title: H111 bapR mutant

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Bc H111 genome using CLC Genomics Workbench v4.9 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: CAFQ00000000.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample

organism: Burkholderia cenocepacia H111

source_name: Bc H111 BapR mutant planktonic cells

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) and DNA was removed. rRNA was removed using the MicrobExpress kit. First-and second strand cDNA synthesis was performed using the nugen protocol (Ovation Prokaryotic RNA-Seq kit).
The librairies were constructed using The Ovation® Ultralow Library Systems from Nugen (Dedicated read barcode sequences for barcoded adaptors) and the librairies size was controlled with Bioanalyzer.

tag: strain

value: bapR mutant

tag: growth

value: planktonic cells, OD600 equal 2.04

tag: medium

value: complex medium LB


title: H111 wt (control for bapR mutant)

status: Public on Mar 26 2014

type: SRA

library_source: transcriptomic

molecule: total RNA

source_name: Bc H111 planktonic cells

value: wt

value: planktonic cells, OD600 equal 2.08


title: Control shRNA-unstim

city: Cleveland

first: Julian

last: Wong

state: OH

address: 10900 Euclid Ave

department: Molecular Biology & Microbiology

country: USA

institute: Case Western Reserve University

description: Nuclear DNA

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
FASTQ files were aligned with Bowtie to hg19 using standard parameters and peaks prediced with MACS also using default parameters except bandwidth=100.
Individual WIG files for both control and treatment conditions produced by MACS as well as peaks region files were uploaded to GEO.
the wig files are processed WIG format output by MACS used for browsing peaks in a browser (wiggle format). They are formatted to be imported in a browser for a histogram style plot/view in software such as UCSC genome bowser or the Integrated genome viewer by the Broad Institute.
The *_treat.wig or *_conrol.wig is in reference to treat being the test condition and the control being the baseline comparison plot for each respective pair analyzed.
The peaks.txt files are the tab delimited files of the co-ordinates of regions of ChIP-Seq signal enrichment, together with FDR rates and p-values for each region predicted by MACS
The BED files contain data lines that are displayed in an annotation track as defined by UCSC. It contains the peak locations http://genome.ucsc.edu/FAQ/FAQformat#format1
Genome_build: hg19
Supplementary_files_format_and_content: WIG files and Peak files were generated by MACS using default parameters except bandwidth=100

molecule: genomic DNA

organism: Homo sapiens

source_name: Control shRNA-unstim

growth_protocol: RPMI-1640 Medium, supplimented with 5% fetal bovine serum. Passaged every 3-5 days to maintain cell density between 2x10^5 and 2x10^6 cells/ml.

extract_protocol:
Cells were crosslinked with formaldehyde, washed twice with phosphate buffered saline and and nuclei isolated with hypotonic buffer and centrifugation. EMBO J. 25, 3596–3604. Samples were immunoprecipitated with rabbit-anti-RNA Pol II (N-20) antibody from Santa Cruz (catalog # sc-899).
Illumina library preparation standard protocol

treatment_protocol: TNF-a 10ng/ml activation for 30 minutes

tag: tissue origin

value: Peripherial Blood

tag: cell line

tag: cell type

value: T lymphocyte supension

tag: infected with

value: lentiviral vector expressing control shRNA

tag: stimulated with

value: none (unstimulated control)

tag: chip antibody

value: rabbit-anti-RNA Pol II (N-20) antibody

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: NELF-E shRNA-unstim

description: Nuclear DNA

source_name: NELF-E shRNA-unstim

value: lentiviral vector expressing shRNA to NELF-E


title: Control shRNA+TNF stim

description: Nuclear DNA

source_name: Control shRNA+TNF stim

value: 10ng.ml TNF-a for 30min


title: WT-UUO-G233

city: Hongkong

first: Qin

last: ZHOU

address: Room 601, Inflammation Lab. Li Ka Shing Institute of Medical Building, Shatin, NT

department: The Chinese University of Hong Kong

country: China

institute: Li Ka Shing Institute of Health Sciences

data_processing:
The Illumina HiSeq 2000 was used for sequencing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mm9 whole genome using bowtie-0.12.7.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, A. et al.,Nature Methods. 5(7): 621-8.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text files include RPKMs.

organism: Mus musculus

source_name: kidney tissue, WT, UUO

extract_protocol:
Kidney tissues were immediately frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Trizol reagent (Life Technologies, Carlsbad, CA, USA) was used to isolate total RNA from the kidney tissues in accordance with the manufacturer's instructions.
Then, total RNA samples were used to remove highly abundant ribosomal RNAs. For each sample, RNA samples were fractionated with a denaturing polyacrylamide gel (urea-PAGE). Then RNAs over 150 bp were used for cDNA synthesis. After adenylating 3' end and ligating the adapter, the RNA samples were then used for library construction following the protocol suggested by the manufacturer.

treatment_protocol: The animal model of UUO was induced in Smad3 KO and WT mice following the well-established protocol. Briefly, groups of 8 mice (both genders, 22-25g body weight) were anesthetized using the Anesthesia Combo (Ketamine/Xylazine 2:1, i.m). Then, the left ureter was ligated by the autoclaved surgical suture and the UUO kidney was harvested at day 5 post-surgery for the further analysis. In addition, mice with sham operation were used as the control. The anti-GBM model was also performed according to previously described. Anti-GBM globulin was prepared from serum of a sheep immunized against a particulate fraction of mouse GBM. C57BL/6J mice were immunized with sheep IgG in Freund's complete adjuvant (Sigma Chemical Co., St. Louis, MO, USA) followed 5 days later by administration of sheep anti-mouse GBM immunoglobulin at a dose of 60 μg/g of bodyweight (termed day 0). Ten days later, GN was initiated by intravenous injection of sheep anti-mouse GBM globulin. A group of age and weight matched normal C57BL/6J mice were used as normal control. The experimental procedure was performed following the approved protocol by Animal Experimentation Ethics Committee at The Chinese University of Hong Kong.

tag: strain/background

tag: genotype/variation

value: WT

tag: tissue

value: kidney

tag: disease model

value: UUO


title: NELF-E shRNA+TNF stim

description: Nuclear DNA

source_name: NELF-E shRNA+TNF stim


title: WT-Normal-Y214

source_name: kidney tissue, WT, normal

value: normal (untreated)


title: WT-Normal-Y217


title: Smad3-KO-UUO-X544

source_name: kidney tissue, Smad3-KO, UUO


title: Smad3-KO-GBM-L762

source_name: kidney tissue, Smad3-KO, anti-GBM GN

value: anti-GBM GN


title: Smad3-KO-Normal-H106

source_name: kidney tissue, Smad3-KO, normal


title: Smad3-KO-Normal-U409


title: WT-GBM-Y541

source_name: kidney tissue, WT, anti-GBM GN


title: Smad3-KO-GBM-H482


title: 4C_Escape_rep2

city: Chapel Hill

first: Joshua

middle: W

last: Mugford

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: The University of North Carolina at Chapel Hill

description: 4C Biological replicate 2 for 8 anchor points

data_processing:
Library strategy: 4C-Seq
Sequences processed by CASAVA v1.8
Raw sequences were filtered for 4C-primers to identify anchor and allele of origin.
Raw sequences were mapped to mm9 using Bowtie 0.12.7 (-n 2 -l 100 -m 1 --best --strata)
Mapped sequences were processed using custom Perl and R scripts to identify interacting regions of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: Text files containing genomic coordinates and allele calls for each interaction.

source_name: Trophoblast stem cells

growth_protocol: TS cells were derived and cultured as described previously (Calabrese et al., 2012; Himeno et al., 2008)

extract_protocol:
Genomic DNA was extracted and processed using a modified protocol for 4C. See supplemental methods in Mugford et al., 2013.
4C libraries were constructed using a modified protocol for 4C-seq. See supplemental methods in Mugford et al., 2013.

value: F1 hybrid trophoblast stem cells derived from blastocyst

tag: passage

value: Cast/EiJ x C57B6/N


title: 4C_Escape_rep1

description: 4C Biological replicate 1 for 8 anchor points


title: Whole genome sequencing of the IMR90 cell line; IMR90-05_Genome_PE

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: Whole genome sequencing of the IMR90 cell line
Library name: IMR90-05_Genome_PE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18898
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: IMR90 Cell Line, biological replicate 2; IMR90-05_Genome_PE

extract_protocol: Library construction protocol: Genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA). The DNA was used to create one fragmented DNA library as described in the Applied Biosystems SOLiDTM 4 System Library Preparation Guide (Applied Biosystems, Foster City, CA).

tag: sra sample accession

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Fetal lung fibroblast

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

tag: Sex

value: Female

value: Whole Genome Sequencing

value: Qiagen DNeasy Mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles


title: E15.5 miR-1s dHET

city: New York City

first: Yong

last: Zhao

state: NY

address: 1470 Madison Ave

department: Mindich Child Health and Development Institute

institute: Icahn School of Medicine at Mount Sinai

description: paired-end (100bp)

data_processing:
Reads were aligned to the mouse reference genome using TopHat program (Bowtie algorithm)
Transcript assembles and identification of differentially expressed genes were achieved using Cufflinks package
To account for expression bias due to transcript length, each sample transcript expression was normalized by using cufflinks algorithm with a FDR of 0.05
Genome_build: NCBI Build 37/mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: whole heart, embryonic 15.5 days

extract_protocol:
Total RNAs were extracted using TRIzol Reagent. mRNAs were purified using a poly-A selection approach.
Sequencing libraries were prepared according to a standard protocol. Barcode (P2.5 miR-1s dHET): TGACCA  Barcode (P2.5 miR-1s dKO): CGATGT; Barcode (E15.5 miR-1s dHET): AGTCAA; Barcode (E15.5 miR-1s dKO): AGTTCC

value: whole heart

tag: developmental stage

value: embryonic 15.5 days

tag: strain

value: dHET


title: E15.5 miR-1s dKO

description: paired-end (100bp)

value: dKO


title: P2.5 miR-1s dHET

description: single read (100bp)

source_name: whole heart, postnatal 2.5 days

value: postnatal 2.5 days


title: CAGE Mtr4

city: Copenhagen N

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

description: For the 5' end, an extra G in position 10 of the reads, right after the barcode, needs to be trimmed. This is due to an artifact in the reverse transcription of the capped G. For the 3'end, the last 8 nt also needs to be trimmed due to 3' end adaptors.

data_processing:
CAGE: basecalling by CASAVA version 1.8.2. The first 11 nt from 5'end and the last 6 nt from 3'end are trimmed off.  All the reads are then filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50 and mapped to hg19 by bowtie version 0.12.7 using --strata --best -k 10. Only 5'end of single mapped reads are used in the analysis.
Genome_build: Hg19
Supplementary_files_format_and_content: CAGE bed files contain positions of 5' calls.

growth_protocol: HeLa cells grown in DMEM medium supplemented with 10% fetal bovine serum at 37°C and 5% CO2.

extract_protocol:
Purelink (Ambion)
HeLa cells were grown in DMEM medium supplemented with 10% fetal bovine serum at 37°C and 5% CO2. siRNA-mediated knockdown of either EGFP (control), DCP2, or hMTR4 (SKIV2L2) were performed using 22 nM of siRNA and Lipofectamin2000 (Invitrogen) as transfecting agent. A second hit of 22 nM siRNA was given after 48 hr. Cells were harvested an additional 48 h after the second hit, and protein depletion was verified by western blotting analysis as described elsewhere (PMID: 19056938).    CAGE libraries were prepared from 5 μg of total RNA purified from 2x10^6 HeLa cells using the Purelink mini kit (Ambion) with 1% 2-Mercaptoethanol (Sigma) and on-column DNAse I treatment (Ambion) as recommended by manufacturer. CAGE libraries were prepared according to the published protocol by Takahashi, et al. (PMID: 22362160). Prior to sequencing four libraries with different barcodes were pooled and applied to the same sequencing lane. The libraries were sequenced on a HiSeq2000 instrument (Illumina). To compensate for the low complexity in 5’end of the CAGE libraries 30% Phi-X spike-in were added to each sequencing lane as recommended by Illumina.    CAGE reads were assigned to their respective originating sample according to identically matching barcodes. Assigned reads were trimmed to remove linker sequences and subsequently filtered for a minimum sequencing quality of 30 in 50% of the bases using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Mapping to the human genome (hg19) was performed using Bowtie24 (version 0.12.7), allowing for multiple good alignments and subsequently filtering for uniquely mapping reads. Reads that mapped to unplaced chromosome patches or chrM were discarded.

