title: BFU-E plus Dexamethasone and GW764, rep1

city: Cambridge

first: Xiaofei

last: Gao

institute: Whitehead Institute for Biomedical Research

description:
Sample name: mBFU_C15Dx_1
PolyA RNA

data_processing:
Sequences were trimmed using fastq_quality_trimmer tool from the FASTX-Toolkit: "fastq_quality_trimmer -v -t 20 -l 25".
Sequences were mapped to the mouse genome assembly mm9 with TopHat 1.4.1 using the following commands: "-p 8 --no-coverage-search --library-type=fr-unstranded --solexa1.3-quals --segment-length 20".
We counted the number of reads mapping to each gene with htseq-count using the parameters "--mode=intersection-strict --stranded=no " and a GTF file version NCBIM37.67 downloaded from ENSEMBL from which we had removed the genes mapped to contigs "NT_".
We normalized the RNA-seq counts and assayed differential expression with DEseq.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Dx_versus_C15Dx.DESeq: Tab-delimited text file that contains raw reads, reads normalized with DESeq and differential expression analysis comparing samples treated with Dexamethasone to samples treated with Dexamethasone and GW7647. The differential expression analysis was performed with DESeq (Simon Anders, Wolfgang Huber. Differential expression analysis for sequence count data. Genome Biology 11 (2010) R106. PMID 20979621. doi:10.1186/gb-2010-11-10-r106).
Supplementary_files_format_and_content: C15Dx_versus_Untr.DESeq.txt: Tab-delimited text file that contains raw reads, reads normalized with DESeq, and differential expression analysis comparing samples treated with Dexamethasone and GW7647 to untreated samples. The differential expression analysis was performed with DESeq (Simon Anders, Wolfgang Huber. Differential expression analysis for sequence count data. Genome Biology 11 (2010) R106. PMID 20979621. doi:10.1186/gb-2010-11-10-r106).

source_name: burst-forming unit erythroid (BFU-E), dexamethasone and GW7647

growth_protocol: Mouse BFU-E erythroid progenitors were isolated from E14.5 fetal livers. The first step includes a negative selection for erythroid progenitors by magnetic depleting of mature blood cells (lineage positive cells), early multipotent GEMM colony forming cells (Sca-1 positive cells), and myeloid colony-forming cells (CFU-G/M/Mk) (CD16/32 positive, CD41 positive, or CD34 positive cells). The second step includes a FACS-based positive selection of BFU-E erythroid progenitor process (c-kit positive and CD71 10%low cells).

extract_protocol:
Total RNA from mouse BFU-Es was purified with TRIzol (Invitrogen).
Samples were prepared for sequencing with the Illumina TruSeq RNA Sample Prep kit according to the standard protocol.

treatment_protocol: Mouse BFU-E erythroid progenitors were isolated from E14.5 fetal livers, and cultured in SFELE medium (StemSpanTM SFEM with 100 ng/mL rmSCF, 40 ng/mL rmIGF-1, and 2 U/mL rhEpo) alone or treated with 100 nM Dexamethasone with or without 10 μM GW7647 for 12 hrs.

value: burst-forming unit erythroid (BFU-E) from E14.5 fetal liver

tag: treatment

value: dexamethasone and GW7647 for 12 hrs


title: H3K4me1_CD24DC

status: Public on Jun 08 2015

type: SRA

city: St Louis

first: Gary

middle: E

last: Grajales-Reyes

state: Mo

address: Room 7766, CSRB

department: Immunology

country: USA

institute: Washington University in St. Louis

library_source: genomic

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were alignted using Bowtie 1.0.1
Uniquely mapped reads were masked using samtools with blacklist of ENCODE project and RepeatMasker in the UCSC genome browser
Bedgraph were made using makeUCSCfile program of the Homer Software package
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

organism: Mus musculus

source_name: Flt3L cultured dendritic cells

growth_protocol: Bone marrow was harvested with mortar and pestle. Afterlysing red blood cells, whole bone maroow was cultured in 100 ng/ml Flt3 ligand for 9 days.  CD24+DCs, CD172a+DCs and pDCs were sorted to >95% purity using by FACS AraFusion.  CD24 DCs: CD11c+ MHC II+ CD24+ CD172a- BST2- CD45RA-; CD172a DCs: CD11c+ MHC II+ CD24- CD172a+ BST2- CD45RA-, pDCs: BST2+ CD45RA+

extract_protocol:
For ChIP of p300, sorted cells were incubated in fresh media with Flt3L for 2 hours before crosslinking; for ChIP of IRF8, Batf3, H3K27ac, and H3K4me1, cells fixed before purification.  Cells were crosslinked with 1% formaldehyde, quenched with 1.25M Glycine, twice washed with PBS.  Chromatin was sonicated for shearing DNA size from 140 to 500 bp. Chromatin fragments were immunoprecipitated overnight at 4 °C with Dynabeads Protein A or G bound to anti-p300 (sc-585X, Santa Cruz Biotechnology), anti-IRF-8 (sc-6058x, Santa Cruz Biotechnology), or anti-Batf3, anti-H3K27ac (Ab 4729, Abcam) and H3K4me1 (Ab 8895, Abcam).  ChIPed DNA was eluted and reverse-crosslinked for 6 hr.  DNA was purified with phenol:chloroform extraction followed by ethanol precipitation.
Libraries for ChIP-seq were prepared using ThruPLEX-FD kit (Rubicon Genomics) and sequenced using Illumina HiSeq 2500 as single reads extending 50 bases.

tag: cell type

tag: chip antibody

tag: antibody vendor/catalog#

value: Ab 8895, Abcam


title: p300_CD24DC

value: sc-585X, Santa Cruz Biotechnology


title: BFU-E plus Dexamethasone and GW764, rep2

state: MA

description:
Sample name: mBFU_C15Dx_2
PolyA RNA

library_source: transcriptomic

molecule: total RNA

tag: strain/background


title: H3K4me1_CD172DC


title: BFU-E plus Dexamethasone, rep2

description:
Sample name: mBFU_Dx_2
PolyA RNA

source_name: burst-forming unit erythroid (BFU-E), dexamethasone

value: dexamethasone for 12 hrs


title: BFU-E untreated, rep2

description:
Sample name: mBFU_untrt_2
PolyA RNA

source_name: burst-forming unit erythroid (BFU-E), untreated


title: Batf3_CD24DC


title: BFU-E untreated, rep1

description:
Sample name: mBFU_untrt_1
PolyA RNA


title: BFU-E plus Dexamethasone, rep1

description:
Sample name: mBFU_Dx_1
PolyA RNA


title: input DNA

data_processing:
Adapter sequences were removed with "cutadapt -m 20 -b adapter_sequence".
We removed sequence artifacts  with fastx_artifacts_filter from the FASTX-Toolkit.
Reads were mapped against the mouse genome assembly mm9 with "bowtie  -k 1 -n 1 -l 20 --best".

source_name: burst-forming unit erythroid (BFU-E)

growth_protocol: Mouse BFU-E erythroid progenitors were isolated from E14.5 fetal livers. The first step includes a negative selection for erythroid progenitors by magnetic depleting of mature blood cells (lineage positive cells), early multipotent GEMM colony forming cells (Sca-1 positive cells), and myeloid colony-forming cells (CFU-G/M/Mk) (CD16/32 positive, CD41 positive, or CD34 positive cells). The second step includes a FACS based positive selection of BFU-E erythroid progenitor process (c-kit positive and CD71 10%low cells).

extract_protocol:
Isolated chromatin was sonicated and pre-cleared with isotype-matched rabbit non-specific IgG. Chromatin immunprecipitation was carried out with a GR antibody (Santa Cruz, sc-8992) or a PPARalpha antibody (Santa Cruz, sc-9000). 107 cells were used per IP condition. The formaldehyde crosslinks were reversed by heating to 65-degrees for 4 hours. RNA and protein were removed by RNAse A and Proteinase K treatment, and the DNA was isolated using phenol-chloroform extraction. Libraries were prepared according to Illumina's standard protocol, with instructions accompanying the DNA Sample Kit.
Immunoprecipitated DNA, along with input control, was prepared for sequencing with the Illumina TruSeq DNA Sample Prep kit according to the standard protocol with the following revisions. A 50-fold dilution of the Adapter mix was used in the ligation reaction. Additionally, the final libraries were size selected for fragments between 200 and 400 bp with a Pippin Prep system prior to sequencing.

treatment_protocol: Mouse BFU-E erythroid progenitors were isolated from E14.5 fetal livers, and cultured in SFELE medium (StemSpanTM SFEM with 100 ng/mL rmSCF, 40 ng/mL rmIGF-1, and 2 U/mL rhEpo) alone or treated with 100 nM Dexamethasone with or without 10 μM GW7647 for 4 hrs. Then cells were crosslinked by 1% formaldehyde and quenched by 2.5M glycine for ChIP analysis.

tag: develomental stage

tag: tissue

value: liver

value: burst-forming unit erythroid (BFU-E)

value: Dexamethasone and GW7647 4 hrs

tag: strain

value: none (input)


title: PPAR alpha_ChIP-seq_Dexamethasone and GW7647

data_processing:
Adapter sequences were removed with "cutadapt -m 20 -b adapter_sequence".
We removed sequence artifacts  with fastx_artifacts_filter from the FASTX-Toolkit.
Reads were mapped against the mouse genome assembly mm9 with "bowtie  -k 1 -n 1 -l 20 --best".
Peaks were called with macs14 -g mm --mfold=5,30 and rest of parameter as default using the PPAR alpha_ChIP-seq from cells treated with DEX plus GW7647 as ChiP-seq sample (-t) and the input DNA from cells treated with DEX plus GW7647 as control (-c).
Peaks with a fold change lower than 10 were filtered out.

value: PPAR alpha (Santa Cruz:H-98, sc-9000)


title: PPAR alpha_ChIP-seq_Dexamethasone

value: Dexamethasone 4 hrs


title: Nasonia_vitripennis_24h_adult_male (GAIIx)

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

description: Illumina WGBS-seq

data_processing:
Illumina CASAVA 1.7 software was used for HiSeq2000 basecalling for N.vit data and Illumina CASAVA 1.8.2 software was used for HiSeq2000 basecalling for N.gir data.
Illumina read QC was performed using FastQC software. Adapter containing reads were trimmed by Trimmomatic.
We built C->T converted reference genomes for both the Watson (+) and Crick (-) strand for Nasonia vitripennis reference genome, with all Cs in CpGs context remains Cs (meth_genome) and all CpG Cs converted to Ts (unmeth_genome).
Illumina sequencing reads were aligned to the converted genomes using BWA with a maximum of 4 mismatches for N.vit and 6 mismatches for N.gir. ~85% of all the reads were aligned to the converted genomes in both species and only ~65% uniquely mapped to the genome were kept for the methylation analysis. For uniquely mapped reads with indels, we queried the indel position against the indel database and unmatched spurious indels due to misalignment were excluded. In the end, 50-60% reads survived these QC filtering steps and they were summarized in a single BAM file for methylation analysis.
Of the 14,024,488 CpG sites in Nasonia haploid genome, we only included CpG sites covered by Illumina genome DNA sequencing data (on samples without bisulfite treatment) in our analysis. CpGs sites located in a potential repetitive region were also excluded. Base counts were summarized at 13,451,035 alignable CpGs in N.vit and 9,742,004 alignable CpGs in N.gir.
Genome_build: Nvit_1.0 scaffold
Supplementary_files_format_and_content: gzipped tab-delimited text file includes the C and T counts at alignable CpG positions in Nasonia vitripennis and Nasonia giraulti genome.

organism: Nasonia vitripennis

source_name: 24h adult Nasonia vitripennis male whole body

extract_protocol:
Genomic DNA samples were extracted from a pool of 50 adult whole-body samples 24 hour following eclosion from N.vit (strain AsymCX) and N.gir (strain R16A) males and females, using DNeasy Blood & Tissue Kit (Qiagen, CA).
Whole-genome bisulfite sequencing libraries were made according to the Illumina protocols (WGBS for Methylation Analysis Guide, Part# 15021861 Rev. A) with 15 ug of starting genomic DNA and Illumina TruSeq adapters.

