title: atrimmer2 Rep1


title: OVCAR8_BRD4-KDM6B_rep2

status: Public on Dec 17 2015

type: SRA

city: Boston

first: Gabriela

last: Pregernig

state: Massachusetts

address: 1325 Boylston Street, Suite 500

country: USA

institute: Decibel Therapeutics

library_source: transcriptomic

data_processing:
Basecalls were performed using standard Illumina software.
Trimmed reads were aligned to the human transcriptome (hg19, refFlat GTF given with -G option) using TopHat2 (v 2.0.9) with the options --no-novel-juncs --library-type fr-firststrand.
Cufflinks (v 2.1.1) was used for evaluating gene expression levels in individual samples (hg19, refFlat GTF given with -G option). Options used were --frag-bias-correct --library-type fr-firststrand and masking mitochondrial and rRNA transcripts with -M.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing FPKM (Fragments per Kilobase per Million Reads) values for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: Human ovarian cancer cell line

growth_protocol: OVCAR8-ADR-Cas9 was cultured in RPMI supplemented with 10% heat-inactivated fetal bovine serum and 1X antibiotic-antimycotic at 37 oC with 5% CO2.

extract_protocol:
RNA were extracted from cells using TRIzol Plus RNA Purification Kit (Life Technologies) according to manufacturer’s protocol and treated with PureLink on-column DNase kit (Life Technologies). RNA quality and concentration was determined using NanoDrop Spectrophotometer. RNA samples were reverse-transcribed using SuperScript III Reverse Transcriptase (Life Technologies), Random Primer Mix (New England Biolabs) and RNAse OUT (Invitrogen). Sequencing libraries were prepared using the Illumina Library Prep Kit, starting with an input amount of 1 µg total RNA and following the manufacturer’s recommendations.
Strand-specific libraries were prepared using the Illumina Library Prep Kit according to the manufacturer's instructions. After PCR amplification, the libraries were size-selected to 300 +/- 25 bp on a 2% agarose gel (E-Gel EX, Invitrogen).

treatment_protocol: OVCAR8-ADR-Cas9 cells infected with the indicated sgRNAs for 15 days.

tag: cell line

tag: infected with sgrna


title: atimmer1 (rrp6l1) Rep3

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

data_processing:
sRNAseq: After removing bacodes, adapters and low-quality reads, clean reads of size 18-30 nt or 30-60 nt were mapped to the Arabidopsis genome (TAIR10 version) with Bowtie (Langmead et al., Genome Biology, 2009, 10, R25) allowing no mismatches.sRNA abundance was calculated as reads per million (RPM) or reads per 10 million (RP10M).
BS-Seq: Bisulfite sequencing reads were mapped to Arabidopsis genome (TAIR10) by BRAT-BW (Harris et al., 2012) with parameters -m 3 -i 0 -a 1000, allowing up to three mismatches. Only uniquely mapped reads were retained for further methylation analysis. Copy-duplicates were removed by Remove-dupl command of BRAT-BW package. Acgt-count command of BRAT-BW was used to calculate fractional DNA methylation levels.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq processed data, our provided files were generated by acgt-count command of BRAT-BW and their format is 'Chr,Start,End,Context:Coverage,Methylation level,Strand'. Small RNA-seq samples are associated with files containing genome-matched unique sequence and the read count.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Three-wks-old seedlings

growth_protocol: plants were grown under a 16-hlight/ 8-h-dark photoperiod

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen) followed by PEG precipitation to enrich low molecular-weight sRNAs. The resulting sRNAs were resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-30nt were excised, and the RNAs were eluted and purified for small RNA library contruction.
Small RNA libraries were constructed as previously described (Mi et al., Cell, 2008, 133, 116-127).

tag: ecotype background

value: Columbia

tag: genotype/variation

tag: age

value: Three-weeks-old

tag: tissue

value: seedlings

tag: molecule subtype

value: Small RNA


title: glucose wt  6a

city: Los Angeles

first: Zvi

last: Tamari

state: California

address: 5531 Boelter Hall

institute: UCLA

description: wild type

data_processing:
Illumina Casava1.8 software used for basecalling.
Adaptor and UMI barcodes were trimmed off and reads were aligned to the S288C_reference_sequence_R64-1-1_20110203 reference genome using Bowtie
Genome_build: S288C_reference_sequence_R64-1-1_20110203
Supplementary_files_format_and_content: Processed read count per gene per sample. Each column corresponds to one of twelve strains, either before or after evolution, grown on either glucose or xylulose. Each row corresponds to a gene. Data was averaged over two repeats. Samples containing less than 400,000 reads were not included in the analysis.

organism: Saccharomyces cerevisiae

source_name: cell population

growth_protocol: Cells were inoculated into either YPD or YP-xylulose media with initial OD of 0.1

extract_protocol:
Log phase cells were harvested and frozen in liquid Nitrogen. Total RNA was extracted using a NucleoSpin® 96 RNA kit (Macherey-Nagel), substituting β-mercaptoethanol with DTT
RNA extracts were fragmented and polyadenylation was selected using PolydT beads. cDNA was prepared using Smartscribe and UMI-containing barcoded primers, and subjected to RNnase H treatment. A second adaptor was subsequently ligated.

tag: strain

tag: repetition

value: repetition 1


title: glucose wt  2a

description: wild type


title: OVCAR8_BRD4-KDM6B_rep1


title: atimmer1 (rrp6l1) Rep2


title: atimmer1 (rrp6l1) Rep1


title: glucose wt  1b

description: wild type

value: repetition 2


title: OVCAR8_KDM4C_rep1


title: OVCAR8_KDM4C_rep2


title: H3K4me3_ChIPSeq

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital

department: Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk

molecule: genomic DNA

source_name: Leukaemia cell line (SEM)

growth_protocol: SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5

extract_protocol:
Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040).

value: SEM

tag: cell type

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: chip antibody


title: glucose wt  1a

description: wild type


title: Col-0 (wild-type control for atrimmer1/2) Replicate3

value: Wild type


title: Col-0 (wild-type control for atrimmer1/2) Replicate1


title: Col-0 (wild-type control for atrimmer1/2) Replicate2


title: RNAPII_stage11_control

city: Nijmegen

first: Saartje

last: Hontelez

address: Geert Grooteplein 28

department: Molecular developmental biology

country: Netherlands

institute: Radboud University

description: Three independent biological replicates were pooled.

data_processing:
Reads were mapped to the reference Xenopus tropicalis genome JGI7.1, using STAR (RNA-seq) or the BWA (ChIP-seq) allowing one mismatch
We used MACS2 with standard settings and q-value of 0.05. Fragment size was determined using phantompeakqualtools . Broad settings (--BROAD) were used for H3K27me3 and RNAPII. Broad and narrow peaks were merged for H3K4me3. For H3K9ac narrow peaks were used. For p300 both broad and narrow peaks were used.
Peaks that showed at least 75% overlap with 1 kb regions that have <65 input reads, and peaks that have a ChIP-seq RPKM > 95 percentile of random background regions are excluded from further analysis.
Only scaffolds 1-10 were included in the analysis. Relative RPKM  was calculated by dividing the ChIP-seq RPKM of the peaks by the ChIP-seq RPKM of 95 percentile of random background regions.
Relative RPKM  was calculated by dividing the ChIP-seq RPKM of the peaks by the ChIP-seq RPKM of 95 percentile of random background regions.
RPKM and readcounts were calculated over exons in genes. Gene annotation xtev_v3.4/Jgi_7.1 (available on http://veenstra.ncmls.nl/genomedata.asp).
Genome_build: JGI7.1
Supplementary_files_format_and_content: bigwig files were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw/src); Scores are scaled with scaling factor 1000000/[total #reads]
Supplementary_files_format_and_content: bed files contain peak locations (scaffold, start, stop)
Supplementary_files_format_and_content: txt files contain gene and RPKM (gene,location,strand,readcount,RPKM)

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were obtained by in vitro fertilisation and grown at 22 celcius untill the approptate developmental stage.

extract_protocol:
Protein-DNA complexes were isolated with antibody from whole embryo lysates that were fixed, sonicated and yolk depleted. Total RNA was subjected to depletion of ribosomal RNA (rRNA) using Ribozero Epicenter low input kit.
Libraries were prepared with the Kapa Hyper Prep kit (Kapa Biosystems), and sequencing was done on the Illumina HiSeq2000 platform.

treatment_protocol: Fertilised eggs were injected with 2,3 nl of 2,67 ng/ul α-amanitin and developed until the control embryos reached mid-gastrulation (stage 11)

tag: developmental stage (nf)

tag: treatment

value: not injected

value: anti-RNAPII (Diagenode C15200004)


title: RNAseq_stage11_control

description: Data from one biological replicate.


title: H3K27ac_ChIPSeq


title: RNAseq_stage11_amanitin

description: Data from one biological replicate.

value: alpha-amanitin injected


title: YF/AA complementation line (ago4 dcl2/3/4)

value: ago4 dcl2/3/4


title: OVCAR8_BRD4_rep1


title: OVCAR8_Awp12_rep2


title: p300_stage11_control_rep2

description: Data from one biological replicate.

value: anti-p300 (Santa Cruz sc-585)


title: RNAPII_stage11_amanitin


title: AGO4 complementation line (ago4 dcl2/3/4)


title: OVCAR8_Awp12_rep1


title: p300_stage11_amanitin_rep2

description: Data from one biological replicate.


title: ago4 dcl2/3/4


title: H3K27me3_stage11_control_rep2

description: Data from one biological replicate.


title: col-0(ago4 corresponding wild-type)


title: nprd1 dcl2/3/4 embyro

source_name: Embryo

value: nrpd1 dcl2/3/4

value: Eight-weeks-old

value: Embryo


title: H3K27me3_stage11_amanitin_rep2

description: Data from one biological replicate.


title: dcl2/3/4 embyro

value: Columbia


title: OVCAR8_KDM6B_rep1


title: OVCAR8_BRD4_rep2


title: OVCAR8_KDM6B_rep2


title: H3K4me3_stage11_amanitin_rep2

description: Data from one biological replicate.

value: anti-H3K4me3 (Abcam ab8580)


title: H3K4me3_stage11_control_rep2

description: Data from one biological replicate.


title: nrpd1 dcl2/3/4 endosperm

source_name: Endosperm

value: Endosperm


title: Col-0 endosperm

value: Small RNA


title: LP

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

description: WGBS

data_processing:
bsmap, v2.73, default
Genome_build: Illumina NextSeq:mm10, Illumina HiSeq 2500: mm9
Supplementary_files_format_and_content: Methylation calls could not be located. Processed data are not available for this study.

organism: Mus musculus

source_name: Spermatozoa_WGBS_10weeks_low protein

growth_protocol: Sibling male mice were split at weaning (3 weeks) onto control or low protein, or control or high fat diets. Mice were maintained on these diets until sacrifice at 10 weeks.

