title: HTGTS_PI3K-WT rep3

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells. 24 h post activation cells were co-transduced with pMX-I-SceI retrovirus to induce double strand breaks and PI3K p110delta WT retrovirus as positive control.

value: c-myc 25xI-SceI WT


title: Alveolar EpCAM pos 1

status: Public on Jan 31 2017

type: SRA

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were aligned to the mouse genome by Rsubread version 1.22.2
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

molecule: total RNA

organism: Mus musculus

source_name: normal lung tissue

extract_protocol:
FACS sorted cells were lysed for RNA preparation using QIAGEN RNAeasy micro-kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: mouse

tag: cell type

value: Alveolar cells

tag: facs gate

value: EpCAM pos CD104 lo 1


title: GRO-Seq_Duvelisib rep2

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

country: USA

institute: Children’s Hospital Boston and Harvard Medical School

data_processing:
GRO-seq data were aligned using Bowtie to mouse reference genome (GRCm37/mm9). Uniquely mapped, nonredundant sequence reads were retained. Next, we used HOMER software to count reads and calculate the nascent RNA expression levels as RPKM in whole genes or in focal translocation clusters, and to identify transcripts from both strands of chromosomes. The ConvT region was defined as sense and antisense transcription overlaps that were longer than 100 bp. Statistical analysis for differential expression and log fold-change calculation were performed using DESeq2 in whole genes or in focal translocation clusters.
Genome_build: mm9
Supplementary_files_format_and_content: For GRO-Seq data, tab-delimited text files generated by HOMER present raw counts of sequencing reads for each reference gene.

source_name: CSR activated B cells

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were further activated  with anti-CD40 plus IL-4, and treated with duvelisib. Cells were kept in culture for 2 days.

extract_protocol:
GRO-Seq: BrU labelled nascent transcripts were extracted with Tripure reagent and affinity purified with anti-BrU antibody conjugated agarose beads.
GRO-Seq libraries were prepared as previously described by Core et al., Science 2008.

treatment_protocol: 1 micromolar Duvelisib

tag: tissue

value: spleen

tag: age

value: 8-12 weeks

tag: genotype

value: WT

value: splenic B cells activated with anti-CD40 plus IL-4 for 2 days

tag: treatment

value: duvelisib


title: GRO-Seq_Idelalisib rep1

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were further activated  with anti-CD40 plus IL-4, and treated with idelalisib. Cells were kept in culture for 2 days.

treatment_protocol: 1 micromolar Idelalisib

value: idelalisib


title: GRO-Seq_Duvelisib rep1


title: GRO-Seq_DMSO rep1

data_processing:
GRO-seq data were aligned using Bowtie to mouse reference genome (GRCm37/mm9). Uniquely mapped, nonredundant sequence reads were retained. Next, we used HOMER software to count reads and calculate the nascent RNA expression levels as RPKM  in whole genes or in focal translocation clusters, and to identify transcripts from both strands of chromosomes. The ConvT region was defined as sense and antisense transcription overlaps that were longer than 100 bp. Statistical analysis for differential expression and log fold-change calculation were performed using DESeq2 in whole genes or in focal translocation clusters.
Genome_build: mm9
Supplementary_files_format_and_content: For GRO-Seq data, tab-delimited text files generated by HOMER present raw counts of sequencing reads for each reference gene.

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were further activated  with anti-CD40 plus IL-4, and treated with the control DMSO. Cells were kept in culture for 2 days.

treatment_protocol: 1 micromolar DMSO

value: DMSO


title: GRO-Seq_DMSO rep2


title: HTGTS_PI3K-WT rep1

library_source: genomic

data_processing:
For HTGTS data, we applied prinseq 0.2 to remove sequences with exact PCR duplicates, mean quality score < 20 and length < 50. Next, effect reads for each sample were recognized by designed barcode, primer and bait portion. Lastly,the barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions as previously described(Chiarle et al.,Cell 2011). Briefly, we aligned sequences to the mouse reference genome (GRCm37/mm9) or human genome (GRCh38/hg38) using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
Genome_build: mm9
Supplementary_files_format_and_content: For HTGTS data, BED files contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.

molecule: genomic DNA

extract_protocol:
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%)  containing 10 μg/ml Proteinase K  at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA)
See Supplemental Experimental procedures from Chiarle et al.  Cell 2011, paragraph Generation of HTGTS libraries by adapter-PCR.

treatment_protocol: not applicable

value: splenic  B cells activated with anti-CD40 plus IL-4 for 4 days


title: HTGTS_PI3K-WT rep2


title: GRO-Seq_Idelalisib rep2

value: idelalisb


title: RA.Sarc.Cont microbiome seq_58 pooled samples

city: New York

first: Leopoldo

middle: Nicolas

last: Segal

state: NY

address: 462 First Avenue NBV 6N5-6N8

department: Medicine

institute: NYU School of Medicine

description: ribosomal DNA

data_processing:
demultiplexing and filtering of short (<150 nt) and low quality reads
de novo clustering of the sequences into operational taxonomic units (OTUs) with the UCLUST program using a 97% similarity threshold
taxonomical assignment of each OTU by running the RDP Classifier(8) at 80% bootstrap confidence on a selected representative sequence from each OTU;
alignment of representative sequences using PyNAST(9) with the Greengenes core-set alignment template
phylogenetic tree reconstruction from the representative sequences for each OTUs using the FASSTTREE program
UniFrac distance calculations
Supplementary_files_format_and_content: abundance measurement

organism: human lung metagenome

source_name: Lung BAL_pooled

extract_protocol:
ion exchange column (Qiagen)
Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25μl reactions with the following reaction conditions: 11μl PCR-grade H2O, 10μl Hot MasterMix (5 Prime Cat# 2200410), 2μl of forward and reversed barcoded primer (5μM) and 2μl template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94°C for 3 min followed by 35 cycles of denaturation at 94°C for 45 seconds, annealing at 58°C for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72°C. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions

tag: disease state

value: RA or sarcoid or Control

value: Lung BAL

tag: barcode sequence

value: provided for each sample in complete_metadata.txt

tag: linkerprimersequence

value: CCGGACTACHVGGGTWTCTAAT


title: HTGTS_KO-Duvelisib rep3

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and simultaneously treated with duvelisib. Cells were transduced with pMX-I-SceI retrovirus to induce double strand breaks 24 h post activation.

treatment_protocol: 1 micromolar duvelisib

value: c-myc 25xI-SceI AID -/-

value: Duvelisib


title: HTGTS_KO-Duvelisib rep2


title: Basal 3

source_name: normal trachea tissue

value: Basal cells

value: NGFR pos 3


title: ArgonLT rep3

city: Emeryville

first: Itay

last: Budin

state: CA

address: 5885 Hollis

institute: UC Berkeley

description: long-term hypoxic exposure

data_processing:
demultiplexed fastq data was trimmed using Trimmomatic 0.33 with parameters ILLUMINACLIP:[Truseq v3 SE adapters for HiSeq data and Truseq v3 PE adapters for MiSeq data] TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:26
reads were aligned against the S. cerevisiae genome using Tophat 2.0.14 with parameters --max-intron-length 2500 -r 0 -G
log2 differential expressions were calculated using cuffdiff version 2.2.1 with parameters -b -u
Genome_build: Saccharomyces_cerevisiae_Ensembl_R64-1-1
Supplementary_files_format_and_content: Cuffdiff-calculated log2 differential expression values (columns C-H) and associated q values (columns J-O) for each gene

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cell pellet

growth_protocol: Growth was performed in CSM as described in the methods section of Degreif, et al. 2017

extract_protocol:
RNA extraction was performed using the hot phenol method; mRNA was isolated using magnetic poly-T beads
Illumina paired libraries were constructed with the NEB Next RNA library kit

treatment_protocol: Cells were grown continuously in the presence or absence of methionine, doxycycline, and hypoxia as described

value: S. cerevisiae S288C

value: background strain (BY4742)

value: Growth in a microfermenter

tag: sample type

value: replicate 3


title: ArgonLT rep2

description: long-term hypoxic exposure

value: replicate 2


title: HTGTS_KO-Duvelisib rep1

value: spleen

value: 8-12 weeks


title: Lgr5+T8-, replicate 2

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

institute: the university of Adelaide

data_processing:
Instrument control: HiSeq control software v2.0.12.0.
Base calling and quality scoring: Illumina RTA 1.13.48.
FASTQ file generation and de-multiplexing: CASAVA pipeline version 1.8.2.
Sequenced reads were mapped using the align function in the Rsubread package (version 1.8.0, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.8.0) using the built-in mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.10.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.24.14, Ritchie et al, NAR, 2015).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: FACS-sorted Lgr5+T8- basal cells from mouse mammary gland

growth_protocol: Basal cells defined by Lgr5 and Tspan8 expression were directly isolated from the mammary glands of 10-week-old Lgr5-GFP-IRES-CreERT2 females.

extract_protocol:
Total RNA from FACS-sorted cells was extracted using the QIAGEN RNeasy micro kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment.