tag: developmental stage

value: 24-hour adult

value: whole body

tag: Sex

value: male


title: Glucocorticoid receptor_ChIP-seq_Dexamethasone

value: GR (Santa Cruz:H300, sc-8992)


title: PPAR alpha_ChIP-seq_untreated

value: untreated


title: Irf8_CD24DC

value: sc-6058x, Santa Cruz Biotechnology


title: H3K27ac_CD24DC

value: Ab 4729, Abcam


title: Glucocorticoid receptor_ChIP-seq_untreated


title: small RNAs (18-29nt) from flies containing a Reporter with tree target sites for Zuc-independent piRNAs (zuc RNAi)

status: Public on Jun 07 2015

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description: adult ovary

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings
the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini)
reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3, release 5)
BigWig files were generated with Homertools v4.6
Genome_build: Drosophila melanogaster dm3, release 5
Supplementary_files_format_and_content: *sensor.txt: bedgraph file, presenting miRNA normalized read counts mapping to plus and minus strand of the corresponding sensor construct; genome_mapping_read_counts.txt: table indicating read counts for all genome mapping small RNA sequences in the indicated libraries

organism: Drosophila melanogaster

source_name: small RNAs (18-29nt) from flies containing a Reporter with tree target sites for three distinct Zuc-independent piRNAs from zucchini germline knock-down ovaries

extract_protocol:
total RNA was isolated with Trizol
small RNAs were PAGE selected and 3' and 5' linkers was ligated. 1st strand cDNA synthesis was performed using SuperScript III (Invitrogen) and the library was amplified using the Kapa HiFi Library Amp real time Kit (Peqlab) with Illumina TruSeq compatible primers.

value: 4-6 days old adult females

tag: germline knock-down

value: germline Zuc knockdown

tag: transgenic construct

tag: rna fraction

value: total small RNAs

value: ovary

tag: growth protocol

value: Flies were kept at standard conditions at 25º C.


title: sRNAs (18-29nt) from flies containing a Reporter with two distant target sites for Zuc-independent piRNAs (zuc RNAi)

description: adult ovary

source_name: small RNAs (18-29nt) from flies containing a Reporter with two target sites for two distant Zuc-independent piRNAs spaced 100nt apart from zucchini germline knock-down ovaries

value: Reporter with two target sites for two distand Zuc-independent piRNAs spaced 100nt apart


title: small RNAs (18-29) from OSCs transfected with a control siRNA

description:
processed data file: genome_mapping_read_counts.txt
Ovarian Somatic Cells (OSC)

tag: cell line

value: OSC

value: OSCs were cultured as published in Niki et al.; 2009


title: sRNAs (18-29nt) from flies containing a Reporter with two distant target sites for Zuc-independent piRNAs (control RNAi)

description: adult ovary

source_name: small RNAs (18-29nt) from flies containing a Reporter with two target sites for two distant Zuc-independent piRNAs spaced 100nt apart from control germline knock- down ovaries


title: small RNAs (18-29nt) from flies containing a Reporter with two target sites for Zuc-independent piRNAs (control RNAi)

description: adult ovary

source_name: small RNAs (18-29nt) from flies containing a Reporter with two target sites for two distinct Zuc-independent piRNAs from control germline knock-down ovaries


title: small RNAs (18-29nt) from flies containing a Reporter with abundant trigger piRNA with 5′ mismatch (pos 4/5)

description: adult ovary


title: small RNAs (18-29nt) from flies containing a Reporter with abundant trigger piRNA with 3′ mismatch (pos 16/17)

description: adult ovary


title: small RNAs (18-29nt) from flies containing a Reporter with two target sites for Zuc-independent piRNAs (zuc RNAi)

description: adult ovary

source_name: small RNAs (18-29nt) from flies containing a Reporter with two target sites for two distinct Zuc-independent piRNAs from zucchini germline knock-down ovaries


title: small RNAs (18-29nt) from flies containing a Reporter with tree target sites for Zuc-independent piRNAs (control RNAi)

description: adult ovary

source_name: small RNAs (18-29nt) from flies containing a Reporter with tree target sites for three distinct Zuc-independent piRNAs from control germline knock-down ovaries


title: small RNAs (18-29nt) from flies containing a Reporter with one target site for a Zuc- independent piRNA (control)

description: adult ovary

source_name: small RNAs (18-29nt) from flies containing a Reporter with one target site for a Zuc- independent piRNA from control germline knock-down ovaries

value: Reporter with one target site for a Zuc-independent piRNA


title: AGO3 bound small RNAs (18-29nt) from zucchini germline knock-down ovaries

description:
processed data file: genome_mapping_read_counts.txt
adult ovary

value: AGO3 bound small RNAs

tag: antibody

tag: antibody source

value: custom made rabbit polyclonal antibody


title: small RNAs (18-29nt) from flies containing a Reporter with control target

description: adult ovary

value: Reporter with control target


title: Glucocorticoid receptor_ChIP-seq_Dexamethasone and GW7647

data_processing:
Adapter sequences were removed with "cutadapt -m 20 -b adapter_sequence".
We removed sequence artifacts  with fastx_artifacts_filter from the FASTX-Toolkit.
Reads were mapped against the mouse genome assembly mm9 with "bowtie  -k 1 -n 1 -l 20 --best".
Peaks were called with macs14 -g mm --mfold=5,30 and rest of parameter as default using the Glucocorticoid_receptor_ChIP-seq from cells treated with DEX plus GW7647 as ChiP-seq sample (-t) and the input DNA from cells treated with DEX plus GW7647 as control (-c).
Peaks with a fold change lower than 10 were filtered out.

value: liver

value: burst-forming unit erythroid (BFU-E)

tag: treatment

value: Dexamethasone and GW7647 4 hrs


title: small RNAs (18-29nt) from flies containing a Reporter with one target site for a Zuc- independent piRNA (zuc RNAi)

description: adult ovary

source_name: small RNAs (18-29nt) from flies containing a Reporter with one target site for a Zuc- independent piRNA from zucchini germline knock-down ovaries


title: Piwi bound small RNAs (18-29nt) from rhino germline knock-down ovaries

value: germline Rhi knockdown

value: Piwi bound small RNAs

value: anti-piwi


title: small RNAs (18-29nt) from zucchini germline knock-down ovaries

value: 4-6 days old adult females

value: germline Zuc knockdown


title: Aub bound small RNAs (18-29nt) from rhino germline knock-down ovaries

value: Aubergine bound small RNAs

value: anti-aubergine

value: ovary


title: Piwi bound small RNAs (18-29nt) from zucchini germline knock-down ovaries

value: Flies were kept at standard conditions at 25º C.


title: AGO3 bound small RNAs (18-29nt) from control germline knock-down ovaries

value: control


title: Aub bound small RNAs (18-29nt) from zucchini germline knock-down ovaries


title: Aub bound small RNAs (18-29nt) from control germline knock-down ovaries


title: abundant_trigger_sensor

description: adult ovary

source_name: small RNAs (18-29nt) from flies containing a Reporter with abundant trigger piRNA

value: Reporter with abundant trigger piRNA

value: total small RNAs


title: AGO3 bound small RNAs (18-29nt) from rhino germline knock-down ovaries

value: AGO3 bound small RNAs

value: custom made rabbit polyclonal antibody


title: H1-WT-day10-Rep2

status: Public on Jun 06 2015

city: Bethesda

first: Brian

last: Busser

state: Md

address: 10 Center Drive

institute: NHLBI/NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then paired-end reads were mapped to the human genome (hg19, GRCh37) by Tophat 2.0.14 (bowtie v2.2.1.0, samtools v0.1.19.0) allowing 2 mismatches and 1 best hit
Mapped reads were counted in individual refSeq transcript region of each sample using RSeQC v2.6.1.  The R Bioconductor edgeR package was used to normalize raw reads and compare the difference.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: actual number of raw reads mapped to the indicated RefSeqID for each experimental sample

organism: Homo sapiens

growth_protocol: ES cells were cultured in Essential 8 media

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiation was performed in differentiation basal medium (E8 medium (minus FGF2, TGFβ and insulin), 1x Chemically Defined Lipid Concentrate (100x, Life Technologies) and 1x Pen-Strep (Life Technologies, 15140-122)).  Cardiac lineage differentiation was induced first with the addition of GSK3β inhibitor CHIR99021 (5 mM, Tocris) for the first 24 hours followed by days 2 through 5 with the Wnt inhibitor IWP2 (3 mM, Tocris, 3533).  Insulin (20 mg/ml, Sigma, I9278) was added at day 7 to maintain CMs.

value: H1 embryonic stem cells

tag: cell type

value: day 10 ES cells differentiating along the cardiac lineage

tag: genotype/variation

value: wild-type


title: H1-WT-day10-Rep4


title: H1-WT-day10-Rep1


title: H1-WT-day10-Rep3


title: germline Piwi bound small RNAs (18-29nt) from control germline knock-down ovaries

value: nos driven GFP-Piwi

value: germline Piwi bound small RNAs

value: anti-GFP

value: Memorial Sloan-Kettering Monoclonal AntibodyFacility; clone names: Htz-GFP-19F7 and Htz-GFP-19C8, bioreactor supernatant purity


title: Piwi bound small RNAs (18-29nt) from control germline knock-down ovaries

value: 4-6 days old adult females

value: Piwi bound small RNAs

value: anti-piwi


title: H1-ZEB2-shRNA-day10-Rep3

value: ZEB2 shRNA knockdown


title: small RNAs (18-29nt) from flies containing a Reporter with Us spaced in decreasing intervals from 27-23nt

description: adult ovary

value: ovary

value: Flies were kept at standard conditions at 25º C.


title: H1-ZEB2-shRNA-day10-Rep4


title: H1-NKX2-5-shRNA-day10-Rep2

value: NKX2-5 shRNA knockdown


title: H1-NKX2-5-shRNA-day10-Rep1


title: H1-WT-day6-Rep1

value: day 6 ES cells differentiating along the cardiac lineage


title: small RNAs (18-29nt) from flies containing a Reporter with 4Us spaced in 26nt intervals

description: adult ovary

value: total small RNAs


title: H1-ZEB2-shRNA-day10-Rep2


title: H1-WT-day6-Rep2


title: H1-ZEB2-shRNA-day6-Rep2


title: H1-ZEB2-shRNA-day10-Rep1


title: H1-ZNF503-shRNA-day6-Rep2

value: ZNF503 shRNA knockdown


title: H1-ZNF503-shRNA-day6-Rep1

value: H1 embryonic stem cells


title: H1-ZEB2-shRNA-day6-Rep1


title: H1-NKX2-5-shRNA-day6-Rep2


title: H1-WT-day2-Rep1

value: day 2 ES cells differentiating along the cardiac lineage


title: H1-ZNF503-shRNA-day0-Rep2

value: day 0 ES cells


title: H1-NKX2-5-shRNA-day2-Rep1


title: H1-NKX2-5-shRNA-day6-Rep1


title: H1-WT-day0-Rep2

value: wild-type


title: H1-ZEB2-shRNA-day0-Rep2


title: H1-NKX2-5-shRNA-day0-Rep2


title: H1-NKX2-5-shRNA-day0-Rep1


title: H1-ZEB2-shRNA-day2-Rep2


title: H1-ZNF503-shRNA-day2-Rep2


title: H1-WT-day2-Rep2


title: H1-ZNF503-shRNA-day2-Rep1


title: SP_CT1-7

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and ht-seq-count.
Non-protein coding and mitochondrial genes were filtered out.
Samples were selected for further analysis by using these criteria: unpaired reads examined/FASQ total read >0.75 and median CV coverage <1. Samples that had total counts less than one million were excluded.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization and differential expression analysis were performed in R using function "SAMseq" from "samr" package.
Genome_build: GRCh38
Supplementary_files_format_and_content: (1) brucellosis_processed_data_for_GEO.csv: comma-separated matrix – first 6 columns contain Ensembl gene ID, Ensembl transcript ID, HGNC symbol, location information and chromosome name, remaining columns include read counts assigned for each library; data represents all processing steps up to and including "sample QC and filtering" but not downstream processing/normalization for analysis. (2) brucellosis_combined_metrics.csv: comma-separated matrix – the first column contains library ID, remaining columns include RNA sequencing and alignment metrics.

