title: VS80 Th17_PII STAT3

city: Aalto

first: Kari

last: Nousiainen

country: Finland

institute: Aalto University

data_processing:
Base calling were done using CASAVA version 1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.0  with the following configurations. No more than 3 mismatches. Suppress all alignments for a particular read or pair if more than one reportable alignments exist for it. Print nothing besides alignments. Input qualities are ASCII chars equal to the Phred quality    plus 33. Make Bowtie guarantee that reported singleton alignments are "best" in terms of stratum. If many valid alignments exist and are reportable (e.g. are not disallowed via the -k option) and they fall into more than one alignment "stratum", report only those alignments that fall into the best stratum. Print the amount of wall-clock time taken by each phase. Print alignments in SAM format. The number of megabytes of memory a given thread is given to store path descriptors in --best mode is 2000.
Samfiles were sorted and transformed into BAM format.
Peaks were called using MACS version 1.4.2 with the following parameters effective genome size = 2.70e+09, band width = 300, model fold = 10,30 and pvalue cutoff = 1.00e-05.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files were generated using Macs.

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturers instructions.

extract_protocol:
Cells were fixed using formaldehyde solution, lysed and sonicated to obtain chromatin fragments of 100-500bp size. The sonicated chromatin was then subjected to immunoprecipitation with polyclonal anti-STAT3 antibody (rabbit polyclonal αSTAT3 9132L, Cell Signaling Technology). The STAT3 bound chromatin was isolated using Dynal magnetic beads coated with secondary antibody anti-rabbit IgG (Dynal Biotech). The immunoprecipitated DNA was eluted, reverse crosslinked and purified using Qiagen minielute columns.
The sample preparation for sequencing was performed according to Illumina's recommendations by Illumina service provider, Fasteris Life Sciences, Switzerland.
Having passed quality control, the library is sequenced on Illumina HiSeq 2500

treatment_protocol: Isolated CD4+ T cells were activated with plate-bound anti-CD3 and soluble anti-CD28 in X-vivo 20 serum free medium (Lonza, Basel, Switzerland) supplemented with 2 mM L-Glutamine (#G7513, Sigma, St. Louis, MO, USA), and 50 U/ml Penicillin and cultured at 37°C in 5 % CO2. IL-6 (20 ng/ml, Roche, Basel, Switzerland), IL-1ß (10 ng/ml) and TGFß (10 ng/ml) in the presence of neutralizing anti-IFN (1 µg/ml) and anti-IL4 (1 µg/ml) were used to initiate Th17 polarization. Control Th0 cells were cultured in a medium containing only the neutralizing antibodies. All cytokines and neutralizing antibodies were purchased from R&D Systems (Minneapolis, MN, USA) unless otherwise stated. Cells were harvested after 72h of culture.

value: healthy neonates

value: Umbilical cord blood

value: primary human CD4+ T cells

tag: chip antibody


title: VS80 Th17_PII input

status: Public on May 15 2017

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell type


title: acs11 Female flowers Input

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
The reads were mapped onto Cucumis.melo3.5.1
To identify regions that were significantly enriched, we used MACS2.
MACS2 parameters for peaks detection were set as follows: Number of duplicate reads at a location:1; Bandwidth:300; mfold of 5:50; q-value cutoff:0.05.
For peak detection in H3K27me3 modified regions, we used SICER with the following criteria: Window size:200, Gap size:600
Genome_build: Cucumis.melo3.5.1
Supplementary_files_format_and_content: WIG file format
Supplementary_files_format_and_content: cufflinks file format

organism: Cucumis melo var. cantalupo

source_name: acs11 Female flowers Input

growth_protocol: Monoecious melon (Cucumis melo) cultivar charentais (Cucumis melo L. subsp. melo var cantalupensis ) were used for H3K9ac and H3K27me3 genome-wide descriptive analyses. For each replicate, 7-day old seedlings were transferred to individual pots and incubated in a growth chamber for 30 days (long day conditions, temperature: 27°C (day) and 21°C (night), relative humidity: 60%). Young male and female flowers (3 mm length; Developmental stage 8) were collected, organized according to their location in the plant (i.e. main stem or branches) and conserved at -80°c for epigenomic and transcriptomic analyses.

extract_protocol:
Total RNA were extracted from leaves, root, fruit, male and female flowers using the Nucleospin RNA kit (Macherey-Nagel). ChIP assays were performed using anti-H3K9ac (Millipore) or anti-H3K27me3 (Millipore) antibodies. Chromatin was reverse-crosslinked by adding 20μL of NaCl 5M and incubated over-night at 65°C. Reverse-cross-linked DNA was submitted to RNase and proteinase K digestion, and extracted with phenol-chloroform. DNA was ethanol precipitated in the presence of 20μg of glycogen and resuspended in 50μL of nuclease-free water (Ambion) in a DNA low-bind tube.
10 ng of IP or input DNA was used 501 for ChIP-Seq library construction using NEB-Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s recommendations. For all libraries, twelve cycles of PCR were  used. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent), and  the libraries were subjected to high-throughput sequencing by Illumina Sequencing technology.