tag: strain/background

tag: genotype/variation

value: 10 weeks

tag: gender

value: female

value: mammary gland

tag: cell population

value: basal

tag: expression

value: FACS-sorted cells

tag: batch

tag: sequencing protocol

value: single-end


title: Lgr5+T8hi, replicate 2

source_name: FACS-sorted Lgr5+T8hi basal cells from mouse mammary gland


title: Basal 2

tag: strain

tag: mouse

tag: cell type

value: NGFR pos 2


title: Lgr5-T8-, replicate 2

source_name: FACS-sorted Lgr5-T8- basal cells from mouse mammary gland

tag: age

tag: tissue


title: HTGTS_KO-Idelalisib rep3

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and simultaneously treated with idelalisib. Cells were transduced with pMX-I-SceI retrovirus to induce double strand breaks 24 h post activation.

tag: genotype

value: c-myc 25xI-SceI AID -/-

value: splenic  B cells activated with anti-CD40 plus IL-4 for 4 days

tag: treatment

value: Idelalisib


title: Lgr5-T8-, replicate 1


title: ArgonLT rep1

description: long-term hypoxic exposure

value: S. cerevisiae S288C

value: replicate 1


title: HTGTS_KO-Idelalisib rep2


title: ArgonST rep3

description: short-term hypoxic exposure

value: background strain (BY4742)

value: Growth under argon for 90 min


title: Lgr5-T8hi, replicate 1

source_name: FACS-sorted Lgr5-T8hi basal cells from mouse mammary gland


title: HTGTS_KO-Idelalisib rep1


title: Lgr5+T8-, replicate 1


title: ArgonST rep2

description: short-term hypoxic exposure

value: replicate 2


title: DP1

city: Qingdao

first: Hualong

last: Wang

address: Songling road

country: China

institute: Ocean University of China

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Skeletonema marinoi

source_name: phytoplankton cell

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.   RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA).   RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).   RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment/phase

value: declining phase

tag: location

value: Jiaozhou Bay


title: ArgonST rep1

description: short-term hypoxic exposure

tag: sample type


title: HTGTS_KO-DMSO rep3

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and simultaneously treated with control DMSO. Cells were transduced with pMX-I-SceI retrovirus to induce double strand breaks 24 h post activation.

value: spleen

value: 8-12 weeks

value: DMSO


title: Lgr5-T8hi, replicate 2

tag: strain/background

value: 10 weeks

value: female

value: mammary gland

value: basal


title: HTGTS_KO-DMSO rep2

value: c-myc 25xI-SceI AID -/-


title: BY rep2

description: Aerobic reference

value: aerobic growth


title: HTGTS_KO-DMSO rep1

extract_protocol:
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%)  containing 10 μg/ml Proteinase K  at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA)
See Supplemental Experimental procedures from Chiarle et al.  Cell 2011, paragraph Generation of HTGTS libraries by adapter-PCR

value: splenic  B cells activated with anti-CD40 plus IL-4 for 4 days


title: HTGTS_Ibrutinib rep3

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and simultaneously treated with ibrutinib. Cells were transduced with pMX-I-SceI retrovirus to induce double strand breaks 24 h post activation.

treatment_protocol: 1 micromolar ibrutinib

value: c-myc 25xI-SceI WT

value: Ibrutinib


title: Lgr5+T8hi, replicate 1

tag: genotype/variation

value: FACS-sorted cells

value: single-end


title: HTGTS_Ibrutinib rep1


title: HTGTS_Ibrutinib rep2


title: HTGTS_Duvelisib rep3

value: Duvelisib


title: HTGTS_Duvelisib rep2


title: mga2p90-dox rep1

description: Reference not expressing processed MGA2 fragment

value: S. cerevisiae S288C

value: with doxycycline (repressed)

value: replicate 1


title: mga2p90-dox rep2

value: replicate 2


title: mga2p90-dox rep3

value: replicate 3


title: mga2p90 rep2

description: Expressing processed MGA2 fragment

value: no doxycycline (unrepressed)


title: HTGTS_Idelalisib rep3

value: spleen

value: 8-12 weeks

value: Idelalisib


title: HTGTS_Duvelisib rep1


title: HTGTS_Idelalisib rep2


title: mga2p90 rep1

description: Expressing processed MGA2 fragment


title: spt23p90-dox rep3

description: Reference not expressing processed SPT23 fragment


title: HTGTS_Idelalisib rep1


title: spt23p90-dox rep2


title: HTGTS_AS-604850 rep2

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and simultaneously treated with AS-604850. Cells were transduced with pMX-I-SceI retrovirus to induce double strand breaks 24 h post activation.

treatment_protocol: 1 micromolar AS-604850


title: HTGTS_AS-604850 rep3


title: spt23p90-dox rep1


title: spt23p90 rep3

description: Expressing processed SPT23 fragment


title: BY rep1

description: Aerobic reference

value: background strain (BY4742)


title: HTGTS_AS-604850 rep1


title: s06-suscep-noninf

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
We mapped reads to human genome hg38 (GRCh38) using Subread (v1.5.0-p2) and discarded non-uniquely mapping reads (flag -u).
We downloaded the exon coordinates of 19,800 Ensembl protein-coding genes (Ensembl 83, Dec 2015, GRCh38.p5) using the R(3.2.1)/Bioconductor(3.2) package biomaRt (2.26.1) and assigned mapped reads to these genes using featureCounts (v1.5.0-p2).
We filtered genes based on their expression level by removing all genes with a transformed median log2 counts per million (cpm) of less than zero. This step resulted in a set of 11,336 genes for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_Data_S1.tds (tab-delimited) contains information on the 50 samples. Most variables describe the batch processing steps. “id” is a unique identifier for each sample, “individual” is the individual identifier (“s” = susceptible, “r” = resistant), “status” is the susceptibility status, “treatment” is if the sample was infected or non-infected, “infection” is the date of the infection experiment (12 total), “arrival” is the identifier for the arrival batch (4 total), “extraction” is the batch for RNA extraction (5 total), “master_mix” is the batch for library preparation (3 total), “rin” is the RNA Integrity Number from the Agilent Bioanalyzer, and “outlier” is a Boolean variable indicating if the sample was identified as an outlier and removed from the analysis.
Supplementary_files_format_and_content: Supplementary_Data_S2.tds (tab-delimited) contains the gene expression counts for the 11,336 genes after filtering lowly expressed genes for all 50 samples. Each row is a gene labeled with its Ensembl gene ID. Each column is a sample. Each sample is labeled according to the pattern “x##-status-treatment”, where x is “r” for resistant or “s” for susceptible, ## is the ID number, status is “resist” for resistant or “suscep” for susceptible, and treatment is “noninf” for non-infected or “infect” for infected.

molecule: polyA RNA

organism: Homo sapiens

source_name: monocyte-derived dendritic cells

growth_protocol: We isolated mononuclear cells from the whole blood samples using Ficoll-Paque centrifugation, extracted monocytes via CD14 positive selection, and differentiated the monocytes into dendritic cells (DCs) by culturing them for 5 days in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FCS (Dutscher), L-glutamine (Invitrogen), GM-CSF (20 ng/mL; Immunotools), and IL-4 (20 ng/mL; Immunotools).

extract_protocol:
We extracted RNA using the Qiagen miRNeasy Kit.
We prepared sequencing libraries using the Illumina TruSeq Kit.

treatment_protocol: We infected the DCs with Mycobacterium tuberculosis (MTB) H37Rv at a multiplicity of infection of 1-to-1 for 18 hours.

value: monocyte-derived dendritic cells

tag: individual

tag: status

value: susceptible

value: non-infected

tag: gender

value: male


title: BY rep3

description: Aerobic reference

value: aerobic growth


title: spt23p90 rep2

description: Expressing processed SPT23 fragment


title: s05-suscep-noninf


title: HTGTS_DMSO rep3

value: c-myc 25xI-SceI WT

value: splenic  B cells activated with anti-CD40 plus IL-4 for 4 days

value: DMSO


title: spt23p90 rep1

description: Expressing processed SPT23 fragment

value: S. cerevisiae S288C


title: HTGTS_DMSO rep1

data_processing:
For HTGTS data, we applied prinseq 0.2 to remove sequences with exact PCR duplicates, mean quality score <  20 and length <  50. Next, effect reads for each sample were recognized by designed barcode, primer and bait portion. Lastly,the barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions as previously described(Chiarle et al.,Cell 2011). Briefly, we aligned sequences to the mouse reference genome (GRCm37/mm9) or human genome (GRCh38/hg38) using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
Genome_build: mm9
Supplementary_files_format_and_content: For HTGTS data, BED files contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.


title: HTGTS_DMSO rep2


title: mga2p90 rep3

description: Expressing processed MGA2 fragment


title: s04-suscep-noninf


title: s04-suscep-infect

value: infected


title: s03-suscep-noninf


title: s02-suscep-noninf


title: s01-suscep-noninf


title: r19-resist-noninf

value: resistant


title: s02-suscep-infect


title: s01-suscep-infect


title: F2 365dpf BPA30 replicate 3

city: Calgary

first: Vijayan

middle: M.

last: Mathilakath

state: Alberta

address: 2500 University drive NW

country: Canada

institute: University of Calgary

description:
Eggs from F1 40 ng BPA Females were fertilized using sperm from non treated males
abundance_F2_365dpf.tabular

data_processing:
Data trimmed and filtered using Illumina base calling software bcl2fastq
Sequence reads were mapped to the sequenced genome of rainbow trout (Berthellot et al. 2014) using Bowtie (2.2.6) with the “very-fast-local” option and Tophat (2.1.0).
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) calculation for each sample was performed using Cufflinks.
Genome_build: Used reference genome of rainbow trout : http://www.genoscope.cns.fr/trout/data/
Supplementary_files_format_and_content: tabular files include FPKM values for each sample of a specific life stage and generation.

organism: Oncorhynchus mykiss

source_name: liver

growth_protocol: Rainbow trout were bred and maintained at the Alma Aquaculture Research Station in a flow-through system receiving water at 8-9°C and fed ad libitum.

