title: Bcells RNA-Seq FancC deficient #2

city: Cincinnati

first: Mathieu

last: Sertorio

address: 3333 Burnett Avenue

department: Exp Hem and Cancer Bio

institute: Cincinnati Children's Hospital Medical center

data_processing:
Samples were sequenced at the CCHMC DNA core, on an Illumina HiSeq2500 using a TopHat/Cufflinks pipeline. Refence annotation is based on UCSC known genes table.
BAM files from RNA-Seq were imported into GeneSpring NGS software (v12.6) and aligned to mm9 reference genome. Reference annotations produced by Emsembl. Aligned reads were filtered on base quality >=50.
Aligned read couts quantified and normalized using TMM algorithm. Filtrations removed all genes with fewer than 1 reads in at least one sample of a condition.
Fold change was calculated as FancCKo/WT with a cut-off of 1.5 average fold change.
Genome_build: mm9
Supplementary_files_format_and_content: TXT files exported into Excel containing WT and FancC deficient B cells normalized values, gene symbols, and fold change

source_name: mature mouse B cells

extract_protocol:
RNA was extracted with the Rneasy plus mini kit. This included genomic DNA cleaning on spin column.  Final RNA was aliquoted and submitted for quality control and RNA-Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols. WT and Ko samples were sequenced in 2 independent experiments, each one containing a WT and a Ko samples to test the reproductibility of results

treatment_protocol: B cellspurified from mouse total splenocytes by anti-CD43 magnetic beads purification (Miltenyi)  after Red blood cells lysis treatment.

tag: fanc status

value: KO

tag: genetic background


title: SLJ8666WT-Rep1

status: Public on Jan 08 2016

type: SRA

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

country: USA

institute: Stowers Institute

library_source: transcriptomic

data_processing:
Sequencing data was processed with CASAVA 1.8.2
Data was aligned to yeast genome sacCer3 using tophat 2.0.10 with parameters --segment-mismatches 1 -x 1 -g 1 --no-coverage-search and with a gtf file based on Ensembl 72.
Downstream analysis was done in R 3.0.2. DE genes were called using edgeR 3.4.2.
Genome_build: sacCer3
Supplementary_files_format_and_content: RPM normalized bigWig files separated by strand - pos for forward/plus strand, neg for minus/reverse strand.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: total RNA extract from yeast culture

growth_protocol: yeast cultures were grown to mid-log phase and harvested

extract_protocol:
total RNA was extracted via acid phenol and ethanol precipitated.  QC performed on BioAnalyzer
libraries were prepared according to Illumina instructions, TruSeq universal adapters were ligated and samples were pooled and run on HiSeq 2500 machine.  Single reads, 51 bases.

tag: genotype

value: wild-type


title: Bcells RNA-Seq Control #1

state: OH

organism: Mus musculus

value: Control


title: Bcells RNA-Seq FancC deficient #1


title: SP_Cipro_RNA

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

data_processing:
Illumina Casava 1.8 software was used for basecalling.
S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 2.03, using default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. This was done internally by Rockhopper version 2.03 after aligning reads.
Upper-quartile normalization (to be able to compare expression between samples) and differential gene expression analysis were performed with Rockhopper version 2.03, using default parameters.
Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample. Files describing RNA-Seq (non-control) data also contain information on differential gene expression, including statistics.

organism: Streptococcus pneumoniae

source_name: Ciprofloxacin-treated S. pneumoniae cells

growth_protocol: Strain DLA3 was grown to OD600 = 0.4 in 5 ml tubes and diluted 1:100 in fresh C+Y medium pH 7.4 . To study the effects of antibiotics, cells grown without antibiotics were compared to cells grown with 0.15 μg/ml HPUra, 28 μg/ml kanamycin, 0.4 μg/ml ciprofloxacin, 608 μg/ml hydroxyurea, or 0.04 μg/ml. Cells were grown in microtiter plates and growth and competence development (luc-expression) was followed.

extract_protocol:
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. For RNA isolation, cells were lysed by bead beating and RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation.
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis.

tag: strain

value: bgaA::ssbB_luc (DLA3)


title: SP_Rif_RNA

source_name: Rifampicin-treated S. pneumoniae cells


title: PN_WT3

city: Cleveland

first: Evan

last: Deneris

address: 2109 Adelbert Rd.

department: Neurosciences

institute: Case Western Reserve University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were filtered for low-quality sequence, then mapped to mm9 whole genome using tophat2.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks.
Reads were mapped to the Mus musculus genome (UCSC mm10) using the Burroughs-Wheeler Aligner (BWA) and were filtered to select reads that map to a single location (Li and Durbin, 2009). Peak calling was performed with MACS v1.4.2 modified to accept a custom scaling factor of 0.8195945 derived from the Normalization ChIPseq software (NCIS) (Zhang et al., 2008; Liang and Keleş, 2012).
MycPet-1 ChIP peaks were associated to genes using the GREAT web service v3.0 (mm10) with 5kb intervals upstream and downstream of the TSS and TTS of each gene model along with peaks that overlap the gene body.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample in the time-series gene expression trajectory (E11.5, E15.5, PN; Gene_expression_trajectories_E11.5_E15.5_PN.matrix.txt) and WT vs. Pet-1-/- (E15.5_WT vs E15.5_KO) generated by cufflinks. For ChIP-seq, a BED file of mycPet-1 ChIP peaks is provided.

source_name: 5-HT neuron

growth_protocol: Animals were reared in standard housing conditions.

extract_protocol:
EYFP+ 5-HT neurons were sorted using a BD FACSAria into Trizol reagent and extracted RNA was Dnase I treated and purified using the RNA Clean & Concentrator-5 kit (Zymo). Purified total RNA was amplified with the SMARTer Ultra-low mRNA-Seq kit (Clontech) or Ovation RNA-Seq System V2 (NuGEN). Dissected YFP+ tissue between the mid-hindbrain boundary and rhombomere 4 of E12.5 to E15.5 hindbrains from Pet-1-/-; ePet-mycPet-1; ePet-EYFP embryos was quickly flash frozen on dry ice. Chromatin was isolated and immunoprecipitated using a ChIP grade, goat anti-Myc antibody (Abcam ab9132, Cambridge, MA, validation report at abcam.com) with proprietary protocols (Active Motif, Carlsbad, CA).
RNA libraries were prepared for sequencing using either Clontech SMARTer RNA-seq (E11.5, E15.5C_WT, E15.5C_KO, PN) or NuGen Ovation RNA-Seq v2 (E15.5N_WT, E15.5N_KO). ChIP-seq libraries were prepared using standard Illumina ChIP-seq methods.

tag: tissue

value: 5-HT neuron

tag: developmental stage

value: postnatal day 1-3

value: wild type


title: L20-2

city: Zheng

first: HONG

last: LI

address: 95 Wenhua Road, Jinshui District

country: China

institute: Henan Agriculture University

data_processing:
Basecalling performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version: 0.0.13.
mRNA-seq reads were aligned to the reference genome ensemble Galgal4 using spliced mapping algorithm in TopHat version: 2.0.9
Fragments per kilo base of exon model per million mapped reads (FPKM) of each gene were calculated  according to the Cufflink (version: V2.1.1)
Differential expression were analysed  using cuffdiff in version 2.3.4
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Gallus gallus

source_name: Liver

extract_protocol:
Liver tissues were moved,snap-frozen in liquid nitrogen,total RNA was harvested with TRIzol® Reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Lushi chicken

tag: age

value: 20 weeks

tag: Sex

value: female

value: liver


title: SP_Hxu_DNA

library_source: genomic

molecule: genomic DNA

source_name: Hydroxyurea-treated S. pneumoniae cells

extract_protocol:
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega).
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: the DNA samples were treated with ultrasound (3-5 pulses of 30 sec at 4°C). After end-repair, TruSeq sequencing adapters were ligated to the DNA fragments. Finally, the DNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase (9-11 cycles, depending on the sample). Aliquots of the PCR amplified libraries were examined by capillary electrophoresis.


title: SP_Kan_RNA [GSM1310002]

source_name: Kanamycin-treated S. pneumoniae cells


title: SP_Cont1_RNA [GSM1309998]

source_name: Untreated S. pneumoniae cells


title: E15.5N_KO1


title: SP_HPUra2_RNA [GSM1310001]

source_name: HPUra-treated S. pneumoniae cells


title: PN_WT1


title: E15.5N_WT2


title: PN_WT2


title: SP_Cont2_RNA [GSM1309999]


title: SP_HPUra1_RNA [GSM1310000]


title: E15.5N_WT3


title: SLJ8668-sec66del-Rep3

value: sec66 mutant


title: E15.5N_KO3


title: E15.5N_KO2


title: SP_Rif_DNA


title: SP_Cipro_DNA


title: SP_Cont2_DNA [GSM1309990]


title: E15.5N_WT1


title: SP_HPUra1_DNA [GSM1309991]


title: E15.5C_KO3


title: E15.5C_KO2


title: E15.5C_KO1


title: SP_HPUra2_DNA [GSM1309992]


title: SP_Kan_DNA [GSM1309993]


title: E15.5C_WT3


title: SP_Hxu_RNA


title: SP_Cont1_DNA [GSM1309989]


title: E15.5C_WT2


title: E11.5_WT3


title: E15.5C_WT1


title: E11.5_WT2


title: E11.5_WT1


title: CNBP PAR-CLIP

city: Wuerzburg

first: Sanjay

middle: Kumar

last: Gupta

state: Bavaria

address: Biozentrum, Am Hubland

department: Dept of Biochemistry

country: Germany

institute: University of Wuerzburg

data_processing:
Illumina high-seq 2500 platform was used for sequencing
Paralyzer was used to align the reads to hg19 genome
Binding sites were categorized using the GRCh37.p13 GTF annotation
Genome_build: hg19

organism: Homo sapiens

source_name: HEK293 cells

growth_protocol: HEK293 cells were grown and routinely passaged in DMEM with 10% FCS and 1% pen/strip.

extract_protocol: The PAR-CLIP cDNA library was generated using protocol used in Hafner et al., 2010.

tag: cell type

value: FLAG-HA tagged CNBP

tag: flag-antibody

value: Monoclonal FLAG antibody, Sigma

tag: cell line


title: ClutchB_polyA_23.5_hpf

status: Public on Jan 07 2016

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA47G_012

data_processing:
Read pairs were aligned to Xenopus tropicalis v7 genome along with known off-genome gene sequences and exogenouns ERCC and ArrayControl spike in sequences using tophat v2.010 and parameters "-r 13 --mate-std-dev 60 -g 200 --report-secondary-alignments".
Abundances were estimated using cufflinks v2.1.1 with parameters ""--compatible-hits-norm --max-bundle-frags 10000000 -b xt7.fa -u --max-mle-iterations 50000". This is with exception of mir427, in which reads aligning at least once to the locus and nowhere else in the genome were counted once to calculate the FPKM for the entire locus. Transcript FPKM were converted to TPM.
Relative gene abundances in TPM were absolute normalised against ERCC spiked RNA standards, resulting abundances are reported in transcripts per embryo.
Genome_build: Xtropicalis_v7
Supplementary_files_format_and_content: Tab-delimited text files containing relative and absolute normalised gene and isoform abundances.