treatment_protocol: For the determination of a- and g-related epigenetic changes, we used two families of EMS451 treated C. melo lines carrying missense mutations in CmWIP1 and in CmACS11, both previously reported to lead to gynoecy and androecy, respectively. Germination, growth and flower collecting conditions were the same to the previously described for the monoecious WT plants.

tag: cultivar

value: charentais

value: Flowers

tag: age

value: 30 days in growth chamber


title: VS80_Th17_PI input


title: Male flowers Input replicate 2

source_name: Male flowers Input replicate 2


title: ZZ@E1

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

library_source: transcriptomic

data_processing:
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.13 and cutadapt 1.7.1.
Using FastX and ShortRead 1.16.3, we filtered subsequently small reads (length < 35 bp), polyA-reads (>90% of the bases equal A), ambiguous reads (containing N) and low quality reads (>50% of the bases < Q25).
The reads are aligned to the reference genome with Tophat v2.0.12. As parameter options we use: --library-type unstranded --min-intron-length 70 --max-intron-length 500000.
Counting per gene was performed using the function summarizeOverlap() from the R package GenomicAlignment 1.2.2, using union method and TxDb.Mmusculus.UCSC.mm10.knownGene library for gene annotation.
Genome_build: GRCm38.73 (mm10)
Supplementary_files_format_and_content: raw counts in txt format

molecule: polyA RNA

organism: Mus musculus

source_name: Lysates of E6.25 epiblast (E) or extra-embryonic (ExE) tissues

growth_protocol: Lysates of E6.25 epiblast (E) and extra-embryonic (ExE) tissues were pooled, based on retrospective genotyping, from at least 6 embryos (collected from 2-3 litters). Four pooled biological replicates were collected for each tissue compartment and each genotype (wt, Zwt and ZZ); in 3 of 4 pooled replicates, the E and ExE samples were obtained from the same litters and given the same numbering. One ExE sample of ZZ was lost.

extract_protocol:
RNA was purified using the RNeasy micro Kit (Qiagen) to obtain 1-10 ng of RNA per pool. RNA quality was assessed using a Bioanalyzer 6000 Pico chip and only samples with RNA integrity number (RIN) > 8.0 were processed further.
First-strand cDNA synthesis and amplification was performed by using the SMARTer Ultra Low Input RNA amplification kit v3 (Clontech). Libraries were prepared using NEBNext Ultra DNA library prep for Illumina and sequenced on NextSeq 500 in high-output to generate 75-bp single-end reads.

value: Epiblast

tag: genotype


title: VS78_2_Th17_STAT3

value: polyclonal anti-STAT3 antibody (rabbit polyclonal αSTAT3 9132L, Cell Signaling Technology)


title: Fruit H3K27me3 replicate 1

source_name: Fruit H3K27me3 replicate 1

value: Fruit


title: Zwt@ExE3

value: Extra-embryonic


title: Zwt@ExE2


title: VS78_1_Th17 input


title: Fruit Input replicate 1

source_name: Fruit Input replicate 1


title: Fruit H3K9ac replicate 1

source_name: Fruit H3K9ac replicate 1


title: Root Input replicate 1

source_name: Root Input replicate 1

value: Root


title: RNAseq_A5-rep4

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) by TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads).
Differential gene expression analyses were performed using DEseq.
Genome_build: hg18
Supplementary_files_format_and_content: text file of gene read count values
Supplementary_files_format_and_content: text file of gene RPKM values

molecule: total RNA

source_name: Human primary adult proerythroblasts (ProEs)

growth_protocol: Human primary fetal and adult HSPCs and erythroblasts were expanded and differentiated ex vivo using a serum-free two-phase liquid culture system.

extract_protocol: For RNA-seq analysis using the Illumina HiSeq2500, 0.1-2 ug of total RNA was processed for library generation using the TruSeq RNA Sample Preparation v2 Kit (Illumina) following the manufacturer’s protocol.

value: CD34+ HSPC-derived proerythroblasts

tag: developmental stage

value: bone marrow


title: RNAseq_A5-rep3


title: cmwip1 Female flowers Input

source_name: cmwip1 Female flowers Input


title: Zwt@ExE1


title: MM180_rep3

city: Göttingen

first: Ashish

last: Rajput

state: Niedersachsen

address: Von-Siebold-Straße 3A

department: Research Group for Computational Systems Biology

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description: Sample_MM180_mm_rna_sr_Thuene_E_4_geneCounts