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using  the RNeasy Mini Kit (Qiagen, Hilden, Germany). Illumina TruSeq Stranded mRNA Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eggs from four to six  3+-year class rainbow trout females were pooled and equally distributed among three treatment groups, which were exposed to ovarian fluid supplemented with either vehicle (<0.01% ethanol), 3 mg/l BPA or 30 mg/l BPA. The oocytes were incubated for 3 h at 4-6 °C, after which they were fertilized with 1-2 ml milt pooled from 4-6 males from the same brood stock as the females. Water was added to activate the sperm and the embryos were washed with clean water and placed in Heath incubator trays receiving water (6-8 °C) at a rate of 10 l min-1. The subsequent embryos, larvae and adults were never exposed to BPA and were always maintained in clean water that had BPA levels below detection.

tag: generation

tag: days post fertilization

value: 40 ng BPA


title: F2 365dpf BPA30 replicate 2


title: s06-suscep-infect


title: r18-resist-noninf


title: r18-resist-infect


title: r17-resist-noninf


title: F2 365dpf BPA3 replicate 2

description:
Eggs from F1 4 ng BPA Females were fertilized using sperm from non treated males
abundance_F2_365dpf.tabular

value: 4 ng BPA


title: SHM_KO_Smu_DMSO rep3

data_processing:
For SHM data, sequences with mean quality score < 20 and length < 50 were removed. The remained sequences were used to calculate mutation rate. Sequences obtained from each designed region were aligned to the reference sequence using BLASTN with alignment length > 200. Mutations to be considered valid were calculated after filtering steps, as previously described(Liu, M. et al.,Nature 2008). Briefly, mutations first had to pass a Neighbourhood Quality Standard (NQS) criteria requiring a minimum Phred score of 30 for the mutation itself, and 20 for the five adjacent bases on either side. Mutations that were within five bases of more than two additional mutations were excluded. Mutations within two bases of a deletion or insertion were also excluded. In addition, bases with mutation rate > 0.01 were excluded as a result of overwhelming influence of sequence error or SNP, of which bases with mutation rate > 0.2 were further regarded as SNP and were excluded. Finally, the average base mutation rate of 1-200 bp passing the above criteria were calculated from forward sequence, as well as reverse sequences. For average base mutation rates of C-to-T or G-to-A transitions, only C or G bp sites we counted.
Supplementary_files_format_and_content: For SHM data, tab-delimited text files give mutation information for each base pair incuding mut frequency for all mut, particular C>T|G>A and others. Bases to fail to pass filter criteria were showen as 'NA'.

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplemented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and treated with control DMSO.

extract_protocol:
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%)  containing 10 μg/ml Proteinase K  at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA)
Phusion High Fidelity DNA polymerase was used to amplify selected regions from template genomic DNA. Amplification products were purified using PCR purification kit and GEL extraction kit and sequenced bi-directionally in a Mi-Seq Illumina sequencing platform.

tag: strain

value: spleen

value: AID -/-

value: splenic B cells activated with anti-CD40 plus IL-4 for 4 days


title: r17-resist-infect


title: F2 365dpf BPA30 replicate 1


title: F2 365dpf BPA3 replicate 0


title: F2 365dpf BPA30 replicate 0


title: F2 365dpf BPA3 replicate 1


title: F2 365dpf BPA3 replicate 3


title: s05-suscep-infect


title: r16-resist-infect


title: F2 365dpf Control replicate 2

description:
Eggs from F1 Control Females were fertilized using sperm from non treated males
abundance_F2_365dpf.tabular

value: Control


title: F2 365dpf Control replicate 3


title: F2 365dpf Control replicate 1


title: r16-resist-noninf

value: monocyte-derived dendritic cells


title: s03-suscep-infect

value: susceptible


title: r15-resist-noninf

value: non-infected


title: F2 365dpf Control replicate 0


title: r15-resist-infect

value: male


title: r14-resist-noninf


title: r19-resist-infect


title: F2 140dpf BPA30 replicate 2

description:
Eggs from F1 40 ng BPA Females were fertilized using sperm from non treated males
abundance_F2_112dpf.tabular


title: r14-resist-infect


title: F2 140dpf BPA30 replicate 1


title: r13-resist-infect


title: F2 140dpf BPA30 replicate 0


title: r12-resist-noninf


title: F2 140dpf BPA3 replicate 3

description:
Eggs from F1 4 ng BPA Females were fertilized using sperm from non treated males
abundance_F2_112dpf.tabular


title: F2 140dpf BPA3 replicate 2


title: F2 140dpf BPA3 replicate 1


title: F2 140dpf BPA3 replicate 0


title: r11-resist-noninf


title: r10-resist-noninf


title: F2 140dpf Control replicate 3

description:
Eggs from F1 Control Females were fertilized using sperm from non treated males
abundance_F2_112dpf.tabular


title: F2 140dpf Control replicate 2


title: r13-resist-noninf


title: r09-resist-infect


title: r09-resist-noninf


title: F2 140dpf BPA30 replicate 3


title: r08-resist-noninf


title: F2 140dpf Control replicate 0


title: F2 140dpf Control replicate 1


title: r10-resist-infect


title: F1 365dpf BPA30 replicate 2

description:
F0 eggs were incubated in ovarian fluid supplemented with 3 mg/L BPA  for 3 hours resulting in 40 ng of BPA in the egg and then fertilized with non-treated sperm creating F1 generation
abundance_F1_365dpf.tabular


title: F1 365dpf BPA30 replicate 3


title: r07-resist-noninf


title: r06-resist-noninf


title: r07-resist-infect


title: F1 365dpf BPA30 replicate 0


title: F1 365dpf BPA3 replicate 3

description:
F0 eggs were incubated in ovarian fluid supplemented with 3 mg/L BPA  for 3 hours resulting in 4 ng of BPA in the egg and then fertilized with non-treated sperm creating F1 generation
abundance_F1_365dpf.tabular


title: r08-resist-infect


title: F1 365dpf BPA30 replicate 1


title: F1 365dpf BPA3 replicate 2


title: r05-resist-noninf


title: r11-resist-infect


title: r06-resist-infect


title: r12-resist-infect


title: r05-resist-infect


title: F1 365dpf BPA3 replicate 0


title: r04-resist-infect


title: r04-resist-noninf


title: F1 365dpf Control replicate 3

description:
F0 eggs were incubated in ovarian fluid supplemented with vehicle (<0.01% ethanol) for 3 hours resulting in 0 ng of BPA in the egg and then fertilized with non-treated sperm creating F1 generation
abundance_F1_365dpf.tabular


title: F1 365dpf Control replicate 1


title: F1 365dpf Control replicate 2


title: F1 140dpf BPA30 replicate 3

description:
F0 eggs were incubated in ovarian fluid supplemented with 3 mg/L BPA  for 3 hours resulting in 40 ng of BPA in the egg and then fertilized with non-treated sperm creating F1 generation
abundance_F1_140dpf.tabular


title: F1 140dpf BPA30 replicate 2


title: F1 365dpf Control replicate 0


title: r02-resist-infect


title: r03-resist-infect


title: r01-resist-noninf


title: r01-resist-infect


title: F1 140dpf BPA3 replicate 3

description:
F0 eggs were incubated in ovarian fluid supplemented with 3 mg/L BPA  for 3 hours resulting in 4 ng of BPA in the egg and then fertilized with non-treated sperm creating F1 generation
abundance_F1_140dpf.tabular


title: F1 140dpf BPA3 replicate 1


title: r02-resist-noninf


title: F1 140dpf Control replicate 3

description:
F0 eggs were incubated in ovarian fluid supplemented with vehicle (<0.01% ethanol) for 3 hours resulting in 0 ng of BPA in the egg and then fertilized with non-treated sperm creating F1 generation
abundance_F1_140dpf.tabular


title: F1 140dpf BPA30 replicate 0


title: HTGTS_MEC1.Idelalisib rep2

data_processing:
For HTGTS data, we applied prinseq 0.2 to remove sequences with exact PCR duplicates, mean quality score < 20 and length < 50. Next, effect reads for each sample were recognized by designed barcode, primer and bait portion. Lastly,the barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions as previously described(Chiarle et al.,Cell 2011). Briefly, we aligned sequences to the mouse reference genome (GRCm37/mm9) or human genome (GRCh38/hg38) using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
Genome_build: hg38
Supplementary_files_format_and_content: For HTGTS data, BED files contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.

