title: N-NUP98 BiotinChIP

city: New York

first: Haiming

last: Xu

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Low quality (< 15) bases were trimmed using cutadapt
Reads were aligned to genome assembly mm9 using Bowtie2 with default paramters
Duplicate reads were removed using Picard MarkDuplicates
The coverage data was converted to bed format using a custom script, and then to BigWig format
Genome_build: mm9
Supplementary_files_format_and_content: BigWig format

source_name: cultured N-NUP98 transduced mouse bone marrow LSK cells

growth_protocol: BM LSK cell–derived NUP98-HOXA9 transformed cells were generated by retrovirally transduction with vectors carrying C-terminally Flag-AviTagged NUP98-HOXA9 or NUP98-HOXD13, and were further transduced with a retroviral vector harboring BirA ligase. Cels were maintained in IMDM, supplemented with heat inactivated 10% fetal bovine serum, 50 U/mL penicillin/streptomycin and murine IL3 (10 ng/mL), IL6 (10 ng/mL) and SCF (20 ng/mL).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (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.

tag: cell type

value: BM-derived cultured cells

tag: passages

value: passage 2 to passage 3

tag: chip antibody


title: SLKK_hypoxia_polyA_mRNAseq_rep2 [mRNA]

status: Public on Dec 21 2016

type: SRA

city: Bethesda

first: Coralie

last: Viollet

state: MD

address: 10 Center Dr

country: USA

institute: NIH/NCI

description: Total RNA containing short RNA fraction; DNase treated; polyA enriched fraction

library_source: transcriptomic

data_processing:
For mRNA sequencing: Adapter sequences were trimmed using the Fastx toolkit. Reads were aligned against two target genomes, human (hg19) and KSHV (Genbank accession number NC_009333.1) using TopHat (Trapnell, Pachter, & Salzberg, 2009) to generate spliced alignments. Transcripts were assembled using Cufflinks and Cuffdiff (Trapnell et al., 2010) in order to reveal differentially expressed genes. Significant mRNA fold change was determined by an adjusted p-value lower than 0.05 based on the Benjamini and Hochberg multiple testing correction.
Genome_build: Human genome (hg19) and KSHV genome (Genbank accession number NC_009333.1)
Supplementary_files_format_and_content: bedGraph files were generated using BEDtools
Supplementary_files_format_and_content: Cufflinks ouput
Supplementary_files_format_and_content: Cuffdiff output

molecule: total RNA

organism: Homo sapiens

source_name: SLKK cells

growth_protocol: Human KS-derived SLK and SLKK cells (also known as SLK+rKSHV.219) were a gift from Dr. Don Ganem (UCSF, CA). They were expanded on receipt, frozen in liquid nitrogen, and stored in a cryogenic tank until used in the experiments described hereafter. Cells were thawed and maintained in Dulbecco’s Modified Eagle medium supplemented with 10% v/v fetal bovine serum and 1% Penicillin/streptomycin/glutamine solution. Additionally, KSHV-positive SLKK cells were periodically grown under selection with 10 μg/mL puromycin to maintain the viral episome.

extract_protocol:
Total RNA was extracted from cells using miRVana miRNA isolation kit according to manufacturer’s instructions. RNA abundance and integrity were determined after isolation using a Nanodrop-ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. Only samples of total RNA with an RNA integrity number (RIN) >9 were further used for RNA-sequencing and small RNA-sequencing. All samples were stored at -80°C.
For mRNA-Seq: Total RNA was treated with Turbo DNA-free DNase I and Dynabeads to deplete samples from the residual DNA and to isolate the polyadenylated mRNA transcriptome, respectively. PolyA+ RNA libraries were then prepared with the ScriptSeq v2 RNA-Seq kit (Epicentre). The final concentration and size distribution of the RNA libraries were measured by using a Nanodrop-ND-1000 spectrophotometer, and by running a DNA 100 chip on an Agilent 2100 Bioanalyzer. Finally, a total of 6 polyadenylated mRNA libraries (3 SLK and 3 SLKK samples in hypoxia) were sequenced using the Illumina HiSeq platform.

treatment_protocol: Exposure of cell cultures to 1% oxygen was undertaken in an InVivo2 Hypoxia Work Station (Ruskinn Technology, UK). This was undertaken in parallel with cells maintained in normoxic conditions (21% O2). All cells were harvested for protein and RNA 24hrs post-treatment. All experiments were done at least in triplicate from independent cell cultures.

tag: infection status

value: Chronically KSHV-infected (Human herpesvirus 8)

tag: oxygen concentration

value: Hypoxia (1% O2 for 24hrs)

value: SLKK cells


title: N-NUP98 Bio_Input

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain


title: Day3_rep1_RiboSeq

city: La Jolla

first: Nathan

last: Lewis

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

description:
Ribosome protected RNA
S04

data_processing:
Sequence data for both RNA-Seq and Ribo-Seq were quality controlled using FastQC
Trimmomatic was used to trim adapter sequences and low quality bases from the reads.
Sequence alignment was accomplished using Bowtie2 (Langmead and Salzberg, 2012) and Tophat2 (Kim et al., 2013). Specifically, rRNA sequences were eliminated by aligning reads to CHO-K1 rRNA sequences using Bowtie2. Reads that did not align to rRNA were then aligned to CHO-K1 reference genome using Tophat2. If Tophat2 reports multiple alignments with the same best quality score, we randomly chose one hit by setting the parameter -g as 1
read counts at each base pair of a gene were based on the 5' end of aligned reads for sense mRNA and based on the 3' end of aligned reads for antisense mRNAs.
To recalibrate the distance between the 5' end and the ribosomal A site, we analyzed the sequence coverage around the translation start site and the translation stop site for every alignment length.
Genome_build: GCF_000223135.1
Supplementary_files_format_and_content: Riboseq and RNAseq quantification are stored in text files. Each row represent rawCount.

organism: Cricetulus griseus

source_name: Chinese hamster ovary cells

growth_protocol: CS13-1.0 CHO cells expressing chimeric IgG against S surface antigen of hepatitis B virus (Kim et al., 1998) were maintained in PowerCHO-2 serum free media (Lonza #12-771Q) supplied with 4mM glutamine (Lonza #17-605F) in vented Erlenmeyer shake flasks (Corning, NY) in a shaking incubator operated at 37°C, 5% CO2 and 120rpm. Additionally, cells were supplemented with 0.2% anti-clumping agent (Life Technologies #0010057AE) and, during maintenance, 1µM Methotrexate hydrate (Sigma #M8407-100MG). Due to high degree of clumping, cells were passed through a 40µm Corning cell strainer (Sigma #CLS431750-50EA) at each passage.   CS13-1.0 cells were cultivated in 1L (SR0700) bioreactors (Eppendorf DASGIP, Jülich, Germany) with a working volume of 600mL. Temperature was maintained at 37°C with an agitation rate of 200 rpm using one three-way segmented impellers. Dissolved oxygen was maintained at 50% of air saturation using air, N2, O2 and CO2 operated at a constant flow rate of 0.6 L/h. Culture pH was maintained at 7.15 with a dead-band of 0.15 using intermittent CO2 addition to the gas mix and 2M sodium carbonate. Culture pH and pO2 was measured on-line. Cell number and viability were measured using a hemocytometer with tryphan blue staining (Sigma-Aldrich). Batch cultures were seeded with 0.3x106 cells/mL in triplicates and samples were drawn on a daily basis. On day 3 and day 6 samples were taken for ribosome profiling. The culture was terminated after 170 hours.

extract_protocol:
RNA was extracted from a minimum of 1x106 cells using Trizol (Life Technologies #15596-026) following manufacturer’s protocol. For qPCR analysis, cDNA was made from 500ng TURBO-DNase (Life Technologies #AM1907) treated RNA, using the qScript Flex cDNA kit (Quanta Bioscience # 95049-100) with random priming. qPCR was run in an Mx3005P (Agilent Technologies) using Brilliant III Ultra-Fast SYBR® Green master mix (Agilent Technologies # 600882). Oligos for qPCR are listed in Supplementary table S1. Fold changes was calculated using the ∆∆CT method. GAPDH was used as reference gene in all calculations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: antibody

value: IgG

tag: phase

value: Exponential phase


title: WT_noZn_RNA-seq

city: Livermore

first: Dan

last: Park

address: 7000 East Ave

department: BBTD

institute: Lawrence Livermore National Lab

data_processing:
Reads were mapped using Bowtie v1.1.1
HTSeq-0.6.1p1 was used to quantify the number of counts per genomic feature
HTSeq-0.6.1p1 output was converted to a .bam file, sorted, and indexed using samtools-0.1.19
The DESeq package in R was used to determine differential expresssion
Genome_build: GenBank accession number NC_011916.1
Supplementary_files_format_and_content: RSeQC-2.3.9 was used to normalize the counts data and generate wig files for visualization. Triplicate samples were merged using the median value at each coordinate. Each condition has a forward and reverse wig file associated with it
Supplementary_files_format_and_content: The wig files were generated using the genome browser mochiview and contain the following header:
track
variableStep chrom=NC_011916.1 span=1
which would be broadly compatible with other genome browser

organism: Caulobacter vibrioides

source_name: wild type

growth_protocol: NA1000 and ΔuzcR strains were grown in PYE (peptone, yeast extract) at 30°C to an OD600 of 0.2

extract_protocol:
Cells were harvested and immediately added to ice-cold ethanol containing 5% (vol/vol) water-saturated phenol (pH 6.6). Total RNA was isolated using hot phenol and phenol/chloroform extractions.
5 ug of total RNA was treated with the ScriptSeq Complete Kit - Bacteria from Epicentre, an Illumina company (Cat# BB1224) for ribosomal RNA depletion and library generation with ScriptSeq Index Primers.

treatment_protocol: with or without one hour exposure to 40 µM ZnSO4

tag: genotype background

tag: genotype/variation

value: wild type


title: Day3_rep3_RNAseq


title: SLKK_hypoxia_polyA_mRNAseq_rep1 [mRNA]


title: Day3_rep2_RNAseq


title: uzcR_Zn_ChIP-seq

data_processing:
Reads were mapped using Bowtie v1.1.1
CSDeconv was used to determine signifcantly enriched regions
Genome_build: GenBank accession number NC_011916.1
Supplementary_files_format_and_content: QuEST version 2.4 was used to generate wig files for visualization; The wig files were generated using the genome browser mochiview and contain the following header:
track
variableStep chrom=NC_011916.1 span=1
which would be broadly compatible with other genome browser

organism: Caulobacter vibrioides NA1000

source_name: ΔCCNA_02845 (uzcR)

growth_protocol: NA1000 and ΔuzcR strains were grown in PYE at 30°C to an OD600 of 0.2

extract_protocol:
Formaldehyde crosslinked cells from an initial 50 ml of culture volume were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-1000 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and 10 μl of the UzcR antibody (affinity purified from UzcR polyclonal antiserum) was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.
The ChIP library prep was constructed using PrepX Complete ILMN 32i DNA library kit (Cat#400076, Wafergen) on Apollo 324 and cleaned up with Ampure beads.  The libraries were quantified to measure sequenceable fragments using Kapa Biosystem Illumina Library compilation quantitative PCR reagents on a Roche LightCycler 480 then pooled at 3 nM and seqeunced on the HiSeq4000.