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the mm10 genome assembly using STAR aligner version 2.3.0e_r291 with default options
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for all genes and all exons (Ensembl annotation v72) were obtained using FeaturesCount. DEGs were calculated using DESEQ2

source_name: Brain

extract_protocol:
RNA from different mice brain regions was purified using miRVANA RNA isolation kit following manufacturer’s protocol. RNAs were treated with DNase Set (Qiagen) for 15min to eliminate genomic DNA contamination.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

tag: condition

value: sporadic Creutzfeldt-Jakob MM1 challenged mouse

tag: time point

value: 180 days post infection


title: MM180_rep2

description: Sample_MM180_mm_rna_sr_Thuene_E_3_geneCounts


title: Zwt@E5


title: MM180_rep1

description: Sample_MM180_mm_rna_sr_Thuene_E_1_geneCounts


title: RNAseq_A5-rep2


title: Leaves Input replicate 1

source_name: Leaves Input replicate 1

value: Leaves


title: Con180_rep4

description: Sample_Con180_mm_rna_sr_Thuene_D_4_geneCounts

value: Control challenged mouse


title: VS80_Th17_PI STAT3

value: healthy neonates


title: Zwt@E4


title: RNAseq_A5-rep1


title: Zwt@E3


title: Zwt@ExE5


title: RNAseq_A0-rep4

source_name: Human primary adult CD34+ HSPCs

value: CD34+ HSPCs


title: Fruit Input replicate 2

source_name: Fruit Input replicate 2


title: Fruit H3K27me3 replicate 2

source_name: Fruit H3K27me3 replicate 2


title: Zwt@E2


title: MM180_rep4

description: Sample_MM180_mm_rna_sr_Thuene_E_5_geneCounts


title: Con180_rep2

description: Sample_Con180_mm_rna_sr_Thuene_D_2_geneCounts


title: RNAseq_A0-rep3


title: Root H3K27me3 replicate 2

source_name: Root H3K27me3 replicate 2


title: Con180_rep1

description: Sample_Con180_mm_rna_sr_Thuene_D_1_geneCounts


title: wt@ExE5

value: wild-type


title: Root H3K27me3 replicate 1

source_name: Root H3K27me3 replicate 1

value: charentais


title: RNAseq_A0-rep2


title: wt@ExE4


title: Leaves H3K27me3 replicate 2

source_name: Leaves H3K27me3 replicate 2


title: wt@ExE2


title: RNAseq_F5-rep4

source_name: Human primary fetal proerythroblasts (ProEs)

value: fetal liver


title: MM120_rep3

description: Sample_MM120_mm_rna_sr_Thuene_C_3_geneCounts

value: 120 days post infection


title: Leaves H3K27me3 replicate 1

source_name: Leaves H3K27me3 replicate 1

value: 30 days in growth chamber


title: MM120_rep2

description: Sample_MM120_mm_rna_sr_Thuene_C_2_geneCounts


title: wt@ExE1

source_name: Lysates of E6.25 epiblast (E) or extra-embryonic (ExE) tissues


title: Root Input replicate 2

source_name: Root Input replicate 2


title: MM120_rep1

description: Sample_MM120_mm_rna_sr_Thuene_C_1_geneCounts


title: Con180_rep3

description: Sample_Con180_mm_rna_sr_Thuene_D_3_geneCounts


title: RNAseq_F5-rep3


title: RNAseq_F5-rep2


title: Con120_rep4

description: Sample_Con120old_mm_rna_sr_Thuene_A_4_geneCounts


title: Leaves Input replicate 2

source_name: Leaves Input replicate 2


title: wt@E4

value: Epiblast


title: wt@E5


title: Con120_rep3

description: Sample_Con120old_mm_rna_sr_Thuene_A_3_geneCounts


title: RNAseq_F5-rep1


title: Fruit H3K9ac replicate 2

source_name: Fruit H3K9ac replicate 2

value: Fruit


title: wt@E2


title: Con120_rep2

description: Sample_Con120old_mm_rna_sr_Thuene_A_2_geneCounts


title: RNAseq_F0-rep4

source_name: Human primary fetal CD34+ HSPCs


title: MM120_rep4

description: Sample_MM120_mm_rna_sr_Thuene_C_4_geneCounts


title: wt@E1


title: RNAseq_A0-rep1


title: RNAseq_F0-rep3


title: Root H3K9ac replicate 1

source_name: Root H3K9ac replicate 1


title: Con120_rep1

description: Sample_Con120old_mm_rna_sr_Thuene_A_1_geneCounts


title: Leaves H3K9ac replicate 2

source_name: Leaves H3K9ac replicate 2


title: Hamster_GV_oocyte_br2

city: Zagreb

first: Vedran

last: Franke

address: Horvatovac 102a

department: Department of biology

country: Croatia

institute: University of Zagreb

data_processing:
Reads were Mapped to the mm10/mesAur1 genome versions. Using the STAR aligner.
Coverage tracks were constructed using UCSC tools
Genome_build: mm10, mesAur1
Supplementary_files_format_and_content: bw files were generated in a non stranded mode using UCSC tools. The tracks are not normalized for library size