organism: Xenopus tropicalis

source_name: Whole embryo, 23.5hpf, polyA+ RNA

growth_protocol: We performed IVF and flooding of the eggs with 1/9xMMR after application of sperm to eggs was considered time zero. All fertilizations and subsequent culturing of embryos were performed in a temperature-controlled room maintained at ~24oC, with fluctuations +/- ~1oC over the entire timecourse. Unfertilized eggs and embryos were dejellied and embryos were cultured at low density, ~100 embryos per 150-mm dish containing ~120-150mls of 1/9thX MMR.

extract_protocol:
For most samples, 10 embryos/timepoint were thoroughly homogenized in 200 ml Trizol® and frozen at -80oC, with the exception of egg, 0.5, 1, 1.5, 2, 2.5 and 3hpf timepoints, which were sampled at 25, 30, 20, 20, 20, 15 and 15 embryos, respectively.
For the Clutch A timecourse, ERCC Spike In Mix 1 (10ul) (lot 1205006) was diluted in DEPC-treated water to a final volume of 1045ul. Diluted spike in mix was then pipetted directly into the Trizol homogenates such that 1ul was delivered per embryo, which in most cases required delivery of 10ul diluted spike in mix/sample, with the exception of the first several timepoints. Spike in mix was pipetted into samples in the order of their chronology. Total RNA was purified from the embryo homogenate according to the manufacturer’s recommendations. Following isopropanol precipitation, RNAs were resuspended in DEPC-treated water and any contaminating genomic DNA was removed by a subsequent overnight precipitation in 5M LiCl at 4oC. RNA was pelleted and washed twice with 70% ethanol made with DEPC-treated water. All RNAs were resuspended and quantitated by Bioanalyzer. RNA quality was assessed by Bioanalyzer and RNA Integrity Numbers were all in excess of 9.
For the Clutch B timecourse, ERCC spike in mix 1 (lot 1306008) was similarly diluted and delivered to all Trizol® homogenates, except the pipetting was done in reverse order to the chronology of the samples. Furthermore, we added an additional spike in mix that was pipetted independently and in order of sample chronology. Ambion ArrayControl™ spikes were used. Two microliters of spikes 1, 2 and 4 were diluted  to a final volume of 82ul in DEPC-treated water to create a solution of 2.439ng for each ArrayControl spike-in RNA per microliter. Approximately 5.125ul of this dilution was then further diluted into DEPC-treated water to a final volume of 1000ul as verified by weight to create a solution of ~12.5pg/ul. One microliter per embryo (~12.5pg) was added to Trizol® homogenates by pipetting of 10ul per tube except in the cases of the 0-3hpf samples. In both timecourses these early timepoint spike ins were pipetted by multiple rounds of 10ul (for 20 or 30ul delivery), or readjustment to 5ul (for 15ul delivery). RNAs were subsequently isolated as described above except we omitted the LiCl precipitation step. RNAs were similar quantitated and quality evaluated.
RNA quality and concentration were evaluated by running total RNA on an Agilent RNA Nano Bioanalyzer chip. All samples had an RNA integrity number (RIN) greater than 9. Ribosomal RNA was removed via polyA-selection or ribosomal RNA depletion. For polyA-extraction, polyadenylated RNA transcripts were selected from the total RNA using two rounds of enrichment with oligo(dT)25 beads (Invitrogen). Ribosomal-depletion was completed with the Ribo-Zero (Human/Mouse/Rat) Magnetic Ribosomal rRNA Removal kit (Epicenter) according to the manufacturer's recommendations. The supernatant from both approaches was purified and concentrated using RNAclean XP beads (Beckman Coulter). Following selection, the RNA was fragmented to approximately 140 base pairs and first-strand synthesis was completed with SuperScript III reverse transcriptase (Invitrogen) using random hexamers. Magnetic AMPure XP beads (Beckman Coulter) were used to purify the cDNA and remained with the sample throughout sequencing library construction. During preparation, DNA is selectively precipitated by weight and re-bound to the beads through the addition of a 20% polyethylene glycol, 2.5 M NaCl solution. We used T4 DNA polymerase and T4 polynucleotide kinase to blunt ends and phosphorylate the fragments. The large Klenow fragment then added a single adenine residue to the 3' end of each fragment, custom adapters (IDT) are ligated using T4 DNA ligase, and, for strand-specific libraries, UDG removes uracil residues. The product is then PCR amplified using custom-made primers (IDT) containing unique 6 bp indices.

tag: genotype/variation

value: whole embryo

tag: clutch

value: B

tag: time (hpf)


title: ClutchB_polyA_13.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA27G_006

source_name: Whole embryo, 13.5hpf, polyA+ RNA


title: ClutchB_polyA_18_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA36G_002

source_name: Whole embryo, 18hpf, polyA+ RNA


title: ClutchB_polyA_24_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA48G_004

source_name: Whole embryo, 24hpf, polyA+ RNA


title: ClutchB_polyA_21.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA43G_004

source_name: Whole embryo, 21.5hpf, polyA+ RNA


title: ClutchB_polyA_14.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA29G_012

source_name: Whole embryo, 14.5hpf, polyA+ RNA


title: ClutchB_polyA_18.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA37G_004

source_name: Whole embryo, 18.5hpf, polyA+ RNA


title: ClutchB_polyA_15.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA31G_004

source_name: Whole embryo, 15.5hpf, polyA+ RNA


title: ClutchB_polyA_23_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA46G_007

source_name: Whole embryo, 23hpf, polyA+ RNA


title: ClutchB_polyA_22.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA45G_006

source_name: Whole embryo, 22.5hpf, polyA+ RNA


title: ClutchB_polyA_15_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA30G_002

source_name: Whole embryo, 15hpf, polyA+ RNA


title: ClutchB_polyA_21_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA42G_002

source_name: Whole embryo, 21hpf, polyA+ RNA


title: ClutchB_polyA_16_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA32G_005

source_name: Whole embryo, 16hpf, polyA+ RNA


title: ClutchB_polyA_12.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA25G_004

source_name: Whole embryo, 12.5hpf, polyA+ RNA


title: ClutchB_polyA_20.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA41G_012

source_name: Whole embryo, 20.5hpf, polyA+ RNA


title: ClutchB_polyA_13_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA26G_005

source_name: Whole embryo, 13hpf, polyA+ RNA


title: ClutchB_polyA_14_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA28G_007

source_name: Whole embryo, 14hpf, polyA+ RNA


title: ClutchB_polyA_17.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA35G_012

source_name: Whole embryo, 17.5hpf, polyA+ RNA


title: ClutchB_polyA_22_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA44G_005

source_name: Whole embryo, 22hpf, polyA+ RNA


title: ClutchB_polyA_20_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA40G_007

source_name: Whole embryo, 20hpf, polyA+ RNA


title: ClutchB_polyA_19_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA38G_005

source_name: Whole embryo, 19hpf, polyA+ RNA


title: ClutchB_polyA_16.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA33G_006

source_name: Whole embryo, 16.5hpf, polyA+ RNA


title: ClutchB_polyA_17_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA34G_007

source_name: Whole embryo, 17hpf, polyA+ RNA


title: ClutchB_polyA_19.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA39G_006

source_name: Whole embryo, 19.5hpf, polyA+ RNA


title: ClutchB_polyA_12_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA24G_002

source_name: Whole embryo, 12hpf, polyA+ RNA


title: ClutchB_polyA_11.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA23G_012

source_name: Whole embryo, 11.5hpf, polyA+ RNA


title: ClutchB_polyA_10.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA21G_006

source_name: Whole embryo, 10.5hpf, polyA+ RNA


title: ClutchB_polyA_11_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA22G_007

source_name: Whole embryo, 11hpf, polyA+ RNA


title: ClutchB_polyA_10_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA20G_005

source_name: Whole embryo, 10hpf, polyA+ RNA


title: ClutchB_polyA_9.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA19G_004

source_name: Whole embryo, 9.5hpf, polyA+ RNA


title: ClutchB_polyA_8.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA17G_012

source_name: Whole embryo, 8.5hpf, polyA+ RNA


title: ClutchB_polyA_8_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA16G_007

source_name: Whole embryo, 8hpf, polyA+ RNA


title: ClutchB_polyA_3.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA07G_004

source_name: Whole embryo, 3.5hpf, polyA+ RNA


title: ClutchB_polyA_6.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA13G_004

source_name: Whole embryo, 6.5hpf, polyA+ RNA


title: ClutchB_polyA_5.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA11G_012

source_name: Whole embryo, 5.5hpf, polyA+ RNA


title: ClutchB_polyA_7_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA14G_005

source_name: Whole embryo, 7hpf, polyA+ RNA


title: ClutchB_polyA_7.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA15G_006

source_name: Whole embryo, 7.5hpf, polyA+ RNA


title: ClutchB_polyA_4_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA08G_005

source_name: Whole embryo, 4hpf, polyA+ RNA


title: ClutchB_polyA_5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA10G_007

source_name: Whole embryo, 5hpf, polyA+ RNA


title: ClutchB_polyA_2.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA05G_012

source_name: Whole embryo, 2.5hpf, polyA+ RNA


title: ClutchB_polyA_3_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA06G_002

source_name: Whole embryo, 3hpf, polyA+ RNA


title: ClutchB_polyA_1_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA02G_005

source_name: Whole embryo, 1hpf, polyA+ RNA


title: ClutchB_polyA_1.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA03G_006

source_name: Whole embryo, 1.5hpf, polyA+ RNA


title: ClutchB_polyA_2_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA04G_007

source_name: Whole embryo, 2hpf, polyA+ RNA


title: ClutchB_polyA_9_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA18G_002

source_name: Whole embryo, 9hpf, polyA+ RNA


title: ClutchB_polyA_0_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA00G_002

source_name: Whole embryo, 0hpf, polyA+ RNA


title: ClutchA_ribozero_3.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_7_012

source_name: Whole embryo, 3.5hpf, RiboZero RNA

value: A


title: ClutchA_ribozero_4_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_8_004

source_name: Whole embryo, 4hpf, RiboZero RNA


title: ClutchA_ribozero_4.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_9_005

source_name: Whole embryo, 4.5hpf, RiboZero RNA


title: ClutchA_ribozero_3_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_6_006

source_name: Whole embryo, 3hpf, RiboZero RNA


title: ClutchA_ribozero_2.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_5_005

source_name: Whole embryo, 2.5hpf, RiboZero RNA


title: ClutchB_polyA_6_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA12G_002

source_name: Whole embryo, 6hpf, polyA+ RNA


title: ClutchB_polyA_4.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA09G_006

source_name: Whole embryo, 4.5hpf, polyA+ RNA


title: ClutchA_ribozero_23_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_46_006

source_name: Whole embryo, 23hpf, RiboZero RNA


title: ClutchA_ribozero_23.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_47_012

source_name: Whole embryo, 23.5hpf, RiboZero RNA


title: ClutchA_ribozero_22_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_44_004

source_name: Whole embryo, 22hpf, RiboZero RNA


title: ClutchA_ribozero_21.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_43_012

