title: hESC_derived_liverprogenitors_RNAseq replicate 2

description:
FGC0186_s_8
liver_day8_2


title: Sox9_ChIPSeq

status: Public on Aug 07 2015

type: SRA

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

country: USA

institute: UC San Diego

library_source: genomic

data_processing:
Fastq files were mapped to hg18 genome using Bowtie2 version 2.1.0
SAM files were processed using HOMER into Tag directories
Peaks were called using HOMER tag directories and normalized using the input file
Genome_build: hg18
Supplementary_files_format_and_content: peak calls using HOMER

molecule: genomic DNA

organism: Homo sapiens

source_name: Pancreatic progenitor cells

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012).

extract_protocol:
Chromatin immunoprecipitations were performed as previously described (Bhandare et al., 2010). Briefly, samples were crosslinked in 1.1% formaldehyde/PBS for 15 min at room temperature and then quenched with 0.125M glycine/PBS. Samples were subsequently washed twice with PBS and then lysed in 1% SDS. For sonication, lysates were sonicated with a Bioruptor Sonicator (Diagenode) six times for 5 min each with a 30 sec on and off cycle, resulting in 200-500bp chromatin fragments. Sheared chromatin was incubated overnight at 4 °C with 5 µg rabbit anti-SOX9 antibody (Millipore, AB5535; Lot number 2262679). Chromatin and antibody complex was incubated with 12.5 µl of Dynabeads protein A plus 12.5 µl of Dynabeads protein G (Life Technologies) at 4 °C for 4 hrs. Immunoprecipitated complexes were further eluted, reverse crosslinked, and subjected to library preparation.
ChIP-seq libraries were prepared as per Illumina’s instructions (http://www.illumina.com). For input library preparation, 50 ng of input DNA from each sample was used. After adaptor ligation, DNA fragments were size-fractionated by gel electrophoresis and excised at 200±25 bp. Following gel purification, DNA fragments were amplified with 18 PCR cycles and purified using a MiniElute PCR Purification kit (Qiagen). 10 nM purified DNA was loaded on the flow cell, and sequencing was performed on an Illumina/Solexa Genome Analyzer II in accordance with the manufacturer’s protocols.

tag: cell line

tag: source cell type

value: human embryonic stem cells

tag: cell type

value: hESC-derived pancreatic progenitor cells

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: LNA-54

city: Chapel Hill

first: Praveen

last: Sethupathy

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Chapel Hill

library_source: transcriptomic

data_processing:
Mapsplice alignment to genome
Gene expression analysis using RSEM
Genome_build: mm9

molecule: total RNA

organism: Mus musculus

source_name: liver, 20mg/kg LNA29a, 20mg/kg LNA29bc

extract_protocol: Livers were removed and flash frozen in liquid nitrogen. RNA was extracted with the Norgen Total RNA Purification kit.

treatment_protocol: mice were dosed iv tail vein with 20mg/kg LNA29a and 20mg/kg LNA29bc. Seven days later, the mice were fasted overnight and euthanized by cervical dislocation without anesthesia; organs were collected and flash frozen in liquid nitrogen.

tag: strain

tag: Sex

value: female


title: Rec8-HA red1∆, 4h in SPM

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

country: Austria

institute: University of Vienna, MFPL

data_processing:
Standard Illumina software was used for basecalling.
We used NextGenMap 0.4.12  (http://cibiv.github.com/NextGenMap) for fast and sensitive alignment to the yeast genome version R64-1-1.
Read depth per position was generated in Java, dividing each hit by the number of genome-wide matches in case of multi-mapping reads.  All mapped reads (36bp) were extended to 250bp, to reflect average fragment size.
All subsequent analyses were performed using R (version 2.15.2). After summing up the read depth of both strands, positions not corresponding to any reads were assigned zeros, followed by smoothing with ksmooth (Nadaraja-Watson kernel) with bandwidth 100 and a resolution of 20bp.
Samples were normalized relative to their negative control (untagged) using NCIS, and the negative control was subtracted from the ChIP files.
Genome_build: S288C, R64-1-1
Supplementary_files_format_and_content: Processed data files are tab separated text files, consisting of 5 columns with headers (mmr in the filenames indicates rounded Million Mapped Reads): 1:Cromosome(1-16), 2:Position(steps of 20), 3:negative control (untagged, smoothed bw=100), 4:ChIP(smoothed bw=100, NCIS normalized), 5:normalized ChIP(negative control subtracted, smoothed bw=100, NCIS normalized)

organism: Saccharomyces cerevisiae SK1

source_name: meiotic cells

growth_protocol: For synchronous sporulation in liquid culture, strains were grown at 30°C overnight in SPS pre-sporulation media (0.5% Difco yeast extract, 1% Difco peptone, 0.17% Difco yeast nitrogen base w/o AA&AS, 1% potassium acetate, 0.5% ammonium sulphate, 0.05 M potassium-biphthalate, pH 5.5) to an OD660 of 1.1-1.3 (4x10^7 cells/ml). Meiosis was induced by a subsequent wash and transfer of the cells into pre-warmed supplemented SPM (1% potassium acetate, 0.001% PPG2000, 4 mg/L Ura, 4 mg/L Trp, 4 mg/L His, 4 mg/L Arg, 6 mg/L Leu) at equal volume. Maximum aeration was provided for efficient meiosis.

extract_protocol:
ChIP from meiotic cultures was performed as described by Panizza (2011). In brief, 2x10^9 cells were collected per time point and incubated with para-formaldehyde (1% final concentration) for 15 minutes at 25°C. Cross-linking was stopped by addition of glycine to 131 mM. 2x10^9 cells were divided into 8 aliquots and separately opened using a multibead shocker (YASUI-KIKAI, Osaka) at 2,500 rpm, 15 cycles of 30 sec on and 30 sec off, at 4°C. Extracts were sonicated to an average of 200bp by a Covaris S2 instrument. After removing the cell debris, the supernatant was used for the chromatin immunoprecipitation. For each sample, 50 μl Dynabeads® Pan Mouse IgG (invitrogen) were incubated with the 12CA5 anti-HA (mouse) antibody or anti-V5 (mouse) antibody for 6–15 hr at 4°C. The precipitated DNA was used as a template for quantitative real-time PCR using GoTaq qPCR Master Mix for SYBR assay (Promega) (primer sequences are available upon request).   For genome-wide analysis (ChIP-seq), one-tenth of the ChIP DNA was analyzed by real-time PCR (qChIP) while the remaining DNA was concentrated by precipitation in ethanol.
For the preparation of libraries for Illumina sequencing, we strictly followed the protocols provided by Illumina (Illumina ChIP-seq DNA sample prep protocol). Briefly, DNA-ends were repaired to convert overhangs to phosphorylated blunt ends with T4 DNA polymerase, E. coli DNA Pol I (Klenow fragment), and T4 polynucleotide kinase (PNK). An ‘A’ nucleotide was added to the 3' end of the blunt ended fragments using Klenow fragment (3' to 5' exo minus). This prepared the DNA fragments for ligation to the adapters (Truseq Adaptors) which have a single ‘T’ base overhang at their 3' ends. After ligation, excess adaptors were removed by selecting a certain size range from 200-500bp with QIAquick Gel Extraction Kit (Qiagen). Purified templates were PCR amplified with 15-18 cycles by KAPA-HiFi Hot Start PCR Kit (KAPA biosystems). Before hybridization to the flow cell, the amount and the size of the DNA library was controlled to be at least 10ng/ul (for an average fragment size of 300bp).

tag: protein

tag: antibody

value: 12CA5, monocolonal mouse anti-HA

tag: time in spm

value: 4 hours

tag: mutant background

value: FK4396,  MAT a/alpha ho::LYS2/=, REC8-HA3::URA3/=, red1::LEU/=, leu2::hisG/=, lys2/=, trp1::hisG/=, ura3/=,


title: Sox9_ChIPSeq_input


title: human_fetal_panc_54to57dpc_RNAseq replicate 1

data_processing:
Quality Control. Quality of sequencing data is analyzed using the software FastQC v0.10.1. The results are examined to determine if samples are of questionable quality on an array of metrics.
Mapping. Alignment of sequencing data to reference genomes is performed with the software RNA-Star 2.3.0e. Parameters are set to default and reads are mapped to references along with splice junction databases.
Gene Expression Quantification. To obtain gene expression values, several quantification methods are used (Sailfish 0.6.3, Cufflinks 2.2.0). Expression values are calculated for entries in the gene annotation references.
Genome_build: hg19
Supplementary_files_format_and_content: Txt file of ensemble identifiers with RPKMs of samples used in study

source_name: Human fetal pancreata

growth_protocol: Human embryonic pancreata at day 54 to 57 of gestation were from the University of Washington Birth Defects Research Laboratory.

extract_protocol:
Human embryonic pancreata were lysed in Trizol (Life Technologies) for extraction of total RNA. Residual contaminating genomic DNA was removed using the Turbo DNase kit (Ambion). mRNA was isolated from 2 μg of DNA-free total RNA using the Dynabeads mRNA Purification kit (Life Technologies).
Strand-specific RNA-seq libraries were prepared as previously described (Parkhomchuk et al., 2009), with minor modifications. Briefly, following RNA purification, mRNA was primed with Olig(dT)s and random hexamers and reverse-transcribed to first-strand cDNA. Residual dNTPs were removed using Illustra MicroSpin G-25 columns (GE Healthcare). In the second-strand synthesis reaction, dUTPs were used instead of dTTPs. The double-strand cDNA was fragmented using a Bioruptor Sonicator for 60 cycles of 30 sec on and off. After end-repair and adenine base addition, the cleaved double-strand cDNA fragments were ligated to Pair-end Adaptor Oligo Mix (Illumina) and size-fractionated on a 2% agarose gel (Sigma). cDNA fragments of 200±25 bp were recovered, and incubated with uracil-N-glycosylase (UNG) to digest the second-strand cDNA. Purified single-strand cDNA was then used as template for 15 cycles of amplification using pair-end PCR primers (Illumina). The amplified products were separated on a 2% agarose gel and a band between 225-275 bp excised.

tag: developmental stage

value: fetus

tag: age

value: 54-57 days post conception (gestation)

tag: tissue

value: pancreas


title: HA untagged, 4h in SPM

value: wild type

value: FK1, MAT a/alpha, HO


title: V5 untagged, 4h in SPM

value: SV5 Pk, monocolonal mouse anti-V5


title: V5-Red1 hop1∆rec8∆, 4h in SPM

value: hop1delta rec8delta

value: FK4815, MAT a/alpha ho::LYS2/+, ho::hisG/+, V5-RED1::hphMX4/=, hop1::LEU2/=, rec8delta::kanMX4/=, ura3/=,  lys2/=,leu2::hisG/=, arg4-Bgl2/+


title: V5-Red1, 4h in SPM

value: FK3870, MAT a/alpha  ho:hisG/=, V5-RED1::hphMX4/=, ura3/=, leu2::hisG/=, lys2/=


title: Rec8-HA, 4h in SPM

value: FK1091, MAT a/alpha ho::LYS2/=, REC8-HA3::URA3/=,  leu2::hisG/=, lys2/=, trp1::hisG/=, ura3/=,


title: LNA-44


title: wt 51

source_name: liver, saline

treatment_protocol: mice were dosed iv tail vein with saline. Seven days later, the mice were fasted overnight and euthanized by cervical dislocation without anesthesia; organs were collected and flash frozen in liquid nitrogen.