value: deltaCCNA_02845 (uzcR)

tag: exposed to

value: 40 µM ZnSO4 for 1 hr

value: 10 ul affinity purified UzcR antibody


title: SLK_hypoxia_polyA_mRNAseq_rep3 [mRNA]

source_name: SLK cells

value: Not infected

value: SLK cells


title: NUP98-TOP1 Biotin ChIP_1

source_name: cultured NUP98-TOP1 transformed mouse bone marrow LSK cells

value: BM-derived immortalised cells

value: passage 5 to passage 10


title: Control for ALKBH5 knockdown 1

city: Heidelberg

first: Jan

last: Mauer

state: BW

address: Im Neuenheimer Feld, 583

country: Germany

institute: BioMed X Innovation Center

data_processing:
To generate m6Am_regions.bed, raw miCLIP reads were first trimmed of their 3' linker (sequence: AGATCGGAAGAGCGGTTCAG) using flexbar (version 2.5).
Reads belonging to each of the 6 biological replicates, as well as other nonspecific reads, were demultiplexed using the pyCRAC tool suite (version 1.2.2.3) and the following 5' barcodes: NNNGGTT, NNNTTGT, NNNCAAT, NNNACCT, NNNGGCG, NNNCCGG.
Reads belonging to each of the 6 biological replicates, but not other nonspecific reads, were concatenated together.
PCR duplicates were removed from the concatenated file using the pyCRAC tool suite (version 1.2.2.3).
Unique reads were aligned to the human genome (hg19) using bowtie (version 1.1.1).
m6Am-containing regions were identified using custom bash and perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: The *.results files contain normalized gene counts derived from the standard RNA-Seq by Expectation-Maximization (RSEM) pipeline. m6Am_regions.bed is a .bed format file and contains the coordinates of m6Am-containing regions in HEK293T cells.

source_name: HEK 293T (ATCC CRL-11268)

growth_protocol: Cells were grown as per ATCC guidelines.

extract_protocol:
For RNA-Seq, total RNA was collected using the TRIzol reagent, and was DNase-treated prior to library construction. For miCLIP, total RNA was collected using the TRIzol reagent and treated with DNase. Then, poly(A)+ RNA was selected using oligo(dT) magnetic beads prior to subjecting the samples to the miCLIP protocol.
For RNA-Seq, libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. For miCLIP, libraries were constructed using the iCLIP cloning process, as previously described (see GSE63753).

treatment_protocol: FTO and ALKBH5 knockdown experiments were carried out in HEK293T cells using either Pepmute transfection reagent (Signagen) or Lipofectamine RNAiMAX (ThermoFisher Scientific) with 20 nM dsiRNA duplex directed against FTO (HSC.RNAI.N001080432.12.1, Integrated DNA Technologies) or 50 nM Silencer Select siRNA duplex pool targeting AlkBH5 (s29686, s29687, s29688, ThermoFisher Scientific), respectively.  Scrambled siRNA was used as non-targeting control. DCP2 CRISPR knockout HEK293T cells and wild type control HEK293T cells were treated with actinomycin D for 2 hours at a concentration of 5µg/ml.

value: human embryonic kidney cells

tag: treatment

value: scrambled siRNA transfected

tag: number of replicates

tag: cell line


title: MLL1ChIP_HsiehAb_NUP98-HOXA9-1

source_name: cultured NUP98-HOXA9 transformed mouse bone marrow LSK cells

value: anti-MLL1 (MO453, provide by James Hsieh lab)


title: MLL1ChIP_HsiehAb_NUP98-HOXA9-1-Input


title: SLK_hypoxia_polyA_mRNAseq_rep2 [mRNA]


title: mrna-seq P4 a

status: Public on Dec 20 2016

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

country: China

institute: Nanjing Normal University

data_processing:
The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). analysis.
Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by LC Sciences (Houston, TX, USA).
After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software as described for de novo transcriptome assembly without a reference genome. The quality of the assembly was critically assessed by LC Sciences before subsequent
For homology annotation, non-redundant sequences were annotated based on the following databases: Swiss-Prot (a manually annotated and reviewed protein sequence database); Nr (NCBI non-redundant protein sequences); Pfam (protein family); KEGG (KEGG Ortholog database); and KOG (euKaryotic Ortholog Groups).
Supplementary_files_format_and_content: The expression level of each transcript was measured as the number of clean reads mapped to its sequence. The mapped clean read number was normalized to RPKM (reads per kilo of per million mapped reads) with RSEM 1.2.3. We used DESeq to determine the FDR threshold. FDR < 0.05 and fold change > 2 were considered to indicate significant expression abundance.

organism: Tachysurus vachellii

source_name: liver

growth_protocol: P. vachelli (13 ± 1.12 cm in length, 20 ± 1.77 g in weight) were randomly transferred to three aquaria with bio-filtered water recirculation systems (equipped with cooling and heating functions and a volume of 200 L and flow rate of 5 L/min) and fed with artificial compound feed, including more than 42.0% protein (Zhenjiang Jiaji Feed Co. Ltd., China). Normal oxygen concentration was 6.8 mg/L (measured with an HQd portable meter and LDO101 probe).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analysed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
For six cDNA library constructions, approximately 5μg of total RNA per sample was used for the RNA sample preparations. The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by LC Sciences (Houston, TX, USA). After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software

treatment_protocol: Control fish (P0 a, P0 b, and P0 c) were removed from three aquaria for immediate liver dissection. Next, the oxygen infiltration and recirculation systems in the three aquaria were closed to initiate the hypoxia experiments. The water was deoxygenated for 30-35 min by bubbling pure nitrogen gas in order to decrease oxygen concentration from 6.8mg/L to 0.7mg/L. After oxygen concentration was maintained for 4 h by continuous bubbling of nitrogen gas, the experimental fish (P4 a, P4 b, and P4 c) were quickly removed for liver dissection. Samplings of control fish (P0 a, P0 b, and P0 c) and experimental fish (P4 a, P4 b, and P4 c) had three biological replicates, each made up of five different individual liver tissues. Fish were killed by dissection after mild anaesthetisation in a eugenol bath (1:10,000), after which they were frozen in liquid nitrogen and stored at -80°C.

tag: age

value: juvenile fish

tag: tissue

value: liver

value: hypoxia fish


title: Day3_rep1_RNAseq


title: mrna-seq P4 c


title: WT_noZn_ChIP-seq


title: mrna-seq P4 b


title: NUP98-TOP1 Bio Input


title: mrna-seq P0 c

value: control fish


title: mrna-seq P0 b


title: mirna-seq P4 a

data_processing:
The libraries were sequenced by Illumina Hiseq2500 50SE (single end) at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.
Briefly, the raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, TX, USA), to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats.
Subsequently, unique sequences 18-26 nt in length were mapped to specific species precursors in miRBase 21.0 by Bowtie search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
Supplementary_files_format_and_content: miRNA differential expression based on normalized deep-sequencing counts was analysed by selectively using Student t test based on the experimental design.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analysed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 2.5 ug of total RNA were used to prepare small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA).


title: mirna-seq P0 a


title: WTv-biological rep2

city: Gainesville

first: SANG-JOON

last: AHN

state: Florida

address: 1395 Center Drive

institute: University of Florida

data_processing:
Sequenced reads were mapped on a Galaxy server using Bowtie for Illumina (version 1.1.2)
Mapped reads per gene were counted from BAM files using htseq-count
Count-based differential expression of genes was analyzed by the R package edgeR on RStudio
Supplementary_files_format_and_content: Tab-delimited text files include DE and htseq-count values, and functional descriptions for 10 different comparisons.

organism: Streptococcus mutans

source_name: UA159, vancomycin, 1μg/ml (anaerobic)

growth_protocol: Cultured in BHI medium; To achieve an anaerobic condition, mineral oil was placed on top of the cultures; Cells were harvested at the mid-exponential phase of growth.

extract_protocol:
Collected cells were treated withRNAprotect reagent (Qiagen)
Total RNA was isolated and purified by RNeasy Mini Kits (Qiagen) with on-column digestion by RNase-free DNase I
mRNA was enriched by using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion)
cDNA libraries were constructed from the enriched mRNA samples by using NEBNext Ultra directional RNA library prep kit for Illumina and NEBNext multiplex oligonucleotides for Illumina (New England BioLabs),

treatment_protocol:
For aerobic conditions, cultures were grown on a rotary shaker (115 rpm) without mineral oils.
For high temperature stress, cells were grown at 40°C; For vancomycin stress, cells were grown in BHI supplemeted with vancomycin at the final concentration of 1 μg/ml

tag: genotype

tag: culture condition

value: vancomycin, 1ug/ml (anaerobic)


title: WTv-biological rep3


title: mirna-seq P4 c


title: ABv-biological rep2

source_name: lrgAB-ΩKm (SAB115), vancomycin, 1μg/ml (anaerobic)

value: lrgAB mutant


title: mirna-seq P4 b


title: mirna-seq P0 c


title: mirna-seq P0 b


title: ABv-biological rep3


title: WTv-biological rep1

value: wild type


title: WTh-biological rep1

source_name: UA159, at 40°C (anaerobic)

value: at 40°C (anaerobic)


title: WTh-biological rep2


title: mrna-seq P0 a


title: WT_Zn_ChIP-seq

value: 40 µM ZnSO4 for 1 hr


title: ABh-biological rep3

source_name: lrgAB-ΩKm (SAB115), at 40°C (anaerobic)


title: ABa-biological rep1

source_name: lrgAB-ΩKm (SAB115), aerobic

value: aerobic


title: ABh-biological rep1


title: WTh-biological rep3


title: SLK_hypoxia_polyA_mRNAseq_rep1 [mRNA]

value: Not infected

value: Hypoxia (1% O2 for 24hrs)

tag: cell type


title: AB-biological rep1

source_name: lrgAB-ΩKm (SAB115), anaerobic

value: anaerobic


title: WTa-biological rep1

source_name: UA159, aerobic


title: ABa-biological rep3


title: ABa-biological rep2


title: ABh-biological rep2


title: AB-biological rep2


title: ABv-biological rep1


title: WTa-biological rep2


title: WTa-biological rep3


title: WT-biological rep2

source_name: UA159, control (anaerobic)

value: control (anaerobic)


title: WT-biological rep1


title: AB-biological rep3


title: LuCaP 35.1 CRPC S57 [RNA-seq]