source_name: Whole embryo, 21.5hpf, RiboZero RNA


title: ClutchA_ribozero_21_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_42_006

source_name: Whole embryo, 21hpf, RiboZero RNA


title: ClutchA_ribozero_22.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_45_005

source_name: Whole embryo, 22.5hpf, RiboZero RNA


title: ClutchA_ribozero_20.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_41_005

source_name: Whole embryo, 20.5hpf, RiboZero RNA


title: ClutchB_polyA_0.5_hpf

description:
PolyA+ RNA
clutch_B_poly_A/Sample_KBRNA01G_004

source_name: Whole embryo, 0.5hpf, polyA+ RNA


title: ClutchA_ribozero_2_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_4_004

source_name: Whole embryo, 2hpf, RiboZero RNA


title: Ezh2ff in vitro

city: Aurora

first: Tobias

last: Neff

state: CO

department: Pediatric Oncology

institute: University of Colorado Denver AMC

description: Harvested prior to injection into syngeneic mouse from OP9DL culture after 14 days

data_processing:
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6.  CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d mm9 -v snp128_strict_wholeChrs --use-splicing=ucscRefGeneSpliceSites_mm9 --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using  Samtools. Bam-files were sorted using Samtools.
Differential gene expression was detemined using Cuffdiff. Genes with low levels (<0.5 in both samples, or 0 in one and <5 in the other sample) were excluded. Genes with 'Fail' and 'Notest' Cuffdiff status were exluded.
For GSEA, a ranked genelist between 2 conditions was created using the Cuffdiff log2-value. miRNAs and snoRNA were excluded from the ranked genelist used for GSEA.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM (Cuffdiff). Comparison was conducted between invivo-ff/invivo-ko and between invitro-ff/invitro-ko

source_name: Bone marrow

extract_protocol:
RNA was isolated using Qiagen RNAeasy kit
Illumina Stranded mRNA kit

value: Bone marrow LSK-cells transformed with NRASQ61K

tag: growth conditions

value: Expanded on OP9DL in the presence of IL7,SCF, Flt3L


title: ClutchA_ribozero_19.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_39_012

source_name: Whole embryo, 19.5hpf, RiboZero RNA


title: ClutchA_ribozero_18.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_37_005

source_name: Whole embryo, 18.5hpf, RiboZero RNA


title: ClutchA_ribozero_20_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_40_004

source_name: Whole embryo, 20hpf, RiboZero RNA


title: SIN3 KD rep2

status: Public on Jan 09 2016

city: Detroit

first: Lori

middle: Ann

last: Pile

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

description:
test
replicates 1,2 and 3 combined
SIN3_KD_vs_GFP_RNAi.txt

data_processing:
Illumina bcl2fastq converter was used to demultiplex samples.
Tuxedo pipeline was used to allign reads to dm3, estimation of  transcripts and analyze differential expression. All steps were performed using default settings.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and expression fold change as determined by Cuffdiff.

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila Schneider cell line 2 (S2) cells were cultured at 270C in Schneider's Drosophila medium (1x) + L-glutamine (Life Technologies) with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 mg/ml gentamycin.

extract_protocol:
Total RNA was isolated from treated S2 cells using the EZ1 RNA Universal Kit (Quiagen). Cells were disrupted and homogenized in 750 μl  QIAzol lysis reagent via bead-milling on the TissueLyser II (Qiagen). RNA was collected from the homogenate by chloroform exraction and purified on the EZ1 Advanced (Qiagen) with additional step to remove any residual DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with dsRNA targeting Sin3A gene for 4 days prior to RNA extraction

tag: dsrna target


title: ClutchA_ribozero_18_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_36_004

source_name: Whole embryo, 18hpf, RiboZero RNA


title: Ezh2ff in vivo

description: Harvested from Spleen of moribund mouse, sorted for YFP and Mac1 expression

source_name: Spleen

value: Expanded on OP9DL in the presence of IL7,SCF, Flt3L prior to transplantation, harvested from leukemic mice.


title: Ezh2ko in vitro


title: ClutchA_ribozero_19_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_38_006

source_name: Whole embryo, 19hpf, RiboZero RNA


title: ClutchA_ribozero_17_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_34_006

source_name: Whole embryo, 17hpf, RiboZero RNA


title: ClutchA_ribozero_17.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_35_012

source_name: Whole embryo, 17.5hpf, RiboZero RNA


title: Ezh2ko in vivo


title: Ezh2ko H3K27me3 ChIP

description: Leukemic cells harvested from a moribund mouse were  expanded on OP9DL in the presence of IL7,SCF, Flt3L.

data_processing:
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6.  CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d mm9 -v snp128_strict_wholeChrs --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using  Samtools. Bam-files were sorted using Samtools.
Sorted Bam-files were converted to Bed format and were used as input for Diffreps (PLoS ONE 8(6): e65598.), using ChIP-input input as background controls and using Gtest (-me -gt).
Sorted Bam-files were used to generate peak-files using MACS2, using the callpeak function with parameters  -f BAM -g mm  --nomodel --broad --nolambda --broad-cutoff 0.25. ChIP-input served as control.
Sorted Bam-files were used to generate Homer Tag-directories. Homer 'makeUCSCfile' was used to generate bedGraph files, which were converted to BigWig format using 'bedGraphToBigWig' (UCSC)
Genome_build: mm9

extract_protocol:
DNA was isolated using standard ChIP protocol
Nugen Ovation Ultra low system V2


title: ClutchA_ribozero_16.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_33_005

source_name: Whole embryo, 16.5hpf, RiboZero RNA


title: Ezh2ko input


title: Ezh2ff H3K27me3 ChIP


title: ClutchA_ribozero_16_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_32_004

source_name: Whole embryo, 16hpf, RiboZero RNA


title: Ezh2ff input


title: ClutchA_ribozero_15.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_31_012

source_name: Whole embryo, 15.5hpf, RiboZero RNA


title: ClutchA_ribozero_1.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_3_012

source_name: Whole embryo, 1.5hpf, RiboZero RNA


title: Estradiol/5-ALA-treated double mutant cells, Replicate 2

city: Madison

first: Kyle

last: Hewitt

state: Wisconsin

address: 1111 Highland Ave.

institute: University of Wisconsin

description: Alas2 cis-element-mutant (double mutant)

data_processing:
Illumina Casava-1.8.2 base calling
RSEM reference preparation: RSEM v1.2.20 with Bowtie v1.1.1, rsem-prepare-reference run with options "--bowtie --gtf" Gene annotation: Ensembl v79 filtered for genes of type "protein_coding" or "lincRNA" on standard chromosomes
RSEM abundance estimation: RSEM v1.2.20 with Bowtie v1.1.1, rsem-calculate-expression run with options "--no-bam-output --time -p 10"
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values and counts for each Sample ...

source_name: G1E-ER-GATA-1 cells

growth_protocol: G1E-ER-GATA-1 cells were cultured in IMDM (Gibco) containing 15% FBS (Gemini), 1% penicillin-streptomycin (Gemini), 2 U/ml erythropoietin, 120 nM monothioglycerol (Sigma), 0.6% conditioned medium from a Kit ligand-producing CHO cell line, and 1ug/ml puromycin (Gemini).

extract_protocol:
Total RNA was purified with TRIzol (Life Technologies).
RNA libraries were prepared using TruSeq RNA Sample Prep Kit (Illumina).

treatment_protocol: ER-GATA-1 activity was induced by addition of 1 uM beta-estradiol (Steraloids) to the media. To rescue heme biosynthesis, 1 mM 5-aminolevulinic acid hydrochloride (5-ALA; Sigma) was added to the media.

tag: treatment

value: 48 h beta-estradiol/5-ALA treatment


title: Estradiol/5-ALA-treated double mutant cells, Replicate 3


title: ClutchA_ribozero_15_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_30_006

source_name: Whole embryo, 15hpf, RiboZero RNA


title: Estradiol-treated double mutant cells, Replicate 3

value: 48 h beta-estradiol treatment


title: Estradiol-treated double mutant cells, Replicate 2


title: Estradiol/5-ALA-treated double mutant cells, Replicate 1


title: ClutchA_ribozero_14.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_29_005

source_name: Whole embryo, 14.5hpf, RiboZero RNA


title: ClutchA_ribozero_14_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_28_004

source_name: Whole embryo, 14hpf, RiboZero RNA


title: ClutchA_ribozero_12.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_25_005

source_name: Whole embryo, 12.5hpf, RiboZero RNA


title: Estradiol-treated double mutant cells, Replicate 1


title: ClutchA_ribozero_13_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_26_006

source_name: Whole embryo, 13hpf, RiboZero RNA


title: Estradiol-treated WT cells, Replicate 3

description: WT


title: ClutchA_ribozero_11.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_23_012

source_name: Whole embryo, 11.5hpf, RiboZero RNA


title: Estradiol-treated WT cells, Replicate 1

description: WT


title: ClutchA_ribozero_13.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_27_012

source_name: Whole embryo, 13.5hpf, RiboZero RNA


title: ClutchA_ribozero_11_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_22_006

source_name: Whole embryo, 11hpf, RiboZero RNA


title: ClutchA_ribozero_12_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_24_004

source_name: Whole embryo, 12hpf, RiboZero RNA


title: Estradiol-treated WT cells, Replicate 2

description: WT


title: Untreated WT cells, Replicate 3

description: WT

value: untreated


title: ClutchA_ribozero_10.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_21_005

source_name: Whole embryo, 10.5hpf, RiboZero RNA

value: wild type


title: ClutchA_ribozero_1_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_2_006

source_name: Whole embryo, 1hpf, RiboZero RNA


title: Untreated WT cells, Replicate 1

description: WT


title: KM3_CD133_pos_Isotype

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

data_processing:
Basecalls, demultiplexing and fastq generation was carried out using CASAVA v 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 aligner.
The genome was divided into non-overlapping windows 200 bp, and aligned reads was were considered to be within a window of the midpoint of its estimated fragment. The genomic bins which contained statistically significant ChIP-Seq enrichment were identified by comparison to a Poisson background model, assuming that background reads are spread randomly throughout the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated.