organism: Mesocricetus auratus

growth_protocol: Oocytes and early embryos were obtained from superovulated CBA/CAJxC57Bl6/J F1 hybrid mice as described previously (Nagy, 2003). Hamster fully-grown GV oocytes were collected the same way from as mouse oocytes except of superovulation, which was not used. Resumption of meiosis during culture of GV oocytes was prevented with 0.2 mM 3-isobutyl-1-methyl-xanthine (IBMX, Sigma). Animal experiments were approved by the Institutional Animal Use and Care Committees and were carried out in accordance with the law.

extract_protocol: Total RNA was extracted from 25 oocyte using PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instruction (Thermo Fisher Scientific, Philadelphia, PA). Each sample was spiked in with 0.2pg synthesized Renilla Luciferase mRNA before extraction as normalization control. RNAseq libraries were constructed by using Ovation RNA-seq system V2(NuGEN, San Carlos, CA) followed by Ovation Ultralow Library system(DR Multiplex System, NuGEN, San Carlos, CA).

value: oocyte


title: RNAseq_F0-rep2


title: Leaves H3K9ac replicate 1

source_name: Leaves H3K9ac replicate 1


title: RNAseq_F0-rep1


title: H2A.Z_IP_arp8_4h_Rep2

status: Public on May 14 2017

city: Martinsried

first: Claudio

middle: Amadeo

last: Lademann

address: Am Klopferspitz 18

institute: Max Plack Institute of Biochemistry

description:
Processed data file (IP/Input): H2A.Z_arp8_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

data_processing:
Raw data quality was analyzed using the FastQC tool.
Fastq raw files were mapped to the S. cerevisiae genome using bowtie1 with standard parameters except -m=1.
The genome was split into non-overlapping windows with a size of 500 bp and all successfully mapped reads assigned to their corresponding window(s) using the GenomicRanges R package.
Window counts were TMM-normalized (Robinson and Oshlack, 2010), the dispersion was estimated (Chen et al., 2014) and a negative binomial generalized log-linear model was fitted using a generalized linear model (McCarthy et al., 2012) using the edgeR (Robinson et al., 2010) R package.
For ChIP analysis, IP samples were normalized to the corresponding Input. The mean of the two replicate values was calculated.
Genome_build: R-64-1-1 (http://www.ensembl.org/Saccharomyces_cerevisiae/Info/Index)
Supplementary_files_format_and_content: bedGraph files

organism: Saccharomyces cerevisiae

source_name: ∆arp8, DSB, 4h, H2A.Z ChIP

growth_protocol: Yeast cells were grown in YP-lactate medium to exponential growth phase.

extract_protocol:
Lysates were generated from sheared yeast chromatin and immunoprecipitation performed with antibodies against RPA, Rad51 or H2A.Z. A separate aliquot of lysate was used as Input. DNA from Input (In) and immunoprecipitations (IP) was purified and used for library generation.
Library construction was done according to the manufacturer's protocol using the Diagenode MicroPlex library preparation kit v2 including 48 indices.

treatment_protocol: A DSB was induced in exponentially growing yeast by addition of 2% (w/v) galactose. At 1h or 4h following DSB induction, cells were crosslinked by addition of 1% (final concentration) formaldehyde. 0h time points were transferred to separate shake flasks prior to DSB induction and crosslinked at any point during the time course.

tag: genotype/variation

tag: treatment

value: double-strand break (DSB)

value: anti-H2A.Z (Active Motif, 39647)


title: naïve mice mPFC_RNA-Seq

city: Esch-sur-Alzette

first: Rashi

last: Halder

address: 7, Avenue des Hauts-Fourneaux

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped using tophat Cufflinks with default parameters to produce FPKM values
Genome_build: mm10
Supplementary_files_format_and_content: fpkm

source_name: naïve mice mPFC

extract_protocol:
RNA was extracted using Tri-reagent as per the supliers protocol and Dnase treated proceeding foe library preparation for sequencing.
Illumina TruSeq RNA Sample Preparation v2 Kit

value: medial Prefrontal cortex

value: 3 months

tag: strain

tag: antibody


title: H2A.Z_IP_arp8_1h_Rep1

description:
Processed data file (IP/Input): H2A.Z_arp8_1h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, DSB, 1h, H2A.Z ChIP