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads are mapped to human reference genome hg19 and refSeq annotation database using tophat  version 1.3.2
Raw counts are generated using HtSeq with intersection-strict option
Differential analysis was done using cuflinks and cufdiff 2.0.0
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw count text file

source_name: castration-recurrent prostate cancer  (CRPC)  human prostate cancer LuCaP 35 cell line xenograft tumors in SCID mice

growth_protocol: Ten million cells were grown to 70–80% confluence in a 150 mm culture dish containing ADM for 48 h.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) as per the manufacturer’s instructions
The quality of RNA was determined using an Agilent Bioanalyzer 2100 (Santa Clara, CA), requiring RIN (RNA Integrity Number) value of ≥6.5.  rRNA depletion (cytoplasmic and mitochondrial) was performed on 200-400 ng of total RNA using the RiboZeroGold kit (Illumina, San Diego, CA) as per the manufacturer’s instructions. The entire rRNA-depleted fraction (ranging 4-22 ng) was used as input for library preparation using the ScriptSeq V2 RNA Seq library preparation kit (Illumina, San Diego, CA) as per the manufacturer’s instructions.

treatment_protocol: 10nM DHT or vehicle 16 h

tag: cell line source

tag: cell/tissue type

value: xenograft tumors

tag: host strain

value: SCID mice


title: LuCaP 35.1 AD-mPC P64 [RNA-seq]

source_name: androgen-dependent (AD)  human prostate cancer LuCaP 35 cell line xenograft tumors in SCID mice


title: 22RV1-control [RNA-seq]

source_name: human prostate cancer 22RV1 cell line

value: human prostate cancer cell line


title: 22RV1 + DHT [RNA-seq]

value: dihydrotestosterone  (DHT)


title: LuCaP 35.1 CRPC S58 [RNA-seq]

value: castration-recurrent prostate cancer  (CRPC)  human prostate cancer LuCaP 35 cell line


title: LuCaP 35.1 CRPC S55 [RNA-seq]


title: LuCaP 35.1 AD-mPC P71 [RNA-seq]

value: androgen-dependent (AD)  human prostate cancer LuCaP 35 cell line


title: WT-biological rep3

tag: strain


title: LuCaP 35.1 AD-mPC P79 [RNA-seq]


title: CNCap-C4-2-control [RNA-seq]

source_name: human prostate cancer LNCap-C4-2  cell line


title: LNCap-C4-2 + DHT [RNA-seq]


title: LNCaP-SRC-control [RNA-seq]

source_name: human prostate cancer LNCaP line

value: LNCaP

tag: genetic change

value: Expression of Src-527F


title: NonNF2_MN-249_H3k27me3_ChIPSEQ

city: New Haven

first: Akdes

last: Serin Harmanci

state: Connecticut

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University

description:
ChIP-Seq
processed data file:
MN-249.bed

data_processing:
H3K27me3 reads were aligned uniquely with bowtie to the human genome (hg19). Regions of enrichment were identified with MUSIC algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: bed

growth_protocol: Samples were excised during neurosugical procedures and frozen in OCT for later use. H&E slides were prepared for each sample to confirm tumor histology and assess tissue density. On the day of each experiment, sections were cut using a cryostat (20uM) and immediately prepared for immunoprecipitation.

extract_protocol:
10 to 15 frozen sections of each tumor block or dura sample were collected for each experiment. Tissue was crosslinked with 1% formaldehyde, quenched with glycine, and washed with PBS.  Nuclei were extracted by dounce homogenization and resuspended in nuclear lysis buffer containing 0.3% SDS.  Chromatin was sheared by sonication with a Q800R2 Sonicator by QSonica (60 minutes total, amplitude 30, 10 second pulses, 10 second rest).  Soluble chromatin was incubated with magnetic beads coated with H3K27me3 antibody (ab6002) overnight at 4°C.  Chromatin was precipitated using a magnet, washed extensively, and eluted with TE+1% SDS.  Crosslinks were reversed, and samples were purified.
Prior to sequencing, the enrichment of each sample was calculated using qPCR and well-established control primers for H3K27me3. Samples were subjected to standard Illumina paired-end multiplexed library construction. H3K27me3 ChIP and input samples were sequenced for each tumor (1x75bp, HiSeq 2000).

treatment_protocol: All samples are untreated, primary specimens from brain tumor patients.

tag: tissue type

value: meningioma

tag: grade


title: NonNF2_MN-26_H3k27me3_INPUT

description:
control
processed data file:
MN-26.bed


title: NF2_MN-97_H3k27me3_ChIPSEQ

description:
ChIP-Seq
processed data file:
MN-97.bed


title: NonNF2_MN-105_H3k27me3_ChIPSEQ

description:
ChIP-Seq
processed data file:
MN-105.bed


title: NF2_MN-54_H3k27me3_ChIPSEQ

description:
ChIP-Seq
processed data file:
MN-54.bed


title: LNCaP + DHT [RNA-seq]


title: VCaP-control [RNA-seq]

source_name: human prostate cancer VCaP line

value: VCaP


title: Hedgehog_INPUT [MN-79]

description:
MN-79_INPUT
processed data file:
mn_54_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed

data_processing:
H3K27ac reads were aligned uniquely with bowtie (0.12.7) 77 to the human genome (hg19). Regions of enrichment were identified with MACS (v1.4) 78.
Super-enhancers were separated from typical enhancers using ROSE pipeline with parameters -s (stitching) 12500, -t (promoter exclusion zone) 2000.  We used DiffBind to estimate significance of super-enhancer read change (adjusted p-value threshold = 0.05) between meningioma subtypes.
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: meningioma

extract_protocol:
10 to 15 frozen sections of each tumor block or dura sample were collected for each experiment. Tissue was crosslinked with 1% formaldehyde, quenched with glycine, and washed with PBS.  Nuclei were extracted by dounce homogenization and resuspended in nuclear lysis buffer containing 0.3% SDS.  Chromatin was sheared by sonication with a Q800R2 Sonicator by QSonica (60 minutes total, amplitude 30, 10 second pulses, 10 second rest).  Soluble chromatin was incubated with magnetic beads coated with either H3K27ac antibody (ab4729) overnight at 4°C.  Chromatin was precipitated using a magnet, washed extensively, and eluted with TE+1% SDS.  Crosslinks were reversed, and samples were purified.
Prior to sequencing, the enrichment of each sample was calculated using qPCR and well-established control primers for H3K27ac.. Samples were subjected to standard Illumina paired-end multiplexed library construction. H3K27ac ChIP and input samples were sequenced for each tumor (1x75bp, HiSeq 2000).

tag: mutation subtype

value: Hedgehog

value: benign

tag: chip antibody

value: none (input)


title: NF2/Chr22_INPUT [MN-97]

description:
MN-97_INPUT
processed data file:
mn_97_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed

value: Atypical


title: LNCaP-SRC + DHT [RNA-seq]

tag: treatment


title: LNCaP-control [RNA-seq]


title: VCaP + DHT [RNA-seq]


title: NonNF2_MN-105_H3k27me3_INPUT

description:
control
processed data file:
MN-105.bed


title: NonNF2_MN-26_H3k27me3_ChIPSEQ

description:
ChIP-Seq
processed data file:
MN-26.bed


title: NonNF2_MN-249_H3k27me3_INPUT

description:
control
processed data file:
MN-249.bed


title: NF2/Chr22_INPUT [MN-291]

description:
MN-291_INPUT
processed data file:
mn_292_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2/Chr22_INPUT [MN-288]

description:
MN-288_INPUT
processed data file:
mn_291_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/KLF4_INPUT [MN-191]

description:
MN-191_INPUT
processed data file:
mn_201_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2/Chr22_INPUT [MN-171]

description:
MN-171_INPUT
processed data file:
mn_191_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2_MN-97_H3k27me3_INPUT

description:
control
processed data file:
MN-97.bed


title: TRAF7/PIK3_INPUT [MN-163]

description:
MN-163_INPUT
processed data file:
mn_163_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2_MN-171_H3k27me3_INPUT

description:
control
processed data file:
MN-171.bed


title: NF2_MN-54_H3k27me3_INPUT

description:
control
processed data file:
MN-54.bed


title: Hedgehog_INPUT [MN-1044]

description:
MN-1044_INPUT
processed data file:
mn_1044_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/KLF4_INPUT [MN-1066]

description:
MN-1066_INPUT
processed data file:
mn_1066_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/PIK3_INPUT [MN-1037]

description:
MN-1037_INPUT
processed data file:
mn_1037_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: control_INPUT [CONTROL2]

description:
CONTROL2_INPUT
processed data file:
control_2_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed

source_name: dura

value: dura

value: control


title: NF2/Chr22_INPUT [MN-54]

description:
MN-54_INPUT
processed data file:
mn_171_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2_MN-171_H3k27me3_ChIPSEQ

description:
ChIP-Seq
processed data file:
MN-171.bed


title: control_INPUT [CONTROL1]

description:
CONTROL1_INPUT
processed data file:
control_1_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2/Chr22_ChIP-Seq [MN-54]

description:
MN-54_ChIP-Seq
processed data file:
mn_171_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed

value: H3k27ac (Abcam, ab4729)


title: Hedgehog_INPUT [MN-24]

description:
MN-24_INPUT
processed data file:
mn_249_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/PIK3_INPUT [MN-292]

description:
MN-292_INPUT
processed data file:
mn_297_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/PIK3_ChIP-Seq [MN-292]

description:
MN-292_ChIP-Seq
processed data file:
mn_297_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: FW

city: Ningbo

first: Zhang

last: Hao

address: Fenghua Road No. 818

institute: NINGBO UNIVERSITY

data_processing:
By base calling, the original image data produced by the sequencer is transferred into sequences, which are defined as "raw reads"(or "raw data") and saved as ".fastq" files. As the raw reads may contain low quality reads and or adaptor sequences, preprocessing is necessary before starting further analysis. Normally, data cleaning (or data filtering) is performed to obtain "clean reads" (or "clean data") for further analysis.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample. The related information of gene is also provided (Coverage, Symbol, Description and so on).
The gene expression level is calculated by using FPKM method (Fragments Per kb per Million reads).
Screening of differentially expressed genes (DEGs) between two samples. This analysis includes the screening of genes that are differentially expressed among samples, and GO functional enrichment analysis and KEGG pathway enrichment analysis for these DEGs. Referring to "The significance of digital gene expression profiles[4]", we have developed a strict algorithm to identify differentially expressed genes between two samples.
Genome_build: de novo assembly. FASTA of assembled sequences are available on the series record.
Supplementary_files_format_and_content: results files include transcript_id, gene_id, length, effective_length, expected_count, TPM, and FPKM values for each Sample.