source_name: DSMZ ACC 497

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with idelalisib

value: peripheral blood, Human Chronic Lymphocytic Leukemia

tag: cell line

value: human chronic lymphocytic leukemia B cells

value: Idelalisib


title: F1 140dpf Control replicate 2


title: F1 140dpf BPA3 replicate 0


title: F1 140dpf Control replicate 1


title: OLE1met250 rep3

description: Low lipid unsaturation

value: POLE1::PMET3 integration

value: 0 uM methionine (repressed)

value: replicate 3


title: F1 365dpf BPA3 replicate 1


title: F1 140dpf BPA3 replicate 2


title: F1 140dpf Control replicate 0


title: OLE1met250 rep2

description: Low lipid unsaturation

value: S. cerevisiae S288C

value: replicate 2


title: OLE1met250 rep1

description: Low lipid unsaturation

value: replicate 1


title: OLE1met0 rep3

description: High lipid unsaturation (reference)

value: 0 methionine (unrepressed)


title: OLE1met0 rep1

description: High lipid unsaturation (reference)


title: OLE1met0 rep2

description: High lipid unsaturation (reference)


title: r03-resist-noninf

tag: cell type

value: resistant


title: F1 140dpf BPA30 replicate 1

value: 40 ng BPA


title: mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG

status: Public on Jan 30 2017

city: San Francisco

first: Yan

last: Zhang

address: 600 16th Street

department: Microbiology and Immunology

institute: UC San Francisco

description:
mRNA
mRNA_pCUG

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded.
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1.
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read.
Genome_build: NC000913.2
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

organism: Escherichia coli

source_name: bacteria

growth_protocol: All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4.

extract_protocol:
Extraction was performed as described previously (Li et al., 2012; Oh et al., 2011). For ribosome profiling, 200 mL of cell culture were filtered rapidly and the resulting cell pellet was flash-frozen in liquid nitrogen and combined with 650 µL of frozen lysis buffer (10 mM MgCl2, 100mM NH4Cl, 20mM Tris-HCl pH 8.0, 0.1% Nonidet P40, 0.4% Triton X-100, 100 U/mL DNase I (Roche), 1mM chloramphenicol). Cells were pulverized in 10mL canisters pre-chilled in liquid nitrogen. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. For mRNA-seq and DMS-seq, cells were pelleted by centrifuging for 2 min at 8000rpm. Total RNA was then hot acid phenol extracted. Ribosomal RNA and small RNA were removed with MICROBExpress (Ambion) or Ribozero (Epicenter) and MEGAclear (Ambion), respectively.
The ribosome footprints and fragmented mRNA were ligated to miRNA cloning linker-1 (IDT) using truncated T4 RNA ligase 2 K227Q. The ligated RNA fragments were reverse transribed using the primer 5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC GTATCATT/iSp18/CACTCA/iSp18/CAAGCAGAAGACGGCATACGAATTGATG GTGCCTACAG. The resulting cDNA was circularized with CircLigase (Epicentre) and PCR amplification was done as described previously (Ingolia et al., 2009).

treatment_protocol: For in vivo DMS modification, 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at 37°C. For kasugamycin (ksg) experiments, ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at 37°C prior to DMS modification. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol). For in vitro DMS modifications, mRNA was denatured at 95 °C for 2 min, cooled on ice and refolded in 90 µL RNA folding buffer (10 mM Tris pH 8.0, 100 mM NaCl, 6 mM MgCl2) at 37°C for 30 min then incubated in either .2% DMS for 1 min (95°C) or 4% DMS for 5 min (37°C).

value: 1mM IPTG


title: mRNA-seq 37°C in WT with control plasmid

description:
mRNA
mRNA_pCTRL

value: MG1655 [p-CTRL]


title: ribosome profiling 37°C in WT with plasmid expressing mini-ORF CUG

description:
ribosome protected mRNA
rib_pCUG

data_processing:
Library strategy: ribosome profiling
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded.
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1.
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read.
Genome_build: NC000913.2
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).


title: mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA

description:
mRNA
mRNA_pCUA


title: Ribosome profiling of wild type Salmonella enterica serovar Thyphimurium - strain SL1344 monosomes

city: Gent

first: Petra

middle: Van

last: Damme

state: East Flanders

address: Albert Baertsoenkaai 3

department: Department of Biochemistry

country: Belgium

institute: University of Gent

description: monosome bound mRNA footprints

data_processing:
The Ribosome profiling and RNA-seq sequenced reads were trimmed for adaptor sequences using fastx_clipper 0.0.14.
For the Ribo-seq reads the trimmed reads were sequentially aligned using Bowtie v0.12.7 to the Salmonella enterica rRNA and tRNA allowing for one mismatch. Reads aligning to any of these indices were discarded.
The trimmed RNA-seq and remaining Ribo-seq reads were then aligned using Bowtie V0.12.7 to the Salmonella enterica subsp. Enterica Typ str. SL1344 genome using parameters -v1 -m2 -k1.
The ribosome occupancy position was determined using the 5' end of the reads. For each footprint read the genomic position corresponding to the 5' end of the read was counted. Scores therefore represents the number of reads alignments attributed to each genomic position.
Genome_build: GCA_000210855.2
Supplementary_files_format_and_content: Bedgraph files were generated  for the sense and antisense seperately: The positional scores represent the number of reads aligned to each genomic position.
Supplementary_files_format_and_content: Bed files were generated using bedtools. The scores represents the number of reads aligned to the region.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

growth_protocol: Overnight stationary cultures of wild type S. Typhimurium (Salmonella enterica serovar Typhimurium - strain SL1344) grown in LB media at 37°C with agitation (200 rpm) were diluted at 1:200 in LB and grown until they reached and OD600 of 0.5 (i.e., logarithmic (Log) phase grown cells).

extract_protocol:
The frozen pellet of a 50 ml culture was re-suspended and thawed in 1 ml ice-cold lysis buffer for polysome isolation (10 mM MgCl2, 100 mM NH4Cl, 20 mM Tris.HCl pH 8.0, 20 U/ml of RNase-free DNase I (NEB 2U/µl), 1mM chloramphenicol (or 300µg/ml), 20 µl/ml lysozyme (50mg/ml in water) and 100u/ml SUPERase.In™ RNase Inhibitor (Thermo Fisher Scientific, Bremen, Germany)), vortexed and left on ice for 2 min with periodical agitation. Subsequently, the samples were subjected to mechanical disruption by two repetitive cycles of freeze-thawing in liquid nitrogen, added 5mM CaCl2, 30µl 10% DOC and 1 × complete and EDTA-free protease inhibitor cocktail (Roche, Basel, Switzerland) and left on ice for 5 min. Lysates were clarified by centrifugation at 16,000 x g for 10 min at 4°C. For the monosome sample, the supernatant was subjected to MNase (Roche diagnostics Belgium) digestion using 600 U MNase (about~ 1000 U per mg of protein). Digestion of polysomes proceeded for 1h at 25°C with gentle agitation at 400 rpm and the reaction was stopped by the addition of 10 mM EGTA. Next, monosomes were recovered by ultracentrifugation over a 1 M sucrose cushion in polysome isolation buffer without RNase-free DNase I and lysozyme, and with 2 mM DTT added using a TLA‐120.2 rotor for 4 hr at 75,000 rpm and 4°C.
For the selective purification of monosomes from polysomes (polysome sample), the supernatant was resolved on 10-55% (w/v) sucrose gradients by centrifugation using an SW41 rotor at 35,000 rpm for 2.5 hr at 4°C. The sedimentation profiles were recorded at 260 nm and the gradient fractionated using a BioComp Gradient Master (BioComp) according to the manufacturer's instructions. Polysome-enriched fractions were pooled and subjected to MNase digestion and monosome recovery as described above.Ribosome-protected mRNA footprints with sizes ranging from 26-34 nucleotides were selected and processed as described  previously [23]with some minor adjustments as described

treatment_protocol: Bacterial cells were pre-treated for 5 min with chloramphenicol (Sigma Aldrich) at a final concentration of 100 μg/ml before collection by centrifugation (6000 × g, 5 min) at 4°C. Collected cells were flash frozen in liquid nitrogen.


title: mRNA profiling of wild type Salmonella enterica serovar Thyphimurium - strain SL1344 monosomes

description: mRNA


title: Ribosome profiling of wild type Salmonella enterica serovar Thyphimurium - strain SL1344 polysomes

description: polysome bound mRNA footprints


title: DMS-seq 37°C in vivo dusB-M3 mutant

description:
DMS-modified mRNA
DMS_dusB_M3

data_processing:
Library strategy: DMS-seq
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded.
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1.
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read.
Genome_build: NC000913.2
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

extract_protocol:
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37°C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C.
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, D. Burkhardt, C.A. Gross, J. S. Weissman, Cell 157, 624-635 (2014).