treatment_protocol: 22nM siRNA transfection (doule hit)

tag: barcode

value: ATGCAGCAG

value: Mtr4 knock out (exosome)

tag: cell line


title: CAGE Egfp

value: Egfp knock out (control)


title: H3K27ac_rep2

status: Public on Mar 25 2014

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Mapping: reads were mapped to the O. latipes genome (oryLat2 assembly) using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: oryLat2
Supplementary_files_format_and_content: WIG files (http://genome.ucsc.edu/goldenPath/help/wiggle.html) can be uploaded to UCSC genome browser for data visualization.

organism: Oryzias latipes

source_name: whole organism

growth_protocol: Embryos were raised at 26ºC untill they reached the desired developmental stage. They were dechorionated manually before fixation.

extract_protocol:
Chromatin was extracted from 600 embryos for each sample. After sonication, the DNA was immunoprecipitated using specific antibodies. Samples were purified prior the library construction.
DNA ends were repaired and Illumina adaptors were ligated. DNA fragments were selected by size (200-300 bp) before sequencing.

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#


title: WT-UUO-G232

tag: strain/background

tag: genotype/variation

value: WT

value: kidney

value: UUO


title: RNAseq_ICabE24_rep2

data_processing:
Mapping: reads were mapped to the O. latipes genome (oryLat2 assembly) using Tophat software (http://tophat.cbcb.umd.edu/).
Assigning reads to transcripts: total counts and RPKM for each transcript were calculated using RSeQC package (v2.3.3, http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html)
Genome_build: oryLat2
Supplementary_files_format_and_content: Plain text files with raw counts and RPKM values for each transcript.

growth_protocol: Embryos were raised at 26ºC untill they reached the desired developmental stage. They were dechorionated manually before RNA extraction.

extract_protocol:
60 embryos per sample were suspended in Trizol reagent (Intron Biotechnology) with chloroform. RNA was isolated from the aqueous phase, purified by isopropanol precipitation and cleaned using RNeasy MinElute Cleanup kit (Qiagen).
RNA libraries were prepared for Illumina sequencing using standard protocol.

value: stage 24

tag: tissue

value: embryo


title: WT_8day_DOX_H3K27me3

city: Rehovot

first: Asaf

last: Zviran

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: This is the duplicated sample record of GSM928452 (i.e. the same biological sample) for the convenient retrieval of the complete raw data from SRA

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm9 reference genome using bowtie version 0.12.5.
Data were filtered using the following specifications:  we only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.
We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (wce) as control in order to define a background model.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using  MACS version 1.4.1, representing enriched peaks.

source_name: WT 8 days after dox induction

growth_protocol: MEFs were expanded in 2i/LIF condition with Doxycycline as indicated.

extract_protocol:
Approximately 60*10^6 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature (RT)), and then quenched with glycine (5 min at RT). Fixed cells were lysed in 50mM HEPES KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4°C (Roche, 04693159001), centrifuged at 950 x g for 10 min and re-suspended in 0.2% SDS, 10mM EDTA, 140mM NaCl and 10mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at -4°C to a size range between 200 and 800 bp, and precipitated by centrifugation. 10 ug of antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 hours at room temperature. Washed beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65°C. Eluate was incubated in 65°C for 4 hours, and then treated sequentially with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for two hours. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881).
120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

treatment_protocol: DOX induction at day 0 at the relevant plate in final concentration of 2ug/ml

tag: cell type

value: Embryonic Fibroblast Cells (MEF)

value: MBD3+/+  transgenic for DOX inducible OSKM reprogramming

tag: stage in reprogramming

value: 8 days after DOX induction

value: Millipore

tag: chip antibody cat. #


title: UP

city: Lanzhou

first: Ruiqing

last: Zhu

state: Gansu

address: DingxiSouth Road 197

department: Instituye of biology

institute: Gansu Academy of Sciences

data_processing:
Sequencing-received raw image data were transformed by base calling into sequence data. Prior to mapping reads to the reference database, all sequences were filtered to remove 3′ adaptor sequence, low quality sequences (tags with unknown sequences ‘N’), tags with a copy number of 1 (probably sequencing error), and tags which are too long or too short, leaving clean tags of 21 nt. For annotation, all clean tags were mapped to the reference sequences, and a mismatch of only 1 bp was considered.
The clean reads mapped to reference database from multiple genes were filtered.
The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags)

organism: Reaumuria songarica

source_name: leaf

growth_protocol: The three-year-old plants were transferred to a greenhouse under the following conditions: 150 µmol m-2∙s-1 (fluorescent tubes), photoperiod 16 h light/8 h darkness, day/night temperature of 25/20 °C. The plants were washed with deionized water to remove surface contaminants. Soil attached to roots was also rinsed off with deionized water, and then the plants were cultivated in 1/8 Murashige and Skoog medium solution with insufflating air for two weeks to accommodate the liquid environment during treatments.

extract_protocol:
CTAB-method
library construction, and sequencing were carried out at Beijing Genome Institute at Shenzhen, China. An extract of 8 μg of total RNA was obtained and treated with oligo(dT) magnetic bead adsorption to purify mRNA; oligo(dT) was then used as a primer to synthesize the first- and second-strand cDNA. The 5′-ends of tags can be generated by two types of endonuclease: NlaIII or DpnII. Then, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and severs the CATG sites. Fragments other than the 3′-cDNA fragments connected to oligo(dT) beads are washed away, and the Illumina adaptor 1 is ligated to the sticky 5′-end of the digested bead-bound cDNA fragments. The junction of the Illumina adaptor 1 and the CATG site constitutes the recognition site of MmeI, which is a type of endonuclease with separate recognition and digestion sites; it breaks 17 bp downstream of the CATG site, producing tags with adaptor 1. After removal of 3′ fragments with magnetic beads precipitation, the Illumina adaptor 2 is ligated to the 3′-ends of tags, acquiring tags with different adaptors of both ends to form a tag library.

treatment_protocol: The experiment was arranged with five groupss (untreated, PEG-treated, UV-B radiation treated, combined stresses by PEG and UV-B treatments, and combined stresses by PEG, UV-B and NaCl treatments).

tag: age

tag: treatment

value: combined stresses by UV-B and PEG


title: H3K27ac

data_processing:
Mapping: reads were mapped to the O. latipes genome (oryLat2 assembly) using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Peak calling: detection of peaks was performed with MACS software (http://liulab.dfci.harvard.edu/MACS/) using default parameters.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: oryLat2
Supplementary_files_format_and_content: WIG files (http://genome.ucsc.edu/goldenPath/help/wiggle.html) can be uploaded to UCSC genome browser for data visualization.

extract_protocol:
Chromatin was extracted from 600 embryos for each sample. After sonication, the DNA was immunoprecipitated using specific antibodies. Samples were purified prior the library construction.
Chromatin was extracted from 600 dechorionated embryos for each sample. Embryos were disrupted and cells lysed. Then chromatin was released from nuclei and sonicated in Bioruptor (two cycles of 15 min in high intensity with intervals of 30 sec on 30 sec off, 15 min in ice in between). After sonication, the DNA was incubated with DynaBeads (Invitrogen) coupled with specific antibodies for immunoprecipitation. The precipitated DNA fragments were eluted from the DynaBeads, and protein-DNA interactions were de-crosslinked. DNA was cleaned with phenol, purified using Quiaquick columns (Quiagen) and measured with Quant-It PicoGreen (Invitrogen) before library construction.
DNA ends were repaired and Illumina adaptors were ligated. DNA fragments were selected by size (200-300 bp) before sequencing.

value: H3K27ac, Abcam, ref. ab4729, batch n. GR6802


title: H3K4me3

extract_protocol:
Chromatin was extracted from 600 dechorionated embryos for each sample. Embryos were disrupted and cells lysed. Then chromatin was released from nuclei and sonicated in Bioruptor (two cycles of 15 min in high intensity with intervals of 30 sec on 30 sec off, 15 min in ice in between). After sonication, the DNA was incubated with DynaBeads (Invitrogen) coupled with specific antibodies for immunoprecipitation. The precipitated DNA fragments were eluted from the DynaBeads, and protein-DNA interactions were de-crosslinked. DNA was cleaned with phenol, purified using Quiaquick columns (Quiagen) and measured with Quant-It PicoGreen (Invitrogen) before library construction.
DNA ends were repaired and Illumina adaptors were ligated. DNA fragments were selected by size (200-300 bp) before sequencing.

value: H3K4me3, Diagenode, ref. pAb-003-050, batch n. A3152-001P


title: RNAseq_ICabE24_rep1


title: U

value: UV-B treated


title: 3

value: combined stresses by UV-B, PEG and NaCl


title: WT-GBM-Y555

tag: disease model

value: anti-GBM GN


title: KO H3K4me1_Input [ChIP-Seq]

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

data_processing:
RTA 1.8.70.0 software was used for basecall analysis and aligned to the reference genome was performed at a mismatch error rates =<0.05%.
Reads that mapped to multiple locations in the genome were discarded.
Reads from two biological replicates were merged.
Peak detection was performed using Partek Genomics Suite at a window of 150bp and selected at an FDR<0.0001 over their respective input for autosomes only.
For identification of potential enhancers only peaks were selected that had no overlap with any H3K4me3 peaks and were at least 2kb distant of transcriptional start sites.
Genome_build: MM9
Supplementary_files_format_and_content: TXT files with peak position

source_name: KO MEF_input

growth_protocol: Lsh WT and Lsh KO MEFs were maintained in DMEM supplemented with 10% (vol/vol) FBS (Gibco), 2 mM Glutamax (Invitrogen), and 1% penicillin and streptomycin (Invitrogen).

extract_protocol:
Cells were cross-linked with formaldehyde and nuclear DNA was sonicated with 200-300bp,  then the H3K4me1-DNA complexes were isolated with antibody.
ChIP DNA libraries were made following Illumina ChIP-Seq library preparation kit and subjected to Solexa sequencing (Illumina) at the CCR-Sequencing Facility, National Cancer Institute. Sequencing was performed on Illumina Genome Analyzer IIx.

treatment_protocol: Primary  MEF cells were derived from the body of E13.5 C57Bl/6 mouse embryos and genotyping was performed to select Lsh WT and Lsh KO.