title: 1024_wk-3_TGACCA_L004

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

data_processing:
Basecalls and sample de-multiplexing performed by CASAVA
Sequenced reads were quality check with fastqc default parameters and then mapped against the revised woodchuck transcriptome with Bowtie2 and prioritized for concordant paired alignments with unique hits.
The resulting SAM/BAM files were processed with SAMtools to yield count data that was normalized and processed by DESeq
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, the number of reads mapping to transcripts were counted and normalized by the size of the longest transcript of a gene and by the size of the library.
Genome_build: In-house woodchuck transcriptome assembly
Supplementary_files_format_and_content: tab-delimited text files include RPKM and read count values for each sample

organism: Marmota monax

extract_protocol:
Sequencing libraries were created using Illumina’s TruSeqTM RNA sample preparation kit (San Diego, CA) according to manufacturer’s protocol. Total RNA was purified using oligo dT magnetic beads, fragmented, and reverse-transcribed using SuperScript II (Invitrogen, Inc., Carlsbad, CA) to synthesize first strand cDNA. After second strand synthesis, Illumina specific adapters containing unique barcodes were ligated to the ends of the double-stranded cDNA. Fragments containing adapters on both ends were then enriched and amplified with PCR, quantified with qPCR, and run on the Agilent Bioanalyzer DNA-1000 chip to estimate fragment size. Samples were then multiplexed and sequenced on the Illumina 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: chronic woodchuck hepatitis virus (WHV)

value: Liver

tag: individual name

tag: gender

value: Female

tag: agent

value: Placebo

tag: time point [week]


title: 1024_wk12_CTTGTA_L007


title: 1024_wk4_ACAGTG_L004


title: 1024_wk12_CTTGTA_L003


title: 1024_wk1_CAGATC_L004


title: 1023_wk-3_AGTTCC_L008

value: IFN-alpha


title: 1024_FoundDead_AGTTCC_L005

value: Died


title: 1023_wk-3_AGTTCC_L007


title: 1023_wk1_GTCCGC_L006


title: 1023_wk1_GTCCGC_L003


title: 1022_wk20_GCCAAT_L004


title: 1022_wk24T_CCGTCC_L008


title: 1022_wk16_CCGTCC_L004


title: 1022_wk20_TGACCA_L007


title: V5-Red1 hop1∆, 4h in SPM

value: 4 hours

value: hop1 delta

value: FK4833, MAT a/alpha ho::LYS2/+,ho:hisG/+, V5-RED1::hphMX4/=, hop1::LEU2/=, ura3/=,  lys2/= ,leu2::hisG/=, trp1::hisG/=


title: 1022_wk4_TGACCA_L006


title: 1021_wk8_GTCCGC_L006


title: 1021_wk24T_ATGTCA_L006


title: 1022_wk12_ATGTCA_L008


title: 1022_wk12_ATGTCA_L006


title: 1021_wk-3_CCGTCC_L006


title: 1022_wk1_GCCAAT_L004


title: 1022_wk-3_ACAGTG_L004


title: 1024_wk8_AGTTCC_L003


title: 1021_wk16_AGTTCC_L006


title: 1021_wk8_GTCCGC_L007


title: 1021_wk12_ATGTCA_L005


title: 1021_wk1_AGTTCC_L007


title: 1020_wk16_ACAGTG_L003


title: 1020_wk12_CTTGTA_L005


title: 1020_wk-3_CAGATC_L002


title: 1020_wk-3_CAGATC_L007


title: 1023_Died_TGACCA_L005


title: 1020_wk12_CTTGTA_L007


title: 1022_wk8_ACAGTG_L006


title: 1020_wk4_AGTTCC_L005


title: 1020_wk1_CAGATC_L004


title: 1021_wk4_CGATGT_L003


title: 1019_wk24T_CAGATC_L005


title: 1019_wk-3_AGTCAA_L005


title: 1019_wk4_CCGTCC_L006


title: 1020_wk8_GTCCGC_L003


title: 1018_wk4_GTCCGC_L007


title: 1019_wk24T_CAGATC_L008


title: 1019_wk16_GCCAAT_L007


title: 1018_wk8_ACAGTG_L004


title: 1018_wk8_ACAGTG_L003


title: 1018_wk8_ACAGTG_L005


title: 1019_wk20_TGACCA_L006


title: 1019_wk8_ATGTCA_L008


title: 1019_wk12_AGTTCC_L008


title: 1018_wk-3_ATGTCA_L003


title: 1018_wk20_GTGAAA_L003


title: 1019_wk1_AGTCAA_L003


title: 1018_wk20_GTGAAA_L006


title: 1020_Died_GCCAAT_L002


title: 1018_wk4_GTCCGC_L004


title: 1018_wk16_CGATGT_L007


title: 1018_wk24T_GCCAAT_L004


title: 1018_wk16_CGATGT_L006


title: 1017_wk8_CTTGTA_L005


title: 1017_wk4_AGTTCC_L004


title: 1018_wk12_ATGTCA_L003


title: 1017_wk-3_CGATGT_L006


title: 1018_wk1_ACAGTG_L007


title: 1017_wk16_CAGATC_L002


title: 1017_wk12_AGTTCC_L004


title: 1017_Euthwk18_CCGTCC_L007


title: 1017_wk1_AGTCAA_L006


title: 1016_wk4_GTGAAA_L005


title: 1016_wk-3_CCGTCC_L008


title: 1016_wk1_CAGATC_L005


title: 1015_wk-3_GTGAAA_L005


title: 1015_wk16_GTGAAA_L004


title: 1016_wk12_GTGAAA_L007


title: 1015_wk4_GTGAAA_L004


title: 1015_wk8_AGTCAA_L004


title: 1016_wk20_GCCAAT_L006


title: 1015_wk24T_CCGTCC_L003


title: 1014_wk8_CCGTCC_L007


title: 1015_wk12_CTTGTA_L004


title: 1014_wk24T_ACAGTG_L008


title: 1014_wk24T_ACAGTG_L003


title: 1014_wk8_CCGTCC_L008


title: 1015_wk1_GCCAAT_L005


title: 1014_wk20_GTCCGC_L007


title: 1014_wk16_CCGTCC_L007


title: 1014_wk4_CAGATC_L006


title: 1014_wk20_GTCCGC_L006


title: 1014_wk12_GTCCGC_L008


title: 1014_wk-3_CGATGT_L006


title: 1016_wk8_TGACCA_L002


title: 1016_wk16_AGTCAA_L008


title: 1016_wk24T_ATGTCA_L007


title: 1018_wk1_ACAGTG_L003


title: 1013_wk8_AGTCAA_L004


title: 1013_wk-3_CTTGTA_L004


title: 1013_wk4_CGATGT_L002


title: 1013_wk24T_GTGAAA_L006


title: 1013_wk20_AGTCAA_L008


title: 1013_wk1_GTCCGC_L005


title: 1013_wk24T_GTGAAA_L008


title: 1013_wk12_TGACCA_L002


title: 1012_wk-3_CGATGT_L003

value: Male


title: 1013_wk20_AGTCAA_L007


title: 1012_wk8_ACAGTG_L006


title: 1013_wk16_ATGTCA_L004


title: 1014_wk1_GTCCGC_L003


title: 1012_wk24T_GTGAAA_L006


title: 1012_wk4_ACAGTG_L002


title: 1011_wk8_CTTGTA_L007


title: 1012_wk16_ACAGTG_L007


title: 1012_wk24T_GTGAAA_L007


title: 1012_wk1_ACAGTG_L007


title: 1012_wk12_CAGATC_L006


title: 1011_wk24T_GTCCGC_L005


title: 1011_wk-3_GTGAAA_L007


title: 1012_wk1_ACAGTG_L002


title: 1011_wk4_TGACCA_L004


title: 1011_wk16_CTTGTA_L006


title: 1011_wk20_GCCAAT_L006


title: 1011_wk1_CGATGT_L004


title: 1011_wk12_GCCAAT_L003


title: 1010_wk8_CGATGT_L008


title: 1010_wk8_CGATGT_L007


title: 1010_wk-3_AGTCAA_L005


title: 1009_wk8_CTTGTA_L003


title: 1010_Euth_wk18_CAGATC_L003


title: 1009_wk4_AGTTCC_L003


title: 1009_wk24T_CAGATC_L003


title: 1010_wk4_TGACCA_L003


title: 1011_wk8_CTTGTA_L005


title: 1012_wk20_CCGTCC_L005


title: 1009_wk-3_GTCCGC_L004


title: 1008_wk4_Replicate_1_CAGATC_L002


title: 1008_wk4_Replicate_2_GTCCGC_L008


title: 1008_wk8_CAGATC_L007


title: 1008_wk24T_Replicate_1_CGATGT_L002


title: 1008_wk24T_Replicate_2_AGTCAA_L008


title: 1008_wk-3_CGATGT_L005


title: 1008_wk20_GCCAAT_L003


title: 1008_wk1_Replicate_2_ATGTCA_L008


title: 1008_wk16_TGACCA_L005


title: 1008_wk12_ACAGTG_L003


title: 1008_wk12_ACAGTG_L007


title: 1008_wk1_Replicate_1_ACAGTG_L002


title: 1007_wk8_GCCAAT_L002


title: 1010_wk1_CGATGT_L002


title: 1009_wk24T_CAGATC_L007


title: 1007_wk-3_CGATGT_L004


title: 1006_wk-3_AGTCAA_L008


title: 1006_wk3_TGACCA_L007


title: 1007_Died_GCCAAT_L005


title: 1007_wk4_TGACCA_L003


title: 1007_wk1_CGATGT_L005


title: 1006_wk-3_AGTCAA_L007


title: 1009_wk1_CGATGT_L005


title: 1008_wk16_TGACCA_L003


title: 1005_wk4_CTTGTA_L006


title: 1005_wk4_CTTGTA_L003


title: 1005_wk-3_GTCCGC_L005


title: 1005_wk24T_AGTCAA_L006


title: 1005_wk20_ACAGTG_L005


title: 1005_wk8_AGTCAA_L003


title: 1005_wk16_ATGTCA_L007


title: 1005_wk16_ATGTCA_L004


title: 1005_wk1_CCGTCC_L004


title: 1004_wk12_GCCAAT_L007


title: 1005_wk12_GCCAAT_L008


title: 1004_wk1_ATGTCA_L007


title: 1005_wk12_GCCAAT_L003


title: 1004_wk20_GTCCGC_L008


title: 1006_wk1_TGACCA_L005


title: 1004_wk8_AGTTCC_L006


title: 1004_wk-3_GTGAAA_L005


title: 1003_wk8_ATGTCA_L004


title: 1004_wk16_CCGTCC_L005


title: 1003_wk4_GCCAAT_L005


title: 1004_wk1_ATGTCA_L005


title: 1003_wk12_AGTTCC_L006


title: 1003_wk16_CAGATC_L005


title: 1003_wk-3_AGTCAA_L004


title: 1003_wk12_AGTTCC_L004


title: 1003_wk24T_CCGTCC_L006


title: 1003_wk20_TGACCA_L007


title: 1003_wk1_CAGATC_L007


title: 1002_wk-3_Replicate_2_AGTTCC_L008


title: 1002_wk8_CGATGT_L003


title: 1004_wk4_ATGTCA_L008


title: 1003_wk1_CAGATC_L003


title: 1002_wk4_GTCCGC_L006


title: 1002_wk-3_Replicate_1_TGACCA_L002


title: 1002_wk1_AGTTCC_L006


title: 1001_wk4_CCGTCC_L004


title: 1002_wk16_Replicate_1_GCCAAT_L002


title: 1001_wk8_ACAGTG_L005


title: WT + 2µ-URA3-PDE2 without mtDNA_0

city: Sariyer

first: Cory

middle: David

last: Dunn

state: Istanbul

address: Rumelifeneri Yolu

department: Molecular Biology and Genetics

country: Turkey

institute: Koç University

description:
b89rhominus 0
[Paired end files] P25 / median / P75: 121 / 153 / 197

