title: DC_MTB_H3K4me1_rep2 (ChIP-Seq)


title: Sox2-ChIP

status: Public on Jun 01 2015

type: SRA

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

library_source: genomic

data_processing:
reads generated from the sequencing were mapped against the mouse genome (mm9) using the BWA (Burrows-Wheeler Aligner)(Li and Durbin 2009) alignment program with the default parameters (allowing 2 mismatches).
Mapped reads were submitted to the HOMER (Hypergeometric Optimization of Motif EnRichment) software for the identification of DNA binding sites
HOMER was used with the default parameters after removing of the duplicated reads.
peak finding was done by comparing the tags to the input tags (background removal)
Genome_build: mm9
Supplementary_files_format_and_content: text file: peak ID, chromosome, start, end, strand, Normalized Tag Count, Focus ratio, FindPeaks score, Total tags, control tags, Fold change vs control, p-value vs control, Fold change vs local, p-value vs local, Clonal fold change

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: mES cells were grown on 0.1% gelatin (Sigma #G1890) coated dishes in DMEM high glucose medium (Life technologies #41965) supplemented with 15% Fetal Bovine Serum (FBS HyClone, Thermo Scientific #SH30070), 2mM L-glutamine (Life technologies #25030), 1mM Sodium pyruvate (Life technologies #11360), 100units/ml penicillin/streptomycin (Bioconcept #4-01F00-H), 0.1mM 2-mercaptoethanol (Life technologies #31350), 1000units/ml Leukemia Inhibitory Factor (LIF, Millipore #ESG1107) and 1μg/ml tetracycline (Sigma #T7660). Cells were incubated at 37°C in a 5% CO2 atmosphere. Medium was changed every day and cells were passed every 1 or 2 days using 1X Trypsin-EDTA (Sigma #T4174).

extract_protocol:
ChIP was performed using the SimpleChIPTM Enzymatic Chromatin IP Kit (Cell Signaling #9003) according to manufacturer’s instructions.
Preparation of the libraries for high throughput sequencing was performed using the ChIP-Seq DNA sample Prep Kit (Illumina #IP-102-1001), following the manufacturer’s instructions

treatment_protocol: Induction of Sim2 expression was performed by culturing the cells in  tetracycline-free medium for 26h

tag: cell line

value: Sim2-expressing cells

tag: clone

tag: antibody

value: anti-Sox2 (Santa Cruz #sc-17320)


title: DC_MTB_H3K27ac_rep2 (ChIP-Seq)

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Adapter sequences and low quality score bases (Phred score < 20) were first removed from reads.
Trimmed reads were mapped in bisulfite mode to human reference genome (GRCh37/hg19) and control sequences and PCR duplicates were removed.
genome build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedgraph files using bedGraphToBigWig (UCSC); Scores represent the number of reads that mapped within a genomic region.

organism: Homo sapiens

source_name: Monocyte-derived dendritic cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats by Ficoll-Paque centrifugation. Blood monocytes were then purified from PBMCs by positive selection with magnetic CD14 MicroBeads (Miltenyi Biotech). Pure monocytes were cultured for 5 days in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FCS (Dutscher), L-glutamine (Invitrogen), GM-CSF (20 ng/mL; Immunotools), and IL-4 (20 ng/mL; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned. Before infection, we systematically checked the differentiation/activation status of the monocyte-derived DCs by flow cytometry, using antibodies against CD1a, CD14, CD83, and HLA-DR. Only samples presenting the expected phenotype for non-activated DCs – CD1a+, CD14-, CD83-, and HLA-DRlow – were used in downstream experiments.

extract_protocol:
DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems).
Samples from infected and non-infected DCs from two individuals were crosslinked with 1% w/v formaldehyde for 10 min at RT and immediately quenched for 5 min with 125mM Glycine at RT. The formaldehyde fixed samples were then sonicated to 100-400 bp using a Bioruptor (Diagenode) and then ChIP-DNA prepared using the IP-Star Compact (Diagenode) Indirect method with an Antibody-Antigen incubation of 10 hr, Bead incubation of 2 hr, and 4x 20 min wash steps. Approximately 1 million cells were used for each ChIP and ~50,000 cells for the input. The following antibodies were used: H3K4me1 (Company: CST, Cat. No.: 5326P, Lot No.: 1), H3K4me3 (CST, 9751BC, 7), H3K9me3 (MABI, 0318, 13001), H3K27me3 (MABI, 0323, 13001), H3K27ac (Abcam, Ab4729, GR119051), and H3K36me3 (MABI, 0333, 12003). ChIP and Input libraries were prepared using the Illumina Truseq Nano DNA kit, with alterations including: PCR enrichment (14 cycles) prior to size selection and utilizing the PippinPrep method (SAGE Science) instead of the SPRI method for size selection (200-400 bp).

treatment_protocol: Dendritic cells (DCs) were infected with a Mycobacterium tuberculosis (MTB) strain expressing green-fluorescent protein (H37Rv) for 18 h at a multiplicity of infection of 1-to-1. Full details can be found in Barreiro et al. (2012).

tag: condition

value: MTB-infected

tag: chip anitbody


title: DC_MTB_H3K27me3_rep2 (ChIP-Seq)


title: Sim2-EB3-input

value: EB3 control cells


title: DC_MTB_H3K36me3_rep2 (ChIP-Seq)


title: Nanog-ChIP

value: anti-Nanog (D2A3) XP® (Cell Signaling #8822)


title: DC_NI_H3K4me3_rep2 (ChIP-Seq)

value: Non-infected


title: Oct4-ChIP

value: anti-Oct3/4 (N-19) (Santa Cruz #sc-8628)


title: DC_NI_Input_rep1 (ChIP-Seq)


title: Sim2-C4-input


title: DC_NI_H3K4me3_rep1 (ChIP-Seq)


title: Sim2-C4-ChIP

value: anti-FLAG M2 antibody (Sigma #F3165)


title: Sim2-EB3-ChIP


title: DC_NI_H3K9me3_rep1 (ChIP-Seq)


title: Sim2-B8-ChIP


title: Sim2-B8-input


title: DC_MTB_H3K9me3_rep2 (ChIP-Seq)


title: DC_NI_H3K27me3_rep1 (ChIP-Seq)


title: DC_NI_H3K4me1_rep1 (ChIP-Seq)

value: H3K4me1 (Company:CST, Cat. No.:5326P, Lot No.:1)


title: Sim2-A6-input


title: DC_NI_H3K27ac_rep1 (ChIP-Seq)


title: DC_MTB_H3K9me3_rep1 (ChIP-Seq)


title: EB3-1

library_source: transcriptomic

data_processing:
mRNA-Seq reads were mapped against the mouse genome (mm9) using the default parameters of BWA.
For each gene, a custom pipeline was used to calculate the exon coverage. This coverage was normalized in reads per kilobase per million (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: txt file: chromosome, start, end, cDNA length, gene length, gene name, strand, RPKM values in Sim2-A6, Sim2-B8, Sim2-C4, EB3-0, EB3-1 and EB3-2

molecule: total RNA

extract_protocol:
RNA samples were prepared using TRIzol® reagent (Life technologies™ #15596) as per the manufacturer’s instructions.
mRNA-Sequencing libraries were prepared from 500ng of total RNA using the TruSeq RNA Sample Preparation kit (Illumina #RS-122-2001) following Illumina’s instructions.

tag: cell type

value: embryonic stem cells


title: EB3-2


title: DC_MTB_Input_rep1 (ChIP-Seq)


title: EB3-0


title: DC_MTB_H3K4me1_rep1 (ChIP-Seq)


title: DC_MTB_H3K4me3_rep1 (ChIP-Seq)


title: DC_MTB_H3K36me3_rep1 (ChIP-Seq)


title: Sim2-C4


title: Sim2-B8


title: Sim2-A6


title: DC_MTB_H3K27me3_rep1 (ChIP-Seq)


title: DC_MTB_H3K27ac_rep1 (ChIP-Seq)


title: Small RNA Seq Dnmt3L KO 10dpp

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: RNA-seq (18-35nt size fractionation)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The 3' adapter sequences were searched in the reads (3' adapter sequence “TGGAATTCTCGGGTGCCAAG”)
The trimmed sequencing reads of each sRNA-seq library were analyzed with ncPRO-seq (v1.5.1, Chen CJ., et al 2012).
Genome_build: mm9
Supplementary_files_format_and_content: Text files with the trimmed sequencing reads and the number of times sequenced.

source_name: Testis

extract_protocol:
Trizol
Illumina small RNA TruSeq

tag: strain background

tag: genotype/variation

value: Dnmt3L knockout

tag: age

value: post-natal day 10

tag: tissue

value: testis


title: DC_NI_H3K36me3_rep1 (ChIP-Seq)


title: Small RNA Seq Dnmt3L WT 16.5dpc

description: RNA-seq (18-35nt size fractionation)

value: Dnmt3L wildtype

value: pre-natal day 16.5


title: Small RNA Seq Dnmt3L KO 16.5dpc

description: RNA-seq (18-35nt size fractionation)


title: Small RNA Seq Dnmt3L WT 10dpp

description: RNA-seq (18-35nt size fractionation)


title: human HER2/ERBB2, overexpressed in HMEC cells 2

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

country: USA

institute: University of Utah

data_processing:
Quality checking with FASTQC
Alignment and quantification with R package Rsubread
FPKM normalization with edgeR and limma
TPM normalization from the FPKM values
TCGA RNA-Seq pipeline processed expected gene counts and normalized gene results
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Raw sequence files as .fastq.gz, processed files are tab-delimited for gene counts as .featureCounts.txt, normalized in fpkm as .fpkm, normalized in TPM as .tpm files. TCGA RNA-Seq Level 3 pipeline processed expected gene counts as GFP18_HER2_TCGA_Pipeline_Expected_Gene_Counts.txt and Level 3 upper quartile normalized data as GFP18_HER2_TCGA_Pipeline_Normalized_Genes_Results.txt

source_name: human HER2/ERBB2_overexpressed in HMEC cells

growth_protocol: Human mammary epithelial cells, grown in Stemgent WIT-P culture medium at 3% CO2 and 37°C

extract_protocol:
Cells were scraped into RNA-Later and stored on ice until processing.  Then RNA was isolated from pelleted cells using a Qiagen Rneasy mini kit (with Rnase-free DNase set) and QIAshredders.
Illumina TruSeq stranded mRNA kit

treatment_protocol: Genes were introduced for over-expression by way of adenovirus.  Cells were infected with MOI 500 Adenovius for 18 hours.

value: Human mammary epithelial cells (HMEC)

value: HER2/ERBB2 overexpression


title: human HER2/ERBB2, overexpressed in HMEC cells 3


title: human HER2/ERBB2, overexpressed in HMEC cells 1


title: human HER2/ERBB2, overexpressed in HMEC cells 4


title: GFP control, overexpressed in HMEC cells 12

source_name: GFP control_overexpressed in HMEC cells

value: GFP overexpression (control)


title: J1-SB431542

city: Yangling

first: Juan

last: Du

state: China/Shaanxi

address: 3 Taicheng Road

country: China

institute: College of Life Sciences

data_processing:
Basecalls performed using Perl package developed by BGI
We will get rid of some contaminant reads from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
The data is processed by the following steps: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Genome_build: mm9

source_name: J1 mESCs treated with SB431542 for 24 hours

growth_protocol: The J1 mouse embryonic stem cell line purchased from ATCC (Manassas, VA, USA) was gelatin adapted and grown on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF (ESGRO, Millipore, USA).