value: MG1655 dusB-M3


title: ribosome profiling 37°C in WT with control plasmid

description:
ribosome protected mRNA
rib_pCTRL


title: ribosome profiling 37°C in WT with plasmid expressing mini-ORF CUA

description:
ribosome protected mRNA
rib_pCUA


title: DMS-seq 37°C in vivo WT_2

description:
DMS-modified mRNA
DMS_WT


title: DMS-seq 37°C in vivo ∆gcvB

description:
DMS-modified mRNA
DMS_gcvB

value: MG1655 delta_gcvB


title: DMS-seq 37°C in vivo dusB-M3:2 mutant

description:
DMS-modified mRNA
DMS_dusB_M32


title: 0.04 nM Fe'_rplC

city: Geneva

first: Sonia

last: Blanco-Ameijeiras

state: GE

address: 66 Boulevard Carl Vogt

department: F.-A. Forel Institute

country: Switzerland

institute: University of Geneva

data_processing:
Quality control was performed using FastQC tool (Babraham Bioinformatics, UK)
Mapping was performed using TopHat 2.0 mapper software (Trapnell et al., 2009)
Table of counts were obtained using the HTSeq 0.5.3.p9 (Anders et al., 2015)
Genome_build: Reads were aligned to the genome of Synechococcus sp. PCC7002 build from the Cyanobase (Fujisawa et al., 2013)
Supplementary_files_format_and_content: Normalized_counts_cpm_replicates.txt

organism: Picosynechococcus sp. PCC 7002

source_name: cells

growth_protocol: Cyanobacterium Synechococcus sp. PCC7002, bioreporter BMB04, grown in Aquil culture medium amended with iron (Fe)-EDTA to maintain Fe concentration constant during the incubation time and achieve desired concentrations of dissolved inorganic Fe (Fe’) (10.9, 0.41, 0.04 and 0.003 nM). Cultures acclimated to grow under the selected Fe’ concentrations for at least 22 generations in diluted batches (<8 × 106 cell ml-1) were incubated in three biological replicates (inoculated with a biomass equivalent to 0.5 mg Chla l-1) in 2 l PC bottles for physiological and genomic analysis, at 22°C, with 50 μmol quanta m-2 s-1 (cool white fluorescent tubes) under a 12:12 light:dark cycle.

extract_protocol:
Cells for RNA extraction were harvested in mid-exponential growth phase by filtration through 0.4 mm polycarbonate membrane and cemtrifugated at 6000 × g for 8 min at 4 ºC. The pellets were snap frozen in liquid nitrogen. RNA was isolated using TRI Reagent (Sigma-Aldrich, Buch, Switzerland) following provider’s instructions. Ribosomal RNA (rRNA) was depleted using Ribo-Zero™ rRNA Removal Kit using gram-negative bacteria-specific capture oligonucleotides (Epicentre, Madison, WI, USA). RNA purity and integrity was determined using the Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies, Inc., Santa Clara, CA, USA).
Libraries were prepared using 200 ng of RNA with the Illumina TruSeq Stranded mRNA kit and sequenced generating 100 bp single reads on an Illumina HiSeq 2500 System (Illumina, San Diego, CA, USA).
Quality control was performed using FastQC tool (Babraham Bioinformatics, UK). Reads were aligned to the genome of Synechococcus sp. PCC7002 build from the Cyanobase (Fujisawa et al., 2013) and further analyzed using TopHat 2.0 mapper software (Trapnell et al., 2009). Table of counts were obtained using the HTSeq 0.5.3.p9 (Anders et al., 2015). Reads mapped to the reference genome at 88.7 ±6.9 %.

treatment_protocol: Sample labels starting with 1_06_A, 2_06_B and 3_06_C, respectively represent the biological replicated of the iron (Fe) treatment with 0.6 nM of total Fe, which is equivalent to 0.003 nM of dissolved inorganic Fe (Severe Fe limitation). Sample labels starting with 4_2_A, 5_2_B and 6_2_C, respectively represent the biological replicated of the Fe treatment with 2 nM of total Fe, which is equivalent to 0.04 nM of dissolved inorganic Fe (Strong Fe limitation). Sample labels starting with 7_20_A, 8_20_B and 9_20_C, respectively represent the biological replicated of the Fe treatment with 20 nM of total Fe, which is equivalent to 0.41 nM of dissolved inorganic Fe (Mild Fe limitation). Sample labels starting with 10_200_A, 11_200_B and 12_200_C, respectively represent the biological replicated of the Fe treatment with 200 nM of total Fe, which is equivalent to 10.9 nM of dissolved inorganic Fe (Fe replete=control).

tag: developmental stage

value: exponential growth phase

tag: label in the processed file

value: Fe limited


title: 10.9 nM Fe'_rplA

value: Fe replete_control


title: 10.9 nM Fe'_rplC


title: 0.04 nM Fe'_rplA


title: 0.41 nM Fe'_rplB


title: 0.41 nM Fe'_rplA


title: 0.003 nM Fe'_rplC


title: mRNA profiling of wild type Salmonella enterica serovar Thyphimurium - strain SL1344 polysomes

description: mRNA


title: 0.04 nM Fe'_rplB


title: 0.003 nM Fe'_rplB


title: 0.003 nM Fe'_rplA


title: H3K27me3 ChIP-Seq

city: Los Angeles

first: Paul-Joseph

middle: P

last: Aspuria

state: California

address: 8400 Beverly Blvd.

department: Women's Cancer Program

institute: Cedars-Sinai Medical Center

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (50 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: BAM = standard BAM alignment format
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks

source_name: G401 (rhabdoid tumor of the kidney)

growth_protocol: Cells were grown in RPMI +15% FBS and grown to 80% confluency

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.

tag: tissue

value: kidney

tag: tumor type

value: rhabdoid tumor of the kidney

tag: chip antibody

value: Active Motif


title: Pol II ChIP-Seq


title: H3K27Ac ChIP-Seq


title: H3K4me3 ChIP-Seq


title: DMS-seq 37°C in vivo ∆gcvB+ksg

description:
DMS-modified mRNA
DMS_gcvB_ksg

value: MG1655 delta_gcvB+ksg

tag: treatment

value: 10mg/ml kasugamycin (ksg) for 2min and 5% DMS for 2min


title: Cold treatment2 of K326

city: singapore

first: JINGJING

last: JIN

address: singapore

country: Singapore

institute: Temasek LifeScience Laboratory

description: cold

data_processing:
NGSToolkits used to filter low quality reads
Trinity is used for denovo assembly of RNA-seq
FPKM are used to measure the expression level

organism: Nicotiana tabacum

source_name: leaf

growth_protocol: For the RNA-seq experiments, their seeds were first germinated and cultivated in plastic pots under normal conditions until the plants grew to six-leaf stage.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cold treatments plants were transferred to 4oC for one day

value: leaf

value: six leaf stage

tag: ecotype


title: Cold treatment1 of K326

description: cold


title: HOXB13 ChIP-Seq

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (50 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

value: HOXB13 (H-80, Santa Cruz sc-66923)


title: Input DNA


title: 10.9 nM Fe'_rplB

tag: sample type


title: control2 of K326

description: control


title: 0.41 nM Fe'_rplC


title: Cold treatment2 of CB-1

description: cold


title: Cold treatment1 of CB-1

description: cold


title: control1 of K326

description: control


title: control1 of CB-1

description: control


title: DMS-seq 37°C 16S rRNA

description:
RNA
16S rRNA


title: DMS-seq 95°C in vitro WT

description:
DMS-modified mRNA
DMS_95_WT_vitro


title: DMS-seq 37°C in vitro WT

description:
DMS-modified mRNA
DMS_37_WT_vitro


title: ribosome profiling 37°C in WT

description:
ribosome protected mRNA
rib_37_WT


title: mRNA-seq 37°C in WT

description:
mRNA
mRNA_37_WT


title: siRNA22 ZBTB33 RNASeq

city: Salt Lake City

first: Bethany

last: Buck-Koehntop

state: Utah

department: Chemistry

institute: University of Utah

data_processing:
Illumina Genome Analyzer (Homo sapiens)
Illumina Fastq files were aligned to the hg19 genome with all known and theoretical splice junctions using Novocraft’s novoalign aligner with the following parameters: -r All 50 -t 40 -o SAM 90 –k. The USeq NovoalignParser application was then used to parse the alignment files into binary point data by setting the posterior probability to 0 and alignment score threshold to 60.
The MultipleReplicaDefinedRegionScanseqs USeq application, which utilizes the DESeq R package22, identified statistically significant differentially expressed genes between cells treated with the scrambled siRNA and ZBTB33 depleted cells.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: HeLa S3

growth_protocol: Cell were cultured in Dulbecco's Modified Eagle medium supplemented with 4.5 g/L glucose, 10% FBS and 2 nM glutamine in humidified incubator at 37 deg. C with 5% CO2.

extract_protocol:
Transfected cells were washed with PBS and resuspended in TRIzol prior to RNA extraction with the Direct-zol RNA Kit (Zymo Research). RNA quality was measured on a Bioanalyzer RNA 6000 Nano Chip.
RNA libraries were prepared for sequencing by Illumina TruSeq Stranded mRNA Sample Prep with poly(A) selection

treatment_protocol: HeLa cells were transfected with either a scrambled siRNA or one of two ZBTB33 siRNAs (Thermo Fisher Scientific) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 24 hr.

value: HeLa

tag: passage

value: 5 to 8

tag: transfection

value: siRNA2 ZBTB33


title: siRNA23 ZBTB33 RNASeq


title: scramble RNASeq3

value: scramble control


title: siRNA13 ZBTB33 RNASeq

value: siRNA1 ZBTB33


title: siRNA12 ZBTB33 RNASeq


title: siRNA21 ZBTB33 RNASeq


title: HeLa_S3 (WGSBS).