molecule: polyA RNA

source_name: healthy control

extract_protocol:
Total RNA was isolated using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Ambion, TX) and RNA sample was globin reduced wit GLOBINclear (Ambion, TX) according to manufacturer’s instructions.
Libraries were prepared from globin reduced RNA samples using the Illumina TrueSeq RNA Sample Preparation kit according to manufacturer's instructions.

tag: group

value: Control

tag: subgroup

tag: history of brucellosis

value: NA; healthy control

tag: response to treatment of brucellosis

tag: country

value: Spain

value: Whole blood


title: H1-WT-day0-Rep1


title: SP_CT1-3

tag: tissue


title: SP_CT1-1


title: SP_CT0-7


title: SP_CT0-6


title: H1-ZEB2-shRNA-day2-Rep1


title: H1-NKX2-5-shRNA-day2-Rep2


title: MK_226

source_name: patients with leishmaniasis

value: Leishmaniasis

value: Macedonia


title: SP_022

source_name: patients with suspected brucellosis

value: Brucellosis

value: Group 1

value: Acute brucellosis

value: Complete remission


title: H1-ZNF503-shRNA-day0-Rep1


title: H1-ZEB2-shRNA-day0-Rep1

value: ZEB2 shRNA knockdown


title: MK_208


title: MK_213


title: MK_204


title: MK_160


title: SP_CT2


title: SP_CT0-8


title: MK_206


title: SP_CT1-6


title: MK_190


title: SP_CT1-5


title: SP_CT1-4


title: MK_147


title: MK_153


title: SP_CT1-2


title: MK_055


title: MK_012


title: SP_CT0-5


title: SP_CT0-2


title: SP_CT0-3


title: SP_CT0-4


title: SP_CT0-1


title: SP_036


title: MK_202


title: MK_205


title: MK_223


title: MK_221


title: MK_201


title: MK_030


title: MK_224


title: MK_031


title: MK_225


title: MK_027


title: MK_028


title: MK_222


title: MK_022


title: MK_025


title: MK_015


title: MK_138


title: MK_018


title: MK_136


title: MK_220


title: MK_219


title: MK_135


title: MK_137


title: MK_133


title: MK_134


title: MK_026


title: MK_016


title: MK_233


title: MK_102


title: MK_126


title: MK_024


title: MK_021


title: MK_019


title: MK_229


title: MK_232


title: MK_139


title: MK_130


title: MK_162

value: Group 5a

value: Chronic brucellosis (<10 years)


title: MK_128


title: MK_228


title: MK_196

value: Group 4a

value: Chronic brucellosis (>10 years)


title: MK_127


title: MK_215


title: MK_184


title: MK_216


title: MK_020


title: MK_189

value: Group 3

value: Reinfection


title: MK_191


title: MK_217

value: Group 2

value: Relapse


title: MK_192


title: MK_230


title: MK_200


title: MK_151


title: MK_157


title: MK_150

value: Group 5b


title: MK_182

value: Whole blood


title: MK_091


title: MK_092


title: MK_193


title: MK_146


title: MK_172


title: MK_173


title: MK_181


title: MK_176


title: MK_188


title: MK_187


title: MK_158


title: MK_195


title: MK_076


title: MK_185


title: MK_183


title: MK_071


title: MK_072


title: MK_179


title: MK_165


title: MK_154


title: MK_163


title: MK_169


title: MK_168


title: MK_017


title: MK_175


title: MK_167


title: MK_084


title: MK_083


title: MK_171


title: MK_170


title: MK_077


title: MK_177


title: MK_082


title: MK_156


title: MK_070


title: MK_161


title: MK_062


title: MK_063


title: MK_065


title: MK_066


title: MK_039


title: MK_036


title: MK_059


title: MK_047


title: MK_043


title: MK_042


title: MK_093


title: MK_080


title: MK_075


title: MK_079


title: MK_010


title: MK_085


title: MK_007


title: MK_060


title: MK_064


title: MK_086


title: MK_069


title: MK_049


title: MK_014


title: MK_106


title: MK_103


title: MK_101


title: MK_056


title: MK_078


title: MK_050


title: MK_038


title: MK_045


title: MK_105


title: MK_218

value: Control

value: NA; healthy control


title: MK_095

value: Brucellosis

value: Macedonia


title: MK_140

value: Group 1

value: Acute brucellosis


title: MK_046

value: Complete remission


title: MK_013

value: Group 5a


title: MK_009

value: Chronic brucellosis (<10 years)


title: MK_006


title: MK_035


title: MK_098


title: MK_011


title: MK_003


title: MK_094


title: MK_057


title: MK_120


title: MK_108


title: MK_107


title: C. elegans RNA dauer rep 1

status: Public on Jun 05 2015

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Minneapolis

description: first-strand, single-end, read_length= 75 bp

data_processing:
Gene expression quantifiation: Stranded, single-ended RNA-seq library reads from the embryonic, L1, IJ, and adult stages of S. feltiae, S. carpocapsae, and C. elegans were trimmed to 35 bp to remove low quality bp. Prior to mapping the reads, indexes were prepared for each respective species annotations (C. elegans: ce10/WS220) using the RSEM command (version 1.2.12) rsem-prepare-reference.   Reads were mapped to the respective species annotations using Bowtie 0.12.8 with the following options: -S --best, --strata, -k 10, -m 10, -v 1. Isoform expression was quantified using RSEM command, rsem-calculate-expression, with the following options: --bam, --fragment-length-mean. Isoform expression was summed to obtain the expression for each gene.
Genome_build: S. carpocapsae RNA-seq data was mapped to carpocapsae annotations from genome version 1: GCA_000757645.1 (http://www.ncbi.nlm.nih.gov/assembly/GCA_000757645.1/). Annotations can be found on Wormbase.
Genome_build: S. feltiae RNA-seq data was mapped to S. feltiae annotations from genome version 1: GCA_000757705.1  (http://www.ncbi.nlm.nih.gov/assembly/GCA_000757705.1). Annotations can be found on Wormbase.
Genome_build: C. elegans RNA-seq data was mapped to WS220 transcripts sequences.
Supplementary_files_format_and_content: Each sample expression file (*.isoforms.results) contains the isoform IDs, and the corresponding RPKMs, TPMs, and counts for each gene isoform.
Supplementary_files_format_and_content: S. carpocapsae gene identifier: L569_g1, S. carpocapsae isoform identifier: L569_g1.t1 (http://parasite.wormbase.org/Steinernema_carpocapsae_prjna202318/Info/Index)
Supplementary_files_format_and_content: S. feltiae gene identifier: L889_g1, S. feltiae isoform identifier: L889_g1.t1 (http://parasite.wormbase.org/Steinernema_feltiae_prjna204661/Info/Index)

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: S. carpocapsae (strain All), S. scapterisci (strain FL), S. feltiae (strain SN), S. glaseri (strain NC), and S. monticolum (Mount Jiri strain) were reared and maintained using standard methods (Kaya and Stock 1997). Briefly, 5 last-instar Galleria mellonella waxmoth larvae or a single adult cricket for S. scapterisci (American Cricket Ranch, Lakeside, CA) were placed in a 5 cm Petri dish with a 55 mm Whatman 1 filter paper acting as a pseudo-soil substrate in the bottom of the dish. ≤250 ml containing 500-1000 IJs suspended in water was evenly distributed on the filter paper. After 7-10 days the insect cadavers were placed on White traps (White 1927). Waxmoth cadavers infected with S. glaseri were placed in a petri dish partially filled with plaster of Paris and harvested from this, since S. glaseri emerge as pre-IJs that will not properly develop if they emerge directly into water (Kaya and Stock 1997). Emerging IJs from all species were harvested, washed for 10 minutes in 0.4% Hyamine 1622 solution (Fluka), and rinsed 3 times with water.

extract_protocol:
To harvest bulk genomic DNA and IJ RNA, infective juveniles from each species were washed in a low percent Hyamine when collected, as above. They were then re-washed and collected in Ringer’s solution. After the last wash in Ringers, the worms were suspended in for 15- 30 minutes. For DNA extraction a Wizard® Genomic DNA Purification Kit (Promega) was used, following the manufacturers protocol. The genomic DNA was then treated with RNase A to remove any RNAs present in the sample. For RNA extractions, the nematodes were snap-frozen in liquid nitrogen in ~100-μL aliquots and stored at −80°C. Worms were then freeze-thawed three or four times to break the cuticle before extracting bulk RNA. Bulk RNA was then extracted using a Phenol-Chloroform extraction using Trizol® (Invitrogen). This sample was treated with DNAse to remove lingering DNA and then treated to poly-A selection to isolate Eukaryotic messenger RNA, reducing if not removing bacterial contaminant. To isolate embryonic, L1, and adult stage-specific RNA from S. carpocapsae, one to two thousand IJs were placed onto 10cm lipid agar plates seeded with overnight cultures of Xenorhabdus nematophila. These cultures were allowed to grow for ~42 hours to collect adults or 3 days to collect embryos and L1s. To collect embryos and L1s, gravid females were harvested from the 10cm plates 3 days after IJs were placed there. The females were harvested by adding enough distilled H2O to the cover the surface of the plates, which were then swirled by hand to lift the nematodes into suspension and pour them into conical tubes. These were then pelleted by gentle centrifugation and rinsed several times with distilled H2O until the supernatant was clear. The nematodes were then placed in separate conical tubes in 5ml aliquots. These were then topped of to 50ml with bleach solution (16.6ml of 12% bleach, 5ml of 1M KOH, and 80ml of distilled H2O). Eggs were harvested by bleaching the nematodes until all nematode tissue was dissolved, leaving only the eggs. These embryos were then either harvested for total RNA as described above or they were allowed to hatch in Ringers solution, where the L1s were then harvested for total RNA as described above. To isolate embryonic, L1, and adult stage-specific RNA from S. feltiae, one to two thousand IJs were placed onto 10 cm lipid agar plates seeded with overnight cultures of Xenorhabdus bovienii. These cultures were allowed to grow for ~36 hours to collect adults or ~55 hours to collect embryos and L1s. The same procedure was used to harvest embryos and L1s as S. carpocapsae. To isolate embryonic, L1, and adult stage-specific RNA from C. elegans N2s, worms were placed onto 10 cm NGM plates seeded with overnight cultures of Escherichia coli  (OP50 strain). 200 uL aliquots OP50 were added every day. Plates with lots of gravid adults were bleached according to the guide for Maintenance of C. elegans in Wormbook (Stiernagle, 2006). The embryos were either collected to harvest embryos, placed in Ringer’s solution for ~ 20 hours to harvest L1s, or plated on fresh NGM plates seeded with E. coli OP50 and collected ~47 hours  later to collect young adults.
The RNA-seq libraries used for genome annotation were built using an unstranded, paired-end library construction protocol (Mortazavi et al. 2008; Mortazavi et al. 2010) . Libraries were quantified using Qubit fluorometer (Invitrogen) and size distributions were verified using Agilent Bioanalyzer and the High Sensitivity DNA Kit. These RNA-seq libraries were sequenced on the Illumina Genome Analyzer IIx sequencer in paired-end mode to a read length of 76 nt. The RNA-seq libraries that were used for the gene expression analyses were built using a first-strand protocol, and sequenced on the NextSeq 500 sequencer in single-end mode to a read length of 75 nts.