extract_protocol:
Total cellular RNA was isolated from J1 mESC using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: J1 mESCs maintained in medium containing 1000 U/mL LIF and treated by 3 μΜ SB431542 or equal volum DMSO for 24h.

tag: strain

value: Inner Cell Mass


title: J1-DMSO

source_name: J1 mESCs treated with DMSO for 24 hours


title: GFP control, overexpressed in HMEC cells 7


title: GFP control, overexpressed in HMEC cells 10


title: GFP control, overexpressed in HMEC cells 6


title: GFP control, overexpressed in HMEC cells 11


title: GFP control, overexpressed in HMEC cells 4


title: GFP control, overexpressed in HMEC cells 5


title: GFP control, overexpressed in HMEC cells 3


title: GFP control, overexpressed in HMEC cells 2


title: human HER2/ERBB2, overexpressed in HMEC cells 5


title: GFP control, overexpressed in HMEC cells 1


title: CON

city: Beijing

first: Shuhui

last: Song

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

data_processing:
The sequenced reads were subjected to adapter-removal using fastx_clipper (0.1.13 version) of FASTX-Toolkit tools (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads less than 13 nt in length or containing an ambiguous nucleotide were discarded. After trimming, the remaining clean reads were aligned to mouse genome sequences (NCBIM37) of Ensembl (release 62) by the BWA 0.5.8 algorithm [1], with up to two mismatches allowed. For multiple mapped reads, only one location reported for the optimal mismatch-stratum. All these matched reads (including unique and multiple mapped reads) were used for further analysis.
The mapped reads in the same strand were grouped into islands by overlapping at least one single nucleotide for each control and RIP sample. The location of grouped islands that contained at least three reads relative to a known gene was determined based on the ENSEMBL database (release 62). Islands that aligned anti-sense strand to know transcripts which likely represent false positive due to amplification and mapping artifacts were discarded. The significant RNA-binding locations were detected by DEGseq [2] software and annotated to gene region based on the chromosome coordinate and GenBank annotation.
Genome_build: ENSEMBL 62 (NCBI 37)

source_name: testis RNA pulled down with IgG

growth_protocol: 10-week old ICR mice was used for this experiment.

extract_protocol:
cDNA library was constructed according to Illumina® TruSeq™ Small RNA Sample Preparation protocol.
library_strategy: PAR-CLIP

treatment_protocol: Mice was injected twice with 4-thiouridine in DMSO and mouse testis lysates were irridated under UV 365nm for crosslinking of protein to RNA molecules. subsequently rabbit polyclonal ALKBH5 antibody, or IgG as a negative control was used to immunoprecipitate ALKBH5 protein together with its binding RNA. After IP, RNA was digested with Rnase T1 and recovered after proteinase K treatment.

value: ICR

value: IgG


title: HD291 line after 15 enzymatic passages

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

institute: PhyMedExp INSERM U1046

description: Transcriptome human embryonic cell line HD291 after 15 enzymatic passages + initial passages 13 mechanic passages

data_processing:
TopHat (http://tophat.cbcb.umd.edu)/Cuffinks(http://cufflinks.cbcb.umd.edu) was used in order to map reads to the refence genome according to annotated trasncripts.
The coverage depth of each unique exon was computed from the Tophat alignement. From the alignment generated by TopHat, the program htseq-count (part of the DESeq software package developed by Simon Anders (2010)) was used to retrieve the counts of reads which aligned to each transcript's exon. The exon annotations are based on Ensembl reference GTF 63. For each unique exon, the count information is reported for all related transcripts. If 2 transcripts contain one common exon, the count information for this exon is the same for both transcripts.
The program Cuffdiff  (part of the Cufflinks software package) was used to compute the abundance of transcripts in each sample. From the Tophat mapping results it eval- uates the abundance of each Ensembl annotated transcript.
The metric used by Cufflinks to estimate the abundance of transcripts is the FPKM: Fragments Per Kilobase of exon per Million fragments mapped. The FPKM was introduced by Trapnell C et al. (2010). The Fraction of Major Isoform (FMI) indicate the relative proportion of each isoform for gene having multiple transcripts. It is equal to 100 for transcripts having the highest FPKM.
Genome_build: GRCh37.63
Supplementary_files_format_and_content: text files containing calculated FPKM and FMI for each annotated gene and transcript (Ensembl).

source_name: Embryonic stem cell line

growth_protocol: These lines were maintained in culture media consisting of 80% KO-DMEM, 20% KOSR, 2 mM L-glutamine, 1% non-essential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and complemented with 10 ng/mL bFGF (Abcys, Paris, France). These cells were maintained in 35-mm dishes with pre-coated irradiated (40 Gy) human foreskin fibroblast (hFF) feeders and were either enzymatically or mechanically passaged every week.

extract_protocol:
In mechanically passaged culture, the hESC colonies were exscinded carefully using a scalpel. In enzymatic-passaged culture, the singles cells were released as described above. As SSEA4 is one of most obstinate pluripotence markers (Ramirez et al., 2011), hESC cells were purified and enriched using the magnetic beads Dynabeads® SSEA-4 (Invitrogen) and the manufacture’s instructions were rigorously followed. The quality control of the purification showed high efficiency and no over-selection of SSEA4+ sub-population.  Total RNA was purified from cell culture using the RNeasy Mini Kit (Qiagen, Courtaboeuf, France) following manufacture’s instructions. We added an RNAse-Free DNase step in RNA extraction and an RNsae A treatment in DNA extraction to eliminate residual DNA or RNA.
QC of the quantity of the total RNA using nanodrop. Library construction using TruSeq RNA Sample Prep Kits. Library Quality Control and quantification by Bioanalyzer Agilent 2100, qPCR and Picogreen.

treatment_protocol: Mechanical passaging was carried out under an inverted microscope under the hood using scalpels (Assou et al., 2009; Bai et al., 2011). For enzymatic single cell passaging, the cells were pre-treated with Y-27632 for 1h and dissociated with TrypLE™ Select (Invitrogen) for 10 mn at 37ºC. The reaction was stopped by hESC culture media and single hESC were released by pipetting and passed through a 20 µm strainer to eliminate hFF feeders, then counted and seeded on newly prepared feeder in density of 20 000 cells/cm2 at beginning and progressively to 3 000 cells/cm2 when cells were adaptated to enzymatic passaging. Both mechanic and enzymatic passaging were performed weekly. Experiments on HD291, HD129 and HS306 lines were initiated at p13, p16 and p25 respectively (termed initiating passages) and maintained independently using mechanic passaging (+MP) or enzyamatic passaging (+EP). All cell cultures were regularly checked for mycoplasma contamination and remained negative throughout the experiments.

tag: gender

value: male

tag: passage


title: HD291 line after 15 mechanic passages

description: Transcriptome human embryonic cell line HD291 after 15 mechanic passages + initial passages 13 mechanic passages


title: LNCaP-Sicontrol-rep1

city: San Antonio

first: Zhenqing

last: Ye

state: Texas

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: The University of Texas Health Science Center at San Antonio

description: Sample 1

data_processing:
Sequenced reads were  mapped to hg19 by TopHat, and those uniquely mapped reads were used for further analysis.
Differentially expressed genes are retrived by edgeR software with p<0.001.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed gene list from edgeR output

source_name: LNCaP-SiControl

growth_protocol: LNCaP cells were routinely cutured in RPMI medium supplemented with 10% FBS.

extract_protocol: RNA mRNA was isolated with Rneasy Mini kit from Qiagen.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample KitPart # 15008136. Briefly, the polyA containing mRNA was purified, fragmented, and reverse transcribed. This was followed by second strand cDNA synthesis. The cDNA fragments went through end repair, adapter ligation, and PCR amplification processes. The final cDNA library was sequenced by Illumina HiSeq2000 in OSUCCC sequencing core.

treatment_protocol: 4 days before ChIP assay, the full medium was changed to RPMI medium supplied with 5% charcal treated FBS without anti-biotics.

value: LNCaP

value: prostate cancer cells

tag: passages


title: RIP

source_name: testis RNA pulled down with ALKBH5 antibody


title: LNCaP-SiGATA2-REP2

description: Sample 4

tag: treated with


title: LNCaP-SiGATA2-REP1

description: Sample 3


title: LNCaP-Sicontrol-rep2

description: Sample 2


title: BisulfiteSeq – PolV+ / SPT- (Replicate 2)

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

data_processing:
BisulfiteSeq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).
Supplementary_files_format_and_content: Concatenated per-chromosome plain text UCSC Genome Browser wiggle files with UNIX-style line endings, compressed with GNU gzip, files are variable step with each value represented the %methylation of a single cytosine of a CHG context at a given position.

organism: Arabidopsis thaliana

source_name: 3 week leaf tissue

growth_protocol: For plant growth, seeds were stratified at 4°C for 2 days before growth on soil at 23°C with 16-h light and 60-70 % relative humidity.

extract_protocol:
Samples 1..27 were extracted by phenol-chloroform extraction followed by bisulfite treatment
Libraries 1..27 were constructed using the TruSeq DNA LT kit (Illumina) and Epitect Bisulfite Kit (Qiagen). converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013.

tag: genotype

value: F2 progeny of intercross between PolV- and SPT- lines

value: 3-week leaf


title: BisulfiteSeq – PolV+ / SPT- (Replicate 3)


title: GFP control, overexpressed in HMEC cells 8


title: BisulfiteSeq – SPT+(1) (Replicate 3)

value: SPT5+ transgene ; spt5l-1 (eco. Columbia)


title: BisulfiteSeq – PolV- / SPT- (Replicate 2)


title: BisulfiteSeq – PolV- / SPT- (Replicate 1)


title: BisulfiteSeq – PolV+ / SPT- (Replicate 1)


title: BisulfiteSeq – SPT-(1) (Replicate 3)

value: SPT5- transgene ; spt5l-1 (eco. Columbia)


title: BisulfiteSeq – SPT+(1) (Replicate 2)


title: BisulfiteSeq – SPT+(1) (Replicate 1)


title: BisulfiteSeq – PolV- / SPT- (Replicate 3)


title: BisulfiteSeq – SPT-(1) (Replicate 1)


title: BisulfiteSeq – PolV+(2) (Replicate 3)

value: PolV+ transgene ; nrpe1-11 (eco. Columbia)


title: BisulfiteSeq – SPT-(1) (Replicate 2)


title: BisulfiteSeq – PolV+(2) (Replicate 2)


title: Sim2-A6-ChIP

value: Sim2-expressing cells

value: anti-FLAG M2 antibody (Sigma #F3165)


title: HD291 line at initial passage 13

description: Transcriptome human embryonic cell line HD291 at initial passage 13

value: embryonic stem cells


title: BisulfiteSeq – PolV-(2) (Replicate 2)

value: PolV- transgene ; nrpe1-11 (eco. Columbia)


title: BisulfiteSeq – PolV-(2) (Replicate 1)


title: BisulfiteSeq – PolV+(2) (Replicate 1)


title: BisulfiteSeq – spt5l (Replicate 2)

value: spt5l-1 (eco. Columbia)


title: BisulfiteSeq – nrpe1 (Replicate 3)

value: nrpe1-11 (eco. Columbia)


title: BisulfiteSeq – PolV-(2) (Replicate 3)


title: BisulfiteSeq – nrpe1 (Replicate 2)


title: BisulfiteSeq – spt5l (Replicate 1)


title: BisulfiteSeq – Columbia (Replicate 2)

value: Wild type (eco. Columbia)


title: BisulfiteSeq – Columbia (Replicate 3)


title: BisulfiteSeq – nrpe1 (Replicate 1)


title: BisulfiteSeq – Columbia (Replicate 1)


title: 2EcR

city: Baltimore

first: Allan

middle: C

last: Spradling

state: MD

address: 3520 San Martin Dr.