organism: Plecoglossus altivelis

source_name: multiple tissues_fresh water

growth_protocol: Ayu larvae were kept in BW or FW tanks at 20–22 °C in a recirculating system with filtered water after hatching, and fed with commercial pellets once a day.

extract_protocol:
Heart, liver, spleen, gill, kidney, skin, muscle, intestine, and brain tissues from ayu after BW or FW acclimation for 4 weeks were mixed.
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.

treatment_protocol: Groups of 20 fish each were subjected to BW (containing 0.17 M NaCl, 10 ppt) in four tanks (BW group) or to FW in the other four tanks (FW group).

tag: developmental stage

value: larvae


title: NF2/Chr22_ChIP-Seq [MN-291]

description:
MN-291_ChIP-Seq
processed data file:
mn_292_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/KLF4_INPUT [MN-249]

description:
MN-249_INPUT
processed data file:
mn_288_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2/Chr22_INPUT [MN-169]

description:
MN-169_INPUT
processed data file:
mn_169_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/PIK3_INPUT [MN-105]

description:
MN-105_INPUT
processed data file:
mn_105_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/KLF4_INPUT [MN-201]

description:
MN-201_INPUT
processed data file:
mn_24_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2/Chr22_INPUT [MN-297]

description:
MN-297_INPUT
processed data file:
mn_79_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: Hedgehog_ChIP-Seq [MN-79]

description:
MN-79_ChIP-Seq
processed data file:
mn_54_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2/Chr22_ChIP-Seq [MN-97]

description:
MN-97_ChIP-Seq
processed data file:
mn_97_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2/Chr22_ChIP-Seq [MN-171]

description:
MN-171_ChIP-Seq
processed data file:
mn_191_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/PIK3_ChIP-Seq [MN-105]

description:
MN-105_ChIP-Seq
processed data file:
mn_105_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: control_ChIP-Seq [CONTROL1]

description:
CONTROL1_ChIP-Seq
processed data file:
control_1_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: BW

source_name: multiple tissues_brackish water

value: Heart, liver, spleen, gill, kidney, skin, muscle, intestine, and brain


title: NF2/Chr22_ChIP-Seq [MN-297]

description:
MN-297_ChIP-Seq
processed data file:
mn_79_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: NF2/Chr22_ChIP-Seq [MN-288]

description:
MN-288_ChIP-Seq
processed data file:
mn_291_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: RD RNA-seq

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using TopHat.
Gene expression values were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks and the UCSC reference at the gene level.
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM files are provided in txt format at the gene-level

source_name: RD Fusion Negative Rhabdomyosarcoma cell line

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
RNA was extracted from RMS cell lines using the RNeasy mini kit (Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: no treatment

tag: cell line


title: Hedgehog_ChIP-Seq [MN-24]

description:
MN-24_ChIP-Seq
processed data file:
mn_249_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/KLF4_ChIP-Seq [MN-249]

description:
MN-249_ChIP-Seq
processed data file:
mn_288_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: RH18 RNA-seq

source_name: RH18 Fusion Negative Rhabdomyosarcoma cell line


title: TRAF7/KLF4_ChIP-Seq [MN-201]

description:
MN-201_ChIP-Seq
processed data file:
mn_24_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/KLF4_ChIP-Seq [MN-191]

description:
MN-191_ChIP-Seq
processed data file:
mn_201_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: Ad.sh-NKX2.2-3 LG8

city: Aurora

first: Lori

last: Sussel

state: CO

address: 1775 Aurora Ct.

institute: University of Colorado

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 1.8.4) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped  to a reference genome (Human: NCBI/build37.2) using Tophat (Trapnell C et al 2009 Bioinformatics) (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Relative abundance (aka expression level) of genes and splice isoforms was determined using cufflinks (Trapnell C et al 2010 Nature Biotech) (version 2.0.2) with default settings.
Differentially expressed genes were calculated using Deseq (Anders S et al 2010 Genome Biology).
Genome_build: build37.2
Supplementary_files_format_and_content: csv-files includse FPKM values for all genes/isoforms in a sample
Supplementary_files_format_and_content: csv-file includes DeSeq analysis for all samples

source_name: pancreatic islets

extract_protocol:
Human islets from 3 donors were obtained through the NIH-supported Integrated Islet Distribution Program (IIDP) via Mt Sinai Human Islet Core facility. The islets were harvested from deceased donors without any identifying information at NIH-approved centers with informed consent and IRB approval at the islet-isolation centers.
Total RNA was isolated using QIAGEN RNeasy Micro kit. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dispersed human islets were transduced with either experimental (Ad.sh-Nkx2.2) or control (Ad.Scrambled) at 300 MOI in serum free media for 2 hrs. Transduction was stopped by adding complete medium containing 10% FCS and cultured for 96 hrs

tag: sample name

value: pancreatic islets


title: NF2/Chr22_ChIP-Seq [MN-169]

description:
MN-169_ChIP-Seq
processed data file:
mn_169_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: Ad.Scramble-1 LG3

tag: tissue


title: Ad.Scramble-2 LG6


title: HCT116 - CNOT3_ChIPseq

city: Boston

first: Paloma

last: Cejas

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
Cell line
CNOT3_ChIPseq
Cells were cross-linked with 1% formaldehyde for 20 min at 37oC, and sonicated for 40 minutes using Covaris Instrument followed by ChIP with 10 µg CNOT3 Ab. DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).

data_processing:
Alignment: For ChIPseq experiments we used Bowtie2 (2.1.0) with settings (--no-unal). For RNAseq we used Tophat, version 2.0.9, default options.
ChIPseq analyses: For peak calling we used MACS2 using Q:0.01.
RNAseq analyses: normalized and differential expression: Cufflinks, version 2.2.1; settings: -b, -u, and default; Cuffmerge was used with reference gtf and default settings; Cuffquant was used with default settings; Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Genome_build: Hg19
Supplementary_files_format_and_content: ChIPseq: Wiggle files were generated by NPS software using parameters by default. Bed files (the 5 columns are 1: chromosome, 2: start location, 3: end location, 4: peak number, 5: score).
Supplementary_files_format_and_content: RNAseq: Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals.  There are two processed data matrices that apply to all the samples.  There exists a differential expression table, prepared using Cuffdiff with an FDR of 5%, which contains average normalized FPKM values for Controls infected with a non specific NS_shRNA construct (Scr) and CNOT3-depleted by infection with shRNA_#3 construct (silenced), as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.

source_name: Colorectal cancer cell line

growth_protocol: Sections of snap-frozen tissues were either micrococcal nuclease treated or cross-linked with 1% formaldedyde for 20 minutes and sonicated for ChIPseq experiments followed b ChIP with 10ug of antibody. HCT116 cells were cross-linked with 1% formaldehyde for 20 min at 37oC, followed by ChIP with 10 µg CNOT3 for ChIPseq. For RNAseq experiments cells were washed with PBS and total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic.

extract_protocol:
ChIPseq: Lysates were clarified from micrococcal nuclease digested or sonicated or and histone-DNA or CNOT3-DNA complexed were  isolated with antibody.
RNAseq: Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.
For ChIPseq:ThruPLEX-FD kits (Rubicon Genomics) was used and 50 bp single-end reads were sequenced on a HiSeq2000 instrument (Illumina).
For RNAseq: TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: CNOT3 (Novus Biologicals, catalog# H00004849_M01, lot# A1171-4B8)


title: TRAF7/PIK3_ChIP-Seq [MN-163]

description:
MN-163_ChIP-Seq
processed data file:
mn_163_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: Hedgehog_ChIP-Seq [MN-1044]

description:
MN-1044_ChIP-Seq
processed data file:
mn_1044_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: TRAF7/PIK3_ChIP-Seq [MN-1037]

description:
MN-1037_ChIP-Seq
processed data file:
mn_1037_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: control_ChIP-Seq [CONTROL2]

description:
CONTROL2_ChIP-Seq
processed data file:
control_2_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: Ad.sh-NKX2.2-2 LG5


title: Ad.sh-NKX2.2-1 LG2


title: Ad.Scramble-3 LG9


title: Adenoma_9_Input - Input_DNA

description:
Adenoma_9_from_patient_9
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).

source_name: Primary colonic adenoma, snap-frozen tissue

value: Primary colonic adenoma

tag: patient


title: Adenoma_4_Input - Input_DNA

description:
Adenoma_4_from_patient_4
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Carcinoma_9 - CNOT3_ChIPseq

description:
Carcinoma_9_from_patient_9
CNOT3_ChIPseq
20 tissue sections from were cross-linked with 1% formaldehyde for 20 min at 37oC, and sonicated for 40 minutes using Covaris Instrument followed by ChIP with 10 µg CNOT3 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)

source_name: Primary colorectal carcinoma, snap-frozen tissue

value: Primary colorectal carcinoma


title: Carcinoma_10_Input - Input_DNA

description:
Carcinoma_10_from_patient_10
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Carcinoma_2 - CNOT3_ChIPseq

description:
Carcinoma_2_from_patient_2
CNOT3_ChIPseq
20 tissue sections from were cross-linked with 1% formaldehyde for 20 min at 37oC, and sonicated for 40 minutes using Covaris Instrument followed by ChIP with 10 µg CNOT3 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Carcinoma_9_Input - Input_DNA

description:
Carcinoma_9_from_patient_9
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Carcinoma_8_Input - Input_DNA

description:
Carcinoma_8_from_patient_8
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Carcinoma_6 - H3K4me2_ChIPseq

description:
Carcinoma_6_from_patient_6
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)

value: H3K4me2 (Millipore, catalog# 07-030, lot# 2019745)


title: Carcinoma_7_Input - Input_DNA

description:
Carcinoma_7_from_patient_7
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Carcinoma_5 - H3K4me2_ChIPseq

description:
Carcinoma_5_from_patient_5
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Carcinoma_1_Input - Input_DNA