data_processing:
Illumina data processing pipeline (v1.5)
fastq_groomer on FASTQ files (Galaxy Tool Version 1.0.4)
TopHat 2.0.14 on groomed FASTQ files (Galaxy tool version 0.9) with settings: paired-end data; Mean Inner Distance between Mate Pairs: 300; Std. Dev for Distance between Mate Pairs: 50; Report discordant pair alignments: Yes; Reference Genome from History: S288C R64-2-1; TopHat settings to use: preSet; Specify read group: no; job resource parameters: no.
Cuffdiff 2.2.1.1 (Galaxy Tool Version 2.2.1.1) with settings: Transcripts: gffread on Reference Genome R64-2-1.gff; Library normalization method: geometric; Dispersion estimation method: per-condition; False Discovery Rate: 0.05; Min Alignment Count: 10; Use multi-read correct: True; Perform Bias Correction: Yes, using R64-2-1 sequence FASTA file; Include Read Group Datasets: No; Include Count Based output files: Yes; apply length correction: cufflinks effective length correction; Set Additional Parameters for single end reads: No; Set Advanced Cuffdiff parameters: No; Job Resource Parameters: No.
SQLiteExport to extract data from the cummeRbund SQLite database produced by Cuffdiff
Qualimap 2.1.1 on BAM files to determine P25 / median / P75.  PicardInsertSize Galaxy Tool Version 1.56 (beta) to determine average insert size and standard deviation, with settings:  Deviations: 10.0; Histogram width: 0; Minimum percentage: 0.05, Metric Accumulation Level: All reads (default)
Genome_build: R64-2-1
Supplementary_files_format_and_content: "Akdogan_Expression_Across_Samples_JUL232015.xlsx" contains normalized FPKM reads produced from Cuffdiff analysis of both replicates of each sample.  "Akdogan_RNASeq_Cuffdiff_JUL232015.xlsx" contains Cuffdiff output.

organism: Saccharomyces cerevisiae

source_name: BY4743 cells

growth_protocol: BY4743 cells (CDD3) were transformed with the indicated plasmids and cultured in synthetic complete medium lacking uracil (SC-Ura).

extract_protocol:
Total RNA was extracted from 5 OD600 units of cells using the TRIzol reagent according to the manufacturer's instructions.  RNA was treated with RNase-free DNase I at a concentration of 1 U/µg to remove any remaining genomic DNA.  mRNAs were purified from 2µg total RNA using oligo (dT) magnetic beads and fragmented in fragmentation buffer using the TruSeq mRNA Sample Preparation Kit.
Fragmented RNA was used for first-strand cDNA synthesis using a random hexameric primer, and the second strand was synthesized by using DNA polymerase I and RNase H.  Double-stranded cDNAs were purified with AMPure XP beads and eluted with re-suspension buffer, followed by 3'end adenine addition.  Sequencing adaptors were ligated to the fragments, and cDNA fragments were enriched by PCR amplification.  Enriched cDNA libraries were used for cluster generation and sequencing.  Paired-end sequencing of the cDNA libraries was performed using the Illumina Miseq platform.  All sequence data are PE 2x75 bp.  Image processing, base calling, and quality calue calculation were performed by the Illumina data processing pipeline (v1.5). High quality reads were saved in FASTQ format.

treatment_protocol: For samples deleted of mtDNA, transformants were treated with 25 µg/ml EtBr for 24 hours in SC-Ura medium, then harvested in the logarithmic phase. For samples containing mtDNA, cells were permitted to carry out at least three divisions in SC-Ura before harvesting in the logarithmic phase.

tag: genetic background

tag: etbr concentration

value: 25 µg/ml

tag: treatment

value: 2µ-URA3-PDE2 without mtDNA


title: WT + 2µ-URA3-TIP41 without mtDNA_1

description:
b28rhominus 1
[Paired end files] P25 / median / P75: 120 / 151 / 197

value: 2µ-URA3-TIP41 without mtDNA


title: 1001_wk24_AGTCAA_L006


title: 1002_wk12_TGACCA_L003


title: WT + 2µ-URA3 vector without mtDNA_1

description:
b13rhominus 1
[Paired end files] P25 / median / P75: 121 / 154 / 200

value: 2µ-URA3 vector without mtDNA


title: WT + 2µ-URA3-PDE2 without mtDNA_1

description:
b89rhominus 1
[Paired end files] P25 / median / P75: 119 / 151 / 198


title: 1001_wk-3_AGTCAA_L003


title: WT + 2µ-URA3-TIP41 without mtDNA_0

description:
b28rhominus 0
[Paired end files] P25 / median / P75: 123 / 156 / 203


title: 1002_wk16_Replicate_2_CCGTCC_L008


title: 1002_wk26_CGATGT_L007


title: WT + 2µ-URA3 vector without mtDNA_0

description:
b13rhominus 0
[Paired end files] P25 / median / P75: 121 / 154 / 202


title: 1001_wk1_GCCAAT_L007


title: WT + 2µ-URA3 vector with mtDNA_0

description:
b13rhoplus 0
[Paired end files] P25 / median / P75: 120 / 151/ 198

value: 0 µg/ml

value: 2µ-URA3 vector with mtDNA


title: yw_RNA

status: Public on Aug 06 2015

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description: yw RNA-seq

data_processing:
RNA-seq reads were mapped to the dm3 genome assembly using Bowtie and Tophat.
Transcript abundances for annotated RNAs were called by Cufflinks
Data from each sample were normalized to total read number (reads per kb of sequence, per million mapped reads; FPKM)
Ratios of transcript abundance was determined in R, and differentially expressed genes were identified.

organism: Drosophila melanogaster

source_name: stage 5 embryo

extract_protocol:
RNA-seq: Embryos depleted for maternal zld and paired yw controls were dechorionated and analyzed under halocarbon oil to determine stage. Individual paired stage 5 embryos were selected and oil was removed. Embryos were lysed in TRIzol (Life Technologies, Grand Island, NY) supplemented with 150 µg/ml glycogen, and RNA was prepared according to the manufacturer’s instruction.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: yw

value: embryo

value: stage 5


title: zld_RNA

description: zld- RNA-seq

value: zld depleted


title: 1001_wk16_ATGTCA_L006

value: chronic woodchuck hepatitis virus (WHV)

value: Liver

value: Placebo


title: 1001_wk12_ACAGTG_L007


title: WT + 2µ-URA3 vector with mtDNA_1

description:
b13rhoplus 1
[Paired end files] P25 / median / P75: 121 / 152 / 197


title: 884-M1

city: Stanford

first: Gokul

last: Ramaswami

address: 300 Pasteur Drive Alway M305

institute: Stanford University

data_processing:
Library strategy: mmPCR-seq
Paired-end sequencing reads were combined and mapped onto a combination of the dm3 genome and 100 bp exonic sequencing surrounding known splicing junctions using BWA samse allowing 9 mismatches per read.
Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
We used samtools mpileup to count the number of 'A' and 'G' reads at each editing site to calculate the editing levels.
Genome_build: dm3
Supplementary_files_format_and_content: The processed data files contain editing level measurements. The columns are formatted: editing site chromosome, editing site position, editing site gene, editing site strand, editing site annotation1, editing site annotation2, sequencing coverage, number of edited reads, editing level.

source_name: Male whole body

growth_protocol: Male adult flies were 3-5 days old

extract_protocol:
Total RNA was extracted from fly whole bodies.
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.

tag: replicate

tag: Sex

value: male

value: whole body


title: 887-M2


title: 887-M1


title: 93-M1


title: 93-M2


title: 861-M1


title: 859-M2


title: 857-M2


title: 884-M2


title: 857-M1


title: 882-M2


title: 855-M2


title: 852-M2


title: 882-M1


title: 879-M2


title: 861-M2


title: 852-M1


title: 859-M1


title: 850-M1


title: 855-M1


title: 879-M1


title: 850-M2


title: 821-M2


title: 822-M2


title: 822-M1


title: 818-M1


title: 818-M2


title: 812-M2


title: 812-M1


title: 810-M2


title: 805-M1


title: 810-M1


title: 808-M1


title: 805-M2


title: 801-M1


title: 801-M2


title: 802-M2


title: 804-M2


title: 804-M1


title: 808-M2


title: 802-M1


title: 821-M1


title: 820-M2


title: 796-M1


title: 820-M1


title: 796-M2


title: 787-M2


title: 786-M2


title: 787-M1


title: 783-M2


title: 786-M1


title: 783-M1


title: 776-M2


title: 776-M1


title: 774-M2


title: 761-M2


title: 761-M1


title: 774-M1


title: 799-M2


title: 75-M1


title: 75-M2


title: 799-M1


title: 757-M2


title: 737-M1


title: 732-M1


title: 73-M2


title: 738-M2


title: 748-M1


title: 737-M2


title: 727-M1


title: 732-M2


title: 757-M1


title: 721-M2


title: 738-M1


title: 721-M1


title: 716-M1


title: 707-M2


title: 716-M2


title: 714-M2


title: 707-M1


title: 748-M2


title: 727-M2


title: 73-M1


title: 714-M1


title: 705-M1


title: 69-M1


title: 646-M2


title: 703-M1


title: 69-M2


title: 646-M1


title: 705-M2


title: 642-M2


title: 642-M1


title: 589-M1


title: 639-M2


title: 563-M1


title: 517-M1


title: 59-M1


title: 595-M2


title: 639-M1


title: 589-M2


title: 703-M2


title: 584-M2


title: 555-M2


title: 57-M1


title: 49-M2


title: 584-M1


title: 49-M1


title: 57-M2


title: 492-M1


title: 563-M2


title: 555-M1


title: 595-M1


title: 508-M2


title: 508-M1


title: 461-M1


title: 492-M2


title: 517-M2


title: 491-M1


title: 486-M2


title: 491-M2


title: 461-M2


title: 441-M1


title: 443-M1


title: 441-M2


title: 59-M2


title: Honey 1

city: Tai'an

first: Lanting

last: Ma

state: Shandong

address: Daizong street, No. 61

country: China

institute: Shandong Agricultural University

description: fed honey only, queens were caged to successively reduce the size of brood

data_processing:
Illumina GA Pipeline v1.5 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence,and filtered for reads with more than 10% unknown bases, then aligned to The DFCI Apis mellifera Gene Index (AMGI) by  SOAP2 aligner,no more than 2 mismatches are allowed in the alignment
Sequencing saturation analysis, distribution of reads on reference genes, and coverage analysis were employed for the quality control purpose.
The level of gene expression was calculated as FPKM (Fragments Per Kilobase of exon per Million fragments mapped), differentially expressed Genes (DEGs) were identified using an FDR≤0.001 (false discovery rate no greater than 0.05)
Cluster v3.0 and javaTreeview v1.1.1 were used forExpression pattern analysis of DEGs. Gene Ontology functional analysis was based on GO::TermFinder. KEGG (major public pathway-related database) is used in our pipeline to perform pathway enrichment analysis of DEGs for  further understand genes biological functions.
Genome_build: The DFCI Apis mellifera Gene Index (AMGI)
Supplementary_files_format_and_content: text files include Gene_position, Length,Strand, raw_fragment_number, normalized_count and FPKM values for each Sample.