department: Embryology

institute: Carnegie Institution/HHMI

data_processing:
basecalling: CASAVA v1.8.2
reads aligned to genome using Bowtie2 v 2.0.6
identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtf
calculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtf
Genome_build: Refseq annotation file: dm3 (Release 5) and dm3-iGenomes.gtf
Supplementary_files_format_and_content: Cufflinks output file (.xlsx)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: stage 10 EcRts follicles sample 2

growth_protocol: Fertilized adult females 4-14 days of age were employed to ensure that follicle production has reached steady state. Females were kept at a controlled density in fresh vials, at 25°C and provided with a optimal nutrition 36hr prior to analysis. Under these conditions, follicle progression in the ovary is stable and reproducible.

extract_protocol:
Ovarian follicles of the indicated stage and genotype were dissected under a dissecting microscope at room temperature in Grace's medium and transferred to iced tripure (Roche/Boehringer Mannheim cat: 11667157001) to avoid RNA degradation. Samples of 100 follicles were homogenized. 600μl of fresh tripure was added, mixed, and allowed to stand at room temperature for 5-10 min. After adding 180μl chloroform, samples were vortexed 2 x 45 secs, and incubated at room temperature for 10 minutes. Samples were then centrifuged for 15 min at 12,000 rpm at 4°C, and the aqueous layer was moved to a fresh tube. RNA was precipitated by adding 400μl of isopropanol, vortexing for 15 seconds, and incubating at room temperature for 15 min, and centrifuging at 12,000 rpm for 15 min at 4°C. After washing the pellet with 75% EtOH, the RNA was dried in air dry for 5 minutes, resuspended in 50μl nuclease free H2O, and stored at -80°C.
cDNA libraries were constructed from poly(A)-selected RNA using Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: EcR mutant flies were shifted to the restrictive temperature 2 days after eclosion.

value: Oregon R

value: female

value: 6-14 days old

tag: developmental stage

value: adult

tag: subregion

value: stage 10 EcR mutant

value: follicle


title: 1EcR

source_name: stage 10 EcRts follicles sample 1


title: 3_10

source_name: stage 10 follicle sample 3

value: stage 10


title: C24741_G07ZQ7Q02

city: Ann Arbor

first: Ryan

last: Mills

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

institute: University of Michigan

description:
clusters_positions.txt
clusters_isoforms.txt
clusters_pas.txt

data_processing:
Reads were aligned to C. elegans genome (WS190) using Bowtie2version 2.0.0-beta6 with the parameters --local --very-sensitive-local -X 750.
Aligned reads were converted to PSL format for clustering and poly A site analysis by custom scripts (Mangone et al., 2010).
Custom scripts (Mangone et al., 2010) were used to identify recurrent polyA signal sequences in the clustered reads and perform additional analyses.
Genome_build: WS190
Supplementary_files_format_and_content: clusters_positions.txt: Tab-delimited text file with gene, chromosome, strand, and 3'UTR start position(s). Used to compile polyA signal statistics in clusters_pas.txt.
Supplementary_files_format_and_content: clusters_isoforms.txt: Tab-delimited text file with gene, # of isoforms and # of 3'UTR start positions. Used to compile polyA signal statistics in clusters_pas.txt.
Supplementary_files_format_and_content: clusters_pas.txt: Tab-delimited text file with genep=gene, chr=chromosome, utr_start=3'UTR start position, utr_end=3'UTR end position, utr_length=3'UTR length, variable number of sample names, tot=# of mapped reads in the cluster, src=one or both samples has a PAS site, class=annotated genic feature (CDS, 5UTR, 3UTR, intron), pas=polyA signal sequence, pas_pos=position of PAS in 3'UTR, pas1=annotation as canonical AATAAA signal or alternative PAS signal, isocnt=# of UTR isoforms, isolen=which of the isoforms is represented by the mapped read clusters, neuron=annotation as present in neuronal (sydn-1) mutant sample, abun_pass=Y/N if passed abundance filter, abun_count=# of samples with PAS present, iso_pass=Y/B if passed isoform filter.

organism: Caenorhabditis elegans

source_name: Whole worm RNA extraction

extract_protocol:
Worms were maintained, propagated and collected at RT. Tens of L4 worms were seeded on each large (15cm) agar plate with E.coli OP50 as the food. 5 days later, the gravid  hermaphrodites were collected and lysed with bleach. Eggs were transferred to large agar  plates with E.coli OP50 and larvae were harvested 1 day (L1-L2 stage) or 2 days (L3-L4 stage) later.
We generated 3’UTR libraries from wild type and sydn-1 mutant by oligo (dT) priming (Mangone et al., 2010), which were later subjected to 454 sequencing.


title: 1_10

source_name: stage 10 follicles sample 1


title: 2_8

source_name: stage 8 follicles sample 2

value: stage 8


title: 3EcR

source_name: stage 10 EcRts follicles sample3


title: 1_8

source_name: stage 8 follicles sample 1


title: C24741_GVN0EHB02


title: 2_10

source_name: stage 10 follicles sample 2


title: N2_GVN0EHB01


title: N2_G07ZQ5M02


title: BisulfiteSeq – spt5l (Replicate 3)

value: 3-week leaf


title: Sample_H3K4me3_Index_7_lane6

city: new york

first: Thadeous

middle: James

last: Kacmarczyk

state: ny

address: 1300 York Ave

department: Medicine/Hematology-Oncology

institute: Weill Cornell Medicine

data_processing:
Basecalling performed using Illumina CASAVA v1.8.2.
ChIP-seq reads aligned to hg19 genome assembly using ELANDv2e from the Illumina CASAVA v1.8.2.
Peak calling performed using ChIPseeqer with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: targets files, the peak files generated by ChIPseeqer, are tab delimited with columns representing:  chromosome, start_position, end_position, avg_p-value, score, posmaxpeakheight, maxpeakheight, relposmaxpeakheight(%), peak_size, mid_point

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly24

growth_protocol: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly1 was grown in medium containing 90% Iscove's, 10% fetal calf serum and supplemented with penicillin G and streptomycin.

extract_protocol:
Chromatin was then subjected to phenol:chloroform extraction followed by purification using a PCR purification kit (Qiagen, Germantown, Maryland). Quantitative real time PCR (qRT-PCR) on positive housekeeping genes was performed on both input and eluted chromatin, to validate the ChIP efficacy.
Libraries compatible with Illumina TruSeq adapter sequencing (Illumina Inc, San Diego, CA) were made as follows: 10 ng of either immunoprecipitated or input DNA were end-repaired using 3 units of T4 DNA polymerase, 1 unit of Klenow DNA polymerase and 10 units of T4 DNA polymerase with 30 minutes incubation at 20ºC;  A-tailing was performed with 5 units of Klenow fragment and 10mM dATP (New England Biolabs, Ipswich, MA) for 30 minutes at 37ºC. 2 ul of 1uM of annealed Illumina TruSeq adapters (Integrated DNA Technologies, Coralville, IA) were used in an overnight ligation at 4ºC with 2000 units of T4 DNA Ligase. To account for the migration pattern of Y-forked Illumina adaptors ligated products from 250-350bp were size selected in a 1% agarose gel. After purification, the PCR reaction was carried out with 300uM dNTP, 200uM of primers and 1 unit of Phusion High-Fidelity DNA Polymerase (Thermo Scientific, Rockford, IL). Initial denaturation of 94ºCx5 min, was followed by18 cycles of 94ºCx20secs, 60ºCx30secs, 72ºCx30secs, with a final extension/elongation step of 72ºCx5min. PCR product was cleaned by the use of SPRI beads as per manufactor’s recommendation [Beckman Coulter, Indianapolis, IN]. Final product was resuspended in 20 ul of TrisEDTA. Final yields were quantified in a Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and quality of the library was assessed by running on a DNA1000 Bioanalyzer chip (Agilent Technologies, Santa Clara, CA). Libraries were normalized to 2nM and loaded on an Illumina HiSeq 2500 at 6pM, per manufacturer’s recommended protocol for 50bp single-read runs.

treatment_protocol: Immunoprecipitation using anti-histone H3 trimethyl K4 (ab8580, Abcam, Cambridge, MA) was performed in crosslinked sonicated extracts. Cells were grown at 1-1.5 million per ml and protein and DNA were crosslinked for a 10 minute treatment with 1% Formaldehyde (Thermo Scientific, Rockford, IL) and harvested. 100 x 106 cells were lysed by flash freezing in liquid N2 and stored at -80ºC. Chromatin shearing was performed using a Covaris S220 sonicator (Covaris, Woburn, MA) using the following conditions: 1 ml tubes with approximately 30 million cells in buffer containing 0.1% SDS (Covaris Buffer D3) were sonicated using peak intensity power of 140, duty factor of 5.0 and 200 cycles per burst, for 18 minutes. Extent of shearing was monitored with a 1% agarose gel and confirmed by separation on an 2100 High sensitivity Bioanalyzer chip (Agilent Technologies, Santa Clara, CA) at the completion of the immunoprecipitation. Immunoprecipitation was carried out at 4ºC with overnight incubation using 97.5 x 106 cell equivalents of chromatin and 15ug of antibody. Immunoprecipitates were captured with Protein A Dynabeads (Novex Life Technologies,Grand Island, NY), washed, and resuspended in buffer containing 100ug of RNAse A and 20ug of PCR grade Proteinase K (Qiagen, Germantown, Maryland). Crosslinks were reversed by incubation at 65ºC in the presence of 1% SDS and 0.3M NaCl.

tag: cell line

tag: chip antibody


title: Sample_H3K4me3_Index_6_lane6

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly23

value: anti-histone H3 trimethyl K4 (ab8580, Abcam, Cambridge, MA)


title: Sample_H3K4me3_Index_5_lane6

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly22


title: Sample_H3K4me3_Index_4_lane6

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly21


title: Sample_H3K4me3_Index_3_lane6

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly20


title: Sample_H3K4me3_Index_2_lane6

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly19


title: GFP control, overexpressed in HMEC cells 9

source_name: GFP control_overexpressed in HMEC cells

value: Human mammary epithelial cells (HMEC)

value: GFP overexpression (control)