source_name: mouse Tumor intitating stem cells

growth_protocol: TICs were grown in DMEM/F12 or Kubota medium for all experiments

extract_protocol:
Four pairs of TICs and Nanog-/CD133-/CD49f+ control cells (~1x10^5 per mouse) were isolated from four independent mouse liver tumors. ChIP was performed with NANOG antibody using CD 133+ as well as CD133– cell lines following a standard protocol as suggested by manufacturer (Millipore). In parallel, isotype control antibody was used as a control.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired and blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters.  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 Illumina Hi-Seq  following the manufacturer's protocols.sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Tumor inititating stem cells

tag: cell marker

value: liver tumor

tag: chip antibody

value: Isotype antibody


title: Untreated WT cells, Replicate 2

description: WT


title: ClutchA_ribozero_10_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_20_004

source_name: Whole embryo, 10hpf, RiboZero RNA


title: KM4_CD133_neg_Isotype

tag: strain


title: ClutchA_ribozero_9.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_19_012

source_name: Whole embryo, 9.5hpf, RiboZero RNA

tag: tissue


title: ClutchA_ribozero_9_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_18_006

source_name: Whole embryo, 9hpf, RiboZero RNA


title: KM2_CD133_neg_NANOG_IP

value: Nanog, Abcam ab21624


title: ClutchA_ribozero_8.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_17_005

source_name: Whole embryo, 8.5hpf, RiboZero RNA


title: KM1_CD133_Pos_NANOG_IP


title: E7.5_EPC_DKO-3 Bisulfite-Seq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.7, default parameters) and mapped to the mouse NCBIM37 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk)
Genome_build: NCBIM37
Genome-wide quantification files: Gene expression files were generated by normalising and transforming raw count data (variance stabilizing transformation) using DEseq.
Bismark coverage report: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Ectoplacental cone

extract_protocol:
DNA was bisulfite converted using the Imprint DNA Modification Kit (Sigma). Whole-genome BS-seq libraries were prepared from 25-70 ng genomic DNA, using a post-bisulfite adaptor tagging protocol, as previously described (Peat et al. 2014).
Genomic DNA and RNA were isolated from the same samples using the Allprep DNA/RNA kit (Qiagen).

tag: background strain

tag: developmental stage

tag: epc genotype

tag: oocyte genotype

value: Dnmt3a/b KO

value: trophoblast


title: ClutchA_ribozero_7_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_14_006

source_name: Whole embryo, 7hpf, RiboZero RNA


title: E7.5_EPC_DHet-3 Bisulfite-Seq


title: ClutchA_ribozero_5.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_11_012

source_name: Whole embryo, 5.5hpf, RiboZero RNA


title: E7.5_EPC_DHet-2 Bisulfite-Seq


title: E7.5_EPC_DKO-2 Bisulfite-Seq


title: E7.5_EPC_DHet-1 Bisulfite-Seq


title: E7.5_EPC_DKO-1 Bisulfite-Seq


title: ClutchA_ribozero_6_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_12_004

source_name: Whole embryo, 6hpf, RiboZero RNA


title: ClutchA_ribozero_8_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_16_004

source_name: Whole embryo, 8hpf, RiboZero RNA


title: E7.5_EPC_Ctrl-1 Bisulfite-Seq

value: Dnmt3a/b WT


title: ClutchA_ribozero_0.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_1_005

source_name: Whole embryo, 0.5hpf, RiboZero RNA

value: whole embryo


title: ClutchA_ribozero_0_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_0_004

source_name: Whole embryo, 0hpf, RiboZero RNA


title: ClutchA_ribozero_5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_10_006

source_name: Whole embryo, 5hpf, RiboZero RNA


title: ClutchA_polyA_64_hpf_repeat

description:
PolyA+ RNA
clutch_A_poly_A/Sample_BKXtRNA_rerun_88_012

source_name: Whole embryo, 64hpf, polyA+ RNA


title: E7.5_EPC_Ascl2_KO-3 RNA-Seq

extract_protocol:
RNA was DNase treated with the DNA-free kit (Life Technologies). Messenger RNA was purified using a Dynabeads mRNA Purification Kit (Life Technologies). Strand-specific libraries were generated using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre).
Genomic DNA and RNA were isolated from the same samples using the Allprep DNA/RNA kit (Qiagen).

value: Ascl2 lacZ/+

value: Ascl2 lacZ


title: E7.5_EPC_Ctrl-2 Bisulfite-Seq


title: ClutchA_polyA_52_hpf_repeat

description:
PolyA+ RNA
clutch_A_poly_A/Sample_BKXtRNA_rerun_76_007

source_name: Whole embryo, 52hpf, polyA+ RNA

value: A


title: E7.5_EPC_Ascl2_WT-2 RNA-Seq

value: Ascl2 +/+

value: Ascl2 WT


title: E7.5_EPC_Ascl2_KO-2 RNA-Seq


title: ClutchA_polyA_30_hpf_repeat

description:
PolyA+ RNA
clutch_A_poly_A/Sample_BKXtRNA_rerun_54_005

source_name: Whole embryo, 30hpf, polyA+ RNA


title: E7.5_EPC_Ascl2_KO-1 RNA-Seq


title: ClutchA_polyA_33_hpf_repeat

description:
PolyA+ RNA
clutch_A_poly_A/Sample_BKXtRNA_rerun_57_006

source_name: Whole embryo, 33hpf, polyA+ RNA


title: E7.5_EPC_Ascl2_WT-1 RNA-Seq


title: ClutchA_ribozero_7.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_15_012

source_name: Whole embryo, 7.5hpf, RiboZero RNA


title: E7.5_EPC_3aKO-3 RNA-Seq


title: ClutchA_ribozero_6.5_hpf

description:
RiboZero RNA
clutch_A_ribozero/Sample_BlitzKhokhaXtRibo-ExProfile_13_005

source_name: Whole embryo, 6.5hpf, RiboZero RNA


title: Mice liver tissue_cold storage

city: Luzhou

first: Bo

last: Li

state: Sichuan Province

address: Taiping Street No. 25, Jiangyang District

department: Department of Hepatobiliary Surgery

institute: the Affiliated Hospital of Luzhou Medical College

data_processing:
Sequencing was performed using the high-throughput, high-sensitivity HiSeq 2500 sequencing platform (Illumina Company, USA). Bioinformatics analyses were conducted using the MAS3.0 system (CapitalBio, Beijing, China) and GeneSpring GX v 12.0 software package (Agilent Technologies, Santa Clara, CA, USA).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Mice liver tissue_cold storage

growth_protocol: Mice were housed on a constant 12 h light/12 h dark cycle in a temperature (22.2℃)-controlled room and given ad libitum access to ordinary chow

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and purified using ZR RNA microprep kit (Zymo Research). The RNA sequencing was performed by Beijing Genomics Institute (BGI) (Beijing, China).
cDNA libraries were generated using the cDNA Library Construction Kit (TaKaRa, China) according to the manufacturer’s instruction. After purification, end repair, base A and sequencing joint adding, the generated cDNA was fragmented using uracil-N-glycosylase (UNG). Then, PCR amplification was performed to establish the complete sequencing cDNA library.

treatment_protocol: Mice were anesthetized by intramuscular injection of sodium pentobarbital (50 mg/kg of body weight). After opening the abdominal cavity, the livers were procured and flushed with 30 mL of UW solution. Then, livers were stored for 12 or 24 h at 4 °C in the UW solution. Sham treatment as a control.

value: liver

tag: age

value: 8-12 week

tag: gender

value: male

value: cold storage


title: ClutchA_polyA_11.5_hpf_repeat

description:
PolyA+ RNA
clutch_A_poly_A/Sample_BKXtRNA_rerun_23_002

source_name: Whole embryo, 11.5hpf, polyA+ RNA

value: wild type


title: E7.5_EPC_Ascl2_WT-3 RNA-Seq


title: E7.5_EPC_DKO-3 RNA-Seq


title: E7.5_EPC_DHet-3 RNA-Seq


title: E7.5_EPC_3bKO-3 RNA-Seq


title: Mice liver tissue_control

source_name: Mice liver tissue_control

value: Sham


title: ClutchA_polyA_65_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_89

source_name: Whole embryo, 65hpf, polyA+ RNA


title: ClutchA_polyA_64_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_88


title: NOD naïve

first: Jenny

last: Chen

address: 16 Divinity Ave

institute: Harvard

description: naïve ESCs from NOD mouse

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and aligned using TopHat v2.0.10 (-N 3 --read-edit-dist 3 --library-type fr-secondstrand --prefilter-multihits --max-multihits 15 --segment-length 20).  Optical duplicates were removed using Picard's MarkDuplicates utility
Transcripts were reconstructed from TopHat alignments using Scripturev3.1 (-coverage 0.2)
Fragments per Kilobase of exon per Megabase of library size (FPKM) was calculated using Cufflinks v2.1.1
Genome_build: mm9, rn5, hg19
Supplementary_files_format_and_content: tab-delimited text file of cufflinks estimation of coding gene FPKMs
Supplementary_files_format_and_content: tab-delimited text file of cufflinks estimation of lncRNA FPKMs
Supplementary_files_format_and_content: wig file representing RNA-Seq coverage of aligned reads

source_name: naïve ESC

extract_protocol:
Briefly, 10ug of total RNA was polyA selected twice using Oligo(dT)25 beads (Life Technologies) and NEB oligo(dT) binding buffer.
PolyA-selected RNA was fragmented, repaired and cleaned using Zymo RNA concentrator-5 kit.  30ng of polyA-selected RNA per sample were used to make RNA-seq libraries. Adapter was ligated to RNA, RNA was reverse transcribed and second adapter was ligated on cDNA.

value: NOD

tag: cell state

value: naïve


title: 129SvEv primed

description: primed epiSCs from 129SvEv mouse

source_name: primed EpiSC

value: epiblast


title: 129SvEv naïve

description: naïve ESCs from 129SvEv mouse


title: E7.5_EPC_3aKO-2 RNA-Seq

source_name: Ectoplacental cone

value: Dnmt3a/b KO

value: trophoblast


title: ClutchA_polyA_21.5_hpf_repeat

description:
PolyA+ RNA
clutch_A_poly_A/Sample_BKXtRNA_rerun_43_004

source_name: Whole embryo, 21.5hpf, polyA+ RNA

tag: genotype/variation

value: whole embryo


title: E7.5_EPC_DKO-2 RNA-Seq


title: input-Hela_rep2-B

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

data_processing:
ChIP-seq and related datasets (IP and Input control) were quality certified with NGS-QC Generator tool (www.ngs-qc.org). Specifically, this methodology allows providing enrichment quality descriptors discretized in a scale ranging from “AAA” (Best) to “DDD” (worst). The quality scores reports associated to these datasets are available at : http://www.ngs-qc.org/certdb.php
bigWig files were generated with a read elongation of 150nts and a resolution of 20nts
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM 1g/L glucose, 5% Fetal Calf Serum and 40μg Gentamicin to a density of 15–20 millions cells/15cm plates. Cells were fixed for 30min with paraformaldehyde (1% in PBS). Fixation was quenched with 0.2M glycine in PBS, then cells were washed three times with PBS, collected and stored at -80°C.