value: primary mouse embryonic fibroblasts

tag: h3k4me1 chip antibody


title: WT H3K4me1_Input [ChIP-Seq]

source_name: WT MEF_input


title: Pm nitrate-limited C

city: Seattle

first: E. Virginia

last: Armbrust

state: WA

department: School of Oceanography

institute: University of Washington

description: Pm expression.tab

data_processing:
Sequence reads were converted from raw color-space into fastq format and then trimmed based on quality score using trimfastq (Iverson et al., 2012; SEAStAR, http://armbrustlab.ocean.washington.edu/seastar). The appropriate read error probability cutoff (Ò-pÓ) was determined based on a subsample of reads trimmed at 10 equally spaced cutoff values.  The cutoff value that yielded the highest number of bases aligned was chosen. Trimmed reads with a length shorter than 30 colorspace transitions (Ò-lÓ) or an entropy value less than 3.0 (Ò-eÓ) were discarded.
Trimmed reads were aligned with BWA (v.0.5.9) to predicted genes for Thalassiosira pseudonana (http://genome.jgi.doe.gov/Thaps3/Thaps3.home.html), Fragilariopsis cylindrus (http://genome.jgi.doe.gov/Fracy1/Fracy1.home.html) or Pseudo-nitzschia multiseries (http://genome.jgi.doe.gov/Psemu1/Psemu1.home.html). Parameters for Òbwa alnÓ were Ò-n .001 -c -l 18 -k 2Ó, and parameters for Òbwa samseÓ were Ò-n 500000Ó (Li and Durbin, 2009).
Counts, the number of sequence reads that aligned to predicted genes, were calculated from the resulting SAM alignment files using ref_select as part of the SEAStAR package. Only those sequences that aligned to predicted genes were used for subsequent analyses.
Transcriptomes from biological triplicates for each condition and species (N=18) were analyzed with the R software package edgeR from Bioconductor (Robinson et al., 2010). Alignment counts generated from ref_select in the SEAStAR package were normalized to library size for each replicate in edgeR. Then, an estimate of common dispersion of normalized counts for the three biological replicates within each treatment was calculated so that triplicates could be pooled for further analyses (Robinson and Smyth, 2007). Pairwise comparisons of pooled counts (i.e. transcript abundances) between treatments (nitrate-limited versus nutrient-replete) were made with the exactTest function. A false discovery rate (fdr) of 0.01 was used to account for Type I errors; all p values provided have been fdr-corrected. P-values < 0.01 reflect statistically significant differences between nitrate-limited and nutrient-replete gene transcription. Up-regulated genes exhibit greater transcript abundances in response to nitrate-limited growth and down-regulated genes exhibit lower transcript abundances under nitrate-limited growth. For each diatom, the nitrate-limited transcript abundances were normalized to the nutrient-replete ÒcontrolÓ abundances to give a log fold-change value, also referred to as the expression ratio.
Genome_build: Thalassiosira pseudonana (http://genome.jgi.doe.gov/Thaps3/Thaps3.home.html)
Genome_build: Fragilariopsis cylindrus (http://genome.jgi.doe.gov/Fracy1/Fracy1.home.html)
Genome_build: Pseudo-nitzschia multiseries (http://genome.jgi.doe.gov/Psemu1/Psemu1.home.html)
Supplementary_files_format_and_content: Tp expression.tab - tab delimited text files generated from edgeR that contain log fold change, log abundance, p-values, and fdr-corrected p-values for 3 biological replicates per condition; protein identification is also given
Supplementary_files_format_and_content: Fc expression.tab - tab delimited text files generated from edgeR that contain log fold change, log abundance, p-values, and fdr-corrected p-values for 3 biological replicates per condition; protein identification is also given
Supplementary_files_format_and_content: Pm expression.tab - tab delimited text files generated from edgeR that contain log fold change, log abundance, p-values, and fdr-corrected p-values for 3 biological replicates per condition; protein identification is also given

molecule: polyA RNA

organism: Pseudo-nitzschia multiseries

source_name: diatom culture

growth_protocol: Thalassiosira pseudonana (Hustedt) Hasle et Heimdal (Provasoli-Guillard National Center for Marine Algae and Microbiota, Maine, USA; CCMP 1335), Fragilariopsis cylindrus (Provasoli-Guillard National Center for Marine Algae and Microbiota, CCMP 1102), and Pseudo-nitzschia multiseries (S. Bates, Fisheries and Oceans Canada; CLNN-17) were maintained at their optimum growth temperatures without bubbling in semi-continuous batch cultures under continuous light (100 μmol photons m−2 s−1) in modified artificial seawater with f/2 concentrations of nutrients (882 μM NaNO3, 106 μM Na2SiO3, 36.2 μM NaH2PO4; Guillard and Ryther, 1962). Growth of non-axenic triplicate cultures of T. pseudonana at 20oC, F. cylindrus at 4°C and P. multiseries at 13°C were monitored with a 10-AU fluorometer (Turner, California, USA). Cultures were considered acclimated to these growth conditions when the growth rates of three consecutive transfers were not significantly different from one another (ANCOVA).  Each acclimated diatom culture was then transferred into a batch culture with nutrient-replete media (882 μM NaNO3, 106 μM Na2SiO3, 36.2 μM NaH2PO4) and a batch culture with low nitrate media (55 μM NaNO3, 212 μM Na2SiO3, 72.4 μM NaH2PO4) in artificial seawater, maintaining three biological replicates per condition and per diatom. The reduced amount of nitrate relative to other nutrients, including a doubling of Na2SiO3 and NaH2PO4 concentrations, ensured that the onset of stationary phase in the low nitrate media was caused by availability of nitrate. In total, there were triplicate biological replicates of the low-nitrate and the replete-media conditions for each diatom (N=18). Experiments were conducted in 10 L (T. pseudonana and F. cylindrus) or 4 L (P. multiseries) bottles; all cultures were bubbled with sterile filtered air. Pseudo-nitzschia multiseries was also stirred continuously. Photosynthetic yield of photosystem II (Fv/Fm) was monitored with a PhytoPAM fluorometer (Walz, Germany). The onset of stationary phase was defined by when chlorophyll a fluorescence of a culture no longer increased exponentially and Fv/Fm values decreased.  Nitrate limitation of growth in the low nitrate media was confirmed by removing two 50 mL aliquots from the remaining cultures and adding 1764 μM NaNO3 to aliquot one, no nutrients to aliquot two, and 1764 μM NaNO3 to the remaining post-harvest large-volume cultures. All samples were monitored for at least two more days to confirm that chlorophyll a fluorescence and Fv/Fm increased after the addition of nitrate to aliquot one and the large-volume cultures.

extract_protocol:
RNA was extracted from frozen cells on filters using the Totally RNA extraction kit (Life Technologies, New York, USA). The RNA was incubated with DNase I (Ambion, New York, USA) at 37°C for 2 hr and purified by DNase inactivation reagent (Ambion). Messenger RNA was polyA-selected from total RNA using the Ambion Micro Poly(A)Purist Kit (Life Technologies, New York, USA) to minimize bacterial RNA sequencing.
The mRNA was then prepared for sequencing according to the SOLiD Total RNA-Seq Kit protocol. For each sample, 700 million beads were loaded onto a slide and run on a Life Technologies (New York, USA) SOLiD sequencer version 4.

treatment_protocol: Between 4.5 and 1.5 L of the experimental cultures (approximately half of the volume of each culture) were filtered onto 0.8 mm polycarbonate filters (Millipore, Massachusetts, USA) during mid-exponential growth (nutrient-replete) or at the onset of stationary phase due to nitrate limitation. Filtered cells were immediately flash frozen in liquid nitrogen and stored at 80°C until later RNA extraction.

tag: nutrient condition

value: nitrate-limited

tag: culture strain


title: Pm replete C

description: Pm expression.tab

value: nutrient-replete control


title: KO H3K4me1_IP [ChIP-Seq]

source_name: KO MEF_IP

tag: strain

value: ab8895, abcam


title: Pm nitrate-limited A

description: Pm expression.tab


title: Pm replete A

description: Pm expression.tab


title: Pm replete B

description: Pm expression.tab


title: P2.5 miR-1s dKO

description: single read (100bp)

value: whole heart

tag: developmental stage

value: postnatal 2.5 days

value: dKO


title: WT H3K4me1_IP [ChIP-Seq]

source_name: WT MEF_IP


title: 24 hours after infection, sequenced by HiSeq 2000

city: Melbourne

first: MAOSHAN

last: CHEN

state: Victoria

address: La Trobe University, Bundoora

department: Department of Biochemistry and Genetics

country: Australia

institute: La Trobe University

data_processing:
Filtering low quality reads, adapters, and other contaminants with self-designed Perl program
TopHat was employed to identify all the splicing junction sites in the library.
Genome_build: Human adenovirus C RefSeq Genome  NC_001405.1
Genome_build: Human adenovirus 2 RefSeq Genome AC_000007.1

source_name: Human primary lung fibroblast cells infected by adenovirus type 2

growth_protocol: Human primary lung fibroblast cells (IMR-90) purchased from American Type Culture Collection(ATCC) were cultured in Eagle’s minimum essential medium (ATCC) supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin. After reaching confluence, the cells were cultured for two more days in order to synchronize them.

extract_protocol:
Total RNA from adenovirus or mock-infected IMR-90 cells was extracted using TRIZOL Reagent (Invitrogen). The quality of the input RNA was controlled by the Bioanalyzer (Agilent Technologies). RNA was treated with RiboZero (Epicentre) to remove ribosomal RNA and the libraries were constructed using ScriptSeq? v2 RNA-Seq library preparation kit according to the manufacturer’s protocol (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Synchronized cells were mock-infected or infected with Ad2 at a multiplicity of 100 fluorescence-forming units (FFU) per cell in serum-free medium (Philipson, 1961). After 1 h adsorption at 37°C, the medium was replaced with complete EMEM containing 10% FBS and incubated at 37°C. Infected cells were collected at 6, 12, 24, and 36 hours post infection (hpi). Mock-infected cells were collected at 6 hpi.

tag: cell line

tag: infection

value: adenovirus type 2

tag: time point

value: 24 hours after infection


title: 12 hours after infection, sequenced by HiSeq 2000

value: 12 hours after infection


title: 12 hours after infection, sequenced by GA II


title: Pm nitrated-limited B

description: Pm expression.tab


title: 36 hours after infection, sequenced by HiSeq 2000

value: 36 hours after infection


title: Fc nitrate-limited C

description: Fc expression.tab

organism: Fragilariopsis cylindrus

value: CCMP 1102


title: 24 hours after infection, sequenced by GA II


title: Fc nitrate-limited B

description: Fc expression.tab


title: RNAseq_E10.5_rep1

description: Replicate 1.

data_processing:
Mapping: reads were mapped to the mouse genome (mm9 assembly) using Tophat software (http://tophat.cbcb.umd.edu/).
Assigning reads to transcripts: total counts and RPKM for each transcript were calculated using the RSeQC package (v2.3.3, http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html).
Genome_build: MGSCv37
Supplementary_files_format_and_content: Plain text files with raw counts and RPKM values for each transcript.

source_name: whole organism, E10.5

growth_protocol: CBA/Ca×C57Bl/10 crosses. Embryos taken at 10.5dpc, taking the day in which the plug was found as 0.5dpc.

extract_protocol:
TRI-reagent followed by chloroform extraction, phenol:chloroform:methyl-butanol (25:24:1) extraction and propanol precipitation.
RNA libraries were prepared for Illumina sequencing using the standard protocol.

treatment_protocol: No treatment. Normal embryonic development.

tag: strain/background

value: whole body


title: RNAseq_E10.5_rep2

description: Replicate 2.


title: Fc nitrate-limited A

description: Fc expression.tab


title: Fc replete B

description: Fc expression.tab


title: mbt_meRich.lane5

city: Bethesda

first: David

last: McGaughey

address: 10 Center Dr

department: NEI

institute: NIH

data_processing:
Aligned with bwa 0.5.8c against zv9
Called peaks with macs2 2.0.10.20120703 (-g 1.4e9)
Used meRich as "-t" and mePoor as "-c l" sample for macs2 peak calls (matched by lane as indicated in the sample titles. Brain used for both lane4 and lane5  as control)
Took centers of peaks and added 100bp to each side with bedtools
Genome_build: zv9
Supplementary_files_format_and_content: bed file with areas of high methylation in the zebrafish tissues (methylation peak locations)

organism: Danio rerio

source_name: danio rerio whole embryo

growth_protocol: Tubigen AB fish were crossed and embryos raised in embryo media until proper age was reached, with standard practices used

extract_protocol:
Embryos/tissue were flash frozen in Liquid Nitrogen and later gDNA was extracted with Gentra PureGene
ChIP-Seq DNA Sample Prep Kit was used

tag: Sex

tag: treated with

value: whole embryo


title: eye_meRich.lane4

source_name: danio rerio tissue

value: female

tag: tissue

value: eye


title: Smad3-KO-UUO-X547

source_name: kidney tissue, Smad3-KO, UUO

tag: genotype/variation

value: kidney

value: UUO


title: sperm_meRich.lane5

value: sperm


title: brain

description: processed data file: brain_macs2_me_peaks.bed

value: brain


title: cntl_neo_1hr_1

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Data was processed with CASAVA version 1.8.2
Sequence reads in fastq format were mapped to danRer7using tophat-1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3.
Genome_build: danRer7
Supplementary_files_format_and_content: FPKM values per gene.

