title: Sc_RS453-Tho2

city: Göttingen

first: Carlo

last: Bäjen

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

description: Protocol: PAR-CLIP

data_processing:
Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15nt, or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.1.1) using the short read aligner Bowtie (version 0.12.7)  with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals)
Genome_build: S. cerevisiae genome (sacCer3, version 64.1.1)
Supplementary_files_format_and_content: tab delimited text files containing genomic locations, p-values and occupancies

source_name: PAR-CLIP of TAP-Tho2

growth_protocol: Yeast cells expressing the TAP-tagged protein were grown at 30 °C from OD600 ∼0.1 to OD600 ∼0.5 in CSM minimal medium (Formedium) supplemented with 10 mg/l uracil, 100 µM 4-thiouracil (4tU) and 2 % glucose. After reaching OD600∼0.5, another 900 µM 4tU were added and cells were grown further for 4 h (OD600∼1.3-1.6).

extract_protocol:
Cells were lysed by bead beating and the lysate was sonicated. Immunoprecipitation was performed on a rotating wheel for 2 h at 4 °C with rabbit IgG-conjugated Protein G magnetic Dynabeads (Invitrogen). Crosslinked RNA was partially digested with RNase T1 and prepared for cDNA library preparation.
Data acquisition were performed as described by Schulz and Schwalb et al. (Cell, 2013) with minor modifications. Following adapter ligation, RNA was recovered by Proteinase K digestion for 2 h at 55 °C, and subsequent acidic phenol/chloroform extraction. Reverse transcription was done for 1 hr at 44 °C using SuperScript III RTase (Invitrogen). PCR amplification was performed using the NEXTflex barcode primer kit (Bioo Scientific).

treatment_protocol: 4tU-labeled yeast cells were UV-irradiated with an energy dose of 12 J/cm2 at 365 nm.

tag: tagged protein

tag: growth medium

value: Minimal complete medium with 4tU


title: Sc_BY4741-Yra1

status: Public on Jul 23 2014

type: SRA

country: Germany

description: Protocol: PAR-CLIP

library_source: transcriptomic

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: PAR-CLIP of Yra1-TAP

tag: strain


title: Sc_BY4741-Sub2

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Sub2-TAP


title: 34766_PBMC_PEG-IFNa2a_D7

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

description:
s_2_1_25_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

data_processing:
RNA-Seq data were aligned to a provisional assembly of Indian Macaca mulatta  (MuSuRCA rhesus assembly v.4) using STAR version 2.3.0e. {Dobin 2012}; parameters were set using the annotation as a splice junction reference, un-annotated non-canonical splice junction mappings and non-unique mappings were removed from downstream analysis.
Transcripts were annotated using the provisional UNMC annotation v4.12 Norgren Accession pending. Transcript assembly, abundance estimates, and differential expression analysis was performed using Cufflinks v2.1.1 and Cuffdiff 2{Trapnell 2013}.
Group 1 was comprised of 166 samples and contained the samples from PBMCs from the saline+SIV, IFN-1ant+SIV, and pegylated IFN_2a-treated+SIV animals, and from samples for the analysis of PBMCS, LN CD4+ T cells and rectal biopsies of uninfected, IFNa treated animals; the average number of mapped reads was 12,188,890 (range: 3,237,374-87,371,564).
Group 2 was comprised of the LN CD4 T cells from the three SIV-infected groups consisting of 37 samples, the average mapped read count for this group was 4,898,448 (range: 1,173,455-19,310,483).
Genome_build: MuSuRCA rhesus assembly v.4
Supplementary_files_format_and_content: Tab delimited text with rows of transcript ID's and columns of sample ID's and sample FPKMs

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Total RNA was extracted from samples using RNAzol RT and was enriched for polyadenylated transcripts by hybridization with oligo-dT(25) magnetic beads.
Enriched polyadenylated RNA was fragmented randomly with heat and divalent cations, and reverse-transcribed from random hexamer primers.  Second strand synthesis was then performed using RNAse-H and DNA Polymerase I.  Double-stranded cDNA was end repaired and A-tailed, and then ligated to a hairpin-loop sequencing adaptor (New England Biolabs).  Libraries were then enriched and barcoded by PCR, validated on a Bioanalyzer, and quantified by qPCR.  Individually libraries were then pooled and quantified again before cluster generation and sequencing.

tag: animal id

tag: treatment group

tag: day post infection


title: 5F0_PBMC_Placebo_D10

description:
s_6_1_20_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

value: Placebo


title: 33880_PBMC_PEG-IFNa2a_D7

description:
s_2_1_23_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: T4226_PBMC_Placebo_D7

description:
s_1_1_12_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: Sc_BY4741-Nam8

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Nam8-TAP


title: Sc_BY4741-Npl3

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Npl3-TAP


title: OF9_PBMC_Placebo_D10

description:
s_6_1_25_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: Sc_BY4741-Pub1

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Pub1-TAP


title: Sc_BY4741-Pab1

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Pab1-TAP


title: 7_68_PBMC_Placebo_D7

description:
s_3_1_4_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_58_PBMC_IFNRa_D7

description:
s_5_1_2_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

value: IFNRa


title: Sc_BY4741-Mud1

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Mud1-TAP


title: Sc_BY4741-Mpe1

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Mpe1-TAP


title: 7_70_PBMC_Placebo_D7

description:
s_6_1_5_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF9_PBMC_Placebo_D7

description:
s_6_1_23_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: OF1_PBMC_Placebo_D7

description:
s_1_1_7_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 5F0_PBMC_Placebo_D7

description:
s_5_1_27_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: Sc_BY4741-Ist3

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Ist3-TAP


title: Sc_BY4741-Mex67

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Mex67-TAP


title: Sc_BY4741-Hrb1

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Hrb1-TAP


title: 6D7_PBMC_Placebo_D7

description:
s_5_1_21_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_Rectum_Uninf_D7

description:
s_6_1_20_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

source_name: Rectum

value: Uninf


title: Sc_BY4741-Snp1

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Snp1-TAP


title: AV21_Rectum_Uninf_D7

description:
s_6_1_21_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_Rectum_Uninf_D7

description:
s_6_1_22_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: Sc_BY4741-Cbc2

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Cbc2-TAP


title: ZE89_PBMC_Placebo_D7

description:
s_6_1_2_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: BB85_PBMC_Placebo_D7

description:
s_2_1_6_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: Sc_BY4741-Hpr1

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Hpr1-TAP


title: Sc_BY4741-Nab2

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Nab2-TAP


title: Sc_BY4741-Gbp2

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Gbp2-TAP


title: AZ28_PBMC_Uninf_D7

description:
s_5_1_15_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_LN CD4_Uninf_D7

description:
s_6_1_12_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

source_name: lymph node CD4 T cells


title: AV21_PBMC_Uninf_D3

description:
s_5_1_11_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

source_name: PBMC


title: AV21_PBMC_Uninf_D7

description:
s_5_1_14_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_PBMC_Uninf_D3

description:
s_5_1_10_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_LN CD4_Uninf_D7

description:
s_6_1_10_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_LN CD4_Uninf_D7

description:
s_6_1_11_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_PBMC_Uninf_D3

description:
s_5_1_12_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_50_PBMC_IFNRa_D0

description:
s_5_1_5_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_52_PBMC_IFNRa_D0

description:
s_6_1_6_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_66_PBMC_IFNRa_D0

description:
s_1_1_4_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 30297_PBMC_PEG-IFNa2a_D0

description:
s_1_1_20_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_58_PBMC_IFNRa_D0

description:
s_1_1_2_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE06_PBMC_IFNRa_D0

description:
s_2_1_7_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 34766_PBMC_PEG-IFNa2a_D0

description:
s_1_1_25_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE89_PBMC_Placebo_D0

description:
s_2_1_2_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 7_70_PBMC_Placebo_D0

description:
s_3_1_5_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_PBMC_Uninf_D7

description:
s_5_1_13_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: T4226_PBMC_Placebo_D0

description:
s_6_1_12_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mE65ExE-2

city: San Francisco

first: Michelle

middle: M

last: Chan

state: CA

institute: UCSF

description: RRBS

library_source: genomic

data_processing:
Alignment using Maq with the following params: maq map -D -s 0 -M c -e 100
Count the number methylated vs unmethylated CpGs (C vs T; G vs A on reverse)
Join the cpg files together
Add the CpG density column (#CpGs +/- 50bp)
Tile the cpg file
Average technical replicates
Supplementary_files_format_and_content: .cpgs: (chromosome,position,seenCount,methylatedCount);hDev100bpMeFinal.txt/mDer100bpMe.txt: (position,100bp methylation value,CpG density)
Genome Build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: E6.5 Extraembryonic endoderm

growth_protocol: hESCs were derived and cultured on gamma-irradiated mouse embryonic fibroblasts (MEFs) in derivation media consisting of KO-DMEM (Life Technologies), 15% KO-SR (Life Technologies), 2.5% Fetal Bovine Serum (FBS) (Hyclone), 2mM Glutamax, 1% non-essential amino acids, 50units/ml penicillin and 50μg/ml streptomycin (Life Technologies), 0.055mM β-mercaptoethanol (Life Technologies), 10ng/ml bFGF (Millipore).  mESCs were derived from immunosurgically isolated ICM of E3.5 blastocysts from C57Bl/6 x 129S1/SvIMJ hybrid crosses and propogated on gamma-irradiated MEFs in one of three conditions: mES - 15% Fetal Bovin Serum (Hyclone) supplemented KO-DMEM plus LIF (Millipore); mPD - 15% FBS supplemented KO-DMEM plus LIF and 1 µM PD0325901 (Stemgent), or in N2/B27 supplemented KO-DMEM containing LIF, 1 µM PD0325901 and 3 µM CHIR99021 (Stemgent) (m2i).  All mouse media were additionally supplemented with 2mM Glutamax, 1% non-essential amino acids, 50units/ml penicillin and 50μg/ml streptomycin (Life Technologies), 0.055mM β-mercaptoethanol (Life Technologies).

extract_protocol:
DNA was extracted from all tissue using 14 hour incubation in 300 ug/mL Proteinase K followed by ethanol precipitation and elusion in EB buffer
Reduced representation bisulfite libraries were prepared from Proteinase K treated, MspI digested DNA following ligation with methylated standard adapters, size selection, bisulfite conversion, and amplification of the final libraries. Reduced representation bisulfite sequencing libraries are designed to enrich for a consistent subset of CpGs in the genome using MspI digestion (C'CGG cutting), adapater ligation and bisulfite conversion to generate base resolution maps of cytosine methylation on a consistent genome scale

treatment_protocol: hICM, hTE,mICM and mTE were isolated using standard micromanipulation equipment and a Hamilton Thorne XYClone laser with 300 µs pulsing at 100% intensity. hBlast and 8c embryos were thawed using the Quinn’s Advantage Embryo Thaw Kit (SAGE), screened for morphology, and purified from the Zona Pellucida using Acid Tyrode's solution (Sigma).  Human sperm was purified via centrifugation through a PureCeption gradient solution  (PureCeption 100% Isotonic Solution, Quinn’s Advantage Medium with HEPES, In-Vitro Fertilization Inc) of 90% and 47% in a 15ml conical tube.  C57Bl/6 x 129S1/SvIMJ E6.5 Epi and ExE were dissected from implanted deciduae and purified of visceral endoderm via incubation in 0.5% trypsin/2.5% pancreatin (Sigma) dissolved in PBS for 20 minutes at 4ºC.