title: Sample_H3K4me3_Index_7_lane5

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly15


title: Sample_H3K4me3_Index_12_lane5

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly16


title: Sample_Input_Index_12_lane6

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly17

value: input


title: Sample_H3K4me3_Index_2_lane5

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly12


title: Sample_H3K4me3_Index_4_lane5

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly13


title: Sample_H3K4me3_Index_5_lane5

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly14


title: Sample_H3K4me3_Index_1_lane6

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly18


title: Sample_Input_Index_6_lane5

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly11


title: 3_8

source_name: stage 8 follicles sample 3


title: Sample_H3K4me3_Index_5_lane4

description:
Targets_lane4.tar
Targets_lane34.tar

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly10


title: Sample_Input_Index_12_lane4

description:
Targets_lane4.tar
Targets_lane34.tar

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly8


title: Sample_H3K4me3_Index_4_lane4

description:
Targets_lane4.tar
Targets_lane34.tar

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly9


title: Sample_Input_Index_4_lane3

description:
Targets_lane3.tar
Targets_lane34.tar

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly3


title: Sample_Input_Index_5_lane3

description:
Targets_lane3.tar
Targets_lane34.tar

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly4


title: Sample_H3K4me3_Index_6_lane3

description:
Targets_lane3.tar
Targets_lane34.tar

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly5


title: Sample_H3K4me3_Index_12_lane3

description:
Targets_lane3.tar
Targets_lane34.tar

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly6


title: Sample_4B-M1T1_DPTP

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

institute: Ohio State University

data_processing:
Primary sequencing data that produced by Illumina Hiseq 2000, called as raw reads were subjected to quality control to determine if resequencing step is needed. After QC, raw reads were filtered into clean reads which was then aligned to reference sequence Streptococcus pyogenes MGAS5005 NC_007297.1 with SOAPaligner/SOAP2 v2.20 [Li. R, Yu,C., LiY et al  Bioinformatics :Doi:10.1093/bioinformatics/btp336.  259(15)1966-1967]. The alignment data were utilized to calculate distribution of reads on reference genes and perform coverage analysis. Upon QC pass, down stream analysis including gene expression, novel transcript prediction and annotation were done. Gene ontology enrichment analysis were used for pathwat enrichment analysis. In order to assess the effectiveness of selected mapping tool, the comparative analysis between SOAPAligner/SOAP2 and other popular-alignment tool BOWTIE [Langmead B. et al (2009) genome biology 10:25-34/ http://Bowtie-bio.sourceforge.net/index.shtml].  Because the SOAPaligner/SOAP2 performed better, quantification analysis of gene expression was done with SOAPaligner/SOAP2. For significance of didgital gene expression profile alogorithms as published [Audic et al (1997) Gemome Res. 7:986-985].. We used FDR< 0.001 [benjamini and Yekutieli(2001)Ann Statistics29:1165-1188] and the absolute value Log2 ratio > 1 as the threshold to judge the significance of gene expression difference. KEGG was used to perform Pathway enrichment analysis. For gene refinement, transcripts reads were assemble by using CUFFLINK software [Roberts et al Bioinformatics: doi:10.1093/bioinformatics. btr355].
Genome_build: NC_007297.1

organism: Streptococcus pyogenes

source_name: Late-log phase culture

growth_protocol: All cultures were grown in Todd Hewitt broth supplemented with 0.5% yeast extract. Cultures were grown at 37oC till O.D. reached at 0.8. (wt) mutant (0.65) i.e. till late log phase. The cultures were then centrifuges at 4oC  and washed once with sterile autoclaved PBS. The cell were then resuspended in PBS in the 1/50th of the starting culture volume.

extract_protocol:
total RNA was extracted using  Norgen RNA isolation kit (canada).
The high quality total RNA samples were obtained by DNase treatment. The samples were then sent to BGI Americas. rRNA was removed from the total RNA samples.cDNA was then made using mRNA as template. Short fragments were made by heat treatment amd the shortfragment were purifiedand resolved  with EB buffer for endreparation and single nucleotide A ( adenine) addition. Short fragments were then connected to adapters. Subsequently, folowwing agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification. All qc steps i.e. for quatification and quality of sample library ABI bioanalyzer and ABI StepOnePlus realtime PCR system were used. Library were sequenced using IlluminaHiseq 2000.

treatment_protocol: Using pFW6 vector, S. pyogenes mutants lacking SP-PTP were derived. The washed concentrated bacterial pellet suspension was treated with phage-lysin to lyse the bacterial cells.

tag: phenotype

value: Lacking -SP-PTP


title: Sample_4A-M1T1_DPTP


title: Sample_1B-M1T1_WT

value: wild-type

value: Intact SP-PTP


title: Sample_H3K4me3_Index_2_lane2

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly2


title: Sample_Input_Index_2_lane1

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly1


title: DC_NI_rep2 [wtRNA-Seq]

data_processing:
Adaptor sequences and low quality score bases were trimmed and resulting reads were aligned to the human genome reference sequence (GRCh37/hg19).
genome build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedgraph files using bedGraphToBigWig (UCSC); Scores represent the number of reads that mapped within a genomic region. Tab-delimited text files include expression count values for each sample.

source_name: Dendritic cells

extract_protocol:
Total RNA was extracted from the same samples using the miRNeasy kit (Qiagen). RNA quantity was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with no evidence for RNA degradation (RNA integrity number > 8) were kept for further experiments.
For three individuals, we also performed RNA-Seq on the whole transcriptome following ribosomal depletion using the Ribo-Zero Gold depletion and the Illumina Total Stranded RNA Library kits (Illumina).

tag: cell-type

value: Monocyte-derived dendritic cells

tag: condition

value: Non-infected


title: DC_MTB_rep2 [wtRNA-Seq]

value: MTB-infected


title: DL3

city: Berlin

first: Dmitriy

last: Ignatov

address: Charitéplatz 1

country: Germany

institute: Max Planck Unit for the Science of Pathogens

data_processing:
Basecalls performed using CASAVA version 1.4
The reads were aligned to the reference sequence of Mycobacterium tuberculosis H37Rv (GenBank accession code AL123456.3) with Bowtie 2, setting parameters: -q --local.
Transcriptional profiles for visualization in Artemis genome browser were made with custom Perl script. For each nucleotide of the genome the quantity of reads mapped to this nucleotide in forward and reverse orientation were counted. The files "Profile_XXX.txt" represent these counts. The rows correspond to nucleotides of the M. tuberculosis H37Rv genome, the columns correspond to quantities of reads mapped to these nucleotides in forward and reverse orientation.
Annotation of the genome was retrieved from GenBank AL123456.3. For every annotated gene, the number of reads overlapping the gene at least by one nucleotide was calculated using custom Perl script. These calculations were made separately for reads in the same orientaion as the gene (sense), and in the opposite orientation (antisense). The results of these calculations are deposited in file "Counts.xls".
RPKM values were calculated for every CDS using custom R script. Only reads in sense orientation were counted. To calculate the proportion of a gene to which reads could be unambiguously mapped, 77 nucleotide sequences were stimulated from the genome sequence and aligned to the sequence under the settings used for mapping the RNA-seq reads. RPKM values were not calculated for genes with no regions, to which sequence reads could be unambiguously mapped, and for instances where less than five reads were mapped to the gene. The RPKM values are in the file "RPKM.xls".
Search for differentially expressed genes was done with edgeR package. The results are represented in file "DiffExpression.xls"
Genome_build: ASM19595v2
Supplementary_files_format_and_content: Profile_XXX.txt (where XXX = Log1, Log2, Log3, DE1, DE2, DE3, DM1, DM2, DM3, DL1, DL2, DL3) - transcriptional profiles for visualization in Artemis genome browser. The rows correspond to nucleotides of the M. tuberculosis H37Rv genome, the columns correspond to quantities of reads mapped to these nucleotides in forward and reverse orientation. The profiles can be visualized in Artemis as "User Plot" with M. tuberculosis H37Rv genome build AL123456.3 as a reference.
Supplementary_files_format_and_content: Counts.xls - The numbers of overlapping reads for every annotated gene in each sample. The number of overlapping reads in the same orientation as a gene (sense) and in the opposite orientation (antisense) is shown
Supplementary_files_format_and_content: RPKM.xls - RPKM values for every annotated CDS in each sample. RPKM values were not calculated for genes with no regions, to which sequence reads could be unambiguously mapped, and for instances where less than five reads were mapped to the gene. For calculation of RPKM for a CDS in a library, the following formula was used: (N reads mapped to the CDS * 10^9)/(N reads mapped to all CDSs in the library * Length of the CDS region, to which the reads could be unambigously mapped)
Supplementary_files_format_and_content: DiffExpression.xls - the results of search for differentially expressed genes using edgeR package. Differentially expressed genes were searched by comparisons of samples: DE relative to Log, DM relative to DE, DL relative to DE and DL relative to DM. For every gene in each of these comparisons log2 fold change (logFC) and FDR-adjusted p-value of test for differential expression (FDR) are represented.

organism: Mycobacterium tuberculosis

source_name: Cells grown in the K+-deficient media for 14 days, and incubated under rifampicin (5 μg/ml) for 20 days

growth_protocol: M. tuberculosis strain H37Rv was initially grown from frozen stocks for 10 days in Sauton medium, containing 0.5 g KH2PO4, 1.4 g MgSO4 · 7H2O, 4 g L-asparagine, 60 ml glycerol, 0.05 g ferric ammonium citrate, 2 g sodium citrate, 0.1 ml 1% ZnSO4 · 7H2O, H2O to 1 liter, pH 7.0 (adjusted with 1M NaOH) and supplemented with ADC and 0.05% Tween 80 (37°C; 200 rpm). This starter culture was then sub-cultured into fresh media (same composition) and incubated for another 10 days to an optical density at 600 nm (OD600) of 4.0, and served as an inoculum that was added to potassium-deficient Sauton medium supplemented with ADC and 0.05% Tween 80 (37°C; 200 rpm) at a concentration of 5·105 cells per ml. Potassium-deficient Sauton medium contains 8.9 g Na2HPO4 · 12H2O, 1.4 g MgSO4 · 7H2O, 4 g/L-asparagine; 60 ml glycerol, 0.05 g ferric ammonium citrate, 2 g sodium citrate, 0.1 ml 1% ZnSO4 · 7H2O, H2O to l liter, pH 7.0 (adjusted with 1M NaOH). Cultures were incubated in K+-deficient Sauton media at 37 °C and shaken at 200 rpm. Sample "Log" represents cells grown in the K+-deficient media for 4 days. Sample "DE" represents cells grown in the K+-deficient media for 14 days  After 14 days of incubation, rifampicin (5 μg/ml) was added and the cells were additionally cultivated for 20 days. Sample "DM" represents cells incubated under rifampicin for 10 days, and sample "DL" - incubated under rifampicin for 20 days.

extract_protocol:
RNA was isolated using phenol-chloroform extraction and cell disruption with BeadBeater (BioSpec Products, Bartlesville, OK).
RNA was treated with Turbo DNase (Life Technologies) to remove traces of genomic DNA, and purified with the RNeasy mini kit (Qiagen, Venlo, Netherlands). RNA samples were depleted of 16S and 23S rRNA with MicrobExpress kit (Life Technologies) (Samples Log 1-3, DM 1-3 and DE 1) or Ribo-Zero (Epicentre) (Samples DE 2,3 and DL 1-3). cDNA for Illumina sequencing was prepared according to “Directional mRNA-Seq Sample Preparation” guide (Part # 15018460 Rev. A) issued by Illumina: RNA was sheared with RNA Fragmentation Reagents (Ambion) for 10 minutes, and ethanol precipitated. Fragmented RNA was dephosphorilated with Antarctic phosphatase (NEB) and 5' phosphate was added with T4 Polynucleotide Kinase (NEB). RNA was purified with RNeasy MinElute kit according to modified protocol from "Directional mRNA-Seq Sample Preparation" guide. Illumina 3' and 5' RNA adapters were ligated according to "TruSeq™ Small RNA Sample Preparation Guide". RNA was reverse transcribed and amplified for 11 cycles. PCR products were fractionated on PAGE and those with the lengths of cDNA inserts 30-80 nt were excized and eluted from the gel. These fragments were sequenced by running 77 cycles on Illumina HiSeq 2000 sequencer.

treatment_protocol: Bacterial cultures were cooled rapidly on ice and centrifuged.

tag: time point in the model of dormancy

value: DL


title: DC_NI_rep6 (RNA-Seq)

data_processing:
Adaptor sequences and low quality score bases were trimmed and resulting reads were aligned to the human genome reference sequence (GRCh37/hg19).
The number of read fragments overlapping with annotated exons of genes was tabulated using HTSeq using the following parameters: -q -m intersection-nonempty -s no.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include expression count values for each sample.