description:
Carcinoma_1_from_patient_1
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Carcinoma_1 - H3K4me2_ChIPseq

description:
Carcinoma_1_from_patient_1
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Carcinoma_3 - H3K4me2_ChIPseq

description:
Carcinoma_3_from_patient_3
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Carcinoma_4_Input - Input_DNA

description:
Carcinoma_4_from_patient_4
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Carcinoma_3_Input - Input_DNA

description:
Carcinoma_3_from_patient_3
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Adenoma_9 - H3K4me2_ChIPseq

description:
Adenoma_9_from_patient_9
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Carcinoma_6_Input - Input_DNA

description:
Carcinoma_6_from_patient_6
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Adenoma_10 - H3K4me2_ChIPseq

description:
Adenoma_10_from_patient_10
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Adenoma_10_Input - Input_DNA

description:
Adenoma_10_from_patient_10
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Adenoma_4 - H3K4me2_ChIPseq

description:
Adenoma_4_from_patient_4
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Adenoma_5 - H3K4me2_ChIPseq

description:
Adenoma_5_from_patient_5
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: TRAF7/KLF4_ChIP-Seq [MN-1066]

description:
MN-1066_ChIP-Seq
processed data file:
mn_1066_h3k27ac_peaks_Gateway_SuperEnhancers_forDiffBind.bed


title: Adenoma_8_Input - Input_DNA

description:
Adenoma_8_from_patient_8
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Adenoma_7_Input - Input_DNA

description:
Adenoma_7_from_patient_7
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Adenoma_3_Input - Input_DNA

description:
Adenoma_3_from_patient_3
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Carcinoma 10 - H3K4me2_ChIPseq

description:
Carcinoma_10_from_patient_10
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Carcinoma 9 - H3K4me2_ChIPseq

description:
Carcinoma_9_from_patient_9
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Adenoma_1 - H3K4me2_ChIPseq

description:
Adenoma_1_from_patient_1
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Restricted 8 TP2 [liver]

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL4-35

data_processing:
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned to UMD3.1 genome using Tophat
Raw counts were enumerated using HTSEQ-count (settings: mode = union)
The raw read counts were normalized using scaling factors estimated by the Trimmed mean of M-Values (TMM) method implemented  the edgeR software package. The normalised values represent read counts per million mapped reads, adjusted for sample library size.
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: Tab delimited txt files (First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene)
Supplementary_files_format_and_content: [Normalized counts] Tab delimited txt files (First row contains the ENSEMBL gene IDs and second row the normalized values that map to each gene)

organism: Bos taurus

source_name: Liver

growth_protocol: Purebred Holstein Friesian bulls (n=20) were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=10) followed by ad libitum access to feed for a further 55 days or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=10).  The first 125 days of the trial were denoted as Peirod 1, during which treatment groups were fed differentially. the subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependnet on each treatment group. restricted fed animals were fed to grow at 0.6 kg /day during Peirod 1, with ad libitum animals expected to gain in excess of 1.5 to 2 kg/day

extract_protocol:
Total RNA was extracted from frozen liver tissue by homogenisation using the Qiagen Rneasy RNA isolation kit.
Single-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

treatment_protocol: 20 bulls fed a restricted diet for 125 days to grow at 0.6kg/day, after which they were fed ad libitum for a further 55 days. The remaining 20 bulls in the control group were fed ad libitum throughout

tag: breed

value: Holstein-Friesian

tag: gender

value: male

tag: diet

value: 70% concentrate, 30% grass silage diet

value: Liver

tag: biopsy day

value: day 55 of Period 2

tag: feeding period

value: Realimentation period

tag: restriction model

value: Undergoing compensatory growth


title: Restricted 9 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL4-57


title: Restricted 7 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL3-56


title: Carcinoma 7 - H3K4me2_ChIPseq

description:
Carcinoma_7_from_patient_7
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Carcinoma_4 - H3K4me2_ChIPseq

description:
Carcinoma_4_from_patient_4
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Carcinoma 8 - H3K4me2_ChIPseq

description:
Carcinoma_8_from_patient_8
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Restricted 2 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL1-41


title: Restricted 1 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL1-38


title: Adenoma_6_Input - Input_DNA

description:
Adenoma_6_from_patient_6
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).

value: none (input)


title: Adenoma_1_Input - Input_DNA

description:
Adenoma_1_from_patient_1
Input_DNA
DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: Adenoma_8 - H3K4me2_ChIPseq

description:
Adenoma_8_from_patient_8
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Control 9 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL3-34

value: Control


title: Adenoma_7 - H3K4me2_ChIPseq

description:
Adenoma_7_from_patient_7
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Control 8 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL3-31


title: Adenoma_6 - H3K4me2_ChIPseq

description:
Adenoma_6_from_patient_6
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Control 5 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL2-42


title: Adenoma_3 - H3K4me2_ChIPseq

description:
Adenoma_3_from_patient_3
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Control 2 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL2-47


title: Adenoma_2 - H3K4me2_ChIPseq

description:
Adenoma_2_from_patient_2
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Restricted 10 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL4-46


title: Restricted 10 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL4-06

value: day 125 of Period 1

value: Differential feeding

value: Undergoing restricted feed intake


title: Restricted 9 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL4-25


title: Restricted 8 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL3-11


title: Restricted 7 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL3-30


title: Restricted 3 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL1-19


title: Carcinoma_2 - H3K4me2_ChIPseq

description:
Carcinoma_2_from_patient_2
H3K4me2_ChIPseq
10 sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: Restricted 6 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL3-53


title: Restricted 5 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL2-55


title: Control 9 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL4-20


title: Control 8 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL4-04


title: Restricted 3 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL1-44


title: Control 10 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL4-54


title: Control 7 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL3-36


title: Control 7 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL4-17


title: Control 6 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL2-37


title: Control 4 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL3-15


title: Control 3 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL2-40


title: Restricted 4 TP2 [liver]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
KKL2-45


title: Restricted 6 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL2-09


title: Input wtE9.5Tailbud 10min fix2

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR
genome build: mm9
processed data files format and content: bed and bw

source_name: Input wtE9.5Tailbud 10min fix2

extract_protocol:
Crosslinking 10mins RT, lysis, sonication according to Amin and Bobola (2014).
Illumina Truseq DNA library protocol

value: E9.5 embryo tailbud

tag: experiment type

value: ChIP-seq

tag: antibody


title: H3K27ac wtE9.5Anterior tissue rep2

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR --nomodel --extsize 300 --llocal 100000
Input control: Input_wtE9.5Anterior_10min_fix2
genome build: mm9
processed data files format and content: bed and bw

source_name: H3K27ac wtE9.5Anterior tissue rep2

extract_protocol:
Crosslinking 10mins RT, lysis, sonication and immunoprecipiation according to Amin and Bobola (2014).
Illumina Truseq DNA library protocol

value: E9.5 embryo anterior

value: Abcam, ab4729


title: Restricted 5 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL2-27


title: Restricted 4 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL2-13


title: TH-LN683_CD19-_Thy+ [RNA-Seq-TH-LN683_Delta_Day_14_19-Thy+_3]

city: Linkoping

first: Rajesh

last: Somasundaram

address: Dept of Clinical and Experimental Medicine (IKE)

department: Microbiology and Molecular Medicine

country: Sweden

institute: Linkoping University

description: RNA-seq-50-norm-tags-count-exons-condenseGenes-T-Kinetic.txt

data_processing:
RNA-Sequencing and data analysis: Each biological sample was processed and sequenced in duplicate or triplicate.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using TopHat. If not indicated, further  analyses were performed using the HOMER platform (Heinz et al. 2010). For further analyses we used normalization to 10M mapped reads by the analyzeRepeats.pl command with the  option –count exons condeseGenes. For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option, and filtered by ≥ 50 tags repeats followed by the getDiffExpression.pl  command using edgeR. Data normalized to 10M mapped reads  per experiment in log scale was visualized by Java Treeview   following hierarchical clustering in Cluster3 (centering genes on mean, average  linkage cluster). BED files were created from HOMER tagdirectories.
ATAC-Sequencing and data analysis:Libraries  were single-end sequenced on a NexSeq500. Each biological sample was processed  for ATAC-Seq and sequenced in triplicate. The data was mapped to mm10 using Bowtie2 with standard  settings. Tag directories with reads mapped to the mitochondrial chromosome filtered  out were created.  ATAC-seq peaks were identified using findPeaks.pl in HOMER with the settings: -style histone -size 75 -minDist 75 -minTagThreshold 6 -L 8 -F 8.  BED files were created from Tag directories using the HOMER package. Annotation on ATAC-seq peaks or on ChIP-seq Peaks from previously published ChIP-seq data retrived from GEO (EBF1: GSE69227, PAX5:GSE38046, GATA3:GSE31235, TCF1:GSE46662, CEBPa:GSM537983) was done in HOMER using the annotatePeaks.pl command. Peakfinding on data from GEO was also performed in HOMER using the findPeaks.pl command with the option -style factor.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include .txt files with ATAC data on annotated peak positions and .txt files of RNA-seq expression matrix. All genomic coordinates are relative to mm10 mouse assembly.

extract_protocol:
Cell culture:  Normal lineage negative Sca1+Kit+ (LSK) cells or lymph node pro-B cells (Lin- (CD11b, Gr1, Ter119 and CD11c) NK1.1-IgM-CD3-CD19+CD43+ were sorted and expanded in vitro by co-culture on OP9 stroma cells using OptiMEM supplemented with 10% heat inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand (FLT3L), and 10ng/ml Interleukin-7. For constitutively active Notch1 expression experiments, ICN1-pMIG or pMIG (control) retrovirus (MSCV) transduced cells were differentiated on OP9 for 14 days. For extra-cellular Notch experiment control cells were co-cultured on OP9 or OP9-DL1 stroma cells for 14 days.  Both for extracellular Notch and the constitutive Notch1 signal experiments, the above-mentioned media and the cytokines were used. During C/EBPα transduction experiment C/EBPα-ER-pMIG or pMIG (Control) retrovirus were transduced into pro-B cells and cultured either with or without 4-HydroxyTamoxifen (1μM; Sigma; H7904) supplemented with 10% heat inactivated Charcoal stripped fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/mL Fms-like tyrosine kinase 3 ligand (FLT3L), 10ng/ml Interleukin-7, 10ng/ml IL3, 10ng/ml SCF 10ng/mL M-CSF and analysed by flow cytometry and the cells were sorted for RNA-Seq or ATAC-Seq.    FACS staining.  Frozen lymph node cells were CD16/CD32 (Fc)–blocked, stained and sorted based on the following markers (Lin- (CD11b,Gr1,Ter119 and CD11c) NK1.1-CD3-CD19+CD43+ and expanded in vitro by co-culture on OP9 stroma cells. For in vitro differentiation (pro-B to T cells) experiments, CD16/CD32 (Fc)–blocked cells were stained with antibodies against CD3, CD19 and Thy1.2. For in vitro  (pro-B to Myleoid) differentiation analysis CD16/CD32 (Fc)–blocked cells were stained with antibodies against CD11b/Mac1 and CD19. Analysis and cell sorting was performed on a BD FACSAriaTM (BD Biosciences, San Jose, California) using propidium iodide (PI, In vitrogen, Paisly UK) as viability marker.
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer’s recommendations. For ATAC-seq: Cells were washed in ice cold PBS prior to Assay for Transposase Accessible Chromatin  (ATAC-seq) library preparation as described in (Buenrostro et al. 2013).
RNA-seq: Libraries were constructed using NuGEN’s  Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,  CA). ATAC-seq: ATAC-seq library preparation was done as described in (Buenrostro et al. 2013) using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego) and custom primers.