tag: developmental stage

value: E6.5 Extraembryonic endoderm

tag: passage

tag: sequenced molecule

value: Msp1 digested bisulfite converted genomic DNA


title: mTE-2

description: RRBS

source_name: Trophectoderm

value: Trophectoderm


title: mE65Epiblast-2

description: RRBS

source_name: E6.5 Epiblast

value: E6.5 Epiblast


title: mESp0-3-2

description: RRBS

source_name: ESC outgrowth - mES

value: ESC outgrowth - mES


title: BB85_PBMC_Placebo_D0

description:
s_4_1_6_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mESp0-1

description: RRBS


title: mESp0-2

description: RRBS


title: 7_68_PBMC_Placebo_D0

description:
s_5_1_4_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: m2ip5-3

description: RRBS

source_name: ESC passage 5 - 2i

value: ESC passage 5 - 2i


title: OF9_PBMC_Placebo_D0

description:
s_6_1_22_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 5F0_PBMC_Placebo_D0

description:
s_5_1_25_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: m2ip5-1

description: RRBS


title: m2ip5-5

description: RRBS


title: OF1_PBMC_Placebo_D0

description:
s_4_1_7_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: ZE80_PBMC_IFNRa_D0

description:
s_3_1_12_run1
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: 33880_PBMC_PEG-IFNa2a_D0

description:
s_1_1_23_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mPDp5-1

description: RRBS

source_name: ESC passage 5 - PD

value: ESC passage 5 - PD


title: AV21_PBMC_Uninf_D0

description:
s_5_1_8_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mESp5-2

description: RRBS

source_name: ESC passage 5 - mES

value: ESC passage 5 - mES


title: 6D7_PBMC_Placebo_D0

description:
s_5_1_20_130430_SN622_0218_AC192CACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AS60_PBMC_Uninf_D0

description:
s_5_1_7_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mESp5-1

description: RRBS


title: mICM-2

description: RRBS

source_name: Inner Cell Mass

value: Inner Cell Mass


title: AZ28_PBMC_Uninf_D0

description:
s_5_1_9_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_Rectum_Uninf_D-7

description:
s_6_1_19_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mPDp0-4

description: RRBS

source_name: ESC outgrowth - PD

value: ESC outgrowth - PD


title: mPDp5-3

description: RRBS


title: mPDp0-2

description: RRBS


title: AV21_Rectum_Uninf_D-7

description:
s_6_1_18_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

source_name: Rectum


title: AS60_Rectum_Uninf_D-7

description:
s_6_1_16_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mPDp0-1

description: RRBS


title: mE65Epiblast-1

description: RRBS


title: mE65ExE-1

description: RRBS


title: AZ28_LN CD4_Uninf_D-7

description:
s_6_1_9_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_LN CD4_Uninf_D-7

description:
s_6_1_8_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mPDp5-2

description: RRBS


title: Sc_BY4741-Yth1

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Yth1-TAP


title: AS60_LN CD4_Uninf_D-7

description:
s_6_1_7_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AV21_PBMC_Uninf_D-7

description:
s_5_1_2_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: Sc_BY4741-Rna15

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Rna15-TAP


title: m2ip0-2

description: RRBS

source_name: ESC outgrowth - 2i

value: ESC outgrowth - 2i


title: AZ28_PBMC_Uninf_D-7

description:
s_5_1_3_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: m2ip0-1

description: RRBS


title: mTE-1

description: RRBS


title: Sc_BY4741-Mud2

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Mud2-TAP


title: AS60_PBMC_Uninf_D-7

description:
s_5_1_1_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: Sc_BY4741-Luc7

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Luc7-TAP


title: Sc_BY4741-Cft2

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Cft2-TAP


title: AS60_PBMC_Uninf_D-4

description:
s_5_1_4_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt

source_name: PBMC


title: AV21_PBMC_Uninf_D-4

description:
s_5_1_5_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: AZ28_PBMC_Uninf_D-4

description:
s_5_1_6_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt


title: mICM-1

description: RRBS


title: m2ip0-3

description: RRBS


title: AP006

status: Public on Jul 22 2014

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Raw reads were aligned to hg19 using Tophat2 with --no-novel-juncs.
Expression levels (FPKM) were computed using Cufflinks2.
Genome_build: hg19

molecule: polyA RNA

organism: Homo sapiens

source_name: non-neoplastic brain tissue

extract_protocol:
Total RNA was isolated from the tissue specimens using the Qiagen TissueLyzer system with Qiazol and steel beads.
Poly(A)+ RNA-Seq libraries were constructed using the Illumina TruSeq v2 RNA-Seq kit.

tag: tissue type

value: non-neoplastic brain


title: AP005


title: AP004


title: AP003


title: EM2-R

city: Durham

first: Joshua

middle: Aaron

last: Granek

state: NC

address: Box 3568, 213 Research Drive

department: Department of Biostatistics and Bioinformatics

institute: Duke University School of Medicine

description: FK506 resistant epimutant

data_processing:
Basecalls performed using CASAVA v.1.8.2
Raw sRNA sequences were processed using fastx_clipper <http://hannonlab.cshl.edu/fastx_toolkit/> to remove adapter sequences
Trimmed reads were then mapped to the reference genome using TopHat (TopHat version 2.0.5, Bowtie version 2.0.0.7, Samtools version 0.1.18)
Per gene read counts were determined using htseq-count <http://dx.doi.org/10.1101/002824>
Genome_build: Mucor circinelloides CBS277.49 v2.0 genome, JGI <http://genome.jgi-psf.org/Mucci2/Mucci2.home.html>
Supplementary_files_format_and_content: .tab files were generated using htseq, for each row, column 1 is gene name, and column 2 is the raw (not normalized) read count for that gene for reads on the either the sense strand (*sense_counts.tab), antisense strand (*anti_counts.tab), or sense and antisense strands (*both_counts.tab)

organism: Mucor lusitanicus

growth_protocol:
grown on MMC media pH 4.5, supplemented with 1 μg/mL of FK506
grown on MMC media pH 4.5

extract_protocol:
mycelia were frozen in liquid nitrogen, RNA was extracted with the mirVana miRNA isolation kit (Ambion), extracted RNA was size-fractioned by electrophoresis and the 18-24 nt fraction purified from the gel
strand-specific sRNA libraries were prepared from 18-24nt fraction using the TruSeq Small RNA Sample Prep Kit (Illumina)

treatment_protocol: epimutants were obtained by growth on YPD containing 1 μg/mL of FK506 for three days to three-four weeks at room temperature, until patches with hyphal growth were observed, followed by at least three generations of vegetative growth in the presence of FK506 to ensure a high proportion of the nuclei in the mycelium syncytium were silenced

value: NRRL 3631

tag: genotype/variation

value: FK506 resistant epimutant

tag: phenotype

value: FK506 resistant


title: AP002


title: EM1-R

description: FK506 resistant epimutant


title: AP001


title: WT

description: wildtype

source_name: WT

growth_protocol:
grown on MMC media pH 4.5
grown on MMC media pH 4.5

value: wildtype

value: FK506 susceptible


title: JJ014


title: EM3-S

description: FK506 susceptible revertant derived from EM3-R

treatment_protocol: revertants were obtained by passage on drug free media


title: JJ013


title: JJ015


title: BJ030


title: EM3-R

description: FK506 resistant epimutant


title: BJ029


title: BJ031


title: BJ024


title: BJ028


title: Sc_BY4741-Msl5

description: Protocol: PAR-CLIP

source_name: PAR-CLIP of Msl5-TAP

value: Minimal complete medium with 4tU


title: BJ027


title: BJ026


title: JJ035

source_name: glioma tissue - contrast-enhancing sample

value: glioma - contrast-enhancing sample


title: JJ039


title: JJ037


title: BJ022


title: BJ023


title: EM1-S

description: FK506 susceptible revertant derived from EM1-R


title: BJ019


title: BJ010


title: BJ009


title: BJ017


title: BJ005


title: BJ001


title: PC115


title: BJ011


title: BJ002


title: PC52


title: BJ004


title: PC112


title: BJ014


title: BJ025


title: PC138


title: PC141


title: PC123


title: PC120


title: PC56


title: PC71


title: PC67


title: PC140


title: PC64


title: PC132


title: PC136


title: PC135


title: PC131


title: PC133


title: BJ006


title: PC63


title: PC118


title: PC125


title: PC47


title: PC124


title: JJ038

source_name: glioma tissue - non-enhancing FLAIR+ sample

value: glioma - non-enhancing FLAIR+ sample


title: PC119


title: JJ036


title: PC61


title: PC57


title: PC117


title: PC110


title: JJ034


title: PC116


title: PC53


title: PC137


title: PC55


title: PC60


title: PC66


title: PC134


title: PC128


title: PC129


title: PC68


title: PC114


title: PC65


title: PC127


title: PC130


title: PC121


title: PC126


title: BJ018


title: PC122


title: BJ021


title: BJ020


title: PC72


title: BJ013


title: BJ016


title: PC139


title: BJ003


title: BJ015


title: BJ008


title: BJ012


title: BJ007


title: WGBS_human_postimplantation_embryo_liver_lane3

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

country: China

institute: Liangzhu Laboratory

description: processed data file: WGBS_Liver_methylation_calling.bed.txt.gz

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
For RRBS and WGBS samples, bisulfite-converted reads were aligned to the reference genome (hg19) using Bismark software (version 0.7.0). For the RNA-Seq samples, cleaned reads were mapped to the reference genome (hg19) using BWA tools (version 0.6.2-r126).
For RRBS and WGBS samples, the DNA methylation levels of the cytosines (in CpG, CHH or CHG context) were estimated using comstomized Perl scripts. While the genes expression levels were calculated using the comtomized Perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: For RRBS and WGBS samples, the processed txt files include the DNA methylation levels of cytosines in CpG, CHH and CHG context. And for the RNA-Seq samples, the processed textfiles include the normalized expression levels of the genes.

source_name: liver

extract_protocol:
For RRBS samples, cells or embryos were directely picked into the lysis buffer which contained protease to release the naked DNAs. For WGBS samples, genomic DNAs were extracted from the embryos using the Dneasy Blood & Tissue Kit (Qiagen). And for the RNA-Seq samples, total RNAs were extracted using the RNeasy Mini Kit (Qiagen).
For RRBS samples, cells were picked into the lysis buffer to release naked DNA; then the released DNAs were digested with MspI, then filled-in and tailed with an extra "A" , then ligated with Illumina indexed adaptors. Bisulfite conversion was performed under the manufacturer’s instructions of the MethyCode DNA Methylation Kit (Invitrogen) with minor modification, the converted DNAs were enriched by two rounds of PCR amplifications and size-selected after running 12% native polyacrylamide TBE gel. For WGBS samples, DNAs isolated from the embryos were sonicated into small fragments, then the endsof the DNAs were blunted, dA-tailed and ligated with the premethylated adapters. Then the ligated DNAs were bisulfite-converted and amplified. As for the RNA-Seq samples, total RNAs were extracted from the postimplantation embryos using RNeasy Mini Kit (Qiagen), and RNA sequencing libraries were constructed under the standard protocol of illumina. The quality-ensured libraries were used for pair-ended deep sequencing on Illumina HiSeq2000 Sequencer.