tag: strain

value: N2 strain

tag: developmental stage

value: dauer


title: C. elegans RNA adult rep 1

value: young adult


title: C. elegans RNA adult rep 2


title: C. elegans RNA L1 rep 2

value: first larval


title: C. elegans RNA L1 rep 1


title: C. elegans mixed embryo RNA rep 2

value: mixed embryo


title: C. elegans mixed embryo RNA rep 1


title: p53-/-, untreated, input RS69

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

description: RNA with Poly A tail

data_processing:
Base calling: RTA 1.12.4.2 (performed at the Next Generation Sequencing Facility at the Center for Cancer Research at the National Cancer Institute)
Alignment and filtering: Casava 1.8.2 (performed at the Next Generation Sequencing Facility at the Center for Cancer Research at the National Cancer Institute)
Re-analyzing: Tophat (TopHat v2.0.8) with parameters:tophat -G mm9_Ensemble_v67.gtf -o ./ -r 10 --mate-std-dev 200 -p 16 read1.fastq read2.fastq
Generation of normalized abundance measurements: After obtaining the aligned bam files, the Cufflinks algorithm was used to calculate FPKM with a .gft file for Refseq transcripts downloaded in May 07, 2014.
Genome_build: mm9
Supplementary_files_format_and_content: bam file format of aligned tags for each sample

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were grown in mESC growth medium, Knockout DMEM (KO-DMEM), 15% Fetal Bovine Serum, 100mM MEM non-essential amino acids, 0.1mM 2-mercaptoethanol, 2mM L-glutamine and 1X penicillin-streptomycin (All from Invitrogen) plus 1000 units/ml leukemia inhibitory factor (Lif, Life Technologies)

extract_protocol:
RNAs were extracted using the GenElute Mammalian total RNA Miniprep kit (Sigma, Cat: RTN350-1kt).
Illumina TruSeq RNA, Protocol RS-930-2001 withIllumina TruSeq V3.0

treatment_protocol: Untreated or treated with 0.5 uM Adriamycin for 8 hours.

value: untreated

tag: genotype

value: embryonic stem cells

tag: type

value: cell culture

tag: passage

value: less than 20 passages

value: C57BL/6X129Sv mix


title: p53+/+, untreated, hnRNP L, RIP RS71

description: RIP RNA

value: hnRNP


title: p53+/+, Adriamycin, hnRNP L, RIP RS72

description: RIP RNA

value: Adriamycin


title: p53+/+, Adriamycin, input RS68

description: RNA with Poly A tail


title: p53+/+, untreated, input RS67

description: RNA with Poly A tail


title: p53-/-, Adriamycin, input RS70

description: RNA with Poly A tail


title: C. elegans RNA dauer rep 2


title: p53-/-, untreated, hnRNP L, RIP RS73

description: RIP RNA


title: mir-80; mir-58; mir-81-82 rep 3 [RNA-Seq]

city: Zurich

first: Deni

last: Subasic

address: Wintethurerstr. 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

data_processing:
Raw fastq files were uploaded to the ClipZ server (www.clipz.unibas.ch; Khorshid et al., Nucleic Acids Res, 2011 ) for mapping and annotation.
DESeq (Anders and Huber, Genome Biol, 2010) was used to compare read counts of transcripts in 3 replicates of a miR-58 family mutant with those of wild type worms and to calculate fold changes and significances thereof.
Genome_build: ce6
Supplementary_files_format_and_content: The txt file contains a table with log2 fold changes of transcripts in a miR-58 family mutant compared to wildtype and the adjusted p-values for this comparison, which was calculated based on 3 replicates each using DESeq (Anders & Huber, Genome Biol, 2010).

source_name: Whole animals

growth_protocol: Light labeled samples were prepared by feeding with light labelled bacteria (light labelled lysine (14N2,12C6-L-Lysine) and arginine (14N4,12C6-L-Arginine)) for two generations, respectively. Both generations were synchronized by bleaching (Stiernagle, 2006). 40 000 larvae that hatched on unseeded plates overnight were transferred to the plates with light labelled bacteria (20 000 worms / plate), and collected at the late L4 stage for subsequent protein and RNA isolation (33 hours post-transfer for wild-type and mir-58). Appropriate staging was determined by examining a characteristic vulval structure for at least 100 animals under an inverted microscope (Leica MZ125). mir-80; mir-58 double mutant was collected 6h post wild-type and mir-80; mir-58; mir-81-82 quadruple mutant 15 hours post wild-type due to an observed developmental delay. Worms were washed with M9 three times before freezing in liquid nitrogen.

extract_protocol:
RNA was isolated by TRIZOL (Life Technologies) according to the manufacturer’s protocol and additionally purified by acidic phenol: chloroform (5:1) solution pH 4.5 (Ambion) / chloroform extraction to obtain high-grade RNA for sequencing. RNA concentration was measured by Nanodrop device (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nDf53 III; mir-58(n4640) IV; nDf54 X

value: whole animals at L4 stage


title: mir-80; mir-58; mir-81-82 rep 2 [RNA-Seq]


title: mir-80; mir-58 rep 3 [RNA-Seq]

value: nDf53 III; mir-58(n4640) IV


title: Wild Type rep 3 [RNA-Seq]

value: N2 Bristol

value: WT


title: mir-58 rep 3 [RNA-Seq]


title: mir-58 rep 1 [RNA-Seq]


title: mir-58 rep 2 [RNA-Seq]


title: Wild Type rep 2 [RNA-Seq]


title: MK_142

value: Brucellosis

value: Group 5a

value: Chronic brucellosis (<10 years)

value: Complete remission

value: Macedonia

value: Whole blood


title: Wild Type rep 1 [RNA-Seq]


title: mir-80; mir-58; mir-81-82 rep 2 [miRNA-Seq]

data_processing:
Raw fastq files were uploaded to the ClipZ server (Khorshid et al. 2011) for adapter removal.
Reads that mapped to mature miRNA sequences and the four calibration sequences were identified using Segemehl (Hoffmann et al. 2009).
miRNA reads were normalized to the sum of reads mapping to the four calibration sequences and then averaged over the three replicates obtained for each mutant condition.
Genome_build: miRbase, release 20 (Kozomara et al. 2011)
Supplementary_files_format_and_content: The txt file contains a table of normalized read numbers of C. elegans miRNAs and of four calibration sequences in wildtype and in three mutant conditions.

growth_protocol: Light labeled samples were prepared by feeding with light labelled bacteria (light labelled lysine (14N2,12C6-L-Lysine) and arginine (14N4,12C6-L-Arginine)) for two generations, respectively. Both generations were synchronized by bleaching (Stiernagle, 2006). 40 000 L1 larvae that hatched on unseeded plates overnight were transferred to the plates with light  bacteria (20 000 worms / plate), and collected at the late L4 stage for subsequent protein and RNA isolation (33 hours post-transfer for wild-type and mir-58). Appropriate staging was determined by examining a characteristic vulval structure for at least 100 animals under an inverted microscope (Leica MZ125). mir-80; mir-58 double mutant was collected 6h post wild-type and mir-80; mir-58; mir-81-82 quadruple mutant 15 hours post wild-type due to an observed developmental delay. Worms were washed with M9 three times before freezing in liquid nitrogen.

extract_protocol:
RNA was isolated by TRIZOL (Life Technologies) according to the manufacturer’s protocol and additionally purified by acidic phenol: chloroform (5:1) solution pH 4.5 (Ambion) / chloroform extraction to obtain high-grade RNA for sequencing. RNA concentration was measured by Nanodrop device (Thermo Fisher Scientific).
1 µg of total RNA isolated as described above was processed for small RNA sequencing. Four calibrator oligonucleotides (Cal 01-04 5 fMol each) were added as a reference as described previously (Hafner et al. 2012a; Hafner et al. 2012b). Briefly, RNA was dephosphorylated using FastAP (Fermentas) and radiolabelled according to the described method (Hafner et al. 2012a) with the 10 fold reduction of γ-32P-ATP (final concentration 0.05 μCi/μl). Subsequently, RNA was separated with denaturing PAA (15%) gelelectrophoresis and fractions between 18 and 25 nt in size were excised from the gel. Thereafter, preadenylated 3’-adapter (IDT DNA Technologies, 5’-TGGAATTCTCGGGTGCCAAGG-3’) was ligated with truncated T4 RNA Ligase 2 (1-249, K227Q, final concentration 2000 U/µL, NEB) overnight on ice. After a denaturing 15% PAA gel separation, RNA ranging from 35 to 70 nt was cut out of the gel and extracted with 0.4 M NaCl overnight. The RNA was recovered by acidic phenol/chloroform extraction, ethanol precipitation, and addition of Glycoblue (Ambion) followed by 5’-RNA Adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’) ligation using T4 RNA ligase (Fermentas) at 37°C for 1 h. After an additional gel-purification step performed RNA was reverse transcribed into cDNA with SuperScript III reverse transcriptase (Invitrogen) according to the manufacturer’s description. Library amplification step was performed with minimal number of PCR as determined by a preceding pilot PCR using different PCR cycle numbers. PCR was performed using Taq DNA-Polymerase (Sigma-Aldrich as described) with Index primers described in IlluminaTruSeq Small RNA Sample Prep Kit protocol. Amplicons were extracted using QiaExII (Qiagen) according to the purchaser’s protocol. The recovered DNA was sequenced using single end, 50 cycle sequencing on HiSeq2000 (Illumina).


title: mir-80; mir-58; mir-81-82 rep 1 [miRNA-Seq]


title: p53-/-, Adriamycin, hnRNP L, RIP RS74

description: RIP RNA

value: embryonic stem cells


title: mir-80; mir-58 rep 1 [miRNA-Seq]


title: mir-80; mir-58 rep 3 [miRNA-Seq]


title: mir-80; mir-58; mir-81-82 rep 1 [RNA-Seq]


title: mir-80; mir-58 rep 1 [RNA-Seq]


title: mir-80; mir-58; mir-81-82 rep 3 [miRNA-Seq]


title: mir-58 rep 2 [miRNA-Seq]


title: Wild Type rep 1 [miRNA-Seq]


title: mir-80; mir-58 rep 2 [RNA-Seq]


title: mir-58 rep 1 [miRNA-Seq]


title: Mouse_Brain_Input_Rep2

city: Tianjin

first: Ping

last: Zhu

address: 288, Nanjing Road, Heping District

department: State Key Laboratory of Experimental Hematology

country: China

institute: Institute of Hematology and Blood Disease Hospital

description: barcode: NNNNATCGNN

data_processing:
library strategy: CAP-seq
Tirm_galore[version 0.3.7, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] was used to remove or trim adaptor contained reads and low quality reads, requiring the minimum length of trimmed reads to be 20 bases. Artificial sequences, two bases added during library construction at the 5 prime of reads, were also removed
Remained reads were mapped to the human or mouse transcriptome (downloaded from UCSC genome tables) using BWA[0.7.5a-r405, Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]]
Genome_build: hg19, mm9
Supplementary_files_format_and_content: txt format; containing 7 columns are: 1)mRNA 2)Position 3)Base on this position 4)Reads with mapping position start at the (Pos+1) 5)Reads covered this position 6) sum of (column 4 and 5) 7)Stop rate estimated as column 4 devided by column 6

extract_protocol:
total RNA was isolated from cell lines or tissues with Trizol(invitrogen). 10 ug mRNA was enriched from 1 mg total RNA with two rounds of polyA selection using Dynabeads Oligo(dT)25 (invitrogen) and one round of rRNA depletion using Ribominus Transcriptome kit (invitrogen).
The Biotin-CMC labeling of ψ was performed as previously described with some modification. The mRNA was was added to 0.2 M Chemically-synthesized N3-CMC in BEU buffer followed by incubated at 37 °C for 20 minutes. The Chemically-synthesized N3-CMC was removed by ethanol precipitation. The RNA pellet was dissolved in sodium carbonate buffer and incubated at 37°C for 6h to remove N3-CMC RNA was purified by ethanol precipitation and dissolved in H2O. Click reaction was performed with addition of 20 mM DBCO-(PEG)4-biotin (sigma) to a final concentration of 150 μM followed by incubating at 37°C for 2h.The mock sample was treated as above only without addition of Chemically-synthesized N3-CMC.The biotin-CMC-Ψ RNA was enriched by Streptavidin C1 Dynabeads (Invitrogen).The library construction was performed according to the iCLIP library construction protocol with some modifications. For dephosphorylation of 3'ends, RNA were treated with rSAP (NEB) and incubated at 37 °C for 30 minutes.RNA linker ligation was performed with T4 RNA ligase 1 (NEB) at 16 °C overnight.Reverse Transcription was performed with Superscript III reverse transcriptase (Invitrogen). The cDNA was purified with 6% UREA-PAGE to remove excessive RT primers. Purified cDNA was circligated with CircLigase II (Epicentre) followed by ethanol precipitation. Linearization of cDNA was performed with annealing with a cut oligo and followed by BamHI digestion. The cDNA was amplified by PCR with primers. PCR products were purified by 8% TBE gel and sequenced on Illumina Hiseq2000 or Hiseq2500 with single end reads (50bp).

