title: NT Kdm4b H3K9me3 ChIP-Seq 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using masc2(v 2.0.10.20131216) with the parameters "macs2 callpeak –n Sample -g mm -B -q 0.05 --nomodel --broad --shiftsize=73 --SPMR" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 pileup function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

source_name: NT Kdm4b H3K9me3 ChIP-seq

extract_protocol:
500-1000 cells were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to illumina TruSeq DNA LT Sample Prep Kit( FC-121-2001, FC-121-2002)

value: Kdm4b overexpression

tag: chip antibody vendor

value: active motif

tag: chip antibody cat. #


title: NT input ChIP-Seq

status: Public on May 16 2016

type: SRA

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

country: China

institute: Tongji University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: NT input ChIP-seq

tag: strain background

tag: development stage

tag: genotype/variation

value: wild type

tag: tissue

value: nuclear transfer embryo


title: WT input ChIP-Seq

source_name: WT input ChIP-seq

value: normal embryo


title: NT 4-cell arrest 3 [RRBS]

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “-D C-CGG -w 100 -s 12 -v 0.1 -m 32 -x 1000 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.

source_name: NT 4-cell arrest

extract_protocol:
Harvested cells were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. After lysed for 3h at 50°C, naked genomic DNA were relesed.
The released naked DNA was digested by MspI(Fermentas,ER0541),The digested DNA was then end-repaired and tailed with an extra A to the 3'blunted ends.Illumina standard premethylated indexed adaptors were ligated with the dA-tailed DNA fragments. Bisulfite conversion was then performed using the MethyCode bisulfite conversion kit (Invitrogen,MECOV-50) followed by two rounds of PCR enrichment.After PCR enrichment, DNA fragments between 200 and 500bp were size-selected by a 12% native polyacrylamide TBE gel.

treatment_protocol: We separated the blastomeres of lived 2- or 4-cell stage embryos. One blastomere was harvested for single-cell sequencing, and the rest were further cultured in an aggregation plate to record the final development fate

tag: strain


title: NT 2-cell arrest 5 [RRBS]

source_name: NT 2-cell arrest


title: NT 2-cell arrest 4 [RRBS]


title: NT Kdm4b H3K9me3 ChIP-Seq 1

tag: chip antibody


title: WT Zygote 5 [RNA-seq]

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v1.3.3 with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v 1.2.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript.

molecule: total RNA

source_name: WT Zygote

extract_protocol:
Harvested cells were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. cDNA were synthesized using primers with 24-nt poly(dT),then a universal tail was added to the second strand cDNAs. After 18-20 cyclesof PCR, the PCR product is purified by QIAquick PCR purification kit(28104).
The prepared cDNA are sheared using Covaris S220. Fragment ends are repaired using NEBNext End Repair Module(E6050), then a NEBNext dA-Tailing Module(E6053) was used to yield a protruding 3- 'A' base for ligation of Illumina's adapters.After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles. library fragments of 200-500bp were band isolated from an agarose gel.

value: zygote


title: WT H3K9me3 ChIP-Seq 2

source_name: WT H3K9me3 ChIP-seq


title: WT Zygote 3 [RNA-seq]


title: WT Zygote 2 [RNA-seq]


title: NT H3K9me3 ChIP-Seq

source_name: NT H3K9me3 ChIP-seq


title: NT 2-cell arrest 6 [RRBS]


title: CC H3K9me3 ChIP-Seq

source_name: CC H3K9me3 ChIP-seq

value: 6-8 weeks post natal

value: cumulus cell


title: WT Zygote 4 [RNA-seq]


title: NT Kdm4b input ChIP-Seq

source_name: NT Kdm4b input ChIP-seq


title: NT 2-cell arrest 3 [RRBS]


title: WT H3K9me3 ChIP-Seq 1


title: CC input ChIP-Seq

source_name: CC input ChIP-seq


title: WT Zygote 1 [RNA-seq]


title: WT TE 2 [RNA-seq]

source_name: WT TE

value: trophoblast


title: WT TE 5 [RNA-seq]


title: WT TE 6 [RNA-seq]


title: WT TE 1 [RNA-seq]


title: WT MII oocyte 6 [RNA-seq]

source_name: WT MII oocyte

value: MII oocyte

value: oocyte


title: WT TE 4 [RNA-seq]


title: WT MII oocyte 2 [RNA-seq]


title: WT MII oocyte 4 [RNA-seq]


title: WT TE 3 [RNA-seq]


title: WT MII oocyte 1 [RNA-seq]


title: WT MII oocyte 5 [RNA-seq]


title: WT ICM 4 [RNA-seq]

source_name: WT ICM

value: inner cell mass


title: WT ICM 5 [RNA-seq]


title: WT Morula 3 [RNA-seq]

source_name: WT Morula

value: morula


title: WT MII oocyte 3 [RNA-seq]


title: WT Morula 2 [RNA-seq]


title: WT Morula 4 [RNA-seq]


title: UNINF_THY_Rep12

status: Public on May 17 2016

city: Edmonton

first: James

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

country: Canada

institute: University of Alberta

data_processing:
Base calling: Real-time analysis and base calling were performed using the Hi-seq Control Software, version 2.2.38 (Illumina) to generate sequence reads with associated base quality scores.
Removal of low quality reads: RNA-seq reads, flagged as low quality by CASAVA 1.8 (Illumina), or with an average PHRED read quality score below 15, or in which ≥5 of the last 10 bases had a quality score below 2, were removed.
Sequence alignment: Reads were aligned to the pig reference genome sequence assembly (Sscrofa10.2) using TopHat 1.4.0 with default parameters. The number of reads uniquely mapped to each gene was determined using Ht-seq count (v0.5.3.p3).
Differential gene expression analysis: Differentially expressed genes (DEG) were identified using the Bioconductor package ‘edgeR’. Raw expression counts were converted to counts per million (CPM). Genes with very low expression levels were filtered out of the dataset by setting an expression threshold of CPM>1 in at least 12 samples. Compositional differences between libraries due to difference in library size were normalized using the ‘Trimmed mean of M values’ (TMM) method. A negative binomial model was fitted to the data and gene and tag-wise dispersions were estimated using the quantile-adjusted conditional maximum likelihood (qCML) method. Differential expression was determined using an exact test for the following three contrasts for both tissues: UNINF v CON, INF v UNINF, and MEC v INF. Genes were classified as differentially expressed if they had an absolute fold change >1.5 and a False Discovery Rate (FDR) <0.05.
Weighted Gene Network Correlation Analysis: Gene co-expression network analysis was performed using the software package ‘WGCNA’ for each of the three contrasts in two tissues described above.  The normalized CPM expression data generated by ‘edgeR’ were transformed using the function log2 (x+1) to stabilize variance prior to use in WGCNA. To construct the network, a matrix of co-expression similarity, pairwise correlations, for all genes across all samples in each contrast was made. Next, a weighted network adjacency matrix was obtained by raising the co-expression similarity to a power β whose value was determined by application of the approximate scale-free topology criterion [29]. After network construction, average linkage hierarchical clustering was used to identify clusters of highly interconnected gene ‘modules’ using the topological overlap measure of network interconnectedness as the input. A dynamic hybrid tree cutter was used to identify the branches of the hierarchical clustering dendogram corresponding to modules. Network construction and module detection were performed using the function ‘blockwiseModules’, with the following parameter values: a maximum block size of 15000 (sufficiently large to analyze all genes in a single block), a minimum module size of 30, a medium sensitivity to cluster splitting of 2, and a cut height for module merging of 0.25. The value of β ranged from 6-10. The gene expression profile of a module can be summarized by the module ‘eigengene’, defined as the first principal component of the expression matrix. Correlations between the module eigengene and the two categorical traits in each contrast were determined. Correlations between the eigengene and viral RNA titers were also calculated for the appropriate contrasts. The threshold for association significance was set at an absolute correlation of >0.3 and a P value of <0.1.
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Text files that contain the raw sequence counts for each gene (Ensembl gene identifier) produced by the program Ht-seq count.

organism: Sus scrofa

source_name: fetal thymus

growth_protocol: 133 Landrace gilts were obtained from a high-health nucleus herd that was free of PRRSV according to clinical signs and serologic testing. Groups of gilts were selected over 12 bi-weekly replicates, estrus-synchronized, and bred homosperimcally to Yorkshire boars. Pregnant gilts were housed in gestation stalls until gestation day 80±1, and then transferred to a biosafety level 2 facility at the University of Saskatchewan. After a period of acclimation, 114 gilts were inoculated on gestation day 85±1 (Experiment day 0) with 1x105 TCID50 PRRSV isolate NVSL 97-7895: 2 mL intramuscularly and 1 mL into each nostril. Nineteen control gilts were mock inoculated in a similar manner with Minimal Essential Medium (MEM). Gilts were humanely euthanized on Experiment day 21. The gravid uterus of each gilt tract was removed intact, placed in a trough, and orientated from left oviduct to right oviduct. The uterine horns were opened and fetuses numbered sequentially according to their position within the horn. The preservation status of each fetus was recorded in situ as: viable (live at the time of gilt necropsy, normal pink appearance), meconium-stained (live at time of gilt necropsy, stained with meconium), decomposed (dead prior to gilt necropsy, with primarily white skin), autolysed (dead prior to gilt necropsy, with over 50% brown-colored skin), or mummified (dead, <20 cm in length and considered dead prior to PRRSV-inoculation). Mummified fetuses were counted, but excluded from sampling and further analyses. After clamping the umbilical cord, each fetus (starting with live fetuses i.e. those classified as viable or meconium-stained) was removed from the uterus together with its umbilical cord, and a portion of allantochorion and uterus adjacent to the umbilical stump.

extract_protocol:
Total RNA was isolated from 10-20 mg of endometrium and thymus of each fetus using an ‘All Prep RNA/DNA isolation Mini kit’ (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was quantified by spectrophotometry using a Nanodrop ND 2000 (Thermo Fisher Scientific, Waltham, USA). RNA quality was assessed by digital electrophoresis using a ‘2200 Tapestation’ (Agilent Technologies, Santa Clara, USA). The mean RNA Integrity Number (RIN) sample value was 9.0 for thymus (range 8.0-9.8) and 8.3 for endometrium (range 7.5-8.8).
A total of 96 cDNA libraries were constructed for RNA-sequencing (RNA-seq) from thymus and endometrium samples of individual fetuses. Libraries were constructed from 1 μg of input total RNA using the TruSeq RNA sample preparation kit v2 (Illumina, San Diego, USA) according to the manufacturer’s instructions. DNA libraries were sequenced at the Genome Quebec Innovation Centre (McGill University, Montreal, Canada). Library insert size distribution was assessed on a LabChip GX instrument (Perkin Elmer, Waltham, USA) using a high sensitivity chip. Library concentration was determined using a KAPA Library Quantification Kit (KAPA Biosystems) on a Lightcycler 480 II instrument (Roche Life Science, Indianapolis, USA). Cluster formation was performed on the cBot instrument (Illumina) with eight libraries per lane (7 pM per library) using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Paired-end 100 bp cycle sequencing was performed on a HiSeq 2000 (Illumina) using the TruSeq SBS kit v3-HS (Illumina).

treatment_protocol: Samples of endometrium (including adherent placental layers) adjacent to the umbilical attachment site and fetal thymus were snap-frozen in liquid nitrogen and immediately stored at -80°C.