title: H2A.Z_In_arp8_1h_Rep2

source_name: ∆arp8, DSB, 1h, input


title: H2A.Z_IP_arp8_4h_Rep1


title: H2A.Z_IP_arp8_1h_Rep2


title: Root H3K9ac replicate 2

source_name: Root H3K9ac replicate 2

value: Root


title: H2A.Z_In_arp8_0h_Rep2

description:
Processed data file (IP/Input): H2A.Z_arp8_0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, 0h, input


title: H2A.Z_IP_arp8_0h_Rep1

source_name: ∆arp8, 0h, H2A.Z ChIP


title: H2A.Z_IP_arp8_0h_Rep2


title: H2A.Z_In_arp8_4h_Rep2

source_name: ∆arp8, DSB, 4h, input


title: H2A.Z_IP_WT_4h_Rep2

description:
Processed data file (IP/Input): H2A.Z_WT_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, DSB, 4h, H2A.Z ChIP

value: WT


title: H2A.Z_IP_WT_4h_Rep1


title: H2A.Z_In_WT_4h_Rep1

source_name: WT, DSB, 4h, input


title: H2A.Z_In_WT_4h_Rep2


title: H2A.Z_IP_WT_1h_Rep2

description:
Processed data file (IP/Input): H2A.Z_WT_1h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, DSB, 1h, H2A.Z ChIP


title: H2A.Z_IP_WT_1h_Rep1


title: H2A.Z_In_WT_1h_Rep2

source_name: WT, DSB, 1h, input


title: H2A.Z_In_WT_1h_Rep1


title: H2A.Z_IP_WT_0h_Rep1

description:
Processed data file (IP/Input): H2A.Z_WT_0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, 0h, H2A.Z ChIP


title: H2A.Z_In_WT_0h_Rep2

source_name: WT, 0h, input


title: H2A.Z_In_WT_0h_Rep1


title: Rad51_IP_arp8htz1_4h_Rep2

description:
Processed data file (IP/Input): Rad51_arp8htz1_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8 ∆htz1, DSB, 4h, Rad51 ChIP

value: delta-arp8 delta-htz1

value: anti-Rad51 (Santa Cruz y-180, lot number:K1209)


title: Rad51_IP_arp8htz1_4h_Rep1


title: Rad51_In_arp8htz1_4h_Rep2

description:
Processed data file (IP/Input): Rad51_arp8htz1_4h.bedgraph
Processed data file (Input only): Input_Rad51_arp8htz1_4hnorm0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8 ∆htz1, DSB, 4h, input


title: Rad51_In_arp8htz1_4h_Rep1


title: H2A.Z_In_arp8_0h_Rep1


title: H2A.Z_In_arp8_1h_Rep1


title: Rad51_IP_arp8htz1_1h_Rep1

description:
Processed data file (IP/Input): Rad51_arp8htz1_1h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8 ∆htz1, DSB, 1h, Rad51 ChIP


title: Rad51_In_arp8htz1_1h_Rep1

source_name: ∆arp8 ∆htz1, DSB, 1h, input


title: Rad51_In_arp8htz1_0h_Rep2

description:
Processed data file (IP/Input): Rad51_arp8htz1_0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8 ∆htz1, 0h, input


title: Rad51_In_arp8htz1_1h_Rep2


title: Rad51_IP_arp8htz1_0h_Rep2

source_name: ∆arp8 ∆htz1, 0h, Rad51 ChIP


title: Rad51_IP_htz1_4h_Rep1

description:
Processed data file (IP/Input): Rad51_htz1_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆htz1, DSB, 4h, Rad51 ChIP


title: Rad51_In_arp8htz1_0h_Rep1


title: Rad51_IP_htz1_4h_Rep2


title: Rad51_In_htz1_4h_Rep1

description:
Processed data file (IP/Input): Rad51_htz1_4h.bedgraph
Processed data file (Input only): Input_Rad51_htz1_4hnorm0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆htz1, DSB, 4h, input


title: Rad51_IP_arp8htz1_0h_Rep1


title: H2A.Z_IP_WT_0h_Rep2


title: Rad51_In_htz1_1h_Rep2

description:
Processed data file (IP/Input): Rad51_htz1_1h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆htz1, DSB, 1h, input


title: Rad51_IP_htz1_1h_Rep2

source_name: ∆htz1, DSB, 1h, Rad51 ChIP


title: Rad51_IP_htz1_1h_Rep1


title: Rad51_In_htz1_1h_Rep1


title: Rad51_IP_htz1_0h_Rep2

description:
Processed data file (IP/Input): Rad51_htz1_0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆htz1, 0h, Rad51 ChIP