value: postimplantation embryo

tag: molecule subtype

value: bisulfite treated genomic DNA


title: WGBS_human_ICM_lane2

description: processed data file: WGBS_ICM_methylation_calling.bed.txt.gz

source_name: inner cell mass

value: late blastocyst


title: WGBS_human_postimplantation_embryo_liver_lane2


title: Bulk_RNA_human_postimplantation_embryo3

source_name: postimplantation embryo

value: cDNA


title: Bulk_RNA_human_postimplantation_embryo1


title: scRRBS_human_Sperm4

source_name: sperm

value: sperm

value: MspI digested and bisulfite treated genomic DNA


title: scRRBS_human_Sperm2


title: scRRBS_human_MII_Oocyte1

source_name: metaphase II oocyte

value: oocyte


title: scRRBS_human_Sperm1


title: scRRBS_human_PN28

source_name: pronucleus

value: zygote


title: scRRBS_human_MII_Oocyte3


title: scRRBS_human_PN25


title: scRRBS_human_PN27


title: scRRBS_human_PN24


title: scRRBS_human_PN26


title: WGBS_human_ICM_lane1


title: scRRBS_human_PN23


title: WGBS_human_postimplantation_embryo_liver_lane1


title: scRRBS_human_PN19


title: scRRBS_human_PN18


title: scRRBS_human_PN21


title: scRRBS_human_PN16


title: scRRBS_human_PN17


title: scRRBS_human_PN20


title: scRRBS_human_MII_Oocyte2


title: scRRBS_human_Sperm3


title: scRRBS_human_PN15


title: scRRBS_human_PN13


title: scRRBS_human_PN8


title: scRRBS_human_PN11


title: scRRBS_human_PN10


title: scRRBS_human_PN12


title: scRRBS_human_PN9


title: scRRBS_human_PN7


title: scRRBS_human_PN4


title: scRRBS_human_PN6


title: scRRBS_human_PN3


title: R-PHH-GW4064

city: Piscataway

first: Le

last: Zhan

state: NJ

address: 170 Frelinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

description: PHH_GW vs DMSO_RNA seq_gene exp.diff

data_processing:
For RNA-seq, the obtained reads were aligned to the Homo sapiens reference genome (hg19) using TopHat (version 2.0.0)
The resulted alignments were then assembled into transcripts using Cufflinks (version 2.0.2).
Cuffdiff, a component of the Cufflinks package, was used to estimate FPKM (fragments per kilobase of exon model per million mapped fragments) and identify differentially expressed transcripts.
Finally the Baggerley’s test was used to perform the differential expression analysis.
Genome_build: hg19, ENSEMBL version 65 human genes
Supplementary_files_format_and_content: excel file with altered gene expression

source_name: primary human hepatocytes

growth_protocol: Primary human hepatocytes were cultured in 37 °C, 5% CO2 upon arrival. Three hours later, medium were refreshed with serum-free HMM Hepatocyte Maintenance Medium supplemented with dexamethasone, insulin, and GA-1000 (Lonza, Switzerland)

extract_protocol:
RNA extraced with TRIZol reagent followed by standard protocol
Illumina TrueSeqTM RNA Sample Prep Kit (San Diego, CA)

treatment_protocol: cells were treated with 5 μM GW4064 compound dissolved in 0.1% DMSO for 24 hours

tag: tissue

value: Liver


title: Bulk_RNA_human_postimplantation_embryo2


title: R-PHH-DMSO

description: PHH_GW vs DMSO_RNA seq_gene exp.diff

treatment_protocol: cells were treated with 0.1% DMSO control for 24 hours


title: scRRBS_human_PN2


title: PHH-GW4064-rIgG

data_processing:
After sequencing, raw data files were processed through Genome Analyzer Pipeline Software (Illumina)
For ChIP-seq, all sequenced paired-end reads were aligned to Homo sapiens version 19 (hg19) reference genome using bowtie (version 0.12.7).
Regions with read enrichment were detected using Model-based Analysis of ChIP-Seq (MACS v 1.4.1) method
By comparing with the rIgG background, non-specific peaks with false discovery rate (FDR) greater than 0.1 were eliminated.
Identified peaks were further split by Mali Salmon's Peak Splitter (http://www.ebi.ac.uk/bertone/software.html) and filtered by p-value of Poisson distribution lower than 10-5.
Peaks were annotated using R packages (http://www.r-project.org) based on the ENSEMBL version 65 human genes.
Genome_build: hg19, ENSEMBL version 65 human genes
Supplementary_files_format_and_content: processed files are in BEDGRAPH format; scores represent FXR antibody pull down normalized to rIgG control antibody

extract_protocol:
Cells were fixed, lysed, sonicated. Chromatin were pulled down by antibody
Illumina TrueSeqTM DNA Sample Prep Kit (San Diego, CA)

treatment_protocol: cells were treated with 5 μM GW4064 compound dissolved in 0.1% DMSO for 1 hour

tag: chip antibody

value: normal rabbit IgG (sc-2027, Santa Cruz)


title: PHH-GW4064-FXR

value: FXR (1:1 mixture of sc-1204x and sc-13063x, ChIP grade, Santa Cruz)


title: PHH-DMSO-FXR

treatment_protocol: cells were treated with 0.1% DMSO control for 1 hour


title: scRRBS_human_PN1


title: scRRBS_human_PN14


title: PHH-DMSO-rIgG


title: scRRBS_human_PN22


title: RRBS_Sperm2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Sperm2_methylation_calling.bed

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Bisulfite-converted reads were aligned to the human refference genome (hg9) using Bismark software with the default parameters.
CpG methylation level was estimated using comstomized Perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bed files which include the methylation level of cytosines in CpG, CHH and CHG context.

extract_protocol:
Single cells were picked into the lysis buffer which contained protease to release the naked DNAs
Cells were picked into the lysis buffer to release naked DNA; then the released DNAs were digested with MspI, then filled-in and tailed with an extra "A" , then ligated with Illumina indexed adaptors. Bisulfite conversion was performed under the manufacturer’s instructions of the MethyCode DNA Methylation Kit (Invitrogen) with minor modification, the converted DNAs were enriched by two rounds of PCR amplifications and size-selected after running 12% native polyacrylamide TBE gel. The quality-ensured libraries were used for pair-ended deep sequencing on Illumina HiSeq2000 Sequencer.


title: RRBS_Zygote2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Zygote2_methylation_calling.bed

source_name: zygote


title: RRBS_TE1_rep2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_TE1_methylation_calling.bed

source_name: trophectoderm cells

value: late blastocyst embryo


title: RRBS_TE3

description:
MspI digested and bisulfite treated genomic DNA
RRBS_TE3_methylation_calling.bed


title: RRBS_TE2_rep1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_TE2_methylation_calling.bed


title: RRBS_Postimplantation_embryo2_rep1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Postimplantation_embryo2_methylation_calling.bed


title: RRBS_Postimplantation_embryo1_rep2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Postimplantation_embryo1_methylation_calling.bed


title: RRBS_Postimplantation_embryo3_rep1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Postimplantation_embryo3_methylation_calling.bed


title: RRBS_Sperm1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Sperm1_methylation_calling.bed


title: RRBS_TE2_rep2


title: RRBS_Postimplantation_embryo1_rep1


title: RRBS_1st_PB3

description:
MspI digested and bisulfite treated genomic DNA
RRBS_1st_PB3_methylation_calling.bed

source_name: polar body

value: the first polar body


title: RRBS_Zygote1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Zygote1_methylation_calling.bed


title: RRBS_Sperm3

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Sperm3_methylation_calling.bed


title: RRBS_Postimplantation_embryo2_rep2


title: scRRBS_human_PN5


title: RRBS_TE1_rep1


title: RRBS_Postimplantation_embryo3_rep2


title: RRBS_Morula2_rep2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Morula2_methylation_calling.bed

source_name: morula

value: morula embryo


title: RRBS_Morula3_rep2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Morula3_methylation_calling.bed


title: RRBS_Sperm4

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Sperm4_methylation_calling.bed


title: RRBS_Morula3_rep1


title: RRBS_Morula2_rep1


title: input DNA

city: Leuven

first: Ksenia

last: Pougach

address: Gaston Geenslaan 1

department: CMPG

country: Belgium

institute: KU Leuven

description: sequenced with Illumina

data_processing:
Data were filtered using the following specifications (low quality reads (q< 30) and adaptor sequences were first trimmed by using Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
ChIP-exo reads were aligned to the S288C genome version R64-1-1 using BWA version 0.7.4 with the default parameters
Resuled bam files were sorted by picard version 1.100
Peaks were called using GEM version 2.41 with the following setting: --smooth 3 --mrc 20.
Genome_build: S288C, R64-1-1
Supplementary_files_format_and_content: bam files were generated by using BWA, samtools and picard

source_name: Saccharomyces cerevisiae s288c

growth_protocol: Cells were grown in YP+2% palatinose till the OD600=0,4. Approx. 10*8 cells were taken for each sample

extract_protocol:
Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to standart ChIP-exo protocol (Rhee, H.S., and Pugh, B.F. (2012). ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr. Protoc. Mol. Biol. Chapter 21, Unit 21.24.).

treatment_protocol: Cells were lysed according to standart ChIP-exo protocol (Rhee, H.S., and Pugh, B.F. (2012). ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr. Protoc. Mol. Biol. Chapter 21, Unit 21.24.).

tag: tag

value: HA

tag: library strategy

value: ChIP-exo

tag: chip-antibody


title: Yfl052w-HA tagged ChIP-exo 1

description: sequenced with Illumina

value: Anti-HA High Affinity; Rat monoclonal antibody (clone 3F10), Roche


title: RRBS_Morula1_rep2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_Morula1_methylation_calling.bed


title: RRBS_Morula1_rep1


title: RRBS_MII_Oocyte2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_MII_Oocyte2_methylation_calling.bed


title: RRBS_MII_Oocyte1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_MII_Oocyte1_methylation_calling.bed


title: RRBS_ICM3

description:
MspI digested and bisulfite treated genomic DNA
RRBS_ICM3_methylation_calling.bed


title: Drosophila sechellia male body small RNA

city: Stanford

first: Jaaved

last: Mohammed

address: 265 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
3' adapter sequences were trimmmed using the fastx_clipper utility
reads < 15nt in size were filtered
identical read sequences were collapsed using the fastq_collapser utility
Supplementary_files_format_and_content: read count table files (columns are read read sequence and number of reads)

organism: Drosophila sechellia

source_name: male bodies

extract_protocol:
Male bodies were isolated in bulk using sieves. Animals were flash frozen in liquid nitrogen followed by vortexing. This procedure severs heads from the thorax and abdomen allowing separation of these two body parts when sifted through chilled fine mesh sieves. Here we used a .600mm sieve to collect male bodies. Total RNA was then extracted from the bodies using TRIzol according to manufacturer protocol.
For Illumina GAII Libraries: From total RNA, ~18-26 nt fraction was isolated using PAGE and cloned using ligation to adapters requiring 5' monophosphate and 3' OH.     For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol. Small RNAs in the 18-29nt size range were first isolated from total RNA by PAGE purification before cloning. PAGE purification was also performed after ligation of RNAs to 3’ and 5’ linkers before processing in subsequent steps. All enzymatic reactions and oligos were used as indicated by manufacturer.

value: abdomen and thorax


title: Drosophila yakuba male body small RNA

organism: Drosophila yakuba


title: Drosophila simulans male body small RNA

organism: Drosophila simulans


title: MAF9_Mll4mm_Foxo3wt

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7.0 or 1.8.0 software used for basecalling.
Sequenced reads were trimmed, and masked for low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.8 determined uniquely aligned reads with at most 2 mismatches.
RNA-Seq sequenced reads were mapped to mm9 using Tophat v2.0.11. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using exons of each transcript annotated by BioConductor's GenomicFeatures 1.10.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files including read counts per entrez gene id.

growth_protocol: WT and MLL4-/- bone marrow cells were co-transformed with MLL-AF9-neo and either EV or a retrovirus encoding FOXO3-IRES-GFP. One week after selection in G418, GFP+ cells were sorted.

extract_protocol: Total RNA was isolated using TRIzol (Ambion). RNA was isolated  using RNeasy kit (Qiagen) following manufacturer's protocol. Quality was determined using Agilent BioAnalyzer. RNA was then prepared for sequencing using the TruSeq RNA sample prep kit (Illumina).  Four libraries were sequenced on one lane of HiSeq 2000.