tag: strain

value: Cultured on OP9-DL1


title: TH-LN683_CD19-_Thy+ [RNA-Seq-TH-LN683_Delta_Day_14_19-Thy+_2]


title: Restricted 2 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL1-05

value: Holstein-Friesian


title: Restricted 1 TP1 [liver]

description:
Experimental: day 125 with restricted diet Period 1
KKL1-21

value: male


title: Control 4 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL2-58

value: 70% concentrate, 30% grass silage diet


title: Control 10 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL4-01

value: Liver


title: Control 6 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL3-03


title: TH-LN683_CD19-_Thy+ [RNA-seq-TH-LN683_Delta_Day_6_19-Thy+_1]


title: Control 5 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL3-02


title: Control 3 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL1-23


title: Control 1 TP2 [liver]

description:
Control: day 55 with ad libitum diet Period 2
KKL1-59

value: day 55 of Period 2


title: Input wtE9.5Anterior 10min fix2

description: ChIP-seq

source_name: Input wtE9.5Anterior 10min fix2


title: Control 1 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL1-12


title: TH-LN683_CD19-_Thy+ [RNA-Seq-TH-LN683_Delta_Day_14_19-Thy+_1]


title: H3K27ac wtE9.5Tailbud tissue rep2

description: ChIP-seq

source_name: H3K27ac wtE9.5Tailbud tissue rep2


title: TH-LN-619-CEBPa-ER-pMIG-CD19-_CD11b+ [RNA-seq-TH-LN-619-CEBPa-ER-pMIG-CD19-_CD11b+_Day_5_2]

description: RNA-seq-50-norm-tags-count-exons-condenseGenes-M-diff.txt

value: Transduced with pMIG-C/EBPa -ER


title: TH-LN-381-CEBPa-ER-pMIG_CD19-_CD11b+ [RNA-seq-TH-LN-381-CEBPa-ER-pMIG_CD19-_CD11b+_Day_5_2]

description:
RNA-seq-50-norm-tags-count-exons-condenseGenes-M-diff.txt
RNA-seq-50-norm-tags-count-exons-condenseGenes-M-Kinetic.txt


title: TH-LN683_CD19-_Thy+ [RNA-Seq-TH-LN683_Delta_Day_6_19-Thy+_3]


title: TH-LN683_CD19+_Thy+ [RNA-Seq-TH-LN683_Delta_Day_6_19+Thy+_2]


title: TH-LN683_CD19+_Thy+ [RNA-Seq-TH-LN683_Delta_Day_6_19+Thy+_1]


title: TH-LN683_CD19-_Thy+ [RNA-seq-TH-LN683_Delta_Day_6_19-Thy+_2]


title: LSK_differentiated_to_Thy1_2+ [RNA-seq-LSK_T-cells_Thy1_2+_2]

description: RNA-seq-50-norm-tags-count-exons-condenseGenes-T-diff-LN-RNA-and-LSK-T.txt

source_name: Wt-BM-LSK-cells

value: Cultured on OP9-DL1 in T-cell condition


title: TH-LN683_CD19+_Thy+ [RNA-Seq-TH-LN683_Delta_Day_6_19+Thy+_3]


title: LSK_differentiated_to_CD11b+ [RNA-Seq-LSK_Myleoid_CD11b+_3]

value: Cultured on OP9 in myeloid condition


title: Control 2 TP1 [liver]

description:
Control: day 125 with ad libitum diet Period 1
KKL1-28

value: Control


title: TH-LN619-pMiG-CD19+ [RNA-seq-TH-LN619-pMiG-CD19+-Day1_2]

value: Transduced with pMIG


title: LSK_differentiated_to_CD19+ [RNA-seq-LSK_B-cells_CD19+_1]

description:
RNA-seq-50-norm-tags-count-exons-condenseGenes-M-diff.txt
RNA-seq-50-norm-tags-count-exons-condenseGenes-M-Kinetic.txt
RNA-seq-50-norm-tags-count-exons-condenseGenes-T-diff-LN-RNA-and-LSK-T.txt
RNA-seq-50-norm-tags-count-exons-condenseGenes-T-Kinetic.txt

value: Cultured on OP9 in B-cell condition


title: TH-LN381-pMiG-CD19+ [RNA-seq-TH-LN381-pMiG-CD19+-Day1_1]


title: LSK_differentiated_to_CD11b+ [RNA-Seq-LSK_Myleoid_CD11b+_1]


title: TH-LN-381-CEBPa-ER-pMIG-19+_11b+ [RNA-seq-TH-LN-381-CEBPa-ER-pMIG-19+_11b+_Day_2_1]

description: RNA-seq-50-norm-tags-count-exons-condenseGenes-M-Kinetic.txt


title: TH-LN-381-CEBPa-ER-pMIG-19+_11b+ [RNA-seq-TH-LN-381-CEBPa-ER-pMIG-19+_11b+_Day_2_2]


title: TH-LN-619-CEBPa-ER-pMIG-CD19-_CD11b+ [RNA-seq-TH-LN-619-CEBPa-ER-pMIG-CD19-_CD11b+_Day_5_1]


title: LN-619-Thy1.2+CD19+-pMiG-transduced [RNA-seq-TH-LN619-pMiG-Thy+_CD19+_2]


title: TH-LN619-pMiG-CD19+ [RNA-seq-TH-LN619-pMiG-CD19+-Day1_1]


title: RsaL-VSV-2

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Bacterial ChIP-seq reads were mapped to the P. auruginosa genomes, using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The enriched peaks were identified using MACS software (version 2.0.0)
Genome_build: P. aeruginosa PAO1

organism: Pseudomonas aeruginosa

source_name: liquid culture in LB

growth_protocol: LB medium with Amp

extract_protocol:
Wild type P. aeruginosa MAPO1 containing empty pAK1900 or pAK1900-VqsM-VSV was cultured in LB medium supplemented with ampicillin until the mid-log phase (OD=0.6), before was treated with 1% formaldehyde for 10 min at 37 °C. Cross-linking was stopped by addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and then re-suspended in 500 µl IP buffer (50 mM Hepes-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail (Roche) and sonicated the DNA to sizes of 100-300 bp. Insoluble cellular debris was removed by centrifugation and the supernatant used as input sample in IP experiments. Both control and IP samples were washed by protein A beads (General Electric), and then incubated with 50 ul agarose-conjugated anti-VSV antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted by following previously published protocols.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)

treatment_protocol: grow until mid-log phase


title: TH-LN-381-CEBPa-ER-pMIG_CD19-_CD11b+ [RNA-seq-TH-LN-381-CEBPa-ER-pMIG_CD19-_CD11b+_Day_5_1]


title: LSK_differentiated_to_Thy1_2+ [RNA-seq-LSK_T-cells_Thy1_2+_3]


title: LN-619-Thy1.2+-ICN-transduced [RNA-seq-TH-LN619-ICN-Thy+_1]

value: Transduced with pMIG-ICN1 (Intracellular Notch)


title: RsaL-VSV-1


title: LN-377-Thy1.2+CD19+-pMiG-transduced [RNA-seq-TH-LN377-pMiG-Thy+_CD19+_2]


title: LSK_differentiated_to_Thy1_2+ [RNA-Seq-LSK_T-cells_Thy1_2+_1]


title: LN-377-Thy1.2+-ICN-transduced [RNA-seq-TH-LN377-ICN-Thy+_2]


title: LSK_differentiated_to_CD11b+ [RNA-Seq-LSK_Myleoid_CD11b+_2]


title: TH-LN381-pMiG-CD19+ [RNA-seq-TH-LN381-pMiG-CD19+-Day1_2]


title: WT-1377-ProB [ATAC-seq-WT-1377-ProB-2]

description:
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-EBF1-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-GATA3-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-PAX5-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-CEBPa-peaks.txt

value: Fresh-sorted


title: WT-1380-ProB [ATAC-seq-WT1380-ProB-1]


title: LSK_differentiated_to_CD19+ [RNA-seq-LSK_B-cells_CD19+_2]


title: LN-619-Thy1.2+CD19+-pMiG-transduced [RNA-seq-TH-LN619-pMiG-Thy+_CD19+_1]


title: LN-377-Thy1.2+-ICN-transduced [RNA-seq-TH-LN377-ICN-Thy+_1]


title: WT-1380-ProB [ATAC-seq-WT1380-ProB-2]


title: LN-683-CD19+_Thy1_2- [ATAC-seq-TH-LN683-OP9-day2-CD19+_Thy1_2-_2]

description:
Annotation-T-Kinetic-on-EBF1-peaks.txt
Annotation-T-Kinetic-on-GATA3-peaks.txt
Annotation-T-Kinetic-on-PAX5-peaks.txt
Annotation-T-Kinetic-on-Tcf1-peaks.txt

value: Cultured on OP9


title: LN-683-CD19+_Thy1_2+ [ATAC-seq-TH-LN683-Delta-day2-CD19+_Thy1_2+_2]


title: LN-683-CD19+_Thy1_2- [ATAC-seq-TH-LN683-Delta-day2-CD19+_Thy1_1-_1]


title: WT-1377-ProB [ATAC-seq-WT-1377-ProB-1]


title: LN-683-CD19+_Thy1_2- [ATAC-seq-TH-LN683-OP9-day2-CD19+_Thy1_2-_1]


title: LN-683-CD19-_Thy1_2+ [ATAC-seq-TH-LN683-Delta-day14-CD19-_Thy1_2+_2]