extract_protocol:
Cauda epididymis and vas deferens was rapidly dissected and punctured, and was incubated in 500 ¼L of human tubule fluid (HTF - Millipore MR-070-D) at 37 C for 30 minutes. Supernatant was removed, sperm were pelleted at 2000 g for 5 minutes, washed once with 1 mL water and then pelleted. Sperm were washed again with 1 mL PBS, and pelleted again. Sperm were resuspended in 400 ¼L DNA Lysis Buffer (10mM Tris, 5mM EDTA, 0.5% SDS, and 200mM NaCl) with 10mM DTT, and incubated at 37oC for 30 minutes. Sperm were subjected to needle homogenization. 20 ¼g/mL Proteinase K was added to the homogenate and incubated at 55oC for 16 hours.  DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol and precipitated with 100% EtOH.
DNA was sheared to an average length of ~100-500 bp with a Covaris sonicator, fragment ends were cleaned up and A-tailed. Fragments were ligated to pre-methylated Illumina paired-end adaptors, bisulfite converted, and PCR-amplified.

value: 10 weeks

value: C57BL/6; FVB/NJ

value: Cauda epididymis and vas deferens

value: Spermatozoa


title: 35S:GUS transgenic plants nrpd1 T6

source_name: Five-wks-old flowers

value: Five-weeks-old

value: flowers


title: 35S:GUS transgenic plants dcl2/3/4 T6


title: 35S:GUS transgenic plants nrpd1 dcl2/3/4 T6


title: C2

description: WGBS

treatment_protocol: Sibling male mice were split at weaning (3 weeks) onto control or low protein, or control or high fat diets. Mice were maintained on these diets until sacrifice at 10 weeks.


title: HF

description: WGBS

source_name: Spermatozoa_WGBS_10weeks_high fat


title: dcl2/3/4 endosperm


title: 35S:GUS transgenic plants Col-0 T6

value: Wild type


title: Col-0 embryo


title: 35S:GUS transgenic plants nrpd1 T5


title: 35S:GUS transgenic plants nrpd1 dcl2/3/4 T5


title: C1

description: WGBS


title: 35S:GUS transgenic plants dcl2/3/4 T5


title: mm_rep2_cont_Input

city: Easter Bush

first: Alasdair

middle: W

last: Jubb

state: Midlothian

address: The Roslin Institute

department: Roslin Institute

institute: University of Edinburgh

description:
ChIP DNA
mBMDM_GR_ChIP_dex100nM_2h_combined_peaks.txt

data_processing:
Base calls were generated using CASAVA 1.8
Trimming of adapters, Trimmomatic v0.27, ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment, Bowtie2 for PE sequencing (defaults)
Formation of tag directories, HOMER
peak calling(cmd = ./homer/bin/findPeaks ./homer/homer_out/combined_1119_dexAb_tags/ -style factor -o auto -i ./homer/homer_out/combined_dex_input_1119_tags/), production of bedGraphs, HOMER.
combination of replicates after checking for concordance (86% peak overlap) and formation of bedGraph for visualization, HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bedGraphs for treated and untreated IP, an input bedGraph and a tab-delimited peak file

source_name: mouse bone marrow derived macrophages

growth_protocol: Bone marrow from 2x 10 week old male C57BL/6 was extracted and differentiated in culture with 10% fetal calf serum, penicillin/streptomycin, Glutamax and recombinant human CSF1 (10,000U/ml) for 1 week. They were then replated in fresh medium, supplemented as above, at 0.5M cells/ml.

extract_protocol:
10M Cells per condition were fixed in 1% formaldehyde for 10min at RT, lysed and sonicated. GR-DNA complexes were then isolated from soluble chromatin using BuGR2 monoclonal antibody (Pierce), crosslinks reversed at 65 degrees and DNA cleaned up using Minielute columns(Qiagen)
Multiplex libraries were prepared by Edinburgh Genomics using Illumina standard protocols and reagents. Libraries were sequenced on the Hiseq2500 following the manufacturer's protocols.

treatment_protocol: Treated with either 100nM dexamethasone (Sigma) or ethanol vehicle for 2h.

value: control

tag: gender

value: male

value: 10 week old

tag: antibody

value: input


title: mm_rep2_dex_IP

description:
ChIP DNA
mBMDM_GR_ChIP_dex100nM_2h_combined_ucsc.bedGrapg
mBMDM_GR_ChIP_dex100nM_2h_combined_peaks.txt

value: dex

value: BuGR2, monoclonal (Pierce/ThermoFisher)


title: mm_rep2_cont_IP

description:
ChIP DNA
mBMDM_GC_ChIP_control_combined_ucsc.bedGrapg
mBMDM_GR_ChIP_dex100nM_2h_combined_peaks.txt


title: mm_rep2_dex_Input


title: mm_rep1_cont_IP


title: 35S:GUS transgenic plants nrpd1 T4

value: Columbia


title: ago4

value: Three-weeks-old

value: seedlings


title: mm_rep1_dex_Input


title: 35S:GUS transgenic plants Col-0 T5

value: Small RNA


title: mm_rep1_cont_Input


title: 35S:GUS transgenic plants nrpd1 dcl2/3/4 T4

value: nrpd1 dcl2/3/4


title: mm_rep1_dex_IP


title: 35S:GUS transgenic plants Col-0 T4


title: 35S:GUS transgenic plants nrpd1 T3


title: 35S:GUS transgenic plants nrpd1 T2


title: 35S:GUS transgenic plants nrpd1dcl2/3/4 T2


title: 35S:GUS transgenic plants Col-0 T3


title: 35S:GUS transgenic plants dcl2/3/4 T1


title: 35S:GUS transgenic plants dcl2/3/4 T3


title: 35S:GUS transgenic plants dcl2/3/4 T4


title: 35S:GUS transgenic plants Col-0 T2


title: 35S:GUS transgenic plants nrpd1 dcl2/3/4 T1


title: 35S:GUS transgenic plants nrpd1 T1


title: 35S:GUS transgenic plants dcl2/3/4 T2


title: AGO4 IP in dcl2/3/4 rep2


title: 35S:GUS transgenic plants Col-0 T1


title: AGO4 IP in dcl2/3/4 rep1


title: AGO4 IP in dcl2/3/4 rep3


title: AGO4 IP in Col0 rep3


title: AGO4 IP in Col0 rep2


title: rdr2 dcl2/3/4 rep1

value: rdr2 dcl2/3/4


title: rdr2 dcl2/3/4 rep2


title: AGO4 IP in Col0 rep1


title: rdr2 rep1


title: nrpd1 dcl2/3/4 rep2


title: 35S:GUS transgenic plants nrpd1 dcl2/3/4 T3


title: dcl1/2/3/4 31-60-nt RNAs

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen) followed by PEG precipitation to enrich low molecular-weight sRNAs. The resulting sRNAs were resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 31-60nt were excised, and the RNAs were eluted and purified for small RNA library contruction.
Small RNA libraries were constructed as previously described (Mi et al., Cell, 2008, 133, 116-127).


title: rdr2 rep2


title: nrpd1 dcl2/3/4 rep1


title: nrpd1 rep2


title: Col-0 rep2


title: nrpd1 rep1


title: Col-0 rep1


title: Col-0 31-60-nt RNAs


title: dcl2/3/4 rep3


title: dcl2/3/4 rep2


title: dcl2/3/4 31-60-nt RNAs


title: RN2_H3K36me2_ChIP

city: Cold Spring Harbor

first: Christopher

middle: R.

last: Vakoc

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Lab

data_processing:
With Bowtie software, raw reads were mapped to the mouse genome (mm9) allowing 2 mismatches.
MACS (Model based Analysis of ChIP-Seq) software was used to indentify ChIP-Seq peaks.
A p value threshold of enrichment of 1e-5 was used for identifying significant peaks within each dataset. For BRD4 peaks, a false discovery rate (FDR) of less than 1%, and 10-fold enrichment relative to input control cutoffs were applied as well.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were converted from wiggle files generated by MACS 1.4 software.

source_name: MLL-AF9/NrasG12D murine cell line

growth_protocol: RN2 cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with appopriate sizes were prepared for sequencing.
ChIP-Seq libraries were constructed with TruSeq ChIP Sample Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.The quantity and quality of all libraries were determined by Bioanalyzer with high-sensitivity chips.

tag: strain background

value: Acute myeloid leukemia (AML) cells

tag: chip antibody info.

value: Active Motif #39255


title: dcl1/2/3/4 rep2


title: dcl2/3/4 rep1


title: dcl1/2/3/4 rep3


title: rdr2 dcl2/3/4

extract_protocol:
Genomic DNA was isolated by CTAB method
Bisulfite sequencing libraries were constructed using the NEXTflex Bisulfite-Seq kit (BIOO SCIENTIFIC) according to the manufacturer’s instructions.


title: rdr2

extract_protocol:
Genomic DNA was isolated by CTAB method
Bisulfite sequencing libraries were constructed using the NEXTflex Bisulfite-Seq kit (BIOO SCIENTIFIC) according to the manufacturer’s instructions. The libraries were paired-end sequenced on the Illumina HiSeq 2000 generating 2x104-mer reads


title: nrpd1 dcl2/3/4

extract_protocol:
Genomic DNA was isolated by CTAB method
Bisulfite sequencing libraries were constructed using the NEXTflex Bisulfite-Seq kit (BIOO SCIENTIFIC) according to the manufacturer’s instructions. The libraries were paired-end sequenced on the Illumina HiSeq 2000 generating 2x103-mer reads


title: shCHD8.3190_RNASeq

data_processing:
With Tophat software, raw reads were mapped to the mouse genome (mm9) allowing no mismatch.
Differentially expressed genes were analyzed with Cuffdiff software and structural RNAs were masked during this step to get rid of undesired effects on global analysis. PRKM (reads per million per kilobase) from shRen.713/sgRosa26 control samples and biological replicates of shRNAs/sgRNAs  samples were used to calculate fold change with log2 scale.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include only genes with OK test status. For Poly-a selected library, only genes with RPKM above 5 are considered

extract_protocol:
Total RNA was prepared using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol.
Libraries with PolyA selection were constructed with the TruSeq Sample Prep Kit v2 (Illumina, San Diego, CA) following the manufacturer’s protocol. 2ug of total RNA was used for Poly-A selection and fragmentation, subsequently followed by cDNA systhesis, end repairing, dA tailing, adapter ligation and final library amplification. For “not-so-random” primer-based RNA-Seq library preparation, libraries were constructed following protocols described previously (Armour et al., 2009, Nature Methods). 1ug of total RNA was used for first-strand synthesis with Superscript III system (#18080044 Life Technologies, Grand Island, NY) and then performed second-strand synthesis with Klenow fragment (#M0212L, NEB). The final PCR amplification was performed with Expand High Fidelity Plus PCR system (#11732641001, Roche).

treatment_protocol: shRNA expression were induced with dox for 48 hours in RN2 cells retrovirually transduced with TRMPV-Neo constructs. sgRNAs were induced with Lenti virus for 4 days.