organism: Apis mellifera

source_name: Hypopharyngeal gland

extract_protocol:
Hypopharyngeal glands were dissected, flash frozen with liquid nitrogen, and RNA was harvested using Total RNA Kit II (50) (R6934-01). The NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The six colonies were divided into three treatments (Honey group, Pollen group and Brood group), and each treatment included two colonies. In the Honey group (fed honey only) and the Pollen group (fed honey and abundant rape pollen), the queens were caged to successively reduce the size of brood. In the Brood group (fed honey and abundant rape pollen), the queen was not restricted and was allowed to lay eggs normally.

tag: caste

value: worker bee

value: hypopharyngeal gland

value: day 11 after emergence from the comb


title: Pollen 2

description: fed honey and abundant rape pollen, queens were caged to successively reduce the size of brood

value: day 10 after emergence from the comb


title: 443-M2


title: 427-M1


title: 45-M1


title: 440-M2


title: 426-M2


title: Brood 2

description: fed honey and abundant rape pollen, queen was not restricted and was allowed to lay eggs normally

value: day 14 after emergence from the comb


title: 440-M1


title: Brood 1

value: day 13 after emergence from the comb


title: 41-M1


title: 406-M1


title: Honey 2

value: day 12 after emergence from the comb


title: 427-M2


title: 41-M2


title: 426-M1


title: 45-M2


title: 486-M1


title: 405-M1


title: 437-M2


title: 40-M1


title: 406-M2


title: 399-M1


title: 392-M1


title: 391-M2


title: 391-M1


title: 405-M2


title: 386-M2


title: 40-M2


title: 385-M1


title: Pollen 1

value: day 9 after emergence from the comb


title: 399-M2


title: 392-M2


title: 437-M1


title: 385-M2


title: 383-M2


title: 383-M1


title: 381-M1


title: 377-M2


title: 380-M1


title: 382-M1


title: 380-M2


title: 382-M2


title: spleen10

city: Shanghai

first: Peng

last: Hu

address: Huchenghuan Road 999

institute: Shanghai Ocean University

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were assessed for their quality using FASTX_toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Reads with a Phred quality score less than 5 over the 95% nt would be removed.
TopHat was used to map the reads to the reference genome. Then HTSeq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html), which is a python based script, was then applied to count the number of reads mapped to the genes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Danio rerio

source_name: spleen

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: fish were maintained 12h to adapt low temperatures and then killed by pithing

value: spleen

tag: temperature

value: Tubingen

value: Six months old


title: 377-M1


title: spleen18


title: muscle18

source_name: muscle

value: muscle


title: 375-M2


title: muscle10


title: spleen28


title: muscle28


title: liver18

source_name: liver

value: liver


title: liver10


title: 375-M1


title: liver28


title: 374-M1


title: kidney10

source_name: kidney

value: kidney


title: 374-M2


title: 386-M1


title: kidney18


title: intestine10

source_name: intestine

value: intestine


title: 371-M2

value: male


title: kidney28


title: 381-M2

value: whole body


title: intestine18


title: intestine28


title: 370-M2


title: 362-M2


title: 370-M1


title: heart18

source_name: heart

value: heart


title: 362-M1


title: heart28


title: 361-M2


title: 361-M1


title: gill10

source_name: gill

value: gill


title: gill18


title: gill28


title: brain28

source_name: brain

value: brain


title: brain18


title: brain10


title: 371-M1


title: 359-M1


title: 360-M2


title: 360-M1


title: 359-M2


title: 356-M2


title: LA2A

city: Taizhou

first: Baoying

last: Qian

state: Zhejiang

address: 1139 Shifu Road, Jiaojiang, Taizhou, Zhejiang 318000, P. R. China

department: School of life science

institute: Taizhou University

data_processing:
Output statistics, such as raw sequence data, and then generate clean reads from raw reads after remove reads with adaptors, remove reads with unknown nucleotides larger than 5% and remove low quality reads which the percentage of low quality bases(base quality≤10) is more than 20%.
Transcriptome de novo assembly is carried out with short reads assembling program - Trinity.
Unigene function annotation. Unigene sequences are firstly aligned by blastx to protein databases like NR, Swiss-Prot, KEGG and COG (e-value<0.00001), and aligned by blastn to nucleotide databases nt(evalue<  0.00001), retrieving proteins with the highest sequence similarity with the given Unigenes along with their protein functional annotations,the results about this are inculding in  the folder annotation.
Unigene GO Classification, Metabolic Pathway Analysis, Protein Coding Region Prediction (CDS), Unigene SSR Analysis and Heterozygous SNP Analysis
GO Classification of Differentially Expressed Unigene and Pathway Analysis,

organism: Larimichthys crocea

source_name: cold stress group

extract_protocol:
Livers were removed, stored in the liquid of RNAstore (CWBIO, China), and RNA was harvested using Trizol reagent. Seqencing libraries were constructed from 1 ug of total RNA using Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: cold stress treated with 12 h


title: 356-M1


title: LF1A

source_name: 21 day fasting group

value: fasting with 21 days


title: LB2A

source_name: control group

value: no treatment


title: 350-M2


title: heart10


title: LC2A

source_name: thermal stress group

value: thermal stress treated with 12 h


title: 350-M1


title: 352-M2


title: 352-M1


title: 336-M2


title: 336-M1


title: 335-M2


title: 340-M2


title: 325-M2


title: 335-M1


title: 325-M1


title: H6309 Input biological replicate 1

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

data_processing:
Sequencing reads were mapped to the S288C (sacCer2) genome using Bowtie unless specified otherwise, only perfect matches across all 51bp were considered during mapping. Multiple alignments were not taken into account, which means each read only mapped to one location in the genome. Reads were also mapped to the SK1 genome with similar results. Reads were extended towards 3’ ends to a final length of 200bp in MACS (http://liulab.dfci.harvard.edu/MACS/) (Zhang et al., 2008).
To identify axis protein enriched regions (peaks), the observed sequence read tag density along the chromosome was normalized against the measured background (INPUT DNA). Median coverage of all base positions in the ChIP sample was calculated. The coverage at each position was then divided by the calculated median. The same division was also performed for the input sample, followed by subtraction of the input from the ChIP sample at each position. Peak identification was performed using MACS (http://liulab.dfci.harvard.edu/MACS/) (Zhang et al., 2008) using a P-value of 1e-15. Peak summits were defined as the local maximum of read coverage within Red1 peaks.
Genome_build: SacCer2
Supplementary_files_format_and_content: Wiggle file: ChIP enrichment at each base position.

source_name: Input of H6309 biological replicate 1

growth_protocol: To induce synchronous meiosis, strains were inoculated at OD600 = 0.3 in BYTA medium for 16.5 hours at 30°C. Then cultures were washed twice with water and resuspended into SPO medium at OD600 = 1.9 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013).
Library preparation was performed using Illumina TruSeq DNA Sample Prep Kits v1 but adaptors were used at 1:20 dilution. Amplified ChIP DNA between 300 and 500bp was gel purified on 1.8% agarose and sequentially quantified using the Qubit assay HS kit as well as an Agilent 2100 Bioanalyzer. Fragments were sequenced on an Illumina HiSeq 2500 instrument using a 51-bp single-end sequencing protocol.

tag: meiotic timepoint

value: 3 hour

tag: genotype

tag: antibody


title: H6309 Smc3 ChIP biological replicate 1

source_name: Smc3 ChIP of H6309 biological replicate 1

value: Anti-3HA (Cat#:11867431001, Roche Applied Science)


title: 324-M2

tag: tissue


title: 324-M1


title: 318-M1


title: 317-M1


title: 317-M2


title: 318-M2


title: FOXA2 ChIP-seq Replicate 1

city: Chicago

first: Ann

last: Harris

state: IL

address: 2430 N Halsted Street Box 211

institute: Lurie Children's Hospital of Chicago Research Center

data_processing:
Fastq files were aligned to the hg19 version of the human genome using Bowtie (v 1.0.0) with a seed length of 40 and a maximum number of 3 mismatches allowed in the seed. Only unique reads were used.
Using Homer (v 1.2) software, tag directories were created using the makeTagDirectory command with default settings.
Using Homer (v 1.2) peaks were called using the findPeaks command with an FDR of .1%, factor style, input tag directory as the control library, and all other settings as default.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing FOXA2 peaks for each replicate

source_name: Colorectal adenocarcinoma cells

growth_protocol: Caco2 cells were grown in DMEM Low Glucose with 10% FBS.

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with the FOXA2 antibody.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.

tag: cell line

value: FOXA2 (Santa-Cruz sc-6554)

tag: style parameter used for peak calling

value: factor

tag: input used for peak calling

value: Caco2 Input


title: 315-M1

source_name: Male whole body


title: FOXA2 ChIP-seq Replicate 2


title: 310-M1


title: 309-M1


title: Caco2 Input


title: 309-M2


title: 340-M1


title: 304-M2


title: 306-M2


title: 301-M1


title: 304-M1


title: 301-M2


title: 28-M1


title: 287-M2


title: 287-M1


title: 320-M2


title: 26-M1


title: 320-M1


title: 26-M2


title: 315-M2


title: 239-M2


title: 239-M1


title: 310-M2


title: 235-M1


title: 235-M2


title: 233-M1


title: 228-M2


title: 227-M1


title: 306-M1


title: 233-M2


title: 223-M2


title: 228-M1


title: 223-M1


title: 21-M2


title: 21-M1


title: 217-M2


title: 217-M1


title: 28-M2


title: 208-M2


title: 195-M2


title: 208-M1


title: 195-M1


title: RibosomeProfiling_Liver_Se0.1_mouse5.2

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

data_processing:
Sequence reads were trimmed of adapter sequences using Hannon lab Fastx toolkit
rRNA sequences were removed using bowtie alignments to mouse 43SrRNA
RefSeq FASTA sequences were obtained from the UCSC genome browser (mm9). These FASTA files were reduced to a single entry for each mRNA corresponding to the longest isoform. Uniquely aligning sequences, allowing for 2 mismatches, were identified using the Bowtie sequence aligner. Differential expression was analyzed using Bioconducter and EdgeR.
Supplementary_files_format_and_content: 10423_EdgeR.txt: ribosome profiling EdgeR output