source_name: GFP negative cells from 5 dpf larvae

growth_protocol: Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild-type larvae at 48 hpf under fluorescent stereoscope.

extract_protocol:
Two hundred 5dpf untreated Tg(sqET20) control or neomycin treated Tg(sqET20) larvae were anesthetized, collected in a 2mL tube, dissociated with trypsin and filtered to remove un-dissociated tissue. A two-gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions (see Materials and Methods of associated manuscript for detailed FACS protocol). Approximately 30,000 GFP- or GFP+ cells were used for total RNA extraction using Trizol (Invitrogen) following the manufacturer’s manual.
Libraries for RNA sequencing were made with poly-A selected mRNA using the Illumina TruSeq RNA library construction kit v2 (Illumina). The resulting libraries were purified using Agencourt AMPure XP system (Backman Coulter), then quantified using a Bioanalyzer or Qubit Fluorometer (Life Technologies).

treatment_protocol: For neomycin treatment, 5dpf larvae were treated for 30min with 300μM neomycin (Fisher BioReagents) diluted in 0.5X E2 medium, rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.

tag: drug

value: neomycin

tag: time

tag: gfp status

value: negative

tag: genotype


title: Mock-infected, sequenced by HiSeq 2000


title: 6 hours after inferction, sequenced by HiSeq 2000

value: 6 hours after inferction


title: heart_meRich.lane4

value: heart


title: Fc replete C

description: Fc expression.tab

value: nutrient-replete control


title: liver_meRich.lane4

value: liver


title: Tp nitrate-limited A

description: Tp expression.tab

organism: Thalassiosira pseudonana

value: nitrate-limited

value: CCMP 1335


title: Tp replete C

description: Tp expression.tab


title: Tp replete B

description: Tp expression.tab


title: Tp replete A

description: Tp expression.tab


title: brain_mePoor.lane4


title: Tp nitrate-limited C

description: Tp expression.tab


title: 1cell_meRich.lane5


title: brain_mePoor.lane5


title: Tp nitrate-limited B

description: Tp expression.tab


title: DMBA treatment 1

status: Public on Mar 24 2014

city: New Haven

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

data_processing:
base-calling using CASAVA version 1.8.2
Alignment with tophat version 2.1 againt mm9 transcriptome.  Parameters:  -a12 --b2-fast  --prefilter-multihits --max-multihits=5 -G $transcriptomeGtf --transcriptome-only
Count of each gene is calculated with htseq-count.
Count Per Million (CPM) is calculated with EdgeR R package version 3.2.3
Genome_build: mm9
Supplementary_files_format_and_content: A matrix of CPM for each gene, sample.  CPM stands for Count of reads uniquely and unambiguously mapped to a gene Per Million filtered reads in the library.

source_name: Keratoacanthoma tumor

growth_protocol: Mice were treated with DMBA for 20 weeks to obtain Keratoacanthoma skin tumors

extract_protocol:
RNA was collected from FACS purified cells (Tomato+/Pcadherin+) by using the RNAesay Kit from Qiagen.
The samples were prepared using the RiboZero Kit. We use a custom 'dUTP Stranded mRNA Protocol' that utilizes dUTP to tag a specific strand fragment for adapter ligation.

treatment_protocol: Mice were kept in DMBA treatment for the collection of tumors at timepoint 0 (0 weeks post DMBA) and maintained in absence of DMBA for a week to collect tumors at 1 week post DMBA

tag: mouse id

value: A

tag: cell type

value: Epi


title: 1 week post DMBA 2

value: D

value: 1 week


title: FVB/N lactation day-12 Argonaute 2 A8

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

country: France

institute: INRA

description:
whole organ
mmu_mirDeep2_prediction.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for poly-A stretches, then filtered for their size (17-28 nt). The cleaned sequences were clustered into unique reads and then mapped to the mouse (GRCm38.71) and bovine (UMD3.1.71) reference genomes using the mapper.pl module from miRDeep2 with defaut parameters.
Novel miRNA and precursors were identified using miRDeep2 core module miRDeep2.pl using defaut parameters. Then Novel miRNA datasets were created by adding to known miRNA of the species (miRBase v20) miRNA predicted with a miRDeep2 score> 0. The same procedure was performed to create a new data set of precursors for both species.
Quantification was performed using quantifier.pl module from miRDeep2 with defaut parameters using the unique reads, novels miRNA datasets, precursor datasets and know miRNA (miRBase v20). Results were then filtered with a custom perl script parse_miRDeep2_outputs.pl (https://mulcyber.toulouse.inra.fr/projects/bioinfoutils/) to eliminate redundancy between known and putative novel miRNA.
Genome_build: mm10 (GRCm38.71) and UMD3.1.71
Supplementary_files_format_and_content: Quantification files (*_quantification.txt) are the resulting files generated by the quantifier.pl module of miRDeep2. These tab-delimited text files include for each miRNA its associated precursor, raw abundance measurements, normalized abundance, and sequence. Prediction files (*_prediction.txt) are the resulting files generated by the miRDeep2 prediction process (miRDeep2.pl) for each species. These tab-delimited text files include predicted miRNA and precursors, associated miRDeep2 scores, and their genome location.

source_name: Mammary gland

extract_protocol:
Total RNA were isolated from mouse tissue biopsies or from the samples obtained after AGO2 co-immunoprecipitation using the RNA NOW kit (Ozyme), with overnight precipitation so as to guarantee a maximum yield of small RNA. Bovine total RNA were prepared from about 50 mg mammary tissue using the Nucleospin® miRNA isolation kit (Macherey-Nagel Inc.) according to the manufacturer’s instructions. Both mouse and bovine samples were precipitated using sodium acetate 3M, 96% ethanol and 5 mg/mL glycogen.
Libraries were prepared using the Illumina small RNA kit (Illumina) from GATC Biotech Company, according to the manufacturer’s instructions.

value: Mammary gland

value: FVB/N

tag: physiological stage

value: lactation day-12

tag: protein co-immunoprecipitation

value: Argonaute 2 (Abnova, EIF2C2 monoclonal antibody (M01), clone 2E12-1C9; Cat. No. H00027161-M01)


title: 1 week post DMBA 1

value: C


title: 3dpf_mtx-treated

value: 400 uM methotrexate applied at 1-cell stage

value: whole embryo


title: DMBA treatment 2

value: B


title: Fc replete A

description: Fc expression.tab

tag: nutrient condition

tag: culture strain

value: CCMP 1102


title: FVB/N lactation day-12 Argonaute 2 A7

description:
whole organ
mmu_mirDeep2_prediction.txt

tag: strain


title: FVB/N lactation day-12 none A5

description:
whole organ
mmu_mirDeep2_prediction.txt


title: Bulk RNA-Seq, 72 hrs, replicate 3

status: Public on Mar 23 2014

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Reads were mapped with TopHat 2.0.9 and Bowtie 2.0.6. TopHat was provided with GENCODE version 17
Mapped reads were analyzed with Cuffdiff 2.2 to generate normalized per-cell expression profiles.
Cells were pseudo-temporally ordered with Monocle
Genome_build: hg19
Supplementary_files_format_and_content: FPKM expression matrix; fpkm_matrix.txt for Cell* samples and truseq_fpkm_matrix.txt for *Bulk RNA-Seq samples

source_name: Bulk RNA-Seq_72 hrs

growth_protocol: Human Skeletal Muscle Myoblasts (HSMM) derived from quadricep biopsy (Lonza, catalog #CC-2580, lot #257130) were expanded in 10% FBS SkGM-2 (Lonza).  All procedures have been performed using HSMM within P10 from explant.

extract_protocol:
For single-cell mRNA sequencing, dissociated cells were captured and processed with the C1™ Single-Cell Auto Prep System (Fluidigm) following manufacturer’s protocol 100-5950.  Starting with a suspension of cells at a concentration of approximately 250 cells/µL, up to 96 single cells are captured in each C1 microfluidic device.
[TruSeq] - HSMM in either growth or differentiation medium were dissociated, washed and resuspended in complete media containing 0.1U/ul of RNaseOUT (Lifetech). Each time point was collected in three independent biological replicates for regular mRNA sequencing while for single cell mRNA sequencing the independent replicates were pooled in equal amounts.  For bulk RNA-Seq libraries, total RNA was extracted with Trizol and mRNA libraries were produced starting from 100ng of total RNA using the TruSeq mRNA-Seq library kit (Illumina) according to manufacturer’s instructions.
[Single Cell] - After imaging with a microscope to identify which sites have captured a single cell, processing of the cells occurs within the C1 instrument to perform the steps of cell lysis, cDNA synthesis with reverse transcriptase, and PCR amplification of each cDNA library.  The cDNA synthesis and PCR use reagents from the SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing (Clontech 634936).  The SMARTer chemistry utilizes a strand-switching mechanism so that both the 1st and 2nd strands of cDNA are synthesized in a single reaction.  Following harvest from the C1 microfluidic device, each cDNA library is subjected to tagmentation (simultaneous fragmentation and tagging with sequencing adapters) using the Nextera XT DNA Sample Preparation Kit (Illumina FC-131-1096) as described in Fluidigm protocol 100-5950.  PCR amplification of the tagmented cDNA uses Index Primers from the Nextera XT DNA Sample Preparation Index Kit (Illumina FC-131-1002).  Following PCR, the cDNA libraries from individual cells are pooled and purified using AMPure® XP beads (Agencourt Bioscience Corp A63880) as described in Fluidigm protocol 100-5950.

treatment_protocol: HSMM cells were differentiated for the via switch to 2% HS aMEM (Lifetech).