value: Acute myeloid leukemia

tag: genotype


title: sgRosa26_RNASeq


title: sgCHD8 e12.1_RNASeq


title: nrpd1


title: shCHD8.2934_RNASeq


title: dcl2/3/4


title: shNSD3.1653_RNASeq rep2


title: Col-0


title: shNSD3.1019_RNASeq rep2


title: shRen.713_RNASeq


title: shNSD3.1653_RNASeq rep1


title: shNSD3.1019_RNASeq rep1


title: shRen.713_RNASeq rep1


title: shRen.713_RNASeq rep2


title: dcl1/2/3/4 rep1


title: sgCHD8 e17.1_RNASeq


title: RN2_CHD8_ChIP_r2

treatment_protocol: no treatment


title: CFP1_ChIPSeq

tag: cell line

value: SEM

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: CFP1 Input DNA

value: none (input)


title: RN2_CHD8_ChIP_r1


title: Input_RN2_ChIP_r2


title: Input_RN2_ChIP_r1.1


title: hMDM_GR_input

description: ChIP DNA

data_processing:
Base calls were generated using CASAVA 1.8
Trimming of adapters, Trimmomatic v0.27, ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment, Bowtie2 for PE sequencing (defaults)
Formation of tag directories, HOMER
peak calling and removal of low absolute value peaks(cmd = ./homer/bin/findPeaks ./homer/homer_out/combined_1119_dexAb_tags/ -style factor -o auto -i ./homer/homer_out/combined_dex_input_1119_tags/), production of bedGraphs, HOMER.
Formation of bedGraph for visualization, HOMER
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph for visualization of treated IP data,  tab-delimited peak file

source_name: human monoycte derived macrophages

growth_protocol: CD14+ monocytes were extracted from whole blood donated by healthy volunteers using MACS separation (Miltenyi). They were differentiated in culture for 1 week in the presence of recombinant human CSF1 (10000U/ml),penicillin/streptomycin, Glutamax and 10% fetal calf serum then replated in fresh medium, also supplemented as above, for the time series experiment.

extract_protocol:
rinsed with PBS, fixed in 1% formaldehyde for 7.5min at RT, lysed and sonicated to fragment size 400-600bp. GR-DNA complexes were then isolated from soluble chromatin using Sigma Imprint anti GR monoclonal antibody , crosslinks reversed at 65 degrees and DNA cleaned up using Minielute columns(Qiagen)
ChIP DNA samples were split into 3 aliquots and blunt ended with Klenow (Roche), PNK (NEB) and T4 DNA polymerase (Roche). An overhanging A base was added using Klenow (-exo) (NEB) and Illumina adapters ligated overnight at 16 degrees C with T4 DNA ligase (NEB). The IP samples were recombined after ligation and then split again into 7 aliquots. Libraries were amplified from each of these aliquots using Illumina Tru-seq multiplex primers and Phusion high-fidelity DNA polymerase (NEB) and the resulting material pooled and sequenced by Edinburgh Genomics on a Hiseq-2500.

treatment_protocol: They were treated with either 100nM dexamethasone (Sigma) or ethanol vehicle for 2h.

tag: pooled

value: yes

tag: fully anonymized

value: human monoycte derived macrophages


title: Ribo-depleted total RNA-Seq

city: Rehovot

first: Yehoshua

last: Enuka

address: Herzl 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used previously described computational pipelines for detection of circRNAs (Memczak et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: The processed file contains genomic coordinates of the circRNA candidates. For each circRNA we show the total number of reads (from all replicates) that align to its non-canonical splice junction.

growth_protocol: MCF10A cells were cultured as described (Tarcic et al., 2012) in DME:F12 medium (Gibco BRL, Grand Island, NY) supplemented with 10 µg ml-1 insulin, 0.1 µg ml-1 cholera toxin, 0.5 µg ml-1 hydrocortison, 5% heat-inactivated horse serum (Biological Industries, Beit-Haemek, Israel) and 10 ng ml-1 EGF.

extract_protocol:
Total RNA was isolated from MCF10A cells using Trizol (Invitrogen). Ribosomal RNA was removed using the Ribominus kit (Invitrogen).
cDNA library was generated and sequenced using an Illumina Hiseq 2500 (1 × 100bp runs), as instructed by Illumina’s RNA-seq protocols.


title: RN2_BRD4_ChIP

value: BRD4 (A301-985A; Bethyl)


title: hMDM_GR_IP

description: ChIP DNA

value: Sigma Imprint anti-GR, monoclonal


title: H3K27Ac_ChIPSeq

data_processing:
Chromatin immunoprecipitation (ChIP) sequencing reads were mapped to the hg19 genome assembly using Bowtie2 (Langmead and Salzberg, 2012)
Genome_build: hg19
Supplementary_files_format_and_content: Tag read densities were generated by the makeTagDirectory from the Homer suite

growth_protocol: MCF10A cells were cultured as described (Tarcic et al., 2012) in DME:F12 medium (Gibco BRL, Grand Island, NY) supplemented with 10 µg ml-1 insulin, 0.1 µg ml-1 cholera toxin, 0.5 µg ml-1 hydrocortison, 5% heat-inactivated horse serum (Biological Industries, Beit-Haemek, Israel) and 10 ng ml-1 EGF. Cells were starved overnight in medium without additives before sequencing

extract_protocol:
Cell fixation and chromatin immunoprecipitation were performed as described (Blecher-Gonen et al., 2013)
Library construction and sequencing were performed as described (Blecher-Gonen et al., 2013)

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #


title: BisSeq_toSerum

status: Public on Dec 16 2015

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Bis-seq reads were processed with QuasR and positions covered by at least 10 reads were used.
Genome_build: mm9

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells were cultivated without feeders on 0.2% gelatine-coated dishes in DMEM, supplemented with 15% fetal calf serum, 1× non-essential amino acids, 2 mM L-glutamine, LIF and 0.001% β-mercaptoethanol (37°C, 7% CO2). Serum-free cultivation was performed in N2B27 medium, supplemented with 1× non-essential amino acids, 2 mM L-glutamine, LIF and 0.001% β-mercaptoethanol as well as MEK inhibitor PD0325901 (1 µM) and GSK3 inhibitor CHIR99021 (3 µM), together known as 2i. For reversal between culturing conditions, cells were cultured for at least three weeks under the new conditions prior to performing downstream experiments.

extract_protocol:
DNA was isolated by phenol chloroform extraction, followed by ethanol precipitation.
Library Construction Protocol: 5 μg of sonicated genomic DNA were end repaired and 3′-end adenylated using the Illumina TruSeq DNA LT Sample Preparation kit (Illumina 15025064). Paired-end adapters were ligated to the DNA fragments and adaptor-ligated DNA was purified by 2% agarose gel electrophoresis. The gel-purified DNA was converted with the EpiTect Bisulfite kit (Qiagen). Converted libraries were enriched by 10 cycles of PCR using PfuTurbo Cx Hotstart DNA Polymerase (Agilent) and purified using AMPure XP beads. Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (100 bp read length, paired end) according to Illumina standards.

value: WT

tag: growth condition

value: adaptation from 2i back to serum (3 weeks)


title: H3K27AC_CHIP_WT_2

data_processing:
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Read mapping was performed using Bowtie version 1.0.0 with parameters -v 3 -m 1 --best --strata.
Bigwig files were generated by extending the reads to 200bp and calculating for each genomic position the read density normalized to one million reads in the library.
Genome_build: mm9

growth_protocol: Mouse embryonic stem cells were cultivated without feeders on 0.2% gelatine-coated dishes in DMEM, supplemented with 15% fetal calf serum, 1× non-essential amino acids, 2 mM L-glutamine, LIF and 0.001% β-mercaptoethanol (37°C, 7% CO2).

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out essentially as previously described (Jermann et al. PNAS 2014).
Library Construction Protocol: Libraries for ChIP-seq were prepared according to standard Illumina library preparation protocols. Twelve cycles of PCR (NEB Q5 Hot Start HiFi PCR) were performed on end-repaired, A-tailed and adapter-ligated DNA prior to gel size-selection. Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.

tag: strain

value: serum

value: H3K27ac (Abcam, ab4729)


title: H3K27AC_CHIP_TKO_2

value: DNMT TKO


title: H3K27AC_CHIP_TKO_1


title: RN2_NSD3_ChIP_r2

value: NSD3 (polyclonal antibody made in house raised against the peptide:PTDYYHSEIPNTRPHEC)


title: shNSD3.218_RNASeq rep2


title: NRF1_CHIP_TKO_2

value: NRF1 (Abcam, ab55744)


title: NRF1_INPUT_NP_2

source_name: neuronal progenitors

growth_protocol: WT mouse ES cells (159) were differentiated to neuronal progenitors as previously described (Bibel et al. Nature Protocols 2007).


title: NRF1_CHIP_NP_1


title: NRF1_CHIP_NP_2


title: NRF1_INPUT_NP_1


title: H3K27AC_CHIP_WT_1


title: NRF1_CHIP_TKO_1


title: RN2_NSD3_ChIP_r1


title: NRF1_CHIP_WT_2


title: NRF1_INPUT_WT


title: RNA_TKO_NRF1_KD_2

data_processing:
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Read mapping was performed using tophat version 1.3.1 with parameter --no-novel-juncs.
Bigwig files were generated by using split RNA-seq reads and calculating for each genomic position the read density normalized to one million reads in the library
Genome_build: mm9

extract_protocol:
RNA was isolated with the RNeasy Mini kit (Qiagen) with on-column DNA digestion. Two micrograms of total RNA were depleted from ribosomal RNA using the Ribo-Zero rRNA removal kit (Epicentre).
Library Construction Protocol: Strand-specific libraries for RNA-seq were prepared using the ScriptSeq v2 protocol (Epicentre). Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.

treatment_protocol:
siRNA targeting Nrf1 for 72h (Qiagen, Mm_Nrf1_7 FlexiTube siRNA, SI05183738)
siRNA targeting Nrf1 for 72h (Qiagen, Mm_Nrf1_7 FlexiTube siRNA, SI05183738)


title: RNA_TKO_NRF1_KD_3


title: NRF1_CHIP_WT_1


title: Input_RN2_ChIP_r1


title: BisSeq_to2i

value: adaptation to 2i (> 3 weeks)


title: RNA_TKO_NRF1_KD_1


title: RNA_TKO_CTRL_KD_2

treatment_protocol:
Negative control siRNA for 72h (Qiagen, AllStars Negative Control siRNA, SI03650318)
Negative control siRNA for 72h (Qiagen, AllStars Negative Control siRNA, SI03650318)


title: BisSeq_TKO


title: RNA_TKO_CTRL_KD_3


title: NRF1_INPUT_TKO


title: NRF1_CHIP_Over_2

treatment_protocol: For transient overexpression of NRF1, a plasmid containing Nrf1 under the control of the CAG promoter was reverse transfected into 159 cells 12 h prior to harvesting


title: NRF1_INPUT_Over


title: NRF1_CHIP_toSerum_1


title: NRF1_CHIP_Over_1

treatment_protocol:
For transient overexpression of NRF1, a plasmid containing Nrf1 under the control of the CAG promoter was reverse transfected into 159 cells 12 h prior to harvesting
For transient overexpression of NRF1, a plasmid containing Nrf1 under the control of the CAG promoter was reverse transfected into 159 cells 12 h prior to harvesting