value: brain

tag: enrichment


title: Mouse_Brain_Pulldown_Rep1

description: barcode: NNNNTGACNN

value: N3-CMC treat and pull down


title: Mouse_Brain_Pulldown_Rep2

description: barcode: NNNNGCTANN


title: Mouse_Liver_Pulldown_Rep1

description: barcode: NNNNATGCNN

value: liver


title: Mouse_Brain_Input_Rep1

description: barcode: NNNNCAGTNN


title: Mouse_Liver_Pulldown_Rep2

description: barcode: NNNNTGCANN


title: E24

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to miRBase Version19 using miRDeep2.
The expression of miRNAs in each library was normalized to counts per million reads (CPM) by the following method: CPM = (miRNA reads number / total reads number per library) × 1000000
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: Tab-delimited text files include reads number for each Sample

organism: Bos taurus

source_name: mammary epithelial cell line

extract_protocol:
Rumen, mid-jejunum and ileum were collected from cavles, flash frozen on dry ice, and RNA was harvested using mirVana™ miRNA Isolation Kit (Ambion, Carlsbad, CA). Illumina TruSeq Small 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

value: MAC-T cell

value: Challenged by Escherichia coli (E. coli) strain P4

tag: time points

value: 24 hours


title: E48

value: 48 hours


title: mir-80; mir-58 rep 2 [miRNA-Seq]

value: nDf53 III; mir-58(n4640) IV

value: whole animals at L4 stage


title: C48

value: control


title: C24


title: S24

value: Challenged by Staphylococcus aureus (S. aureus) strain Smith CP


title: S48


title: S06

value: 6 hours


title: E12

value: 12 hours


title: Mouse_Liver_Input_Rep1

description: barcode: NNNNGCATNN


title: C00

value: 0 hour


title: Short OG-mix 1

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

country: Finland

institute: University of Helsinki

data_processing:
The SOLiD™ Software platform was used for basecalling, read trimming and quality control.
Mapping to the Arabidopsis genome TAIR9 was performed using SHRiMP v. 2.2.3 using the parameters   -N 8 -m 20 -i -25 -g -40 -e -10 -E
Read counts were summarized and analyzed using HT-Seq version 0.6.0 and subsequent relative gene expression between treatments was calculated using DESeq 2 version 1.10
Genome_build: tair9
Supplementary_files_format_and_content: read count tab delimited csv tables contains read counts for each sample

organism: Arabidopsis thaliana

source_name: Whole-plant Seedlings

growth_protocol: For the growth inhibition assay, Arabidopsis seedlings were placed in individual wells with 1 ml of liquid 1/2MS medium in 12-well plates (Gómez-Gómez et al., 1999). The plates were sealed with Parafilm to minimize evaporation. Seeds were stratified for 3 days then allowed to grow in a 12 h light cycle at 20°C. After 8 days the medium was replaced with fresh liquid 1/2MS and the seedlings were grown for 2 more days

extract_protocol:
Total RNA was extracted from seedlings as described by Ferrari et al. (2007). Briefly, the protocol for treating plants was similar to that used in growth inhibition studies with the difference that 12 seeds were placed in each well for germination. For each biological replicate, plants were harvested from 3 wells, rinsed in MQ and blotted dry before freezing in liquid nitrogen. The plant material was crushed by using metal beads in a shaker. The RNA was extracted using the GeneJET Plant RNA Purification mini kit (ThermoScientific) following the manufacturer’s protocol. Sample quality was assessed by gel electrophoresis and measured using a NanoDrop (ThermoScientific). 2 µg of total RNA was treated with DNAseI, Rnase-free (ThermoScientific) and used for cDNA synthesis using Maxima Reverse Transcriptase and Ribolock Rnase Inhibitor (ThermoScientific) following the manufacturer’s protocol. Primers used for cDNA synthesis were random hexamers and oligo dT primers.
The library was constructed using the standard protocols for the ABI SOLiD system. Two pools containing all samples were made and run on seperate lanes.

treatment_protocol: Treatment was performed with OG-containing suspensions of either 200 µM trimeric OGs (Sigma-Aldrich, trimers) or a 2 mM mixture of short (DP<10) OGs (short OG-mix). 1/2 MS medium was used as a mock treatment. Plants were subjected to the suspensions for 3 hours.

tag: ecotype

value: Colombia 0

value: Short OG-mix

tag: sample time

value: 3 hours post treatment


title: C06

tag: cell type

tag: treatment


title: Short OG-mix 3


title: mir-58 rep 3 [miRNA-Seq]


title: C12


title: Short OG-mix 2


title: S12


title: E06


title: Mock 3

value: Mock


title: Trimers 1

value: Trimer


title: Trimers 3


title: Trimers 2


title: Mock 2


title: Mock 1


title: tagged-726_S1

city: cambridge

first: oren

last: ram

state: MASSACHUSETTS

address: 415 Main Street

department: epigenomics

institute: Broad institute

description:
Single cell RNA-seq
Read1: 3' end of polyA transcripts
Read2: single cell barcodes

data_processing:
extracting single cell by barcodes
alignment with TOPHAT
filtering duplicates
aggregating mES cells and Mef cells
Genome_build: mm9
Supplementary_files_format_and_content: mEF.sorted.bed: bed file (bam->bed): aggregating all mEF single cells
Supplementary_files_format_and_content: mES.sorted.bed: bed file (bam->bed): aggregating all mES single cells

source_name: mES and mEF

growth_protocol:
mESCs were grown using Knockout DMEM: ~410mL (Gibco)
15% Fetal Bovine serum: 75mL (lot# F12101121)
1% Pen/Strep: 5mL (Gibco)
1% Non-essential amino acids: 5mL (Gibco)
1% Glutamax: 5mL (Gibco)
.01% LIF: 50ul (Millipore: ESG1107)
.0004% BME: 2ul
mEFs were grown using Knockout DMEM: ~410mL (Gibco)
15% Fetal Bovine serum: 75mL (lot# F12101121)
1% Pen/Strep: 5mL (Gibco)
1% Non-essential amino acids: 5mL (Gibco)
1% Glutamax: 5mL (Gibco)

extract_protocol:
Mouse embryonic Stem cells (V6.5) and mouse embryonic fibroblast cells (10.5 p.c.) are cultured from cell-lines. The cells are dissociated prior to encapsulation using trypsin and re-suspended in PBS at a concentration of about 5•106/mL. Human derived K562 cells are cultured from cell-line in suspension and re-suspended prior to encapsulation in PBS at a concentration of about 5•106/mL. The cell suspension is loaded in a syringe together with the magnetic stirrer bar that prevents sedimentation of the cell suspension. The cell suspension is injected into a co-flow drop-maker device (Figure 3B) with a 2X lysing buffer containing 100 mM Tris-HCl, 300 mM NaCl and 1 % Triton X-100 and dispersed in oil with 0.2 % w/w surfactant. We use OEM syringe pumps (KD Scientific, MA, USA) with typical flow rates of 1.8 mL/hr for the oil and 250 µL/hr for each of the aqueous phases, resulting in a drop diameter of ~50 µm. Drops are collected and incubated off chip at 4ºC for 15 minutes to complete cell lysis. The lysing protocol was optimized to maximize product after amplification and lysis is verified visually after 15 min.
To label cells in drops, cell-bearing drops and barcode-library drops are re-injected into a “three point merger” device. Drops are spaced on chip by oil with 0.2% w/w surfactant and are then electrocoalesced. An additional RT buffer is pico-injected as the drops are coalesced. The buffer contains 1X Affinity Script buffer (Agilent), 10 mM DTT, 8 mM dNTPs, Rnase inhibitor (Rnasin, Promega) diluted 1:10 and Affinity Script Multi Temp RT enzyme (Agilent) diluted 1.5:10. The device electrodes are connected to a high voltage amplifier (TREK 2210) which supplies a 100 V sine wave at a frequency of 25 kHz. The flow rates used to inject the drops are chosen to ensure that no more than one barcode drop fuses with a single cell-bearing drop, even at the expense of some drops not fusing with other drops. The flow rate of the buffer containing RT-enzyme is chosen to ensure that the buffer is added at ~1:1 ratio upon coalescence of the two drops. Typical flow rates fulfilling these requirements are 1 mL/hr for the oil, 100 µL/hr for the cell-bearing drops, 30 µL/hr for the barcode-drops and 170 µL/hr for the RT-enzyme buffer. To control the number of cells collected per sample, we measure the filling number λ at the cell encapsulation stage and use a fast camera (HiSpec1, Fastec Imaging,USA) to measure the frequency f of pairs of barcode-drops and cell-bearing drops that fuse at the labeling stage. The time T100 required to collect 100 cells is then calculated as T100= 100/λf. Typically, f=100 Hz and λ=0.1, so that 1000 pairs of fused drops are collected to sample 100 cells, and the collection lasts 10 seconds. To protect the collected drops from evaporating and adsorbing to the walls of the collection vial, they are collected into a vial containing ~50 µL of oil and 1 % w/w surfactant and 30 µL of emulsion of ~70 µm carrier drops containing 0.25X Affinity Script buffer, 25 mM Tris-HCl, 75 mM NaCl and 0.25 % Triton X-100. The sample is collected and incubated at 42 ºC for 1 hour to allow the RT reaction to occur; thereafter it is maintained at 4 ºC.
Barcodes were commercially synthesized (IDT) and delivered in three 384 well-plates at concentrations of 150 µM. To encapsulate the barcodes in drops we design 96 parallel drop-makers on a single microfluidic chip (Figure 3A), so that the aqueous inlets of each drop-maker (22 gauge stainless steel capillaries, New England Small Tube) precisely fit one quarter of a 384 well-plate and are immersed in 96 different wells, each containing a unique barcode. Oil with 1% w/w surfactant is distributed to all drop-makers via a common inlet that is connected to a pressurized oil reservoir. The plate and the microfluidic parallel device are placed in a pressure chamber while a common outlet for all 96 barcode drop-makers is located outside the pressure chamber. Upon pressurizing the chamber, each of the 96 barcode solutions is forced through its own drop-maker, thereby forming an emulsion where every drop contains about 1 billion copies of one of the 96 barcodes. We pressurize the oil reservoir to 9 psi and the pressure chamber to 6 psi, producing ~35 µm drops at a rate of about 500 µL/min from 96 wells. After encapsulation the device is washed with water by placing it in a petri dish filled with water and pressurizing the chamber for 2 minutes. Then the device is similarly washed with isopropanol with the exception that the oil inlet is also fed with isopropanol. Finally, the device is dried by placing it in the pressurized chamber with all inlets exposed for several minutes. The process is repeated 12 times in 6 hours until a total of 1152 different barcodes are encapsulated to form the final barcode-library emulsion. A total volume of about 10 mL is produced from 10 µL in each well.
RT preformed within the microfluidic drops. The RT primers includes polyT barcode and illumina anchor. after breaking the drops we followed with RNAse treatment and ligated a ss-DNA adapter containg a second illumina anchor to the cDNA 3' end.
Size selected for 100bp-500bp