tag: infection status

value: UNINF

value: fetal thymus


title: WT ICM 3 [RNA-seq]


title: WT ICM 2 [RNA-seq]


title: WT Blastocyst 3 [RNA-seq]

source_name: WT Blastocyst

value: blastocyst


title: WT Morula 1 [RNA-seq]


title: WT Blastocyst 2 [RNA-seq]


title: WT Morula 5 [RNA-seq]


title: WT Blastocyst 1 [RNA-seq]


title: WT Morula 6 [RNA-seq]


title: WT 8-cell 3 [RNA-seq]

source_name: WT 8-cell


title: WT 8-cell 2 [RNA-seq]


title: WT 8-cell 4 [RNA-seq]


title: WT 8-cell 5 [RNA-seq]


title: WT 8-cell 1 [RNA-seq]


title: WT 4-cell 3 [RNA-seq]

source_name: WT 4-cell


title: WT 4-cell 5 [RNA-seq]


title: WT 4-cell 6 [RNA-seq]


title: WT 4-cell 4 [RNA-seq]


title: WT 4-cell 1 [RNA-seq]


title: WT 4-cell 2 [RNA-seq]


title: WT Blastocyst 4 [RNA-seq]


title: WT 2-cell 5 [RNA-seq]

source_name: WT 2-cell


title: WT 2-cell 1 [RNA-seq]


title: NT TE 4 [RNA-seq]

source_name: NT TE


title: WT 2-cell 4 [RNA-seq]


title: NT ICM 5 [RNA-seq]

source_name: NT ICM


title: WT 8-cell 6 [RNA-seq]


title: NT ICM 3 [RNA-seq]


title: NT ICM 4 [RNA-seq]


title: NT TE 2 [RNA-seq]


title: NT ICM 2 [RNA-seq]


title: NT TE 3 [RNA-seq]


title: NT TE 1 [RNA-seq]


title: Cumulus cell 6 [RNA-seq]

source_name: Cumulus cell


title: NT ICM 1 [RNA-seq]


title: Cumulus cell 5 [RNA-seq]


title: Cumulus cell 4 [RNA-seq]


title: WT 2-cell 2 [RNA-seq]


title: Cumulus cell 2 [RNA-seq]


title: NT 4-cell to blastocyst 9 [RNA-seq]

source_name: NT 4-cell to blastocyst


title: Cumulus cell 1 [RNA-seq]


title: NT 4-cell to blastocyst 8 [RNA-seq]


title: NT 4-cell to blastocyst 6 [RNA-seq]


title: NT 4-cell to blastocyst 4 [RNA-seq]


title: NT 4-cell to blastocyst 7 [RNA-seq]


title: NT 4-cell to blastocyst 2 [RNA-seq]


title: NT 4-cell to blastocyst 5 [RNA-seq]


title: NT 2-cell to blastocyst 8 [RNA-seq]

source_name: NT 2-cell to blastocyst


title: NT 2-cell to blastocyst 7 [RNA-seq]


title: NT 2-cell to blastocyst 2 [RNA-seq]


title: NT 2-cell to blastocyst 6 [RNA-seq]


title: NT 2-cell to blastocyst 3 [RNA-seq]


title: NT 2-cell to blastocyst 1 [RNA-seq]


title: NT 4-cell to blastocyst 3 [RNA-seq]


title: NT Kdm5b TE 5 [RNA-seq]

source_name: NT Kdm5b TE

value: Kdm5b overexpression


title: NT 4-cell to blastocyst 1 [RNA-seq]


title: NT 2-cell to blastocyst 5 [RNA-seq]


title: NT 2-cell to blastocyst 4 [RNA-seq]


title: NT Kdm5b TE 1 [RNA-seq]


title: Cumulus cell 3 [RNA-seq]


title: NT Kdm5b TE 2 [RNA-seq]


title: NT Kdm5b 4-cell 5 [RNA-seq]

source_name: NT Kdm5b 4-cell


title: NT Kdm5b 4-cell 3 [RNA-seq]


title: WT ICM 1 [RNA-seq]


title: NT Kdm5b 4-cell 2 [RNA-seq]


title: NT Kdm5b 4-cell 4 [RNA-seq]


title: NT Kdm5b 4-cell 1 [RNA-seq]


title: NT Kdm5b TE 3 [RNA-seq]


title: NT Kdm4d 2-cell 1 [RNA-seq]

source_name: NT Kdm4d 2-cell

value: Kdm4d overexpression


title: NT Kdm4d 2-cell 3 [RNA-seq]


title: NT Kdm4b TE 5 [RNA-seq]

source_name: NT Kdm4b TE

value: Kdm4b overexpression


title: NT Kdm4d 2-cell 2 [RNA-seq]


title: NT Kdm5b TE 4 [RNA-seq]


title: NT Kdm4b TE 3 [RNA-seq]


title: NT Kdm4b ICM 4 [RNA-seq]

source_name: NT Kdm4b ICM


title: NT Kdm4b ICM 3 [RNA-seq]


title: NT Kdm4b TE 1 [RNA-seq]


title: NT Kdm4b ICM 5 [RNA-seq]


title: NT Kdm4b TE 4 [RNA-seq]


title: NT Kdm4b TE 2 [RNA-seq]


title: NT Kdm4b ICM 2 [RNA-seq]


title: NT Kdm4b ICM 1 [RNA-seq]


title: NT Kdm4b 2-cell 5 [RNA-seq]

source_name: NT Kdm4b 2-cell


title: NT Kdm4b 2-cell 4 [RNA-seq]


title: Sclero Day 15 Rep 1

city: Aberdeen

first: Sophie

last: Shaw

state: Aberdeen City

address: 23 St. Machar Drive

department: Centre for Genome Enabled Biology and Medicine

country: United Kingdom

institute: University of Aberdeen

description: processed data column: 15_10

data_processing:
Base Calling carried out using CASAVA v1.8.2
Fastq-Mcf was used to remove adapter sequences and trim reads of a phred quality score < 20 with the following parameters: -q 20 -l 35 -k 0  -p 15  --max-ns 0 -m 3. ERCC reads were removed using Bowtie v1.0.0 with the following parameters: -S -X 600
Reads were aligned to the reference genomes for Trichoderma hamatum GD12 and Sclerotinia sclerotiorum isolate 1980 using TopHat v2.0.8b with the following parameters: -r 200 --mate-std-dev 375 --library-type fr-unstranded.
Reads were quantified at each predicted gene location using htseq-count v0.6.0 with the following parameters: -m union -s yes
DESeq2 was used to calculate normalised counts and identify genes with statistically significant differential expression.
Genome_build: Trichoderma hamatum GD12 and Sclerotinia sclerotiorum 1980
Supplementary_files_format_and_content: Tab delimited matrix containing the normalised count for each gene in each sample.

organism: Sclerotinia sclerotiorum

source_name: Mixed species soil sample

growth_protocol: 50 g of sieved sphagnum moss peat (Shamrock) was supplemented with a treatment and split between the wells of a 6 well plate. Two lettuce seeds were sown into each well. The first seedling to emerge was preserved and the second removed upon emergence. Plants were watered with sterile water.

extract_protocol:
2 g of soil from each sample was used for RNA extraction. Samples were prepared for RNA extraction by homogenisation in a blender in the presence of liquid nitrogen. RNA was extracted using RNA PowerSoil® Total RNA Isolation Kit (Cambio UC-12866-25). Remaining soil was stored at -80˚C.
2 µl of diluted ERCC RNA control spike-in mix 1 or control spike-in mix 2 (Life Technologies) was added to 1 µg of sample RNA and the volume adjusted to 50 µl.   Sequencing Libraries were prepared using the Maestro-based TruSeq RNA application from Perkin Elmer for Illumina TruSeq RNA library preparation on a Sciclone NGS platform. Samples were processed in 96 well hard shell PCR plates (Biorad HSP-9631). Washes were done in 150 µl bead washing solution instead of the 200 µl used in the manual process. Incubations at 65°C and 16°C for mRNA denaturation, and second-strand synthesis were performed on the Sciclone deck. However, the 80°C and 94°C incubations for mRNA elution and fragmentation, and first-strand cDNA synthesis reactions were performed on a thermocycler with heated lid to avoid excess evaporation. Purification and size selection was by Ampure XP bead clean up rather than gel based size selection. Library quality and quantity was determined by LabChipGX high sensitivity assay, after diluting the libraries 2µl in 20 µl.

treatment_protocol: Soils were supplemented with one of the following treatments; T. hamatum GD12, S. sclerotiorum, both fungal treatments or no treatment (control). T. hamatum GD12 was prepared as a bran inoculum by culturing five plugs taken from the leading edge of a three day old T. hamatum GD12 plate in a mixture of sterile 10 g bran + 30 ml water for 5 days at 26˚C under a 16 h light regime. The soil was inoculated with this mixture at a ratio of 1.3 g for every 50 g of soil (2.6% w/w).  S. sclerotiorum was prepared as a poppy seed inoculum by culturing 10 g poppy seeds (sterilised as a mixture with 10 ml water) with 10 1 mm plugs for 10 days at 26˚C under a 16 h light regime before incorporating into soil at 2.6% (w/w)  Soil from 2 wells of the same treatment were combined, snap frozen in liquid nitrogen and stored at -80˚C at six timepoints over a time course of 15 days (1d, 2d, 4d, 7d, 10d, 15d).

tag: isolate


title: Sclero Day 7 Rep 3

description: processed data column: 7_12


title: Sclero Day 15 Rep 3

description: processed data column: 15_12


title: Sclero Day 10 Rep 1

description: processed data column: 10_10


title: Sclero Day 10 Rep 3

description: processed data column: 10_12


title: Sclero Day 15 Rep 2

description: processed data column: 15_11


title: Sclero Day 10 Rep 2

description: processed data column: 10_11


title: NT Kdm4b 2-cell 3 [RNA-seq]


title: NT Kdm4b 2-cell 1 [RNA-seq]


title: NT Kdm4b 2-cell 2 [RNA-seq]

value: Kdm4b   overexpression


title: Sclero Day 7 Rep 2

description: processed data column: 7_11


title: Sclero Day 7 Rep 1

description: processed data column: 7_10


title: U2OS+Tetra-Pt(bpy)

city: Guangzhou

first: Yong

last: Zhao

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment 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: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples ...

organism: Homo sapiens

source_name: human osteosarcoma (U2OS) cells

extract_protocol:
Total RNA was extracted using the Trizol reagent (Takara). A total of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s recommendations.

tag: cell line

tag: treatment

value: Tetra-Pt(bpy)-treated


title: U2OS

value: control


title: HeLa+Tetra-Pt(bpy)

source_name: human cervical cancer (HeLa) cells

value: HeLa


title: HeLa


title: NT Kdm4b+Kdm5b TE 2 [RNA-seq]

source_name: NT Kdm4b+Kdm5b TE

value: Kdm4b and Kdm5b overexpression

value: nuclear transfer embryo


title: Sclero Day 4 Rep 1

description: processed data column: 4_10


title: Sclero Day 4 Rep 2

description: processed data column: 4_11


title: Sclero Day 2 Rep 3

description: processed data column: 2_12


title: NT Kdm4b+Kdm5b ICM 3 [RNA-seq]

source_name: NT Kdm4b+Kdm5b ICM


title: FL-HSPC sh-HOXA7_infected experiment_4 (HOXA7 in shHOXA7gene_exp.diff)

city: Los Angeles

first: Hanna

middle: Katri Annikki

last: Mikkola

state: CA

address: 621 Charles E Young Drive South, 2204, Mailbox 160606

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

data_processing:
Alignment: TopHat v2.0.14
parameters --no-coverage-search -M -T -x 1
Coverage file: Genomecov, Bedtools
parameters -bg -split –ibam
Abundance estimations: Cufflinks v2.2.1
parameters --compatible-hits-norm -N -u --GTF gencode.v19.annotation.gtf
Merging assemblies: Cuffmerge
Differential expression: Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: output of cuffdiff (text file .diff); Please note that the '#NAME' is the program output for log2 value of 0.