tag: cell type

value: sorted MLL4-/- WBM cells co-infected with MLL-AF9-neo and EV

tag: genotype

tag: growth duration

value: 14 days


title: MAF9_Mll4mm_Foxo3pp

value: sorted MLL4-/- WBM cells co-infected with MLL-AF9-neo and FOXO3-IRES-GFP

tag: strain


title: MAF9_Mll4wt

growth_protocol: MLL4f/f MxCre or WT MxCre bone marrow cells were retrovirally transformed with MLL-AF9 and subsequently infected with retroviruses containing either Cre-recombinase (MSCV-Cre-IRES-Tomato Red, “Cre”) or an empty vector (MSCV-IRES-Tomato Red, “EV”). GFP+/Tomato+ cells were sorted 5 days after infection.

value: sorted WBM MLL-AF9 transformed cells

value: sorted Mll4f/f + EV, WBM MLL-AF9 transformed


title: RRBS_8-cell2_rep1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_8-cell2_methylation_calling.bed

source_name: 8-cell embryo

value: 8-cell embryo


title: RRBS_8-cell3_rep1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_8-cell3_methylation_calling.bed


title: RRBS_ICM2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_ICM2_methylation_calling.bed

value: late blastocyst


title: RRBS_8-cell3_rep2


title: RRBS_ICM1_rep1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_ICM1_methylation_calling.bed


title: RRBS_ICM1_rep2


title: RRBS_8-cell2_rep2


title: Yfl052w-HA tagged ChIP-exo 2

description: sequenced with AB SOLiD

data_processing:
The entire length of the sequenced tags were aligned to the reference genome using Corona Lite software provided by the SOLiD system, allowing up to three mismatches. This process was repeated for the remaining tags, after removal of the 3? most 6 bp, which tend to have higher error rates
For Peak calling GeneTrack algorithm  was used with fine-grain smoothing (s5, e=10)
Singleton peaks were filtered out. Singletons are defined as peaks wherein all associated reads are located at a single chromosomal coordinate.
Peak-pairing is performed individually for each locus rather than a global shift of tags on each strand, which is intended to maximize the resolution for bound locations. Peakpairs are matched based on the genome-wide mode for all possible peak-pairs  for a given data set.Default Parameters:Upstream peak-pairing limit: u=0, Downstream peak-pairing limit: d = 80, Bin size (bp): b=2, Peak-pairing method: m=mode
Genome_build: s288c R64-1-1
Supplementary_files_format_and_content: The Detailed (D_) output reports the peak interval for each peak within a peak-pair, as well as the peak pair midpoint coordinate, the sum of the tags and peak pair distance.
Supplementary_files_format_and_content: A peak pair is the matching of a peak on one strand with a peak on the opposite strand within the limits set by parameters listed in the file name.  Typically the genomic coordinate that is midway between a peak-pair is either the point of crosslinking or the center of its binding location.

extract_protocol:
Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody.
Libraries were prepared by Peconic Gemomics according to standart ChIP-exo protocol (Rhee, H.S., and Pugh, B.F. (2012). ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr. Protoc. Mol. Biol. Chapter 21, Unit 21.24.).


title: RRBS_2-cell2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_2-cell2_methylation_calling.bed

source_name: 2-cell embryo

value: 2-cell embryo


title: WT cells no tag ChIP-exo

description: sequenced with AB SOLiD

value: no


title: RRBS_8-cell1_rep1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_8-cell1_methylation_calling.bed


title: RRBS_2nd_PB2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_2nd_PB2_methylation_calling.bed

value: the second polar body


title: RRBS_2nd_PB1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_2nd_PB1_methylation_calling.bed


title: QS deficient ES∆IR (pBR1MCS-3)

city: Blacksburg

first: Roderick

last: Jensen

address: 970 Washington Street

institute: Virginia Tech

data_processing:
The P. stewartii subsp. stewartii transcriptome sequencing read files in FASTQ format were transformed into FASTA format using the SeqIO module of BioPython (11) v.1.63 (www.biopython.org) through Python 2.7.6.
Then the standalone BLAST+ suite (12, 13) v.2.2.29 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/) was used to align the reads to the partially assembled version v5b P. stewartii DC283 genome sequence provided on the ASAP website (14).
). First, a BLAST database and its index were created using the FASTA files for each of the samples with the makeblastdb and makembindex BLAST+ routines.  Second, for each sample, standalone blastn (-task megablast) queries were performed using the nucleotide sequences for the P. stewartii DC283 protein coding genes against the BLAST databases for each sample with a maximum e-value of 1.e-10 for alignment.  The table format output (-outfmt 6) of each blastn query was subsequently processed using an awk-based shell script to count and list the total number of BLAST hits for each of the protein-coding genes in the P. stewartii subspecies stewartii data set.
Subsequent data processing was done using Microsoft Excel and Lasergene (DNASTAR Inc., Madison, WI).
Normalized gene expression levels in the two samples was determined by first removing all of the potentially repetitive transposases, insertion element sequences, and unnamed hypothetical proteins and normalizing the read counts to the total number of reads aligned to the remaining genes in each sample.  The error bars for the ratios of normalized gene expression levels were conservatively estimated using the standard deviation of the log (base 2) ratios across all genes.
genome build: v5b
processed data files format and content: Excel file with read counts for each annotated feature in the v5 and v8 version of the P. stewartii genome. Also, in a separate worksheet, the Normalized Read counts Per Million aligned reads (RPM)

organism: Pantoea stewartii

source_name: prokaryotic whole transcriptome

growth_protocol: Grown to an OD at 600nm of 0.5 and harvested in RNA-protect reagent.

extract_protocol:
miRNeasy kit (Qiagen) per manufacturer's protocol
Ribo-zero rRNA removal kit for Gram-negative bacteria (Epicentre, Madison, WI)
TruSeq RNA Sample Preparation Kit v2

treatment_protocol: RNA protect Reagent (Qiagen, Valencia, CA) was added and incubated with cells for 5 min at room temperature to stabilize mRNA,

value: esaR-, esaI-

tag: plasmid

value: pBBR1MCS-3:Empty expression vector

tag: strain phenotype

value: Quorum sensing deficient

value: rRNA depleted mRNA


title: Drosophila erecta male body small RNA

organism: Drosophila erecta


title: RRBS_1st_PB2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_1st_PB2_methylation_calling.bed

tag: developmental stage

value: the first polar body


title: RRBS_8-cell1_rep2


title: LSK_WT

source_name: LSK Cells

growth_protocol: Lin-negative, Sca1-positive, c-Kit positive cells (LSK) cells from polyIC-treated WT MxCre+ and MLL4f/f MxCre+ littermates at 2 months of age were sorted.

extract_protocol: To perform RNA-seq in LSK cells, we followed a protocol for single cell RNA-seq (Tang, F. et all. Nature protocols 5, 516-535, (2010)). In brief, approximately 50 cells was manually picked and transferred into lysate buffer, followed by reverse transcription directly on the whole-cell lysate. Following this procedure, terminal deoxynucleotidyl transferase was used to add a poly(A) tail to the 3′ end of first-strand cDNAs, which was followed by 20 + 9 cycles of PCR to amplify cDNAs. After generation of the target cDNA, 100 ng cDNA (0.5–3 kb) was sheared into 80–130 bp fragments. Adaptors were ligated to each end, and the fragments were subjected to 8–10 cycles of PCR amplification.

value: Sorted LSK Cells

value: WT

value: 0 day


title: RRBS_2-cell1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_2-cell1_methylation_calling.bed


title: RRBS_4-cell2

description:
MspI digested and bisulfite treated genomic DNA
RRBS_4-cell2_methylation_calling.bed

source_name: 4-cell embryo

value: 4-cell embryo


title: QS proficient ES∆IR (pSVB60)

value: esaR+, esaI-

value: pSVB60:esaR expressed from native promoters

value: Quorum sensing proficient


title: MAF9_Mll4mm

value: sorted WBM MLL-AF9 transformed cells

value: sorted Mll4f/f + Cre, WBM MLL-AF9 transformed

value: 14 days


title: RRBS_4-cell1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_4-cell1_methylation_calling.bed


title: LSK_Mllmm

value: Mll4f/f + Cre


title: RRBS_1st_PB1

description:
MspI digested and bisulfite treated genomic DNA
RRBS_1st_PB1_methylation_calling.bed


title: Depleted RNA

status: Public on Jul 21 2014

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

description: Sample 2

data_processing:
SCS 2.8/RTA 1.8... real time basecalling, resulting in .cif, .pos, .bcl files.
BclConverter-1.7.1 (setupBclToQseq.py)...  bcl conversion producing qseq.txt files
demultiplex.pl (packaged with CASAVA-1.7.0)... separating out the barcodes
GERALD.pl (packaged with CASAVA-1.7.0)... converting to .fastq format
CLC genomics Workbench 4.8 for mapping and RPKM values
Genome_build: ASM18366v1 (NC_014774.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values Lso genes

organism: Candidatus Liberibacter solanacearum

source_name: Adult psyllids

growth_protocol: Insects were maintained in tomato plants at room temperature and photoperiod of 12:12 (L:D)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was removed using RNA depletion using RiboMinus Transcriptome Isolation kit (Life Technologies) and polyA RNA was purified using Dynabeads mRNA Purification kit  (Life Technologies)
The library from the polyA purified RNA was prepared using the RNA-TruSeq Library kit (Illumina) and the library from the depleted RNA was prepared using ScriptSeq RNA (Epicenter Biotechnologies).

tag: psyllid vector

value: Bactericera cockerelli

tag: rna prep

value: Depleted total RNA


title: PolyA purified RNA

description: Sample 1

value: PolyA purified RNA


title: tof1_a-_input9

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description:
source of  scaled coverage, and tRec114
processed data: tRec114_tof1_a-.txt.gz
processed data: tof1_Rec114_ChIP_scaled_a-.txt.gz