tag: mescs

tag: mefs


title: tagged-741_S2


title: RNA Pol II, Adriamycin

description: ChIP DNA

data_processing:
Base calling: RTA 1.12.4.2 and sequencing chemistry: Illumina TruSeq 3.0. All raw files were generated using this method.
Alignment: Illumina Casava 1.8.2. All processed data files were generated using this method.
Processed files are peak files. Peak calling was performed using MACS (version 1.4.1 2011_06_27; band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05)
Genome_build: mm9

source_name: ESC, RNA Pol II, Adriamycin

extract_protocol:
ChIP DNA was extracted by standard phenol approach.
NEB ChIP-seq prep kit

value: embryonic stem cells

value: less than 20 passages

tag: background strain

value: C57BL/6X129Sv mix


title: RNA Pol II, untreated

description: ChIP DNA

source_name: ESC, RNA Pol II, untreated


title: tagged-954_S3


title: tagged-630_S3


title: tagged-375_S2


title: hnRNP L, untreated

description: ChIP DNA

source_name: ESC, hnRNP L, untreated


title: H3K79me2, Adriamycin

description: ChIP DNA

source_name: ESC, H3K79me2, Adriamycin


title: S. feltiae RNA young adult rep 1

organism: Steinernema feltiae

value: SN strain

value: young adult


title: H3K27me3, Adriamycin

description: ChIP DNA

source_name: ESC, H3K27me3, Adriamycin


title: S. feltiae RNA young adult rep 2


title: S. feltiae RNA IJ rep 2

value: infective juvenile


title: S. feltiae RNA IJ rep 1


title: H3K27me3, untreated

description: ChIP DNA

source_name: ESC, H3K27me3, untreated


title: hnRNP L, Adriamycin

description: ChIP DNA

source_name: ESC, hnRNP L, Adriamycin


title: KO_Input_Rep2

description: barcode: NNNNCGATNN

growth_protocol: cells was maintained in DMEM with 10% FBS and penicillin/streptomycin.

tag: cell line

value: human embryonic kindey cells

tag: genotype/variation

value: PUS1 KO


title: H3K79me2, untreated

description: ChIP DNA

source_name: ESC, H3K79me2, untreated


title: Mouse_Liver_Input_Rep2

description: barcode: NNNNCATGNN

tag: tissue

value: liver


title: KO_Pulldown_Rep2

description: barcode: NNNNTAGCNN

value: N3-CMC treat and pull down


title: KO_Pulldown_Rep1

description: barcode: NNNNGACTNN


title: S. feltiae RNA L1 rep 1

tag: strain

value: first larval


title: KO_Input_Rep1

description: barcode: NNNNTCGANN


title: KO_Ctrl_Input_Rep2

description: barcode: NNNNAGCTNN


title: S. feltiae RNA L1 rep 2

tag: developmental stage


title: S. feltiae RNA embryo rep 2

value: embryo


title: KO_Ctrl_Pulldown_Rep1

description: barcode: NNNNGTACNN


title: H3K4me3, Adriamycin

description: ChIP DNA

source_name: ESC, H3K4me3, Adriamycin


title: Input

city: Houston

first: Francesco

middle: J

last: DeMayo

state: Texas

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
50-nt sequence reads identified by the Sequencing Service (using Ilumina's Hi-seq)
reads mapped to the genome using the BWA algorithm with default settings
tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp
density of fragments, in 32-nt bins divided genome, defined in BAR files
peaks were defined using MACS for FOXO1 and SICER for RNA Pol II
Genome_build: GRCh37.p2-Primary Assembly

source_name: endometrial stromal cells

growth_protocol: DMEM F12, 10% fetal bovine serum, antibiotic-antimycotic, HEPES and NaHCO3

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the  3 -ends. Illumina genomic adapters were ligated and the sample was  size-fractionated (200-300 bp) on a 2% agarose gel. After a final PCR  amplification step (18 cycles), the resulting DNA libraries were  quantified and sequenced on HiSeq 2000.

treatment_protocol: 10nM 17β-estradiol, 100nM medroxyprogesterone acetate, and 1mM  cAMP OPTI-MEM I  reduced serum media supplemented with 2% stripped fetal bovine serum and antibiotic and antimycotics

value: primary cells

tag: passages

tag: health status

value: healthy, proliferative phase


title: KO_Ctrl_Input_Rep1

description: barcode: NNNNACGTNN


title: S. carpocapsae RNA IJ rep 2

description: first-strand, single-end, read_length= 50 bp

organism: Steinernema carpocapsae

value: ALL strain


title: S. carpocapsae RNA L1 rep 2


title: S. carpocapsae RNA young adult rep 1


title: S. carpocapsae RNA L1 rep 1


title: H3K4me3, untreated

description: ChIP DNA

source_name: ESC, H3K4me3, untreated

tag: passage


title: S. feltiae RNA embryo rep 1

source_name: whole organism


title: p53-/-, untreated

description: RNA with Poly A tail

data_processing:
Base calling: RTA 1.12.4.2 (performed at the Next Generation Sequencing Facility at the Center for Cancer Research at the National Cancer Institute)
Alignment and filtering: CASAVA-1.8.1 (performed at the Next Generation Sequencing Facility at the Center for Cancer Research at the National Cancer Institute)
Re-analyzing: Tophat (v2.0.5) with parameters: /usr/local/tophat/bin/tophat -r 230 -o
Generation of normalized abundance measurements: After obtaining the aligned bam files, the Cufflinks algorithm was used to calculate FPKM with a .gft file for Refseq transcripts downloaded in May 07, 2014.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reports FPKMs

source_name: embryonic stem cells

extract_protocol:
RNAs were extracted using the GenElute Mammalian total RNA Miniprep kit (Sigma, Cat: RTN350-1kt).
TruSeq Exome Enrichment Kit-24 Catalog (FC-121-1024) with Illumina TruSeq PE Cluster kit v3-HS & TruSeq SBS kit v3-HS

tag: cell culture

tag: agent

value: untreated


title: WT_Input_Rep3

description: barcode: NNNNGTCANN

tag: enrichment


title: p53-/-, Adriamycin

description: RNA with Poly A tail

value: Adriamycin


title: WT_Pulldown_Rep2

description: barcode: NNNNCTAGNN


title: WT_Pulldown_Rep3

description: barcode: NNNNAGTCNN


title: H2O2_Pulldown_Rep2

description: barcode: NNNNGTCANN

treatment_protocol: Cells were incubated with Hydrogen peroxide (50 uM) for 30min


title: WT_Input_Rep2

description: barcode: NNNNACTGNN


title: p53+/+, Adriamycin

description: RNA with Poly A tail

value: embryonic stem cells


title: p53+/+, untreated

description: RNA with Poly A tail

value: less than 20 passages


title: S. carpocapsae RNA young adult rep 2


title: S. carpocapsae RNA embryo rep 1


title: RNA PolII_ChIPseq

tag: antibody

value: RNA PolII

tag: antibody catalog

value: Abcam ab5095


title: FOXO1_ChIPseq

tag: cell type


title: WT_Input_Rep1

description: barcode: NNNNCGATNN


title: S. carpocapsae RNA IJ rep 1


title: S. carpocapsae RNA embryo rep 2


title: KO_Ctrl_Pulldown_Rep2

description: barcode: NNNNGATCNN


title: WT_Pulldown_Rep1

description: barcode: NNNNTCGANN


title: tagged-908_S4

tag: mescs


title: H2O2_Pulldown_Rep1

description: barcode: NNNNACTGNN

tag: treatment


title: H2O2_Input_Rep2

description: barcode: NNNNCTAGNN


title: Sample_LSD18a_SH-SY5Y_B0_S56

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

description: LSD1+8a ChIP-seq is done in SH-SY5Y infected control shRNA at B0

data_processing:
base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-1.0.0
peaks were called using macs14 with the following setting:--pvalue=1e-5
Genome_build: hg19
Supplementary_files_format_and_content: txt and peak list; bedgraph files.

source_name: Cultured SH-SY5Y cells

growth_protocol: SH-SY5Y were maintained in Dulbecco's Modified Eagle Medium (DMEM) containing 4,500 mg/L glucose, 10% heat-inactivated fetal bovine serum, 110 mg/L sodium pyruvate, 2 mM L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature before termination with 0.125 M glycine. Cells were then lysed in ChIP buffer (0.6% SDS, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) and cross-linked chromatin was sonicated to obtain DNA fragments of 300–800 bp. Immunoprecipitations were performed following the Upstate protocol (http://www.upstate.com). DNA was recovered by phenol-chloroform extraction and ethanol precipitation.
ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6000) and the protocol and reagents concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads.

treatment_protocol: SH-SY5Y cells were seeded onto collagen-coated plates at an initial density of 104 cells/cm2. Retinoic acid (RA) (Sigma) was added at a final concentration of 10 μM the next day after plating. After 4 days, the cells were washed three times with PBS and incubated with 50 ng/mL of Brain Derived Neural Factor (BDNF) (Millipore) in serum-free medium for 3 days.

value: Homemade polyclonal antibody against LSD1+8a

tag: infection

value: control shRNA

tag: neuronal maturation


title: Stress_Ctrl_Pulldown_Rep2

description: barcode: NNNNAGTCNN

tag: cell line

value: human embryonic kindey cells


title: Sample_SVIL_SH-SY5Y_B3

description: SVIL ChIP-seq is done in SH-SY5Y infected control shRNA at B3

value: SVIL (S8695; Sigma)


title: Sample_LSD18a_shLSD18a_B3_S60

description: LSD1+8a ChIP-seq is done in SH-SY5Y infected LSD1+8a shRNA at B3

value: LSD1+8a shRNA


title: H2O2_Input_Rep1

description: barcode: NNNNTCGANN


title: HS_Input_Rep1

description: barcode: NNNNGACTNN

treatment_protocol: cells were incubated at 42°C for 8 hours

value: mild heat shock


title: HS_Pulldown_Rep2

description: barcode: NNNNTAGCNN

value: N3-CMC treat and pull down


title: IgG_ChIPSeq

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to human genome hg19 using bowtie 1.0 with n = 1 and m = 3
Peaks were called using MACS (p = 10e-4) within the Cistrome Platform
The wiggle file has been created in the Cistrome platform using MACS
Genome_build: hg19
Supplementary_files_format_and_content: wiggle
Supplementary_files_format_and_content: called peaks

growth_protocol: PC3 cells were cultured in DMEM, supplemented with 10% FCS and Penicillin/Streptavidin.

extract_protocol:
Genomic DNA were extracted using ALKBH3 or IgG antibodies and subsequent purified.
Libraries were constructed of 50 ng of ChIP DNA following Illumina’s® protocol

treatment_protocol: For ChIP cells were crosslinked with 1% formaldehyd for 10 min and sonicated to 200 bps.

tag: chip antibody

value: IgG Abcam (#ab37415)


title: Sample_LSD1_SH-SY5Y_B3

description: LSD1 ChIP-seq is done in SH-SY5Y infected control shRNA at B3

value: LSD1 (ab-17721; Abcam)


title: Sample_LSD1_SH-SY5Y_B0_S63

description: LSD1 ChIP-seq is done in SH-SY5Y infected control shRNA at B0


title: HS_Input_Rep2

description: barcode: NNNNAGTCNN


title: ALKBH3_ChIPSeq

value: ALKBH3 Millipore (#09-882)


title: Sample_LSD1_shLSD18a_B0_S57

description: LSD1 ChIP-seq is done in SH-SY5Y infected LSD1+8a shRNA at B0


title: Sample_LSD18a_SH-SY5Y_B3

description: LSD1+8a ChIP-seq is done in SH-SY5Y infected control shRNA at B3


title: Stress_Ctrl_Input_Rep2

description: barcode: NNNNGACTNN


title: Sample_Input_SH-SY5Y_B0_S53

description: input


title: Input

data_processing:
50-nt sequence reads identified by the Sequencing Service (using Ilumina's Hi-seq)
reads mapped to the genome using the BWA algorithm with default settings
tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp
density of fragments, in 32-nt bins divided genome, defined in BAR files
peaks were defined using MACS at the default settings
Genome_build: GRCh37.p2-Primary Assembly