source_name: FL-HSPC sh-HOXA7_infected

growth_protocol: Cells in culture were cultured at 37C and 5% CO2 in alpha-MEM (Invitrogen), 20% FBS (Hyclone), 2 mM L-glutamine and 1% penicillin/streptomycin (10,000 U/ml, Invitrogen) supplemented with SCF (25 ug/ml, Peprotech), Flt-3 (25 ug/ml, Peprotech) and TPO (25 ug/ml, Peprotech)

extract_protocol:
RNA was purified from sorted cells using RNeasy Mini Kit (QIAGEN), according to manufacturer's instructions.
Ovation Rna-seq system System v2 (Nugen), followed by KAPA LTP Library Preparation Kit

treatment_protocol: Cells were infected with VSV-g pseudotyped lentivirus encoding shRNA and puromicin resistance and selected with puromycin and sorting

tag: cell type

value: human fetal liver, CD34+CD38-CD90+CD45+

value: fetal liver-hematopoietic stem/progenitor cell (FL-HSPC)

tag: infected with

value: lentiviral shRNA vector targeting HOXA7


title: EB cells infected with FUGW-GFP-HOXA7

data_processing:
Alignment: TopHat v2.0.14
parameters --no-coverage-search -M -T -x 1
Coverage file: Genomecov, Bedtools
parameters -bg -split –ibam
Abundance estimations: Cufflinks v2.2.1
parameters --compatible-hits-norm -N -u --GTF gencode.v19.annotation.gtf
Merging assemblies: Cuffmerge
Differential expression: Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: output of cuffdiff (text file .diff)

value: lentiviral FUGW vector encoding HOXA7 protein (FUGW-GFP-HOXA7)


title: FL-HSPC sh-HOXA7_infected experiment_3 (HOXA7 in shHOXA7gene_exp.diff)


title: EB cells infected with the empty FUGW-GFP

description: EB-CTR

value: empty lentiviral FUGW vector (FUGW-GFP)


title: Sclero Day 2 Rep 2

description: processed data column: 2_11


title: FL-HSPC LKO_infected experiment_4 (LKO in shHOXA7gene_exp.diff)

source_name: FL-HSPC LKO_infected

value: emtpy lentiviral vector (LKO)


title: NT Kdm4b+Kdm5b ICM 1 [RNA-seq]

value: inner cell mass


title: Sclero Day 2 Rep 1

description: processed data column: 2_10


title: FL-HSPC sh-HOXA7_infected experiment_1 (HOXA7 in shHOXA7gene_exp.diff)


title: Sclero Day 4 Rep 3

description: processed data column: 4_12


title: NT Kdm4b+Kdm5b 4-cell 5 [RNA-seq]

source_name: NT Kdm4b+Kdm5b 4-cell


title: NT Kdm4b+Kdm5b TE 3 [RNA-seq]

value: trophoblast


title: FL-HSPC LKO_infected experiment_2 (LKO in shHOXA7gene_exp.diff)


title: FL-derived HSPC sorted at day 0 (at the time of OP9 seeding)

data_processing:
Alignment: TopHat v2.0.14
parameters --no-coverage-search -M -T -x 1
Coverage file: Genomecov, Bedtools
parameters -bg -split –ibam
Abundance estimations: Cufflinks v2.2.1
parameters --compatible-hits-norm -N -u --GTF gencode.v19.annotation.gtf
Merging assemblies: Cuffmerge
Differential expression: Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: output of cuffdiff (text file .diff); Bigwig tracks

treatment_protocol: Cells were treated with 0.2uM AM580 on OP9 co-culture


title: FL-HSPC LKO_infected experiment_1 (LKO in shHOXA7gene_exp.diff)


title: NT Kdm4b+Kdm5b ICM 2 [RNA-seq]


title: NT Kdm4b+Kdm5b TE 1 [RNA-seq]


title: EB-derived HSPC sorted at day 0 (at the time of OP9 seeding)

value: human EB, CD34+CD38-CD90+CD43+

value: EB-derived hematopoietic stem/progenitor cell (HSPC)


title: FL DMSO-treated day12 on OP9, experiment 2 (q8 in the EB_AM580gene_exp.diff)

source_name: FL DMSO-treated day12 on OP9

tag: treated with

value: DMSO on OP9 for 12 days


title: FL DMSO-treated day12 on OP9, experiment 1 (q8 in the EB_AM580gene_exp.diff)


title: NT Kdm4b+Kdm5b 4-cell 3 [RNA-seq]


title: FL-HSPC sh-HOXA7_infected experiment_2 (HOXA7 in shHOXA7gene_exp.diff)


title: EB AM580-treated day12 on OP9, experiment 2 (q7 in the EB_AM580gene_exp.diff)

source_name: EB AM580-treated day12 on OP9

value: human EB, CD34+CD38-CD90+CD45+

value: 0.2uM AM580 on OP9 for 12 days


title: EB AM580-treated day12 on OP9, experiment 1 (q7 in the EB_AM580gene_exp.diff)


title: FL-HSPC LKO_infected experiment_3 (LKO in shHOXA7gene_exp.diff)


title: RCShNPCs replicate 2 (R3G)

first: Melissa

middle: Kaye

last: Jones

address: 8700 Beverly Blvd.

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

data_processing:
Raw reads were filtered and trimmed with the FASTX toolkit.
Reads were aligned to the rat reference genome rn5.
FPKM (fragment per kilobase of gene per million reads sequenced) values were calculated with Cufflinks 2.0.8 software (Trapnell et al., 2012).
Genome_build: rn5
Supplementary_files_format_and_content: abundance measurements

organism: Rattus norvegicus

source_name: Retina

extract_protocol:
Neural retinas were isolated from enuclated eyes, and oriented so that only the portion of the retina with hNPCs was used (approximately half of the retina). In animals with sham surgeries, a corresponding half was used. RNA was extracted with the PureLink RNA Mini Kit (Life Technologies).
Libraries were constructed using Ion Total RNA-seq Kit v2 (Life Technologies) per standard protocols.

treatment_protocol: hNPCs were transplanted by subretinal injection at postnatal day 21 (P21) into RCS animals. LE and RCS animals receiving sham surgeries received the same surgery with cell-carrying media only.

value: Royal College of Surgeons

value: Retina

tag: age

value: postnatal day 60


title: Sclero Day 1 Rep 1

description: processed data column: 1_10


title: Sclero Day 1 Rep 2

description: processed data column: 1_11


title: RCShNPCs replicate 1 (R1G)


title: EB DMSO-treated day12 on OP9, experiment 1 (q5 in the EB_AM580gene_exp.diff)

source_name: EB DMSO-treated day12 on OP9


title: NT Kdm4b+Kdm5b 4-cell 1 [RNA-seq]

value: Kdm4b and Kdm5b overexpression

value: nuclear transfer embryo


title: Sclero Day 1 Rep 3

description: processed data column: 1_12


title: FL DMSO-treated day6 on OP9, experiment 2 (q4 in the EB_AM580gene_exp.diff)

source_name: FL DMSO-treated day6 on OP9

value: human fetal liver, CD34+CD38-CD90+CD45+

value: fetal liver-hematopoietic stem/progenitor cell (FL-HSPC)

value: DMSO on OP9 for 6 days


title: FL DMSO-treated day6 on OP9, experiment 1 (q4 in the EB_AM580gene_exp.diff)


title: RCSsham replicate 2 (R4S)


title: RCSsham replicate 1 (R2S)


title: EB AM580-treated day6 on OP9, experiment 1 (q3 in the EB_AM580gene_exp.diff)

source_name: EB AM580-treated day6 on OP9

value: 0.2uM AM580 on OP9 for 6 days


title: NT Kdm4b+Kdm5b 2-cell 6 [RNA-seq]

source_name: NT Kdm4b+Kdm5b 2-cell


title: NT Kdm4b+Kdm5b 2-cell 5 [RNA-seq]


title: EB DMSO-treated day6 on OP9, experiment 1 (q1 in the EB_AM580gene_exp.diff)

source_name: EB DMSO-treated day6 on OP9


title: EB AM580-treated day6 on OP9, experiment 2 (q3 in the EB_AM580gene_exp.diff)


title: EB DMSO-treated day6 on OP9, experiment 2 (q1 in the EB_AM580gene_exp.diff)


title: EB AM580-treated day6 on OP9, experiment 2

data_processing:
library strategy: ATAC-seq
Alignment: Bowtie2 v2.2.5; parameters --local -X 2000 -N 1 --no-mixed
Coverage file: Bamcoverage, Deeptools; parameters default
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, tracks for each of the samples

extract_protocol:
Chromatin was tagmented and DNA extracted (Nextera DNA Library Prep Kit, Illumina) and incubated at 37oC for 30 minutes, (see methods)
Transposed DNA was column purified and used for library amplification with custom made adaptor primers (see primer table) using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs)

tag: molecule subtype

value: Tagmented DNA


title: NT Kdm4b+Kdm5b 2-cell 4 [RNA-seq]


title: NT Kdm4b+Kdm5b 4-cell 2 [RNA-seq]


title: EB DMSO-treated day12 on OP9, experiment 2 (q5 in the EB_AM580gene_exp.diff)


title: NT Kdm4b+Kdm5b 2-cell 3 [RNA-seq]


title: EB AM580-treated day6 on OP9, experiment 1


title: EB DMSO-treated day6 on OP9, experiment 1


title: NT Kdm4b+Kdm5b 2-cell 2 [RNA-seq]


title: EB DMSO-treated day6 on OP9, experiment 2


title: NT Kdm4b+Kdm5b 2-cell 1 [RNA-seq]


title: NT 4-cell arrest in 2-cell stage 6 [RNA-seq]

source_name: NT 4-cell arrest

value: wild type


title: Control - rep1

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
The raw reads were trimmed for an adaptor sequence by cutdapt, and reads less than 17 bases after trimming were discarded. Aligning read to known human miRNAs precursors (miRBase release 20) and counting the aligned read for quantitative miRNA expression were conducted by miRExpress analysis pipline. The -t parameter (alignment identity between query and reference sequences) for miRExpress was set to be 0.9.
Genome_build: GRCh37

source_name: Neuroblastoma cells

growth_protocol: SK-N-BE(2)-C Cells were obtained from ATCC (American Type Culture Collection, Manassas, VA). Cell were grown in DMEM/F12 (Gibco Laboratories, Grand Island, NY) supplemented with 10% fetal bovine serum (Gibco Laboratories) at 37°C and 5% CO2 and routinely passaged when 80% to 90% confluent. All the cells were free of mycoplasma as determined by a PCR-based mycoplasma detection method (MBI Fermentas, Vilnius, Lithuania).

extract_protocol:
After 48 hours of transfection, cells were harvested using 1 ml TRIzol reagent and RNA was extracted TRIzol reagent (Invitrogen) as indicated in the manufacturer's protocol.
The RNA concentration and purity were determined photometrically by measuring absorbance at 260 nm and A260/A280 ratio using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc, Rockland, DE). The RNA integrity was evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). 20 µg of total RNA was used for the library construction following the protocol supplied with the Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA) and the Solexa sequencing was performed by Beijing Genomics Institute (BGI) according to the manufacturer's instructions.

treatment_protocol: Cells (4 × 105) were plated into 6-well plate and transiently transfected with 150 picomoles double-stranded RNA (dsRNA) oligonucleotides against MYCN (Dharmacon, Lafayette, CO, USA; SMARTpool(TM), J-003913-16, 5’-CGAGCUGGGUCACGGAGAU-3’; 5’-GAACCCAGACCUCGAGUUU-3’; 5’- GGACAGUGAGCGUCGCAGA-3’; 5’-CCUCCAUGACAGCGCUAAA-3’). Double stranded oligonucleotide was diluted into 250 μl of serum-free DMEM, mixed with 250 μl serum-free DMEM containing 7.5 microliter of Lipofectamine 2000 reagent (Invitrogen, Carlsbad, CA, USA), and incubated for 20 min at room temperature before being added to the cells growing in 1.5 ml of complete medium.