title: NRF1_CHIP_to2i_1


title: NRF1_CHIP_to2i_2


title: RNA_TKO_2


title: RNA_TKO_1


title: RNA_TKO_3


title: RNA_WT_3


title: DNASE_TKO_2

data_processing:
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Raw reads were trimmed of illumina adaptors. Read mapping was performed using Bowtie version 1.0.0 with parameters -v 3 -m 1 --best --strata.
Bigwig files were generated by using the 1bp 5'-end of the reads and calculating for each genomic position the read density normalized to one million reads in the library.
Genome_build: mm9

extract_protocol:
DNase treatment was performed essentially as previously described, with some modifications (John et al. Curr Prot Mol Biol 2013). Briefly, intact nuclei were extracted using 0.03% NP-40 in an isotonic buffer. After NP-40 removal, batches of 5 million nuclei were incubated for 4 min at 37°C with a range of DNase I (DPRF, Worthington) concentrations in the presence of Ca2+. The digestion was stopped by addition of EDTA/SDS and the samples were treated with proteinase K and RNase A. Phenol-chloroform extracted DNA was separated on a 5-30% sucrose gradient by ultracentrifugation for 24 h and fractionated with a Gilson fraction Collector FC 203B. Fractions were precipitated with ethanol and resuspended in TE buffer. Both successful digestion and size separation were verified by agarose gel electrophoresis. Low-coverage sequencing of a bar-coded pool of samples derived from different fractions of the sucrose gradient and treated with different DNase concentrations was used to select the sample with the highest information content.
Library Construction Protocol: Libraries for DNase-seq were prepared essentially according to standard Illumina protocols, using 40 ng of the precipitated fractions of the sucrose gradient as starting material. To reduce amplification bias, end-repaired, A-tailed and adapter ligated DNA was amplified in 6 cycles of PCR with KAPA HiFi Hot Start polymerase. Adapter dimers were subsequently removed with Agencourt AMPure XP beads (Beckman Coulter). Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.


title: RNA_WT_1


title: NRF1_INPUT_toSerum


title: IgG CHIP-seq control in LCL

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
All chip-seq files were generated by Illumina GA II and base calling was done with CASAVA 1.5
Chip-seq files were aligned to human genome hg19 using bowtie using "-v 2 -m 1 -best -strata" option on unique reads
Peak calling was done with homer (v1.0) software
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains Homer peak calling output

source_name: LCL cell line

growth_protocol: EBV positive B-cell (Mutu I, LCL) were grown in RPMI with 10% FBS and Glutamax

extract_protocol:
ChIP-Seq protocol is as described previously (Lu et al, 2010  Virology journal 7, 262).
Library was constructed using the TruSeq ChIP Sample Prep kit (Illumina) according to manufacturers instructions

treatment_protocol: Cells were maintained and isolated in logarihmic growth phase for ChIP-assays

value: LCL

value: EBV positive B-cells

value: IgG

value: Santa Cruz Biotechnology

tag: chip antibody lot #


title: DNASE_TKO_1


title: IgG CHIP-seq control in MutuI

source_name: MutuI cell line

value: MutuI

tag: cell type


title: NRF1_CHIP_toSerum_2

tag: chip antibody


title: H3K27me3 CHIP-seq in LCL

value: Active Motif


title: RNA_TKO_CTRL_KD_1


title: DNASE_WT_2


title: DNASE_WT_1


title: H3K4me1 CHIP-seq in LCL


title: H3K4me3 CHIP-seq in LCL

value: EMD Millipore


title: H3K27me3 CHIP-seq in MutuI


title: H3K4me3 CHIP-seq in MutuI


title: RBP-jk CHIP-seq in LCL

value: RBP-jk

value: Abcam


title: RBP-jk CHIP-seq in MutuI


title: EBF1 CHIP-seq in LCL


title: EBF1 CHIP-seq in MutuI


title: RNA_WT_2

value: WT


title: EBNA1 CHIP-seq in C6661

data_processing:
All chip-seq files were generated by Illumina GA II and base calling was done with CASAVA 1.5
Chip-seq files were aligned using bowtie version 0.12.9 to human genome hg19
Peak calling was done with homer (v1.0) software with -center -o,  -fdr 0.2
RNA-Seq data analyzing was done with rsem(ver. 1.2.3) and Hg19 genome with UCSC known gene set.
edgeR was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains Homer peak calling output while expression file contains the edgeR output; details in the 'readme.txt'

source_name: EBNA1 CHIP-seq in C6661

growth_protocol: EBV positive B-cell (Raji, Mutu I, LCL) were grown in RPMI with 10% FBS and Glutamax.  EBV positive NPC-line C666-1 was grown in DMEM with 10% FBS and Glutamax.

extract_protocol:
Lu et al, 2010  Virology journal 7, 262
The EBNA1 antibody is a rabbit polyclonal antibody raised to full length EBNA1(lacking Gly-Ala repeats).  The rabbit  injections and bleeds were provided by Pocono Rabbit Farm.  Reactive serum was affinity purified against full length EBNA1, and 10 ug of affinity purified antibody was used for 50 million cells for each ChIP experiment.
TruSeq ChIP Sample Prep kit
ChIP-Seq protocol is as described previously (Lu et al, 2010  Virology journal 7, 262).  Total RNA was isolated for RNA-Seq using Trizol reagent.

treatment_protocol:
maintained and isolated in logarihmic growth phase
Cells were maintained and isolated in logarihmic growth phase for ChIP-assays.   RNA Seq analysis was performed with LCL cells transduced with either pLKO.1 shControl or shEBNA1 lentivirus after 5 days of puromycin selection.

value: EBV positive nasopharyngeal carcinoma (NPC) line


title: IgG CHIP-seq in MutuI

description: CHIP.MutuI.IgG

source_name: IgG CHIP-seq in MutuI

extract_protocol:
Lu et al, 2010  Virology journal 7, 262
TruSeq ChIP Sample Prep kit
ChIP-Seq protocol is as described previously (Lu et al, 2010  Virology journal 7, 262).  Total RNA was isolated for RNA-Seq using Trizol reagent.

value: EBV positive B-cell


title: IgG CHIP-seq in LCL

description: CHIP.LCL.IgG

source_name: IgG CHIP-seq in LCL


title: IgG CHIP-seq in Raji

description: CHIP.Raji.IgG

source_name: IgG CHIP-seq in Raji

value: Raji


title: EBNA1 CHIP-seq in MutuI

source_name: EBNA1 CHIP-seq in MutuI


title: IgG CHIP-seq in C6661

source_name: IgG CHIP-seq in C6661


title: EBNA1 CHIP-seq in LCL

source_name: EBNA1 CHIP-seq in LCL


title: GLD-8

city: Berkeley

first: Claire

last: Dugast-Darzacq

address: LI KA SHING Center

department: Molecular and Cell Biology

institute: UC Berkeley

description: Normal human Dermal Fibroblast (NHDF)

data_processing:
Base calling was performed using Casava version 1.7.0
The analysis was performed on aggregated transcripts (non-redundnant list of all exons of all transcripts for a given gene, based on genes from Ensembl v58
Reads were trimmed and mapped with bowtie using the Eoulsan pipeline (version 1.0.7) onto the human reference genome sequence hg19 masked for repeats (identified by RepeatMasker) and for pseudogenes (identified by Ensembl version 58)
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, including all replicates.

source_name: NHDF, TGFbeta

growth_protocol: Normal human dermal fibroblasts (NHDF) were isolated from human explants (Promocell, C-12302). Two female donors were studied. Primary fibroblast cultures were maintained at 37°C in DMEM-F12 (Invitrogen, 31331-028), supplemented with 10% FCS (Invitrogen, 10270106), 5µg/mL of insulin and 1ng/mL of b-FGF (PromoKine, C-60212 and C-60240), in a humidified atmosphere of 5% CO2. Cells were trypsinized (Promocell, C-41220) at 80% confluency and split 1:5 for subsequent passaging.

extract_protocol:
RNA was purified using TRIzol Reagent (Invitrogen (Life Technologies), 15596-018) according to manufacter’s insctructions. Total RNA was quantified on the NanoDrop 2000c Spectrophotometer (Thermo Scientific) and their quality was evaluated on the RNA Nano Chips (Agilent 2100 bioanalyzer, Agilent, 5067-1511).
libraries were prepared by FASTERIS. 1)Transcripts purification; 2) Transcripts breaking in presence of Zn; 3) Double-stranded cDNA synthesis using random primers and RNase H; 4) Ends repair; 5) 3’ A addition; 6) Ligation of adapters; 7) Gel purification to isolate fragments of specified inserts size; 8) PCR amplification to generate the DNA Colonies Template Library, library purification; 9) Library quantification and dilution at 10 nM. 10 )Library Quality Control, done by titration run on the HiSeq. All the libraries to be quality controlled are multiplexed in 1 channel of 1x50 bp run on the HiSeq. After demultiplexing of the reads according to the indexes, we typically provide 50 fasta reads and 100'000 fast-q reads from each library. We can then blast the fasta sequences to check the quality of the library. In addition, the titration run helps us for quantification of the libraries.

treatment_protocol: For differentiation experiments, cells were deprived of insulin and b-FGF during 48 hours. Then, primary cell cultures between passages 4 and 7 were transferred into collagen (Life Technologies, A10483-01) coated culture plates and maintained during four days in DMEM-F12, supplemented with 10% FCS, 10ng/mL of TGF-β1 (Promocell, C-63504) and 500µg/mL of total proteins of exudate. Within the text of this article TGF-β1 is mentionned as TGF-β.

value: human primary dermal fibroblast

tag: donor

value: donor A

tag: passage

value: between 4 and 7


title: GLD-16

description: Normal human Dermal Fibroblast (NHDF)

source_name: NHDF, TGFbeta + exudate


title: GLD-7

description: Normal human Dermal Fibroblast (NHDF)

source_name: NHDF, no treatment


title: GLD-11

description: Normal human Dermal Fibroblast (NHDF)

source_name: NHDF, exudate

value: donor B


title: GLD-13

description: Normal human Dermal Fibroblast (NHDF)


title: GLD-15

description: Normal human Dermal Fibroblast (NHDF)


title: GLD-12

description: Normal human Dermal Fibroblast (NHDF)


title: GLD-10

description: Normal human Dermal Fibroblast (NHDF)


title: 4096

city: Columbia

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

data_processing:
Reads were quality trimmed (error probability 0.001, max 2 ambiguous bases, discard reads <15 nt) with CLC Genomics Workbench 8.0.3
Trimmed reads were mapped to Ensembl genes with CLC Genomics Workbench 8.0.3 (CLC bio, Aarhus, Denmark) using default settings.
Associated gene names and descriptions were downloaded from the Ensembl Genes 75 database with BioMart and used to annotate the RNA-seq experiment table.
Expression values were calculated as reads per kilobase of transcript per million mapped reads (RPKM)
Genome_build: Ovis aries Oar_v3.1.75
Supplementary_files_format_and_content: Tab-delimited text file containing individual and mean RPKM values, gene name, Ensembl ID and description.