source_name: Monocyte-derived dendritic cells

extract_protocol:
Total RNA was extracted from the same samples using the miRNeasy kit (Qiagen). RNA quantity was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with no evidence for RNA degradation (RNA integrity number > 8) were kept for further experiments.
RNA-Seq libraries for the six samples for which we collected MethylC-Seq were generated via polyA+ selection of mRNA from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina).


title: DL1


title: DC_MTB_rep3 [wtRNA-Seq]


title: DL2


title: DC_NI_rep5 (RNA-Seq)


title: DC_MTB_rep1 [wtRNA-Seq]


title: DC_MTB_rep6 (RNA-Seq)


title: DM2

source_name: Cells grown in the K+-deficient media for 14 days, and incubated under rifampicin (5 μg/ml) for 10 days

value: DM


title: DM3


title: DC_NI_rep1 [wtRNA-Seq]


title: Sample_Input_Index_6_lane4

description:
Targets_lane4.tar
Targets_lane34.tar

source_name: Diffuse large B-cell lymphoma (DLBCL) cell line OCI-Ly7


title: DE3

source_name: Cells grown in the K+-deficient media for 14 days

value: DE


title: DM1


title: DC_MTB_rep5 (RNA-Seq)


title: DC_MTB_rep4 (RNA-Seq)


title: Sample_1A-M1T1_WT

tag: genotype/variation


title: DC_NI_rep3 [wtRNA-Seq]


title: DC_MTB_rep3 (RNA-Seq)


title: DE1


title: Log2

source_name: Cells grown in the K+-deficient media for 4 days

value: Log


title: DC_MTB_rep2 (RNA-Seq)


title: Log1


title: DE2


title: DC_NI_rep2 (RNA-Seq)


title: Log3


title: DC_NI (ATAC-Seq)

data_processing:
ATAC-Seq reads were mapped to the human reference genome (GRCh37/hg19) and reads that had a unique alignment and mapping quality of ≥10 were retained for downstream analyses.
genome build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedgraph files using bedGraphToBigWig (UCSC); Scores represent the number of reads that mapped within a genomic region.

extract_protocol:
DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems).
To prepare nuclei, we spun 100,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.05% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using 25 uL of 2X NEBnext PCR master mix, 0.3 uL of 100X SYBR Green I, 2.5 uL each of Nextera primer index 1 (i7) and 2 (i5), and 10 uL of the transposed DNA, in a final volume of 50 uL. We used the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do so, we amplified the full libraries for four cycles, after which we took an aliquot (5 ul) of the PCR reaction and added 10 μl of the previous PCR cocktail. We ran this reaction for 19 cycles to determine the additional number of cycles needed for the remaining 45 uL reaction. Libraries were amplified for a total of 9 cycles. The libraries were purified using a Qiagen MinElute kit in 20 μL. Quality of the libraries was verified on a polyacrylamide gel and Bioanalyzer. Libraries were then quantifed by qPCR using the KAPA Library Quantification Kit.


title: DC_NI_rep3 (RNA-Seq)


title: DC_NI_rep1 (RNA-Seq)


title: DC_MTB_rep1 (RNA-Seq)


title: DC_MTB (ATAC-Seq)


title: iPGCs_2

city: Los Angeles

first: Juehua

last: Yu

state: CA

address: 615 Charles E. Young South BSRB 457

institute: UCLA

data_processing:
Reads with low quality and reads containing sequencing adapters were first filtered out before mapping raw reads (single-end, 50bp in length) to the Mus Musculus reference genome (GRCm38/mm10) with the gapped aligner Tophat2
Transcript expression levels were quantified using FPKM units (Fragments per Kilobase of exon per Million reads mapped) using Cufflinks
The FPKM values of repeats were calculated according to coding transcripts. We filtered out genes with FPKM<1 in all groups. The multiple testing errors were corrected by the false discovery rate (FDR). In addition to the FDR of <0.05, we considered differentially expressed genes as having >2-fold difference.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: iPGC

growth_protocol: Sorted PGCs were cultured in 7-factor (7F) media which was based on the formulation of (Farini et al., 2005) without the addition of retinoic acid. Therefore, 7F media includes 15% FBS (Hyclone), DMEM high glucose (Gibco), 1X non-essential amino acids (Gibco),  0.1mM 2-Mercaptoethanol (Gibco), 0.25mM Pyruvate (Gibco 100mM), 1X PSG [100 U/mL Penicillin, 100 µg/mL Streptomycin, 292 µg/mL L-Glutamine (Gibco)], 50 ng/mL SCF (Peprotech), 10 ng/mL bFGF (Biological Resources Branch of the Frederick National Laboratory for Cancer Research), 10 ng/mL SDF1 (R&D Systems),  25 ng/mL human BMP4 (R&D Systems),  500 U/mL LIF (Millipore), 5µM Forskolin (Sigma), 1mg/mL N-Acetyl-L-Cysteine (Sigma).  Cells were plated directly on 0.4 µM PET membranes (Falcon) in 24-well plates and cultured at 37°C with 5% CO2 with daily medium changes.  For some downstream experiments, cultured PGCs were detached from the membrane with 0.05% Trypsin for 5 min at 37°C. ESCs and EGC growth in serum + LIF on MEFs and EB differentiation was performed as described (Vincent et al., 2011).  Maintenance of BVSC ESCs in 2i+ LIF on Laminin followed by EpiLC induction and PGCLC generation in aggregates was performed as previously described (Hayashi et al., 2011).

extract_protocol:
Total RNA was extracted from E9.5 endogenous PGCs, iPGCs, PGCLCs and EGCs using Qiagen RNeasy Micro Kit (Qiagen) and eluted in 8 μl of RNase free water.
2 biological replicate samples were used with following start cell numbers: E9.5 PGCs (about 250 cells), iPGCs (1500 cells), PGCLCs (300-500 cells) and EGCs (500 cells). RNA was amplified and converted to cDNA using the Ovation RNA-Seq System V2 (Nugen). cDNA was diluted to 130 μl using TE buffer (Tris pH 8.0 10mM, Cat#15568-025; EDTA 0.1mM, Cat#15575, both from Invitrogen) transferred to Snap-Cap MicroTUBEs with AFA fiber (Covaris, Cat# 520015) and sonicated to DNA fragments within the 200bp range using a Covaris S2 sonicator according to manufacturer’s instructions (Duty cycle 10%, Intensity 5, Cycles per burst 200 and time 180 sec). Subsequently libraries were generated using the Encore Rapid Library System according to manufacturers instructions. Library concentration was estimated using a Kapa library quantification kit (Cat# 4827) according to manufacturer’s instructions on a ViiA 7 Real-time PCR System (Invitrogen). Libraries were run using 50bp single-end reads on the HiSeq 2500 System (Illumina). 8 libraries were multiplexed and run in two lanes. ERCC RNA Spike-In Mix (Cat#4456740, Invitrogen) was used according to manufacturer’s instructions.

tag: cell type

value: ESC derived in vitro primordial germ cells using hanging drop method

value: BVSC (from Dr. Saitou)


title: EGC_7

value: EGCs derived from E9.5 sorted PGCs


title: EGC_4


title: E95PGCs_2

source_name: E9.5 PGC

value: E9.5 endogenous primordial germ cells


title: PGCLCs_1

source_name: PGCLC

value: ESC derived PGCLCs using Hayashi et al. 2013


title: E95PGCs_1


title: wt hyperproliferative rep2

city: Cincinnati

first: Steven

last: Potter

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Children's hospital Medical Center

data_processing:
Tophat version April 2012 was used for basecalling
Genespring 12.6.1 was used for analyzing Bam files
post alignment read metrics were used to remove reads that ligned to more than one place in the genome
Duplicate reads were filtered out
Genome_build: mouse genome  build: mm10
Supplementary_files_format_and_content: GeneSpring generated RPKM values

source_name: wt hyperproliferative_forelimb zeugopod

extract_protocol:
isolation protocol: samples were isolated by laser capture microdissection
Total RNA was extracted from fresh tissue using the Qiagen RNeasy Mini kit
RNA was amplified with NOvation® RNA-Seq System V2 (NuGen), Tagmented with Nextera, and libraries prepared according to Illumina HiSeq 2500 protocols

tag: strain background

value: mixed 129/CD-1

value: wild type

tag: compartments purified by lcm

value: hyperpfoliferative

tag: tissue

value: Forelimb zeugopod


title: DC_NI_rep4 (RNA-Seq)


title: wt proliferative rep3

source_name: wt proliferative_forelimb zeugopod

value: proliferative


title: PGCLCs_2

tag: passage

tag: strain


title: wt proliferative rep2


title: wt hyperproliferative rep3


title: wt hyperproliferative rep1


title: wt resting rep1

source_name: wt resting_forelimb zeugopod

value: resting


title: wt resting rep2


title: Hoxa9,10,11/Hoxd9,10,11 mutant rep3


title: Hoxa9,10,11/Hoxd9,10,11 mutant rep1


title: Hoxa9,10,11/Hoxd9,10,11 mutant rep2


title: Nes-GFP;Nes-Cre;PDGFRα+/[S]D842V 3

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Data quality was monitored using FastQC. Adapters were removed using Cutadapt v1.1. Sequences were mapped to the mouse mm9 genome assembly using TopHat v2.0.4.
Mapped reads were summarized using htseq-count v0.5.3
Differentially expressed genes were identified using Deseq2 in R/Bioconductor programming environment
Genome_build: mm9
Supplementary_files_format_and_content: htseq-count gene counts

source_name: White Adipose Tissue

growth_protocol: Cell suspensions from juvenile cutaneous WAT were prepared from P3 pup skin as described (Lichti et al., 2008). Briefly, the whole skin was floated on 0.25% cold trypsin overnight with the epidermis up. The next day the epidermis was removed and discarded, and the remaining tissue was digested with 0.35% collagenase type I (GIBCO) in DMEM for 60 minutes at 37¼C. Hair follicles were removed by low speed centrifugation. Subsequently, Nestin-GFP+ single cells were sorted from cell suspensions with a MoFlo XDP (Beckman Coulter) cell sorter and the purity of sorted cells was verified by re-running the sorted population.

extract_protocol:
Using the dermis and attached subcutaneous WAT from three 3-day old Nestin-GFP;Nestin-Cre;PDGFRα+/D842V mice and three Nestin-GFP mice, we prepared freshly sorted Nestin-GFP+ cells for isolation of total RNA.
We constructed cDNA libraries from each of the six RNA samples and then pooled the individually indexed libraries for sequencing.

value: White Adipose Tissue

tag: age


title: Nes-GFP;Nes-Cre;PDGFRα+/[S]D842V 1


title: iPGCs_1


title: Nes-GFP+ cells 2

value: Nes-GFP+ cells


title: Nes-GFP+ cells 1


title: Nes-GFP+ cells 3


title: Small RNA Seq Miwi2 KO 10dpp

description: RNA-seq (18-35nt size fractionation)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The 3' adapter sequences were searched in the reads (3' adapter sequence “TGGAATTCTCGGGTGCCAAG”)
The trimmed sequencing reads of each sRNA-seq library were analyzed with ncPRO-seq (v1.5.1, Chen CJ., et al 2012).
Genome_build: mm9
Supplementary_files_format_and_content: Text files with the trimmed sequencing reads and the number of times sequenced.