data_processing:
For ChIP-seq, DNA from Rec114 ChIP and input samples collected from the ARS+ and ars∆ strains (same samples as used for ChIP-qPCR) were further sheared by sonication to an average fragment sizes of ~300 bp. These were sequenced (75 bp and 50 bp paired-end reads for TOF1 and tof1∆ cultures, respectively) on the HiSeq platform (Illumina). Reads were mapped to the SacCer2 genome assembly using BWA (aln) version 0.5.9-r16 to generate coverage maps for each time point from each strain. Each ChIP coverage map was divided by the corresponding input map. Then, to scale the ChIP-seq coverage relative to absolute ChIP efficiency, we calculated the total coverage within ± 1 kb of the center of each qPCR amplicon, plotted these as a function of the corresponding qPCR ChIP efficiency, and calculated regression lines by least squares. The resulting regression line for each time point was then used to scale the ChIP-seq coverage maps. The scaled ChIP-seq coverage maps were smoothed using a 2004-bp Parzen (triangular) sliding window. Using the smoothed, scaled coverage map of the 4-h and 3-h samples from the TOF1 ARS+ and the tof1∆ ARS+ strains, respectively, a total of 2,010 and 2290 peaks were called using as a threshold 0.8 x each chromosome’s mean coverage. A Rec114 ChIP kinetic profile at each peak position was assembled by collecting the ChIP signals from the smoothed, scaled coverage map for each time point. For each Rec114 kinetic profile, we first fitted a modified log-normal curve to all of the qPCR data to define the empirical peak position in the Rec114 ChIP profile. Next, we used this peak to fit a saturating exponential growth (logistic) curve to just the early time points. For the first step, we estimated the peak position and peak height by fitting normal distribution curves to data with log-transformed time values [t’ = ln(t+1)]. We employed an equation that is a modification of the normal probability density function [y = a+b*exp((-(t’-c)^2)/d^2), where y is ChIP efficiency (% of input), a is the background, b is the peak height, c is the peak position, and d is the equivalent of standard deviation]. We set the background parameter (a) to the ChIP efficiency at 0 h, then fitted the equation to the data points by least squares to estimate the other parameters (b, c and d) using the “nls” function in R. From these parameters, parameter c was reverse-transformed to show the time (t, in hours) when the fitted curve reaches its maximum.Next, we fitted a modified logistic function to the upward sloping part of the Rec114 kinetic profile (time points before the peak time in the log-normal fitting) as follows: [y = a + b/(1 + exp(c*(d – t))), were: y (ChIP efficiency (% of input)), a (background), b (maximum value), c (shaping factor), and d (inflection point)]. We set the background parameter (a) to the value of the 0 h sample and the maximum parameter (b) to the peak height parameter from the log-normal fitting, then fitted the logistic equation to the data points by least squares to estimate the other parameters (c and d). We used parameter d as tRec114, i.e., the time when Rec114 ChIP signal reached 50% of maximum. For tof1∆ strains, we fitted regression curves consisting of two log-normal curves [y = a+b*exp((-(t’-c)^2)/d^2)+b2*exp((-(t’-c2)^2)/d2^2), where y is ChIP efficiency (% of input), a is the background, b and b2 are the heights of the first and second peaks, c and c2 are the positions of the first and second peaks, and d and d2 are the standard deviations of the first and second log-normal curves]. Parameters from the curve fitting were assigned to the first-derivative of the regression equation and then solved for the first value of t at which the equation is zero using the “uniroot” function on R. This peak time and the fitted parameters were then assigned to the equation of the regression curve to determine the peak height. Once the peak time and peak height were determined, tRec114 was estimated using fits of pre-peak time points to the modified logistic function as described above. To evaluate the fitting quality for the kinetic profile at each Rec114 peak, absolute distances between the data points and the fitted log-normal curve (residuals) were summed and divided by the peak height from the fitted curve (normalized-total residuals). We excluded peaks with poorly fitted profiles, defined as those for which normalized-total residuals exceeded a value of 3. Next, sites with total residuals from logistic regression exceeding 0.0125 (TOF1 ARS+), 0.006 (TOF1 ars∆) and 0.01 (tof1∆ ARS+ and tof1∆ ars∆) were also excluded from each data set. We also excluded Rec114 peaks with insufficient signal, defined as those with a log-normal fitted peak height less than 0.1 or 0.06 for TOF1 or tof1∆ data sets, respectively. From the tof1∆ data sets, we also excluded Rec114 peaks that exhibited aberrant curve fits, defined as those with a fitted second standard deviation (parameter d2) less than 0.02 or greater than 0.4. Finally, we removed outliers (a few peaks), defined as Rec114 peaks with tRec114 values more than 4 standard deviations from the mean of tRec114 values. After these filtering steps, totals of 1029 (TOF1 ARS+), 1035 (TOF1 ars∆), 957 (tof1∆ ARS+), and 2020 (tof1∆ ars∆) Rec114 peaks were processed for further analyses. Replication index maps were generated from coverage maps from the ChIP input samples using the same approach described above for the generation of replication index maps using total genomic DNA, except that coverage in the masked map was binned using non-overlapping 5-kb windows. For the comparison with Rec114 chromatin association timing, coverage in 5-kb windows centered on the called Rec114 peak positions was used to calculate the replication profile. Coverage maps from 0-h and 2-h samples were used as G1 and meiotic S phase samples for TOF1 strains. For tof1∆ ARS+ and tof1∆ ars∆ strains, 1.5-h and 2.5-h samples, respectively, were used for S phase samples.
Supplementary_files_format_and_content: (replication profile: RepPro_tof1_A+.txt and RepPro_tof1_a-.txt) tab delimited text files include relative coverage map for 1.5-h (ARS+) and 2.5-h(ars∆) time points at the center position of each bin in the genome
Supplementary_files_format_and_content: (scaled tof1 Rec114 ChIP coverage map: tof1_Rec114_ChIP_scaled_A+.txt and tof1_Rec114_ChIP_scaled_a-.txt) tab delimited text files include each schaled ChIP efficiency (ChIP/input) for the each time point at each nucleotide position in the genome
Supplementary_files_format_and_content: (time of Rec114 chromatin association: tRec114_A+.txt, tRec114 _a-.txt, tRec114_tof1_A+.txt and tRec114_tof1_a-.txt) tab delimited text files include each replication index, tRec114, scaled ChIP signals, parameters and residuals from log-normal and logistic curve fittings at each called Rec114 peak position in the genome

source_name: meiotic culture

growth_protocol: Synchronized meiotic cultures were prepared in 2% potassium acetate at 30°C by the SPS pre-growth method as described in Murakami et al. (2009) Methods Mol Biol 557: 117-142.

extract_protocol: ChIP was performed as described (Aparicio et al., 2004; Mendoza et al., 2009; Metivier et al., 2003; Panizza et al., 2011) with modifications. REC114-Myc diploids were sporulated and 50 mL of meiotic culture (2 x 109 cells) was collected at different times and crosslinked with 1% formaldehyde for 30 min at room temperature. Crosslinking was terminated by 5 min incubation with 131 mM glycine. Cells were washed twice with ice-cold TBS, flash frozen with liquid nitrogen and stored at -80°C. Cells were suspended in 1 mL of Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 7 ug/mL aprotinin, 1% protease inhibitor cocktail (Sigma), 1x Complete Protease Inhibitor Cocktail (Roche)) with ca. 900 uL of 0.5 mm zirconia/silica beads (BioSpec Products) in 2 mL screw-cap tubes. Cells were disrupted by vigorous shaking 3 min x 6 times in Mini-beadbeater-16 (BioSpec Products) or at 6.5 m/s for 1 min x 8 times in FastPrep24 (MP Biomedicals). 1 mL of Lysis buffer was added after cell disruption. Subsequently, chromatin in the whole cell extracts (WCE) was sheared by sonication with "M" intensity, 30 sec ON/ 30 sec OFF for 15 min x 2 times in Bioruptor Sonication System UCD200 (Diagenode) in 15 mL polystyrene conical tubes. Insoluble fraction (cell debris) was removed by centrifugation at 21,130 g, 5 min, 4°C. WCE was further sonicated with the same conditions 1-3 times to yield average DNA size less than 500 bp. WCE was flash frozen and stored at -80°C.

value: meiotic pophase

value: REC114-Myc tof1-delta ars-delta

tag: time in meiosis

value: time = 4.5 hr  in meiosis


title: tof1_a-_input12

value: time = 7 hr  in meiosis


title: tof1_a-_input11

value: time = 6 hr  in meiosis


title: tof1_a-_input8

value: time = 4 hr  in meiosis


title: tof1_a-_input7

value: time = 3.5 hr  in meiosis


title: Rex1-high_RRBS

city: Pasadena

first: Michael

last: Elowitz

state: Ca

address: 1200 E California Blvd MC 114-96

department: Bioengineering

institute: Caltech

data_processing:
Reads were aligned to the mm9 genome using Bismark v0.7
Genome_build: mm9
Supplementary_files_format_and_content: BED files are provided reporting the number of methylated reads over the total number of reads per base

source_name: E14 Embryonic Stem Cells

growth_protocol: ES cells were grown on gelatin in standard conditions containing LIF and 10% serum

extract_protocol: Libraries were prepared from 200-500 ng genomic DNA digested with 60 units of TaqI and 30 units of MspI (NEB) sequentially. Size-selected TaqI-MspI fragments (40–120 bp and 120–350 bp) were filled in and 3’-terminal-A extended, extracted with Zymo Research (ZR) DNA Clean & Concentrator™-5 kit (Cat#: D4003). Ligation to pre-annealed adapters containing 5’- methyl-cytosine instead of cytosine (Illumina) was performed using the Illumina DNA preparation kit and protocol. Purified, adaptor ligated fragments were bisulphite-treated using the EZ DNA Methylation-Direct™ Kit (ZR, Cat#: D5020). Preparative-scale PCR was performed and DNA Clean & Concentrator™ -purified PCR products were subjected to a final size selection on a 4% NuSieve 3:1 agarose gel. SYBR-green-stained gel slices containing adaptor-ligated fragments of 130–210 bp or 210–460 bp in size were excised. Library material was recovered from the gel (Zymoclean™ Gel DNA Recovery Kit, ZR Cat#: D4001) and sequenced on an Illumina HiSeq 2000.

tag: strain background

value: E14 Embryonic Stem Cells

tag: genotype/variation

value: Rex1-dGFP knockin reporter line

tag: cell population

value: Rex1-high cells


title: Rex1-low_RRBS

value: Rex1-low cells


title: tof1_a-_input10

value: time = 5 hr  in meiosis

tag: chip antibody


title: tof1_a-_input6

value: time = 3 hr  in meiosis


title: tof1_a-_input5

description:
source of  scaled coverage, and tRec114
processed data: tRec114_tof1_a-.txt.gz
processed data: tof1_Rec114_ChIP_scaled_a-.txt.gz
RepPro_tof1_a-.txt.gz

value: time = 2.5 hr  in meiosis


title: tof1_a-_input4

value: time = 2 hr  in meiosis


title: tof1_a-_input2

value: time = 1 hr  in meiosis


title: tof1_A+_input1

description:
source of  scaled coverage, and tRec114
processed data: tRec114_tof1_A+.txt.gz
processed data: tof1_Rec114_ChIP_scaled_A+.txt.gz
RepPro_tof1_A+.txt.gz

value: REC114-Myc tof1-delta RS+

value: time = 0 hr  in meiosis


title: tof1_A+_input4

description:
source of  scaled coverage, and tRec114
processed data: tRec114_tof1_A+.txt.gz
processed data: tof1_Rec114_ChIP_scaled_A+.txt.gz

value: meiotic pophase


title: tof1_A+_input3

value: time = 1.5 hr  in meiosis


title: tof1_A+_input8


title: tof1_A+_input10


title: tof1_a-_input3

value: REC114-Myc tof1-delta ars-delta


title: tof1_A+_input12

value: time = 7 hr  in meiosis


title: tof1_A+_input9

value: time = 4.5 hr  in meiosis


title: tof1_A+_input2


title: tof1_a-_ChIP12

value: anti-Myc antibody (9E10)