value: Human Skeletal Muscle Myoblasts (HSMM)

tag: hour post serum-switch

tag: debris

value: FALSE

tag: control well

tag: cells in well

tag: library protocol

value: Bulk RNA-Seq (TruSeq)


title: A4 (LF)

description:
pool of 2 biopsies from 2 dairy cows. Diet was an grass natural hay-based diet with cows receiving a mixture of concentrates to give approximately a 46:54 forage-to-concentrate ratio, called “low forage” (LF).
bta_mirDeep2_prediction.txt

organism: Bos taurus

source_name: Mammary biopsy

tag: tissue

value: Mammary biopsy

value: Holstein

value: mid-lactation


title: Bulk RNA-Seq, 72 hrs, replicate 2


title: Bulk RNA-Seq, 72 hrs, replicate 1


title: Bulk RNA-Seq, 48 hrs, replicate 3

source_name: Bulk RNA-Seq_48 hrs


title: Bulk RNA-Seq, 48 hrs, replicate 2


title: Bulk RNA-Seq, 48 hrs, replicate 1


title: Bulk RNA-Seq, 24 hrs, replicate 2

source_name: Bulk RNA-Seq_24 hrs


title: 3dpf

tag: Sex

tag: treated with


title: Bulk RNA-Seq, 24 hrs, replicate 1


title: Bulk RNA-Seq, 24 hrs, replicate 3


title: Bulk RNA-Seq, 0 hrs, replicate 3

source_name: Bulk RNA-Seq_0 hrs


title: Bulk RNA-Seq, 0 hrs, replicate 2


title: Cell T48_CT_H11

source_name: Myoblast_Cell T48_CT_H

value: Single-cell


title: Cell T48_CT_H10


title: Cell T48_CT_H08


title: Cell T48_CT_H07


title: Cell T48_CT_H09


title: A2 (LF)

description:
pool of 2 biopsies from 2 dairy cows.
Diet was an grass natural hay-based diet with cows receiving a mixture of concentrates to give approximately a 46:54 forage-to-concentrate ratio, called “low forage” (LF).
bta_mirDeep2_prediction.txt