extract_protocol:
25μL of ChIP-IT Protein G  Magnetic Beads (ActiveMotif) were incubated with the antibody  under evaluation (the amounts of antibody in use corresponded to  that indicated by the supplier’s information) in presence of 100μL  PIC-containing Lysis Buffer. After two hours at 4°C on a rotating  shaker, chromatin from 3 million cells was added and the final vol-  ume was adjusted to 500μL with PIC-containing Lysis Buffer and  incubation on a rotating shaker was continued overnight at 4°C. The immunoprecipitated chromatin was recovered by magnetic bead separation, followed by multiple washing steps on a custom liquid handling platform (TECAN EVO75). Specifically, the washing is performed as follows: (1) Low salt washing (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM TrisHCl pH 8, 150mM NaCl); (2) High salt washing (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM TrisHCl pH 8, 500mM NaCl); (3) LiCl-washing (0.25M LiCl, 1% IGEPAL CA630, 1% Na-deoxycholate, 1mM EDTA, 10mM Tris pH 8) and (4) 1×TE washing. The immunoprecipitated chromatin was eluted and de-crosslinked in 100μL of elution buffer (1%  SDS, 100mM NaHCO3, 250mM NaCl, 0.2mg/ml Proteinase K) and incubated for 4 hours at 65°C. The eluted chromatin was supplemented with 200μL H2O and 300μL phenol/chloroform/isoamyl alcohol (25/24/1) mix was added. After two extraction steps, the aqueous phase was subjected to ethanol precipitation in presence of 1μL GlycoBlue (Invitrogen; 15mg/ml). The precipitated material was re-suspended in 45μL H2O; 5μL was used for validation by quantitative PCR, the remaining 40μL was used for DNA library preparation.
The DNA library preparation for massive parallel sequencing was performed according to standard procedures (NEXTFlex ChIP-Seq Kit (Biooscientific)) adapted to automation by our custom liquid handling platform (TECAN EVO75). Prior to DNA sequencing library preparation was monitored using a Tapestation (Agilent). Samples were sequenced on an Illumina HiSeq 2000 platform following manufacturer’s standard procedures and certified on the basis of the NGS-QC Generator  concept (Mendoza-Parra et al; NAR 2013).

treatment_protocol: 40 million cells were sonicated in 500μL of Lysis Buffer (1% Na-deoxychlorate, 50mM TrisHCl pH8, 140mM NaCl, 1mM EDTA, 1% Triton X-100) containing 5-times diluted Protease Inhibitor Cocktail (PIC;  Roche Diagnostic; 1 tablet solubilized in 10ml Lysis Buffer). Sonication was performed with a Bioblock Scientific instrument (Vibra Cell 75043; 40 cycles, 30s ON end 59s OFF; 38% power). Chromatin fragmentation was evaluated by agarose gel electrophoresis as follows: 20μL of sonicated chromatin was diluted with 20μL TE (10mM Tris-HCl pH 8, 1mM EDTA) and 5μL 5M NaCl was added. Diluted chromatin was incubated at 100°C for 30 min, centrifuged at 12,000 rpm at room temperature and the supernatant was loaded onto a 2% agarose gel.

tag: cell line

value: HeLa cells

value: Paraformaldehyde fixation (1%, 30 minutes)


title: ClutchA_polyA_63_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_87

source_name: Whole embryo, 63hpf, polyA+ RNA

tag: clutch

value: A

tag: time (hpf)


title: ClutchA_polyA_62_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_86

source_name: Whole embryo, 62hpf, polyA+ RNA


title: input-Hela_rep1-B


title: input-Hela_rep1-A


title: E7.5_EPC_3bKO-2 RNA-Seq


title: H3K9ac-mono_rep2-A

value: H3K9ac monoclonal Ref:Active motif 61251


title: ClutchA_polyA_66_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_90

source_name: Whole embryo, 66hpf, polyA+ RNA


title: ClutchA_polyA_61_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_85

source_name: Whole embryo, 61hpf, polyA+ RNA


title: H3K9ac-mono_rep1-D


title: H3K9ac-mono_rep1-C


title: ClutchA_polyA_60_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_84

source_name: Whole embryo, 60hpf, polyA+ RNA


title: E7.5_EPC_3aKO-1 RNA-Seq


title: H3K9ac-mono_rep2-B


title: H3K9ac-mono_rep1-B


title: NOD primed

description: primed epiSCs from NOD mouse


title: input-Hela_rep2-A


title: H3K9ac-mono_rep1-A


title: ClutchA_polyA_59_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_83

source_name: Whole embryo, 59hpf, polyA+ RNA


title: E7.5_EPC_Ctrl-3 RNA-Seq

value: Dnmt3a/b WT


title: H3K9ac-poly_rep2

value: H3K9ac polyclonal Ref:Active motif 39917


title: E7.5_EPC_DKO-1 RNA-Seq


title: ClutchA_polyA_57_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_81

source_name: Whole embryo, 57hpf, polyA+ RNA


title: H3K4me3-poly_rep1-D

value: H3K4me3 polyclonal Ref:Active motif 39159


title: H3K4me3-poly_rep1-C


title: H3K4me3-poly_rep2-B


title: ClutchA_polyA_54_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_78

source_name: Whole embryo, 54hpf, polyA+ RNA


title: H3K4me3-poly_rep1-A


title: E7.5_EPC_3bKO-1 RNA-Seq


title: H3K4me3-poly_rep1-B


title: E7.5_EPC_Ctrl-2 RNA-Seq


title: E7.5_EPC_Ctrl-1 RNA-Seq


title: E7.5_EPC_DHet-2 RNA-Seq


title: H3K4me3_mono-rep2-A

value: H3K4me3 monoclonal Ref:Active motif 61379


title: ClutchA_polyA_56_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_80

source_name: Whole embryo, 56hpf, polyA+ RNA


title: ClutchA_polyA_55_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_79

source_name: Whole embryo, 55hpf, polyA+ RNA


title: E7.5_EPC_DHet-1 RNA-Seq


title: H3K9ac-poly_rep1


title: ClutchA_polyA_53_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_77

source_name: Whole embryo, 53hpf, polyA+ RNA


title: ClutchA_polyA_52_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_76

source_name: Whole embryo, 52hpf, polyA+ RNA


title: ClutchA_polyA_58_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_82

source_name: Whole embryo, 58hpf, polyA+ RNA


title: H3K4me3-poly_rep2-A


title: H3K27ac-poly_rep1-B

value: H3K27ac polyclonal Ref:Active motif 39133


title: H3K4me3_mono-rep1-A


title: H3K4me3_mono-rep1-D


title: ClutchA_polyA_51_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_75-2

source_name: Whole embryo, 51hpf, polyA+ RNA

value: wild type


title: H3K27ac-mono_rep2

value: H3K27ac monoclonal Ref:Active motif 39685


title: H3K4me3_mono-rep2-B


title: ClutchA_polyA_50_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_75-1

source_name: Whole embryo, 50hpf, polyA+ RNA


title: H3K27ac-poly_rep2


title: H3K27ac-mono_rep1


title: KO-chow_2

city: Chicago

first: Richard

last: Green

state: IL

address: Tarry 15, 303 E. Chicago Av.

institute: Northwestern University

data_processing:
Adapters were removed and reads were removed that had either more than 5% unknown bases, or more than 50% of the reads had a phred score less than 10
The remaining reads were aligned to mm10 (UCSC) with TopHat v2.0.7 with parameters -p 12 -G genes.gtf
Differential expression was performed with cuffdiff v2.1.1 using parameters -p 12 -b genome.fa.  RPKM values were extracted from the cuffdiff results.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Livers were removed, snap frozen in liquid nitrogen and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed either regular chow or a high fat diet with high frucose corn syrup equivalent for 4 weeks.

tag: genotype

value: liver


title: H3K4me3_mono-rep1-B

tag: treatment


title: KO-chow_1


title: A1 anti-Flag-SIRT7

city: Heidelberg

first: Renate

last: Voit

address: Im Neuenheimer Feld 581

department: Division Molecular Biology of the Cell

institute: German Cancer Research Center

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to human hs37 reference genome (including human rRNA sequence) using Tophat2 with default parameters.
The RPKM values were calculated for all genes with annotation in Gencode V17 including mRNA and snoRNAs.
The SIRT7 reads distributions on genes transcribed by different polymerases (PolI, Pol II, Pol III) were calculated and normalized to the total number of mapped reads.
Genome_build: hs37
Supplementary_files_format_and_content: The snoRNAs  identified in SIRT7 CLIP-seq are listed in the file snoRNAs_identified_SIRT7_CLIP_seq.xlsx

source_name: Flag-SIRT7-293T cells

growth_protocol: HEK293T cells expressing Flag-SIRT7 were cultured in DMEM/10% FCS. For CLIP-seq cells were harvested at 70% of confluence.

extract_protocol:
RNA-protein cpmplexes were crossslinked by irradiating cells with UV (254 nm) and Flag-SIRT7-RNA complexes were isolated with anti-Flag antibody from nuclear lysates.
RNA libraries were prepared for sequencing using standard Illumina protocols, Briefly, the CLIP-seq experiments were performed in biological duplicates. Co-immunoprecipitated RNA from anti-Flag-SIRT7 and IgG control immunoprecipitations was purified with TRIZOL, and treated with DNase I. The RNA-seq libraries were created using the NEBNext Ultra RNA Library Prep kit for Illumina (E7530) with NEBNext Multiplex Oligos for Illumina (E7300). 50 cycles of sequencing were performed on the Illumina HiSeq 2000 Instrument. cDNA libraries from total RNA were used as Input.

treatment_protocol: transfected cells, no particular treatment

tag: cell line background

value: expressing Flag-SIRT7

tag: clip antibody

value: anti-Flag (Sigma F1804)


title: A1 IgG

value: mouse IgG (Dianova 115-035-062)


title: A1 Input


title: ClutchA_polyA_49_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_73

source_name: Whole embryo, 49hpf, polyA+ RNA


title: ClutchA_polyA_48_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_72

source_name: Whole embryo, 48hpf, polyA+ RNA


title: Flox-highfat_2

tag: strain


title: H3K27ac-poly_rep1-A

source_name: HeLa cells

tag: chip antibody


title: KO-highfat_2

tag: tissue


title: Flox-highfat_1


title: pCDNA3.1 B

city: Danville

first: anne

last: moon

state: PA

address: 100 North Academy Ave

institute: Geisinger CLinic

data_processing:
Sequence reads were aligned (98.5% mapped) to the human genome build 37.2 with Tophat (v2.0.8b) using default parameters
Aligned reads were assembled into transcripts and their relative abundance was measured using Cufflinks (v2.1.1) with fragment bias correction (frag-bias-correct) and multi-read correction (multi-read-correct).
Cuffdiff was used to test for differential expression between samples and controls
Genome_build: GRCh 37.2
Supplementary_files_format_and_content: cufflinks FPKM

extract_protocol:
Total RNA was isolated from negative control, TBX3 and CAPERa KD HFFs using the nucleospin Kit (Clontech) according to the manufacturer's protocol
Poly-A RNA was purified, fragmented, primed with random hexamers and used to generate first strand cDNA using reverse transcriptase. Samples that passed quality control steps were used for Illumina library preparation using the Illumina TruSeq RNA Sample Prep protocol
Single-end 50 bp reads

treatment_protocol: HFFs were incubated with TBX3 or CAPER a shRNA encoding retrovirus for 48hs followed by incubation for 2 days with antibiotic selection medium.