source_name: Testis

extract_protocol:
Trizol
Illumina small RNA TruSeq

value: Miwi2 knockout

value: post-natal day 10

value: testis


title: Small RNA Seq Miwi2 WT 10dpp

description: RNA-seq (18-35nt size fractionation)

value: Miwi2 wildtype


title: RNA Seq Dnmt3L KO 10dpp

data_processing:
Illumina Casava1.8.2 software used for basecalling.
RNA-seq libraries were first depleted of reads coming from rRNA by subtracting those reads that map to rRNA sequences (GenBank identifiers: 18S NR_003278.3, 28S NR_003279.1, 5S D14832.1, 5.8S K01367.1) with Bowtie
The rRNA depleted libraries were then mapped on the Mouse reference genome (mm9) using the Bowtie software allowing zero mismatch and 10 000 best alignments per read.
Reads were annotated using the RepeatMasker database and were weighted by the number of mapping sites.
Genome_build: mm9
Supplementary_files_format_and_content: Text files with the quantification of repeated elements.

extract_protocol:
TRIZOL
Illumina TruSeq Stranded mRNA LT

value: Dnmt3L knockout


title: RNA Seq Dnmt3L WT 20dpp

value: Dnmt3L wildtype

value: post-natal day 20


title: Nes-GFP;Nes-Cre;PDGFRα+/[S]D842V 2


title: RNA Seq Dnmt3L HET 10dpp

value: Dnmt3L heterozygous


title: RNA Seq Dnmt3L KO 16.5dpc

value: pre-natal day 16.5


title: RNA Seq Dnmt3L HET 16.5dpc


title: wt proliferative rep1

value: mixed 129/CD-1


title: Tomato_HG6-61_42DAF

city: Wuhan City

first: JIE

last: YE

state: Hubei Province

address: No. 1, Shizishan Road

institute: Huazhong Agricultural University

description: Sample name: H6

data_processing:
Illumina  GIIAX used for RNA-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S. lycopersicum whole genome by Tophat
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: SL2.40
Supplementary_files_format_and_content: Reads.txt includes the number of reads in each gene of each Sample.
Supplementary_files_format_and_content: RPKM.txt includes the RPKM values of each gene in each Sample.

organism: Solanum lycopersicum

source_name: fruit

growth_protocol: Plant growth and cultivation was carried out according to commercial practices with a day/night temperature of 28/20°C. Plants were pruned so that fruits were on one vine per plant.

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
The AC and HG6-61 fruits harvested at 7, 14, 21, 28, 35, 42 and 49 DAF were frozen in liquid nitrogen and kept at -80°C until use. Total RNA was extracted using a ZP411-2 GREENspin RNA quick extraction kit (ZOMANBIO, Beijing), excluding polyphenols and polysaccharides from the sample according to the manufacturer’s instructions

treatment_protocol: To collect fruit samples from various developmental stages, flowers were tagged when fully opened (anthesis) and fruits were harvested from 5 individual plants of each genotype at 7, 14, 21, 28, 35 (mature green stage), 42 (breaker stage) and 49 (ripening) days after flowering (DAF)

tag: days after flowering

value: breaker stage

value: fruit

tag: cultivar


title: Tomato_HG6-61_49DAF

description: Sample name: H7

tag: developmental stage

value: ripening


title: M3

city: Cleveland

first: Andrea

middle: N

last: Ladd

address: 9500 Euclid Ave NC-10

department: Cellular and Molecular Medicine

institute: Cleveland Clinic

data_processing:
All reads were treated as single-end reads in this analysis, to maximize coverage
Reads were trimmed to 50nt by removing one base at the 3' end
Reads for each specimen were mapped using tophat v.2.0.9 (bowtie2)
Transcriptome files were generated for each sample using cufflinks v.2.1.1 and then merged
Differencecs between treatment groups were generated using cuffdiff with a cutoff of q<0.05
Genome_build: galGal4 (ensembl release 73)
Supplementary_files_format_and_content: cuffdiff expressed genes output file containing all transcripts that are differentially expressed with q<0.05. The file is supplemented with gene names or ensembl IDs where available

organism: Gallus gallus

source_name: chicken embryonic primary cardiomyocytes

growth_protocol: Plated on fibronectin, at 250,000 cells/35mm plate

extract_protocol:
Total RNA was extracted with Trizol according to manufacturer's instructions
Samples were multiplexed

treatment_protocol: Transfected (Lipofectamine 2000) at 24 hours post-plating; collected (by scraping) at 72 hours post-transfection

value: embryonic day 8

value: heart

value: Cardiomyocyte

tag: treatment

value: Mock-transfected


title: AL2

value: siRNA-transfected


title: AL3


title: M1


title: AL1


title: Tomato_HG6-61_28DAF

description: Sample name: H4

value: mature green stage


title: Tomato_HG6-61_35DAF

description: Sample name: H5


title: Tomato_HG6-61_21DAF

description: Sample name: H3


title: Tomato_HG6-61_14DAF

description: Sample name: H2


title: Tomato_HG6-61_7DAF

description: Sample name: H1


title: Tomato_AC_49DAF

description: Sample name: A7

value: Ailsa Craig


title: Tomato_AC_42DAF

description: Sample name: A6


title: Tomato_AC_35DAF

description: Sample name: A5


title: Tomato_AC_14DAF

description: Sample name: A2


title: Tomato_AC_21DAF

description: Sample name: A3


title: RNA Seq Dnmt3L KO 20dpp

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

value: testis


title: H3K4me3_ChIPSeq_chaetocin

status: Public on May 31 2015

city: Shimotsuke

first: Ruri

last: KANEDA

state: Tochigi

address: 3311-1 Yakushiji

country: Japan

institute: Jichi Medical University

description: high salt_chaetocin treatment

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the rn4/Baylor 3.4 genome assembly using Bowtie (version 0.12.7).
Enriched regions were detected using MACS (version 1.4.2) with default parameters except -gsize=1980000000, and -mfold=5,30
Genome_build: rn4
Supplementary_files_format_and_content: wig

organism: Rattus norvegicus

source_name: heart tissue

growth_protocol: Five-week-old male Dahl salt-sensitive (DS) rats were purchased from Sankyo Labo Service Corporation, INC. (Tokyo, Japan). The rats were divided into three groups: control [normal-salt diet containing 0.3% NaCl, NS (-)], heart failure (HF) [high-salt diet containing 8% NaCl, HS (-)] and treatment [high-salt diet with 0.25 mg/kg of chaetocin (Sigma-Aldrich Co. LLC.) treatment, HS (+)] group.

extract_protocol:
Lysates were extracted from one gram of crushed left ventricular tissue per group,  cross-linked with 0.5% formaldehyde, sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions (TruSeq ChIP Sample Preparation Guide Rev. A) accompanying TruSeq ChIP Sample Prep Kit. Briefly, DNA were blunted, phosphorylated, protruded with 3- 'A' base, and ligated with adapters. After adapter ligation DNA was isolated from an agarose gel and amplified with PCR. The DNA was captured for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: Chaetocin was dissolved in dimethyl sulfoxide (DMSO). Rats in the treatment group were administered chaetocin intraperitoneally twice a week from 6 weeks of age until 13 weeks old.

value: Dahl salt sensitive

tag: sample group

value: treatment [high-salt diet with 0.25 mg/kg of chaetocin treatment, HS (+)]

tag: chip-antibody

tag: chip-antibody vendor

value: abcam

tag: chip-antibody cat. #


title: Tomato_AC_7DAF

description: Sample name: A1


title: M2


title: H3K9me3_ChIPSeq_chaetocin

description: high salt_chaetocin treatment

value: Millipore


title: H3K9me3_ChIPSeq_HF

description: high salt_no treatment

value: heart failure (HF) [high-salt diet; HS (-)]


title: H3K4me3_ChIPSeq_cont

description: normal salt_no treatment

value: control [normal-salt diet, NS (-)]


title: H3K9me3_ChIPSeq_cont

description: normal salt_no treatment


title: input DNA

description: normal salt_no treatment


title: wt resting rep3

value: mixed 129/CD-1

value: wild type

value: resting

value: Forelimb zeugopod


title: H3K4me3_ChIPSeq_HF

description: high salt_no treatment

value: heart


title: Osaba1-1-clean.txt

first: Qiu

last: Jin-Long

state: Beijing

address: 1 Beichen West Road,Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
The adaptor sequences in Illumina sequencing reads were removed by using vectorstrip in the EMBOSS package. The small RNA reads with high sequencing accuracy and with length of 18 -30 nt were were retained for further analysis.
Small RNAs were mapped to rice genome (http: //rapdb.dna.affrc.go.jp/download/irgsp1.html), Rfam10.1 (http://rfam.sanger.ac.uk/), Genbank (http://www.ncbi.nlm.nih.gov/genbank/) , miRBase19 (http://www.mirbase.org/) and exons and introns of rice mRNA.
Supplementary_files_format_and_content: length | number | sequence

organism: Oryza sativa Japonica Group

source_name: Osaba1-1 rice leaves

growth_protocol: Seeds of rice (Oryza sativa L. japonica. cv. Nipponbare and Osaba1-1 mutant) were disinfected by 5% NaClO for 30min followed by washing with distilled water for 6 times and then soaked in distilled water at 37℃ for 1 d in darkness. The soaked seeds were put in distilled 96 well microplate without bottoms and then subject the microplate to 1/2 Kimura nutrient solution, and then removed the solution every 3 days for 10 days. The 10-day seedlings were transplated into sterilized soil (loess: nutrient =1:1). The cultivated seedlings were grown at 28℃ and 90% relative humidity in a 14-h-light/10-h-dark condition.

extract_protocol:
The fifth and sixth stage leaves of 40 days old rice were chose and tissue that 2cm within the cut site which was 4 cm from the leaf opex were collected and frozen in liquid nitrogen and used for total RNA isolation. 15 seedlings of each line at least were collected as a mix. Total RNA was isolated using TRIZOL® reagent (Invitrogen, USA) in accordance with the manufacture’s protocol for miRNA high-throughput sequencing.
Small RNA sized at 18-30 nt was gel-purified on a 15% polyacrylamide denaturing gel from the total RNA for each sample. The isolated small RNAs were sequentially ligated to RNA/DNA chimeric oligonucleotide adapters, reversely transcribed, and amplified with 15 cycles of PCR to produce sequencing libraries. The Illumina sequencing was performed by Beijing Genomics Institute.

tag: genotye

value: Japonica

tag: variety

value: Nipponbare

value: leaves


title: WT-clean.txt

source_name: wild type rice leaves


title: C24xCol_ZT15_mRNAseq

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
Alignment: mRNA-seq reads each were mapped to the TAIR9 genome and cDNA sequence using BFAST software (http://bfast.sourceforge.net)
RPKM values were calculated using a previously published method (Shi, X., Ng, D.W.-K., Zhang, C., Comai, L., Ye, W. and Chen, J.Z. (2012) Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nat. Commun. 3, 950.)
Genome_build: TAIR9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. FIELD #1: AGI number; #2: RPKM

source_name: Rosette leaves

growth_protocol: All plants were grown on soil under a 16/8-hour light/dark cycle with temperatures of 22C (light) and 20C (dark).