source_name: Liver, 0.1 ppm Se

extract_protocol:
Total RNA was isolated by bead beating.
100mg of Liver tissue was homogenized, and crude polysomes digested with RNase1, isolated by centrifugation through sucrose, and ribosome footprints (~30nts) size purified by denaturing polyacrylamide gel electrophoresis. Libraries were constructed using illumina TruSeq Small RNA Sample Preparation kit. Sequencing was done using the Illumina HiSeq 2000 instrument

treatment_protocol: Mice were fed diets supplemented with 0 or 0.1 ppm Se for 6 weeks

value: FVB/N

value: liver


title: RibosomeProfiling_Liver_Se0.1_mouse4.2

source_name: Liver, 0.1 ppm Se diet


title: 181-M2

value: male


title: 181-M1

value: whole body


title: RibosomeProfiling_Liver_Se0_mouse2.2

source_name: Liver, 0 ppm Se diet


title: RibosomeProfiling_Liver_Se0_mouse1.2


title: 161-M2


title: RibosomeProfiling_Liver_Se0.1_mouse4.1


title: RibosomeProfiling_Liver_Se0.1_mouse5.1


title: 158-M2


title: 161-M1


title: 158-M1


title: RibosomeProfiling_Liver_Se0_mouse1.1


title: RibosomeProfiling_Liver_Se0_mouse2.1


title: 153-M2


title: 153-M1


title: RNASeq_Liver_Se0.1_mouse4

data_processing:
Sequence reads were trimmed of adapter sequences using Hannon lab Fastx toolkit
rRNA sequences were removed using bowtie alignments to mouse 43SrRNA
RefSeq FASTA sequences were obtained from the UCSC genome browser (mm9). These FASTA files were reduced to a single entry for each mRNA corresponding to the longest isoform. Uniquely aligning sequences, allowing for 2 mismatches, were identified using the Bowtie sequence aligner. Differential expression was analyzed using Bioconducter and EdgeR.
Supplementary_files_format_and_content: 10422_EdgeR.txt: RNA-Seq profiling EdgeR output

extract_protocol:
Total RNA was isolated by grinding in liquid nitrogen cooled mortar and pestle.
Liver total RNA was isolated. rRNA was removed using Ribo-Zero (Illumina), fragmented, primed with random hexamers, and libraries prepared using Illumina TruSeq stranded total RNA sample preparation kit. Sequencing was done using the Illumina HiSeq 2000 instrument.


title: 149-M2


title: RNASeq_Liver_Se0_mouse2


title: 142-M1


title: 149-M1


title: RNASeq_Liver_Se0.1_mouse5


title: 142-M2


title: 138-M2


title: RNASeq_Liver_Se0_mouse1


title: 109-M2


title: 105-M2


title: 136-M1


title: yw_faire

description: yw FAIRE-seq

data_processing:
Basecalls performed using CASAVA1.8.2
FAIRE reads were aligned to the dm3 genome assembly using Bowtie2 with the --sensitive and --end-to-end flags.
Aligned reads with a MAPQ score less than 10 were removed using samtools, reads were extended to 110bp, and replicates were pooled.
FAIRE peaks were called with MACS2 using a shift size of 125bp.
Differential FAIRE peaks between yw and zldM- were identified with edgeR, using the "classic analysis". The input file consisted of a table of FAIRE read counts for each yw and zldM- replicate intersecting the union set of the top 5000 FAIRE peaks. FAIRE peaks with a p-value lower than 0.05 were called as differential (the content of each processed data file and column headers are described further in readme.txt).

source_name: yw FAIRE-seq

growth_protocol: Embryos lacking maternally supplied ZLD were generated as described by Liang et al., 2008.  zld294FRT19A/FM7 females were crossed with C(1) Dx/ovoD1 FLP122 FRT19A males and allowed to lay for 24 hours. The resulting offspring were heat-shocked twice for 30 minutes at 37°C with a 24 hour interval between (at ~24-48 hours and 48-72 hours after laying) to generate germ-line clones.  In parallel, yw FRT19A females were crossed to C(1) Dx/ovoD1 FLP122 FRT19A males, and the offspring were heat-shocked to serve as paired controls.  Since only females with the desired germ-line clones should produce embryos, non-heat-shocked offspring from each cross were preserved and allowed to mature to check for escapers. Any crosses resulting in escapers that produced embryos without heat-shock were discarded.

extract_protocol:
FAIRE-seq: Embryos ranging in age from 2.5 to 3 hours were collected, dechorionated, and crosslinked for 10 min with 3:1 heptane:fix solution at room temperature.  Following washing, embryos were flash frozen in liquid nitrogen and stored at -80°C.  FAIRE was performed on approximately 0.1 g of embryos, as previously described in McKay and Lieb (2013) with the following exceptions.  The homogenized embryos were filtered through Miracloth (EMD Millipore, Billerica, MA).  After resuspension in Lysis Buffer (10 mM Tris-Cl pH 8, 100 mM NaCl, 1 mM EDTA, 2% Triton X-100, 1% SDS), the nuclei were subjected to four rounds of bead-beating with 0.5mm glass beads.  The chromatin was sonicated three times for 30 seconds using a Branson Sonifier 250 at a power setting of 1.5 to achieve a size range of 200bp-1kb.
FAIRE-seq libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: yw

value: paired control

value: embryo

tag: developmental stage

tag: age

value: ranging in age from 2.5 to 3 hr


title: yw_faire_input

source_name: yw FAIRE-seq_input


title: 105-M1


title: zld_faire_input

source_name: zld- FAIRE-seq_input

value: zld depleted

value: lacking maternal ZLD; zldM-


title: zld_faire

description: zld- FAIRE-seq

source_name: zld- FAIRE-seq


title: WT_Ctrl 4

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: Zv9 (Ensembl gene-build 66)
Supplementary_files_format_and_content: matrix_table.txt contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

molecule: polyA RNA

source_name: Heart

growth_protocol: All experiments were conducted with adult zebrafish between 6 and 9 months of age, raised at a density of 3 fish/l.

extract_protocol: Four biological replicates consisting of 3 pooled hearts were used per sample. Index-tagged cDNA libraries were constructed from total RNA (1 μg) with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA).

value: WT

tag: stress

value: Control

value: heart


title: WT_Ctrl 3


title: WT_Cryoinjury 3

value: cryoinjury

tag: time

value: 3 days post cryoinjury


title: WT_Cryoinjury 1


title: WT_Cryoinjury 2


title: WT_Cryoinjury 4


title: WT_Ctrl 1


title: WT_Ctrl 2


title: 136-M2

tag: strain


title: 138-M1

tag: replicate


title: KO_Cryoinjury 2

value: Tert (AB/hu3430) KO mutant


title: ISTS oviduct

city: Jokioinen

first: Anu

last: Sironen

address: Myllytie 1

department: Biotechnology and Food Research

country: Finland

institute: Agrifood Research Finland

description: Sample 4

data_processing:
The Solid 4 color-space reads were mapped against the pig genome build 10.2 using LifeScope v2.1.
Sequenced reads associated with ribosomal RNA, transfer RNA, repeats and other uninformative reads were filtered out and remaining reads were mapped to Sus scrofa 10.2 whole genome using LifeScope v2.1.
After alignment to the reference genome, reads with more than 10 potential alignments and low mapping quality reads were discarded (mapQV(<10)) and unique reads were associated with known genes based on UCSC annotations, and the number of reads aligned within each gene was counted. FPKM values were calculated using the Cufflinks software v2.0.2.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include Cufflinks FPKM values for each sample.

organism: Sus scrofa

source_name: Oviduct

extract_protocol:
Tissue samples were collected at slaughter house, stored in RNAlater (Qiagen) at −80°C prior to RNA extraction. RNA was extracted using RNeasy Midi kit (Qiagen) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Solid 4 protocols

value: Finnish Large white

value: oviduct

value: > 6 months

value: ISTS


title: KO_Cryoinjury 3


title: WT oviduct

description: Sample 3

value: wild type


title: KO_Cryoinjury 4


title: WT testis

description: Sample 1

source_name: Testis

value: testis


title: ISTS testis

description: Sample 2


title: KO_Ctrl 4


title: KO_Cryoinjury 1


title: KO_Ctrl 3


title: 109-M1

tag: Sex

value: male

value: whole body


title: KO_Ctrl 2


title: KO_Ctrl 1


title: Input rep 2

status: Public on Aug 05 2015

city: Irvine

first: Haoping

last: Liu

address: Med. Sci. I, Rm D234

department: Dept. of Biological Chemistry

institute: University of California

description: input

data_processing:
ChIP-seq reads were aligned to the Ca21 genome assembly using bowtie version 0.12.7 with the following parameters: -S -n 2 --best --strata --chunkmbs 256 -p 3 -m 1
WT IN vs WT IP peaks were called using QuEST version 2.4 with recommended stringency
IN1 vs IP1 peaks were called using QuEST version 2.4 with recommended stringency
IN2 vs IP2 peaks were called using QuEST version 2.4 with recommended stringency
Called peaks were annotated to the Ca21 genome
Genes present in IN1 vs IP1 and IN2 vs IP2 analyses, but not in the control WT IN vs WT IP were selected. Selected genes were validated by visual confirmation by uploading the data to MochiView
Genome_build: C. albicans SC5314 A21 (Ca21)
Supplementary_files_format_and_content: Tab delimited files include annotated peak regions (QUEST*.txt) and Cph2 bound genes from ChIP-seq analysis

organism: Candida albicans

source_name: fungus

growth_protocol: Wild type cells containing Mal2p-Cph2N were grown in YPM overnight to OD600 ~10

extract_protocol:
Cells were broken using a FastPrep and zirconium beads
Library was generated using the BioScientific NextFlex ChIP-Seq kit

treatment_protocol: ChIP was performed using a modified protocol from the Snyder lab


title: Untagged WT IP

description:
ChIP-seq of Cph2
antibody: EZview Red Anti-c-Myc Affinity Gel from Sigma, catalog number E6654


title: Input rep 1

description: input


title: IP rep 2


title: IP rep 1


title: E347 ablation replicate 2

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

data_processing:
Reads were aligned to the UCSC dm3 genome using tophat2
FPKM were calculcated and compared using cufflinks (cuffdiff)
Genome_build: dm3
Supplementary_files_format_and_content: cuffdiff

source_name: 91 larval brains

growth_protocol: Animals were reared at 25uC on modified Bloomington media  (with malt) containing 35 g yeast per liter.

extract_protocol: Brains were frozen in Trizol and RNA extracted

treatment_protocol: Brains were dissected at wandering stages

value: larval brain


title: E347 ablation replicate 1

source_name: 100 larval brains


title: E347 activation replicate 2

source_name: 97 larval brains

value: w, E347-GAL4/yw;+;UAS-NachBac


title: E347 activation replicate 1


title: pooled thymus tissue miRNA from 3 non-drinking male adolescent control rats