organism: Ovis aries

source_name: extracellular vesicles

growth_protocol: Intact day 14 conceptuses were cultured for 24 hours. Each conceptus was placed in a sterile petri dish containing 10 ml of exosome-depleted conceptus culture medium [DMEM/F-12 supplemented with 10% exosome-depleted fetal bovine serum (Exo-FBS; System Biosciences, Cupertino, CA), glutamine (2 mM), insulin (700 nM), pyruvate (1.0 mM), nonessential amino acids (0.1 mM), and antibiotics (50 U penicillin, 50 μg streptomycin)] and cultured with gentle rocking at 37ºC under 5% CO2 and 5% O2 in a humidified incubator.

extract_protocol:
EVs were isolated from culture media by adding 200 µl ExoQuick-TC (System Biosciences) precipitation solution per ml of filtered (0.2 µm) media per the manufacturer's instructions. Total RNA from day 14 conceptus EVs isolated from conceptus-conditioned culture media (n=3) was purified using the miRNeasy kit (Qiagen, Valencia, CA). RNA concentration was determined by quantitative high sensitivity RNA analysis on the Fragment Analyzer instrument (Catalog # DNF-472, Advanced Analytical Technologies, Inc., Ankeny, IA).
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Clontech SMART-Seq® v4 Ultra™ Low Input RNA Kit for Sequencing kit (Catalog # 634888) and Low Input Library Prep Kit (Catalog # 634947, Clontech Laboratories, Inc., Mountain View, CA) according to the manufacturer’s instructions using 5 ng of total RNA. Libraries were diluted and sequenced according to Illumina’s standard sequencing protocol on a HiSeq 2500 (paired-end 50 bp).

tag: tissue origin

value: conceptus

tag: day

tag: cellular compartment

value: extracellular vesicles


title: GLD-9

description: Normal human Dermal Fibroblast (NHDF)


title: H3K4me1 CHIP-seq in MutuI

value: EBV positive B-cells


title: 4141


title: 4020


title: Amphioxus_36hpf (62)

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

description: European amphioxus

data_processing:
library strategy: 4C-Seq
For 4C: Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the danRer7 assembly and Sc_hox scaffold using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: danRer7/Sc_hox (see Sc_hox fasta linked as supplementary file on Series record)
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 4Cseq of viewpoint that can be directly uploaded to UCSC for visualization.
For ATAC-seq: Alignment: reads were aligned using Sc_hox scaffold as reference genome and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using local browser
Genome_build: Sc_hox (see Sc_hox fasta linked as supplementary file on Series record)
Supplementary_files_format_and_content: bigWig format for visualization

organism: Branchiostoma lanceolatum

source_name: 36hpf amphioxus embryos

growth_protocol: Embryos were obtained and raised as previously described (Fuentes et al 2007 J Exp Zoolog B Mol Dev Evol 308:484–493)

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

treatment_protocol: No treatment

tag: age

tag: tissue

value: whole embryos


title: Amphioxus_36hpf (61)

description: European amphioxus


title: Amphioxus_36hpf (60)

description: European amphioxus


title: Amphioxus_36hpf (59)

description: European amphioxus


title: Amphioxus_36hpf (58)

description: European amphioxus


title: GLD-14

description: Normal human Dermal Fibroblast (NHDF)


title: Amphioxus_36hpf (57)

description: European amphioxus


title: EBNA1 CHIP-seq in Raji

source_name: EBNA1 CHIP-seq in Raji

tag: cell line


title: Amphioxus_36hpf (55)

description: European amphioxus


title: Amphioxus_36hpf (53)

description: European amphioxus


title: Amphioxus_36hpf (52)

description: European amphioxus


title: Amphioxus_36hpf (56)

description: European amphioxus


title: Amphioxus_36hpf (54)

description: European amphioxus


title: Amphioxus_36hpf (51)

description: European amphioxus


title: NRF1_INPUT_to2i

source_name: embryonic stem cells

tag: genotype

value: adaptation to 2i (> 3 weeks)


title: Amphioxus_36hpf (49)

description: European amphioxus


title: Amphioxus_8hpf (44)

description: European amphioxus

source_name: 8hpf amphioxus embryos


title: Amphioxus_8hpf (45)

description: European amphioxus


title: Amphioxus_8hpf (43)

description: European amphioxus


title: Amphioxus_36hpf (47)

description: European amphioxus


title: Amphioxus_8hpf (41)

description: European amphioxus


title: Amphioxus_8hpf (42)

description: European amphioxus


title: Amphioxus_8hpf (38)

description: European amphioxus


title: Amphioxus_36hpf (48)

description: European amphioxus


title: Amphioxus_36hpf (50)

description: European amphioxus


title: Amphioxus_8hpf (39)

description: European amphioxus


title: Amphioxus_8hpf (36)

description: European amphioxus


title: Amphioxus_8hpf (35)

description: European amphioxus


title: Amphioxus_8hpf (46)

description: European amphioxus


title: Amphioxus_8hpf (34)

description: European amphioxus


title: Amphioxus_8hpf (33)

description: European amphioxus


title: Amphioxus_8hpf (32)

description: European amphioxus


title: Amphioxus_15hpf (30)

description: European amphioxus

source_name: 15hpf amphioxus embryos


title: Amphioxus_8hpf (31)

description: European amphioxus


title: Amphioxus_15hpf (29)

description: European amphioxus


title: Amphioxus_15hpf (28)

description: European amphioxus


title: Amphioxus_15hpf (26)

description: European amphioxus


title: Amphioxus_8hpf (40)

description: European amphioxus


title: Amphioxus_15hpf (27)

description: European amphioxus


title: Amphioxus_15hpf (21)

description: European amphioxus


title: Amphioxus_15hpf (22)

description: European amphioxus


title: Amphioxus_36hpf (74)

description: European amphioxus

data_processing:
library strategy: ATAC-Seq
For 4C: Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the danRer7 assembly and Sc_hox scaffold using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: danRer7/Sc_hox (see Sc_hox fasta linked as supplementary file on Series record)
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 4Cseq of viewpoint that can be directly uploaded to UCSC for visualization.
For ATAC-seq: Alignment: reads were aligned using Sc_hox scaffold as reference genome and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using local browser
Genome_build: Sc_hox (see Sc_hox fasta linked as supplementary file on Series record)
Supplementary_files_format_and_content: bigWig format for visualization

extract_protocol:
Cells were processed for ATAC-seq as previously described (Buenrostro et al., 2013) with the following modifications: 12 total cycles of PCR were used, and DNA cleanups were performed using a Nucleospin Gel and PCR Clean up kit (Macherey-Nagel).
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.


title: Amphioxus_8hpf (37)

description: European amphioxus


title: Amphioxus_15hpf (24)

description: European amphioxus


title: Amphioxus_15hpf (25)

description: European amphioxus


title: Amphioxus_15hpf (7)

description: European amphioxus


title: Amphioxus_15hpf (12)

description: European amphioxus


title: Amphioxus_15hpf (20)

description: European amphioxus


title: Amphioxus_15hpf (18)

description: European amphioxus


title: Amphioxus_15hpf (13)

description: European amphioxus


title: Amphioxus_15hpf (5)

description: European amphioxus


title: Amphioxus_15hpf (14)

description: European amphioxus


title: Amphioxus_15hpf (3)

description: European amphioxus


title: Amphioxus_15hpf (4)

description: European amphioxus


title: Amphioxus_15hpf (17)

description: European amphioxus


title: Amphioxus_15hpf (19)

description: European amphioxus


title: Amphioxus_15hpf (16)

description: European amphioxus


title: Amphioxus_15hpf (15)

description: European amphioxus


title: Amphioxus_15hpf (10)

description: European amphioxus


title: Amphioxus_15hpf (9)

description: European amphioxus


title: Amphioxus_15hpf (11)

description: European amphioxus


title: Amphioxus_15hpf (2)

description: European amphioxus


title: Amphioxus_15hpf (1)

description: European amphioxus


title: Amphioxus_15hpf (23)

description: European amphioxus


title: SoxC morphlino oligo knockdown

city: Bethesda

first: Robert

middle: C

last: Angerer

state: MD

address: 30 Convent Drive

institute: NIDCR

data_processing:
Base-calling software was CASAVA 1.8. Reading alignment software was Bowtie.
Genome_build: PRJNA81157
Supplementary_files_format_and_content: Tab-delimited text files with abundance measurements

organism: Strongylocentrotus purpuratus

source_name: morpholino oligo injected

growth_protocol: Embryos developed in 15-degee artificial sea water to 30 hours.

extract_protocol: After 30 hours of development, total RNA was extracted with the NucleoSpin RNAII kit from Mcherey-Nagel GmbH.

treatment_protocol: Fertilized eggs were either microinjected with glycerol as control or Soxc morpholino oligos.

value: whole embryo

tag: development stage

value: 30 hours post fertilization


title: PV_HET_7-het_A1_pe

city: Chapel Hill

first: Corbin

middle: D

last: Jones

state: NC

address: 250 Bell Tower

department: Biology

institute: University of North Carolina

data_processing:
CASAVA 1.8
BWA 0.7.12 alignment to transcriptome of D. melanogaster (r6.)
Call counts, custom script
format for R, custom script
DEseq2, modeled both genotype and time
Genome_build: D. melanogaster r6.1
Supplementary_files_format_and_content: Tab-seperated, normalized counts, non-normalized counts

organism: Drosophila melanogaster

source_name: Adult Antennae

extract_protocol:
RNA was extracted with RNeasy kit (Qiagen
Illumina Stranded mRNA seq

value: antennae

tag: developmental stage

value: Adult


title: PV1118_8-WT_A2_pe


title: PV_RN_8-rn_A2_pe


title: PV_RN_7-rn_A1_pe


title: PV1118_7-WT_A1_pe


title: Glycerol control

source_name: glycerol injected


title: PV_HET_8-het_A2_pe


title: Amphioxus_15hpf (6)

description: European amphioxus


title: Amphioxus_15hpf (8)

description: European amphioxus


title: PV_RN_6-rn_P40_2_pe

source_name: 40hr APF pupal antennae

value: 40 hours after pupation


title: PV_HET_6-het_P40_2_pe


title: PV1118_6-WT_P40_2_pe


title: PV1118_5-WT_P40_1_pe


title: PV_RN_5-rn_P40_1_pe


title: PV_HET_4-het_P8_2_pe

source_name: 8hr APF pupal antennae

value: 8 hours after pupation


title: PV1118_4-WT_P8_2_pe


title: PV_RN_3-rn_P8_1_pe


title: PV_RN_2-rn_L2_pe

source_name: larval imaginal disc

value: imaginal disc

value: wandering larvae


title: PV_HET_3-het_P8_1_pe


title: PV_HET_1-het_L1_pe


title: PV_HET_2-het_L2_pe


title: PV1118_1-WT_L1_pe


title: PV_RN_1-rn_L1_pe


title: PV1118_3-WT_P8_1_pe


title: RNA-seq in LCL, EBNA1 shRNA, replicate 2

source_name: LCL_EBNA1 shRNA_RNA-seq

extract_protocol:
total RNA isolated using Trizol reagent
TruSeq Stranded Total RNA Library Preparation kit
ChIP-Seq protocol is as described previously (Lu et al, 2010  Virology journal 7, 262).  Total RNA was isolated for RNA-Seq using Trizol reagent.