title: LN-377-Thy1.2+CD19+-pMiG-transduced [RNA-seq-TH-LN377-pMiG-Thy+_CD19+_1]


title: LN-683-CD19-_Thy1_2+ [ATAC-seq-TH-LN683-Delta-day14-CD19-_Thy1_2+_1]


title: LN-683-CD19-_Thy1_2+ [ATAC-seq-TH-LN683-Delta-day6-CD19-_Thy1_2+_2]


title: LN-683-CD19-_Thy1_2+ [ATAC-seq-TH-LN683-Delta-day6-CD19-_Thy1_2+_1]


title: TH-ProB-cell-1381 [ATAC-seq-TH-1381-ProB-2]

description:
Annotation-TH-LSK-diff-on-EBF1-peaks.txt
Annotation-TH-LSK-diff-on-GATA3-peaks.txt
Annotation-TH-LSK-diff-on-PAX5-peaks.txt
Annotation-TH-LSK-diff-on-CEBPa-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-EBF1-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-GATA3-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-PAX5-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-CEBPa-peaks.txt


title: LN-683-CD19+_Thy1_2+ [ATAC-seq-TH-LN683-Delta-day2-CD19+_Thy1_2+_1]


title: BM-LSK-cells-differentiated-to-Thy1.2+ [ATAC-seq-LSK-diff-Thy1_2-1]

description:
Annotation-Thy-conversion-and-LSK-Thy-on-EBF1-peaks.txt
Annotation-Thy-conversion-and-LSK-Thy-on-GATA3-peaks.txt
Annotation-Thy-conversion-and-LSK-Thy-on-PAX5-peaks.txt
Annotation-T-conversion-on-merge-LSK_B-LSK_T-Top20K-peaks.txt
Annotation-TH-LSK-diff-on-EBF1-peaks.txt
Annotation-TH-LSK-diff-on-GATA3-peaks.txt
Annotation-TH-LSK-diff-on-PAX5-peaks.txt
Annotation-TH-LSK-diff-on-CEBPa-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-EBF1-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-GATA3-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-PAX5-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-CEBPa-peaks.txt


title: TH-ProB-cell-1376 [ATAC-seq-TH-1376-ProB-1]


title: BM-LSK-cells-differentiated-to-CD19+ [ATAC-seq-LSK-diff-CD19-1]

description:
Annotation-M-conversion-on-merge-LSK_B-LSK_M-Top20K-peaks
Annotation-T-conversion-on-merge-LSK_B-LSK_T-Top20K-peaks.txt


title: BM-LSK-cells-differentiated-to-CD19+ [ATAC-seq-LSK-diff-CD19-2]


title: LN-683-CD19+_Thy1_2- [ATAC-seq-TH-LN683-Delta-day2-CD19+_THy1_2-_2]


title: BM-LSK-cells-differentiated-to-CD11b+ [ATAC-seq-LSK-diff-CD11b-2]

description:
Annotation-M-conversion-on-merge-LSK_B-LSK_M-Top20K-peaks
Annotation-Cd11b-conversion-and-LSK-Cd11b-on-EBF1-peaks.txt
Annotation-Cd11b-conversion-and-LSK-Cd11b-on-PAX5-peaks.txt
Annotation-Cd11b-conversion-and-LSK-Cd11b-on-CEBPa-peaks.txt
Annotation-TH-LSK-diff-on-EBF1-peaks.txt
Annotation-TH-LSK-diff-on-GATA3-peaks.txt
Annotation-TH-LSK-diff-on-PAX5-peaks.txt
Annotation-TH-LSK-diff-on-CEBPa-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-EBF1-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-GATA3-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-PAX5-peaks.txt
Annotation-WT-TH-LSK-Thy-LSK-Cd11b-on-CEBPa-peaks.txt


title: BM-LSK-cells-differentiated-to-CD11b+ [ATAC-seq-LSK-diff-CD11b-1]


title: LN-619-Thy1.2+-ICN-transduced [RNA-seq-TH-LN619-ICN-Thy+_2]


title: LN-381-CD19+_pMiG-transduced [ATAC-seq-TH-LN381-pMiG-CD19+_day1-1]

description:
Annotation-M-cond-on-EBF1-peaks-161012.txt
Annotation-M-cond-on-PAX5-peaks-161012.txt
Annotation-M-cond-on-CEBPa-peaks-161012.txt


title: BM-LSK-cells-undifferentiated [ATAC-seq-LSK_3]


title: LN-381-CD19+_pMiG-transduced [ATAC-seq-TH-LN381-pMiG-CD19+_day1-2]


title: LN-381-CD11b+-CEBPa-transduced [ATAC-seq-TH-LN381-CEBPa-CD11b+_day5-2]


title: LN-381-CD11b+-CEBPa-transduced [ATAC-seq-TH-LN381-CEBPa-CD11b+_day5-1]


title: LSK_differentiated_to_CD19+ [RNA-Seq-LSK_B-cells_CD19+_3]


title: TH-ProB-cell-1381 [ATAC-seq-TH-1381-ProB-1]


title: LN-619-Thy1.2+_CD19- [ATAC-seq-TH-LN619-OP9delta_Thy+_CD19-_2]

description:
Annotation-Thy-conversion-and-LSK-Thy-on-EBF1-peaks.txt
Annotation-Thy-conversion-and-LSK-Thy-on-GATA3-peaks.txt
Annotation-Thy-conversion-and-LSK-Thy-on-PAX5-peaks.txt
Annotation-T-conversion-on-merge-LSK_B-LSK_T-Top20K-peaks.txt


title: TH-ProB-cell-1376 [ATAC-seq-TH-1376-ProB-2]


title: LN-619-Thy1.2+_CD19+ [ATAC-seq-TH-LN619-OP9_Thy+_CD19+_2]

description:
Annotation-Thy-conversion-and-LSK-Thy-on-EBF1-peaks.txt
Annotation-Thy-conversion-and-LSK-Thy-on-GATA3-peaks.txt
Annotation-Thy-conversion-and-LSK-Thy-on-PAX5-peaks.txt
Annotation-T-conversion-on-merge-LSK_B-LSK_T-Top20K-peaks.txt
Annotation-TH-LSK-diff-on-EBF1-peaks.txt
Annotation-TH-LSK-diff-on-GATA3-peaks.txt
Annotation-TH-LSK-diff-on-PAX5-peaks.txt
Annotation-TH-LSK-diff-on-CEBPa-peaks.txt


title: LN-619-CD11b+-CEBPa-transduced [ATAC-seq-TH-LN619-CEBPa_CD11b+_2]

description:
Annotation-M-conversion-on-merge-LSK_B-LSK_M-Top20K-peaks
Annotation-Cd11b-conversion-and-LSK-Cd11b-on-EBF1-peaks.txt
Annotation-Cd11b-conversion-and-LSK-Cd11b-on-PAX5-peaks.txt
Annotation-Cd11b-conversion-and-LSK-Cd11b-on-CEBPa-peaks.txt


title: LN-619-CD19+-pMiG-transduced [ATAC-seq-TH-LN619-pMiG_CD19+_1]


title: BM-LSK-cells-differentiated-to-Thy1.2+ [ATAC-seq-LSK-diff-Thy1_2-2]


title: BM-LSK-cells-undifferentiated [ATAC-seq-LSK_2]


title: LN-381-Thy1.2+_CD19- [ATAC-seq-TH-LN381-OP9delta_Thy+_CD19-_2]


title: BM-LSK-cells-undifferentiated [ATAC-seq-LSK_1]


title: LN-381-CD19+_CD11b+_CEBPa-transduced [ATAC-seq-TH-LN381-CEBPa-CD19+_Cd11+_day2-1]


title: LN-381-Thy1.2+_CD19+ [ATAC-seq-TH-LN381-OP9_Thy+_CD19+_2]


title: LN-619-Thy1.2+_CD19+ [ATAC-seq-TH-LN619-OP9_Thy+_CD19+_1]


title: LN-619-CD19+-pMiG-transduced [ATAC-seq-TH-LN619-pMiG_CD19+_2]


title: LN-619-Thy1.2+_CD19- [ATAC-seq-TH-LN619-OP9delta_Thy+_CD19-_1]


title: LN-381-Thy1.2+_CD19+ [ATAC-seq-TH-LN381-OP9_Thy+_CD19+_1]


title: LN-381-CD19+-pMiG-transduced [ATAC-seq-TH-LN381-pMiG-CD19+_1]


title: CEL-Seq Embryos WT 3

description: CEL-Seq

data_processing:
After sequencing the right mate of each read was aligned to the mm10 RefSeg mouse transcriptome downloaded from the UCSC genome browser4 using bwa3 with default parameters. The left mate of each read contains a barcode identifying the sample from which the read originated. CEL-seq only sequences the most 3’ prime end of a transcript so only one read per transcript is generated.
genome build: mm10
processed data files and content: csv file with raw read counts per gene.

source_name: CEL-Seq Embryos WT 3

extract_protocol:
Trizol and Qiagen total RNA extraction according to Young et al. (2009)
For the mRNA sequencing 10ng of total RNA was used as starting material. The RNA was processed using the CEL-seq protocol (Hashimshony, 2012 Cell reports) and sequenced on an Illumina Nextseq using 75bp paired end sequencing.

value: microdissected tailbud E8.0 embryo


title: LN-381-Thy1.2+_CD19- [ATAC-seq-TH-LN381-OP9delta_Thy+_CD19-_1]


title: CEL-Seq Embryos Triple 1

description: CEL-Seq

source_name: CEL-Seq Embryos Triple 1


title: CEL-Seq Embryos Cdx1-4 3

description: CEL-Seq

source_name: CEL-Seq Embryos Cdx1-4 3


title: LN-381-CD19+-pMiG-transduced [ATAC-seq-TH-LN381-pMiG-CD19+_2]


title: LN-381-CD11b+-CEBPa-transduced [ATAC-seq-TH-LN381-CEBPa-CD11b+_2]


title: CEL-Seq Embryos Cdx1-4 2

description: CEL-Seq

source_name: CEL-Seq Embryos Cdx1-4 2


title: CEL-Seq Embryos WT 2

description: CEL-Seq

source_name: CEL-Seq Embryos WT 2


title: CEL-Seq Embryos WT 1

description: CEL-Seq

source_name: CEL-Seq Embryos WT 1


title: CEL-Seq Embryos Cdx1-4 1

description: CEL-Seq

source_name: CEL-Seq Embryos Cdx1-4 1


title: CEL-Seq Embryos Triple 3

description: CEL-Seq

source_name: CEL-Seq Embryos Triple 3


title: LN-619-CD11b+-CEBPa-transduced [ATAC-seq-TH-LN619-CEBPa_CD11b+_1]


title: CEL-Seq Cell Lines WT 24h 2

description: CEL-Seq

source_name: CEL-Seq Cell Lines WT 24h 2

growth_protocol: Pre-streak embryos (E6.0) were isolated in M2 medium; extraembryonic tissue and surrounding primitive endoderm was removed. Explants were put on MEFs and cultured in presence of Wnt inhibitor IWP2 (2 µM, Sigma Aldrich, dissolved in DMSO) in medium containing 20% KOSR, 77% DMEM/F12, 1x penicillin/streptomycin (100 units/mL, Thermo Fisher Scientific), 2 mM L-glutamine, 1x non-essential amino acids, 0.01% β-mercaptoethanol, Fgf-basic (12 ng/mL, ThermoFisher Scientific ), Activin A (20 ng/mL, R&D Systems).  MEF-free culture took place on surface coated by fibronectin (ThermoFisher Scientific) in medium containing 48% DMEM/F12, 48% Neurobasal Medium 1% B27 Supplement, 0.5% N2 Supplement B (all Thermo Fisher Scientific), 1x penicillin/streptomycin, Fgf-basic (12 ng/mL), Activin A (20 ng/mL), IWP2 (2 µM), 0.01% β-mercaptoethanol. Medium was refreshed on daily basis.