title: Knockdown of MYCN - rep2


title: Control - rep2


title: LEsham replicate 2 (L2S)

value: Long Evans


title: NT 4-cell arrest in 2-cell stage 5 [RNA-seq]


title: ABL siSMARCA4

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

data_processing:
Sequence reads were aligned to the hg19 genome using TopHat
Coding gene expression levels were called using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: FPKM expression level

source_name: LNCaP-abl

growth_protocol: The prostate cancer cell line LNCaP-abl cells were maintained in phenol-red-free RPMI 1640 medium supplemented with 10% charcoal stripped fetal bovine serum (CDT), 2mM glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin.

extract_protocol:
After 72hrs of siRNA transfection, RNA was extracted using Qiagen Rneasy Mini Kit following manufacturer's instruction
Libraries were prepared according toIllumina TruSeq RNA Sample Prep Kit v2
RNAseq were performed in the platform Hiseq2000.

treatment_protocol: LNCaP-abl cells were transfected with control siRNAs or target gene siRNAs (ON-target smart pool from Thermo Scientifc ) using Lipofectamine RNAiMAX from Life Technologies.

value: LNCaP-abl

value: prostate cancer cell line

tag: passage

tag: transfected with


title: NT 4-cell arrest in 2-cell stage 3 [RNA-seq]


title: ABL siRAD21


title: IgG_ChIP-seq

data_processing:
The 49-nt read were aligned to the human genome GRCh37 using Bowtie 266. Only reads mapped uniquely to the genome were retained for binding-peak identification. The Model-based Analysis of ChIP-seq (MACS version 1.4.2) algorithm67 was used to identify the enriched-regions with the 0.001 p-value cutoff and modified parameter (bw=500).
Genome_build: GRCh37
Supplementary_files_format_and_content: bed files with peak or summit coordinates, text file with peak info

extract_protocol:
The ChIP assay was performed using the EZ-Magna ChIPTM A (Upstate-Millipore, Billerica, MA, USA). Cells were cross-linked in 1% formaldehyde (Sigma-Aldrich, St Louis, MO, USA) for 30 minutes. Nuclear lysates were extracted and the chromatin fraction was sheared to 200- to 500-bp fragments using an ultrasonic probe (Labsonic M, Sartorius, Tagelswangen, Switzerland). Immunoprecipitations were performed using 1 μg of anti-MYCN antibody (Abcam, Cambridge, UK) or 1 μg of anti-mouse IgG1κ antibody (Abcam) as control overnight at 4°C. After washed off unspecific DNA binding, the protein/DNA complexes were eluted and reverse corsslinked to free DNA fragments as described in manual. Purified fragmented DNA was subjected to ChIP-seq analysis for determining MYCN binding regions.
Then DNA fragments 150–400 bp long were gel purified following the adaptor ligation step. The PCR-amplified DNA libraries were quantified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and diluted for cluster generation. The ChIP-seq libraries assayed by single-end sequencing on an Illumina HiSeq platform sequencing in Beijing Genomics Institute (BGI).

value: neuroblastoma

value: IgG (Abcam ab18443)


title: MYCN_ChIP-seq

value: MYCN (Abcam ab16898)


title: Knockdown of MYCN - rep1


title: LEsham replicate 1 (L1S)


title: NT 4-cell arrest in 2-cell stage 4 [RNA-seq]


title: NT 4-cell arrest in 2-cell stage 2 [RNA-seq]


title: ABL siMALAT1


title: Nano_3dpi_B

city: Leiden

first: Wouter

last: Veneman

state: Zuid-Holland

address: Einsteinweg 55

department: Institute Biology Leiden

country: Netherlands

institute: Leiden University

data_processing:
GeneTiles was used for quantification and visualization of the RNAseq data
Bowtie2 is used to align the reads in the fastq file to the genome (obtained from Ensemble). Bowtie2 generates SAM files that contain the reads together with the location on the genome.
Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome, resulting in a sorted BAM file.
The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome, i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file.
Using the available annotation from Ensemble we can search the BAM file for reads within a gene (using exon starting positions and lengths). This is done with a python script. The output of this script is a tab separated file (tsv) containing the read counts per gene.
We used DESeq, an R-script to perform statistical analysis. The DESeq script is used to normalise the reads per gene, based on (divided by) the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P-value, by calculating the dispersion per gene using DESeq. The size factors as well as the P-values are stored in ‘tsv’ files.
Using a script, all tsv files are combined into xlsx files , e.g. per experiment, chromosome, per filtered results of most significant reads or highest ratio between measurement and control.
Genome_build: GRCz10
Supplementary_files_format_and_content: counts

organism: Danio rerio

source_name: Danio rerio embryo 5 days post fertilization

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zebrafish embryos were micro-injected into the yolk (2dpf) with 1nl of  5mg/ml of 700nm red fluorescent polystyrene particles suspended in PVP (Polyvinylpyrrolidone) (n=3), or mock-injected (n=2) containting PVP only or Non-injected as a control (n=3). At 1 and 3 days post injection (3 and 5 days post fertilization) 10 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

tag: sample type

value: Wildtype; injected with 1nl of  5mg/ml of 700nm red fluorescent polystyrene particles into the yolk at 2 dpf; RNA isolated at 5 days post fertilization (= 3dpi timepoint). Biological replica 2

value: embryo


title: NT 4-cell arrest in 2-cell stage 1 [RNA-seq]

tag: development stage


title: Nano_3dpi_C

value: Wildtype; injected with 1nl of  5mg/ml of 700nm red fluorescent polystyrene particles into the yolk at 2 dpf; RNA isolated at 5 days post fertilization (= 3dpi timepoint). Biological replica 3


title: Nano_3dpi_A

value: Wildtype; injected with 1nl of  5mg/ml of 700nm red fluorescent polystyrene particles into the yolk at 2 dpf; RNA isolated at 5 days post fertilization (= 3dpi timepoint). Biological replica 1


title: ABL siKDM1A


title: ABL siFOXM1


title: NT 4-cell arrest 5 [RNA-seq]

tag: genotype/variation

value: nuclear transfer embryo


title: NT 4-cell arrest 3 [RNA-seq]

tag: tissue


title: ABL siPCAT1


title: NT 4-cell arrest 2 [RNA-seq]

tag: strain


title: ABL siEZH2


title: ABL siEED

description: EED

value: siEED


title: NT 4-cell arrest 4 [RNA-seq]


title: ABL siFOXA1


title: Control_3dpi_B

value: Wildtype:non-injected control; RNA isolated at 5 days post fertilization (= 3dpi timepoint). Biological replica 2


title: Mock_3dpi_A

value: Wildtype:mock-injected control with PVP; RNA isolated at 5 days post fertilization (= 3dpi timepoint). Biological replica 1


title: NT 4-cell arrest 1 [RNA-seq]


title: ABL siCTCF

description: CTCF

value: siCTCF


title: Control_3dpi_C

value: Wildtype:non-injected control; RNA isolated at 5 days post fertilization (= 3dpi timepoint). Biological replica 3


title: Control_3dpi_A

value: Wildtype:non-injected control; RNA isolated at 5 days post fertilization (= 3dpi timepoint). Biological replica 1


title: Nano_1dpi_C

source_name: Danio rerio embryo 3 days post fertilization

value: Wildtype; injected with 1nl of  5mg/ml of 700nm red fluorescent polystyrene particles into the yolk at 2 dpf; RNA isolated at 3 days post fertilization (= 1dpi timepoint). Biological replica 3


title: ABL siControl2

value: LNCaP-abl


title: NT 2-cell arrest 8 [RNA-seq]

source_name: NT 2-cell arrest

value: wild type


title: NT 2-cell arrest 7 [RNA-seq]


title: WT 2-cell 3 [RNA-seq]

source_name: WT 2-cell

value: normal embryo


title: ABL siBRCA1

value: prostate cancer cell line


title: ABL siBRD4


title: NT 2-cell arrest 6 [RNA-seq]


title: NT 2-cell arrest 5 [RNA-seq]


title: ABL siBRCA2


title: Mock_3dpi_B

value: Wildtype:mock-injected control with PVP; RNA isolated at 5 days post fertilization (= 3dpi timepoint). Biological replica 2


title: Nano_1dpi_A

value: Wildtype; injected with 1nl of  5mg/ml of 700nm red fluorescent polystyrene particles into the yolk at 2 dpf; RNA isolated at 3 days post fertilization (= 1dpi timepoint). Biological replica 1


title: NT 2-cell arrest 4 [RNA-seq]


title: Control_1dpi_C

value: Wildtype:non-injected control; RNA isolated at 3 days post fertilization (= 1dpi timepoint). Biological replica 1

value: embryo


title: Control_1dpi_B

value: Wildtype:non-injected control; RNA isolated at 3 days post fertilization (= 1dpi timepoint). Biological replica 2


title: Mock_1dpi_A

value: Wildtype:mock-injected control with PVP; RNA isolated at 3 days post fertilization (= 1dpi timepoint). Biological replica 1


title: ABL siAR

description: AR

value: siAR


title: NT 2-cell arrest 3 [RNA-seq]

value: nuclear transfer embryo


title: Nano_1dpi_B

value: Wildtype; injected with 1nl of  5mg/ml of 700nm red fluorescent polystyrene particles into the yolk at 2 dpf; RNA isolated at 3 days post fertilization (= 1dpi timepoint). Biological replica 2


title: NT 2-cell arrest 1 [RNA-seq]


title: Mix Day 15 Rep 1

description: processed data column: 15_7

organism:
Sclerotinia sclerotiorum
Trichoderma hamatum GD12

source_name: Mixed species soil sample


title: Mock_1dpi_B

value: Wildtype:mock-injected control with PVP; RNA isolated at 3 days post fertilization (= 1dpi timepoint). Biological replica 2


title: Mix Day 15 Rep 3

description: processed data column: 15_9


title: H3K27ac_siRAD21

description: H3K27ac ChIP

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using BWA with default parameters
Bigwig traces were generated using MACS2 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files containing genomic wiggle traces

source_name: prostate cancer

growth_protocol: LNCaP-abl cells were maintained in phenol red-free RPMI 1640 medium with 10% charcoal/dextran-treated FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Library construction was performed using the ChIP-seq DNA sample Prep Kit (Illumina) according to the manufacture’s instruction.

treatment_protocol: Cells were transfected with 20nM siRNA oligos by RNAiMax reagent (Invitrogen) in 12 well plates according to manufacturer’s instructions.

tag: transfection

tag: antibody


title: H3K27ac_siSMARCA4

description: H3K27ac ChIP


title: GD12 Day 15 Rep 3

description: processed data column: 15_6

organism: Trichoderma hamatum GD12

tag: isolate


title: NT 2-cell arrest 2 [RNA-seq]


title: Mix Day 10 Rep 3

description:
processed data column: 10_9
*Sample removed from analysis due to unexpected alignment profile


title: mot1 spt16 MNase rep 1

first: David

last: Auble

address: Box 800733 Jordan Hall University of Virginia Health System

department: Biochemistry and Molecular Genetics

data_processing:
Reads were aligned to the SacCer3 reference genome using bowtie2-2.2.6 with default mapping settings.
Unmapped reads and reads with mapping quality scores < 30 were removed from the bowtie2-generated bam file using samtools-0.1.19
For viewing the data in IGV, bam files were converted to BigWig by first sorting and indexing using samtools, then creating .bed and .cov files using BEDTools 2.18.2, and finally converting the .cov files to BigWig using the bedGraphToBigWig converter.
Gene average plots were produced using ngs.plot-2.4.7
Nucleosome mapping and differential nucleosome analyses were performed using the dpos tool in the DANPOS-2.2.2 package with default settings.
Genome_build: SacCer3
Supplementary_files_format_and_content: BigWig files were generated as described above.