treatment_protocol:
LCL cells transduced with either pLKO.1 shControl or shEBNA1 lentivirus after 5 days of puromycin selection
Cells were maintained and isolated in logarihmic growth phase for ChIP-assays.   RNA Seq analysis was performed with LCL cells transduced with either pLKO.1 shControl or shEBNA1 lentivirus after 5 days of puromycin selection.

value: LCL

value: EBV positive B-cell

tag: transduced with

value: shEBNA1 lentivirus


title: Orangutan testis 2

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

institute: University of Cambridge

description: Sample1 and Sample2 correspond to two distinct RNA-seq runs performed from the same library

data_processing:
Reads were pre-processed by removing the last nucleotide at their 3’-end (artificially included by the protocol) using trimmomatic (version 0.32) and adaptors were trimmed using Skewer (version 0.1.114).
Reads were mapped using TopHat (version 2.0.9) on the genome using the gene annotation (GTF file including the Ensembl annotated genes and the retrocopies detected using our pipeline) as a guide; the comman used was: tophat -p 8 -o -a 8-i 40 -I 1000000 -G --microexon-search --read-realign-edit-dist 0  --library-type fr-firststrand
Retrocopy transcripts were reconstructed using Cufflinks (version 2.1.1) usign the aligned reads from all samples to perform a transcriptome assembly (cufflinks options: cufflinks -o  -p 12 --library-type fr-unstranded --min-frags-per-transfrag 50 --max-multiread-fraction 1 --trim-3-dropoff-frac 0.25 --overlap-radius 1). The boundaries of the transcipts overlapping the retrocopies were then trimmed if their RNA-Seq coverage was below 10% of the mean transcript coverage.
Gene expression levels (in FPKM) were calculated using Cufflinks; Cufflinks options: cufflinks -o  -G  -p 8 --library-type fr-<$strand> --multi-read-correct -b. The GTF files for expression level calculation was obtained by Ensembl (version 65), and was modified by including our reconstructed retrocopy transcripts (after removing all Ensembl transcripts overlapping our retrocopy annotation).
Genome_build: ponAbe2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of all genes (from Ensembl65 and our own retrocopy reconstruction) obtained from Cufflinks.

organism: Pongo pygmaeus

source_name: testis

extract_protocol:
Total RNA was extracted from using the RNAeasy kit (Qiagen) using standard protocol
mRNA was purified from total RNA using the Dynabeads® mRNA Purification Kit. Purified mRNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module Protocol and then purified using the NucleoSpin RNA Clean-up XP kit. Paired-end strand-specific RNA-seq libraries were prepared using NEBNext RNA First Strand Synthesis Module (using Actinomycin D) and NEBNext Ultra Directional RNA Second Strand Synthesis Module. Sequencing was perfomed on the Illumina MiSeq platform using MiSeq Reagent Kits v2 to generate 150-bp paired-end sequencess.

value: testis

tag: rin value


title: RNA-seq in LCL, control shRNA, replicate 2

source_name: LCL_contorl shRNA_RNA-seq

value: pLKO.1 control shRNA


title: RNA-seq in LCL, EBNA1 shRNA, replicate 1


title: PV1118_2-WT_L2_pe


title: RNA-seq in LCL, control shRNA, replicate 1


title: NRF1_INPUT_HCC1954

data_processing:
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Read mapping was performed using Bowtie version 1.0.0 with parameters -v 3 -m 1 --best --strata.
Bigwig files were generated by extending the reads to 200bp and calculating for each genomic position the read density normalized to one million reads in the library.
Genome_build: hg19

source_name: breast cancer cells

growth_protocol: HCC1954 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum, 1× nonessential amino acids and 1× L-glutamine (37°C, 5% CO2).

value: WT

value: none (input)


title: NRF1_CHIP_HCC1954_2

value: NRF1 (Abcam, ab55744)


title: Orangutan testis 1


title: NRF1_CHIP_HCC1954_1


title: NRF1_CHIP_HMEC_1

source_name: mammary epithelial cells

growth_protocol: HMECs were purchased from Lonza (CC-2551), cultivated according to the distributor's instructions and harvested after two passages.

value: HMEC


title: TSC_D4_PF1-3_2

city: Freiburg

first: Maria

middle: Josefina

last: Castex

address: BreisacherStrasse 66

country: Germany

institute: Freiburg Uniklinik

description:
TSC treated with PF1-3 compound in differentiation conditions
processed data file: D4_analyzed.txt

data_processing:
Illumina Casava1.7 software used for basecalling. RTA 1.17.21.3
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: trophoblast stem cells derived from E3.5 mouse blastocysts

growth_protocol: Trophoblast Stem cells medium +/- Fgf4

extract_protocol:
Qiagen RNA total extraction
Illumina

treatment_protocol: 2 micromolar PF1-3 during 1 (stemness) or 4 (differentiation) days  or 10 micromolar control compound

tag: strain


title: NRF1_CHIP_HMEC_2


title: PV_RN_4-rn_P8_2_pe


title: PV_HET_5-het_P40_1_pe


title: TSC_D4_Ctrl

description:
TSC treated with control compound in differentiation conditions
processed data file: D4_analyzed.txt


title: TSC_DO_PF1-3_2

description:
TSC treated with PF1-3 compound in stemness conditions
processed data file: DO_analyzed.txt


title: TSC_DO_PF1-3_1


title: TSC_DO_Ctrl_1

description:
TSC treated with control compound in stemness conditions
processed data file: DO_analyzed.txt


title: TSC_DO_Ctrl_2


title: SLBP_CLIP_low_MW_low_MNase

city: Hanover

first: Michael

last: Whitfield

state: NH

address: Geisel School of Medicine; HB 7400

institute: Geisel School of Medicine at Dartmouth

description:
nuclease-resistant RNA fragments
SLBP HITS-CLIP

data_processing:
Raw fastq files were quality-filtered and adapter-clipped using default parameters of the FASTX toolkit http://hannonlab.cshl.edu/fastx_toolkit/
The remaining sequence was aligned to the human genome reference hg19 using default parameters of the bwa aligner (Li H. And Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics, Epub. [PMID: 20080505] )
Post-processing of the alignment files was performed using the python programming language and the library known as PySAM (by Andreas Heger and contributors, https://code.google.com/p/pysam/), which is a wrapper for samtools (Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. And 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943] )
Genome_build: hg19
Supplementary_files_format_and_content: the genomic coordinates and quantity of single-basepair deletions, aligned fragment termini, and raw coverage are submitted in bedgraph format

source_name: HeLa S3 monolayer cell culture

growth_protocol: HeLa S3 cells were propogated in monolayer culture. Culture medium used was DMEM with 10% FBS.

extract_protocol:
The irradiated cells were lysed in NP-40 lysis buffer
Illumina sRNA adapters v1 were ligated to the immunopreciptated RNA fragments. The adapter-ligated fragments were reverse transcribed, PCR-amplified and sie selected according to the manufacturers protocol.

treatment_protocol: The RNP were crosslinked prior to lysis by irradiating the monolayer with 7400 mJ of 254 nm UV light. Notably,

value: HeLa S3

tag: antibody used

value: α-SLBP

tag: molecular weight

tag: mnase concentration

value: low (0.03 gel units/μL)


title: GLD-2

description: Normal human Dermal Fibroblast (NHDF)

source_name: NHDF, TGFbeta

tag: cell type

value: human primary dermal fibroblast

tag: donor

value: donor B

value: between 4 and 7


title: mock_RIP_seq_03

description:
RNP-bound mRNA
mock RIP-seq

data_processing:
Raw fastq files were quality-filtered and adapter-clipped using default parameters of the FASTX toolkit http://hannonlab.cshl.edu/fastx_toolkit/
The remaining sequence was aligned to the human genome reference hg19 using default parameters of the bwa aligner (Li H. And Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics, Epub. [PMID: 20080505] )
Post-processing of the alignment files was performed using Aaron Quinlan's BEDTools (Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, [PMID: 20110278]). The genomecov command was used to generate bedgraph files.
Genome_build: hg19
Supplementary_files_format_and_content: the genomic coordinates and quantity of single-basepair deletions, aligned fragment termini, and raw coverage are submitted in bedgraph format

source_name: polyribsomal fractions of HeLa S3 cells that were propagated in suspension culture

growth_protocol: HeLa S3 cells were propogated in suspension culture.

extract_protocol:
The HeLa S3 cells were lysed and fractionated by sucrose gradient centrifugation
Illumina sequencing adpaters were ligated to double-stranded cDNA, which was synthesized from the immunopreciptated RNA. Note that this is a strand-agnostic library prepartion protocol.
Illumina adpaters were ligated to double-stranded cDNA, which was synthesized from the immunopreciptated RNA. Note that this is a strand-agnostic library prepartion protocol.

tag: antibody

value: mock


title: mock_RIP_seq_01

description:
RNP-bound mRNA
mock RIP-seq


title: mock_RIP_seq_02

description:
RNP-bound mRNA
mock RIP-seq


title: SLBP_RIP_seq_03

description:
RNP-bound mRNA
SLBP RIP-seq


title: SLBP_RIP_seq_02

description:
RNP-bound mRNA
SLBP RIP-seq


title: SLBP_RIP_seq_01

description:
RNP-bound mRNA
SLBP RIP-seq


title: Zebrafish_24hpf (73)

description: zebrafish

organism: Danio rerio

source_name: 24 hpf zebrafish embryos

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated with pronase before fixation.

value: 24 hpf

value: whole embryos


title: GLD-1

description: Normal human Dermal Fibroblast (NHDF)

source_name: NHDF, no treatment

tag: passage


title: SLBP_CLIP_high_MW_high_MNase

value: high (3.0 gel units/μL)


title: Zebrafish_24hpf (71)

description: zebrafish


title: NRF1_INPUT_HMEC

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out essentially as previously described (Jermann et al. PNAS 2014).
Library Construction Protocol: Libraries for ChIP-seq were prepared according to standard Illumina library preparation protocols. Twelve cycles of PCR (NEB Q5 Hot Start HiFi PCR) were performed on end-repaired, A-tailed and adapter-ligated DNA prior to gel size-selection. Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.

tag: chip antibody


title: mock_CLIP_high_MW_high_MNase

description:
nuclease-resistant RNA fragments
mock HITS-CLIP


title: mock_CLIP_low_MW_high_MNase


title: Zebrafish_24hpf (69)

description: zebrafish

tag: age


title: Zebrafish_24hpf (66)

description: zebrafish

tag: tissue


title: Zebrafish_24hpf (70)

description: zebrafish


title: Zebrafish_24hpf (64)

description: zebrafish


title: Zebrafish_24hpf (63)

description: zebrafish


title: Zebrafish_24hpf (68)

description: zebrafish


title: Zebrafish_24hpf (67)

description: zebrafish


title: MethylC-seq_xt_st9

status: Public on Dec 15 2015

description: Data from one biological replicate.

data_processing:
Data were mapped to the reference genome Xenopus tropicalis (JGI 7.1)
JGI 7.1
Genome_build: JGI7.1
Supplementary_files_format_and_content: For "*.allC" processed data file (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.