title: tof1_a-_ChIP11

value: time = 6 hr  in meiosis


title: tof1_a-_ChIP10


title: tof1_a-_ChIP9


title: tof1_a-_ChIP5


title: tof1_a-_ChIP6


title: tof1_a-_ChIP8

value: time = 4 hr  in meiosis


title: tof1_a-_ChIP1


title: tof1_A+_input5


title: tof1_a-_input1


title: tof1_A+_input11


title: tof1_a-_ChIP2


title: tof1_a-_ChIP3


title: tof1_A+_input7

value: time = 3.5 hr  in meiosis


title: tof1_A+_input6


title: tof1_a-_ChIP7


title: WT_a-_input11

description: source of  scaled coverage, and tRec114

data_processing:
Base calls were made using HiSeq Control Software v.2.0.10.0
For ChIP-seq, DNA from Rec114 ChIP and input samples collected from the ARS+ and ars∆ strains (same samples as used for ChIP-qPCR) were further sheared by sonication to an average fragment sizes of ~300 bp. These were sequenced (75 bp paired-end) on the HiSeq platform (Illumina). Reads were mapped to the SacCer2 genome assembly using BWA (aln) version 0.5.9-r16 to generate coverage maps for each time point from each strain. Each ChIP coverage map was divided by the corresponding input map. Then, to scale the ChIP-seq coverage relative to absolute ChIP efficiency, we calculated the total coverage within ± 1 kb of the center of each qPCR amplicon, plotted these as a function of the corresponding qPCR ChIP efficiency, and calculated regression lines by least squares. The resulting regression line for each time point was then used to scale the ChIP-seq coverage maps. The scaled ChIP-seq coverage maps were smoothed using a 2004-bp Parzen (triangular) sliding window. Using the smoothed, scaled coverage map of the 4-h sample from the ARS+ strain, a total of 2,010 peaks were called using as a threshold 0.8´ each chromosome’s mean coverage. A Rec114 ChIP kinetic profile at each peak position was assembled by collecting the ChIP signals from the smoothed, scaled coverage map for each time point. To estimate the time of Rec114 association to chromatin (tRec114), Gaussian curves were fitted to each kinetic profile. To create positive skew in the regression curves, times (t, in hours) were log-transformed [t’ = ln(t+1)]. We employed an equation that is a modification of the Gaussian probability density function [y = a+b*exp((-(t’-c)^2)/d^2), where y is ChIP efficiency (% of input), a is the background, b is the peak height, c is the peak position, and d is the equivalent of standard deviation]. We set the background parameter (a) to the ChIP efficiency at 0 h, then fitted the equation to the data points by least squares to estimate the other parameters (b, c and d) using the “nls” function in R. From these parameters, the time when the second derivative reaches its maximum (tRec114) was calculated as [tRec114 = -1+exp((2*c-d^2-sqrt(6*d^2+d^4))/2)]. To evaluate the fitting quality for the kinetic profile at each Rec114 peak, absolute distances between the data points and the fitted curve (residuals) were summed and divided by the peak height (parameter b) from the fitted curve (normalized-total residuals). We excluded peaks with poorly fitted profiles, defined as those for which normalized-total residuals exceeded a value of 2. We also excluded Rec114 peaks with insufficient signal, defined as those with a fitted peak height (parameter b) less than 0.13. Finally, we removed outliers (~1% of peaks), defined as Rec114 peaks with tRec114 values more than 3 SD from the mean. After these filtering steps, totals of 1153 and 1108 Rec114 peaks from ARS+ and ars∆ strains, respectively, were processed for further analyses.
Replication profiles were generated from coverage maps from the ChIP input samples. Coverage maps from 0-h and 2-h samples were used as G1 and meiotic S phase samples to generate relative coverage map (S/G1).To remove regions with spurious mapping, the map from the 0 h sample of the wild-type ARS+ strain was used to define “mask regions” where the coverage was out of a fixed range (>40 from mean coverage). The mask regions were further extended by 1 kb on other side, and these regions were censored from further analysis. Coverage in the masked map was binned non-overlapping 5-kb windows. The binned coverage was normalized to the mean coverage calculated from the masked map and then divided by coverage in the 0-h map. For the comparison with Rec114 chromatin association timing, coverage in 5-kb windows centered on the called Rec114 peak positions were used to calculate the replication profile.
Genome_build: SacCer2
Supplementary_files_format_and_content: (replication profile: RepPro_A+.txt and RepPro_a-.txt) tab delimited text files include relative coverage map for the 2 h time point at the center position of each bin in the genome
Supplementary_files_format_and_content: (scaled Rec114 ChIP coverage map: Rec114_ChIP_scaled_A+.txt and Rec114_ChIP_scaled_a-.txt) tab delimited text files include each schaled ChIP efficiency (ChIP/input) for the each time point at each nucleotide position in the genome
Supplementary_files_format_and_content: (time of Rec114 chromatin association: Rec114_ChIP_scaled_A+.txt and Rec114_ChIP_scaled_a-.txt) tab delimited text files include each relative coverage (2 h / 0 h, represent replication timing), tRec114.sdm (time Rec114 ChIP measured by second derivative max), tRec114.peak (time Rec114 ChIP measured by the peak position of the fitted curve), peak.height (parameter b from the fitted curve), sd (parameter c from the fitted curve), and nor.total.res (normalized total residuals: represents curve fitting quality) for the each time point at each called Rec114 peak position in the genome

value: REC114-Myc ars-delta

value: 7 hr  in meiosis


title: tof1_a-_ChIP4


title: WT_a-_input12

description: source of  scaled coverage, and tRec114

value: 8 hr  in meiosis


title: tof1_A+_ChIP9


title: tof1_A+_ChIP12


title: tof1_A+_ChIP11


title: tof1_A+_ChIP10

value: time = 5 hr  in meiosis


title: WT_a-_input8

description: source of  scaled coverage, and tRec114

value: 5 hr  in meiosis


title: WT_a-_input7

description: source of  scaled coverage, and tRec114

value: 4.5 hr  in meiosis


title: tof1_a-_4

description: source of replication profile

data_processing:
Base calls were made using HiSeq Control Software v.2.0.10.0
Reads were mapped onto the S288c reference genome (SGD June 2008 assembly (SacCer2)) using BWA (aln) version 0.5.9-r16 to generate coverage maps. To remove regions with spurious mapping, the map from the 0 h sample of the wild-type ARS+ strain was used to define “mask regions” where the coverage was out of a fixed range (>1.5 SD from mean coverage). The mask regions were further extended by 1 kb on other side, and these regions were censored from further analysis. Coverage in the masked map was binned using 5 kb windows with steps of 2.5 kb. The binned coverage was normalized to the mean coverage calculated from the masked map and then divided by coverage in the 0-h map.
Genome_build: SacCer2
Supplementary_files_format_and_content: tab delimited text files include relative coverage map for each time point at the center position of each bin in the genome

extract_protocol: Standard spheroplasting followed by proteinase K digestion as described in Murakami et al. (2009) Methods Mol Biol 557: 117-142.

value: meiotic S phase

value: tof1∆ ars∆

value: 2 hr  in meiosis


title: tof1_a-_6

description: source of replication profile

value: 3 hr  in meiosis


title: WT_a-_input6

description: source of  scaled coverage, and tRec114

value: meiotic pophase

value: 4 hr  in meiosis


title: tof1_a-_5

description: source of replication profile

value: 2.5 hr  in meiosis


title: tof1_a-_1

description: source of replication profile

value: meiotic G1 phase

value: 0 hr  in meiosis


title: WT_a-_input5

description: source of  scaled coverage, and tRec114

value: 3.5 hr  in meiosis


title: tof1_a-_2

description: source of replication profile

value: 1 hr  in meiosis


title: tof1_A+_ChIP1

value: REC114-Myc tof1-delta RS+

value: time = 0 hr  in meiosis

value: anti-Myc antibody (9E10)


title: tof1_A+_ChIP2

value: time = 1 hr  in meiosis


title: tof1_A+_ChIP7

value: time = 3.5 hr  in meiosis


title: tof1_A+_ChIP6

value: time = 3 hr  in meiosis


title: tof1_A+_ChIP3

value: time = 1.5 hr  in meiosis


title: tof1_A+_ChIP5

value: time = 2.5 hr  in meiosis


title: tof1_A+_ChIP4

value: time = 2 hr  in meiosis


title: tof1_A+_ChIP8

value: time = 4 hr  in meiosis


title: WT_a-_input4

description: source of  scaled coverage, and tRec114

value: meiotic pophase

value: REC114-Myc ars-delta

value: 3 hr  in meiosis


title: tof1_A+_8

description: source of replication profile

value: meiotic S phase

value: tof1∆ ARS+

value: 4 hr  in meiosis


title: WT_a-_input10

description: source of  scaled coverage, and tRec114

value: 6 hr  in meiosis


title: tof1_A+_6

description: source of replication profile


title: WT_a-_input9

description: source of  scaled coverage, and tRec114

value: 5.5 hr  in meiosis


title: tof1_a-_7

description: source of replication profile

value: tof1∆ ars∆

value: 3.5 hr  in meiosis


title: tof1_a-_3

description: source of replication profile

value: 1.5 hr  in meiosis


title: tof1_a-_8

description: source of replication profile


title: WT_a-_input3

description: source of  scaled coverage, and tRec114

value: 2.5 hr  in meiosis


title: tof1_A+_5

description: source of replication profile


title: WT_a-_input2

description: source of replication profile, scaled coverage, and tRec114

value: 2 hr  in meiosis


title: tof1_A+_7

description: source of replication profile


title: tof1_A+_3

description: source of replication profile


title: tof1_A+_4

description: source of replication profile


title: WT_a-_ChIP12

description: source of  scaled coverage, and tRec114

value: 8 hr  in meiosis

value: anti-Myc antibody (9E10)


title: WT_a-_input1

value: 0 hr  in meiosis


title: tof1_A+_2

description: source of replication profile

value: 1 hr  in meiosis


title: WT_a-_ChIP11

description: source of  scaled coverage, and tRec114

value: meiotic pophase

value: 7 hr  in meiosis


title: BCR1 rep1

city: Zürich

first: Markus

middle: S

last: Schröder

state: Zürich

address: Otto-Stern-Weg 7

department: Biology, Molecular Health Sciences

country: Switzerland

institute: ETH Zürich

description: bcr1 deletion biofilm sample 1

data_processing:
Raw Illumina reads were provided by BGI (www.genomics.cn, Hong Kong)
Fastq files were aligned to the C. parapsilosis genome (Candida parapsilosis CDC 317) using TopHat2, using strand-specific option for dUTP, paired-end mode and default arguments.
BAM files were processed with HTSeq version 0.5.3p9 to count mapped reads per transcript. Default options were used with mode set to intersection-nonempty.
DESeq2 was used for expression analysis.   DESeq2 uses raw count data as input, performs normalization internally, and generates result files (e.g., log2 fold change).
Genome_build: ASM18276v1
Supplementary_files_format_and_content: Tab-delimited text files include raw counts per transcript values for each Sample.

organism: Candida parapsilosis

growth_protocol: Biofilms for were grown in SD media with 50 mM glucose at 37C in Nunc 6 well plates.

extract_protocol:
Biofilm was scraped from the bottom of each well and combined for RNA isolation. The number of wells combined depended on the amount of biofilm produced and the amount of biomass needed to obtain sufficient RNA for library preparation (6 weels for CLIB214 and 6-10 wells for the deletion strains). RNA was isolated using an Ambion Ribopure-Yeast RNA kit.
Strand-specific RNA-seq libraries were prepared by BGI (www.genomics.cn, Hong-Kong) for sequencing using standard Illumina protocols.