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3 -ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-300 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on GA2 (GAII).

value: primary cells

value: healthy, proliferative phase


title: FOSL2_ChIPseq


title: Stress_Ctrl_Input_Rep1

description: barcode: NNNNTCGANN


title: Sample_LSD18a_shLSD18a_B0_S58

description: LSD1+8a ChIP-seq is done in SH-SY5Y infected LSD1+8a shRNA at B0


title: Stress_Ctrl_Pulldown_Rep1

description: barcode: NNNNCTAGNN


title: Sample_Input_shSVIL_B3_S61

description: input

value: SVIL shRNA


title: Sample_SVIL_shSVIL_B3_S62

description: SVIL ChIP-seq is done in SH-SY5Y infected SVIL shRNA at B3


title: PGR_ChIPseq

value: PGR


title: Sample_H3K9me2_SH-SY5Y_B3_S31

description: H3K9me2 ChIP-seq is done in SH-SY5Y infected control shRNA at B3

value: H3K9me2 (ab-1220; Abcam)


title: Sample_H3K9me2_SH-SY5Y_B0_S27

description: H3K9me2 ChIP-seq is done in SH-SY5Y infected control shRNA at B0


title: HS_Pulldown_Rep1

description: barcode: NNNNCGATNN


title: Sample_Input_shLSD18a_B3_S59

description: input


title: Sample_H3K9me2_Input_SH-SY5Y_B3_I19

description: input


title: AM15537_Scc1-6HA_2hrNocodazole_scc4-m35::HIS3_IP

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
AM15537 Scc1 6HA 2hrNocodazole scc4 m35 IP
Sample 9 (VM9)

data_processing:
Mapper: BWA Version: 0.6.1-r104
RPM scaling, bedgraph creation and bed intersections: bedtools v2.16.2
additional scripts:https://github.com/AlastairKerr/Hindshaw2015
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: scaled to reads per million mapped reads

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were arrested in G1 with α-factor and synchronously released in medium containing nocodazole and benomyl for 2 hrs to depolymerize microtubules and induce a metaphase arrest.

extract_protocol:
Anti-FLAG ChIP was performed and both input and IP samples were sequenced.
All samples were prepared using a liquid handling robot (Hamilton) by Bianka Baying (EMBL, Heidelberg, Germany). 10ng of each sample mixed with library preparation were assessed according to manufacturer's recommendation (NEBNext Ultra™ DNA Library Prep Kit for Illumina, (#E7370S/L)). Library preparation was done according to manufacturer. Briefly, the Adapter in the Adapter Ligation step was diluted 1:30 in water. The size selection step was performed with Ampure XP Beads from Beckman Coulter (insert size 200-250bp). The PCR amplification was performed in 15 cycles. Finally NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (#E7335S/L) were used for the Indexing. The quality and quantity of the libraries was checked using the Agilent BioAnalyzer and the Qubit dsDNA HS Assay kit (Invitrogen).  ChIP-Seq was performed using Illumina HiSeq 2000 Sequencer with Requested Read Length HiSeq50 SE.

treatment_protocol: Samples of wild type (AM15307) and mutant cells (AM15311) were fixed in formaldehyde for 2h before harvesting.

tag: labeled protein

tag: strain

tag: genotype

tag: chip-antibody

value: Anti-HA (12CA5) (Roche)


title: AM15540_Scc1-6HA_2hrNocodazole_SCC4::HIS3_IP

description:
AM15540 Scc1 6HA 2hrNocodazole SCC4 HIS3 IP
Sample 10 (VM10)

value: wildtype


title: Sample_Input_shLSD18a_B0_S54

description: input


title: Sample_H3K9me2_shLSD18a_B0_S29

description: H3K9me2 ChIP-seq is done in SH-SY5Y infected LSD1+8a shRNA at B0


title: Sample_H3K9me2_Input_shLSD18a_B3_I20

description: input


title: AM1145_Scc1-6HA_2hrNocodazole_IP

description:
AM1145 Scc1 6HA 2hrNocodazole IP
Sample 8 (VM8)


title: Sample_H3K9me2_shLSD18a_B3_S33

description: H3K9me2 ChIP-seq is done in SH-SY5Y infected LSD1+8a shRNA at B3


title: Sample_H3K9me2_Input_shLSD18a_B0_I18

description: input


title: AM1145_Scc1-6HA_2hrNocodazole_Input

description:
AM1145 Scc1 6HA 2hrNocodazole input
Sample 5 (VM5)


title: AM15537_Scc1-6HA_2hrNocodazole_scc4-m35::HIS3_Input

description:
AM15537 Scc1 6HA 2hrNocodazole scc4 m35 input
Sample 6 (VM6)


title: Sample_H3K9me2_Input_SH-SY5Y_B0_I17

description: input


title: by_chx_2_r

status: Public on Jun 04 2015

city: Heidelberg

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

institute: EMBL Heidelberg

description: processed data file: by_chx_r.txt

data_processing:
Base-calling was done during processing of sequencing data with the illumina pipeline casava v1.8.2
Random barcode was extracted for each read
Reads were mapped to a merged genome (S. cerevisiae genome (SGD R64-1-1), S. pombe ASM294v2.20 and IVT sequences) using the Novoalign software with default settings
Reads with multiple alignments, or mapping quality <30, or carrying soft-clipped bases on the 5’ end were excluded from downstream analysis
5' end of reads passing quality filtering were extracted; total number of reads per genome location were calculated; total unique number of reads (or unique molecule, based on random barcode sequences) per genome location were calculated
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3), downloaded from SGD(http://www.yeastgenome.org/). Schizosaccharomyces pombe reference genome ASM294v2.20, downloaded from pombase.org (http://www.pombase.org/).
Supplementary_files_format_and_content: Processed data contain the  genomic location of the identified unique identified molecules after controlling for presence of molecular barcodes (unum) and reads per million (rpm) for each biology replicate.

growth_protocol: Strains were grown to mid-log phase (OD~1) at 30ºC. S. cerevisiae was gown in YPD (1% yeast extract, 2% peptone, 2% glucose), Complete Synthetic Media (SD) or Synthetic Media without Histidine (SD-His) S. pombe (h-) was grown  using YES media (0.5% yeast extract, 3% glucose, supplemented with 225 mg/l of adenine, histidine, leucine, uracil and lysine hydrochloride).

extract_protocol:
All  samples were collected by centrifugation and frozen in liquid N2. Total RNA was isolated by a standard hot phenol method and treated with RNase-free DNaseI using Turbo DNA-free kit (Ambion)
We used 10-100 µg of DNA-free total RNA as starting material. As an internal control, we added polyadenylated in vitro transcripts (ATCC 87482, 87483 and 87484, that were modified to be enriched respectively in 5?cap, 5?PPP or 5?P ends) and S. pombe RNA. For 5?P sequencing (5PSeq), samples were directly subjected to RNA ligation. To generate a negative control of 5?P molecules (5PSeq-fragmented) RNA sample was chemically fragmented by incubating the samples at 80ºC for 5 min in the presence of RNA fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc). Fragmented 5?OH sites were then phosphorilated by treatment with 5 unit of T4 Polynucleotide Kinase (T4 PNK, NEB) for 1 hour at 37ºC in the presence of RNase inhibitor (RNasin +, Promega). The sample was phenol:chloroform purified and ethanol precipitated and subjected to RNA ligation. From the ligation step we used the same protocol all the methods. The treated RNA sample was incubated overnight at 16ºC with 20 units of T4 RNA ligase 1 (NEB) in the presence of 10 mM DNA/RNA rP5_RND oligo (CTTTCCCTACACGACGCTCTTCCGATrCrUrNrNrNrNrNrNrNrN). RNA integrity was controlled by RNA Bioanalyzer and then polyA purified using Oligotex (Quiagen) according to manufacturer?s instructions. For the ribosomal depleted samples (5µg total RNA), polyA purification was substituted by treatment with Ribo-Zero Magnetic Gold Kit (Epicentre). PolyA enriched RNA was fragmented at 80ºC for 5 min in the presence of RNA fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc). RNA was retrotranscripted with Superscript II (Life Technologies) and primed with random hexamers. The retrotranscription reaction was incubated for 10 minutes at 25ºC, 5 minutes at 42ºC and heat inactivated for 15 minutes at 72ºC. Second cDNA strand was perform by a unique cycle of PCR (1 min at 98ºC; 2 min at 50ºC and 15 at 72ºC) using Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) and priming with BioNotI-P5-PET (Biotin-TATAGCGGCCGCAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT). From this point libraries were generated as previously described (PMID:23295673). Briefly double stranded cDNA was first purified using HighPrep beads (Magbio) and then bound to Dynabeads M-280 Streptavidin beads (Life Technologies) according to manufacturers instructions. Bound DNA molecules were successively washed and subjected to Ends repair, A addition and adaptor ligation using Nebnext DNA Library Prep Master Mix (NEB). 0.5µL of common adapter (2.5µM) was ligated to each sample. The common adapter was prepared by annealing P7MPX_linker_for and P7MPX_linker_rev. Beads were washed and subjected to PCR amplification (30s 96ºC; 15-18 cycles (30s 96ºC; 30s 65ºC; 30s 72ºC); 5min 72ºC) using Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) and 0.1µM final of PE1.0 and the appropriate indexed PE2_MTX PCR oligo. Sample was size selected using 0.6x-0.9x (v/v) HighPrep beads (Magbio) to 300-500 bp. Libraries were sequenced (single-end) using either an Illumina HiSeq 2000 or a MiSeq. The first experiments were indexed adding a barcoded P7 linker (as in PMID:23295673) and subjected to a paired-end sequencing where first read contains the 8nt molecular barcode followed by the 5?sequence and the reverse read contains a 6 nt index followed by and A and the reverse complementary sequence of the identified transcripts.

treatment_protocol: For cycloheximide (CHX) treatment, CHX was added to 0.1mg/mL final and incubated 5 min at 30ºC. For S. pombe cells CHX was incubated either 5 or 30 min. When combining CHX treatment with H2O2 stress (final 0.2mM H2O2), samples were transferred to watery ice at the specified stress time points and incubated for extra 5 min at 4ºC in presence of 0.1mg/mL CHX final. For 3-amino-1,2,4-triazole (3-AT) treatment S96 strain (MATa lys5∆ gal2∆, S288c background) was grown in CSM-His to mid-log phase (OD600~1). Cells were diluted to OD600~0.15 in either CSM-His (control) or CSM-His + 100mM 3-AT (treated) and harvested at OD600~0.5. For polyribosome fractionation yeast cells were incubated for 5 min with CHX at 0.1mg/mL final and then broken with glass beads using a FastPrep machine in presence of Lysis buffer (20 mM Tris-HCl pH 8, 140 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 100µg/mL CHX, 500µg/mL heparin and supplemented with EDTA-free Complete protease inhibitor). Fractions were separated by ultracentrifugation (2h 40min at 88244 g) using a 10-50% sucrose gradient, the presence of RNA was estimated by measuring Abs at 254 nm.