organism: Saccharomyces cerevisiae

source_name: DNA from mot1-42 spt16-197

growth_protocol: Yeast cells were grown in YPD media at 30°C to an O.D. of ~1.0, except the double mutant was grown at 25°C to an OD of ~1.0.

extract_protocol:
Cells were lysed, sonicated, and clarified by centrifugation.  Lysates were incubated with antibody for either myc-tagged protein or histone H3.  Immunoprecipitated samples were washed twice each with lysis buffer (140 mM NaCl), lysis buffer (500 mM NaCl), LiCl wash buffer, and 1X TE.  DNA was eluted from beads in ChIP elution buffer and cross-links were reversed overnight.  DNA was then purified using Qiagen PCR purification kit.
Libraries were constructed using TruSeq ChIP Library Prep Kit from Illumina (IP-202-1012) according to manufacturer's instructions and are briefly described here.  Purified DNA was end repaired, and 3' ends were adenylated.  Adapters were ligated to adenylated ends and products were gel purified.  DNA with adapters was PCR enriched, quantified via Qubit, and validated using Bioanalyer.

treatment_protocol: Cells were shifted to 35°C for 45 minutes, then crosslinked with a final volume of 1% formaldehyde for 15 minutes, and quenched with 125 mM glycine for 5 minutes.

tag: strain background

tag: chip antibody


title: Mix Day 10 Rep 2

description: processed data column: 10_8


title: Control_1dpi_A


title: spt16 MNase rep 2

source_name: DNA from spt16-197


title: mot1 spt16 MNase rep 2


title: H3K27ac_siPCAT6

description: H3K27ac ChIP

tag: cell line


title: Mix Day 15 Rep 2

description: processed data column: 15_8


title: H3K27ac_siMALAT1

description: H3K27ac ChIP


title: Mix Day 10 Rep 1

description: processed data column: 10_7


title: H3K27ac_siKDM1A

description: H3K27ac ChIP


title: NT Kdm4b+Kdm5b 4-cell 4 [RNA-seq]

source_name: NT Kdm4b+Kdm5b 4-cell

value: Kdm4b and Kdm5b overexpression


title: GD12 Day 7 Rep 2

description: processed data column: 7_5


title: spt16 MNase rep 1


title: H3K27ac_siEZH2

description: H3K27ac ChIP


title: GD12 Day 15 Rep 2

description: processed data column: 15_5


title: H3K27ac_siFOXM1

description: H3K27ac ChIP


title: FOXA1

description: FOXA1 ChIP


title: Mix Day 4 Rep 3

description: processed data column: 4_9


title: GD12 Day 15 Rep 1

description: processed data column: 15_4


title: Mix Day 4 Rep 2

description: processed data column: 4_8


title: H3K27ac_siPCAT1

description: H3K27ac ChIP


title: Mot1 IP spt16 rep 1

source_name: DNA from MOT1-myc spt16-197


title: GD12 Day 10 Rep 2

description: processed data column: 10_6


title: H3K27ac_siFOXF1

description: H3K27ac ChIP


title: mot1 MNase rep 1

source_name: DNA from mot1-42


title: GD12 Day 4 Rep 3

description: processed data column: 4_6


title: H3K27ac_siCTCF

description: H3K27ac ChIP

value: siCTCF


title: GD12 Day 10 Rep 1

description: processed data column: 10_5


title: WT MNase rep 2

source_name: DNA from MOT1-WT


title: WT MNase rep 1


title: H3K27ac_siEED

description: H3K27ac ChIP

value: siEED


title: Mix Day 7 Rep 2

description: processed data column: 7_8


title: GD12 Day 7 Rep 1

description: processed data column: 7_4


title: H3K27ac_siFOXA1

description: H3K27ac ChIP

value: LNCaP-abl


title: Mix Day 7 Rep 3

description: processed data column: 7_9


title: Mot1 IP spt16 rep 2


title: H3K27ac_siE2F1

description: H3K27ac ChIP


title: Mot1 input

source_name: DNA from MOT1-myc

value: none (input)


title: mot1 MNase rep 2


title: Mix Day 7 Rep 1

description: processed data column: 7_7


title: Mix Day 4 Rep 1

description: processed data column: 4_7


title: H3K27ac_siCon3

description: H3K27ac ChIP


title: GD12 Day 4 Rep 1

description: processed data column: 4_4


title: Mix Day 2 Rep 3

description: processed data column: 2_9


title: Mot1 IP WT rep 2


title: H3K27ac_siCon1

description: H3K27ac ChIP


title: Mot1 IP WT rep 1


title: Mix Day 2 Rep 2

description: processed data column: 2_8


title: Spt16 IP mot1 rep 2

source_name: DNA from SPT16-myc mot1-42


title: GD12 Day 2 Rep 2

description: processed data column: 2_5


title: Mix Day 2 Rep 1

description: processed data column: 2_7


title: H3K27ac_siBRD4

description: H3K27ac ChIP


title: H3K27ac_siCon2

description: H3K27ac ChIP


title: GD12 Day 2 Rep 1

description: processed data column: 2_4


title: GD12 Day 4 Rep 2

description: processed data column: 4_5


title: Mix Day 1 Rep 3

description: processed data column: 1_9


title: H3K27ac_siBRCA2

description: H3K27ac ChIP


title: Mix Day 1 Rep 2

description: processed data column: 1_8


title: H3K27ac_siBRCA1

description: H3K27ac ChIP


title: GD12 Day 1 Rep 3

description: processed data column: 1_6


title: GD12 Day 1 Rep 2

description: processed data column: 1_5


title: Mix Day 1 Rep 1

description: processed data column: 1_7


title: Spt16 input

source_name: DNA from SPT16-myc


title: Spt16 IP WT rep 2


title: H3K27ac_siAR

description: H3K27ac ChIP


title: Spt16 IP WT rep 1


title: GD12 Day 1 Rep 1

description: processed data column: 1_4


title: GD12 Day 2 Rep 3

description: processed data column: 2_6


title: Spt16 IP mot1 rep 1


title: 27me3 pri-NPC

status: Public on May 15 2016

city: SAN FRANCISCO

first: Sheng

last: Ding

state: California

address: 1650 Owens Street

department: Gladstone Institute of Cardiovascular Disease

institute: THE J DAVID GLADSTONE INSTITUTES

data_processing:
base-calling was done using CASAVA 1.8.4.
For the histone marker ChIP-seq data: the alignment was done using bowtie (version 1.1.0) with human genome build mm10, reporting only reads with unique genome alignments. The result was then filtered by removed potential PCR duplications with with samtools (version 0.1.19)
Read Intensity of Histone markers  were calculated with bedtools multicov, then normalized by the total number of reads for each samples, result were mered into one single file
Genome_build: mm10
Supplementary_files_format_and_content: histone marker excel file contains the normalized intensity around the TSS of genes (-2kb to +3kb)

source_name: H3K27me3 of pri-NPC

growth_protocol: tdMEFs were cultured in MEF medium (Dulbecco’s modified Eagle’s medium supplemented with 10 % fetal bovine serum, 0.1 mM nonessential amino acids, and 2 mM Glutamax) in 5 % CO2 and 20 % O2 at 37 °C.

extract_protocol:
Cells at indicated time points were cross-linked by 1% formaldehyde, quenched with 0.125 M glycine. The chromatin DNA was extracted and sheared into 200-400 bp, and immuoprecipitated using a EZ-ChIP kit (Millipore, 17-371), and indicated antibodies.
Barcoded ChIP-Seq libraries were made from 1 to 10 ng of chromatin immunoprecipitated DNA (ChIP-DNA) using the NuGen Ovation Ultralow V2 kit. 13 cycles were used for PCR amplification of the libraries. Amplified libraries were checked for adapter artifacts by Agilent Bioanalyzer using DNA high sensitivity reagents and chips (Agilent). All libraries were quantified by qPCR using an Illumina Library Quantification kit (KAPA Biosystems). Libraries were pooled in equimolar amounts and run on the HiSeq 2500 sequencer with a single read 50 cycle run (Illumina).

treatment_protocol: M9-induced neural reprogramming was performed in M9 medium (50% Neural basal, 50% DMEM/F12/Glutamax, 1xN2, 1xB27 without vitamin A, 0.075% BSA, 0.1 mM nonessential amino acids, CHIR99021 3 mM, LDN193189 100 nM, A83-01 0.5 mM, Hh-Ag1.5 0.5 mM, retinoic acid 1 mM, SMER28 10 mM, RG108 10 mM, Parnate 2 mM, bFGF 10 ng/ml) at 5% O2 and 5% CO2 incubator at 37°C.

tag: cell type

value: pri-NPC


title: Sus1-WT heat shock rep2

city: Valencia

first: Susana

last: Rodríguez-Navarro

address: Eduardo Primo Yúfera 3

country: Spain

institute: Centro de Investigación Príncipe Felipe (CIPF)

description:
Replicate 2
library strategy: ChIP-exo

data_processing:
For single end reads from HiSeq, basecalls were performed using CASAVA version 1.7 and for paired end reads from NextSeq, basecalls were performed using Bcl2fq version 2.15
ChIP-exo reads were aligned to the sacCer3 genome assembly using BWA  (Version: 0.6.2 for single end reads and Version: 0.7.9a for paired end reads) with default options. Non-uniquely mapped reads were filtered out in order to remove the reads with low mapping quality.
Genome_build: sacCer3

source_name: Wild type yeast cells

growth_protocol: Normal growth conditions were 25°C in YPD media with shaking at 250 rpm. Yeast cells were grown to mid-log phase (O.D 600 nm of  0.8), and fixed with 1% formaldehyde. Heat shocked samples were abruptly shifted to 37˚C with hot media, for 15 min, then shifted back to 25˚C for crosslinking (Zanton and Pugh, 2004).

extract_protocol:
Cross-linked chromatins were sheared using a sonicator, and immunoprecipitated using the following beads or anti-body: Sepharose to pull down all myc-tagged proteins used in this study. Mock ChIP DNA was prepared by immunoprecipitation with myc-antibody in the wild type strain with no myc-tagged protein expression.
ChIP-exo experiments were carried out essentially as described (PMID: 22258509). This included an immunoprecipitation step with magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and lambda and recJ exonuclease digestion on the beads. After elution, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina adaptor was then ligated, and the products PCR amplified and gel-purified.