tag: cell type

value: human foreskin fibroblasts (HFFs)


title: UCA1 A


title: KO-highfat_1


title: ClutchA_polyA_46_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_70

source_name: Whole embryo, 46hpf, polyA+ RNA

value: whole embryo


title: Flox-chow_2


title: UCA1 B


title: ClutchA_polyA_45_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_69

source_name: Whole embryo, 45hpf, polyA+ RNA


title: Caper B

tag: incubated with

value: CAPERα-shRNA encoding retrovirus for 48hrs


title: Caper A


title: pCDNA3.1 A


title: Control B

value: control vector containing shRNA oligonucleotides targeting luciferase


title: TBX3 B

value: TBX3-shRNA encoding retrovirus for 48hrs


title: Control A


title: ClutchA_polyA_44_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_68

source_name: Whole embryo, 44hpf, polyA+ RNA

value: A


title: Epididymis DNase-seq rep 2

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

data_processing:
Bowtie v 1.0.0 used for alignment after removing first 20 bases of each read.
Sequences are mapped to hg19 reference genome with parameters:  -q -m 1 -l 20 -n 3 --best --strata -p 10.
The peak calls for the DNase-seq data were performed with homer software using default parameters. False discovery rate of 0.1% was used for all samples.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing the locations of DNase hypersensitive sites

source_name: primary human adult epididymis cells

growth_protocol: Cells were grown as decribed in Yang et al. 2015. In review.

extract_protocol:
genomic DNA is digested with different concentrations of DNaseI (NEB) and purified for library construction
DNase-seq libraries were prepared by Drs A. Safa and G. Crawford.

tag: tissue type

value: primary adult human epididymis cells


title: ClutchA_polyA_42_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_66

source_name: Whole embryo, 42hpf, polyA+ RNA


title: Epididymis DNase-seq rep 1


title: Flox-chow_1


title: ClutchA_polyA_41_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_65

source_name: Whole embryo, 41hpf, polyA+ RNA


title: Caco2 DNase-seq rep 2

source_name: colorectal adenocarcinoma cells

value: colorectal adenocarcinoma


title: Caco2 DNase-seq rep 1


title: HBE DNase-seq

source_name: primary human bronchial epithelial cells


title: ClutchA_polyA_40_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_64

source_name: Whole embryo, 40hpf, polyA+ RNA


title: NOMO1R_CPI203_2

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

data_processing:
Sequencing was performed on an Illumina HiSeq 2000.
Tophat 1.4.1 was used to perform sequence alignment, with UCSC human (hg19) as the reference genome.
The Normalized counts of sequence reads (FPKM) mapped to annotated UCSC genes were determined using Cufflinks software.
The data was filtered to keep genes with at least one sample above a 50-read threshold. Samples with fewer than 10 reads FPKM are replaced with the average across samples of 10 reads FPKM, to generate the final gene counts for each sample and gene.
Data processing was performed by Ocean Ridge Biosystems.
Genome_build: hg19
Supplementary_files_format_and_content: Summarized FPKM values per Ensembl-annotated gene for each sample listed.

growth_protocol: NOMO-1 and NOMO-1-t cells were seeded at 2.5x10^5 cells/mL in RPMI+20% FBS. A375 and A375-t cells were seeded at 2e6 cells/T25 flask and grown in DMEM+10% FBS.

extract_protocol: Cell samples were collected and total RNA was prepared using TRIzol (Life Technologies) or RNeasy mini kit (QIAGEN). RNA-sequencing from total RNA samples was carried out using the services of Ocean Ridge Biosciences.

treatment_protocol: NOMO-1 and NOMO-1-t cells were treated with DMSO or 1 uM CPI203 for 24 hours. For treatment samples, A375 and A375-t cells were treated with DMSO or 1 uM CPI203 for 6h or 24 h.

tag: clone

value: NOMO1 resistant clone


title: ClutchA_polyA_47_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_71

source_name: Whole embryo, 47hpf, polyA+ RNA


title: NOMO1R_DMSO_2

value: DMSO


title: ClutchA_polyA_39_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_63

source_name: Whole embryo, 39hpf, polyA+ RNA


title: ClutchA_polyA_38_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_62

source_name: Whole embryo, 38hpf, polyA+ RNA


title: NOMO1_CPI203_2

value: NOMO1 parental


title: NOMO1R_CPI203_1


title: NOMO1_CPI203_1


title: NOMO1R_DMSO_1


title: NOMO1_DMSO_1


title: ClutchA_polyA_36_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_60

source_name: Whole embryo, 36hpf, polyA+ RNA

value: wild type


title: ClutchA_polyA_35_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_59

source_name: Whole embryo, 35hpf, polyA+ RNA


title: A375_Resistant4_CPI203_6h_R1

value: A375 resistant clone 4


title: A375_Resistant4_CPI203_6h_R2


title: ClutchA_polyA_37_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_61

source_name: Whole embryo, 37hpf, polyA+ RNA


title: ClutchA_polyA_34_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_58

source_name: Whole embryo, 34hpf, polyA+ RNA


title: A375_Resistant1_CPI203_6h_R2

value: A375 resistant clone 1


title: A375_Resistant4_DMSO_6h_R2


title: TBX3 A


title: A375_Resistant1_CPI203_6h_R1


title: ClutchA_polyA_33_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_57

source_name: Whole embryo, 33hpf, polyA+ RNA


title: A375_Resistant1_DMSO_6h_R2


title: A375_Resistant4_DMSO_6h_R1


title: ClutchA_polyA_31_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_55

source_name: Whole embryo, 31hpf, polyA+ RNA


title: A375_Parental_DMSO_6h_R2

value: A375 parental


title: A375_Resistant1_DMSO_6h_R1


title: A375_Parental_CPI203_6h_R2


title: A375_Parental_CPI203_6h_R1


title: ClutchA_polyA_30_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_54

source_name: Whole embryo, 30hpf, polyA+ RNA


title: NOMO1_DMSO_2


title: A375_Resistant4_None_0h_R1


title: ClutchA_polyA_32_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_56

source_name: Whole embryo, 32hpf, polyA+ RNA


title: ClutchA_polyA_29_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_53

source_name: Whole embryo, 29hpf, polyA+ RNA


title: A375_Resistant1_None_0h_R2


title: A375_Parental_DMSO_6h_R1


title: A375_Resistant1_None_0h_R1


title: A375_Parental_None_0h_R2


title: A375_Resistant4_None_0h_R2


title: ClutchA_polyA_28_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_52

source_name: Whole embryo, 28hpf, polyA+ RNA


title: SUM159_JQ1_3H_2

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: RNA-Seq in DMSO or JQ1 treated cells

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
For all samples, transcriptome mapping was performed using tophat2 with default settings against the hg19 UCSC genes.gtf build. Quantification was performed using the cufflinks software suite by running the cuffquant command on all samples followed by the cuffnorm command. For all tophat2 and cufflinks data processing steps, default parameters were used.
Supplementary_files_format_and_content: TNBC_RNASEQ.FPKM.txt

molecule: polyA RNA

growth_protocol: Cells were growed with SUM medium

extract_protocol: RNA-Seq libraries were generated on a Sciclone NGS instrument (Perkin    Elmer) using Illumina TrueSeq reagents.  Briefly, mRNA was enriched from 1    ug of total RNA, fragmented and reverse transcribed.  Following 2nd strand    synthesis, next generation sequencing libraries were obtained by end    repair, A-tailing and adapter ligation reactions with reagents from the    Illumina TrueSeq kit.  Libraries were amplified and purified before    sequencing on a HiSeq instrument.

treatment_protocol: Cells were treated with 500nM JQ1 or DMSO for the indicated time

tag: drug treatment

tag: duration

tag: barcode (already removed)

value: TGACCA


title: A375_Parental_None_0h_R1

tag: cell line


title: SUM159_JQ1_3H_1

description: RNA-Seq in DMSO or JQ1 treated cells

value: AGTCAA


title: ClutchA_polyA_27_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_51

source_name: Whole embryo, 27hpf, polyA+ RNA

extract_protocol:
For most samples, 10 embryos/timepoint were thoroughly homogenized in 200 ml Trizol® and frozen at -80oC, with the exception of egg, 0.5, 1, 1.5, 2, 2.5 and 3hpf timepoints, which were sampled at 25, 30, 20, 20, 20, 15 and 15 embryos, respectively.
For the Clutch A timecourse, ERCC Spike In Mix 1 (10ul) (lot 1205006) was diluted in DEPC-treated water to a final volume of 1045ul. Diluted spike in mix was then pipetted directly into the Trizol homogenates such that 1ul was delivered per embryo, which in most cases required delivery of 10ul diluted spike in mix/sample, with the exception of the first several timepoints. Spike in mix was pipetted into samples in the order of their chronology. Total RNA was purified from the embryo homogenate according to the manufacturer’s recommendations. Following isopropanol precipitation, RNAs were resuspended in DEPC-treated water and any contaminating genomic DNA was removed by a subsequent overnight precipitation in 5M LiCl at 4oC. RNA was pelleted and washed twice with 70% ethanol made with DEPC-treated water. All RNAs were resuspended and quantitated by Bioanalyzer. RNA quality was assessed by Bioanalyzer and RNA Integrity Numbers were all in excess of 9.
For the Clutch B timecourse, ERCC spike in mix 1 (lot 1306008) was similarly diluted and delivered to all Trizol® homogenates, except the pipetting was done in reverse order to the chronology of the samples. Furthermore, we added an additional spike in mix that was pipetted independently and in order of sample chronology. Ambion ArrayControl™ spikes were used. Two microliters of spikes 1, 2 and 4 were diluted  to a final volume of 82ul in DEPC-treated water to create a solution of 2.439ng for each ArrayControl spike-in RNA per microliter. Approximately 5.125ul of this dilution was then further diluted into DEPC-treated water to a final volume of 1000ul as verified by weight to create a solution of ~12.5pg/ul. One microliter per embryo (~12.5pg) was added to Trizol® homogenates by pipetting of 10ul per tube except in the cases of the 0-3hpf samples. In both timecourses these early timepoint spike ins were pipetted by multiple rounds of 10ul (for 20 or 30ul delivery), or readjustment to 5ul (for 15ul delivery). RNAs were subsequently isolated as described above except we omitted the LiCl precipitation step. RNAs were similar quantitated and quality evaluated.
RNA quality and concentration were evaluated by running total RNA on an Agilent RNA Nano Bioanalyzer chip. All samples had an RNA integrity number (RIN) greater than 9. Ribosomal RNA was removed via polyA-selection or ribosomal RNA depletion. For polyA-extraction, polyadenylated RNA transcripts were selected from the total RNA using two rounds of enrichment with oligo(dT)25 beads (Invitrogen). Ribosomal-depletion was completed with the Ribo-Zero (Human/Mouse/Rat) Magnetic Ribosomal rRNA Removal kit (Epicenter) according to the manufacturer's recommendations. The supernatant from both approaches was purified and concentrated using RNAclean XP beads (Beckman Coulter). Following selection, the RNA was fragmented to approximately 140 base pairs and first-strand synthesis was completed with SuperScript III reverse transcriptase (Invitrogen) using random hexamers. Magnetic AMPure XP beads (Beckman Coulter) were used to purify the cDNA and remained with the sample throughout sequencing library construction. During preparation, DNA is selectively precipitated by weight and re-bound to the beads through the addition of a 20% polyethylene glycol, 2.5 M NaCl solution. We used T4 DNA polymerase and T4 polynucleotide kinase to blunt ends and phosphorylate the fragments. The large Klenow fragment then added a single adenine residue to the 3' end of each fragment, custom adapters (IDT) are ligated using T4 DNA ligase, and, for strand-specific libraries, UDG removes uracil residues. The product is then PCR amplified using custom-made primers (IDT) containing unique 6 bp indices.