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: miRNA expression data from untreated male control rats

data_processing:
After phasing, prephasing, normalization and cross talk correction are taken into account, base calling was performed by Illumina Real Time Analysis (RTA) software (version 1.17.28) on the MiSeq instrument
Sequenced reads were trimmed for adaptor sequence, FASTQ files were subsequently imported into Partek Flow for alignment and analysis. Base calls below a phred score of 20 were trimmed. Reads were aligned to the rat Rn5 reference genome using the Bowtie algorithm. These were then quantified against both Precursor and Mature miRBase (version 21) sequences and RefSeq transcript miRNA annotations (7-30-14). Raw miRNA counts are reported.
Genome_build: Rn5
Supplementary_files_format_and_content: tab-delimited text files include percent of total read values for each sample

organism: Rattus norvegicus

source_name: thymus

extract_protocol:
Qiagen total RNA
RNA libraries were prepared for sequencing using Illumina TruSeq small RNA protocol

value: thymus

value: postnatal day 35

tag: treatment


title: E347 control replicate 1


title: pooled skin tissue miRNA from 3 non-drinking male adolescent control rats

source_name: skin

value: skin


title: blood serum miRNA from non-drinking male adolescent control rat, replicate 2

source_name: blood serum

value: blood serum


title: pooled spleen tissue miRNA from 3 non-drinking male adolescent control rats

source_name: spleen

value: spleen


title: blood serum miRNA from non-drinking male adolescent control rat, replicate 1


title: pooled skeletal muscle tissue miRNA from 3 non-drinking male adolescent control rats

source_name: muscle

value: muscle


title: pooled liver tissue miRNA from 3 non-drinking male adolescent control rats

source_name: liver

value: liver


title: pooled stomach tissue miRNA from 3 non-drinking male adolescent control rats

source_name: stomach

value: stomach


title: pooled pancreas tissue miRNA from 3 non-drinking male adolescent control rats

source_name: pancreas

value: pancreas


title: pooled testes tissue miRNA from 3 non-drinking male adolescent control rats

source_name: testes

value: testes


title: pooled lung tissue miRNA from 3 non-drinking male adolescent control rats

source_name: lung

value: lung


title: Untagged WT IN

description: input

value: wild type


title: pooled kidney tissue miRNA from 3 non-drinking male adolescent control rats

source_name: kidney

value: kidney


title: pooled large intestine tissue miRNA from 3 non-drinking male adolescent control rats

source_name: large intestine

value: large intestine

value: male


title: pooled heart tissue miRNA from 3 non-drinking male adolescent control rats

source_name: heart

value: heart


title: whole brain hemisphere tissue miRNA from non-drinking male adolescent control rat, replicate 2

source_name: brain

value: brain


title: E347 control replicate 2

source_name: 86 larval brains

value: larval brain


title: pooled subcutaneous abdominal fat tissue miRNA from 3 non-drinking male adolescent control rats

source_name: fat

value: fat

value: postnatal day 35


title: whole brain hemisphere tissue miRNA from non-drinking male adolescent control rat, replicate 3


title: pooled small intesting tissue miRNA from 3 non-drinking male adolescent control rats

source_name: small intestine

value: small intestine


title: blood serum miRNA from non-drinking male adolescent control rat, replicate 3

value: blood serum


title: ecodormant_yes_glyphosate_rep4

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

data_processing:
Raw sequence reads were checked for quality using the FastQC0.10.0 program and quality trimmed using the Sickle-quality-base-triming program in the iPlant discovery environment with the parameters minimum quality = 20 and minimum number of bases = 70.
All trimmed illumina read files from all experiments for each paired end were concatenated and subjected to kmer reduction using the trinity kmer reduction program to a maximum of 30 kmers. The resulting file was assembled using Trinity with iPlant rescources and default parameters.
The program RSEM was used to map individual fragments to the assembled transcriptome and theresulting raw expression data (number of fragments mapping to each contig/gene-counts per million) was normalized using EBseq program associated with RSEM, and likelihood ofdifferential expression was determined by the EBseq program.
Genome_build: trinity -assembled transcriptome from all available RNAseq data.

organism: Euphorbia esula

source_name: crown buds of leafy spurge

growth_protocol: Plants were grown under greenhouse-conditions (18 hr photoperiod) to approximately 4 months of age. They were then placed in a growth chamber and acclimated for 1 week at 27C to acclimate prior to treatment and subsequent harvest.

extract_protocol:
RNA extraction was performed by grinding approximately 0.1 grams of frozen tissue in liquid nitrogen to a fine powder, and adding 1 ml Trizol reagent (Ambion/Life Technologies). Chloroform:Isoamyl (24:1) was added to the Trizol/tissue mixture, centrifuged, and RNA was extracted from the resulting supernatant using an RNeasy Plant Mini kit (Qiagen). Quality control was assessed using a nanodrop bioanalyzer on the RNA setting. Poly A RNA was extracted with the NEBNext Poly(A) mRNA Magnetic Issolation Module.
cDNA libraries were created usining the NEBNext Ultra DirectionalRNA Library Prep Kit for Illumina. In short, 4000 ng of RNA was purified and fragmented into mRNA, followed by first and second strand cDNA synthesis. End repair and adenylation of 3’ ends preceded adapter ligation and PCR amplification. Library quality was assessed using an Agilent Bioanalyzer, and quantified for pooling by qRT-PCR using the PhiX Control Kit v2 according to manufacturer specifications. Libraries were paired-end sequenced on an Illumina HiSeq2000.

treatment_protocol: dormancy transitions with glyphosate: Plants were treated with 2.24 kg ai ha-1 rate of glyphosate (Buccanneer Plus®, 480 g ai L-1, Tenkoz, Inc., Alpharetta, GA, USA) plus 0.25% of surfactant (Class Act® NG® surfactant Agrisolutions - Winfield Solutions, LLC, St. Paul, MN, USA) using a SS8001 nozzle delivering 95 liter ha-1 solution in a positive airflow hood (DeVries Manufacturing Co., Hollandale, MN, USA). Plants were returned to growth-conducive conditions in a greenhouse, and paradormant crown buds were collected from a subset of plants 7 days after the treatments for transcript and phytohormone profiling. To induce endodormancy, remainder of the plants were exposed to a ramp down in temperature and photoperiod (RD) treatment consisting of a reduction in temperature of 1.42 C week-1 (from 27 to 10 C) and a decreasing photoperiod of 40 min week-1 (from 16 to 8 h light) for 12 weeks; half of these plants were further exposed to extended cold treatment (8 weeks at 7 C, under constant 8:16 h day:night cycle) to induce ecodormancy as previously standardized for leafy spurge. Crown buds were collected as noted above following the various treatment regimes.

value: crown buds of leafy spurge

tag: cultivar

value: Glyphosate treated plants not harvested for endodormantdormant buds were placed in a growth chamber set to an 8 hr photoperiod at 7C for 8 weeks to induce ecodormancy. Crown buds from a subset of plants were harvested at ~10:00 am following conclusion of the ecodormant-inducing treatment.

tag: temperature at sampling

value: ~7 C for for 8 weeks after ramp down completed

tag: photoperiod

value: 8 hr for 8 weeks after ramp down

tag: glyphosate

value: 2.24 kg ai ha-1 rate of glyphosate 7 days prior to collection or paradormant buds and subsequent dormancy transition treatments.


title: ecodormant_yes_glyphosate_rep1

tag: tissue


title: ecodormant_yes_glyphosate_rep2


title: endodormant_yes_glyphosate_rep4

value: Glyphosate treated greenhouse-grown plants not harvested for paradormant buds were placed in a growth chamber set to reduce light and temperature over a three month period. Crown buds from a subset of plants were harvested at ~10:00 am following conclusion of the endodormanc-inducing treatment.

value: 27 C ramped down to 10 C over three months

value: 16 hr ramp down to 8 hr over 3 months


title: endodormant_yes_glyphosate_rep3


title: ecodormant_yes_glyphosate_rep3


title: endodormant_yes_glyphosate_rep2


title: paradormant_yes_glyphosate_rep4

value: Plants were greenhouse-grown to ~4 months of age. Treated with gyphosate and one week leter Crown buds were harvested at ~10:00 am from a subset of plants.

value: 16 hr


title: paradormant_yes_glyphosate_rep3


title: paradormant_yes_glyphosate_rep1


title: paradormant_yes_glyphosate_rep2


title: ecodormant_no_glyphosate_rep2

description:
no glyphosate treatment
MD_18

treatment_protocol: dormancy transitions with or without glyphosate: Plants were grown to a 4 months of age in the green house, and paradormant crown buds were collected from a subset of plants. To induce endodormancy, remainder of the plants were exposed to a ramp down in temperature and photoperiod (RD) treatment consisting of a reduction in temperature of 1.42 C week-1 (from 27 to 10 C) and a decreasing photoperiod of 40 min week-1 (from 16 to 8 h light) for 12 weeks; half of these plants were further exposed to extended cold treatment (8 weeks at 7 C, under constant 8:16 h day:night cycle) to induce ecodormancy as previously standardized for leafy spurge. Crown buds were collected as noted above following the various treatment regimes.

value: Plants not harvested for endodormantdormant buds were placed in a growth chamber set to an 8 hr photoperiod at 7C for 8 weeks to induce ecodormancy. Crown buds from a subset of plants were harvested at ~10:00 am following conclusion of the ecodormant-inducing treatment.


title: ecodormant_no_glyphosate_rep3

description:
no glyphosate treatment
MD_19


title: ecodormant_no_glyphosate_rep4

description:
no glyphosate treatment
MD_20


title: endodormant_no_glyphosate_rep4

description:
no glyphosate treatment
MD_12

value: Greenhouse-grown plants not harvested for paradormant budswere placed in a growth chamber set to reduce light and temperature over a three month period. Crown buds from a subset of plants were harvested at ~10:00 am following conclusion of the endodormanc-inducing treatment.


title: endodormant_no_glyphosate_rep3

description:
no glyphosate treatment
MD_11


title: endodormant_no_glyphosate_rep1

description:
no glyphosate treatment
MD_9


title: ecodormant_no_glyphosate_rep1

description:
no glyphosate treatment
MD_17


title: endodormant_no_glyphosate_rep2

description:
no glyphosate treatment
MD_10


title: paradormant_no_glyphosate_rep4

description:
no glyphosate treatment
MD_4

value: Plants were greenhouse-grown to ~4 months of age. Crown buds were harvested at ~10:00 am.


title: whole brain hemisphere tissue miRNA from non-drinking male adolescent control rat, replicate 1

value: brain

value: male


title: paradormant_no_glyphosate_rep2

description:
no glyphosate treatment
MD_2


title: paradormant_no_glyphosate_rep3

description:
no glyphosate treatment
MD_3


title: mES_Eed_KO_2i_r2

city: Munich

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

data_processing:
Base calling was performed with the standard Illumina pipeline 1.83
ChIP-Seq data was aligned to the mm9/NCBI37 reference genome using bwa version  0.5.7 (Li and Durbin, 2009) or with bowtie version 0.12.7 (Langmead et al., 2009) with default parameter settings. Subsequently, reads were filtered for duplicates and extended by 200bp. Visualization of read count data was performed by converting raw bam files to .tdf files using IGV tools (Thorvaldsdottir et al., 2012) and normalizing to 1 million reads.   For the analysis of the ChIP-Seq datasets, we utilized the Irreproducible Discovery Rate (IDR) framework with a cutoff of 0.05 in combination with the MACS2 peak caller version 2.1 to identify peaks taking advantage of both replicates for each condition (except for OCT4). For MACS2 peak calling, we used an initial p-value cutoff of 0.01 and the mouse ESC whole cell extract (WCE) control library as background.
RNA-Seq raw sequence reads were aligned to mm9 using Tophat (Trapnell et al., 2009) and Bowtie version 0.12.7 (Langmead et al., 2009) with parameters set to default values except mate-inner-dist 300 mate-std-dev 500. Subsequently, duplicates were removed and cufflinks 2.2.1 (Grant et al., 2011) was used to conduct RNA expression quantification based on ensembl mm9 gene models.  The –M option of cuffquant/cuffdiff was used to mask out reads mapping to rRNA genes, mitochondrial genes, and any transcripts less than 200 bp long. A pseudo-count of 1 was added to all FPKM values generated from cuffdiff before plotting. An FDR threshold of 0.1 was used for differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data for ChIP-Seq is in ENCODE narrowPeak format. Processed gene expression data is in standard cuffdiff .tracking format.