data_processing:
Illumina Genome Analyzer was used for basecalling
The WGSBS fastq data were aligned in Novoalign bisulfite mode using the following parameters: -oSAM -rRandom -t240 -h120 -b2
sam alignments were sorted with the Picard SortSam.jar script and all duplicates removed using the Picard MarkDuplicates.jar script for WGSBS datasets. The results were converted into .bam files and indexed using Samtools
Peak calling was performed with the USeq NovoalignBisulfiteParser to parse the alignments into four binary PointData sets containing the number of observed converted Cyt and non-converted Cyt at each reference Cyt site sequenced in the genome for both the plus and minus strands
Genome_build: hg19
Supplementary_files_format_and_content: read coverage tracks files were built with Useq

extract_protocol:
Genomic DNA was isolated using the DNeasy Blood & Tissue Kit (QIAGEN)
Library construction was performed using the EpiGnome/TruSeq DNA Methylation Kit. Briefly, genomic DNA (50-100 ng) was denatured and bisulfite converted in a reaction containing 0.5 ng of unmethylated lambda DNA (Promega) as a control. Following purification, the BS converted DNA was hybridized with oligonucleotides consisting of random hexamers linked to Illumina P5 adapter sequences and strand replicated using EpiGnome polymerase. Adapter-ligated DNA molecules were enriched by 10 cycles of PCR.


title: scramble RNASeq1


title: RNAseq-lncRNAs_55

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

data_processing:
AB SOLID data:  Primary alignment with Lifescope software version 2.1
Mark duplicate with PICARD version 1.107
SplitNCigar with GATK version 3.2-2
Read counts using HTSeq version 0.6.1p1
Genome_build: hg19
Supplementary_files_format_and_content: Reads counts based on Ensembl GRCH37 version 75 + lncRNAs from Casero D, Sandoval S, Seet CS, Scholes J, Zhu Y, Ha VL, Luong A, Parekh C, Crooks GM. 2015. Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages. Nat Immunol 16(12): 1282-1291.

source_name: Tumoral biospecimen

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. Following a DNAse I treatment, total or mature RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System.

value: Bone marrow

tag: age diagnosis (month)

tag: Sex

value: M


title: RNAseq-lncRNAs_56

value: F


title: scramble RNASeq2


title: RNAseq-lncRNAs_54


title: Ewing sacroma patient 121 RRBS

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Data acquisition performed with HiSeq Control Software (HCS)  2.2.38
Basecalling performed with Illumina Real-Time Analysis (RTA) software 1.18.61.0
BCL to BAM file conversion and demultiplexing was performed with Illumina2bam tools 1.17
ChIP-seq Alignment performed with Bowtie2 version 2.2.9 with standard options.
ChIP-seq Peak calling was performed with MACS2 version 2.1.0.20151222 via macs2 callpeak --SPMR --bdg --gsize hs
Bisulfite-Seq (reduced representation) read trimming with Trimmomatic version 0.32 and options illuminaclip: ":2:40:7 SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18"
Bisulfite-Seq (reduced representation) alignment with bsmap version 2.90 and options -D C-CGG -D T-CGA -w 100 -v 0.08 -p 4 -r 1 -n 0 -s 12 -S 0 -f 5 -q 0 -u -V 2
Bisulfite-Seq (reduced representation) methylation site calling with biseq-methcalling --restrictionSite="y-CG_R" --minFragmentLength=20 --maxFragmentLength=1000 --pfStatus="All" --maxMismatches=0.1 --baseQualityScoreC=20 --baseQualityScoreNextToC=10 --timeDelay=0 --genomeFraction=50 --smartWindows=250000 --maxProcesses=4
Genome_build: UCSC hg38 based on GRCh38
Supplementary_files_format_and_content: Peak calls from MACS2 in tab-sparated value (TSV) format. File names indicate treatment and control sample names separated by two underscores.

source_name: Ewing sacroma patient 121

extract_protocol:
DNA was isolated from 10 to 25 mg of snap-frozen tumors, cell lines, and MSCs by standard proteinase K digestion and phenol/chloroform extraction. DNA was quantified using a Qubit 2.0 Fluorometer (ThermoFisher Scientific, Q32866) and the Qubit dsDNA BR Assay Kit (ThermoFisher Scientific, Q32850).
ChIP-seq for three primary human tumors was done as described previously (Tomazou EM., et al, Cell Reports, 2015). Chromatin was prepared from 20 to 50 sections (25µm each) of snap-frozen tumors obtained by microtome sectioning. The following antibodies were used: H3K4me3 (Diagenode, C15410003-50, pAb-003-050), H3K27me3 (Diagenode, C15410195, pAb-195-050), H3K4me1 (Diagenode, pAb-194-050), H3K27ac (Diagenode, pAb-196-050), H3K56ac (Active Motif, 39281), H3K9me3 (Diagenode, pAb-193- 050), H3K36me3 (Diagenode, pAb-192-050). Library preparation for ChIP DNA and input control DNA was performed using the NEBNext Ultra kit (New England Biolabs, E7370S/L) following the manufacturer’s instructions. Quality control for the final libraries was done by measuring the DNA concentration with the Qubit dsDNA HS assay (Life Technologies, Q32851) on Qubit 2.0 Fluorometer (Life Technologies, Q32866) and by determining library fragment sizes with the Experion DNA 1K Analysis kit (Bio-Rad, 700-7107) on the Experion Automated Electrophoresis Station (Bio-Rad, 701-7000)
For reduced representation Bisulfite-seq (RRBS), 100 ng of genomic DNA was digested for 12 hr at 37°C with 20 units of MspI (New England Biolabs, R0106L) in 30 μl of 1× NEB buffer 2. To retain even the smallest fragments and to minimize the loss of material, end preparation and adaptor ligation were performed in a single-tube setup. End fill-in and A-tailing were performed by addition of Klenow Fragment 3′ > 5′ exo- (New England Biolabs, M0212L) and dNTP mix (10 mM dATP, 1 mM dCTP, 1 mM dGTP). After ligation to methylated Illumina TruSeq LT v2 adaptors using Quick Ligase (New England Biolabs, M2200L), the libraries were size selected by performing a 0.75× cleanup with AMPure XP beads (Beckman Coulter, A63881). The libraries were pooled in combinations of six based on qPCR data and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit (Zymo Research, D5020) with the following changes to the manufacturer’s protocol: conversion reagent was used at 0.9× concentration, incubation performed for 20 cycles of 1 min at 95°C, 10 min at 60°C, and the desulphonation time was extended to 30 min. These changes increase the number of CpG dinucleotides covered by reducing double-strand break formation in larger library fragments. Bisulfite-converted libraries were enriched using PfuTurbo Cx Hotstart DNA Polymerase (Agilent, 600412). The minimum number of enrichment cycles was estimated by qPCR. After a 2× AMPure XP cleanup, quality control was performed using the Qubit dsDNA HS (Life Technologies, Q32854) and Experion DNA 1k assays (BioRad, 700-7107).

value: Ewing sacroma

tag: tumor stage

value: diagnosis


title: control2 of CB-1

description: control


title: RNAseq-lncRNAs_53


title: Ewing sacroma patient 120 RRBS

source_name: Ewing sacroma patient 120


title: Ewing sarcoma patient 119 RRBS

source_name: Ewing sacroma patient 119


title: Ewing sacroma patient 121 input 1

tag: antibody


title: RNAseq-lncRNAs_49


title: Ewing sacroma patient 121 H3K9me3 1


title: RNAseq-lncRNAs_50


title: DMS-seq 37°C in vivo WT_1

description:
DMS-modified mRNA
DMS_37_WT

tag: strain


title: siRNA11 ZBTB33 RNASeq

tag: cell line


title: Ewing sacroma patient 121 H3K4me3 1

tag: cell type


title: Ewing sacroma patient 121 H3K56ac 1


title: RNAseq-lncRNAs_45


title: Ewing sacroma patient 121 H3K4me1 1


title: Ewing sacroma patient 121 H3K36me3 1


title: Ewing sacroma patient 121 H3K27me3 1


title: Ewing sacroma patient 121 H3K27ac 1


title: Ewing sacroma patient 120 H3K9me3 1


title: Ewing sacroma patient 120 input 1


title: Input

city: Guang-Zhou

first: Can-Ze

last: Huang

address: 107 Yan-Jiang Xi-Road

institute: Sun Yat-Sen Memorial Hospital

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the mm9 genome assembly using MACS sofeware.
Data were filtered using FastQC sofeware.
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MEME-ChIP version 4.11.2.

source_name: Intestinal epithelium stem cells

growth_protocol: Mice were maintained under a 12 h light/12 h dark cycle in a specific pathogen-free animal facility.

extract_protocol:
Lysates were clarified from sonicated nuclei and  transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Gene Lepr was spontaneously mutated.

value: FACS-intestinal epithelium stem cells

value: BKS.Cg-Dock7m +/+ Leprdb/JNju


title: db/db

value: rabbit polyclonal anti-mouse Sox9 antibody (Abcam, UK)


title: Ewing sacroma patient 120 H3K56ac 1


title: db/+


title: RNAseq-lncRNAs_40


title: Ewing sacroma patient 120 H3K4me3 1


title: RNAseq-lncRNAs_39


title: RNAseq-lncRNAs_43


title: NPC_Hsp90i_Rep3

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: processed data file: DESeq2_RepeatCounts_NPC.txt

data_processing:
RNA-seq reads were trimmed with TrimGalore (http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/, v0.4.0) and mapped to Ensembl annotation release 78 using TopHat2 (v2.0.13) with the options mate-inner-dist, mate-std-dev and library-type (fr-firststrand). The distance between read mates (mate-inner-dist and mate-std-dev) were assessed individually using RSeQC (v2.6.1).
After mapping of the RNA-seq reads from all samples, the reads that mapped uniquely to the genome were counted using featureCounts with the following options: -Q 10 -p -B -C -s 2. The annotations present in the Mus musculus gtf file from the Ensembl release 78 were used as reference for counting. DESeq2 was used for differential expression analysis.
To analyze repeats, RNA-seq reads were mapped to the mouse genome assembly mm10 using Bowtie2 with random assignment of multi-mapping reads. Reads with more than 3 mismatches were discarded. RepeatMasker annotation (downloaded from UCSC genome browser on 28 July 2015) was used as input for the bamCoverage to count repetitive element reads with the -split option. Differential expression was analyzed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression of repetitive elements upon Hsp90 inhibition per cell type.