title: Cell T48_CT_H04


title: FVB/N lactation day-12 none A6

description:
whole organ
mmu_mirDeep2_prediction.txt


title: Cell T48_CT_H05


title: Cell T48_CT_H06


title: Cell T48_CT_H01


title: Cell T48_CT_H02


title: Cell T48_CT_G12

source_name: Myoblast_Cell T48_CT_G


title: Cell T48_CT_G10


title: Cell T48_CT_G11


title: Cell T48_CT_G07


title: Cell T48_CT_G09


title: Cell T48_CT_G05


title: Cell T48_CT_G04


title: Cell T48_CT_G03


title: Cell T48_CT_G01


title: Cell T48_CT_G06


title: Cell T48_CT_G02


title: Cell T48_CT_F11

source_name: Myoblast_Cell T48_CT_F


title: Cell T48_CT_F10


title: Cell T48_CT_F08


title: Bulk RNA-Seq, 0 hrs, replicate 1


title: Cell T48_CT_F06


title: Cell T48_CT_F09


title: Cell T48_CT_F07


title: Cell T48_CT_H03

value: TRUE


title: Cell T48_CT_F05


title: Cell T48_CT_F03


title: Cell T48_CT_F02


title: Cell T48_CT_H12


title: Cell T48_CT_F01


title: Cell T48_CT_G08


title: Cell T48_CT_E11

source_name: Myoblast_Cell T48_CT_E


title: Cell T48_CT_E10


title: Cell T48_CT_F12


title: Cell T48_CT_E09


title: Cell T48_CT_E08


title: Cell T48_CT_E12


title: Cell T48_CT_E03


title: Cell T48_CT_E02


title: Cell T48_CT_E04


title: Cell T48_CT_E06


title: Cell T48_CT_E01


title: Cell T48_CT_D12

source_name: Myoblast_Cell T48_CT_D


title: Cell T48_CT_D10


title: Cell T48_CT_E05


title: Cell T48_CT_D11


title: Cell T48_CT_D05


title: Cell T48_CT_E07


title: Cell T48_CT_D02


title: Cell T48_CT_D01


title: Cell T48_CT_D09


title: Cell T48_CT_C11

source_name: Myoblast_Cell T48_CT_C


title: Cell T48_CT_D06


title: Cell T48_CT_C10


title: Cell T48_CT_D04


title: Cell T48_CT_D07


title: Cell T48_CT_D03


title: Cell T48_CT_C08


title: Cell T48_CT_C07


title: Cell T48_CT_C09


title: Cell T48_CT_C04


title: Cell T48_CT_C06


title: Cell T48_CT_C03


title: Cell T48_CT_C02


title: Cell T48_CT_B12

source_name: Myoblast_Cell T48_CT_B


title: Cell T48_CT_F04


title: Cell T48_CT_C05


title: Cell T48_CT_C01


title: Cell T48_CT_B11


title: Cell T48_CT_B10


title: Cell T48_CT_D08


title: Cell T48_CT_B07


title: Cell T48_CT_B06


title: Cell T48_CT_B04


title: Cell T48_CT_B05


title: Cell T48_CT_C12


title: Cell T48_CT_B02


title: Cell T48_CT_B01


title: Cell T48_CT_A12

source_name: Myoblast_Cell T48_CT_A


title: Cell T48_CT_A11


title: Cell T48_CT_A10


title: Cell T48_CT_B03


title: Cell T48_CT_A09


title: Cell T48_CT_A07


title: Cell T48_CT_B08


title: Cell T48_CT_A06


title: Cell T48_CT_A05


title: Cell T48_CT_A04


title: Cell T48_CT_A02


title: Cell T48_CT_A03


title: Cell T48_CT_A01


title: Cell T48_CT_A08


title: Cell T24_CT_H10

source_name: Myoblast_Cell T24_CT_H


title: Cell T24_CT_H12


title: Cell T24_CT_H11


title: Cell T24_CT_H07


title: Cell T24_CT_H08


title: Cell T24_CT_H06


title: Cell T24_CT_H02


title: Cell T24_CT_H01


title: Cell T24_CT_H03


title: Cell T24_CT_G12

source_name: Myoblast_Cell T24_CT_G


title: Cell T24_CT_G11


title: Cell T24_CT_H05


title: Cell T24_CT_G10


title: Cell T24_CT_G06


title: Cell T24_CT_G07


title: Cell T24_CT_G04


title: Cell T24_CT_G03


title: Cell T24_CT_H09


title: Cell T24_CT_F12

source_name: Myoblast_Cell T24_CT_F


title: Cell T24_CT_F11


title: Cell T24_CT_G08


title: Cell T24_CT_G01


title: Cell T24_CT_F10


title: Cell T24_CT_F05


title: Cell T24_CT_H04


title: Cell T24_CT_F07


title: Cell T24_CT_F06


title: Cell T48_CT_B09


title: Cell T24_CT_F09


title: Cell T24_CT_F02


title: Cell T24_CT_F04


title: Cell T24_CT_F08


title: Cell T24_CT_G02


title: Cell T24_CT_F01


title: Cell T24_CT_G09


title: Cell T24_CT_E10

source_name: Myoblast_Cell T24_CT_E


title: Cell T24_CT_E07


title: Cell T24_CT_E08


title: Cell T24_CT_G05


title: Cell T24_CT_E11


title: Cell T24_CT_E01


title: Cell T24_CT_E02


title: Cell T24_CT_D08

source_name: Myoblast_Cell T24_CT_D


title: Cell T24_CT_D12


title: Cell T24_CT_E04


title: Cell T24_CT_D07


title: Cell T24_CT_D05


title: Cell T24_CT_D06


title: Cell T24_CT_D04


title: Cell T24_CT_C11

source_name: Myoblast_Cell T24_CT_C


title: Cell T24_CT_C12


title: Cell T24_CT_E03


title: Cell T24_CT_D01


title: Cell T24_CT_D03


title: Cell T24_CT_D02


title: Cell T24_CT_E05


title: Cell T24_CT_C10


title: Cell T24_CT_E12


title: Cell T24_CT_C08


title: Cell T24_CT_C09


title: Cell T24_CT_E09


title: Cell T24_CT_C06


title: Cell T24_CT_C04


title: Cell T24_CT_F03


title: Cell T24_CT_C05


title: Cell T24_CT_E06


title: Cell T24_CT_D10


title: Cell T24_CT_D09


title: Cell T24_CT_D11


title: Cell T24_CT_C02


title: Cell T24_CT_B11

source_name: Myoblast_Cell T24_CT_B


title: Cell T24_CT_B03


title: Cell T24_CT_B09


title: Cell T24_CT_B04


title: Cell T24_CT_C01


title: Cell T24_CT_B02


title: Cell T24_CT_C03


title: Cell T24_CT_B01


title: Cell T24_CT_B07


title: Cell T24_CT_B10


title: Cell T24_CT_B08


title: Cell T24_CT_B05


title: Cell T24_CT_B06


title: Cell T24_CT_B12


title: Cell T24_CT_A11

source_name: Myoblast_Cell T24_CT_A


title: Cell T24_CT_A10


title: Cell T24_CT_C07


title: Cell T24_CT_A09


title: Cell T24_CT_A07


title: Cell T24_CT_A08


title: Cell T24_CT_A06


title: Cell T24_CT_A05


title: Cell T24_CT_A03


title: Cell T24_CT_A04


title: Cell T72_CT_H11

source_name: Myoblast_Cell T72_CT_H


title: Cell T72_CT_H12


title: Cell T24_CT_A02


title: Cell T24_CT_A01


title: Cell T0_CT_H12

source_name: Myoblast_Cell T0_CT_H


title: Cell T0_CT_H09


title: Cell T72_CT_H06


title: Cell T0_CT_H08


title: Cell T72_CT_H10


title: Cell T72_CT_H05


title: Cell T72_CT_H09


title: Cell T72_CT_H08


title: Cell T72_CT_H04


title: Cell T0_CT_H07


title: Cell T0_CT_H10


title: Cell T72_CT_H03


title: Cell T0_CT_H05


title: Cell T0_CT_H04


title: Cell T72_CT_H02


title: Cell T72_CT_G12

source_name: Myoblast_Cell T72_CT_G


title: Cell T0_CT_H11


title: Cell T0_CT_G12

source_name: Myoblast_Cell T0_CT_G


title: Cell T0_CT_H03


title: Cell T0_CT_H01


title: Cell T72_CT_G10


title: Cell T72_CT_H01


title: Cell T72_CT_G11


title: Cell T0_CT_H06


title: Cell T0_CT_G11


title: Cell T72_CT_G08


title: Cell T72_CT_G09


title: Cell T0_CT_G10


title: Cell T24_CT_A12


title: Cell T0_CT_H02


title: Cell T72_CT_G07


title: Cell T72_CT_G05


title: Cell T0_CT_G06


title: Cell T72_CT_G03


title: Cell T0_CT_G07


title: Cell T0_CT_G05


title: Cell T72_CT_G02


title: Cell T72_CT_F11

source_name: Myoblast_Cell T72_CT_F


title: Cell T72_CT_F10


title: Cell T72_CT_G06


title: Cell T0_CT_G03


title: Cell T0_CT_G02


title: Cell T0_CT_F11

source_name: Myoblast_Cell T0_CT_F


title: Cell T0_CT_G01


title: Cell T0_CT_F12


title: Cell T0_CT_F10


title: Cell T72_CT_F08


title: Cell T0_CT_G04


title: Cell T0_CT_F08


title: Cell T72_CT_F04


title: Cell T72_CT_F02


title: Cell T72_CT_F01


title: Cell T0_CT_F09


title: Cell T72_CT_F05


title: Cell T0_CT_G09


title: Cell T0_CT_F07


title: Cell T0_CT_G08


title: Cell T72_CT_F07


title: Cell T72_CT_G04


title: Cell T72_CT_E12

source_name: Myoblast_Cell T72_CT_E


title: Cell T0_CT_F06


title: Cell T0_CT_F05


title: Cell T0_CT_F04


title: Cell T72_CT_F09


title: Cell T0_CT_F02


title: Cell T0_CT_F03


title: Cell T72_CT_E05


title: Cell T72_CT_E07


title: Cell T72_CT_E03


title: Cell T0_CT_F01


title: Cell T0_CT_E11

source_name: Myoblast_Cell T0_CT_E


title: Cell T72_CT_E02


title: Cell T0_CT_E12


title: Cell T72_CT_D12

source_name: Myoblast_Cell T72_CT_D


title: Cell T72_CT_E04


title: Cell T0_CT_E09


title: Cell T72_CT_E01


title: Cell T72_CT_D09


title: Cell T72_CT_D08


title: Cell T0_CT_E10


title: Cell T72_CT_D07


title: Cell T72_CT_D06


title: Cell T0_CT_E04


title: Cell T0_CT_E06


title: Cell T0_CT_E05


title: Cell T72_CT_D11


title: Cell T72_CT_E06


title: Cell T72_CT_E08


title: Cell T72_CT_D04


title: Cell T0_CT_E03


title: Cell T0_CT_E02


title: Cell T0_CT_D12

source_name: Myoblast_Cell T0_CT_D


title: Cell T0_CT_E01


title: Cell T72_CT_D03


title: Cell T0_CT_E08


title: Cell T72_CT_D05


title: Cell T72_CT_D01


title: Cell T0_CT_D11


title: Cell T72_CT_C12

source_name: Myoblast_Cell T72_CT_C


title: Cell T72_CT_D02


title: Cell T0_CT_E07


title: Cell T0_CT_D09


title: Cell T0_CT_D08


title: Cell T72_CT_C11


title: Cell T72_CT_C10


title: Cell T0_CT_D07


title: Cell T72_CT_C09


title: Cell T72_CT_D10


title: Cell T72_CT_C08


title: Cell T0_CT_D04


title: Cell T72_CT_C07


title: Cell T72_CT_C06


title: Cell T72_CT_C04


title: Cell T0_CT_D05


title: Cell T72_CT_C03


title: Cell T72_CT_C02


title: Cell T0_CT_D10


title: Cell T72_CT_C01


title: Cell T72_CT_B12

source_name: Myoblast_Cell T72_CT_B


title: Cell T0_CT_D01


title: Cell T0_CT_D03


title: Cell T72_CT_B11


title: Cell T0_CT_C10

source_name: Myoblast_Cell T0_CT_C


title: Cell T72_CT_B10


title: Cell T0_CT_D02


title: Cell T0_CT_C09


title: Cell T0_CT_C11


title: Cell T72_CT_B09


title: Cell T0_CT_C08


title: Cell T72_CT_B08


title: Cell T0_CT_C07


title: Cell T0_CT_D06


title: Cell T0_CT_C06


title: Cell T0_CT_C05


title: Cell T72_CT_B06


title: Cell T72_CT_A11

source_name: Myoblast_Cell T72_CT_A


title: Cell T72_CT_B07


title: Cell T0_CT_C04


title: Cell T72_CT_A06


title: Cell T0_CT_B12

source_name: Myoblast_Cell T0_CT_B


title: Cell T0_CT_B08


title: Cell T72_CT_B02


title: Cell T0_CT_C01


title: Cell T72_CT_B05


title: Cell T0_CT_B03


title: Cell T0_CT_C03


title: Cell T0_CT_C02


title: Cell T72_CT_B04


title: Cell T72_CT_B03


title: Cell T0_CT_A09

source_name: Myoblast_Cell T0_CT_A


title: Cell T72_CT_B01


title: Cell T72_CT_A10


title: Cell T0_CT_C12


title: Cell T0_CT_A08


title: Cell T72_CT_A09


title: Cell T0_CT_A06


title: Cell T0_CT_A05


title: Cell T72_CT_A08


title: Cell T0_CT_B07


title: Cell T0_CT_B06


title: Cell T0_CT_A04


title: Cell T0_CT_B05


title: Cell T72_CT_A05


title: Cell T72_CT_A02


title: Cell T0_CT_B04


title: Cell T72_CT_A01


title: Cell T0_CT_A02


title: Cell T0_CT_B11


title: Cell T0_CT_A01


title: Cell T0_CT_B10


title: Cell T0_CT_B09


title: Cell T72_CT_A07


title: FIREWACh_BioRep1_Hae_TechRepA

status: Public on Mar 22 2014

city: New York

first: Matthew

last: Murtha

address: 550 First Ave

department: Microbiology

institute: NYU School of Medicine

description:
NFR DNA selected by GFP expression and rescued from the integrated lentiviral reporter within gDNA by PCR
FIREWACh.bed

data_processing:
Illumina MiSeq 2x 151 bp data were pre-processed by demultiplexing and trimming of 7 bp from the 5' end and 44 bp from the 3' end, yielding a data set of 2 x 100 bp sequence reads.
Basecalls performed using Illumina's RTA software
Paired end sequences were aligned to the mouse reference genome (mm9) using BWA software with default settings.
Read pairs were filtered from the final data set if either read failed to map to the genome, if both reads did not map in the proper orientation, if the mapping quality score of both reads was less than 25, or if neither  read had a unique map location on the genome.  Target sites were identified as loci where paired reads both aligned entirely within a 500 bp genomic region.
Genome_build: mm9
Supplementary_files_format_and_content: .bed files containing the genomic loci of NFR elements within starting library (Library.bed) or elements rescued from sorted cells (FIREWACh.bed)

source_name: Mouse Embryonic Stem Cells

growth_protocol: E14ESCs were obtained from ATCC (ES-E14TG2a, CRL-1821) and were maintained in 2i/LIFwith the inhibitors CHIR99021 (3μM), and PD0325901 (1 μM) (Axon Medchem BV, The Netherlands) and 100 u/ml LIF in N2B27,or in standard ESC medium (DMEM supplemented with 15% FCS (Stem Cell Technologies,“ES cult”), 0.1mM non-essential amino acids, 0.1mM b mercaptoethanol, 1X Glutamax (Invitrogen), and 1000 u/ml LIFon plates coated with 0.2% Gelatin1. 3T3 were maintained in DMEM(Invitrogen), 15% Bovine Calf Serum and Penicillin/Streptomycin.

extract_protocol:
NFR-DNAs were rescued from either the initial lentiviral plasmid libraries or gDNA of GFP+ selected cells using PCR in a method adapted from bacterial rRNA sequencing7. In this method, Illumina sequencing adaptors are included in the primers, permitting one step amplification and sequencing library preparation. Primers (termed FMS-F/R,) were designed such that they contain recognition sequences complimentary to lentiviral sequence flanking NFR-DNA and Illumina adaptor sequence for paired-end sequencing in addition to a 6base pair Index sequence. Six PCR reactions (10 ul Phusion Polymerase buffer, 1 μl 10 mMdNTP, 2.5 μl 10 μM forward and reverse primer, 1.5 μl DMSO, 0.5 μl (NEB) 50 ng DNA, 31 μl H20; 16 cycles with 550C annealing temperature) per plasmid library were pooled and sequenced. FIREWACh elements were recovered from the genomic DNA of a least 1x106 FACS-sorted GFP+ cells using PCR. In this case 10 PCR reactions were performed using the same conditions as above but 100 ng gDNA and 23 cycles of amplification. The 10 reactions were then pooled.
Six PCR reactions (10 ul Phusion Polymerase buffer, 1 μl 10 mMdNTP, 2.5 μl 10 μM forward and reverse primer, 1.5 μl DMSO, 0.5 μl (NEB) 50 ng DNA, 31 μl H20; 16 cycles with 550C annealing temperature) per plasmid library were pooled and sequenced. Quality was assessed determining size distrubution with with bioanalyzer and concentration was confirmed via QPCR
Up to six samples were pooled within a single lane on a MiSeq machine. Input library derived NFRs were sequenced together using three of the indices while FIREWACh NFRS, i.e. NFR’s rescued from GFP+ cells, were run with six samples per lane, each sample representing NFRs rescued from an independent biological replicate (i.e. HaeIII_BioRep1 etc). Technical replicates consisting of independent PCR rescued NFR sequencing libraries were sequenced on separate days.

treatment_protocol: ESCs were transduced at a MOI of 7 (determined  by p24 ELISA) to ensure that the maximum number of cells is transduced while favoring single copy integration. To increase the likelihood that any given NFR-lentiviral genome would be represented, the number of cells transduced was equivalent to more than ten times each library’s complexity. Thus 5x106 E14 ESCs were plated in complete ESC medium plus LIF in feeder free conditions on a 10 cm gelatin coated dish one day prior to transduction. The cells were then transduced overnight in 10 ml of complete ESC medium plus 8 ug/ml polybrene, containing 3.5x107 virus particles for a MOI of 7. The following day the medium was replaced with fresh ESC medium plus LIF. Hygromycin-selection was initiated four days post transduction in ESC medium/LIF containing 250 ug/ml hygromycin B. Cells were selected for hygromycin B resistance for 5 days, with media changed daily. GFP+ cells were selected using fluorescence activated cell sorting (FACS) on a iCyt Reflection HAPS2 cell sorter.

tag: cell line

tag: passages

tag: tag


title: FIREWACh_BioRep1_Hae_TechRepB


title: FIREWACh_BioRep2_Hae_TechRepA


title: Cell T0_CT_B01

tag: cell type


title: Cell T0_CT_A12


title: Cell T0_CT_B02


title: Cell T0_CT_A11


title: FIREWACh_BioRep2_Hae_TechRepB


title: Cell T0_CT_A10


title: Cell T0_CT_A03


title: Cell T0_CT_A07


title: FIREWACh_BioRep1_Rsa_TechRepA


title: FIREWACh_BioRep1_Rsa_TechRepC


title: FIREWACh_BioRep1_Rsa_TechRepB


title: H3K27me3 ChIP-seq

city: Basel

first: Philip

middle: Martin

last: Jermann

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

data_processing:
Alignment against mm9 and wiggle file creation was performed using the qAlign (with default parameters) and qExportWig function (with shift=60, correspond to a fragment length of 120 nts) of the R package QuasR, version 1.2.2 (http://www.bioconductor.org/packages/release/bioc/html/QuasR.html)
Genome_build: mm9
Supplementary_files_format_and_content: Entries of the wiggle file correspond to the summed-up read counts in consecutive windows of length 100 nts.

source_name: DNMT triple knockout ESCs

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 102-1001). 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 (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~250 bp (insert plus adaptor sequences) were band isolated from an agarose gel. DNA was PCR amplified with Illumina primers for 18 cycles and. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: chip antibody

value: H3K27me3 (Millipore, 07-449)

value: ESCs


title: FIREWACh_BioRep1_Hae_TechRepC


title: FIREWACh_BioRep2_Hae_TechRepC


title: Esrrb ChIPseq, Oct3/4KO Day1

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description: On MEF feeders, with FGF4/heparin/Activin A

data_processing:
Basecalls performed using CASAVA version 1.8.2. Sequence reads were aligned to the mouse reference genome (mm9) using Bowtie2 with default parameters. Sequence reads overlapping with repetitive sequences were removed using BedTools and repeat region data from UCSC Genome Browse. Peak Calling was performed using MACS2 with input DNA as a control and with a q-value cutoff of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using MACS2. The signals were normalized by sequencing depth of million mapped reads with the --SPMR option.

source_name: ZHBTc4 ES cells, +Tet, Day 1

growth_protocol: ES cells were maintained in GMEM supplemented with 10% FBS and 1,000 U/ml LIF on MEF feeders.

extract_protocol:
Chromatin was enzymatically sheared into fragments with an average size of 300-500 bp using the ChIP-IT Express Enzymatic Kit (Active Motif).
Sequencing libraries were prepared from ChIP DNA according to the Illumina protocols. Briefly, ChP DNA was end-repaired, A-tailed, ligated to the adapters, size selected to 200-400 bp and amplified by 18 cycles of PCR. Libraries were sequenced on the Genome Analyzer Iix (Illumina) as single-end 50-bp reads.

treatment_protocol: TS cells were induced in GMEM/10% FBS supplemented with 1 ug/ml Tet, 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on MEF feeders.

tag: antibody

value: Esrrb (H6705, Perseus Proteomics)

tag: treatment

value: Tet

tag: time

value: 1 day


title: FIREWACh_BioRep2_Rsa_TechRepA


title: FIREWACh_BioRep2_Rsa_TechRepB


title: Background Populations for Library A & B [L001]

status: Public on Mar 21 2014

first: Panos

last: Oikonomou

state: New York

address: 1150 St. Nicholas Ave

department: Biological Sciences

institute: Columbia University

description:
processed data file: processed_C3U_LibraryA_L10_L20.csv
processed_C3U_LibraryB_L10_L20.csv
processed_C3U_LibraryA_L30_L40.csv
processed_C3U_LibraryB_L30_L40.csv
processed_C3U_LibraryA_H30_H40.csv
processed_C3U_LibraryB_H30_H40.csv
processed_C3U_LibraryA_H10_H20.csv
processed_C3U_LibraryB_H10_H20.csv
Ln1_Idx6_CTTGTAAT_L001_R1

data_processing:
library strategy: Over/under representation patterns for library sequences in every subpopulation
The 5' end of sequence reads was matched to one of the custom identifiers. Reads were trimmed for the universal adaptor sequences and matched to the C3U Library sequences.
Data from technical replicates and from adjacent bins were merged to increase read-counts in each group (L10 & L20; L30 & L40; H10 & H20; H30 & H40).
A frequency was calculated for every probe in every merged population and it was normalized to the frequency in the corresponding background population.
Genome_build: Custom C3U Library Sequences (34 nucleotide sequences that are listed in all the processed data files (first column is sequence ID,  second column is sequence).
Supplementary_files_format_and_content: comma-delimited text files include counts for every sequence in the C3U Library, counts in the background population and log2 normalized frequency.

source_name: FlpIn-293 C3U Library

growth_protocol: FlpIn 293 C3U Library cells were grown in D10F media and 50 μg/ml Hygromycin.