extract_protocol:
Total RNA was isolated from mature leaves (3 week old A. thaliana) prior to bolting using plant RNA purification reagent (Invitrogen, Carlsbad, CA). The integrity of extracted RNA was verified by resolving 1ug RNA in an 1% formaldehyde denaturing agarose gel. An aliquot of 10ug total RNA was used to prepare mRNA-seq libraries using Illumina mRNA-seq sample preparation kit (Illumina Inc., San Diego, CA). Libraries with a range of 200-25 bp were excised and amplified for subsequent cluster generation and massively parallel sequencing using the Illumina Genome Analyzer with read lengths of 84 bp.
mRNA libraries were prepared for sequencing using standard Illumina kit protocols

tag: genotype

value: F1 hybrid between Col and C24 with C24 as the maternal parent

tag: time point (zt time)

tag: Stage

value: Before bolting

value: 3 weeks old


title: ColxC24_ZT6_mRNAseq

value: F1 hybrid between Col and C24 with Col as the maternal parent


title: C24_ZT6_mRNAseq

value: C24 ecotype


title: Col_ZT6_mRNAseq

value: Columbia ecotype


title: ColxC24_ZT15_mRNAseq


title: ColxC24_ZT0_mRNAseq


title: Tomato_AC_28DAF

description: Sample name: A4

value: mature green stage

tag: tissue

value: fruit

value: Ailsa Craig


title: C24xCol_ZT0_mRNAseq


title: Col_ZT15_mRNAseq


title: Gene expression modulated by TUDCA1

city: Xiamen

first: Dawang

last: Zhou

state: Fujian

address: Xiang'An south Rd

department: State Key Laboratory of Cellular Stress Biology

institute: School of Life Sciences,Xiamen Univeristy

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the genome using the split read aligner TopHat (v2.0.7) and Bowtie2 using default parameters.
HTSeq for estimating their abundances
Genome_build: Mus_musculus.NCBIM38.70
Supplementary_files_format_and_content: The rpkm.txt files include abundance measurements (RPKM values) for each sample

source_name: Gene expression modulated by TUDCA1

growth_protocol: primary hepatocyte culture:see reference :Cell Rep. 2013 May 30;3(5):1663-77. Mouse primary hepatocytes were isolated by the two-step liver perfusion method of Seglen, 1976 with some modifications. Briefly, the mouse was anesthetized with intraperitoneal injection of xylazine (0.1 mg/10 g body weight) and ketamine (1 mg/10 g body weight). The abdomen was then cut open, and the portal vein was catheterized. The liver was first perfused in situ with D-Hank’s buffered solution (containing 0.5 mM EGTA, pre-warmed to 37°C) for 8–10 min with the inferior vena cava cut for drainage and then perfused for 5 min with 0.12 PZ-U/ml collagenase perfusate (containing 2 mM Ca2+). The livers were extirpated and transferred into plates filled with DMEM at 4°C. The hepatic capsules were torn, and the livers were gently shaken to help the cells detach. The cell suspension was collected and filtered through 70 μm cell strainers (BD Falcon, Bedford, USA). Cell viability, as determined by trypan blue exclusion, was generally >90%. The cells were plated in 24-well gelatin-coated plates (8 × 104) in Williams’ Medium E (Invitrogen) containing 10% fetal bovine serum, 100 U/ml penicillin/streptomycin and 1 × 10-7 M insulin and cultured at 37°C with 5% CO2.

extract_protocol:
Trizol purification :see reference :Cell Rep. 2013 May 30;3(5):1663-77.
mRNA extraction was performed using Dynabeads oligo(dT) (Dynal; Invitrogen Corp.). Double-stranded cDNAs were synthesized using reverse transcriptase (Superscript II; Invitrogen Corp.) and random hexamer primers. The cDNAs were then fragmented by nebulization, and the standard Illumina protocol was followed thereafter to create the mRNA-seq libraries.

treatment_protocol: TUDCA treatment:100mM for 24 hours

tag: cell type

value: Primary mouse hepatocyte

tag: passage


title: C24xCol_ZT6_mRNAseq

tag: age


title: Col_ZT0_mRNAseq


title: Input DNA F-H9S3

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

institute: Stem Cell and Brain Research Institute

data_processing:
ChIP-Seq reads were aligned using the Bowtie software to GRCh build 37 (hg19) of the human genome.
The SICER program was used to detect peaks of ChIP enrichment. It was run with the default settings using a a fragment size of 150 and a gap size of 600.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using SICER via Galaxy with the variableStep data and the value data

source_name: F-H9S3 hESCs

growth_protocol: hESCs were routinely cultured at 37°C in 5% O2 in a medium containing Knockout DMEM, 20% KO-SR, 1 mM glutamine, 0.1 mM β-mercaptoethanol (Sigma), and 1% nonessential amino acid (NEAA, Gibco), on growth-inactivated MEF. For F-H9S3 cells, the complete ESC medium was supplemented with 4-8 ng/mL FGF2.  For TL2i-H9S3 cells, the culture medium was supplemented with 10,000 U/mL hLIF, 250 nM 4’OHT, 3 μM CHIR99021, and 1 μM PD325901 (Stemgent).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and formaldehyde was inactivated by the addition of 125 mM glycine. Chromatin from each cell line was sonicated to a length of around 250-500bp and immunoprecipitated using custom made antibodies provided bu Huck-Hui Ng. Samples were sequenced using the SOLEXA platform.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: hESCs in primed state

tag: antibody


title: H3K27me3_ChIPSeq F-H9S3

value: H3K27me3 (Diagenode,pAb-195-050)


title: H3K27me3_ChIPSeq TL2i-H9S3

source_name: TL2i-H9S3 hESCs

value: hESCs in naive state


title: H3K4me3_ChIPSeq TL2i-H9S3

value: H3K4me3 (Diagenode, pAb-003-050 )


title: Input DNA TL2i-H9S3


title: C24_ZT15_mRNAseq


title: C24_ZT0_mRNAseq


title: H3K4me3_ChIPSeq F-H9S3


title: Gene expression modulated by TUDCA2

source_name: Gene expression modulated by TUDCA2

tag: strain


title: Gene expression modulated by DMSO

source_name: Gene expression modulated by DMSO

treatment_protocol: DMSO


title: ChIP of MNase dinucleosome selected cerebellum material INPUT

status: Public on May 30 2015

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

description:
ChIP-seq, INPUT
processed_data: TSSCOUNT_CHIP_MNASE_DIN_CEREB.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt

data_processing:
Illumina Genome Analyzer
Illimina Pipeline 1.6
Alignment with bwa  0.5.7 against the MM9 genome
Feature analysis with Seqmonk version 0.20.0
Description of the processed data files format and contents are included in the 'readme.txt' file linked to Series records.
Genome_build: MM9
Supplementary_files_format_and_content: Tab delimited txt files containing genomic feature counts of various sequence reads and enrichment, fold change values [available on Series records]

growth_protocol: MeCP2 null and wild type brain tissue was used

extract_protocol:
ChIP and Methylminer libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.
RNA expression libraries were prepared according to Illumina's instructions accompanying the mRNA Sample Kit.
RNA immunoprecipitated libraries were prepared according to NEBnext intructions accompanying the mRNA library prep mix set kit.

tag: genotype/variation

value: wild type

tag: gender

value: male

value: Cerebellum

tag: chip/rip antibody

tag: chip/rip antibody vendor

value: Sigma

tag: chip/rip antibody cat. #


title: Methyl miner of cerebellum DNA - HIGH methylation capture

description:
Methylminer-seq (MBD-seq), HIGH METHYLATION DENSITY
processed_data: TSSCOUNT_METHYL_CEREB.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt


title: ChIP of MNase mononucleosome selected whole brain material INPUT

description:
ChIP-seq, INPUT
processed_data: TSSCOUNT_CHIP_MNASE_MONON_WB.txt

value: Wholebrain


title: ChIP of MNase mononucleosome selected cerebellum material MECP2 IP

description:
ChIP-seq, BOUND
processed_data: TSSCOUNT_CHIP_MNASE_MONON_CEREB.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt


title: Methyl miner of cerebellum DNA - LOW methylation capture

description:
Methylminer-seq (MBD-seq), LOW METHYLATION DENSITY
processed_data: TSSCOUNT_METHYL_CEREB.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt


title: RNA expression in MECP2 wild type cerebellum 2 of 2

description:
RNA-seq, EXPRESSION
processed_data: EXPRESSION_CEREB_FOLD_CHANGE.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt
processed_data: EXPRESSION_LEVEL_WT_CEREB_RPKM.txt


title: RNA expression in MECP2 wild type cerebellum 1 of 2


title: ChIP of MNase mononucleosome selected whole brain material MECP2 IP

description:
ChIP-seq, BOUND
processed_data: TSSCOUNT_CHIP_MNASE_MONON_WB.txt


title: MECP2 RNA immunoprecipitation in female cerebellum 3 of 3

description:
RNA-IP-seq (RIP-seq), BOUND
processed_data: RIP_COUNT_GENE.txt
processed_data: RIP_COUNT_LNCRNA.txt
processed_data: RIP_COUNT_REL_EXPRESSION.txt

value: female


title: ChIP of MNase dinucleosome selected cerebellum material MECP2 IP

description:
ChIP-seq, BOUND
processed_data: TSSCOUNT_CHIP_MNASE_DIN_CEREB.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt


title: MECP2 RNA immunoprecipitation in male cerebellum 2 of 3


title: MECP2 RNA immunoprecipitation in female cerebellum 1 of 3


title: RNA expression in MECP2 null cerebellum

description:
RNA-seq, EXPRESSION
processed_data: EXPRESSION_CEREB_FOLD_CHANGE.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt

value: MeCP2 null


title: ChIP of sonicated whole brain MECP2 IP

description:
ChIP-seq, BOUND
processed_data: TSSCOUNT_CHIP_SONICATED_WB.txt


title: ChIP of sonicated whole brain INPUT

description:
ChIP-seq, INPUT
processed_data: TSSCOUNT_CHIP_SONICATED_WB.txt


title: SA11 + glucose C (single)

status: Public on May 29 2015

city: Seattle

first: E.

middle: Virginia

last: Armbrust

address: Ben Hall IRB, 616 NE Northlake Pl, Room 306

department: Oceanography

institute: University of Washington

data_processing:
SOLiD reads were aligned to the P. multiseries gene catalog transcripts provided by JGI (Psemu1_GeneCatalog_transcripts_20111011.nt.fasta) using in-house pipelines and SAM tools.
Reads mapping to transcripts were assigned and tallied using seastar.
Seastar counts were then analyzed with edgeR for differential expression and significance testing using Benjamini Hochberg multiple testing corrections.
Count tables were then merged with KEGG annotations provided by JGI.
Genome_build: Sulfitobacter sp. SA11 (https://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2519103045)
Genome_build: Pseudo-nitzschia multiseries (http://genome.jgi.doe.gov/Psemu1/Psemu1.home.html)
Supplementary_files_format_and_content: SA11-expression.tab - tab delimited text files generated from edgeR that contain log fold change, log abundance, p-values, and fdr-corrected p-values for 3 biological replicates per condition; protein identification is also given
Supplementary_files_format_and_content: PC9-expression.tab - tab delimited text files generated from edgeR that contain log fold change, log abundance, p-values, and fdr-corrected p-values for 3 biological replicates per condition; protein identification is also given

organism: Sulfitobacter sp. SA11

source_name: diatom-associated bacterial culture

growth_protocol: P. multiseries was maintained at its optimum growth temperature (13C) without bubbling in semi-continuous batch cultures under a light/dark cycle (16/8 hr, 80 μmol photons m−2 s−1) in Aquil. Axenic culture was generated by applying a suite of antibiotics (per mL: 50 μg streptomycin, 67 μg gentamycin, 20 μg ciprofloxacin, 2.2 μg chloramphenicol, and 100 μg ampicillin). For cocultures, the diatom was inoculated from an early to mid-exponential phase growing culture was used to inoculate fresh media to achieve an initial diatom cell density of ~4000 cells/mL. Bacteria were plated freshly before each experiment on marine agar and were grown from single colonies in marine broth overnight (30oC, 150 rpm). Cells were centrifuged (5000 rpm for 5 min) and washed 2x with sterile Aquil and diluted to a stock cell density of ~ 1×10^8 cells/mL with sterile Aquil. This stock was used to inoculate the freshly prepared diatom culture to achieve a final bacterial cell density of ~1 ×10^5 cells/mL. Bacteria-only cultures were supplemented with 1 μM glucose.