source_name: whole embryo

growth_protocol: Embryos were obtained by in vitro fertilisation and grown at 22 celcius untill the approptate developmental stage.

extract_protocol:
MethylC-seq: Genomic DNA was obtained as described before (Bogdanovic and Veenstra; BMC Res Notes, 2011).
MethylC-Seq libraries were constructed as descibed previously (Lister et al; Nature, 2011), except library amplification was performed with either PfuTurboCx Hotstart DNA polymerase (Agilent Technologies, Santa Clara, CA, USA) or KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA, USA).

tag: developmental stage (nf)

tag: treatment

value: not injected

value: no antibody


title: SLBP_CLIP_high_MW_low_MNase

tag: cell line


title: SLBP_CLIP_low_MW_high_MNase


title: Sample_KP40

city: New York

first: Jingli

last: Cao

state: NY

department: Cell & Developmental Biology

institute: Weill Cornell Medical College

data_processing:
Illumina CASAVA1.8  software used for basecalling.
Sequenced reads were mapped to the zebrafish genome using Bowtie2.
Transcript expressions were quantified by using RSEM 1.2.12
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files include expected count values for each sample.

source_name: zebrafish epicardial cell

extract_protocol:
Ventricles were collected from adult tcf21:nucEGFP fish at 6 months of age. Ventricles were collected on ice and washed several times to remove blood cells.  Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH (Roche) and 1% sheep serum at 37°C, while stirring gently with a Spinbar® magnetic stirring bar (Bel-Art Products).  Supernatants were collected every 5 min and neutralized with sheep serum.  Dissociated cells were spun down and re-suspended in DMEM plus 10% fetal bovine serum (FBS) medium with 1.5 μg/ml propidium iodide (PI), and sorted using a BD FACSVantage SE sorter for EGFP-positive and PI-negative cells.  Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol.
Libraries were constructed on the C1 platform following the Fluidigm protocol.

value: EK

value: heart epicardium

value: 6 month


title: Sample_KP39


title: Sample_KP38


title: Zebrafish_24hpf (72)

description: zebrafish


title: Sample_KP35


title: Sample_KP32


title: Sample_KP31


title: Sample_KP30


title: Sample_KP26


title: Sample_KP27


title: Sample_KP29


title: Sample_KP28


title: Sample_KP36


title: Sample_KP33


title: Sample_KP37


title: Sample_KP25


title: Sample_KP24


title: Sample_KP22


title: Sample_KP23


title: Sample_KP21


title: MethylC-seq_xt_st10.5

description: Data from one biological replicate.

data_processing:
Data were mapped to the reference genome Xenopus tropicalis (JGI 7.1)
Genome_build: JGI7.1
Supplementary_files_format_and_content: For "*.allC" processed data file (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.


title: Sample_KP19


title: Sample_KP17


title: Sample_KP16


title: Sample_KP18


title: Sample_KP20


title: Sample_KP15


title: Sample_KP34


title: Sample_KP11


title: Sample_KP10


title: Sample_KP14


title: Sample_KP12


title: Sample_KP7


title: Sample_KP8


title: Sample_KP9


title: Sample_KP3


title: Sample_KP6


title: Sample_KP5


title: Sample_KP4


title: SC_280K_rep3

city: Charlestown

first: Joy

middle: Luz

last: Nishikawa

address: Bldg 149, 13th Street

department: Cancer Center / Cell Biology

institute: Massachusetts General Hospital / Harvard Medical School

description: S. cerevisiae iKIX1 + ketoconazole

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S288C saccharomyces cerevisiae genome and draft genome sequence from isolate DSY562 for Candida glabrata respectively using STAR
Counts Per Megabase of library size (CPM) were calculated using HTSeq-count
Genome_build: S288C
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: S. cerevisiae RNA

growth_protocol: Cells were grown in YPD at 30oC with shaking overnight (24 hours) then washed twice in 2x volume of Milli-Q water before being resuspended in YP to an OD600 of 0.8. Cells were grown with shaking overnight (~16 hours) before splitting and treatment.

extract_protocol:
Cells were harvested by centrifugation at 4,000 rpm for 4 minutes at 4oC. Media was aspirated and cells were snap frozen on dry ice and then RNA was isolated according to (Martin R, Moran GP, Jacobsen ID, Heyken A, Domey J, Sullivan DJ, et al. The Candida albicans-specific gene EED1 encodes a key regulator of hyphal extension. PLoS One.6(4):e18394. Epub 2011/04/23.) RNA was then DNase treated using recombinant DNaseI, RNase-free (Roche) according to manufacturer’s instructions.
Multiplexed RNA-Seq libraries were constructed using PolyA selection and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Cells were treated with vehicle (DMSO) or 10 μM iKIX1 then grown with shaking another 8 hours before harvest of non-azole induced samples. Remaining cultures were induced to a final concentration of 40 μM ketoconazole and harvested after 15 minutes.

value: 10 μM iKIX1 + 40 μM ketoconazole


title: SC_DK_rep2

description: S. cerevisiae DMSO + ketoconazole

value: 1/1000 volume of DMSO + 40 μM ketoconazole


title: SC_280_rep3

description: S. cerevisiae iKIX1

value: 10 μM iKIX1


title: SC_280K_rep2

description: S. cerevisiae iKIX1 + ketoconazole


title: SC_DK_rep3

description: S. cerevisiae DMSO + ketoconazole


title: SC_280K_rep1

description: S. cerevisiae iKIX1 + ketoconazole


title: Sample_KP1


title: Sample_KP2


title: SC_DK_rep1

description: S. cerevisiae DMSO + ketoconazole


title: TSC_D4_PF1-3_1


title: SC_280_rep1

description: S. cerevisiae iKIX1


title: SC_D_rep2

description: S. cerevisiae DMSO

value: 1/1000 volume of DMSO


title: mcm21_2

first: Isabel

last: Lam

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (RStudio version 0.98.1091, R version 3.0.1)
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

source_name: meiotic culture

growth_protocol:
Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 30°C, harvested, resuspended to OD600=6.0 in 2% potassium acetate, 0.2 × supplements (2 μg/mL adenine, 2 μg/mL histidine, 6 μg/mL leucine, 2 μg/mL tryptophan, 2 μg/mL uracil) and sporulated at 30°C.
Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 30°C, harvested, resuspended to OD600=6.0 in 2% potassium acetate, 0.2 × supplements (2 μg/mL adenine, 2 μg/mL histidine, 6 μg/mL leucine, 2 μg/mL tryptophan, 2 μg/mL uracil) and sporulated at 30°C.

extract_protocol:
Based on Pan et al. 2011 Cell, and Zhu and Keeney 2015 Genetics, with modifications. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Flag fusion with Protein-G Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell, and Thacker et al. 2014 Nature. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: genotype/variation

value: mcm21 null

tag: epitope tag

tag: time

value: 4 hr in meiosis


title: SC_D_rep3

description: S. cerevisiae DMSO

tag: strain


title: Sample_KP13


title: SC_D_rep1

description: S. cerevisiae DMSO


title: mcm21_1

description: Spo11-associated DNA oligonucleotides


title: EryA ATAC_seq

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

description: ATAC-seq

data_processing:
Basecalls performed using CASAVA version 1.4
bowtie2 using default parameters
Using uniquely maped tag only
Genome_build: mm9

source_name: EryA cells

growth_protocol: Cells were sorted by FACS according to stablished markers

extract_protocol:
pelleted by centrifugation
two sets of 9 cycles of PCR using indexing primers from Nextera kit

value: EryA cells

tag: passages

value: In vivo FACS purified cells


title: polyN Puf2p rep 2

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

data_processing:
Library strategy: CLIP-Seq
PCR duplicates were removed using a random barcode.
The first five nucleotides of the read (the random barcode) were removed.
Reads were mapped to the S. Cerevisiae EF4 genome using the --local parameter.
Reads with MAPQ below 20 were removed.
Peaks were called by custom CLIP-seq processing scripts, requiring at least 10 reads in a peak, enrichment relative to RNA-seq and to local CLIP-seq signal, and only one peak permitted per gene.
Genome_build: EF4
Supplementary_files_format_and_content: Processed data files are bed files of peak locations, with the name column as the target gene and the score column as the maximum height reached in the peak region.

source_name: BY4742 PUF2 null mutants with TAP tagged Puf2p vector-expressed

growth_protocol: CLIP-seq was performed in BY4742 S. cerevisiae grown in log phase, and using 2 replicates of TAP-tagged proteins.

extract_protocol:
Cells were lysed by mortar and pestle, and libraries prepared by CLIP-seq methods.
CLIP-seq, by either HITS-CLIP or PAR-CLIP. Five random nucleotides were included in the 5' RNA linker, such that the first five nucleotides in each read are the random barcode.


title: Untagged cells negative control rep 1

source_name: BY4742 PUF2 null mutants with an empty vector


title: Zebrafish_24hpf (65)

description: zebrafish


title: polyN Puf2p rep 1


title: PUF domain alone Puf2p rep 1


title: R1 SNE Puf2p rep 1


title: Genomic WT Puf2p PAR-CLIP rep 2

source_name: BY4742 with a TAP tag C-terminally added to PUF2


title: polyN RRM Puf2p rep 1


title: PUF domain alone Puf2p rep 2


title: R1 SNE Puf2p rep 2


title: Genomic WT Puf2p PAR-CLIP rep 1


title: At rz-1b At rz-1c mRNA-seq replicate 2

city: Norwich

first: Zhe

last: Wu

address: Colney

institute: John Innes Centre

description: high-throughput profiling of transcriptome in At rz-1b At rz-1c(mutant), replicate 2, single end

data_processing:
Total RNA was extracted from two-week-old seedlings using TRIzol (Invitrogen) according to the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was purified using the PolyATtract® mRNA Isolation System (Promega, USA) following the manufacturer’s instructions. Strand-specific RNA-seq libraries generated from the WT and double mutant plants were constructed according dUTP method (replicate 1) or the Illumina Directional mRNA-Seq library prep protocol v1.5 (replicate 2) and sequenced on an Illumina GAII. Replicate 1 is paired ended while replicate 2 is single ended. The RNA-seq reads were aligned to the TAIR10 Arabidopsis Genome using TopHat v2.0 (Trapnell et al., 2009). A summary of reads alignment can be found in supplemental table 4. Only uniquely mapped reads were retained for subsequent analysis. The expression levels for gene models from the TAIR10 Arabidopsis Genome were measured and normalized as reads per kilobase of exon model per million mapped reads (RPKM) (Mortazavi et al., 2008). Next, P-values for each gene were calculated by DEGseq based on the MA-plot-based method with random sampling model (MARS) (Wang et al., 2010). Genes with more than 1.5-fold change and P < 0.01 were regarded as differentially expressed genes. For pathway analysis, the list of differential expressed genes and their corresponding log2 fold-changes were analyzed using MapMan (Thimm et al., 2004). Differentially spliced introns were detected as previously reported (Deng et al., 2010). In brief, Fisher's exact test was performed to identify introns with differential splicing between wild type plants and double mutants using read counts from each intron and its two flanking exons. In total, introns with more than 95% read coverage, intron RPKM greater than 5, and a two-sided P-value less than 0.01 were regarded as differentially spliced introns.
Genome_build: TAIR10 Arabidopsis genome
Supplementary_files_format_and_content: wig files were generated using MACS program

source_name: mutant_14DAG seedlings

growth_protocol: Arabidopsis thaliana seedling were grown for 14days on MS+1% sucrose plate and harvested for total RNA extraction, from which the mRNA were purified for subsequent mRNAs-seq

extract_protocol:
Total RNAs were extracted from 14DAG seedlings with TRIzol Reagent (15596–026; Invitrogen).
Strand-specific RNA-Seq libraries generated by using dUTP method (sample 1 and 2) or according to the Illumina Directional mRNA-Seq library prep v1.5 protocol (sample 3 and 4) and sequenced on Illumina GAII.