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen) from each subpopulation."
Libraries were prepared by PCR amplifying the cloned 3’UTR sequences from each subpopulation’s total DNA. Samples were multiplexed using standard Illumina adapters (TruSeq adapters 2, 4, 5, 6, 7, 9, 12).  Additionally we included 6 custom designed identifiers (ATCACG, TTAGGCG, ACTTGACG, GATCAGTAG, TAGCTTACAG, GGCTACGAGTG) at the 5’ end of the amplified sequences from each subpopulation, which were used to further multiplex but also to stagger the library sequences to achieve the necessary variability in the initial bases. Illumina Index CGATGTAT: Library A sub-populations L10 I & II (custom identifiers ATCACG, TTAGGCG); Library B sub-populations L10 I & II (custom identifiers ACTTGACG, GATCAGTAG); Library A sub-populations L20 I & II (custom identifiers TAGCTTACAG, GGCTACGAGTG). Illumina Index TGACCAAT: Library A sub-populations L30 (custom identifiers ATCACG, TTAGGCG); Library B sub-populations L30 (custom identifiers ACTTGACG, GATCAGTAG); Library B sub-populations L20 (custom identifiers TAGCTTACAG, GGCTACGAGTG). Illumina Index ACAGTGAT: Library A sub-populations L40 (custom identifiers ATCACG, TTAGGCG); Library B sub-populations L40 (custom identifiers ACTTGACG, GATCAGTAG); Library A sub-populations H40 (custom identifiers TAGCTTACAG, GGCTACGAGTG). Illumina Index GCCAATAT: Library A sub-populations H30 (custom identifiers ATCACG, TTAGGCG); Library B sub-populations H30 (custom identifiers ACTTGACG, GATCAGTAG); Library B sub-populations H40 (custom identifiers TAGCTTACAG, GGCTACGAGTG). Illumina Index CAGATCAT: Library B sub-populations H20 (custom identifiers TAGCTTACAG, GGCTACGAGTG). Illumina Index GATCAGAT: Library A sub-populations H10 (custom identifiers ATCACG, TTAGGCG); Library B sub-populations H10 (custom identifiers ACTTGACG, GATCAGTAG); Library A sub-populations H20 (custom identifiers TAGCTTACAG, GGCTACGAGTG). Illumina Index CTTGTAAT: Library A background populations (custom identifiers ATCACG, TTAGGCG); Library B background populations (custom identifiers ACTTGACG, GATCAGTAG).

tag: sample type

value: pooled FlpIn-293 C3U Library subpopulation

tag: molecule subtype

value: PCR from total genomic DNA


title: Esrrb ChIPseq, Oct3/4KO Day0

description: On MEF feeders, with LIF

source_name: ZHBTc4 ES cells, untreated

tag: strain

value: control

value: 0 day


title: Library A-H10 I & II; Library B-H10 I & II; Library A-H20 I & II [L002]

description:
processed data file: processed_C3U_LibraryA_H10_H20.csv
processed_C3U_LibraryB_H10_H20.csv
Ln2_Idx7_GATCAGAT_L002_R1


title: FIREWACh_BioRep2_Rsa_TechRepC


title: Library B-H20 I & II [L002]

description:
processed data file: processed_C3U_LibraryB_H10_H20.csv
Ln2_Idx5_CAGATCAT_L002_R1


title: Library_Rsa_Rep2

description:
nucleosome free genomic DNA isolated by HaeIII digest
Library.bed


title: Library_Hae_Rep1

description:
nucleosome free genomic DNA isolated by RsaI digest
Library.bed


title: Library_Hae_Rep2


title: Library_Rsa_Rep1


title: Esrrb ChIPseq, Oct3/4KO Day2

source_name: ZHBTc4 ES cells, +Tet, Day 2

value: 2 days


title: Library A-H30 I & II; Library B-H30 I & II; Library B-H40 I & II [L002]

description:
processed data file: processed_C3U_LibraryA_H30_H40.csv
processed_C3U_LibraryB_H30_H40.csv
Ln2_Idx4_GCCAATAT_L002_R1


title: Background Populations for Library A & B [L002]

description:
processed data file: processed_C3U_LibraryA_L10_L20.csv
processed_C3U_LibraryB_L10_L20.csv
processed_C3U_LibraryA_L30_L40.csv
processed_C3U_LibraryB_L30_L40.csv
processed_C3U_LibraryA_H30_H40.csv
processed_C3U_LibraryB_H30_H40.csv
processed_C3U_LibraryA_H10_H20.csv
processed_C3U_LibraryB_H10_H20.csv
Ln2_Idx6_CTTGTAAT_L002_R1


title: Library A-L10 I & II; Library B-L10 I & II; Library A-L20 I & II [L002]

description:
processed data file: processed_C3U_LibraryA_L10_L20.csv
processed_C3U_LibraryB_L10_L20.csv
Ln2_Idx1_CGATGTAT_L002_R1


title: Esrrb ChIPseq, Oct3/4KO Day4

source_name: ZHBTc4 ES cells, +Tet, Day 4

value: 4 days


title: Library A-H10 I & II; Library B-H10 I & II; Library A-H20 I & II [L001]

description:
processed data file: processed_C3U_LibraryA_H10_H20.csv
processed_C3U_LibraryB_H10_H20.csv
Ln1_Idx7_GATCAGAT_L001_R1


title: Esrrb ChIPseq, Oct3/4KO Day3

source_name: ZHBTc4 ES cells, +Tet, Day 3

value: 3 days


title: Library A-L40 I & II; Library B-L40 I & II; Library H-L40 I & II [L002]

description:
processed data file: processed_C3U_LibraryA_H30_H40.csv
processed_C3U_LibraryA_L30_L40.csv
processed_C3U_LibraryB_L30_L40.csv
Ln2_Idx3_ACAGTGAT_L002_R1


title: Library A-L30 I & II; Library B-L30 I & II; Library B-L20 I & II [L002]

description:
processed data file: processed_C3U_LibraryB_L10_L20.csv
processed_C3U_LibraryA_L30_L40.csv
processed_C3U_LibraryB_L30_L40.csv
Ln2_Idx2_TGACCAAT_L002_R1


title: Library A-H30 I & II; Library B-H30 I & II; Library B-H40 I & II [L001]

description:
processed data file: processed_C3U_LibraryA_H30_H40.csv
processed_C3U_LibraryB_H30_H40.csv
Ln1_Idx4_GCCAATAT_L001_R1


title: Library B-H20 I & II [L001]

description:
processed data file: processed_C3U_LibraryB_H10_H20.csv
Ln1_Idx5_CAGATCAT_L001_R1


title: Library A-L40 I & II; Library B-L40 I & II; Library A-H40 I & II [L001]

description:
processed data file: processed_C3U_LibraryA_H30_H40.csv
processed_C3U_LibraryA_L30_L40.csv
processed_C3U_LibraryB_L30_L40.csv
Ln1_Idx3_ACAGTGAT_L001_R1


title: Library A-L10 I & II; Library B-L10 I & II; Library A-L20 I & II [L001]

description:
processed data file: processed_C3U_LibraryA_L10_L20.csv
processed_C3U_LibraryB_L10_L20.csv
Ln1_Idx1_CGATGTAT_L001_R1


title: Library A-L30 I & II; Library B-L30 I & II; Library B-L20 I & II [L001]

description:
processed data file: processed_C3U_LibraryB_L10_L20.csv
processed_C3U_LibraryA_L30_L40.csv
processed_C3U_LibraryB_L30_L40.csv
Ln1_Idx2_TGACCAAT_L001_R1


title: V6.5_12.5minTRP_#2

city: Ithaca

first: Iris

middle: Helene

last: Jonkers

address: Biotechnology Building 417

department: Molecular Biology & Genetics

institute: Cornell University

description:
GRO-seq
V6.5_12.5minTRP_Plus.bedGraph
V6.5_12.5minTRP_Minus.bedGraph

data_processing:
All the GRO-seq libraries were sequenced in 50 nt runs on the Illumina HiSeq and split by barcode. Sequences that contained the Illumina adaptor were clipped with the cutadapt tool (https://code.google.com/p/cutadapt/) and remaining sequences were trimmed down to 32-mers, aligned to the ribosomal genome to remove rRNAs, and then aligned uniquely to the mm9 reference genome, with up to 2 mismatches with bowtie (http://bowtie-bio.sourceforge.net/index.shtml).  Replicates were highly correlated and were pooled for further analysis, with exception of one of the 25 min Trp-treated #1 replicate, which suffered from extensive RNA degradation during the library preparation, and was subsequently discarded. Spike-in RNA controls were aligned similarly to a spike-in reference genome.
Sequences that contained the Illumina adaptor were clipped with the cutadapt tool (https://code.google.com/p/cutadapt/) and remaining sequences were trimmed down to 32-mers,
32-Mers were aligned to the ribosomal genome to remove rRNAs, and then aligned uniquely to the mm9 reference genome, with up to 2 mismatches with bowtie (http://bowtie-bio.sourceforge.net/index.shtml).
Replicates were highly correlated and were pooled for further analysis, with exception of one of the 25 min Trp-treated #1 replicate, which suffered from extensive RNA degradation during the library preparation, and was subsequently discarded. Spike-in RNA controls were aligned similarly to a spike-in reference genome.
Instead of using total read counts to normalize between treatments within either the FP or Trp time course, we chose to normalize with the spike-in RNA read counts instead.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, nascent RNA read density of combined replicates, normalized to spike-in controls for each time course. Split by Plus and Minus strand

source_name: mouse embryonic stem cells

growth_protocol: Cell culturing of the V6.5 mES cell line was done as in (Monkhorst et al., 2008), and drug treatment was performed on pre-plated mES cells, grown for one passage before isolation of nuclei to remove irradiated MEF-feeder cells.