extract_protocol:
Trizol and Qiagen total RNA extraction according to Simmini et al. (2014)
For the mRNA sequencing 10ng of total RNA was used as starting material. The RNA was processed using the CEL-seq protocol (Hashimshony, 2012 Cell reports) and sequenced on an Illumina Nextseq using 75bp paired end sequencing.

treatment_protocol: Wnt and Fgf stimulation was done after at least two passages feeder-free culturing by withdrawal of IWP2 and addition of Chiron (3 µM) and Fgf8 (120ng/ml).

value: EpiSCs


title: CEL-Seq Cell Lines WT 24h 1

description: CEL-Seq

source_name: CEL-Seq Cell Lines WT 24h 1


title: CEL-Seq Cell Lines Null 24h 2

description: CEL-Seq

source_name: CEL-Seq Cell Lines Null 24h 2

growth_protocol: CdxKO pre-streak embryos (E6.0) were isolated in M2 medium; extraembryonic tissue and surrounding primitive endoderm was removed. Explants were put on mitotically inactivated mouse embryonic fibroblasts (MEFs) and cultured in presence of Wnt inhibitor IWP2 (2 µM, Sigma Aldrich, dissolved in DMSO) in medium containing 20% KOSR, 77% DMEM/F12, 1x penicillin/streptomycin (100 units/mL, Thermo Fisher Scientific), 2 mM L-glutamine, 1x non-essential amino acids, 0.01% -mercapto-ethanol, Fgf-basic (12 ng/mL, ThermoFisher Scientific ), Activin A (20 ng/mL, R&D Systems). Wnt3 null EpiSCs were genotyped once cultured free of MEFs to avoid contamination of wild type alleles. MEF-free culture took place on surface coated by fibronectin (ThermoFisher Scientific) in medium containing 48% DMEM/F12, 48% Neurobasal Medium 1% B27 Supplement, 0.5% N2 Supplement B (all Thermo Fisher Scientific), 1x penicillin/streptomycin, Fgf-basic (12 ng/mL), Activin A (20 ng/mL), IWP2 (2 µM), 0.01% -mercapto-ethanol. Medium was refreshed on daily basis.


title: CEL-Seq Cell Lines Null 24h 1

description: CEL-Seq

source_name: CEL-Seq Cell Lines Null 24h 1


title: LN-381-CD11b+-CEBPa-transduced [ATAC-seq-TH-LN381-CEBPa-CD11b+_1]


title: CEL-Seq Cell Lines Null 0h 2

description: CEL-Seq

source_name: CEL-Seq Cell Lines Null 0h 2


title: CEL-Seq Cell Lines Null 0h 1

description: CEL-Seq

source_name: CEL-Seq Cell Lines Null 0h 1


title: 4C-seq Wnt3a 0h EpiSCs

data_processing:
Library strategy: 4C-seq
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII sites (4C fragment ends), using custom Perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome mm9.
genome build: mm9
processed data files format and content: wig

source_name: 4C-seq Wnt3a 0h EpiSCs

extract_protocol:
The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics (PMID 17033623)), remain unchanged. Cells are cross-linked using 2% formaldehyde for 10 min at room temperature in PBS 10% FCS and nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme treatment (Csp6I). After a second re-ligation step, the sample is purified and a 4C PCR is performed.
4C PCR

treatment_protocol: Wnt stimulation was done after at least two passages feeder-free culturing by withdrawal of IWP2 and addition of Wnt3a (Cell Guidance Systems, 125 ng/mL) or Chiron (3 µM).


title: 4C-seq Wnt3a 24h Chiron EpiSCs

source_name: 4C-seq Wnt3a 24h Chiron EpiSCs


title: 4C-seq Wnt3a E9.5 embryo

source_name: 4C-seq Wnt3a E9.5 embryo

value: posterior part E9.5 embryo


title: 4C-seq Sp5 24h Chiron EpiSCs

source_name: 4C-seq Sp5 24h Chiron EpiSCs


title: 4C-seq Sp5 0h EpiSCs

source_name: 4C-seq Sp5 0h EpiSCs


title: CEL-Seq Embryos Triple 2

description: CEL-Seq

source_name: CEL-Seq Embryos Triple 2


title: 4C-seq Rspo3 distal1 rep

source_name: 4C-seq Rspo3 distal1 rep


title: 4C-seq Lef1 E9.5 embryo

source_name: 4C-seq Lef1 E9.5 embryo


title: 4C-seq Rspo3 distal2 rep

source_name: 4C-seq Rspo3 distal2 rep


title: 4C-seq Lef1 24h Chiron EpiSCs

source_name: 4C-seq Lef1 24h Chiron EpiSCs


title: 4C-seq Fgf4-15 0h EpiSCs

source_name: 4C-seq Fgf4-15 0h EpiSCs


title: CEL-Seq Cell Lines WT 0h 1

description: CEL-Seq

source_name: CEL-Seq Cell Lines WT 0h 1


title: LN-381-CD19+_CD11b+_CEBPa-transduced [ATAC-seq-TH-LN381-CEBPa-CD19+_Cd11+_day2-2]


title: CEL-Seq Cell Lines WT 0h 2

description: CEL-Seq

source_name: CEL-Seq Cell Lines WT 0h 2


title: 4C-seq Cdx2 0h EpiSCs

source_name: 4C-seq Cdx2 0h EpiSCs


title: 4C-seq Cdx2 24h Chiron EpiSCs

source_name: 4C-seq Cdx2 24h Chiron EpiSCs


title: 4C-seq Lef1 0h EpiSCs

source_name: 4C-seq Lef1 0h EpiSCs


title: 4C-seq Fzd10 24h Chiron EpiSCs

source_name: 4C-seq Fzd10 24h Chiron EpiSCs


title: 4C-seq Fzd10 E9.5 embryo

source_name: 4C-seq Fzd10 E9.5 embryo


title: ATAC-seq CdxKO EpiSCs Chiron48h

description: ATAC-seq

data_processing:
Library strategy: ATAC-seq
Adapter trimming: Cutadapt (1.8.1), parameters: -a CTGTCTCTTATA -A CTGTCTCTTATA
Mapping: Bowtie2 (2.1.0), parameters: -X 2000 -p 8
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Read cleanup: Samtools (0.1.19) reads that were not mapped, paired, uniquely mapped (MAPQ > 1) or mapped to chrM, were removed
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR –nomodel –llocal 100000
genome build: mm9
processed data files format and content: bed and bw

source_name: ATAC-seq CdxKO EpiSCs Chiron48h

growth_protocol: CdxKO pre-streak embryos (E6.0) were isolated in M2 medium; extraembryonic tissue and surrounding primitive endoderm was removed. Explants were put on mitotically inactivated mouse embryonic fibroblasts (MEFs) and cultured in presence of Wnt inhibitor IWP2 (2 µM, Sigma Aldrich, dissolved in DMSO) in medium containing 20% KOSR, 77% DMEM/F12, 1x penicillin/streptomycin (100 units/mL, Thermo Fisher Scientific), 2 mM L-glutamine, 1x non-essential amino acids, 0.01% -mercapto-ethanol, Fgf-basic (12 ng/mL, ThermoFisher Scientific ), Activin A (20 ng/mL, R&D Systems).  MEF-free culture took place on surface coated by fibronectin (ThermoFisher Scientific) in medium containing 48% DMEM/F12, 48% Neurobasal Medium 1% B27 Supplement, 0.5% N2 Supplement B (all Thermo Fisher Scientific), 1x penicillin/streptomycin, Fgf-basic (12 ng/mL), Activin A (20 ng/mL), IWP2 (2 µM), 0.01% β-mercapto-ethanol. Medium was refreshed on daily basis.

extract_protocol:
According to Buenrostro et al. (2013)
Modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: Wnt stimulation was done after at least two passages feeder-free culturing by withdrawal of IWP2 and addition of Chiron (3 µM).


title: 4C-seq Cdx2 E9.5 embryo

source_name: 4C-seq Cdx2 E9.5 embryo


title: ATAC-seq CdxKO EpiSCs

description: ATAC-seq

source_name: ATAC-seq CdxKO EpiSCs


title: TBra wtEpiSCs 24h rep2

description: ChIP-seq

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR
Input control: Input_wtEpiSCs_15min_fix2
Peak calling on pooled: TBra wtEpiSCs 24h rep1 & TBra wtEpiSCs 24h rep2
Input control for pooled: Input_wtEpiScs_15min_fix2
genome build: mm9
processed data files format and content: bed and bw

source_name: TBra wtEpiSCs 24h rep2

extract_protocol:
Crosslinking 15mins RT, lysis, sonication and immunoprecipiation following standard procedures.
Illumina Truseq DNA library protocol

value: Santa Cruz Biotech, sc-17745 X


title: TBra wtEpiSCs 24h rep1

description: ChIP-seq

source_name: TBra wtEpiSCs 24h rep1


title: Input wtEpiSCs 15min fix3

description: ChIP-seq

source_name: Input wtEpiSCs 15min fix3

extract_protocol:
Crosslinking 15mins RT, lysis, sonication following standard procedures.
Illumina Truseq DNA library protocol


title: Input wtEpiSCs 15min fix2

description: ChIP-seq

source_name: Input wtEpiSCs 15min fix2