tag: growth phase

value: 48h biofilm


title: WT_a-_ChIP10

description: source of  scaled coverage, and tRec114

value: REC114-Myc ars-delta


title: BCR1 rep2

description: bcr1 deletion biofilm sample 2


title: CZF1 rep3

description: czf1 deletion biofilm sample 3


title: BCR1 rep3

description: bcr1 deletion biofilm sample 3


title: tof1_A+_1

description: source of replication profile

value: meiotic G1 phase

value: tof1∆ ARS+


title: WT_a-_ChIP7

description: source of  scaled coverage, and tRec114

value: 4.5 hr  in meiosis


title: DDK_a-_8

description: source of replication profile

value: meiotic S phase

value: DDK overproduction ars∆

value: 4 hr  in meiosis


title: UME6 rep3

description: ume6 deletion biofilm sample 3


title: DDK_a-_7

description: source of replication profile

value: 3.5 hr  in meiosis


title: WT_a-_ChIP9

description: source of  scaled coverage, and tRec114

value: 5.5 hr  in meiosis


title: UME6 rep2

description: ume6 deletion biofilm sample 2


title: DDK_a-_6

description: source of replication profile

value: 3 hr  in meiosis


title: UME6 rep1

description: ume6 deletion biofilm sample 1


title: EFG1 rep2

description: efg1 deletion biofilm sample 2


title: WT_a-_ChIP6

description: source of  scaled coverage, and tRec114


title: WT_a-_ChIP5

description: source of  scaled coverage, and tRec114


title: EFG1 rep1

description: efg1 deletion biofilm sample 1


title: DDK_a-_5

description: source of replication profile

value: 2.5 hr  in meiosis


title: WT_a-_ChIP4

description: source of  scaled coverage, and tRec114

value: anti-Myc antibody (9E10)


title: CPH2 rep3

description: cph2 deletion biofilm sample 3


title: DDK_a-_4

description: source of replication profile

value: 2 hr  in meiosis


title: CPH2 rep2

description: cph2 deletion biofilm sample 2


title: CPH2 rep1

description: cph2 deletion biofilm sample 1


title: DDK_a-_3

description: source of replication profile

value: 1.5 hr  in meiosis


title: ACE2 rep3

description: ace2 deletion biofilm sample 3


title: WT_a-_ChIP3

description: source of  scaled coverage, and tRec114

value: meiotic pophase


title: WT_a-_ChIP8

description: source of  scaled coverage, and tRec114

value: 5 hr  in meiosis


title: CZF1 rep2

description: czf1 deletion biofilm sample 2

value: 48h biofilm


title: ACE2 rep2

description: ace2 deletion biofilm sample 2


title: DDK_a-_2

description: source of replication profile

value: 1 hr  in meiosis


title: WT biofilm rep3

description: Wild type biofilm sample 3

source_name: WT biofilm

value: wild type (CLIB214 strain)


title: CZF1 rep1

description: czf1 deletion biofilm sample 1


title: DDK_a-_1

description: source of replication profile

value: meiotic G1 phase

value: 0 hr  in meiosis


title: EFG1 rep3

description: efg1 deletion biofilm sample 3


title: DDK_A+_7

description: source of replication profile

value: meiotic S phase

value: DDK overproduction ARS+


title: DDK_A+_8

description: source of replication profile

value: 4 hr  in meiosis


title: WT biofilm rep1

description: Wild type biofilm sample 1


title: WT biofilm rep2

description: Wild type biofilm sample 2


title: WT_a-_ChIP1

description: source of  scaled coverage, and tRec114

value: REC114-Myc ars-delta


title: WT_A+_input12

description: source of  scaled coverage, and tRec114

value: REC114-Myc ARS+

value: 8 hr  in meiosis


title: DDK_A+_6

description: source of replication profile

value: 3 hr  in meiosis


title: WT_A+_input11

description: source of  scaled coverage, and tRec114

value: 7 hr  in meiosis


title: WT_A+_input9

description: source of  scaled coverage, and tRec114

value: 5.5 hr  in meiosis


title: WT_A+_input10

description: source of  scaled coverage, and tRec114

value: 6 hr  in meiosis


title: DDK_A+_5

description: source of replication profile

value: 2.5 hr  in meiosis


title: WT_A+_input8

description: source of  scaled coverage, and tRec114

value: meiotic pophase

value: 5 hr  in meiosis


title: WT planktonic rep2

description: Wild type planktonic sample 2

source_name: WT planktonic

growth_protocol: Strains were grown to an A600 of 1 in SD media with 50 mM glucose at 37C

extract_protocol:
RNA was isolated using an Ambion Ribopure-Yeast RNA kit.
Strand-specific RNA-seq libraries were prepared by BGI (www.genomics.cn, Hong-Kong) for sequencing using standard Illumina protocols.

value: log phase


title: WT planktonic rep3

description: Wild type planktonic sample 3

value: wild type (CLIB214 strain)


title: WT_a-_ChIP2

description: source of  scaled coverage, and tRec114

value: 2 hr  in meiosis

value: anti-Myc antibody (9E10)


title: ACE2 rep1

description: ace2 deletion biofilm sample 1

value: 48h biofilm


title: WT_A+_input7

description: source of  scaled coverage, and tRec114

value: 4.5 hr  in meiosis


title: WT_A+_input6

description: source of  scaled coverage, and tRec114

value: 4 hr  in meiosis


title: DDK_A+_2

description: source of replication profile

value: meiotic S phase

value: DDK overproduction ARS+

value: 1 hr  in meiosis


title: WT planktonic rep1

description: Wild type planktonic sample 1


title: DDK_A+_1

description: source of replication profile

value: meiotic G1 phase

value: 0 hr  in meiosis


title: DDK_A+_3

description: source of replication profile

value: 1.5 hr  in meiosis


title: WT_a-_8

description: source of replication profile

value: wild type ars∆


title: WT_A+_input4

description: source of  scaled coverage, and tRec114

value: REC114-Myc ARS+

value: 3 hr  in meiosis


title: WT_a-_6

description: source of replication profile


title: WT_a-_7

description: source of replication profile

value: 3.5 hr  in meiosis


title: WT_A+_input3

description: source of  scaled coverage, and tRec114

value: meiotic pophase

value: 2.5 hr  in meiosis


title: WT_A+_input5

description: source of  scaled coverage, and tRec114


title: WT_A+_input2

value: 2 hr  in meiosis


title: WT_a-_4

description: source of replication profile


title: WT_a-_3

description: source of replication profile


title: WT_a-_2

description: source of replication profile


title: WT_A+_input1


title: WT_a-_5

description: source of replication profile


title: WT_A+_ChIP12

description: source of  scaled coverage, and tRec114

value: 8 hr  in meiosis

value: anti-Myc antibody (9E10)


title: WT_A+_ChIP11

description: source of  scaled coverage, and tRec114

value: 7 hr  in meiosis


title: WT_A+_ChIP10

description: source of  scaled coverage, and tRec114

value: 6 hr  in meiosis


title: DDK_A+_4

description: source of replication profile

value: meiotic S phase


title: WT_a-_1

description: source of replication profile


title: WT_A+_8

description: source of replication profile

value: wild type ARS+

value: 4 hr  in meiosis


title: WT_A+_7

description: source of replication profile


title: WT_A+_ChIP8

description: source of  scaled coverage, and tRec114

value: 5 hr  in meiosis


title: WT_A+_ChIP7

description: source of  scaled coverage, and tRec114

value: 4.5 hr  in meiosis


title: WT_A+_ChIP9

description: source of  scaled coverage, and tRec114

value: 5.5 hr  in meiosis


title: WT_A+_ChIP6

description: source of  scaled coverage, and tRec114


title: WT_A+_6

description: source of replication profile


title: WT_A+_5

description: source of replication profile


title: WT_A+_ChIP5

description: source of  scaled coverage, and tRec114


title: WT_A+_ChIP4

description: source of  scaled coverage, and tRec114


title: WT_A+_4

description: source of replication profile


title: WT-IP

city: London

first: Christopher

last: Pin

state: ON

address: 800 Commissioners Road E, 5th floor, Victoria Research labs

department: Pediatrics

country: Canada

institute: Children's Health Research Institute

data_processing:
Enriched DNA fragments sequenced using Illumina 2.0 genome analyzer were mapped to the mm9 mouse genome using the SOAP2.21 alignment program.
The MACS 1.4.0 algorithm was used for peak calling to identify H3K4Me3 enrichment relative to control input samples.
The MACS parameters were as follows:  -c (sample 1-WT-IP is the input sample of sample 2-WT-H3K4, sample 4-M1-IP is the input sample of sample 5-M1-H3K4), --tsize 49, --bw (192 for sample 2-WT-H3K4, 230 for sample 5-M1-H3K4), --gsize mm, --pvalue 1e-5, --wig, --wigextend 300, --space 50, --diag Ture and --mfold 10,30.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files were generated using MACS 1.4.0 and can be used to visualize individual peaks across the genome. Genepeak files showing showing individual peaks and associated genes are also included.

source_name: Pancreatic acinar cells

growth_protocol: Acinar cells were isolated from WT and Mist1-/- mice by collagenase injections in DMEM. After washing the cells with DMEM containing 4% BSA and 1% BSA respectively, the cells were resuspended in DMEM without BSA for crosslinking.

extract_protocol: Isolated nuclei from acinar cells were lysed and sonicated to yield sheared chromatin.  Histone-DNA complexes were isolated with H3K4Me3 antibody antibody.  Libraries were prepared according to established standard protocol at BGI (HK) .

value: WT

tag: antibody

value: Input


title: M1-IP


title: WT_A+_3

description: source of replication profile

value: 1.5 hr  in meiosis


title: WT_A+_ChIP3

description: source of  scaled coverage, and tRec114

value: REC114-Myc ARS+


title: WT_A+_1

description: source of replication profile

value: meiotic G1 phase

value: 0 hr  in meiosis


title: WT_A+_2

description: source of replication profile

value: 1 hr  in meiosis


title: WT_A+_ChIP2

description: source of  scaled coverage, and tRec114

value: meiotic pophase

value: 2 hr  in meiosis


title: WT_A+_ChIP1

description: source of  scaled coverage, and tRec114

value: anti-Myc antibody (9E10)


title: WT-H3K4

value: H3K4Me3 (cat#04-745 Millipore)


title: M1-H3K4


title: Input DMSO 24h, rep1

status: Public on Jul 20 2014

first: Rintaro

last: Hashizume

address: 1450 3rd street

department: Neurosurgery

description:
8628_input_24h_DMSO
DIPG-derived cell line, harboring H3F3A K27M mutation.

data_processing:
ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2 software and preset parameters. Only uniquely mapping reads were used for further analysis.
Informative tags were selected from the aligned ChIP-seq data of each sequenced sample based on the cross-correlation profile of positive- and negative-strand tag densities. Background anomalies resulting from extremely high-density peaks at single chromosome positions were removed. After these filtering steps, the remaining tag list from each K27me3 immunoprecipitated sample was normalized against tag lists from sample matched input DNA (treated only with DMSO). Broad regions of binding enrichment (i.e. ChIP signal over input) for each immunoprecipitated sample were obtained by comparing scaled ChIP and input tag counts to see if their ratio exceeds that expected from a Poisson process. The R library SPP was used to perform all aforementioned steps.
Distance to the nearest transcription start site (TSS) was obtained for each enriched binding region using Bioconductor package ChIPpeakAnno.
Genome_build: GRCh37
Supplementary_files_format_and_content: bed files were generated using R library SPP.

source_name: Pediatric, K27M mutated DIPG cells treated with DMSO for 24h, input

growth_protocol: Primary pediatric human glioma cells, designated with “SF”, were obtained from surgical biopsy of tumor from patients admitted to UCSF Medical Center, and in accord with an institutionally approved protocol. Establishment of glioma cell cultures, from surgical specimens, and tumor cell modification for expression of firefly luciferase, for in vivo bioluminescence imaging, have been described in Hashizume R et al., 2012 (PMID 22983601).

extract_protocol:
Briefly, 1×10^6 cells, treated with vehicle or 6 μM GSKJ4 for 24 and 72 hours, were harvested, washed with PBS and fixed with 1% formaldehyde for 5 minutes at room temperature. Cells were then quenched with 125 mM glycine for 5 minutes. After wash, cell extracts were prepared using lysis buffer (50 mM HEPES/KOH at pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X100, 0.1% Na-deoxycholate, 1 mM PMSF, 1 mM Pefoblock, 1 mM benzamidine, 1 mg/ml bacitracin) on ice for 10 minutes.
Chromatin was sheared by sonication (bioruptor, High power, 15 × 2 cycles), to average lengths of 500 bp, then immunoprecipitated using an antibody against histone H3K27me3 (#9733, Cell Signaling). After repeated washings, the DNA was recovered from the beads by incubating the beads in elution buffer (10 mM Tris at pH 8.0, 10 mM EDTA at pH 8.0, 1% SDS, 150 mM NaCl, 5 mM DTT) at 65 oC. Both input DNA and eluted DNA were subsequently purified using Qiagen Mini Elute PCR purification kit. ChIP DNA libraries were prepared with the Ovation Ultralow DR Multiplex system (NuGEN).

treatment_protocol: Cells were treated with vehicle or 6 μM GSKJ4 for 24 and 72 hours.