tag: strain background

tag: genotype/variation

value: wild type

value: Mat a; his3delta1leu2delta0 ura3delta0 met15delta0

tag: protocol

value: 5PSeq-ribosome depleted

tag: spike-in

value: IVTs

tag: growth/culture condition

value: 5 min CHX treatment


title: AM15540_Scc1-6HA_2hrNocodazole_SCC4::HIS3_Input

description:
AM15540 Scc1 6HA 2hrNocodazole SCC4 HIS3 input
Sample 7 (VM7)


title: Sample_H3K9me2_SH-SY5Y_D0_S23

description: H3K9me2 ChIP-seq is done in SH-SY5Y infected control shRNA at D0

tag: antibody

value: control shRNA


title: by_chx_1_r

description: processed data file: by_chx_r.txt


title: rny1_H2O2_1_p

description: processed data file: rny1_H2O2_p.txt

value: MATa; rny1delta::kanMX4

value: 5 min H2O2 stress


title: rny1_H2O2_2_p

description: processed data file: rny1_H2O2_p.txt


title: by_ypd_1_r

description: processed data file: by_ypd_r.txt

value: grown in YPD


title: by_ypd_2_r

description: processed data file: by_ypd_r.txt


title: rny1_ypd_2_p

description: processed data file: rny1_ypd_p.txt


title: rny1_ypd_1_p

description: processed data file: rny1_ypd_p.txt


title: Sample_H3K9me2_Input_SH-SY5Y_D0_I15

description: input


title: CA923

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and ht-seq-count.
Non-protein coding and mitochondrial genes were filtered out.
Samples were selected for further analysis by using these criteria: unpaired reads examined/FASQ total read >0.75 and median CV coverage <1. Samples that had total counts less than one million were excluded.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh38
Supplementary_files_format_and_content: (1) mexico_processed_data_for_GEO.csv: comma-separated matrix – first 6 columns contain Ensembl gene ID, Ensembl transcript ID, HGNC symbol, location information and chromosome name, remaining columns include read counts assigned for each library; data represents all processing steps up to and including "sample QC and filtering" but not downstream processing/normalization for analysis. (2) mexico_combined_metrics.csv: comma-separated matrix – the first column contains library ID, remaining columns include RNA sequencing and alignment metrics.

source_name: children with diarrhea_Shigella

extract_protocol:
Total RNA was isolated using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Ambion, TX) and RNA sample was globin reduced wit GLOBINclear (Ambion, TX) according to manufacturer’s instructions.
Libraries were prepared from globin reduced RNA samples using the Illumina TrueSeq RNA Sample Preparation kit according to manufacturer's instructions.

tag: age

value: 2 year-old or older

tag: group

value: Diarrhea

tag: organisms

value: Shigella

tag: severity

value: severe

tag: tissue

value: Whole blood

tag: flowcell

value: B

tag: lane


title: CA922

value: mild


title: CA905

value: A


title: by_stat_2_p

description: processed data file: by_stat_p.txt

value: wild type

value: grown in YPD to stationary phase


title: CA900

value: moderate


title: by_stat_1_p

description: processed data file: by_stat_p.txt

value: Mat a; his3delta1leu2delta0 ura3delta0 met15delta0

value: IVTs


title: CA898


title: CA891


title: CA879


title: CA877


title: CA893

value: <2 year-old


title: by_H2O2_1_f

description: processed data file: by_H2O2_f.txt, pomb_f.txt

source_name: negative control H2O2 stress; paired-end library

value: S. Pombe + IVTs

tag: media

value: YPD


title: CA876


title: CA781


title: by_YPD_1_f

description: processed data file: by_YPD_f.txt, pomb_f.txt

source_name: negative control; paired-end library

tag: strain


title: by_YPD_2_f


title: CA821


title: CA863


title: by_H2O2_2_f


title: CA561


title: CA543


title: CA524


title: CA584


title: CA473


title: CA454


title: CA536


title: CA448


title: pomb_chx_2_f

description: processed data file: pomb_fraN.txt

organism: Schizosaccharomyces pombe

value: h-

value: negative control pombe CHX treated 30 min


title: by_mono_1_p

description: processed data file: by_mono_p.txt

source_name: monosome fraction; paired-end library


title: CA438

value: 2 year-old or older

value: Diarrhea


title: by_mono_2_p

description: processed data file: by_mono_p.txt


title: CA434

value: Shigella


title: CA323

value: Whole blood


title: pomb_chx_1_p

description: processed data file: pomb_chxN.txt

value: pombe CHX treated 30 min


title: pomb_chx_2_p

description: processed data file: pomb_chxN.txt


title: pomb_chx_1_f

description: processed data file: pomb_fraN.txt


title: CA330


title: CA236

value: mild


title: CA205

value: A


title: CA120


title: by_poly_1_p

description: processed data file: by_poly_p.txt

source_name: polyribosome fraction; paired-end library


title: by_H2chxt30_2_p

description: processed data file: by_H2chxt30_p.txt

source_name: 30 min H2O2 stress + CHX at 4ºC; single-end read


title: CA059


title: S96_3AT_1_p

description: processed data file: S96_3AT_p.txt

source_name: 3AT treatment;  single-end read

value: MATa; lys5delta gal2delta, S288c background


title: CA275

value: severe


title: CA042

value: moderate


title: CA919

source_name: children with diarrhea_Salmonella

value: Salmonella

value: B


title: CA077

value: <2 year-old


title: CA159


title: CA895


title: CA062


title: CA185


title: by_H2chxt5_2_p

description: processed data file: by_H2chxt5_p.txt

source_name: 5 min H2O2 stress + CHX at 4ºC; single-end read

value: Mat a; his3delta1leu2delta0 ura3delta0 met15delta0

value: IVTs


title: CA881


title: by_H2chxt30_1_p

description: processed data file: by_H2chxt30_p.txt

value: YPD


title: by_H2chxt5_1_p

description: processed data file: by_H2chxt5_p.txt


title: by_chxt0_1_p

description: processed data file: by_chxt0_p.txt

source_name: no H2O2 stress + CHX at 4ºC; single-end read


title: S96_sdh_1_p

description: processed data file: S96_sdh_p.txt

source_name: SD-His growth; single-end read

value: SD-His


title: S96_sdh_2_p

description: processed data file: S96_sdh_p.txt


title: CA888


title: CA878


title: CA712


title: CA807


title: CA545

value: 2 year-old or older


title: CA672

value: Diarrhea


title: CA119

value: Shigella


title: CA682

value: Whole blood


title: CA661


title: CA531


title: xrn_ypd_2_p

description: processed data file: xrn_ypd_p.txt, pomb_p.txt

source_name: xrn1 deletion; same paired-end library in 3 lanes

value: MATa; xrn1delta::kanMX4, BY4741 background

value: S. Pombe + IVTs


title: xrn_ypd_1_p


title: by_sd_2_p

description: processed data file: by_sd_p.txt, pomb_p.txt

source_name: grown in SD; same paired-end library in 3 lanes

value: SD complete


title: by_sd_1_p


title: CA527

value: A


title: by_chx_2_p

description: processed data file: by_chx_p.txt, pomb_p.txt

source_name: 5 min CHX treatment; same paired-end library in 3 lanes


title: CA392

value: mild


title: CA499


title: by_chxt0_2_p

description: processed data file: by_chxt0_p.txt


title: CA447


title: CA476


title: CA710


title: CA394

value: moderate


title: by_H2O2_2_p

description: processed data file: by_H2O2_p.txt, pomb_p.txt

source_name: 5 min H2O2 stress; same paired-end library in 3 lanes


title: CA334

value: Salmonella


title: CA341


title: by_H2O2_1_p


title: CA314


title: CA307


title: CA285


title: by_YPD_2_p

description: processed data file: by_YPD_p.txt, pomb_p.txt

source_name: grown in YPD; same paired-end library in 3 lanes


title: CA268


title: by_YPD_1_p


title: CA456

value: severe


title: by_chx_1_p


title: pomb_chxt0_2_p

description: processed data file: pomb_chx_p.txt

source_name: pombe CHX treated; single-end read

value: h-

value: Schizosaccharomyces pombe (h-)

value: YES


title: CA131

value: <2 year-old


title: CA108


title: CA098


title: CA081


title: CA057


title: CA055


title: CA858

source_name: children with diarrhea_Rotavirus

value: Rotavirus


title: CA864

value: 2 year-old or older


title: CA857

value: Diarrhea


title: CA851


title: CA850


title: CA844


title: CA848


title: CA845


title: CA842


title: CA841


title: CA840


title: CA839


title: CA838


title: CA076


title: CA266


title: CA831


title: CA826


title: CA828


title: CA829


title: CA824


title: pomb_chxt0_1_p

description: processed data file: pomb_chx_p.txt

value: IVTs


title: CA114

value: Whole blood


title: CA832


title: CA867


title: CA820


title: CA817


title: CA808


title: CA810


title: CA814


title: CA279


title: CA804


title: CA789


title: CA793


title: CA784


title: CA779


title: CA785


title: CA774


title: CA787


title: CA818


title: CA773


title: CA815


title: CA760


title: CA771


title: CA758


title: CA756


title: hlh30_OP50_rep2

city: Boston

first: Javier

last: Irazoqui

address: 55 Fruit Street, GRJ802

department: Center for the Study of Inflammatory Bowel Disease

institute: Massachusetts General Hospital, Harvard Medical School

description:
Sample 3_rep2
hlh30_OP50

data_processing:
TopHat alignment to genome
Single-read 1x49-bp sequencing was performed on the Illumina platform to yield 49 bp-long barcoded reads, with 7 bases designated to distinguish between the eight samples in the pool (see Table S1).  After removing barcodes, raw 42-bp reads were aligned to the WS190 (ce6) assembly of the C. elegans genome (both gene transfer format files for protein-coding genes and RNA genes were downloaded from the UCSC Browser) using TopHat (Trapnell et al., 2012). Transcript abundance on a per-gene basis was estimated and normalized as FPKMs (Mortazavi et al., 2008) using Partek® software (version 6.3 Copyright © 2008 Partek Inc., St. Louis, MO, USA).  We used DESeq (Anders and Huber, 2010) to determine S. aureus - induced genes/transcripts, retaining those that were significantly induced in infected vs. uninfected wild type animals, at p ≤ 0.05 after multiple test correction (See Table S2).
Genome_build: WS190
Supplementary_files_format_and_content: FPKMs with expression values for each isoform

source_name: whole organism

growth_protocol: Animals were synchronized by egg prep with bleach, and allowed to grow at 20 C until the young adult stage on NGM plates seeded with E. coli OP50

extract_protocol:
After 8 h incubation at 25 °C, S. aureus infected and HK E. coli uninfected animals were washed twice in water and lysed by resuspension in Tri Reagent (Molecular Research Center).
After purification, RNA was reverse transcribed as described in the Experimental Procedures and analyzed by qPCR or by sequencing.  Two independent replicate sample sets were submitted for pooled sequencing at the Genome Technology Access Center at Washington University in St. Louis.

treatment_protocol: To prepare infection plates, S. aureus NCTC8325 was grown overnight (ON) in tryptic soy broth (TSB, BD) with 10 μg/ml nalidixic acid (NAL, Sigma).  500 μl of the ON culture was uniformly spread onto the entire surface of 10 cm tryptic soy agar plates (TSA, BD) supplemented with 10 μg/ml NAL and incubated 6 h at 37 °C, then stored at 4 °C overnight.  To prepare control plates, 500 μl of heat-killed (HK) E. coli OP50 culture concentrated 10X was plated on TSA + NAL plates. Synchronized wild type and hlh-30 young adults were seeded the next day on infection and control plates that were previously warmed to room temperature

value: hlh-30(-) mutant

tag: infection

value: OP50 e-coli (normal feed)


title: N2_OP50_rep2

description:
Sample 1_rep2
N2_OP50

value: WT (N2)


title: CA812

value: A


title: CA755


title: N2_SA_rep2

description:
Sample 2_rep2
N2_SA

value: S. aureus


title: CA805

value: mild

value: B


title: hlh30_SA_rep1

description:
Sample 4_rep1
hlh30_SA


title: hlh30_OP50_rep1

description:
Sample 3_rep1
hlh30_OP50


title: CA751


title: CA750

value: moderate


title: CA754


title: CA688


title: CA686


title: hlh30_SA_rep2

description:
Sample 4_rep2
hlh30_SA


title: N2_SA_rep1

description:
Sample 2_rep1
N2_SA


title: N2_OP50_rep1

description:
Sample 1_rep1
N2_OP50


title: CA769


title: CA629


title: CA768

value: severe


title: CA622


title: CA602


title: CA595


title: CA683

source_name: children with diarrhea_EPEC

value: EPEC


title: CA615


title: CA616