title: Rad51_IP_htz1_0h_Rep1


title: Rad51_IP_arp8htz1_1h_Rep2


title: Rad51_In_htz1_0h_Rep1

source_name: ∆htz1, 0h, input


title: Hamster_GV_oocyte_br1

extract_protocol:
RNA was released from small number of oocytes upon incubation in water with RNase inhibitor for 5 min at 85°C. RNA was reverse-transcribed using RevertAid First Strand cDNA Synthesis Kit (Fermentas). Real-time PCR was carried out on LightCycler 480 System (Roche). Each reaction (10 µl) consisted of 5 µl Maxima® SYBR Green qPCR Master Mix (Fermentas), 0.4 µl mixed gene-specific forward and reverse primers (30 µM each) and 2 µl diluted cDNA. Each sample was run in triplicate.
Total RNA was extracted from 25 oocyte using PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instruction (Thermo Fisher Scientific, Philadelphia, PA). Each sample was spiked in with 0.2pg synthesized Renilla Luciferase mRNA before extraction as normalization control. RNAseq libraries were constructed by using Ovation RNA-seq system V2(NuGEN, San Carlos, CA) followed by Ovation Ultralow Library system(DR Multiplex System, NuGEN, San Carlos, CA).


title: Rad51_In_arp8_4h_Rep2

description:
Processed data file (IP/Input): Rad51_arp8_4h.bedgraph
Processed data file (Input only): Input_Rad51_arp8_4hnorm0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, DSB, 4h, input


title: Rad51_IP_arp8_1h_Rep1

description:
Processed data file (IP/Input): Rad51_arp8_1h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, DSB, 1h, Rad51 ChIP


title: Rad51_In_htz1_4h_Rep2


title: Rad51_In_arp8_1h_Rep2

source_name: ∆arp8, DSB, 1h, input


title: Rad51_In_arp8_4h_Rep1


title: Rad51_IP_arp8_1h_Rep2


title: Rad51_In_arp8_1h_Rep1


title: Rad51_IP_arp8_0h_Rep2

description:
Processed data file (IP/Input): Rad51_arp8_0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, 0h, Rad51 ChIP


title: Rad51_IP_arp8_0h_Rep1


title: Rad51_IP_WT_4h_Rep2

description:
Processed data file (IP/Input): Rad51_WT_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, DSB, 4h, Rad51 ChIP


title: Rad51_IP_WT_4h_Rep1


title: Rad51_In_arp8_0h_Rep2

source_name: ∆arp8, 0h, input


title: Rad51_In_WT_0h_Rep2

description:
Processed data file (IP/Input): Rad51_WT_0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, 0h, input


title: Rad51_In_WT_1h_Rep1

description:
Processed data file (IP/Input): Rad51_WT_1h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, DSB, 1h, input


title: Rad51_IP_WT_1h_Rep2

source_name: WT, DSB, 1h, Rad51 ChIP


title: Rad51_IP_WT_1h_Rep1


title: Rad51_IP_WT_0h_Rep1

source_name: WT, 0h, Rad51 ChIP


title: Rad51_In_WT_1h_Rep2


title: Rad51_In_WT_0h_Rep1


title: Rad51_In_htz1_0h_Rep2


title: RPA_IP_arp8_4h_Rep2

description:
Processed data file (IP/Input): RPA_arp8_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, DSB, 4h, RPA ChIP

value: anti-RPA (Agrisera, AS07214)


title: Rad51_In_WT_4h_Rep1

description:
Processed data file (IP/Input): Rad51_WT_4h.bedgraph
Processed data file (Input only): Input_Rad51_WT_4hnorm0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, DSB, 4h, input


title: Rad51_IP_WT_0h_Rep2


title: Rad51_IP_arp8_4h_Rep2

description:
Processed data file (IP/Input): Rad51_arp8_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, DSB, 4h, Rad51 ChIP


title: RPA_IP_arp8_4h_Rep1


title: RPA_In_arp8_4h_Rep2

description:
Processed data file (IP/Input): RPA_arp8_4h.bedgraph
Processed data file (Input only): Input_RPA_arp8_4hnorm0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.


title: RPA_In_arp8_4h_Rep1


title: RPA_IP_arp8_1h_Rep2

description:
Processed data file (IP/Input): RPA_arp8_1h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, DSB, 1h, RPA ChIP


title: Rad51_In_arp8_0h_Rep1


title: Rad51_IP_arp8_4h_Rep1


title: Rad51_In_WT_4h_Rep2


title: RPA_IP_arp8_1h_Rep1


title: RPA_In_arp8_0h_Rep2

description:
Processed data file (IP/Input): RPA_arp8_0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.