tag: cell line

tag: age

value: year 3

tag: tissue

value: pons

tag: gender

value: female

tag: treatment

value: DMSO

tag: treatment duration


title: K27 GSKJ4 24h, rep1

description:
8628_K27_24h_6uM
DIPG-derived cell line, harboring H3F3A K27M mutation.

source_name: Pediatric, K27M mutated DIPG cells treated with GSKJ4 for 24h, H3K27me3 ChIP


title: K27 DMSO 24h, rep2

description:
8628_K27_24h_DMSO
DIPG-derived cell line, harboring H3F3A K27M mutation.

source_name: Pediatric, K27M mutated DIPG cells treated with DMSO for 24h, H3K27me3 ChIP


title: K27 DMSO 72h, rep1

description:
8628_K27_72h_DMSO
DIPG-derived cell line, harboring H3F3A K27M mutation.

source_name: Pediatric, K27M mutated DIPG cells treated with DMSO for 72h, H3K27me3 ChIP


title: Input DMSO 24h, rep2


title: K27 DMSO 72h, rep2


title: K27 GSKJ4 72h, rep2

description:
8628_K27_72h_6uM
DIPG-derived cell line, harboring H3F3A K27M mutation.

source_name: Pediatric, K27M mutated DIPG cells treated with GSKJ4 for 72h, H3K27me3 ChIP


title: K27 DMSO 24h, rep1


title: K27 GSKJ4 72h, rep1


title: CGGA_J030

city: Beijing

first: Wanlu

last: Ye

state: Beijing

address: Biodynamic Optical Imaging Center

department: Colleage of Life Sciences

institute: Peking University

data_processing:
Remove duplications using picard-tools-1.80
Detect fusions using Tophat-2.0.6 with parameter -N 1 --read-gap-length 1 -r -50 --mate-std-dev 33 -p 4 -i 50 --bowtie1 --fusion-search --fusion-anchor-length 10 --solexa-quals
Detect fusions using defuse-0.6.1 with parameter --clustering_precision 0.90 --span_count_threshold 2 --split_min_anchor 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of a list of fusions tophat finds. Each row represents a fusion with detailed description of chromosome, break point, number of supporting reads…
Supplementary_files_format_and_content: tab-delimited text files of a list of fusions defuse finds.

source_name: Tumor cells

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions
RNA libraries were prepared using TruSeq RNA library perparation kit following standard Illumina protocols

tag: history

value: oligodendroastrocytomas


title: CGGA_J130

value: recurrent astrocytomas


title: CGGA_J042

value: recurrent oligodendroastrocytomas


title: CGGA_J100

value: recurrent Glioblastomas


title: CGGA_J023

value: anaplastic oligodendrogliomas


title: CGGA_D09

value: primary Glioblastomas


title: CGGA_D07

value: oligodendrogliomas


title: CGGA_J024


title: CGGA_D59

value: secondary Glioblastomas


title: CGGA_D57


title: CGGA_D56


title: K27 GSKJ4 24h, rep2


title: CGGA_D58

value: recurrent anaplastic astrocytomas


title: CGGA_D52


title: CGGA_D48


title: CGGA_D44

value: anaplastic oligodendroastrocytomas


title: CGGA_D47


title: CGGA_D06


title: CGGA_D36


title: CGGA_D37


title: CGGA_D39


title: CGGA_D46


title: CGGA_D33


title: CGGA_D40


title: CGGA_D34


title: CGGA_D03


title: CGGA_D32


title: CGGA_D51


title: CGGA_D27


title: CGGA_D21

value: anaplastic astrocytomas


title: CGGA_D20

value: astrocytomas


title: CGGA_D18


title: CGGA_D02


title: CGGA_D26


title: CGGA_D16


title: CGGA_D15


title: CGGA_D04


title: CGGA_D14


title: CGGA_D38


title: CGGA_247


title: CGGA_1046-1


title: CGGA_1409


title: CGGA_D45


title: CGGA_1411


title: CGGA_1412


title: CGGA_1384


title: CGGA_1381


title: CGGA_1394


title: CGGA_1406


title: CGGA_D29


title: CGGA_D24


title: CGGA_1388


title: CGGA_1343


title: CGGA_1374


title: CGGA_1340


title: CGGA_1338


title: CGGA_1375


title: CGGA_1324


title: CGGA_1330


title: CGGA_1329


title: CGGA_1342


title: CGGA_1314


title: CGGA_D11


title: CGGA_1322


title: CGGA_1301


title: CGGA_1313


title: CGGA_1287


title: CGGA_1284


title: CGGA_1408


title: CGGA_1307


title: CGGA_1280


title: CGGA_1292


title: CGGA_1272


title: CGGA_1271


title: CGGA_1281


title: CGGA_1263


title: CGGA_1246


title: CGGA_1231


title: CGGA_1234


title: CGGA_1237


title: CGGA_1218


title: CGGA_1227


title: CGGA_1215


title: CGGA_1190


title: CGGA_1189


title: CGGA_1175


title: CGGA_1177


title: CGGA_1197


title: CGGA_1160


title: CGGA_1171


title: CGGA_1146


title: CGGA_1170


title: CGGA_1145


title: CGGA_1140


title: CGGA_1124


title: CGGA_1118


title: CGGA_1116


title: CGGA_1136


title: CGGA_1240


title: CGGA_1099


title: CGGA_1113


title: CGGA_1109


title: CGGA_1094


title: CGGA_1251


title: CGGA_1119


title: CGGA_1079


title: CGGA_1077


title: CGGA_1072


title: CGGA_1078


title: CGGA_1081


title: CGGA_1068


title: CGGA_1061


title: CGGA_1060


title: CGGA_1039


title: CGGA_1052


title: CGGA_1045


title: CGGA_1059


title: CGGA_1049


title: CGGA_1050


title: CGGA_1035


title: CGGA_1031


title: CGGA_1026


title: CGGA_1027


title: CGGA_1024


title: CGGA_1022


title: CGGA_1013


title: CGGA_1011


title: CGGA_1007


title: CGGA_1008


title: CGGA_1020


title: CGGA_1004


title: CGGA_1006


title: CGGA_1005


title: CGGA_908


title: CGGA_904


title: CGGA_902


title: CGGA_905


title: CGGA_898


title: CGGA_899


title: CGGA_893


title: CGGA_909


title: CGGA_892


title: CGGA_884


title: CGGA_1034


title: CGGA_864


title: CGGA_876


title: CGGA_1015


title: CGGA_859


title: CGGA_843


title: CGGA_842


title: CGGA_848


title: CGGA_837


title: CGGA_838


title: CGGA_815


title: CGGA_804


title: CGGA_802


title: CGGA_818


title: CGGA_808


title: CGGA_796


title: CGGA_785


title: CGGA_807


title: CGGA_773


title: CGGA_766


title: CGGA_878


title: CGGA_782


title: CGGA_871


title: CGGA_752


title: CGGA_757


title: CGGA_858


title: CGGA_738


title: CGGA_850


title: CGGA_731


title: CGGA_732


title: CGGA_727


title: CGGA_725


title: CGGA_715


title: CGGA_710


title: CGGA_704


title: CGGA_700


title: CGGA_791


title: CGGA_681


title: CGGA_685


title: CGGA_694


title: CGGA_698


title: CGGA_680


title: CGGA_689


title: CGGA_762


title: CGGA_679


title: CGGA_676


title: radish sprouts biological replicate SOLiD

city: Freising

first: Richard

middle: B.

last: Landstorfer

address: Weihenstephaner Berg 3

department: Chair for Microbial Ecology

institute: Technische Universität München

description: rRNA depleted

data_processing:
SOLiD output as QUAL and CSFASTA files was converted to FASTQ with Galaxy. We mapped SOLiD and Illumina FASTQ files to the reference genome using Bowtie (settings for SOLiD data: 28 nt seed length, maximal two mismatches in the seed, a maximal threshold of 70 for the sum of the quality values at mismatched positions; Illumina data: 20 nt seed length, 0 mismatches in the seed) implemented in Galaxy. Using Samtools output SAM files were filtered for mappable reads only. We further converted SAM files to BAM files and indexed them to create BAM.BAI files.
The number of reads were normalized to reads per kilobase per million mapped reads (RPKM). Using this method, the number of reads is normalized with respect to the sequencing depth and the length of a given gene. For determination of counts and RPKM values, BAM files were imported into R (R Development Core Team) using Rsamtools. For further processing, the Bioconductor packages GenomicRanges and IRanges were used. Gene locations were determined by RefSeq and GenBank PTT files. The locations of the 16S rRNA and 23S rRNA are given by the RNT file from RefSeq. The method countOverlaps of IRanges was used to determine the remaining reads overlapping a 16S or 23S rRNA gene. We discarded these reads from further analysis due to the artificial removal of these rRNAs using the Ribominus kit as described above. countOverlaps is also used to determine the number of reads overlapping a gene on the same strand (counts). With these counts, we generated the RPKM values. For the value “million mapped reads”, the number of reads mapped to the genome minus the reads overlapping a 16S or 23S rRNA gene were used (see above). The differential gene expression was analyzed with the Bioconductor package edgeR (version 3.2.3) using the counts.
Genome_build: Escherichia coli (str. O157H7 substr. EDL933: 259
Supplementary_files_format_and_content: The xlsx file contains information for each annotated gene in each condition. For each gene, the first number indicates the logFC of a certain condition compared to LB; RPKM values are shown in parentheses. The magnitude of the absolute value of logFC is indicated by shades of grey. Significantly differentially expressed genes are in bold (i.e., p values ≤ 0.05 in edgeR).

organism: Escherichia coli O157:H7

source_name: whole organisms

extract_protocol:
RNA was extracted using Trizol, rRNA was removed with the Ribominus kit (life technologies).
The read fragments were phosphorylated and the library was constructed using the TruSeq smallRNA sample prep kit.

tag: strain

value: late logarthmic, early stationary phase

tag: growth condition and treatment

value: Radish sprout seeds were sterilized (5 min 70% ethanol, 10 min 1% NaOCl with 0.1% Tween), then washed five times with sterile water and subsequently incubated in sterile MS medium without glucose in sterile plastic boxes (1 L total volume, passively aerated). After germination, seedlings were tested for sterility by plating a sample on LB agar. After 5 days of growth, the shoots were inoculated 10 min with 1 L ¼ concentrated Ringer solution containing 103 cfu/ml EHEC. The superfluous medium was decanted and cfu/g was periodically determined as follows:infected shoots were washed and bacterial numbers of the washing liquid were determined by serial dilution platings. After 120 hours, the transition from exponential to stationary phase could be determined. Bacteria were harvested by gently shaking the seedlings in cold ¼-concentrated Ringer (+1% Tween-20; 4°C) for 1 min. Bacteria were collected by centrifugation from the decanted Ringer as above.


title: CGGA_678


title: minimal medium

description: rRNA depleted

value: M9 minimal medium was prepared as described and cells harvested after 12 h at about 2.5 x 109 cfu/ml.


title: CGGA_669


title: CGGA_675


title: LB-solid

description: rRNA depleted

value: For growth on solid medium, about 500 colonies were grown on undiluted LB agar plates and harvested after 17h at 37°C. Colonies were transferred directly to Trizol (see below) for RNA extraction.


title: spinach juice technical replicate 1

description: rRNA depleted

value: For spinach medium, whole spinach leaves were homogenized (Agienda Agricola Pistelle, Kaufland, Germany) on ice using an Ultraturrax D50. The mush was centrifuged (1 h, 30,000×g, 5°C), decanted, filtered (2.5 µm pore size), centrifuged (2 h, 30,000×g, 5°C), decanted and sterile filtered (0.2 µm). After 5 h of growth, we harvested the cells at 6.0 x 108 cfu/ml.


title: CGGA_761