source_name: Eed knockout mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% Glutamine, 1% NEAA and LIF. For ES cell maintenance dishes were coated with 0.2% gelantin and irradiated CF1 mouse embryonic fibroblasts (MEFs) were plated as confluent layer of feeder cells. ESCs were seeded in a density of 50000 cells/ 6well and were splitted every 2-3 days. The 2i media was prepared according to the following protocol (Ying et al., 2008) and was supplemented with LIF.

extract_protocol:
RNA-Seq: Polyadenylated RNA was isolated using Olig dT beads (Invitrogen). RNA was fragmented to a size of 200-600 base pairs, followed by ligation to RNA adapters using T4 RNA Ligase (NEB). Adapter primers were used for cDNA synthesis, followed by RNA degradation. Each cDNA library was ligated to a DNA adapter, used for barcoding and PCR enrichment of the library. Libraries were pooled and sequenced on the Illumina HiSeq 2000. ChIP-Seq: Cells were crosslinked in 1% formaldehyde for 15 minutes at room temperature, with constant agitation, followed by quenching with 125mM Glycine for 5 minutes at room temperature. Nuclei were isolated and chromatin was sheared using Branson sonifier until the majority of DNA was in the range of 200-700 base pairs. Chromatin was incubated with antibody overnight at 4°C, with constant agitation. Immunoprecipitation of antibody-protein complexes was completed using Protein A or Protein G Dynabeads (Invitrogen) for 2-3 hour at 4°C, with constant agitation
Immunoprecipitated DNA was end repaired using the End-It DNA End-Repair Kit (Epicentre), extended using a Klenow fragment (3’-5’ exo) (NEB), and ligated to sequencing adapter oligos (Illumina). Each library was then PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 was selected for sequencing on the Illumina HiSeq 2000.

tag: cell type

value: mouse embryonic stem cells

tag: culture condition

value: 2i for 3 passages


title: mES_Eed_KO_2i_r1


title: mES_Eed_KO_serum_r2

value: Standard Serum


title: endodormant_yes_glyphosate_rep1

value: crown buds of leafy spurge


title: rhesus_placenta

city: Davis

first: Janine

last: LaSalle

address: Medical Microbiology and Immunology

institute: UC Davis

data_processing:
genome version: rheMac3
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

organism: Macaca mulatta

source_name: placenta

extract_protocol: DNA was purified using Qiagen's Puregene kit. MethylC-seq libraries were made by sonicating the genomic DNA to ~300 bp and ligating methylated Illumina adapters to the ends.  The library was bisulfite converted, amplified for 14 cycles, and sequenced.

value: placenta

tag: developmental timepoint

value: gestation day 60


title: rhesus_trophoblasts

source_name: trophoblasts

extract_protocol: Trophoblast cells were isolated from Rhesus monkey (Macaca mulatta) placental tissue (Gestation Day: 40–65 days) using procedures we have previously described (Douglas and King 1990; Soghomonians et al. 2002; Kumar et al. 2012).  These cells are 95% cytokeratin 7-positive and 5% vimentin-positive, consistent with a predominantly trophoblast population.  DNA was purified using Qiagen's Puregene kit.  MethylC-seq libraries were made using the Epicentre EpiGnome Methyl-Seq kit according to the manufacturer's recommendations except that 14 cycles of amplification were performed.

value: trophoblasts

value: gestation day 66


title: mES_Eed_KO_serum_r1


title: mES_WT_3p_2i_rep2

source_name: KH2 mouse embryonic stem cells


title: mES_WT_3p_2i_rep1


title: mES_WT_24h_2i_rep1

value: 2i for 24 hours


title: mES_WT_Serum_rep2


title: mES_WT_Serum_rep1


title: mES_Sox2_24h_2i_r1

tag: antibody epiptope

tag: antibody-vendor

value: Santa Cruz

tag: antibody-catalog-nr

tag: antibody-lot


title: mES_Sox2_24h_2i_r2


title: mES_Sox2_Serum_r2


title: mES_Sox2_3p_2i_r1


title: mES_Sox2_Serum_r1


title: mES_H3K4me3_24h_2i_r2

value: Millipore


title: mES_H3K4me3_Serum_r2


title: mES_H3K4me3_Serum_r1


title: mES_Nanog_24h_2i_r2

value: 2i for 24 hours_v1

value: Nanog

value: Cosmo Bio Ltd


title: mES_H3K4me3_3p_2i_r1


title: mES_H3K4me3_3p_2i_r2


title: mES_Nanog_24h_2i_r1


title: mES_Nanog_3p_2i_r2


title: mES_Nanog_Serum_r2


title: mES_TKO_Nanog_24h_2i

source_name: DNMT triple knockout mouse embryonic stem cell


title: mES_WT_24h_2i_rep2


title: mES_Nanog_3p_2i_r1


title: mES_Nanog_24h_2i_ab2

value: 2i for 24 hours_v3


title: Caput_sperm_rep2

city: Callaghan

first: Bettina

middle: P

last: Mihalas

state: NSW

address: Level 4 Life Science Building, University Drive

department: Life Sciences

country: Australia

institute: University of Newcastle

data_processing:
Basecalls were dones using CASAVA pipeline version 1.8.2.
Reads were screened and trimmed based on matches to Illumina smallRNA adaptors, PhiX, ChrM and rRNAs using flicker script with Illumina smallRNA kit with default settings
Cleaned reads were aligned using the bowtie ver 1.1.1 against human genome and miRNA database version 21
miRNA gene counts were summarised with custom shell scripts
Differential expression analysis was performed using the R-bioconductor libraries: limma and voom
Genome_build: miRNA database version 21
Supplementary_files_format_and_content: miRNA gene counts

source_name: Sperm

extract_protocol:
Total RNA was extracted from purified sperm cells (caput, corpus and cauda) using a Direct-zol™ RNA MiniPrep Kit (Zymo Research Corporation, Irvine, CA, USA) according to manufacturer’s instructions before being incubated with 1% DNase (Promega) to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epididymis

tag: tissue compartment

value: Caput

value: sperm

value: Swiss

tag: age

value: 8 weeks

value: Male


title: Cauda_sperm_rep2

value: Cauda

tag: strain


title: Corpus_sperm_rep1

value: Corpus

tag: Sex


title: Cauda_sperm_rep1


title: mouse_placenta2

data_processing:
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

extract_protocol: DNA was purified using Qiagen's Puregene kit.  MethylC-seq libraries were made using the Epicentre EpiGnome Methyl-Seq kit according to the manufacturer's recommendations except that 14 cycles of amplification were performed.

tag: genome version


title: Caput_sperm_rep1


title: mES_H3K4me3_24h_2i_r1

value: mouse embryonic stem cells


title: Corpus_sperm_rep2


title: mouse_placenta

data_processing:
genome version: mm10
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

value: placenta


title: mES_Pou5F1_2i

value: 2i for 24 hours


title: mES_Nanog_Serum_r1

value: Standard Serum


title: opossum_brain

data_processing:
genome version: monDom5
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

organism: Monodelphis domestica

value: brain


title: mES_H3K27me3_Serum

value: Millipore


title: mES_Pou5F1_Serum

value: Santa Cruz


title: mES_Nanog_Serum_GFPHigh

value: Nanog

value: Cosmo Bio Ltd


title: mES_WCE


title: opossum_EEM

source_name: extraembryonic membrane

value: extraembryonic membrane


title: mES_H3K27me3_24h_2i


title: cow_placenta4

organism: Bos taurus

tag: biological replicate


title: cow_placenta3


title: dog_placenta3

organism: Canis lupus familiaris

tag: breed

value: terrier

value: gestation day 30-35


title: dog_placenta2

value: pit bull

value: gestation day 21-25


title: cow_placenta2


title: dog_brain

data_processing:
genome version: canFam3
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

source_name: cerebrum

value: cerebrum

value: bulldog

value: 12 years old


title: cow_oocyte_1

data_processing:
genome version: bosTau7
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

source_name: oocytes

extract_protocol: MII oocytes were produced by in vitro maturation of GV oocytes collected from slaughter house derived ovaries according to standard protocols.  Oocyte maturation was confirmed by presence of a polar body. Then, zona pellucida and first polar body were removed by incubation in 0.5% pronase solution for 2 minutes and vigorous pipetting. Zona-free oocytes were snap frozen in liquid nitrogen and stored at -80°C until DNA extraction.  DNA from 100 cells was purified using Zymo's Quick-gDNA MicroPrep kit and the MethylC-seq libraries were prepared using Zymo's Pico Methyl-seq Library Prep Kit according to the manufacturer's instructions.

value: oocytes

value: MII stage

value: biological replicate 1


title: mES_H3K27me3_3p_2i

value: mouse embryonic stem cells

value: 2i for 3 passages


title: dog_placenta

value: placenta

value: Vizsla

value: gestation day 40-45


title: cow_placenta


title: CT53

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

data_processing:
Align raw data using RNA-Seq Unified Mapper (RUM) to the mm9 genome, and RefSeq, UCSC, and Vega transcriptome annotations. RUM also calculated RPKM values for each transcript, exon, and intron in these annotations.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain RPKM values for each exon, intron, and transcript contained in the UCSC, RefSeq, and Vega annotations.
Supplementary_files_format_and_content: bedgraph files contain coverage plots for uniquely-aligned reads.
Supplementary_files_format_and_content: *.bed files contain high-confidence gapped-junctions mapped by uniquely-aligned reads.

source_name: Liver

growth_protocol: C57/BL6 mice were entrained to a 12h light : 12h dark schedule for one week. Mice were then transferred to complete darkness for one day before collection. Mice were housed in light-tight boxes for the duration of the experiment.

extract_protocol: polyA RNA selected from total RNA using Dynabeads

treatment_protocol: Liver chunks were dissected, snap frozen in liquid nitrogen, and RNA was extracted using Trizol reagent & RNeasy columns. RNA from 3 animals was pooled equally to create 40 ug of total RNA. PolyA RNA selected from total RNA using Invitrogen Dynabeads (cat# 610.06). Generate libraries using a modified version of Illumina Paired-End Library protocol (cat# PE-102-1001). RNA was fragmented for 5 minutes using Ambion Fragmentation Reagents (cat# AM8740). Fragmented RNA was converted into cDNA using Invitrogen SuperScript ds-cDNA kit (cat# 11917-010). Blunt ended cDNA fragments generated with Epicentre End Repair kit (cat# ER0720) and 'A' overhang created using NEB Klenow Fragment (cat# MO212s). Illumina Paired-End Adapters (from cat# PE-102-1001) ligated using Promega LigaFast kit (cat# M8221). Ligation products run on a 2% agarose gel and slice between 350-500bp cut from gel. Products purified using Qiagen Gel Extraction Kit (cat# 28704). Ligation products amplified with 13 PCR cycle using Illumina's paired-end primer mix (from cat# PE-102-1001) and NEB Phusion PCR Master Mix (cat# F-531S).