title: RPA_IP_arp8_0h_Rep1

source_name: ∆arp8, 0h, RPA ChIP


title: RPA_In_arp8_1h_Rep1

description:
Processed data file (IP/Input): RPA_arp8_1h.bedgraph
Processed data file (Input only): Input_RPA_arp8_1hnorm0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.


title: RPA_In_arp8_0h_Rep1


title: RPA_In_arp8_1h_Rep2


title: RPA_IP_WT_4h_Rep2

description:
Processed data file (IP/Input): RPA_WT_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, DSB, 4h, RPA ChIP


title: RPA_IP_arp8_0h_Rep2


title: RPA_IP_WT_4h_Rep1


title: RPA_In_WT_4h_Rep2

description:
Processed data file (IP/Input): RPA_WT_4h.bedgraph
Processed data file (Input only): Input_RPA_WT_4hnorm0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.


title: RPA_IP_WT_0h_Rep2

description:
Processed data file (IP/Input): RPA_WT_0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, 0h, RPA ChIP


title: RPA_In_WT_1h_Rep1

description:
Processed data file (IP/Input): RPA_WT_1h.bedgraph
Processed data file (Input only): Input_RPA_WT_1hnorm0h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.


title: RPA_IP_WT_1h_Rep1

description:
Processed data file (IP/Input): RPA_WT_1h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: WT, DSB, 1h, RPA ChIP


title: RPA_In_WT_1h_Rep2


title: RPA_IP_WT_1h_Rep2


title: RPA_In_WT_0h_Rep1


title: RPA_IP_WT_0h_Rep1


title: RPA_In_WT_4h_Rep1


title: 5month old Wild-type_1

status: Public on May 13 2017

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to mm9 using TopHat 1.3.2/bowtie 0.12.7.0 with default settings
RPKM values were calculated with Partek 6.6
Genome_build: mm9
Supplementary_files_format_and_content: Excel, RPKM values

source_name: gastrocnemius muscle

extract_protocol: RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: GAA knockout mice were created by targeted disruption of exon 6 of the acid alpha-glucosidase gene; LOX P sites are inserted in introns 5 and 6; the colony is maintained by brother-sister matings; this is an inbread strain >20 generations; mixed bcgr: BL6/129j

value: mixed background

value: gastrocnemius muscle

value: 5 month old

value: Wild type


title: ATCC52813xATCC52814 - endosymbionts, rep2

city: Ithaca

first: Stephen

middle: James

last: Mondo

state: NY

address: 334 Plant Science Building, Tower Road

department: Plant Pathology and Plant-Microbe Biology

institute: Cornell University

data_processing:
quality control using the FAST-X Toolkit (Gordon and Hannon, 2010) removing reads with quality scores below 20
de novo transcriptome assembly using Trinity (Grabherr, 2011) using all available quality-controlled sequence data
FPKM values were calculated using RSEM (Li and Dewey, 2011)
Genome_build: transcriptomes were assembled de novo from raw data using Trinity (Grabherr et al., 2011)
Transcriptome_Trinity.fasta file contains the transcriptome as assembled by Trinity (Grabherr, 2011) using all available quality-controlled sequence data
Supplementary_files_format_and_content: FPKM_profiles contains the expression profiles for each biological replicate of all six conditions investigated. FPKM values were calculated using RSEM (Li and Dewey, 2011)

organism: Rhizopus microsporus

source_name: mycelium

extract_protocol:
We used the ToTALLY RNA extraction kit (Ambion), followed by rRNA depletion using the Ribo-Zero rRNA removal Human/Mouse/Rat kit as well as the Gram negative kit (Epicentre) prior to library prep
We followed the standard protocol of the TruSeq RNA Sample Preparation Kit

value: day 6

value: mycelium

tag: endosymbiont


title: ATCC52814 + endosymbionts, rep1

source_name: mycelium + asexual sporangia

value: mycelium + asexual sporangia

value: Burkholderia rhizoxinica


title: ATCC52814 - endosymbionts, rep1


title: ATCC52813xATCC52814 - endosymbionts, rep1


title: ATCC52813 - endosymbionts, rep1


title: Control siRNA-transfected SW480 cells_rep2

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

country: South Korea

institute: Korea Institute of Science and Technology Information

description: Control siRNA-transfected SW480 cells replicate2

data_processing:
Quality trimming using FastQC and Fastx-toolkit
Alignment using Mapsplice v2.1.7 to hg19
Differential expression analysis using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include expected count, FPKM, and TPM values for each sample

source_name: Control siRNA-transfected SW480 cells

growth_protocol: HT29 and SW480 cells were cultured in McCoy’s 5A medium and RPMI1840 medium supplemented with 10% fetal bovine serum, respectively.

