPSeq antibody #1

description: ChIP-seq enriched genomic DNA

data_processing:
Reads Mapping: Bowtie
ChIP-seq Peak calling: MACS2
Detection of common bound regions detected by both antibodies: Customized
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing ChIP-seq regions detected by both antibodies

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody
Libraries were prepared using Illumina ChIP-seq sample preparation kit

treatment_protocol: Activin A dependent Serum free in vitro differentiation of ES cells was performed to derive mesoendoderm cells.

value: Anti-Brachyury antibody Rabbit #1, Custom-made, rabbits were immunized with Brachyury residues 249-436 GST fusion protein


title: MockChIPSeq

description: DNA fragments from chromatin immunoprecipitation with pre-immune IgG

value: pre-immune IgG


title: Brachyury ChIPSeq antibody #2

description: ChIP-seq enriched genomic DNA

value: Anti-Brachyury antibody Rabbit #2, Custom-made, rabbits were immunized with Brachyury residues 249-436 GST fusion protein


title: SREBP1 (ZT02)

source_name: SREBP1_ZT02, liver cells


title: Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 12h + acetate

status: Public on Mar 09 2014

city: Los Angeles

first: Sabeeha

last: Merchant

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description:
UGTWs6nA12HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

data_processing:
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length.
Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html)
Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 12h after acetate boost

growth_protocol: Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol.

extract_protocol:
Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012.
For quantitative transcriptomes, RNAs were sequenced at LANL.

treatment_protocol: Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints.

tag: strain/background

tag: treatment

value: 48 h minus nitrogen, then acetate boost

tag: time point

value: 12h after acetate boost


title: Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 48h + acetate

description:
UGTWs6nA48HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 48h after acetate boost

value: 48h after acetate boost


title: Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 24h + acetate

description:
UGTWs6nA24HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 24h after acetate boost

value: 24h after acetate boost


title: Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 4h + acetate

description:
UGTWs6nA4HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 4h after acetate boost

value: 4h after acetate boost


title: Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 0h + acetate

description:
UGTWs6nA0bHS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 0h after acetate boost

value: 0h after acetate boost


title: Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 0.5h + acetate

description:
UGTWs6nA05HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 0.5h after acetate boost

value: 0.5h after acetate boost


title: Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 8h + acetate

description:
UGTWs6nA8HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 8h after acetate boost

value: 8h after acetate boost


title: Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 2h + acetate

description:
UGTWs6nA2HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 2h after acetate boost

value: 2h after acetate boost


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 12h

description:
UGTWs6na12HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 12h

value: minus nitrogen


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 24h

description:
UGTWs6na24HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 24h


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 8h

description:
UGTWs6na8HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 8h


title: Wildtype E10

description: Directional mRNA-seq

tag: genotype

value: Wildtype

tag: tissue


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 4h

description:
UGTWs6na4HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 4h


title: SREBP1 (ZT10)

source_name: SREBP1_ZT10, liver cells

value: wild type

value: male

value: liver

value: Santa Cruz Biotechnology


title: SREBP1 (ZT14)

source_name: SREBP1_ZT14, liver cells


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 0.5h

description:
UGTWs6na05HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 0.5h


title: SREBP1 (ZT06)

source_name: SREBP1_ZT06, liver cells


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 0h

description:
UGTWs6na0bHS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 0h


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 2h

description:
UGTWs6na2HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 2h


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 0h pre-wash

description:
UGTWs6Na0aHS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, pre-wash

value: pre-wash


title: Chlamydomonas reinhardtii CC-4349 48h minus N, 48h + acetate

description:
UGTWcwnA48HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 48h after acetate boost


title: Chlamydomonas reinhardtii CC-4349 48h minus N, 12h + acetate

description:
UGTWcwnA12HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 12h after acetate boost


title: Chlamydomonas reinhardtii CC-4349 48h minus N, 4h + acetate

description:
UGTWcwnA4HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 4h after acetate boost


title: Chlamydomonas reinhardtii CC-4349 48h minus N, 24h + acetate

description:
UGTWcwnA24HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 24h after acetate boost


title: Chlamydomonas reinhardtii CC-4349 48h minus N, 2h + acetate

description:
UGTWcwnA2HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 2h after acetate boost


title: Chlamydomonas reinhardtii CC-4349 48h minus N, 0.5h + acetate

description:
UGTWcwnA05HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 0.5h after acetate boost


title: Chlamydomonas reinhardtii CC-4349 minus N 48h

description:
UGTWcwna48HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, 48h


title: Chlamydomonas reinhardtii CC-4349 48h minus N, 0h + acetate

description:
UGTWcwnA0bHS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 0h after acetate boost


title: Chlamydomonas reinhardtii CC-4349 minus N 8h

description:
UGTWcwna8HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, 8h


title: Chlamydomonas reinhardtii CC-4348 sta6 minus N 48h

description:
UGTWs6na48HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 48h


title: Chlamydomonas reinhardtii CC-4349 minus N 2h

description:
UGTWcwna2HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, 2h


title: Chlamydomonas reinhardtii CC-4349 minus N 24h

description:
UGTWcwna24HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, 24h


title: Chlamydomonas reinhardtii CC-4349 minus N 0.5h

description:
UGTWcwna05HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, 0.5h


title: Chlamydomonas reinhardtii CC-4349 minus N 12h

description:
UGTWcwna12HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, 12h


title: Chlamydomonas reinhardtii CC-4349 minus N 4h

description:
UGTWcwna4HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, 4h


title: 12hr Rpb1 ChIP

status: Public on Mar 08 2014

city: New York

first: Jaspreet

last: Khurana

state: NY

address: 701 West 168th St.

institute: Columbia University

data_processing:
After quality trimming, Input and ChIP-seq reads were mapped to the O.trifallax reference genome (MAC and mitochondrial)
Reads were aligned using BLAT
ChIP-Seq reads were normalized to input by comparing number of reads mapping to the Oxytricha mitochondrial genome
Processed file represents the normalized coverage of Rpb1 across single gene chromosomes.
Genome_build: Genbank accession no. AMCR00000000
Supplementary_files_format_and_content: normalized number of Rpb1 reads mapping to total (polII_normalized_coverage.txt file) and 2-telomere (polII_normalized_coverage_2telo.txt file) MAC chromosomes. MAC genome reference assembly can be found under Genbank accession number AMCR00000000.

organism: Oxytricha trifallax

source_name: 12 hr cell extracts post mixing

growth_protocol: JRB310 and JRB510 strains were grown on Pringsheim medium and mixed in equal numbers at 5000 cells/ml.

extract_protocol:
Formaldehyde fixed chromatin was sheared, clarified and DNA-protein complexes were isolated using Rpb1 antibody
Tru-seq ChIP-seq protocol

value: JRB310 and JRB510


title: Chlamydomonas reinhardtii CC-4349 minus N 0h

description:
UGTWcwna0bHS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, 0h


title: Chlamydomonas reinhardtii CC-4349 minus N 0h pre-wash

description:
UGTWcwNa0aHS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

source_name: Chlamydomonas cultured cells, CC-4349, minus nitrogen, pre-wash