value: wild type

tag: temperature

value: myc

tag: antibody vendor/catalog#

value: Santa Cruz Biotechnology, catalog #:sc-40


title: no-tag heat shock rep1

description:
Replicate 1
library strategy: ChIP-exo


title: Sus1-spt7-deletion heat shock rep2

description:
Replicate 2
library strategy: ChIP-exo


title: Sus1-WT mock rep2

description:
Replicate 2
library strategy: ChIP-exo


title: 27Ac pri-NPC

source_name: H3K27Ac of pri-NPC


title: no-tag mock rep2

description:
Replicate 2
library strategy: ChIP-exo


title: Sus1-spt8-deletion heat shock rep2

description:
Replicate 2
library strategy: ChIP-exo


title: Sus1-spt8-deletion mock rep2

description:
Replicate 2
library strategy: ChIP-exo


title: 4me1 pri-NPC

source_name: H3K4me1 of pri-NPC


title: Input pri-NPC

source_name: Input genomic DNA of pri-NPCs


title: Sus1-spt7-deletion mock rep2

description:
Replicate 2
library strategy: ChIP-exo


title: no-tag heat shock rep2

description:
Replicate 2
library strategy: ChIP-exo


title: 4me3 pri-NPC

source_name: H3K4me3 of pri-NPC


title: no-tag mock rep1

description:
Replicate 1
library strategy: ChIP-exo


title: 27me3 ciNSLC

source_name: H3K27me3 of ciNSLCs

value: ciNSLCs


title: 27Ac ciNSLC

source_name: H3K27Ac of ciNSLCs


title: Sus1-spt8-deletion heat shock rep1

description:
Replicate 1
library strategy: ChIP-exo


title: 4me3 ciNSLC

source_name: H3K4me3 of ciNSLCs


title: Sus1-spt8-deletion mock rep1

description:
Replicate 1
library strategy: ChIP-exo


title: Sus1-spt7-deletion heat shock rep1

description:
Replicate 1
library strategy: ChIP-exo


title: 4me1 ciNSLC

source_name: H3K4me1 of ciNSLCs


title: Input ciNSLC

source_name: Input genomic DNA of ciNSLCs


title: in vitro, KO POVPC Hypoxia 1

first: Gary

middle: K

last: Owens

address: 415 Lane Road MR5 Building Room 1322

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121647

data_processing:
Basecalls performed using CASAVA
Data were aligned to the mm9 genome using STAR version 3.0
Aligned reads were counted against genes from the UCSC mm9 annotation using the featureCounts from the SubRead package
Data were normalized for library size using the DESeq2 median ration normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R
Genome_build: mm9
Supplementary_files_format_and_content: Counts of reads aligning to genes from the mm9 annotation as output from featureCounts

source_name: Primary smooth muscle cell culture

extract_protocol:
For in vivo, BCA were removed and flash frozen and RNA was harvested using standar Trizol reagent/protocol.
For in vitro, RNA was harvested using standard Trizol reagent/protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
For in vivo, animals were maintened in a Western Diet for 18 weeks
For in vitro, cell

value: Smooth Muscle Cells

tag: genotype

tag: treatment

value: POVPC

tag: oxygen levels

value: Hypoxia (1% O2)


title: in vitro, KO Vehicle Hypoxia 3

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121646

value: Vehicle


title: in vitro, KO POVPC Hypoxia 2

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121648


title: Sus1-spt7-deletion mock rep1

description:
Replicate 1
library strategy: ChIP-exo


title: 27Ac D8

source_name: H3K27Ac at day 8 of M9-induced reprogramming

value: tdMEFs at day 8 of reprogramming


title: in vitro, KO Vehicle Hypoxia 2

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121645


title: 27me3 D8

source_name: H3K27me3 at day 8 of M9-induced reprogramming


title: in vitro, KO Vehicle Hypoxia 1

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121644


title: in vitro, WT Vehicle Hypoxia 3

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121640


title: Sus1-WT heat shock rep1

description:
Replicate 1
library strategy: ChIP-exo


title: in vitro, WT POVPC Hypoxia 2

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121642


title: in vitro, WT Vehicle Hypoxia 2

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121639


title: in vitro, WT POVPC Hypoxia 3

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121643


title: 4me3 D8

source_name: H3K4me3 at day 8 of M9-induced reprogramming


title: in vitro, WT Vehicle Hypoxia 1

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121638


title: in vitro, KO POVPC Hypoxia 3

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121649


title: 4me1 D8

source_name: H3K4me1 at day 8 of M9-induced reprogramming


title: Sus1-WT mock rep1

description:
Replicate 1
library strategy: ChIP-exo


title: 11731

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

data_processing:
The raw sequence reads (fastq) were quality checked using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) followed by a windowed adaptive trimming step for base quality of the reads. The quality trimming was performed using Sickle (https://github.com/najoshi/sickle) with default parameters for paired-end reads.  The mean insert size was averaged over first million reads alignments using a python tool getinsersize.py (https://gist.github.com/davidliwei/2323462).
The trimmed paired-end reads were then mapped to the bovine reference genome UMD3.1 using SubRead aligner (Liao et al. 2013).
The number of reads mapped to the exon sequences of annotated genes was determined using FeatureCounts (Liao et al. 2014).
Genes significantly differentially expressed between samples were determined by fitting the read counts to a generalized linear model implemented in edgeRrobust (Zhou et al. 2014 ).
The length-normalized FPKM (fragment per kilobases per million reads) was determined from the sum of exon lengths of each gene.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The file "Processed_Data.txt" contatins both read counts and FPKM values of genes for all samples. The read counts were used in EdgeR to determine significant difference in gene expression between fertility classes.

molecule: polyA RNA

organism: Bos taurus

source_name: endometrium

growth_protocol: All females received PGF on day -18 and GnRH administration on day -15. On day -9, all females received an intravaginal progesterone insert (CIDR) and an injection of 2.5 mg estradiol and 50 mg progesterone. CIDRs were removed and PGF administered on day -2.5. Recipient heifers that did not exhibit estrus by day 0 received GnRH and estrogen (1 mg estradiol benzoate). On day 7, each heifer received an in vivo-produced embryo placed in the uterine horn ipsilateral to the ovary containing a corpus luteum. Following uterine flush, an endometrial biopsy was collected near the greater curvature of the uterine horn ipsilateral to the ovary containing the corpus luteum. Endometrial tissue was obtained using Jackson uterine biopsy forceps (GerMedUSA Inc., Garden City Park, NY).

extract_protocol:
Qiagen Rneasy Mini Kit
Illumina TruSeq mRNA stranded

tag: ferility class

value: Infertile

tag: day of pregnancy


title: 11860


title: in vitro, KO POVPC Normoxia 3

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121637

value: Normoxia


title: in vitro, KO POVPC Normoxia 2

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121636


title: 11879


title: 11687


title: Input D8

source_name: Input genomic DNA of tdMEFs at day 8 of M9-induced reprogramming


title: 11727


title: 27me3 D4

source_name: H3K27me3 at day 4 of M9-induced reprogramming

value: tdMEFs at day 4 of reprogramming


title: 4me3 D4

source_name: H3K4me3 at day 4 of M9-induced reprogramming


title: 11952

value: Sub-fertile


title: in vitro, KO Vehicle Normoxia 3

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121634


title: 4me1 D4

source_name: H3K4me1 at day 4 of M9-induced reprogramming


title: in vitro, WT POVPC Hypoxia 1

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121641


title: 11949


title: Input D4

source_name: Input genomic DNA of tdMEFs at day 4 of M9-induced reprogramming


title: 27Ac D4

source_name: H3K27Ac at day 4 of M9-induced reprogramming


title: 27Ac D0

source_name: H3K27Ac at day 0 of M9-induced reprogramming

value: tdMEFs at day 0 of reprogramming


title: 11778


title: 27me3 D0

source_name: H3K27me3 at day 0 of M9-induced reprogramming


title: 11782


title: in vitro, KO Vehicle Normoxia 2

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121633


title: in vitro, WT POVPC Normoxia 3

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121631


title: 4me3 D0

source_name: H3K4me3 at day 0 of M9-induced reprogramming


title: in vitro, KO Vehicle Normoxia 1

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121632


title: 11690


title: 11981

value: High-fertile


title: in vitro, WT POVPC Normoxia 1

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121629


title: Input D0

source_name: Input genomic DNA of tdMEFs at day 0 of M9-induced reprogramming


title: Gli2 pri-NPC

data_processing:
base-calling was done using CASAVA 1.8.4.
1. Reads are trimmed using the fastq-mcf program
2. The filtered reads are analyzed using the Fastqc program
3. The reads are aligned to the genome mm10 using bowtie2
4. Samtools is used to keep only the reads that do not map uniquely to the genome (mapq score >= 30)
5, bam2bed is used to convert bam files into bed files
6. Normalized Read intensity: The genome is divided into 20bp bins. The tag density is defined as the number of tags that map to within 75bp of each genomic bin. Tag density was then normalized according to method: ENCODE best practices; Landt et al., Genome Research 2012; (http://genome.cshlp.org/content/22/9/1813.full)
7. Peak Calling by comparing the normalized intensity with background tags (Paige et al., Cell 2012; (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462257/)). Enriched bins were merged.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized intensity of the regions with at least one peak in any of the time points from Elk1 ChIP or Gli2 ChIP

source_name: Gli2 chromatin binding in pri-NPC

value: Gli2 antibody (Abcam, 26056, lot GR223520-2)


title: Gli2 ciNSLCs

source_name: Gli2 chromatin binding in ciNSLCs


title: in vitro, WT Vehicle Normoxia 2

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121627

source_name: Primary smooth muscle cell culture


title: in vitro, WT POVPC Normoxia 2

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121630


title: 11912


title: in vitro, WT Vehicle Normoxia 3

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121628


title: in vitro, WT Vehicle Normoxia 1

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121626


title: 11753


title: 4me1 D0

source_name: H3K4me1 at day 0 of M9-induced reprogramming


title: 11976


title: 11704


title: Gli2 D8

source_name: Gli2 chromatin binding at day 8 of M9-induced reprogramming


title: in vivo, WT 4

description:
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60375

source_name: Atherosclerosis lesion

value: Mixture of cell types (SMC, Epithelial, Macrophage, others)

value: Western Diet


title: in vitro, KO POVPC Normoxia 1

description:
oct4-in-vitro-rnaseq-rawcounts.txt
oct4-in-vitro-rnaseq-counts-summary.txt
SL121635


title: in vivo, WT 3

description:
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60374

value: wild type


title: Gli2 D4

source_name: Gli2 chromatin binding at day 4 of M9-induced reprogramming


title: Gli2 D0

source_name: Gli2 chromatin binding at day 0 of M9-induced reprogramming


title: in vivo, WT 2

description:
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60373


title: Elk1 pri-NPC

source_name: Elk1 chromatin binding in pri-NPC

value: pri-NPC

value: Elk1 antibody (Epitomics, 1277-1, lot GR106696-8)


title: in vivo, KO 3

description:
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60370


title: Elk1 ciNSLCs

source_name: Elk1 chromatin binding in ciNSLCs

value: ciNSLCs


title: in vivo, KO 4

description:
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60371


title: Elk1 D8

source_name: Elk1 chromatin binding at day 8 of M9-induced reprogramming


title: in vivo, KO 2

description:
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60369


title: Elk1 D4

source_name: Elk1 chromatin binding at day 4 of M9-induced reprogramming


title: Elk1 D0

source_name: Elk1 chromatin binding at day 0 of M9-induced reprogramming


title: Sus1-spt8-deletion mock rep3

description:
Replicate 3
library strategy: ChIP-exo

source_name: Wild type yeast cells

tag: genotype/variation

value: myc

value: Santa Cruz Biotechnology, catalog #:sc-40


title: in vivo, KO 1

description:
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60368


title: Sus1-spt8-deletion heat shock rep3

description:
Replicate 3
library strategy: ChIP-exo


title: RMS13 DMSO MAL3-101 9 hour repl. A

city: San Francisco

first: Amit

middle: J

last: Sabnis

address: 1550 4th Street

institute: University of California, San Francisco

description: DMSO treatment x 9 hours

data_processing:
Alignment to NCBI build 37 (hg19) of the human genome with RSEM
Differential Expression analysis by DESeq
Genome_build: hg19
Supplementary_files_format_and_content: DESeq expression values

source_name: Rhabdomyosarcoma Cell Line

growth_protocol: RPMI 1640 with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using an RNEasy kit by Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols and a TruSeq RNA sample preparation kit
Paired-end RNASeq

treatment_protocol: 10 micromolar MAL3-101 or DMSO treatment for 9 hours

tag: biomaterial provider

value: ATCC


title: RMS13-R 10 uM MAL3-101 9 hour repl. A

description: Derived resistance to MAL3-101; 10 micromolar MAL3-101 treatment x9 hours


title: RMS13-R 10 uM MAL3-101 9 hour repl. B


title: RMS13 10 uM MAL3-101 9 hour repl. A

description: 10 micromolar MAL3-101 treatment x9 hours


title: Sus1-spt7-deletion mock rep3

description:
Replicate 3
library strategy: ChIP-exo

tag: strain


title: RMS13 DMSO MAL3-101 9 hour repl. B

description: DMSO treatment x 9 hours


title: Sus1-spt7-deletion heat shock rep3

description:
Replicate 3
library strategy: ChIP-exo


title: RMS13 10 uM MAL3-101 9 hour repl. B


title: Sus1-WT mock rep3

description:
Replicate 3
library strategy: ChIP-exo


title: Mse-2 RNA

status: Public on May 14 2016

city: Lincoln

first: Paul

last: Blum

state: NE

address: 1901 Vine St.

department: School of Biological Sciences

institute: University of Nebraska-Lincoln

data_processing:
Alignment of reads to genome using TopHat
Gene counts generated using HTSeq
Gene expression analysis and normalization using DESeq2
Genome_build: NC_009440.1 Metallosphaera sedula
Supplementary_files_format_and_content: excel files with non-normalized read count or normalized read count.

organism: Metallosphaera sedula

growth_protocol: Metallosphaera sedula and its derivative were grown in basal salts medium as modified by Brock. Complex medium contained tryptone 0.2% (w/v) and the medium was adjusted to the desired pH using sulfuric acid. All cultures were incubated at 80°C in glass screw-capped flasks with aeration in orbital baths. Planktonic growth was monitored by light absorption at a wavelength of 540 nanometers using a Cary 50 spectrophotometer.