growth_protocol: Embryonic Stem cells were grown in 2i medium using standard protocols for maintenance and passaging. Neuronal Progenitor Cells were cultured in N2B27 medium (StemCell Sciences) containing 10 ng/mL EGF and FGF (Preprotech). Macrophages were derived from mouse bone marrows using recombinant murine Macrophage Colony stimulating factor (M-CSF; PeproTech cat. No. 315-02) following standard protocols.

extract_protocol:
After treatment, cells were resupended in peqGOLD Trifast (VWR International, Germany, cat. no. 30-2010). RNA was extracted according to the manufacturer’s protocol. DNase-I treatment was carried out for 2 hours to eliminate genomic DNA contamination using TURBO DNase kit (Thermo Fisher Scientific cat. No. AM1907). RNA was analyzed by paired end poly(A) RNA sequencing.
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit.

treatment_protocol: Hsp90 inhibition was carried out using the following concentrations of NVP-AUY922 for 24 hours with the corresponding cell types: 100nM for ESCs, 500nM for macrophages, and 50nM for NPCs.

tag: strain background

value: neuronal progenitor cells (NPCs)

tag: treated with

value: NVP-AUY922 for 24 hours


title: Ewing sacroma patient 120 H3K4me1 1


title: RNAseq-lncRNAs_48

tag: tissue


title: RNAseq-lncRNAs_38


title: NPC_Hsp90i_Rep2


title: RNAseq-lncRNAs_37


title: NPC_Hsp90i_Rep1


title: NPC_Ctrl_Rep3


title: RNAseq-lncRNAs_36


title: Ewing sacroma patient 120 H3K36me3 1


title: Ewing sacroma patient 120 H3K27me3 1


title: NPC_Ctrl_Rep1


title: Ewing sacroma patient 119 input 1


title: NPC_Ctrl_Rep2


title: RNAseq-lncRNAs_34


title: Ewing sacroma patient 120 H3K27ac 1


title: RNAseq-lncRNAs_33


title: Ewing sacroma patient 119 H3K9me3 1


title: Macrophages_Hsp90i_Rep2

description: processed data file: DESeq2_RepeatCounts_Macrophages.txt

value: bone-marrow-derived macrophages


title: RNAseq-lncRNAs_31


title: Ewing sacroma patient 119 H3K4me3 1


title: Macrophages_Hsp90i_Rep3


title: Ewing sacroma patient 119 H3K56ac 1


title: Macrophages_Ctrl_Rep2


title: RNAseq-lncRNAs_29


title: Macrophages_Ctrl_Rep3


title: Ewing sacroma patient 119 H3K4me1 1


title: Ewing sacroma patient 119 H3K36me3 1


title: Macrophages_Ctrl_Rep1


title: Ewing sacroma patient 119 H3K27me3 1


title: Ewing sacroma patient 119 H3K27ac 1


title: RNAseq-lncRNAs_27


title: ESC_Hsp90i_Rep3

description: processed data file: DESeq2_RepeatCounts_mESC.txt

value: embryonic stem cells (ESCs)


title: ESC_ATAC-seq rep2

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

description: Genome-wide library of transposed fragments

data_processing:
Library strategy: ATAC-Seq
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig : un-normalised coverage of filtered fragments (reconstructed, duplicate-filtered fragments : see above),  density of alignments in a moving 300 bp window with an increment of 30  bp

source_name: Embryonic Stem Cell

growth_protocol: ES cell lines were maintained in DMEM (Invitrogen) supplemented with 15% fetal calf serum (Gibco), 1% Penicillin/Streptomycin (Invitrogen), 0.1mM 2-mercaptoethanol (Sigma), 1% Glutamine (Invitrogen), 1% MEM Non-essential amino acids (Gibco), 1mM Sodium Pyruvate (Sigma), 1000U/ml LIF (ESGRO) on gelatin coated plates.

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

treatment_protocol: ES cells (ESC) were seeded in suspension at low density (1x104 cells/ml) in the absence of LIF to form embryoid bodies (EBs). ES cells were seeded in DMEM (Invitrogen) supplemented with 15% fetal calf serum (Gibco), 1% Penicillin/Streptomycin (Invitrogen), 0.1mM 2-mercaptoethanol (Sigma), 1% Glutamine (Invitrogen), 1% MEM Non-essential amino acids (Gibco) and 1mM Sodium Pyruvate (Sigma). On day 2 EBs were transferred into N2B27 medium (Cellartis) supplemented with 20ng/ml ActivinA (R&D systems) and 20ng/ml EGF (Peprotech) to induce DE differentiation (Morrison et al. 2008).

value: Embryonic Stem Cell

tag: day of differentiation

value: Day 0


title: RNAseq-lncRNAs_26


title: ESC_Hsp90i_Rep2


title: ESC_ATAC-seq rep1


title: RNAseq-lncRNAs_24


title: ESC_Ctrl_Rep3


title: Macrophages_Hsp90i_Rep1


title: ESC_Ctrl_Rep2


title: DE_ATAC-seq rep3

source_name: Definitive Endoderm

value: ES_derived Definitive Endoderm

value: Day 5


title: RNAseq-lncRNAs_22


title: DE_ATAC-seq rep2


title: DE_ATAC-seq rep1


title: RNAseq-lncRNAs_21


title: ESC_Ctrl_Rep1


title: Delta Snf5 RNAseq Replicate 3

city: Smithville

first: Solomon

last: Hailu

state: Tx

address: Park road 1c

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

data_processing:
Initial extension steps of cluster generation were performed on cBot (Illumina, San Diego, CA) using TruSeq Rapid Duo cBot Sample Loading Kit (Illumina) followed by additional cluster generation steps and 76 bp paired end sequencing using an Illumina HiSeq 2500 (Illumina) with rapid run mode.
Fragments were mapped to the yeast reference genome sacCer3, using TopHat V2.0.10 and Bowtie V2.1.0.
Differential gene expression analysis was performed using EdgeR 3.8.6. Gene annotations were obtained from the Saccharomyces Genome Database (SGD).
Wild type and mutant samples were then compared. Data was filtered using fold change >=2 and p < 0.05.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab delimited text file with edgeR count values (cpm expression values) for each sample

source_name: Yeast cells

growth_protocol: Yeast strains (wild type and mutants) in the BY4741 background were grown to an OD600 of approximately 0.75 – 1.0 with independent biological triplicates at 30 degree celsius.

extract_protocol:
Total RNA was extracted using the hot acid phenol method (Collart & Oliviero, 2001). Samples were phenol/chloroform extracted and ethanol precipitated before resuspension in 50 µl of diethylpyrocarbonate treated water.
RNA library was prepared using Truseq stranded mRNA LT kit (RS-122-2101/2102)

tag: developmental stage

value: Log phase

tag: genotype

value: mata his3delta_1 leu2delta_0 met15delta_0 ura3delta_0 snf5delta_::kanMX4 snf6::snf6-2FLAG-9 amino acids-LEU2


title: Delta Snf5 RNAseq Replicate 2


title: RNAseq-lncRNAs_28

value: Bone marrow


title: RNAseq-lncRNAs_20

value: F


title: PHS_Enhancer_capture_rep3

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
PHS_Enh_Interacting.txt
PHS_C

data_processing:
Library strategy: Capture-C
Library Strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 1 maintaining strict read order
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates(custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Processing: Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format with count of interactions per fragment (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Erythrocytes

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

treatment_protocol: ES cells (ESC) were seeded in suspension at low density (1x104 cells/ml) in the absence of LIF to form embryoid bodies (EBs). ES cells were seeded in DMEM (Invitrogen) supplemented with 15% fetal calf serum (Gibco), 1% Penicillin/Streptomycin (Invitrogen), 0.1mM 2-mercaptoethanol (Sigma), 1% Glutamine (Invitrogen), 1% MEM Non-essential amino acids (Gibco) and 1mM Sodium Pyruvate (Sigma). On day 2 EBs were transferred into N2B27 medium (Cellartis) supplemented with 20ng/ml ActivinA (R&D systems) and 20ng/ml EGF (Peprotech) to induce DE differentiation (Morrison et al. 2008).  Single cell suspensions of erythrocytes were made from the spleens of phenylhydrazine treated mice (40mg/g body weight, x3 doses 12h apart, sacrificed on day 5). Erythrocytes were isolated from spleens by gentle manual dissociation, resuspension in PBS and passage through a CellTrics 30 µM filter (Sysmex).