tag: genotype/variation

tag: clutch


title: SUM159_JQ1_24H_1

description: RNA-Seq in DMSO or JQ1 treated cells


title: SUM159_JQ1_24H_2

description: RNA-Seq in DMSO or JQ1 treated cells

value: CCGTCC


title: SUM159_JQ1_12H_2

description: RNA-Seq in DMSO or JQ1 treated cells

value: GCCAAT


title: ClutchA_polyA_25_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_49

source_name: Whole embryo, 25hpf, polyA+ RNA

value: whole embryo

tag: time (hpf)


title: SUM159_JQ1_12H_1

description: RNA-Seq in DMSO or JQ1 treated cells

value: ATGTCA


title: SUM159_DMSO_3H_1

description: RNA-Seq in DMSO or JQ1 treated cells

value: CTTGTA


title: ClutchA_polyA_24_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_48

source_name: Whole embryo, 24hpf, polyA+ RNA

value: A


title: SUM159_DMSO_24H_2

description: RNA-Seq in DMSO or JQ1 treated cells


title: ClutchA_polyA_23_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_46

source_name: Whole embryo, 23hpf, polyA+ RNA


title: SUM159_DMSO_12H_2

description: RNA-Seq in DMSO or JQ1 treated cells

value: ACAGTG


title: ClutchA_polyA_23.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_47

source_name: Whole embryo, 23.5hpf, polyA+ RNA


title: SUM159R_JQ1_3H_2

description: RNA-Seq in DMSO or JQ1 treated cells

value: AGTTCC


title: ClutchA_polyA_22.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_45

source_name: Whole embryo, 22.5hpf, polyA+ RNA


title: SUM159R_JQ1_24H_2

description: RNA-Seq in DMSO or JQ1 treated cells


title: SUM159R_JQ1_3H_1

description: RNA-Seq in DMSO or JQ1 treated cells


title: ClutchA_polyA_22_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_44

source_name: Whole embryo, 22hpf, polyA+ RNA


title: SUM159R_JQ1_24H_1

description: RNA-Seq in DMSO or JQ1 treated cells

value: GTCCGC


title: SUM159_DMSO_12H_1

description: RNA-Seq in DMSO or JQ1 treated cells

value: DMSO


title: SUM159R_DMSO_3H_2

description: RNA-Seq in DMSO or JQ1 treated cells


title: ClutchA_polyA_21.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_43

source_name: Whole embryo, 21.5hpf, polyA+ RNA


title: SUM159R_DMSO_3H_1

description: RNA-Seq in DMSO or JQ1 treated cells


title: ClutchA_polyA_26_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_50

source_name: Whole embryo, 26hpf, polyA+ RNA


title: ClutchA_polyA_21_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_42

source_name: Whole embryo, 21hpf, polyA+ RNA


title: SUM159R_DMSO_24H_2

description: RNA-Seq in DMSO or JQ1 treated cells


title: ClutchA_polyA_20.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_41

source_name: Whole embryo, 20.5hpf, polyA+ RNA


title: SUM159R_DMSO_24H_1

description: RNA-Seq in DMSO or JQ1 treated cells


title: SUM159_DMSO_3H_2

description: RNA-Seq in DMSO or JQ1 treated cells

value: CGATGT


title: ClutchA_polyA_20_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_40

source_name: Whole embryo, 20hpf, polyA+ RNA

value: wild type


title: SUM159_BRD4_DMSO_R1

description:
ChIP-Seq for BRD4 in DMSO treated cells
Sample name: SUM159_BRD4_DMSO_R1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Cells were treated with 500 nM JQ1 or DMSO for the indicated time

value: BRD4 (Bethyl, catalog# A301-985A, lot# 2)

value: 3 hour

value: ATCACG


title: HepG2 5C Rep1

city: Worcester

first: Bryan

middle: R

last: Lajoie

address: 368 Plantation St.

department: Program in Systems Biology

institute: UMMS

description:
ENM001CFTR-HepG2-R1
HepG2 replicate 1

data_processing:
Library strategy: 5C
5C read mapping: Sequencing data was obtained from an Illumina GAIIx machine and was processed by a custom pipeline to map and assemble 5C interactions, as previously described.  We used an updated version of the Novoalign mapping algorithm (V2.07.11).
5C bias correction: 5C experiments involve a number of steps that can differ in efficiency, thereby introducing biases in efficiency of detection of interactions.  These biases could be due to differences in the efficiency of crosslinking, the efficiency of restriction digestion (related to crosslinking efficiency), the efficiency of ligation (related to fragment size), the efficiency of 5C probes (related to annealing and PCR amplification) and finally the efficiency of DNA sequencing (related to base composition).  All of these potential biases?several of which are common to other approaches such as chromatin immunoprecipitation (for example, crosslinking efficiency, PCR amplification, base-composition-dependent sequencing efficiency)?will have an impact on the overall efficiency with which long-range interactions for a given locus (restriction fragment) can be detected.  We implemented the following steps to estimate and correct for such technical biases.
Probe filtering - cis purge: Not all probes are represented equally in our 5C dataset due to over- and under-performance in the assay.  As the first step in our data correction pipeline, we remove probes that perform significantly differently than the overall set.  The relative performance of each probe is determined as follows.  First, a global average relationship between interaction frequency and genomic distance is calculated using Loess smoothing for each data set.  Interaction profiles anchored on each probe across the 2.8 Mb region is then compared to this global average.  If the individual Loess is more or less than 0.85 of the scaled Z-score distance (a measurement of the number of standard deviations a data point is from the mean) from the average global Loess, the probe is flagged as problematic.  If a probe is flagged as problematic in more than 40% of the datasets, it is removed from downstream analysis from all datasets.  Using this threshold we removed 34 probes from downstream analysis (Table S5).
Singletonal removal: As we examined the 5C datasets, we noticed several instances when the interaction between two probes was much higher than neighboring interactions by an order or magnitude or more. Although there were not many of these ?blowouts?, we removed them from the dataset to avoid problems downstream during peak calling.  Thus, we removed any interaction that had a Z-score of 12 or more, resulting in the removal of 44 individual interactions (out of 44,770 interrogated interactions) from downstream analysis (Table S6). To calculate the Z-score of a given data point, we used the following equation:  where the Z-score (Z) is the read count (x) minus the population mean read count (µ) divided by the standard deviation (?).  This measurement was calculated for the given genomic distance between the corresponding loci, meaning the average and standard deviation of the read count were calculated only for points separated by the same genomic distance as the data point (x).
Coverage correction: Once the outlier probes and blowout interactions are removed from the 5C data set, the profiles of each probe were normalized so that they could be quantitatively compared to each other.  Here, we applied a slightly modified method compared to the one we used before 25 based only on local (cis) chromatin interaction data (within the 2.8 Mb CFTR region).  First, all 5C datasets were read-normalized (each interaction value was divided by the number of reads obtained for that dataset).  Second, to determine differential performance of probes due to non-biological technical biases (see above) we combined all 10 5C datasets.  Next, a global average relationship between interaction frequency and genomic distance was calculated using Loess smoothing, and the interaction profile detected with each probe was compared to this average.  In the absence of any technical detection bias we assume that the overall profile of each probe is similar to the dataset-wide average profile.  For each probe we then calculated a correction factor by which the profile of that probe should be lifted or lowered in order to match the average Loess profile from the entire combined dataset. This correction factor was calculated as follows:  Interactions were first converted into z-scores using the Loess values for the corresponding genomic distance as average and the standard deviation around that average at the corresponding genomic distance (as described above and in 25).  Zeros were excluded.  We then calculated the average z-score for each row and column of the interaction map (corresponding to all interactions detected with individual forward and reverse 5C probes), leaving out the top and bottom 5% of values.  This calculation yielded average z-score values for each probe, and these were used as correction factors.  To correct individual interactions, detected by pairs of probes, correction factors were combined as follows:  The corresponding averaged z-score values of the two probes were summed.  The corrected interaction frequency was then calculated as: Corrected interaction = Loess value ? (sum of average z-scores) X standard deviation.  The Loess value and standard deviation are calculated for each genomic distance as described above and in Sanyal et  al. 25. This bias correction approach was used to correct each of the 10 individual read-normalized datasets to produce the final bias corrected datasets.  By combining the datasets before correction to calculate correction factors, we reduce the risk of overcorrecting certain probes that were truly giving high biological signals in one cell line.  When the datasets were combined, this biologically high signal was averaged with the other lower signals, giving that interaction a less stringent correction.  If correction factors were calculated for each dataset separately, the interaction profile would be penalized for giving such a high interaction and corrected too harshly. Data corrections did not change the overall structure of the data.  In fact, analysis of specific probes from raw and corrected data show only few differences in their profiles, indicating that probes display only minor differences in detection efficiency.  Further, domains detected with the corrected 5C interaction maps are very similar to those obtained with a completely independently obtained high-resolution Hi-C interaction map 11.
Insulation Index: To define regions of our dataset that contain TAD boundaries we calculated an insulation score along the locus 34; 47.  This method is based on the concept that TAD boundaries act as physical insulators that prevent or inhibit interaction across them.  First, 5C data was binned at 100 kb with a 10x (10 kb) step size.  Next, we calculated for each bin the combined number of observed interactions across it by summing all interactions between loci located up to 250 kb upstream with loci located up to 250 kb downstream of the bin.  This sum was then calculated for each bin along the 2.8 Mb locus, and then divided by the average sum of all bins to obtain insulation scores.  Insulation scores are plotted along the locus to obtain an insulation profile.  (Figure 2, Figure S11).  Local minima in this profile represent bins that display the largest insulation and thus indicate the positions of TAD boundaries.  Local minima in the insulation profiles were detected by identifying the bins with the lowest insulation scores in a local 490 kb window.  We then set the midpoint of this low-value bin as the boundary.
Peak Calling: To detect statistically significant looping interactions at the restriction fragment level we applied a ?5C peak calling? algorithm as described before 25 with the following modifications.  We called peaks on three different sub-sets of the data ? all the data, intra-TAD data and inter-TAD data (Figure 4A and B, Figures S14-S16, Table S7).  Peaks called on intra-TAD and inter-TAD data were called after the TAD boundaries were defined as stated previously.  Peak calling for intra-TAD and inter-TAD interactions is done separately because the background signal is overall higher within TADs than between TADs (shown in Figure 4A).  Thus, by performing peak calling separately for intra-TAD and inter-TAD signals (using different background estimations for the two sets of interactions) we avoid calling many false positives for intra-TAD signals (that tend to be higher) and suffering false negatives for inter-TAD signals (that tend to be of lower frequency).  Peaks were defined as signals that are significantly higher than expected. Expected values were calculated as follows:  For peak calling for the complete dataset we calculated the average interaction frequency for each genomic distance using Loess smoothing (alpha value 0.01).  This provides a weighted average and a weighted standard deviation at each genomic distance.  For peak calling within or between TADs separately, we calculated the average interaction frequency for each genomic distance using Loess smoothing using only intra-TAD or inter-TAD data respectively (alpha value 0.01).  We assume the large majority of interactions are not significant looping interactions and therefore we interpret this weighted average as the expected 5C signal for a given genomic distance.  Observed 5C signals are then transformed into a Z-score by calculating the [(observed-expected)/standard deviation] as described earlier, where the observed value is the detected 5C signal for a specific interaction, expected is the calculated weighted average of 5C signals for a specific genomic distance and standard deviation is the calculated weighted standard deviation of 5C signals for the corresponding genomic distance.  Once the Z-scores have been calculated, their distribution is fit to a Weibull distribution.  P-values are then be mapped to each Z-score and then transformed into q-values for False Discovery Rate (FDR) analysis.  The ?qvalue? package from R (qvalue.cal [siggenes]) was used to compute the q-values for the given set of p-values determined from the fit to the Weibull distribution.  We used a stringent FDR threshold of 0.001%.  This threshold was chosen as it was the most stringent FDR at which all known ?gold standard? looping interactions in the CFTR locus were detected in the appropriate cell lines, as previously detected by 3C studies, while these interactions were not deemed significant in cell lines that do not express the genes and were shown by 3C to not display these long-range interactions 18; 21.  We called peaks in each 5C biological replicate separately and then took only the peaks that intersect across replicates as our final list of significant looping interactions.  Using this cutoff, we saw a comparable fraction of peaks that are observed in both replicates as compared to our previous 5C studies 25.  We note that interactions that were statistically significant in only one replicate were still significantly more frequent in the second replicate as compared to interactions that were not significant in either replicate (Figure S13), similar to our previously published 5C studies 25.  This suggests that these may in fact be bona fide looping interactions, but that the typically low signal to noise ratio in these experiments prevented their reproducible detection.  By limiting our analysis to long-range interactions that were statistically significant, at a very stringent FDR in both replicates we restrict our analysis to the strongest signals, but may introduce false negatives.
Genome_build: hg18