extract_protocol: For the diatom, total RNA was isolated from filters using the ToTALLY RNA™ Total RNA Isolation Kit (Ambion; Life Technologies), and mRNA was purified from the total RNA using the MicroPoly(A)Purist™ Kit (Ambion; Life Technologies). For the bacteria, RNA was isolated from filters using the RNeasy Mini Kit along with RNAprotect Bacteria Reagent (Qiagen, Maryland, USA) according to the manufacturer’s instructions using 1 mg/mL lysozyme solution (Fisher) to lyse the cells. Total RNA was treated for DNA contamination using two successive treatments with Turbo-DNase (Ambion; Life Technologies) and cleaned/concentrated with RNeasy MinElute Cleanup Kit (Qiagen). Ribosomal RNAs (rRNAs) were selectively removed using a subtractive hybridization protocol with biotinylated rRNA probes specific to the organism(s) in each sample (e.g. 16S and 23S for SA11 and/or 16S, 18S and 28S for P. multiseries). Probe-bound RNAs were removed with strepdavidin-coated magnetic beads (New England Biolabs). rRNA-depleted samples were then linearly amplified using the MessageAmp II-Bacteria kit (Ambion; Life Technologies).

treatment_protocol: 2 L of the experimental cultures were filtered onto 3 μm polycarbonate filters (Millipore, Massachusetts, USA) followed by filtration of flow-through onto 0.2 μm polycarbonate filters. Filtered cells were immediately flash frozen in liquid nitrogen and stored at 80°C until later RNA extraction.

tag: culturing condition

value: Axenic control

tag: culture strain


title: SA11 + glucose C (paired-end)


title: SA11 + glucose B (paired-end)


title: SA11 + glucose B (single)


title: SA11 + glucose A (paired-end)


title: MECP2 RNA immunoprecipitation in male cerebellum 3 of 3


title: MECP2 RNA immunoprecipitation in male cerebellum 1 of 3


title: MukB + CA1

city: Pasadena

first: Long

last: Cai

state: California

address: 1200 E.california blvd

department: Chemistry and chemical engineering

institute: Caltech

data_processing:
Reads were aligned and counted using open-source cloud-based platform for biomedical research, Galaxy (https://usegalaxy.org/).
The processed data has two columns. The first column is the genomic coordinates for E.coli K12. The second column is the total ChIPseq reads within a 20 nt bin starting for the coordinate on the first column.
The RefSeq accession number for the genome build is NC_000913

organism: Escherichia coli

source_name: cells

growth_protocol: Cells were grown in LB media at 37C at 200 rpm.

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type, MukB-FLAG

tag: chip antibody

value: ANTI-FLAG, Sigma, F7425


title: TopA

value: wild type, TopA-FLAG


title: ChIP of MNase mononucleosome selected cerebellum material INPUT

description:
ChIP-seq, INPUT
processed_data: TSSCOUNT_CHIP_MNASE_MONON_CEREB.txt
processed_data: ACT_REP_HI_LO_CGAT4_INDIVIDUAL_REGIONS.txt


title: MukB + RIF


title: MECP2 RNA immunoprecipitation in female cerebellum 2 of 3


title: SA11 + glucose A (single)


title: RNAP

value: ANTI-RNAP, Abcam, ab12087


title: ParC

value: wild type, ParC-FLAG


title: PyV 36 hours rep 3

city: Boston

first: Seth

middle: B

last: Garren

state: MA

address: 185 Cambridge St

department: Systems Biology

institute: Massachusetts General Hospital

description:
Time course experiment
Mocks_vs_PyV_sig_diff_pooled.txt
Mocks_vs_PyV_sig_diff_per_condition.txt
gene_fpkm_all_samples_cufflinks_mouse (version 1).xls

data_processing:
CASAVA 1.8.2
Alignments were made using Tophat 2.0.9 and Samtools 1.19
Mouse reference genome was taken from Illumina's IGENOMES collection
Relative expression of host genes between Mock and PyV infected samples was determined using Cuffdiff 2.1.1 using dispersion method pooled and dispersion method per condition
Cluster 3.0 was used to produce k means clustering of time course gene expression
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: NIH 3T6 Cells

growth_protocol: NIH 3T6 mouse fibroblast cells were cultured on 10 cm plates at a density of 600Kcells/plate in Gibco Dulbecco’s Modified Eagle Medium (11995-065) supplemented with 100 units of penicillin/streptomycin, 2mM L-Glutamine, and 5% calf serum.  Cells were serum starved in 2% calf serum 1 day before infection to synchronize cell cycles.

extract_protocol:
Total RNA was harvested at 12, 18, 24, and 36 hours after infection by removing media, washing with PBS, and adding 4M guanidinium isothiocyanate.  RNA was isolated by cesium centrifugation through 2 ml of 5.7M cesium chloride at 39000 rpm at 20°C for 18 hours and DNAse treated with DNAse 1 from the Ambion DNAse I Kit.  1 μg of RNA was used from each sample for library preparation with the Trueseq Stranded Total RNA kit from Illumina
1 μg of RNA was used from each sample for library preparation with the Trueseq Stranded Total RNA kit from Illumina.

treatment_protocol: Polyomavirus strain Py59RA at 180 million plaque forming units per ml was diluted to 15 million PFU/ml to infect cells at an MOI of 50 using 2 ml of virus per plate.  Mock infection was done using 2% media without virus.

tag: cell line

value: NIH 3T6 mouse fibroblast cells

tag: infection

value: polyomavirus strain Py59RA

tag: time

value: 36 hours


title: PyV 36 hours rep 2


title: PyV 18 hours rep 2

value: 18 hours


title: PyV 18 hours rep 1


title: PyV 12 hours rep 3

value: 12 hours


title: PyV 12 hours rep 2


title: MukB


title: Mock 36 hours rep 3

value: uninfected


title: PyV 36 hours rep 1


title: PyV 18 hours rep 3


title: PyV 12 hours rep 1


title: YYM_input

city: ShenZhen

first: Zhixiang

last: Yan

address: Beishan Industrial Zone, Yantian District

institute: BGI

data_processing:
the sequencing data were mapped to hg18 by SOAP
The mappable reads were treated as input of MACS (version 1.4) for peak calling. The MACS parameters for peak calling of each individual were: -g hs --nolambda --nomodel --shiftsize 150
Genome_build: hg18
Supplementary_files_format_and_content: .bed file contains MeDIP peaks and .wig file contains read coverage information of each interval

source_name: blood

extract_protocol:
DNA fragment were sonicated, and isolated by anti-5mC antibody
Genomic DNA was fragmented to 100–500 bp by sonication. Adaptors were ligated to both ends of the fragments. End repair, base addition, and adaptor ligation steps were performed by using Illumina’s Paired-End DNA Sample Prep kit following the manufacturer’s instructions. Adaptor-ligated DNA was immunoprecipitated with anti-5mC antibody, and the MeDIP products were validated by qPCR using SYBR green mastermix. To obtain genomic DNA libraries that were suitable for the Illumina Genome Analyser II, the DNA was amplified, purified, and size selected (200–300 bp, including the adaptor sequence). The sequences of each individual were generated as 44-bp paired-end reads.

tag: tissue

value: blood


title: Mock 36 hours rep 2


title: YYJ_input


title: YYM_MeDIP


title: Mock 36 hours rep 1


title: YYJ_MeDIP


title: Mock 24 hours rep 3

value: 24 hours


title: Mock 24 hours rep 2


title: Mock 24 hours rep 1


title: Mock 18 hours rep 3


title: Mock 18 hours rep 1


title: Mock 12 hours rep 3


title: Mock 18 hours rep 2


title: PyV 24 hours rep 3


title: Mock 12 hours rep 2


title: PyV 24 hours rep 2


title: PyV 24 hours rep 1


title: Mock 12 hours rep 1


title: Control Replicate 2

city: Philadelphia

first: Ellen

last: Elliott

state: PA

address: 12-164 Smilow TRC, 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation .
Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file of raw read counts and tab-delimited file of FPKM normalized read counts

source_name: Perinatal proximal jejunum

extract_protocol:
RNA was isolated from laser-captured cells using PicoPure RNA isolation kit (Applied Biosystems).Total RNA isolated by LCM (2.3 ng to 33.3 ng per sample) was amplified using the Ovation RNA-Seq System V2 (NuGEN).
300 ng of each sonicated cDNA sample was used for RNA-Seq library preparation. cDNA sequencing libraries were completed using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), Illumina multiplexing adaptors, and the NEBNext ChIP-Seq DNA Sample Prep Reagent Set 1 Kit (New England Biolabs). Single-read sequencing was performed on the Illumina HiSeq 2000 (100 bp reads).

treatment_protocol: Neonatal intestines were fixed one hour in cold methacarn solution. Samples were processed and embedded in parrafin. Intervillus cells were collected by laser capture microdissection on an Arcturus PixCell IIe. Mutant intervillus cells were identified by Ki67 immunofluorescence staining on adjacent sections; Ki67-negative intervillus areas were collected from Dnmt1-mutant intestines. Ki67-positive intervillus regions were collected from littermate controls.

tag: genotype

value: Dnmt1 L/+

value: Postnatal Day Zero

tag: cell type

value: Proximal jejunum intervillus cells


title: Mutant Replicate 4

value: Dnmt1 L/L; VillinCre

tag: age


title: Control Replicate 1


title: Mutant Replicate 6


title: PC9 + SA11 C

organism:
Pseudo-nitzschia multiseries
Sulfitobacter sp. SA11

source_name: diatom culture + diatom-associated bacterium

value: + bacterium

value: PC9 + SA11


title: SA11 + PC9 B (single)

source_name: diatom-associated bacterial culture + diatom culture

value: SA11 + PC9


title: Control Replicate 3


title: Infected 2

city: Amsterdam

first: Jeroen

last: Bakker

address: Plesmanlaan 121

department: Cell Biology II

country: Netherlands

institute: NKI

data_processing:
Sequence reads were mapped to mm9 using tophat version 2.0.6 with parameters --bowtie1, --library-type fr-unstranded, --no-coverage-search, --mate-inner-dist, --mate-std-dev, -M, -G, --transcriptome-index, Ensembl GTF version 66
Readcounts (FPKM values) were calculated using cufflinks version 2.1.1 with parameters -G, -b -u --compatible-hits-norm, -N
Ratios were calculated by dividing the FPKM values of the infected samples against the MEF_control sample
Genome_build: mm9
Supplementary_files_format_and_content: The file fpkm_values.txt contains the fpkm values in tab separated format. The file ratios.txt contains the ratios for the infected samples against the MEF_control sample

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEF cells were cultured in anchorage independent (Soft Agar) conditions to mimic transformation.

extract_protocol:
Transformed colonies were isolated from Soft Agar and cultured in monolayer for a short period to increase sample size
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Salmonella infected

tag: culturing conditions

value: Ciprofloxacin added

value: C57BL/6 derived, Arf-deficient, overexpressing c-MYC


title: SA11 + PC9 C (paired-end)

value: + diatom


title: Infected 1


title: MEF Control

value: Non Salmonella infected


title: SA11 + PC9 C (single)


title: PC9 + SA11 A


title: SA11 + PC9 A (single)


title: SA11 + PC9 B (paired-end)