value: Erythrocytes

tag: genes analysed


title: PHS_Enhancer_capture_rep2

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
PHS_Enh_Interacting.txt
PHS_B


title: RNAseq-lncRNAs_19

value: M


title: PHS_Enhancer_capture_rep1

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
PHS_Enh_Interacting.txt
PHS_A


title: ESC_ATAC-seq rep3


title: ESC_Hsp90i_Rep1


title: RNAseq-lncRNAs_18


title: Delta Snf5 RNAseq Replicate 1


title: RNAseq-lncRNAs_25


title: RNAseq-lncRNAs_23


title: Delta Snf2 RNAseq Replicate 3

value: mata his3delta_1 leu2delta_0 met15delta_0 ura3delta_0 snf2delta_::kanMX4 snf6::snf6-2FLAG-9 amino acids-LEU2


title: ESC_Enhancer_capture_rep2

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
ESC_Enh_Interacting.txt
ESC_B


title: RNAseq-lncRNAs_17


title: ESC_Enhancer_capture_rep1

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
ESC_Enh_Interacting.txt
ESC_A


title: RNAseq-lncRNAs_15


title: RNAseq-lncRNAs_16


title: RNAseq-lncRNAs_30


title: Delta Swp82 RNAseq Replicate 3

value: mata his3delta_1 leu2delta_0 met15delta_0 ura3delta_0 swp82delta_::kanMX4 snf6::snf6-2FLAG-9 amino acids-LEU2


title: Delta Snf2 RNAseq Replicate 2


title: DE_Enhancer_capture_rep3

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
DE_Enh_Interacting.txt
DE_C


title: DE_Enhancer_capture_rep2

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
DE_Enh_Interacting.txt
DE_B


title: Delta Swp82 RNAseq Replicate 2


title: RNAseq-lncRNAs_14


title: RNAseq-lncRNAs_12


title: WT Snf2 RNAseq Replicate 2

value: mata his3delta_1 leu2delta_0 met15delta_0 ura3delta_0 snf2::snf2-2FLAG-9 amino acids-LEU2


title: PHS_Promoter_capture_rep3

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
PHS_Pro_Interacting.txt
PHS_C


title: WT Snf2 RNAseq Replicate 3


title: RNAseq-lncRNAs_11


title: PHS_Promoter_capture_rep2

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
PHS_Pro_Interacting.txt
PHS_B


title: WT Snf2 RNAseq Replicate 1


title: PHS_Promoter_capture_rep1

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
PHS_Pro_Interacting.txt
PHS_A


title: High fat Diet+B-LGND2-3

city: Memphis

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

description: sample 9

data_processing:
The sequencing run here had a mean read length of 168 bp
These were aligned to the mouse genome (Ensembl GRCm38.p3, Genbank Assembly ID GCA_000001635.5) using TopHat version 2.0.13, Bowtie 2 version 2.2.4 and Samtools version 0.1.19.
Reads were mapped to known genes using HTseq version 0.6.1p1.  Gene expression was analyzed using DESeq2 version 1.6.3.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: Tab delimited text files

source_name: Liver

extract_protocol:
Total RNA was extracted from liver using the qiagen RNA isolation kit and its quality was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).
1µg of total RNA was enriched for Poly A RNA using the Dynabeads® mRNA DIRECT™ Micro Purification Kit according to manufacturer’s standard protocol. The resulting enriched RNA samples were then used to prepare barcoded libraries for sequencing using the Ion Total RNAseq V2 kit and the Ion Xpress 1-48 Barcode kit. Libraries were amplified 16 cycles and the quality of the libraries was confirmed on an Agilent Bioanalyzer using a DNA High Sensitivity chip. The libraries were pooled based on concentrations from the High Sensitivity chip, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an Ion Torrent Proton sequencer.

value: Liver

tag: diet

value: high fat

tag: treatment


title: ESC_Enhancer_capture_rep3

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
ESC_Enh_Interacting.txt
ESC_C


title: ESC_Promoter_capture_rep3

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
ESC_Pro_Interacting.txt
ESC_C


title: High fat Diet+B-LGND2-2

description: sample 8


title: RNAseq-lncRNAs_8


title: Delta Snf2 RNAseq Replicate 1


title: RNAseq-lncRNAs_9


title: RNAseq-lncRNAs_7


title: ESC_Promoter_capture_rep1

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
ESC_Pro_Interacting.txt
ESC_A


title: High fat Diet+B-LGND2-1

description: sample 7


title: High fat Diet+Vehicle-1

description: sample 4

value: vehicle


title: High fat Diet+Vehicle-3

description: sample 6


title: Delta Swp82 RNAseq Replicate 1


title: ESC_Promoter_capture_rep2

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
ESC_Pro_Interacting.txt
ESC_B


title: DE_Promoter_capture_rep2

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
DE_Pro_Interacting.txt
DE_B


title: High fat Diet+Vehicle-2

description: sample 5


title: DE_Promoter_capture_rep1

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
DE_Pro_Interacting.txt
DE_A

data_processing:
Library strategy: Capture-C
Library Strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 1 maintaining strict read order
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Processing: Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format with count of interactions per fragment (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)


title: Normal Diet+Vehicle-3

description: sample 3

value: normal


title: DE_Input rep3

data_processing:
Mapping : bowtie -m 2 --maxIns 350
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
Processing: Plot of density of alignments in a moving 300 bp window with an increment of 30  bp
Genome_build: mm9
Supplementary_files_format_and_content: bigWig : un-normalised coverage of filtered fragments (reconstructed, duplicate-filtered fragments : see above),  density of alignments in a moving 300 bp window with an increment of 30  bp

growth_protocol: Definitive Endoderm differentiation from ESCs cultured as EBs for 2 days, induced to differentiate to a DE fate in N2B27 medium supplemented with ActivinA and EGF. EBs were dissociated by incubation with 0.25% trypsin (Gibco) for 3 min at 37˚C with constant agitation followed by gentle pipetting to obtain a single cell suspension.

extract_protocol:
Fixed cells were lyzed on ice for 20 minutes (5 mM PIPES, 85 mM KCl, 0.5% Igepal-CA 630) before pelleting and nuclear lysis (50 mM Tris-HCl, 10 mM EDTA, 1% SDS), chromatin was then sonicated to 200bp in a Covaris S220 and incubated overnight with 2 µl of anti-H3K4me3 (07-473; Millipore) and Protein A and Protein G Dynabeads (Invitrogen). Beads were washed seven times with RIPA buffer variants (10 mM Tris-HCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate): RIPA (twice), High Salt RIPA (500 mM NaCl; twice), RIPA with 250mM LiCl (once) and T.E. Buffer (twice) before treatment with RNAse A at 37ºC for 1 hr (Roche) and Proteinase K 65ºC overnight (Thermo Fisher). DNA was recovered by phenol-chloroform extraction.
Libraries were indexed for sequencing using NebNext Ultra II (New England BioLabs); library profiles were visualized using D1000 tape on a TapeStation (Agilent Technologies) and quantified using a universal library quantification kit (KAPA Biosystems).

tag: chip antibody


title: DE_Promoter_capture_rep3

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
DE_Pro_Interacting.txt
DE_C


title: Normal Diet+Vehicle-2

description: sample 2


title: DE_Enhancer_capture_rep1

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
DE_Enh_Interacting.txt
DE_A


title: Normal Diet+Vehicle-1

description: sample 1


title: DE_Input rep2


title: DE_H3K4me3 rep3

value: anti-H3K4me3 (07-473; Millipore)


title: JX1012-Opaque

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using FPKM method (Fragments Per kb per Million reads) according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: RPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: C_tropicalis MYA-3404 genome
Supplementary_files_format_and_content: text files containing FPKM values for each Sample

organism: Candida tropicalis

source_name: Candida tropicalis

growth_protocol: White, gray, and opaque cells were grown at 30°C on solid Lee’s GlcNAc medium for two days.

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: opaque

tag: age

value: 2 days-old


title: JX1012-White

value: white


title: JX1012-Gray

value: gray


title: DE_H3K4me3 rep2

value: ES_derived Definitive Endoderm

value: Day 5


title: 72hpa_rep2

city: Stanford

first: Jessica

middle: Kay

last: Chang

address: 300 Pasteur Drive, Alway Building M311

department: Genetics

institute: Stanford University

data_processing:
Adapter sequences and low quality bases were trimmed using fastx_clipper (fastx_toolkit v 0.13.2) for single end reads and trim_galore v 0.3.3 for paired end libraries.  Reads were subsequently mapped to the v9.0 genome via Tophat v2.0.13 with very-sensitive parameters.
Multimapped or unmapped reads were filtered using samtools v 1.1.
Count data was summarized via HTSeq (python v2.7).  Adjustments for sequencing depth (and prior to clustering, variance stabilization through rlog transformation) were performed using DESeq2 (R v3.2.0).
Genome_build: Xentr9.0
Supplementary_files_format_and_content: Tab delimited file containing normalized count data (adjusted by size factor via DESeq2).  Additional columns concerning whether a gene was called differentially expressed (DE) or if it was assigned to a fuzzy cluster are also included.

organism: Xenopus tropicalis

source_name: Tadpole tail

extract_protocol:
Tadpole tails were amputated and immediately placed in lysis buffer (1% SDS, 0.100M NaCl, 0.010M EDTA, 0.20M Tris ph 7.6, Proteinase K) followed by ethanol precipitation to extract RNA. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tadpole

value: Stage 40

value: Tadpole tails were amputated

tag: time

value: 72hours post-amputation

value: Tail


title: 24hpa_rep2

value: 24hours post-amputation


title: 72hpa_rep1