source_name: liver hepatocellular cells

growth_protocol: All cell lines were grown with antibiotic (1% penicillin–streptomycin).  GM12878 lymphoblastoid cells (Coriell Cell Repositories) were grown in RPMI 1640 medium supplemented with 2mM L-glutamine and 15% fetal bovine serum (FBS).  HepG2 hepatocellular carcinoma cells (ATCC) were grown in MEMα with 10% FBS.  Caco2 colorectal adenocarcinoma cells (ATCC) were grown in MEMα with 20% FBS.  Calu3 lung adenocarcinoma cells (ATCC) were grown in ATCC-formulated E-MEM with 10% FBS.  Capan1 pancreas adenocarcinoma cells (ATCC) were grown in IMDM with 20% FBS.  Cell densities were maintained as recommended using Accutase (Life Technologies) to detach adherent cells from plates.

extract_protocol: 3C was performed with HindIII restriction enzyme as previously described. For Caco2, Calu3, Capan1, GM12878 and HepG2 cells with two biological replicates for each cell line.  The 3C libraries were then interrogated by 5C.  The region was analyzed by pooling all probes for a final concentration of 0.5 fmol μl−1.  In total, 75 reverse probes and 605 forward probes were pooled for a possible 44,770 interactions.  We included control probes in other regions as follows: Enm002 (Chr5) – 45 reverse probes, Enm004 (Chr22) – 46 reverse probes, Enm008 (Chr16) – 28 probes, Enr311 (Chr14) – 67 reverse probes, Enr112 (Chr13) – 53 reverse probes, Enr113 (Chr4) – 53 forward probes, Enr131 (Chr2) – 65 forward probes, Enr232 (Chr9) – 50 forward probes, Enr233 (Chr15) – 52 forward probes, Enr332 (Chr11) – 42 forward probes.  All probes in these ENCODE regions are the same as previously published.  5C was performed as described with the following changes: 10 ligation reactions were performed for each 5C library, each containing an amount of 3C template that represents 400,000 genome equivalents and 2 fmol of each primer.


title: GM12878 5C Rep4

description:
ENM001CFTR-GM12878-R4
GM12878 replicate 2

source_name: lymphoblastoid


title: SUM159_DMSO_24H_1

description: RNA-Seq in DMSO or JQ1 treated cells


title: SUM159R_BRD4_DMSO

description:
ChIP-Seq for BRD4 in DMSO treated cells
Sample name: SUM159R_BRD4_DMSO

value: TTAGGC


title: HepG2 5C Rep2

description:
ENM001CFTR-HepG2-R2
HepG2 replicate 2


title: Capan1 5C Rep2

description:
ENM001CFTR-Capan1-R2
Capan1 replicate 2

source_name: pancreas


title: Capan1 5C Rep1

description:
ENM001CFTR-Capan1-R1
Capan1 replicate 1


title: ClutchA_polyA_19.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_39

data_processing:
Read pairs were aligned to Xenopus tropicalis v7 genome along with known off-genome gene sequences and exogenouns ERCC and ArrayControl spike in sequences using tophat v2.010 and parameters "-r 13 --mate-std-dev 60 -g 200 --report-secondary-alignments".
Abundances were estimated using cufflinks v2.1.1 with parameters ""--compatible-hits-norm --max-bundle-frags 10000000 -b xt7.fa -u --max-mle-iterations 50000". This is with exception of mir427, in which reads aligning at least once to the locus and nowhere else in the genome were counted once to calculate the FPKM for the entire locus. Transcript FPKM were converted to TPM.
Relative gene abundances in TPM were absolute normalised against ERCC spiked RNA standards, resulting abundances are reported in transcripts per embryo.
Genome_build: Xtropicalis_v7
Supplementary_files_format_and_content: Tab-delimited text files containing relative and absolute normalised gene and isoform abundances.

source_name: Whole embryo, 19.5hpf, polyA+ RNA


title: Calu3 5C Rep2

description:
ENM001CFTR-Calu3-R2
Calu3 replicate 2

source_name: lung adenocarcinoma


title: ClutchA_polyA_18_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_36

source_name: Whole embryo, 18hpf, polyA+ RNA


title: ClutchA_polyA_17_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_34

source_name: Whole embryo, 17hpf, polyA+ RNA


title: ClutchA_polyA_16_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_32

source_name: Whole embryo, 16hpf, polyA+ RNA


title: Caco2 5C Rep2

description:
ENM001CFTR-Caco2-R2
Caco2 replicate 2

source_name: epithelial colorectal adenocarcinoma


title: T47D_WCE_DMSO

description: ChIP-Seq whole cell extract input control from DMSO treated cells

value: 12 hour

value: TTCTGTGT


title: ClutchA_polyA_15.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_31

source_name: Whole embryo, 15.5hpf, polyA+ RNA


title: Calu3 5C Rep1

description:
ENM001CFTR-Calu3-R1
Calu3 replicate 1


title: Caco2 5C Rep1

description:
ENM001CFTR-Caco2-R1
Caco2 replicate 1


title: ClutchA_polyA_14.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_29

source_name: Whole embryo, 14.5hpf, polyA+ RNA


title: T47D_BRD4_DMSO

description: ChIP-Seq for BRD4 in DMSO treated cells

value: BRD4 (Bethyl, catalog# A301-985A, lot# 4)


title: T47D_BRD4_JQ1

description: Chip-Seq for BRD4 in JQ1 treated cells


title: SUM185_BRD4_JQ1

description: Chip-Seq for BRD4 in JQ1 treated cells

value: GCCAATGT


title: ClutchA_polyA_19_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_38

source_name: Whole embryo, 19hpf, polyA+ RNA

value: whole embryo


title: SUM185_WCE_DMSO

value: ACAGTGGT


title: SUM149_WCE_DMSO

value: TGGTTGTT


title: GM12878 5C Rep2

description:
ENM001CFTR-GM12878-R2
GM12878 replicate 1


title: ClutchA_polyA_13.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_27

source_name: Whole embryo, 13.5hpf, polyA+ RNA

value: A


title: ClutchA_polyA_14_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_28

source_name: Whole embryo, 14hpf, polyA+ RNA


title: ClutchA_polyA_18.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_37

source_name: Whole embryo, 18.5hpf, polyA+ RNA


title: SUM185_BRD4_DMSO

description: ChIP-Seq for BRD4 in DMSO treated cells


title: ClutchA_polyA_13_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_26

source_name: Whole embryo, 13hpf, polyA+ RNA


title: ClutchA_polyA_12.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_25

source_name: Whole embryo, 12.5hpf, polyA+ RNA


title: SUM149_H3K27AC_JQ1

description: ChIP-Seq for H3K27ac in JQ1 treated cells

value: H3K27AC (Abcam, catalog# ab4729, lot# GR200563-2)


title: ClutchA_polyA_17.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_35

source_name: Whole embryo, 17.5hpf, polyA+ RNA


title: ClutchA_polyA_12_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_24

source_name: Whole embryo, 12hpf, polyA+ RNA


title: ClutchA_polyA_11.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_23

source_name: Whole embryo, 11.5hpf, polyA+ RNA


title: SUM149_H3K27AC_DMSO

description: ChIP-Seq for H3K27ac in DMSO treated cells

value: CTTGTA


title: ClutchA_polyA_11_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_22

source_name: Whole embryo, 11hpf, polyA+ RNA


title: ClutchA_polyA_15_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_30

source_name: Whole embryo, 15hpf, polyA+ RNA


title: ClutchA_polyA_16.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_33

source_name: Whole embryo, 16.5hpf, polyA+ RNA


title: SUM149_BRD4_DMSO

description: ChIP-Seq for BRD4 in DMSO treated cells

value: DMSO

value: ATCACGTT


title: ClutchA_polyA_10.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_21

source_name: Whole embryo, 10.5hpf, polyA+ RNA

value: wild type


title: SUM149R_WCE_DMSO

value: TCTCGGTT


title: ClutchA_polyA_10_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_20

source_name: Whole embryo, 10hpf, polyA+ RNA


title: ClutchA_polyA_9_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_18

source_name: Whole embryo, 9hpf, polyA+ RNA


title: SUM149R_H3K27AC_DMSO

value: CAGATC


title: SUM149R_H3K27AC_JQ1

value: ACAGTG


title: ClutchA_polyA_9.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_19

source_name: Whole embryo, 9.5hpf, polyA+ RNA


title: SUM149R_BRD4_DMSO

description: ChIP-Seq for BRD4 in DMSO treated cells

value: TTAGGC


title: ClutchA_polyA_8.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_17

source_name: Whole embryo, 8.5hpf, polyA+ RNA


title: SUM1315_WCE_DMSO

value: 12 hour

value: TAAGCGTT


title: SUM149R_BRD4_JQ1

description: Chip-Seq for BRD4 in JQ1 treated cells

value: BRD4 (Bethyl, catalog# A301-985A, lot# 4)

value: TGACCA


title: SUM1315_BRD4_JQ1

description: Chip-Seq for BRD4 in JQ1 treated cells

value: ACTTGAAT


title: MDA436_WCE_DMSO

value: TGTACCTT


title: ClutchA_polyA_7.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_15

source_name: Whole embryo, 7.5hpf, polyA+ RNA

value: whole embryo