value: Liver

tag: genotype

value: WT

tag: time


title: CT59

tag: tissue


title: CT65


title: CT29


title: CT41


title: cow_oocyte_2

value: biological replicate 2


title: input DNA

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

data_processing:
Illumina Casava1.7 software used for basecalling.
After QC with Fastqc, reads were aligned with BWA and peaks were subsequently called with MACS1.4 using input DNA as control, p-value cutoff  1.00e-05
Genome_build: hg19
Supplementary_files_format_and_content: ALL_SIL_TLX1_peaks.bed: peak location bed file
Supplementary_files_format_and_content: ALL_SIL_TLX1_peaks.txt: MACS1.4 output including FDR
Supplementary_files_format_and_content: ALL_SIL_TLX1_summits.bed: summit location bed file

organism: Homo sapiens

source_name: ALL-SIL cell line

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol:
DNA was purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime).
standard illumina library prep, unstranded paired end

treatment_protocol: The ChIP-protocol has been adapted from previous studies (Lee et al. 2006). In brief, 100*106 cells were cross-linked with 1,1% formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. Next, the purified chromatin was fragmented to 200-300 bp fragments by sonication (Covaris, S220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 100 ul of protein-A coated beads (Thermo-Scientific, catalog number 53139) and 10 μg of fibrillarin-specific (Abcam, ab5821) or TLX1-specific antibody (Santa-Cruz Biotechnology, sc-880). The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65°C overnight.

tag: cell line

value: ALL-SIL

tag: chip antibody

value: none (input)


title: Clk-Mut CT22

organism: Mus musculus

growth_protocol: C57/BL6 mice with ClockΔ19 mutation as well as the Scg2:tTA and tetO::Clock-HA transgenes, were entrained to a 12h light : 12h dark schedule for one week. Mice were then transferred to complete darkness and housed in light-tight boxes for the duration of the experiment. Collection began one day following the shift to total darkness

extract_protocol: Liver chunks were dissected, snap frozen in liquid nitrogen, and RNA was extracted using Trizol reagent & RNeasy columns. RNA from 3 animals was pooled equally to create 40 ug of total RNA. PolyA RNA selected from total RNA using Invitrogen Dynabeads (cat# 610.06). Generate libraries using a modified version of Illumina Paired-End Library protocol (cat# PE-102-1001). RNA was fragmented for 5 minutes using Ambion Fragmentation Reagents (cat# AM8740). Fragmented RNA was converted into cDNA using Invitrogen SuperScript ds-cDNA kit (cat# 11917-010). Blunt ended cDNA fragments generated with Epicentre End Repair kit (cat# ER0720) and 'A' overhang created using NEB Klenow Fragment (cat# MO212s). Illumina Paired-End Adapters (from cat# PE-102-1001) ligated using Promega LigaFast kit (cat# M8221). Ligation products run on a 2% agarose gel and slice between 350-500bp cut from gel. Products purified using Qiagen Gel Extraction Kit (cat# 28704). Ligation products amplified with 13 PCR cycles using Illumina's paired-end primer mix (from cat# PE-102-1001) and NEB Phusion PCR Master Mix (cat# F-531S).

treatment_protocol: 3 days prior to constant conditions, ClockΔ19, Scg2:tTA and tetO::Clock-HA mice were treated with doxycycline in their drinking water (30 ug/ml). Treatment continued for the duration of the experiment.

value: Clock-delta-19, Scg2:tTA and tetO::Clock-HA

tag: timepoint


title: 3_Day_Rep_1

description:
temperature at sampling: 27 C
photoperiod: 16 hr
no glyphosate treatment

data_processing:
Raw sequence reads were checked for quality using the FastQC0.10.0 program and quality trimmed using the Sickle-quality-base-triming program in the iPlant discovery environment with the parameters minimum quality = 20 and minimum number of bases = 70.
All trimmed illumina read files from all experiments for each paired end were concatenated and subjected to kmer reduction using the trinity kmer reduction program to a maximum of 30 kmers. The resulting file was assembled using Trinity with iPlant rescources and default parameters.
The program RSEM was used to map individual fragments to the assembled transcriptome and the resulting raw expression data in transcripts per million (number of fragments mapping to each contig/gene-counts per million) was normalized using EBseq program associated with RSEM, and likelihood ofdifferential expression was determined by the EBseq program.
Genome_build: trinity -assembled transcriptome from all available RNAseq data.

treatment_protocol:
plants were greenhouse-grown to ~3 months of age and then placed ina growth chamber for 1 week prior to treatment. Crown buds were harvested at ~12:00 am 3 days following excision of the aerial shoot.
paradormancy release: The aerial portion of the stem was excised at soil level and crown buds were collected at the specified times and placed in liquid N2 for storage prior to RNA extraction.

tag: cultivar

value: crown buds of leafy spurge


title: 3_Day_Rep_3


title: 3_Day_Rep_2


title: CT23


title: H3K27ac ChIP-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
reads were aligned with Bowtie2
peaks were called using MACS2.0
Genome_build: hg19
Supplementary_files_format_and_content: txt file with MACS2.0 output  including FDR

extract_protocol:
DNA was purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime).
library preparation was performed using the standard Illumina protocol
unstranded single end sequencing

treatment_protocol: The ChIP-protocol has been adapted from previous studies (Lee et al. 2006). In brief, 100*106 cells were cross-linked with 1,1% formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. Next, the purified chromatin was fragmented to 200-300 bp fragments by sonication (Covaris, S220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 100 ul of protein-A coated beads (Thermo-Scientific, catalog number 53139) and 10 μg of H3K27ac-specific antibody (Abcam, ab4729). The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65°C overnight.

tag: cell type

value: T-cell acute lymphoblastic leukemia (T-ALL) cell line

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: CT35


title: cow_brain

value: cerebrum

tag: developmental timepoint

value: adult


title: Clk-Mut CT28


title: 1_Day_Rep_4

treatment_protocol:
plants were greenhouse-grown to ~3 months of age and then placed ina growth chamber for 1 week prior to treatment. Crown buds were harvested at ~12:00 am 1 day following excision of the aerial shoot.
paradormancy release: The aerial portion of the stem was excised at soil level and crown buds were collected at the specified times and placed in liquid N2 for storage prior to RNA extraction.


title: 1_Day_Rep_3


title: Clk-Mut CT40


title: input DNA [for H3K27ac ChIP-seq]


title: 3_Day_Rep_4


title: human_cordblood

data_processing:
genome version: hg19
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

source_name: cordblood

value: cordblood

value: newborn


title: TLX1 ChIPSeq

value: anti-TLX1 (C-18 rabbit polyclonal antibody (sc-880), Santa Cruz Biotechnology)


title: horse_placenta

data_processing:
genome version: equCab2
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

organism: Equus caballus

value: placenta

value: full term


title: 1_Day_Rep_2


title: Clk-Mut CT34


title: CT47


title: 1_Day_Rep_1


title: paradormant_no_glyphosate_rep1

description:
no glyphosate treatment
MD_1

tag: treatment

value: Plants were greenhouse-grown to ~4 months of age. Crown buds were harvested at ~10:00 am.

tag: temperature at sampling

tag: photoperiod

value: 16 hr


title: 6_Hour_Rep_4

treatment_protocol:
plants were greenhouse-grown to ~3 months of age and then placed ina growth chamber for 1 week prior to treatment. Crown buds were harvested at ~12:00 am 6 hrs following excision of the aerial shoot.
paradormancy release: The aerial portion of the stem was excised at soil level and crown buds were collected at the specified times and placed in liquid N2 for storage prior to RNA extraction.


title: 6_Hour_Rep_1


title: 6_Hour_Rep_3


title: 6_Hour_Rep_2


title: 0_Hour_Rep_3

treatment_protocol:
plants were greenhouse-grown to ~3 months of age and then placed ina growth chamber for 1 week prior to treatment. Crown buds were harvested at ~12:00 am.
paradormancy release: The aerial portion of the stem was excised at soil level and crown buds were collected at the specified times and placed in liquid N2 for storage prior to RNA extraction.


title: 0_Hour_Rep_1


title: 0_Hour_Rep_2


title: M23NDcovS-SP-2

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

data_processing:
Basecalls performed using CASAVA version 1.8
The reads were aligned to the annotated genome of S. pyogenes M23ND using BWA v0.7. Only uniquely mappable reads were retained.
The expression levels were evaluated by counting the reads uniquely mapping to the encoding regions of the annotated genes in the genome and calculated as RPKM by normalizing to the total uniquely mappable reads and gene lengths.
The gene differential expression was evaluated using DESeq package in R environments. The negative binomial test was used to assess the significance p-value of the differential expression and Benjamini-Hochberg procedure was used for multiple test correction.
Genome_build: CP008695 (Streptococcus pyogenes M23ND)
Supplementary_files_format_and_content: Excel file for the gene expression values and differential expression.

organism: Streptococcus pyogenes

source_name: cell pellets

growth_protocol: covS- mutant strain and the isogenic covS+ derivative were grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY; BD-Difco) at 37°C under aerobic conditions. Cells were collected at logarithm phase (OD600=0.6) and stationary phase (OD600=1.0).

extract_protocol:
The cell pellets were harvested by centrifuge at 10,000 rpm for 5 minutes. Total RNA was isolated and purified from the cell pellets using the DNeasy Blood & Tissue Kit (GIAGEN) according to the manufacture’s protocol.
The library was constructed using the Epicentre ScriptSeq v2 Complete Kit (Bacteria) and protocol companion (Illumina, Inc., San Diego, CA). Briefly, the total RNA was treated with rRNA-depletion using the Ribo-Zero rRNA removal solution specifically for gram-positive organisms. The remaining RNA was purified using Agencourt AMPure XP Beads, then heat fragmented at 85°C for 5 minutes. The ends of the fragments were reparied and ligated with adapters. The ligated fragments were PCR amplified and library fragments of ~200 bp band were isolated from the gel. The pair-end 2x79bp sequencing was performed using the Illlumina Miseq platform and Miseq Reagent Kit v3 (Illumina, Inc).

treatment_protocol: The cells were digested with mutanolysin (500u/ml) in 300lm spheroplasting buffer (20mM Tris-HCl pH6.8, 10mM MgCl2, 56% raffinose) and incubated with 100mg/ml chloramphenicol at 37’C for 60 minutes.

tag: strain

tag: growth

value: Stationary phase

value: Replicate 2


title: M23NDcovS-SP-1

tag: biological replicate

value: Replicate 1


title: M23NDcovSplusSP-1

tag: genotype


title: M23NDcovSplusSP-2


title: M23NDcovS-LP-1

value: Logarithm phase


title: squirrel_monkey_ placenta

data_processing:
genome version: saiBol1
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

organism: Saimiri boliviensis

value: full term (Cesarean section)


title: M23NDcovSplusLP-1