extract_protocol:
Nuclei isolation are performed using standard protocols, in brief, after rinsing the 15 cm2 plates with drug-treated cells, 15 ml cell lysis buffer (10 mM Tris-Cl, pH 7.5, 300 mM Sucrose, 3mM CaCl2, 2 mM MgAc2, 0.5% NP-40, 5 mM DTT, 1 mM PMSF, protease inhibitors) was added to the plates and the cells were scraped off, and spun down at 4°C and 185 xg for 5 min in a GS-6R Beckman swing-bucket centrifuge, after which supernatant was discarded. 5 ml fresh cell lysis buffer was added and cells were dounced 50 times in a 5 ml douncer on ice and spun down at 328 xg for 5 min, after which supernatant was discarded and nuclei were taken up in ~250 μl of glycerol storage buffer (50 mM Tris-Cl, pH 8.3, 40% glycerol, 0.1 mM EDTA, 5 mM MgAc2, 5 mM DTT, 1 mM PMSF, protease inhibitors) and snap frozen.
For each nuclear run-on (NRO), 1e7 nuclei were used. An NRO master mix was added containing nucleotides ATP, GTP, CTP and nucleotide analogue bromo-UTP, as well as sarkosyl and 300 mM KCl to remove all impediments that pause Pol II and prevent NRO and to prevent re-initiation of Pol II. The NRO was performed at 37°C for 5 min, which results in ~100 nt addition to the nascent RNA. Immediately after the NRO, a population of ~100 different in-vitro transcribed Arabidopsis thaliana spike-in RNAs with and without Br-UTP was added to the nascent RNA as a way to assess experimental differences between each library, and to use as a normalization tool between timepoints within each timecourse.  The nascent RNA was fragmented to ~150 nts and NRO BrU-RNA was isolated 3 consecutive times with BrdU-antibody beads (sc-32323, Santa Cruz), with enzymatic TAP and PNK treatments to remove the cap and 3’-phosphate and to add a 5’-phosphate, as well as Illumina adaptor ligations between the BrU-RNA isolation steps. The three consecutive isolation steps lead to an approximate 500.000x enrichment of BrU-RNA over background RNA. BrU-RNA was reverse transcribed, amplified, barcoded and sent for sequencing. Each dataset was done in replicate.

treatment_protocol: Cells were treated with 300nM flavopiridol for 2, 5, 12.5, 25 and 50 min, or with 500nM triptolide for 12.5, 25, and 50 min, or with 0.0125% DMSO for 50min.

value: treated 12.5min with 500nM triptolide

value: nascent RNA


title: V6.5_50minTRP_#2

description:
GRO-seq
V6.5_50minTRP_Plus.bedGraph
V6.5_50minTRP_Minus.bedGraph

value: treated 50min with 500nM triptolide


title: V6.5_12.5minTRP_#1


title: V6.5_50minTRP_#1


title: V6.5_25minTRP_#2

description:
GRO-seq
V6.5_25minTRP_Plus.bedGraph
V6.5_25minTRP_Minus.bedGraph

value: treated 25min with 500nM triptolide


title: V6.5_50minDMSO_#2

description:
GRO-seq
V6.5_DMSO_Plus.bedGraph
V6.5_DMSO_Minus.bedGraph

value: treated 50min with 0.0125% DMSO


title: V6.5_50minFP_#2

description:
GRO-seq
V6.5_50minFP_Plus.bedGraph
V6.5_50minFP_Minus.bedGraph

value: treated 50min with 300nM flavopiridol


title: V6.5_12.5minFP_#2

description:
GRO-seq
V6.5_12.5minFP_Plus.bedGraph
V6.5_12.5minFP_Minus.bedGraph

value: treated 12.5min with 300nM flavopiridol


title: V6.5_12.5minFP_#1


title: V6.5_50minDMSO_#1


title: V6.5_25minFP_#1

description:
GRO-seq
V6.5_25minFP_Plus.bedGraph
V6.5_25minFP_Minus.bedGraph

value: treated 25min with 300nM flavopiridol


title: V6.5_25minFP_#2


title: V6.5_50minFP_#1


title: V6.5_untreated_#2

description:
GRO-seq
V6.5_untreated_Plus.bedGraph
V6.5_untreated_Minus.bedGraph

value: untreated


title: V6.5_5minFP_#2

description:
GRO-seq
V6.5_5minFP_Plus.bedGraph
V6.5_5minFP_Minus.bedGraph

value: treated 5min with 300nM flavopiridol


title: V6.5_5minFP_#1


title: V6.5_2minFP_#2

description:
GRO-seq
V6.5_2minFP_Plus.bedGraph
V6.5_2minFP_Minus.bedGraph

value: treated 2min with 300nM flavopiridol


title: V6.5_untreated_#1


title: DMC. Biol. Replicate 1

status: Public on Mar 20 2014

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

data_processing:
Reads were de-multiplexed. Sequence reads were then mapped against the L. interrogans Copenhageni FIOCRUZ L1-130 reference genome using Segemehl with accuracy set to 100%. To increase mapping quality, unmapped reads were sequentially truncated by one nucleotide from the end of the read and were mapped again. This process was iterated until a minimal read length of 20 nucleotides or until a read mapped into a single location on the chromosome.
Genome_build: RefSeq Genome Accession: PRJNA58065, PRJNA10687 ID: 58065. Leptospira interrogans serovar Copenhageni str. FIOCRUZ L1-130. Nascimento AL et al., "Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis.", J Bacteriol, 2004 Apr;186(7):2164-72.
Supplementary_files_format_and_content: .gr files are provided showing uniquely mapped sequence reads (without normalization). Ready to load into Integrated Genome Browser (IGB). The file consists of two columns showing nucleotide position on the chromosome and number of reads mapped at each location. "Plus" and "Minus" refer to the two strands of the Leptospira chromosome

organism: Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130

source_name: RNA from bacteria

growth_protocol: Virulent low-passage Leptospira interrogans sv. Copenhageni strain Fiocruz L1-130 was cultivated in vitro under standard conditions at 30C in EMJH medium supplemented with 1% rabbit serum (Pel-514 Freez Biologicals, Rogers, AR) with 100 μg/ml 5-fluorouracil. To obtain L. interrogans in a mammalian host-adapted state, leptospires were cultivated in dialysis membrane chambers (DMCs). Briefly, DMCs were constructed using standard dialysis membrane tubing (Spectra-Por; 8000 MW cut-off). Prior to use, 8-inch strips of dialysis tubing were tied off at one end and then sterilized by boiling for 20 min in sterile water containing 5 mM EDTA, followed by two successive boiling washes in water alone. Dialysis bags were cooled to room temperature and then filled with ~8-9 mls of EMJH medium (supplemented with 10% vaccine-grade bovine serum albumin to maintain osmotic pressure) containing 10^4 organisms per ml. Once filled, the tubing was tied and excess membrane removed from both ends. For implantation, female Sprague-Dawley rats (150-174 g) were anesthetized by intramuscular injection of a mixture of ketamine (50 mg/kg), xylazine (5 mg/kg), and acepromazine (1 mg/kg). Using strict aseptic technique, a DMC was implanted into the peritoneal cavity of each rat. Analgesia (carprofen; 5 mg/kg) was administered on the day of surgery and once the following day. At designated time points (typically 9-10 days postimplantation), rats were euthanized by CO2 narcosis and DMCs recovered. The contents of each chamber were removed by gentle syringe aspiration with an 18G needle; the needle was removed prior to expelling the DMC dialysate into a sterile 15 ml conical bottom tube. Bacteria were enumerated by dark field microscopy immediately following explant using a Petroff-Hausser counting chamber (Hausser Scientific Co., Horsham, PA).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and digested with DNase I
One hundred ng of total RNA was used for library generation according to Illumina standard protocols (TruSeq RNA Sample Preparation Guide, Low-Throughput Protocol, Part # 15008136 Rev. A). cDNAs were normalized using a duplex-specific nuclease (DSN) approach according to the DSN Normalization Sample Preparation Guide, Early Access Protocol, Part # 15014673 Rev. C, which decreases the prevalence of highly abundant transcripts, such as rRNAs.

value: FIOCRUZ L1-130

value: dialysis membrane chamber


title: DMC. Biol. Replicate 2


title: SB2_ethanol_BR3

city: Ann Arbor

first: Alexey

last: Vorobev

address: 2350 Hayward Street

institute: University of Michigan

description:
Bacterial RNA
Methylocystis strain SB2

data_processing:
The reads were trimmed using Sickle (version 1.100, https://github.com/ucdavis-bioinformatics/sickle.git) with default parameters
The reads were then aligned to the assembled genome using the Burrows-Wheeler alignment tool (BWA) version 0.6.2 (Li and Durbin, 2009), using default parameters for small genomes.
Sequence Alignment/Map (SAM) files, obtained from BWA, were converted to binary SAM (BAM) files and subsequently sorted and indexed using SAMtools 0.1.17 (Li et al., 2009).
The number of fragments was calculated using a protocol described in Haas et., 2012. Properly mapped paired reads were counted as a single fragment. If one of the paired reads was not properly mapped, it was discarded and the remaining unpaired reads were treated as independent fragments.
Sorted and indexed BAM files were analyzed by Cufflinks 2.0.2 (Trapnell et al., 2010) which detected the differentially expressed genes by calculating the number of fragments per kilobase of transcript per million mapped reads (FPKM) for all genes. A negative binomial model estimated from the data was used to obtain variance estimates from which p-values were computed. These p-values were used to determine if the differential expression of each individual transcript was statistically significant as described previously Trapnell et al., 2012).
Cufflinks output files were analyzed using CummeRbund (Goff et al., 2012), which was also used to estimate the variance between replicates within both methane- and ethanol-grown cultures
Genome_build = AYNA00000000 (Methylocystis strain SB2)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all samples (see supplementary files linked to Series record).

organism: Methylocystis sp. SB2

growth_protocol: Methylocystis strain SB2 was grown to the late-exponential phase on nitrate mineral salts (NMS) medium (Whittenbury et al. 1970) with 10 µM of copper added as CuSO4.  Fifty ml cultures were grown in 250 ml Erlenmeyer flasks at 300C with rotation at 225 rpm in the presence of 0.1% (v/v) ethanol as a carbon source or in a methane-to-air ratio of 1:2.

extract_protocol:
RNA was extracted from cultures grown with either methane or ethanol as the sole growth substrate.  Cultures were collected in the late-exponential phase by centrifugation at 4500 x g for 10 min at 4ºC. Cell pellets were re-suspended in 0.75 ml of RNA extraction buffer (0.2 M NaH2PO4/Na2HPO4 buffer, pH 7.5; 5% CTAB in 2.4 M NaCl). The resuspended cell pellets were subjected to bead-beating (1 min at 4800 rpm) in 2 ml plastic tubes containing 0.5 g of 0.1 mm zirconia-silica beads (Biospec Products), 35 µl of SDS 20%, 35 µl of laurylsarcosine 20% and 750 µl of phenol:chloroform:isoamylic alcohol (25:24:1). The samples were then centrifuged at 14000 rpm for 5 min at 4ºC. The aqueous phase was mixed with an equal volume of chloroform:isoamylic alcohol (24:1) and centrifuged at 14000 rpm for 5 min at 4ºC. RNA was precipitated by adding MgCl2 (final concentration, 2.5 mM), 0.1 volume of 3 M sodium acetate and 0.7 volume of isopropanol and incubating overnight at -80 ºC. RNA was then recovered by centrifugation at 14000 rpm for 30 min at 4ºC. The DNase treatment was carried out using the RNase free DNase set (Qiagen) in accordance with the manufacturer’s instructions. The RNA samples were further purified using the RNeasy Plus Kit (Qiagen) using gDNA eliminator columns and RNeasy Mini Spin columns according to manufacturer’s instructions. The rRNA content was reduced using a MICROBExpress Bacterial mRNA purification kit (Ambion). To check for any DNA contamination, PCR was performed with extracted RNA as template. RNA was reverse transcribed to obtain cDNA by using Superscript III Reverse Transcriptase (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using TruSeq mRNA preparation kit

tag: taxonomy

value: Alphaproteobacteria

tag: metabolism

value: Facultative methanotroph

tag: growth protocol

value: ethanol


title: DMC. Biol. Replicate 3


title: SB2_methane_BR2

description:
Bacterial RNA
Methylocystis strain SB2

value: methane


title: SB2_ethanol_BR1

description:
Bacterial RNA
Methylocystis strain SB2


title: SB2_methane_BR1

description:
Bacterial RNA
Methylocystis strain SB2


title: SB2_methane_BR3

description:
Bacterial RNA
Methylocystis strain SB2


title: 30oC. Biol. Replicate 2

value: 30 C in EMJH


title: SB2_ethanol_BR2

description:
Bacterial RNA
Methylocystis strain SB2