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction
Libraries were prepared according to Illumina's instructions

value: DSM 5348T

tag: growth ph


title: Mse-1 RNA

source_name: DSM 5348T_pH2


title: Sus1-WT heat shock rep3

description:
Replicate 3
library strategy: ChIP-exo


title: Adult CNS

city: Denver

first: Scott

middle: A

last: Barbee

state: CO

address: 2190 E. ILIFF Ave.

department: Biological Sciences

institute: University of Denver

data_processing:
Illumina Casava v1.8 software was used for basecalling and de-multiplexing.
For identifying known miRNAs, sequence reads were trimmed for adapter sequences and mapped to known Drosophila miRNAs (miRBase v20) using the CLC Genomics Workbench v7.0 small RNA workflow. Parameters used were: miR length = 18-27;  min reads = 1.
For identifying novel miRNAs, sequence reads were trimmed for adapter sequences and mapped to the Drosophila genome (UCSC assembly dm3) using miRDeep* (An et al. Nucleic Acids Research 2013). Parameters used were: miR length = 18 to 23; min phred = 20; max multimap = 101; min reads = 5; min score = -10.
Anaylsis of differential known miRNA expression including statisitical analysis was done using normlized miRNA counts (in RPM) in CLC Genomics Workbench v7.0. Kal's test (Kal et al. Mol Biol Cell 1999) was used to calculate Bonferroni corrected p-values.
Genome_build: miRBase v20; Release 5
Supplementary_files_format_and_content: Excel spreadsheets including miRNA abundance measurements (normalized to RPM), novel miRNAs, and analysis of differential miRNA expression with statistics.

organism: Drosophila melanogaster

source_name: Adult brain w/antennal lobes

growth_protocol: Flies were grown on standard Bloomington media at 24 C in a humidified diurnal incubator (BioCold). For larval CNS collection, flies were grown in vials initially containing 15 females  and 5 males (P0). Ventral ganlia (including the optic lobes but not the eye imaginal discs) were explanted from wandering third instar larvae (F1). For adult brain collection, remaining larvae in these vials were allowed to pupate and brains explanted from adults collected 3-5 days post-eclosion (F1). In both cases, the male:female ratio was approximately 50:50.

extract_protocol:
For each sample, tissues were explanted from ~100 animals by microdissiction and immediately transferred to ice-cold Trizol reagent (Life Technologies). Total RNA was extracted using Trizol reagent and standard protocols.
Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of both sequencing libraries. Indexes RPI4 and RPI5 were added to adult and larval small RNAs (respectively) for multiplex sequencing. Small RNA libraries were prepared using standard Illumina protocols.

tag: tissue

value: brain (w/antennal lobes)

tag: developmental stage

value: adult

tag: age

value: 3-5 days post-eclosion


title: Larval CNS

source_name: Larval ventral ganglion w/optic lobes

value: brain (ventral ganglion w/optic lobes)

value: larvae

value: third instar


title: genomic DNA from mycelium of cordyceps militaris

status: Public on May 13 2016

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

data_processing:
bisulfite-converted DNA
The resultant DNAs were applied to paired-end sequencing using an ultrahigh-throughput Illumina Genetic Analyzer (GA2)
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle
All clean BS-Seq reads were mapped to the genome using the BSMAP aligner
Genome_build: CM01
Supplementary_files_format_and_content: cytosine type: CG, CHG or CHH

organism: Cordyceps militaris

extract_protocol:
C. militaris fungus were ground into powder in liquid nitrogen,Powder was used to isolate nuclear proteins with EpiQuik™ Nuclear Extraction Kit I
DNA was fragmented by sonication with a Diagenome sonicator to a mean size of approximately 250 bp, followed by DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptors according to the manufacturer’s instructions (Illumina).

value: asexual developmental stage


title: SARC M-1 RNA

source_name: SARC M-1_pH0.95

value: SARC M-1


title: in vivo, WT 1

description:
oct4-atherosclerosis-in-vivo-rnaseq-rawcounts.txt
oct4-atherosclerosis-in-vivo-rnaseq-summary.txt
SL60372

value: Mixture of cell types (SMC, Epithelial, Macrophage, others)

value: Western Diet


title: Input_DNA_H3.3K36M

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

description: 5% input DNA

data_processing:
Reads that passed the quality score were aligned using bowtie 1.0.0 with default parameters
Peaks were called using mosaics (threshold = 20, FDR= 0.05, maxgap = 10000bp, minsize = 5000bp, binSize= 200bp, two component model, Input-Only analysis)
RPKM-normalized read intensities in the peaks were determined for the H3.3WT and H3.3K36M samples
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated file containing genomic coordinates for HA-tagged H3.3/H3.1 K36M peaks
Supplementary_files_format_and_content: tab-separated file containing RPKM enrichment of H3.1WT, H3.1K36M, H3.3WT and H3.3K36M in genomic bins (10000 bp each)

source_name: C3H10T1/2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, CellGro).

extract_protocol:
~2x10^7 cells were fixed with 1% formaldehyde for 10 min at room temperature and then quenched with 125 mM glycine for 5 min. Cells were then lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl) and sonicated for 1 h with Bioruptor (Diagenode) to obtain mononucleosomes. After centrifugation, the lysates were diluted with dilution buffer (167 mM NaCl, 0.01% SDS, 1.1% TritonX-100, 1.2 mM EDTA, 16.7 mM Tris-HCl) and incubated with αCbx2 (Active Motif, 39663) antibody bound to 75 μl protein A Dynal magnetic beads (Invitrogen) and incubated overnight at 4°C, with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). ChIP DNA was eluted, treated with Proteinase K (Roche) and recovered using Qiagen PCR purification kit.
libraries were prepared according to the Illumina TruSeq protocol

value: C3H embryo-derived mesenchymal progenitor cells

value: Stably expressing FLAG-HA-tagged H3.3K36M

tag: passages

value: Passage 10-15


title: genomic DNA from fruitingbody of cordyceps militaris

source_name: NF

value: sexual developmental stage


title: H3.1K36M-HA_ChIPseq_H3.3K36M

description: ChIP-DNA using HA antibody (Biolegend, catalog number 901501, lot number B201938)


title: Input_DNA_H3.1WT

description: 5% input DNA

value: Stably expressing FLAG-HA-tagged wildtype H3.1


title: Cbx2_ChIPseq_H3.3K36M

description: ChIP-DNA using Cbx2 antibody Bethyl Laboratories, catalog number A302-524A)

data_processing:
Reads that passed the quality score were aligned using bowtie 1.0.0 with default parameters
Peaks were called using mosaics (threshold = 20, FDR= 0.05, maxgap = 10000bp, minsize = 5000bp, binSize= 200bp, two component model, Input-Only analysis)
RPKM-normalized read intensities in the peaks were determined for the H3.3WT and H3.3K36M samples
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated file containing genomic coordinates for Cbx2 peaks and rpkm-normalized read-counts for H3.3WT and H3.3K36M samples for each peak

value: Stably expressing FLAG-HA-tagged wildtype H3.3


title: H3.1WT-HA_ChIPseq_H3.3WT


title: H3.1K36M-HA_ChIPseq_H3.1K36M

value: Stably expressing FLAG-HA-tagged H3.1K36M


title: Input_DNA_H3.1K36M

description: 5% input DNA


title: RNA_siRNA_Ring1a-Ring1b_2

data_processing:
Reads were aligned using bowtie 1.0.0 with default parameters
Expression for annotated refseq genes was determined using RSEM 1.2.12 with default parameters
the data-matrix was normalized by median-normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab separated files containing median normalized 'expected-counts' for all genes and genes with >4x differential expression

extract_protocol:
RNA was isolated using Trizol (Invitrogen).
libraries were prepared according to the Illumina TruSeq protocol

treatment_protocol: 2x10^6 H3.3K36M cells were mixed with Matrigel and injected subcutaneously into both flanks of 6-8 weeks old athymic female SCID mice. Tumors were harvested 5-6 weeks post-injection.

value: C3H embryo-derived mesenchymal multipotent cells

value: Parental Cells treated with siRNAs against Ring1a and Ring1b

tag: passage


title: Input_DNA_H3.3WT

description: 5% input DNA

tag: cell type


title: RNA_control_siRNA_3

value: Parental Cells treated with scramble siRNA


title: RNA_siRNA_Ring1a-Ring1b_1


title: Input_DNA_H3.3WT

description: 5% input DNA


title: RNA_control_siRNA_1


title: RNA_control_siRNA_2


title: H3K36me3_ChIPseq H3.3K36M

description:
ChIP-DNA
Peaks_K36me3_RxNormalizedReads

data_processing:
Reads that passed the quality score were aligned to mm9_dm6 custom genome using bowtie 1.0.0 with default parameters.  The  mm9_dm6 custom genome was built by concatenating the mm9 and dm6 genomes.
Sample normalization factor (Rx) was determined as 1 over the number of reads mapping to Drosophila genome per million
Peaks were called using mosaics Input-only, Two-signal analysis. Background was calculated using robust method of moment.   (threshold = 20, FDR= 0.05, maxgap = 10000bp, minsize = 5000bp, binSize= 200bp, two component model, Input-Only analysis)
Reads belonging to peaks were determined for H3.3WT and H3.3K36M samples and normalized by the Rx-normalization factor
Genome_build: mm9/dm6
Supplementary_files_format_and_content: tab-separated file containing genomic coordinates of H3K27me3, H3K36me2 and H3K36me3 peaks in H3.3WT and H3.3K36M cells

source_name: C3H10T1/2 cells & S2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, CellGro). Drosophila S2 cells were cultured in Schneiderís Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS (CellGro).