tag: ecotype background

value: At rz-1b At rz-1c double mutant

value: 14DAG seedlings


title: SC_280_rep2

description: S. cerevisiae iKIX1


title: Genomic WT Puf2p HITS-CLIP rep 2


title: Genomic WT Puf2p HITS-CLIP rep 1


title: Col-0 mRNA-seq replicate 2

description: high-throughput profiling of transcriptome in Col-0 (wild type), replicate 2,single end

source_name: WT_14DAG seedlings

value: wild type


title: Col-0 mRNA-seq replicate 1

description: high-throughput profiling of transcriptome in Col-0 (wild type), replicate 1, paired end


title: At rz-1b At rz-1c mRNA-seq replicate 1

description: high-throughput profiling of transcriptome in At rz-1b At rz-1c(mutant), replicate 1, paired end


title: WT Puf2p RNA-seq 2

data_processing:
Reads were mapped to the EF4 genome using bowtie2 –local
Reads assigned to genes using HTSeq and the EF4 genomic annotation
Differential gene expression was determined using DESeq2
Genome_build: EF4
Supplementary_files_format_and_content: Processed data files represent the absolute number of reads (not normalized) in each gene, as determined by HTSeq

source_name: BY4742 PUF2 null mutants

growth_protocol: Cells were grown to early log phase (0.1 -0.4 OD660) in minimal media.

extract_protocol:
RNA was extracted from 50 ml culture by the hot phenol method, followed by an RNA-cleanup column.
TruSeq Stranded mRNA Sample Preparation Guide Rev E was followed to prepare libraries for sequencing: Poly-A selection, Fragment, Prime, Finish using FPF mix (Frag 6 minutes), cDNA Synthesis,  and finally bead purification (Agencourt AMPure XP)

tag: vector

value: delta(poly(N)) Puf2p


title: R1 SNE Puf2p RNA-seq 4

value: R1 SNE delta(poly(N)) Puf2p


title: R1 SNE Puf2p RNA-seq 2


title: WT Puf2p RNA-seq 3


title: R1 SNE Puf2p RNA-seq 1


title: WT Puf2p RNA-seq 1


title: EV RNA-seq 4

value: Empty


title: R1 SNE Puf2p RNA-seq 3


title: EV RNA-seq 1


title: EV RNA-seq 3


title: AM13833_Rec8-3HA_SPO5hr_input

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

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

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

description: NV3 input

data_processing:
Mapper: BWA Version: 0.7.5a-r405
RPM scaling, bedgraph creation and bed intersections: bedtools v2.16.2
SAMtools Version 1.2
additional scriptshttps://github.com/AlastairKerr/Vincenten2015
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: scaled to reads per million mapped reads

source_name: SK1 diploid cells

growth_protocol: Cells were allowed to sporulate in SPO media (0.3% potassium acetate, pH 7) a OD=1.8-1.9 for 5 hours.

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

treatment_protocol: Cells were fixed using 1% formaldehyde for 2 hours before harvesting.

tag: cell cycle stage

value: Cells harvested after 5 hours in SPO

value: none, input

tag: background


title: AM4016_Rec8-3HA_SPO5hr_input

description: NV2 input

tag: antibody


title: AM10686_Zip1_SPO5hr_IP

description: NV5 IP

extract_protocol:
Anti-Zip1 ChIP was performed and both input and IP samples were sequenced.
All samples were prepared using a liquid handling robot (Hamilton) by Bianka Baying (EMBL, Heidelberg, Germany). 10ng of each sample mixed with library preparation were assessed according to manufacturer's recommendation (NEBNext Ultra™ DNA Library Prep Kit for Illumina, (#E7370S/L)). Library preparation was done according to manufacturer. Briefly, the Adapter in the Adapter Ligation step was diluted 1:30 in water. The size selection step was performed with Ampure XP Beads from Beckman Coulter (insert size 200-250bp). The PCR amplification was performed in 15 cycles. Finally NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (#E7335S/L) were used for the Indexing. The quality and quantity of the libraries was checked using the Agilent BioAnalyzer and the Qubit dsDNA HS Assay kit (Invitrogen). ChIP-Seq was performed using Illumina HiSeq 2000 Sequencer with Requested Read Length HiSeq50 SE.


title: AM11633_Zip1_SPO5hr_input

description: NV6 input


title: AM11633_Zip1_SPO5hr_IP

description: NV6 IP


title: AM4015_Rec8-3HA_SPO5hr_IP

description: NV1 IP

value: Anti-HA


title: AM13833_Rec8-3HA_SPO5hr_IP

description: NV3 IP


title: AM4016_Rec8-3HA_SPO5hr_IP

description: NV2 IP


title: H4K20me3_stage30

city: Nijmegen

first: Saartje

last: Hontelez

address: Geert Grooteplein 28

institute: Radboud University

data_processing:
Reads were mapped to the reference Xenopus tropicalis genome JGI7.1, using the BWA allowing one mismatch
We used MACS2 with standard settings and q-value of 0.05. Fragment size was determined using phantompeakqualtools . Broad settings (--BROAD) were used for H3K4me1, H3K36me3, H3K27me3, H3K9me2, H3K9me3, H4K20me3 and RNAPII. Broad and narrow peaks were merged for H3K4me3. For H3K9ac narrow peaks were used
Peaks that showed at least 75% overlap with 1 kb regions that have <65 input reads, and peaks that have a ChIP-seq RPKM > 95 percentile of random background regions are excluded from further analysis.
Only scaffolds 1-10 were included in the analysis. Relative RPKM  was calculated by dividing the ChIP-seq RPKM of the peaks by the ChIP-seq RPKM of 95 percentile of random background regions.
Relative RPKM  was calculated by dividing the ChIP-seq RPKM of the peaks by the ChIP-seq RPKM of 95 percentile of random background regions.
Genome_build: JGI7.1
Supplementary_files_format_and_content: wig files were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw/src); Scores are scaled with scaling factor 1000000/[total #reads]
Supplementary_files_format_and_content: bed files contain peak locations (scaffold, start, stop)

extract_protocol:
Protein-DNA complexes were isolated with antibody from whole embryo lysates that were fixed, sonicated and yolk depleted.
Libraries were prepared with the Kapa Hyper Prep kit (Kapa Biosystems), and sequencing was done on the Illumina HiSeq2000 platform.

treatment_protocol: Fertilised eggs were injected with 2,3 nl of 2,67 ng/ul α-amanitin and developed until the control embryos reached mid-gastrulation (stage 11)

value: not injected

value: anti-H4K20me3 (Abcam ab9053)


title: H4K20me3_stage16


title: AM10664_Zip1_SPO5hr_IP

description: NV4 IP


title: H4K20me3_stage10.5


title: H3K9me3_stage30

value: anti-H3K9me3 (Abcam ab8898)


title: H4K20me3_stage9


title: H4K20me3_stage12


title: H3K9me3_stage12


title: EV RNA-seq 2


title: AM4015_Rec8-3HA_SPO5hr_input

description: NV1 input


title: H3K9me2_stage12

value: anti-H3K9me2 (Diagenode C15410060)


title: H3K9me2_stage10.5


title: H3K9me2_stage30


title: H3K9me2_stage9


title: H3K9me2_stage16


title: H3K9me3_stage16


title: AM10664_Zip1_SPO5hr_input

description: NV4 input


title: H3K27me3_stage30


title: H3K27me3_stage16


title: H3K27me3_stage12


title: H3K27me3_stage11_amanitin

description: Data from one biological replicate.

value: alpha-amanitin injected


title: H3K27me3_stage11_control

description: Data from one biological replicate.


title: AM10686_Zip1_SPO5hr_input

description: NV5 input


title: H3K27me3_stage9


title: H3K27me3_stage10.5


title: RNAPII_stage16

value: anti-RNAPII (Diagenode C15200004)


title: RNAPII_stage12


title: H3K27me3_stage8


title: RNAPII_stage9


title: RNAPII_stage10.5


title: p300_stage30

value: anti-p300 (Santa Cruz sc-585)


title: H3K9me3_stage10.5


title: p300_stage11_control

description: Data from one biological replicate.


title: H3K9me3_stage9


title: p300_stage11_amanitin

description: Data from one biological replicate.


title: p300_stage12


title: CG_280K_rep3

description: C. glabrata iKIX1 + ketoconazole

organism: Nakaseomyces glabratus

source_name: C. glabrata RNA

value: 10 μM iKIX1 + 40 μM ketoconazole


title: p300_stage9


title: CG_DK_rep3

description: C. glabrata DMSO + ketoconazole

value: 1/1000 volume of DMSO + 40 μM ketoconazole


title: CG_280K_rep1

description: C. glabrata iKIX1 + ketoconazole


title: Input_st30

value: no antibody


title: H3K36me3_stage30

value: anti-H3K36me3 (Abcam ab9050)


title: CG_280K_rep2

description: C. glabrata iKIX1 + ketoconazole


title: CG_DK_rep2

description: C. glabrata DMSO + ketoconazole


title: CG_280_rep3

description: C. glabrata iKIX1

value: 10 μM iKIX1


title: H3K36me3_stage16


title: CG_280_rep2

description: C. glabrata iKIX1


title: H3K36me3_stage12


title: RNAPII_stage30


title: H3K36me3_stage10.5


title: CG_D_rep2

description: C. glabrata DMSO

value: 1/1000 volume of DMSO


title: CG_280_rep1

description: C. glabrata iKIX1


title: CG_DK_rep1

description: C. glabrata DMSO + ketoconazole


title: H3K9ac_stage30

value: anti-H3K9ac (Upstate/Millipore 06-942)


title: CG_D_rep1

description: C. glabrata DMSO


title: H3K9ac_stage10.5


title: H3K9ac_stage9


title: H3K9ac_stage12


title: p300_stage10.5


title: H3K36me3_stage9


title: p300_stage16


title: H3K9ac_stage8


title: H3K9ac_stage16


title: H3K4me3_stage12

description: Previously published under GEO Series accession number GSE14025.

value: anti-H3K4me3 (Abcam ab8580)


title: H3K4me3_stage16


title: H3K4me3_stage30


title: H3K4me3_stage11_control

description: Data from one biological replicate.


title: H3K4me3_stage10.5


title: CG_D_rep3

description: C. glabrata DMSO