extract_protocol:
~2x10^7 C3H10T1/2 cells were lysed using digesting buffer (50 mM Tris-HCl pH 7.6, 1 mM CaCl2 and 0.2% Triton X-100) and digested with micrococcal nuclease to obtain mono-nucleosomes. The chromatin were then dialyzed into RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100) for 2 h at 4°C. After centrifugation, soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5% of the mouse cell chromatin. The mixed soluble chromatin was incubated with αH3K36me3 (Active Motif, 61101), αH3K36me2 (Millipore, 07-369-I) or αH3K27me3 (Cell Signaling Tech, 9733) antibody bound to 75 μl protein A or protein G Dynal magnetic beads (Invitrogen) and incubated overnight at 4°C, with 5% kept as input DNA. Magnetic beads were washed with RIPA buffer and LiCl buffer (0.25 M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate) and chromatin was eluted. ChIP DNA was treated with Proteinase K (Roche) and recovered using Qiagen PCR purification kit.
libraries were prepared according to the Illumina TruSeq protocol

tag: cell line

value: Stably expressing FLAG-HA-tagged K36M mutant H3.3

tag: spike-in

value: soluble chromatin from Drosophila melanogaster S2 cells derived from a primary culture of 20–24 hours old, late stage embryos (equivalent to 5% of the mouse cell chromatin)

tag: chip antibody

value: H3K36me3 antibody (active motif, catalog # 61101, lot # 32412003)


title: H3K27me3_ChIPseq H3.3K36M

description:
ChIP-DNA
Peaks_K27me3_RxNormalizedReads

tag: genotype

value: H3K27me3 antibody (Cell Signaling, catalog # 9733, lot # 10)


title: Input_DNA H3.3K36M

description: 5% input DNA


title: Input_DNA H3.3WT

description: 5% input DNA


title: H3K36me3_ChIPseq H3.3WT

description:
ChIP-DNA
Peaks_K36me3_RxNormalizedReads


title: H3K36me2 ChIPseq H3.3WT

description:
ChIP-DNA
Peaks_K36me2_RxNormalizedReads

value: H3K36me2 antibody (Millipore, catalog # 07-369-I, lot # 2475921)


title: H3K27me3_ChIPseq H3.3WT

description:
ChIP-DNA
Peaks_K27me3_RxNormalizedReads


title: Input_DNA_H3.3K36M

description: 5% input DNA

data_processing:
Reads that passed the quality score were aligned using bowtie 1.0.0 with default parameters
Peaks were called using mosaics (threshold = 20, FDR= 0.05, maxgap = 10000bp, minsize = 5000bp, binSize= 200bp, two component model, Input-Only analysis)
RPKM-normalized read intensities in the peaks were determined for the H3.3WT and H3.3K36M samples
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated file containing genomic coordinates for ring1b peaks and rpkm-normalized read-counts for H3.3WT and H3.3K36M samples for each peak

extract_protocol:
~2x10^7 cells were fixed with 1% formaldehyde for 10 min at room temperature and then quenched with 125 mM glycine for 5 min. Cells were then lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl) and sonicated for 1 h with Bioruptor (Diagenode) to obtain mononucleosomes. After centrifugation, the lysates were diluted with dilution buffer (167 mM NaCl, 0.01% SDS, 1.1% TritonX-100, 1.2 mM EDTA, 16.7 mM Tris-HCl) and incubated with αRing1b (Active Motif, 39663) antibody bound to 75 μl protein A Dynal magnetic beads (Invitrogen) and incubated overnight at 4°C, with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). ChIP DNA was eluted, treated with Proteinase K (Roche) and recovered using Qiagen PCR purification kit.
libraries were prepared according to the Illumina TruSeq protocol

value: Stably expressing FLAG-HA-tagged K36M H3.3


title: RNA_H3.3K36M tumor 6

data_processing:
Reads were aligned using bowtie 1.0.0 with default parameters
Expression for annotated refseq genes was determined using RSEM 1.2.12 with default parameters
the data-matrix was normalized by median-normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab separated files containing median normalized 'expected-counts'

source_name: Tumor derived from C3H10T1/2 H3.3K36M cells

value: Not applicable

value: tumor derived from C3H10T1/2 H3.3K36M cells


title: Input_DNA_H3.3WT

description: 5% input DNA

value: C3H embryo-derived mesenchymal progenitor cells


title: RNA_siRNA_Ring1a-Ring1b_3

value: Passage 10-15


title: RNA_H3.3K36M tumor 5


title: RNA_H3.3K36M tumor 4


title: RNA_H3.3K36M tumor 3


title: RNA_H3.3K36M tumor 2


title: RNA_siRNA_HMT 2

value: Parental Cells treated with siRNAs against Nsd1, Nsd2 and Setd2


title: RNA_siRNA_HMT 3


title: H3K36me2_ChIPseq H3.3K36M

description:
ChIP-DNA
Peaks_K36me2_RxNormalizedReads


title: RNA_siRNA_control 2


title: RNA_siRNA_control 1


title: RNA_siRNA_HMT 1


title: RNA_H3.1 K36M 1

value: Stably expressing FLAG-HA-tagged K36M mutant H3.1


title: RNA_H3.3 K36M 2

description:
RNA_MedianNorm_H33_WT_K36M
RNA_MedianNorm_H31_H33_xenografts
RNA_medianNorm_wt_K36M-siRNA-control


title: Ring1b_ChIPseq_H3.3WT

description:
ChIP-DNA
rpkm_ring1b_WTpeakAssociated.txt

value: Stably expressing FLAG-HA-tagged wildtype H3.3

value: Ring1b antibody (Active Motif, catalog # 39663, lot # 23012002)


title: Ring1b_ChIPseq_H3.3K36M


title: RNA_siRNA_control 3

value: C3H embryo-derived mesenchymal multipotent cells


title: RNA_H3.3 WT 2


title: RNA_H3.3 WT 1


title: RNA_H3.1 K36M

description: exon.vst.tsv

data_processing:
Raw reads are trimmed for quality (phred33 >= 30) and length (n >= 30) using Trimmomatic (v. 0.32). Illumina adaptor sequences are clipped off using the palindromic mode.
Perform a sliding window trimming, cutting once the average quality within the window falls below 30. Cut 3 bases off the start of each read, if below quality 30. Cut 3 bases off the end of each read, if above quality 30. Cut the first 4 bases at the start of each read. Drop short reads (n <= 30).
Reads are aligned to the UCSC mm10 genome with STAR v2.3.0e using default settings, which removes multimapping reads. Feature annotation is provided by UCSC knownGene.
Read counting is done with featureCounts v1.4.4. Unless stated otherwise, default settings are used. Read summarization is done at the gene symbol level. The minimum mapping quality score for a read to be counted is 3. Only primary alignments are counted. Reads rather than fragments are counted. Only reads mapping to exons are considered.
Expression data is variance-stabilized using the VST algorithm provided by the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated file containing read counts normalized with the variance-stabilized transformation


title: RNA_H3.3 K36R

description: exon.vst.tsv

value: Stably expressing FLAG-HA-tagged K36R mutant H3.3


title: RNA_H3.3 K36L

description: exon.vst.tsv

value: Stably expressing FLAG-HA-tagged K36L mutant H3.3


title: RNA_H3.3 K36M

description: exon.vst.tsv

value: Stably expressing FLAG-HA-tagged K36M mutant H3.3


title: RNA_H3.3 WT

description: exon.vst.tsv


title: RNA_H3.3 K36A

description: exon.vst.tsv

value: Stably expressing FLAG-HA-tagged K36A mutant H3.3


title: RNA_H3.3 K36I

description: exon.vst.tsv

value: Stably expressing FLAG-HA-tagged K36I mutant H3.3


title: RNA_H3.3K36M tumor 1


title: WT

city: Wuhan

first: Wang

last: Kun

state: Hubei

address: Ba-yi Road

institute: wuhan university

data_processing:
Sequence reads for ChIP-Seq is 100bp paired-end and quality control was performed by Fastqc, and then low quality reads and adaptor contamination were deleted. For downstream analysis, data were mapped to Release 7 of the Michigan State University Rice Genome using Bowtie and MACS for peaks calling.
For RNA-Seq, the clean reads were mapped to the rice genome using the Cufflink software. Gene expression was calculated according to the fragments per kilobase of exon per Million fragments mapped (FPKM) method.
Genome_build: MSU rice genome 7.0
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each RNA-Seq data. Tab-delimited text file include peaks location for ChIP-Seq data.

organism: Oryza sativa

source_name: The panicles (secondary branch development stage)

extract_protocol:
For ChIP, Lysates were clarified from sonicated nuclei and OsGRF6-DNA complexes were isolated with antibody. For RNA-seq, total RNAs were extracted with Trizol according to manufacturer’s manual.
For ChIP-Seq library construction, cross-linked chromatin was fragmented into 150-300bp, and then fragmented DNA was used for library construction and sequencing by Illumina Hiseq2000. RNA-Seq library construction was performed by using Illumina TruSeq kit

value: Wild Type (Yutai B)


title: MIM396


title: ChIP_Input_seq

source_name: Callus

tag: antibody

value: p35S:GRF6-GFP transgenic lines


title: RNA_H3.1 K36M 2


title: si40-Z8

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

data_processing:
Library strategy: TIF-Seq
De-multiplexed reads containing sequence information on 5’ and 3’ ends, poly(A) tail, and experimental control sequences (chimeras, molecular barcode) were obtained.
The 5’ and 3’ reads were individually aligned to a combined reference consisting of the human genome (GRCh37.68) and the experimental in vitro transcript sequences used in quality control (see PMID: 24967623). Single-end alignment with GSNAP (version 2012-01-11) (PMID: 20147302) allowing splicing and 7% of sequence mismatches was carried out for >17bp read, and the rest were aligned with Bowtie (version 0.12.7) (PMID: 19261174) that can deal with short reads, allowing one mismatch, in order to recover as many reads as possible. Uniquely aligned read pairs were kept for further analysis. Additionally, read pairs with one unique and one ambiguous but high quality, and both ambiguous but uniquely high quality read pairs were included if the read pairs were within the expected distance of approx 40nt-750kb on correct chromosome and strand.
Paired reads were used to form transcript boundary models and PCR amplification removed using molecular barcode information and alignment position of the 5’ and 3’ ends.
Genome_build: Homo sapiens GRCh37.68
Supplementary_files_format_and_content: Custom bam. Constructed transcript boundary models based on paired 5’ and 3’ end information obtained from sequenced reads. TIF-seq reads were discarded,  if their immediate downstream sequence started with 5 or more continuous adenines, or if the first 10 immediate downstream bases had 7 or more than 7 adenines. For each DNA strand, the remaining TIF-seq reads were further removed if they overlapped more than one annotated transcription block (merged overlapping GENCODE v17 transcripts) on the same strand.

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted with TRIzol (Invitrogen).
Protocol based on Pelechano et al. Nat Protoc 2014. Briefly, 5’-to-3’ mapping of capped and poly(A) transcripts was carried out using the TIF-seq protocol from Pelechano et al. (PMID: 24967623). Briefly, total RNA was de-phosphorylated to remove any RNA degradation intermediates that may carry a 5’ phosphate, followed by a tobacco acid pyrophosphatase (TAP) treatment to remove the cap structure and expose the resulting 5’ phosphate for ligation of a single-stranded RNA oligo (used later for primer annealing). Each RNA sample was split in two independent tubes and subjected to reverse transcription followed by generation of double-stranded full-length cDNA by PCR. During this process a tube-specific 4nt sequence is introduced at each end of the cDNA fragments (chimera controls) that allow the identification of inter-molecular ligation events. During these process, we introduce a random octamer sequence at the 3’ end (unique molecular identifier, to control for PCR amplification) and a NotI site to facilitate the circularization and a biotin. Please see Pelechano et al. (PMID: 24967623) for a detailed description. The independently barcoded full-length cDNA samples were then pooled, digested (using NotI) to create sticky ends, and circularized overnight with T4 DNA ligase in conditions favouring intra-molecular ligation. Non-circularized molecules were degraded and circularized cDNAs fragmented by sonication. Biotin containing cDNA fragments were captured using streptavidin conjugated magnetic beads, and followed by standard Illumina library construction (including DNA blunt ending, dA addition, and ligation of forked adapters containing 6 nt barcodes identifying each sample) on beads. Barcoded libraries were pooled and sequenced paired-end (101 bp) at the EMBL Genomics Core Facility using an Illumina HiSeq 2000. Since our main interest was to identify transcript boundaries for PROMPT that are generally short compared with mRNA, no size selection to enrich for long RNA fragments was done.

treatment_protocol: siRNA transfections were done twice with 20 nM of siRNA, with the second hit performed after 48h, with Lipofectamine 2000 (Invitrogen) as transfecting agent.

value: HeLa


title: siEGFP

value: EGFP control