extract_protocol:
Total RNA of 1 mg was extracted from each sample
The mRNA library (insert size of ~300 bp) was created using the TruSeq RNA Library Preparation kit v2 (Illumina)

treatment_protocol: HT29 and SW480 cells were transfected with control siRNA (siCon) and Prdx2 siRNA (siPrdx2) for 36 hr and then subjected to RNA extraction. Experiments were performed in duplicate.

tag: cell line

tag: transfection

value: Control siRNA


title: ATCC52814 + endosymbionts, rep2


title: ATCC52813xATCC52814 + endosymbionts, rep2

source_name: mycelium + asexual sporangia + sexual zygospores


title: 6month old Wild-type_2

value: 6 month old


title: ATCC52813 - endosymbionts, rep2


title: 5month old Wild-type_2


title: PRDX2 siRNA-transfected SW480 cells_rep1

description: PRDX2 siRNA-transfected SW480 cells replicate1

source_name: PRDX2 siRNA-transfected SW480 cells

value: PRDX2 siRNA


title: PRDX2 siRNA-transfected SW480 cells_rep2

description: PRDX2 siRNA-transfected SW480 cells replicate2


title: Control siRNA-transfected SW480 cells_rep1

description: Control siRNA-transfected SW480 cells replicate1


title: 6month old Wild-type_1


title: RPA_In_WT_0h_Rep2

source_name: WT, 0h, input


title: 5month old GAA Knock-out_5

value: GAA knock-out


title: ATCC52814 - endosymbionts, rep2


title: ATCC52813xATCC52814 + endosymbionts, rep1

value: mycelium + asexual sporangia + sexual zygospores


title: ATCC52813 + endosymbionts, rep1


title: cre2

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

data_processing:
Short read FASTQ files were quality trimmed using FASTX toolkit (v. 0.0.14) to trim three bases from the 5’ end of the reads.
Paired-end reads were then mapped to the mm9 genome using tophat2 (Kim et al., 2013) and the UCSC knownGene gtf file. The following parameters were used in the tophat2 call “-N 1 –g 1 –read-gap-length 1 –mate-inner-dis 170”.
Reads that had the same starting location and strand with mate-pairs that also had the same location and strand were considered to be PCR duplicates and removed from subsequent analyses using Picard tools (v. 1.103).
Differentially expressed transcripts were determined using Cufflinks and Cuffdiff (v2.1.1) (Trapnell et al., 2010).
Downstream analyses were performed in R/Bioconductor (Gentleman et al., 2004) and used gene summarized expression levels normalized using Fragments Per Kilobase per Million (FPKM) from Cufflinks.
Hierarchical clustering was performed using the pvclust R package were significance was determined using bootstraping (Suzuki and Shimodaira, 2006).
Principle Components Analysis (PCA) was conducted using the “prcomp” function of the stats package in R / Bioconductor.
Enriched gene ontologies were determined using the package “GOstats” (v. 3.1.1) (Falcon and Gentleman, 2007).
Gene Set Enrichment Analysis (GSEA) was performed using a pre-ranked gene list determined by cuffdiff and GSEA (v. 2.1.0) (Subramanian et al., 2005.)
Hierarchical clustering of gene expression data was performed using average clustering in the heatmap.2 package.  UCSC-style display of gene expression data were plotted using the “rtracklayer” package (Lawrence et al., 2009) and custom R scripts as previously described, available upon request
Genome_build: mm9

source_name: hippocampus

extract_protocol:
Hippocampi were then dissected and snap frozen with liquid nitrogen in 1mL Trizol and stored at -80°C. For RNA isolation, samples were thawed in a 37°C waterbath then kept on ice prior to homogenization with a Polytron homogenizer with a 5 second pulse. After a 5 minute incubation at room temperature, one tenth the sample volume of 1-bromo-3chloropropane was added, mixed by inversion and a 3 minute incubation at room temperature. Samples were then centrifuged at 13,000 X g for 15 minutes at 4°C to separate the aqueous and organic layers. As much of the aqueous layer was recovered as possible, then RNA was precipitated with isopropanol. Pellets were then washed with 75% ethanol and resuspended in 50µL deionized water.
RNA library preparation and sequencing were performed by HudsonAlpha. RNA was Poly(A) selected and 300bp size selected. Libraries were sequenced for 25 million 50bp paired end reads.

treatment_protocol: Mice were anesthetized with a lethal dose of isoflurane, followed by decapitation and brain dissection.

value: hippocampus

tag: gender

value: Female


title: ctrl2


title: Control siRNA-transfected HT29 cells_rep2

description: Control siRNA-transfected HT29 cells replicate2

source_name: Control siRNA-transfected HT29 cells


title: PRDX2 siRNA-transfected HT29 cells_rep2

description: PRDX2 siRNA-transfected HT29 cells replicate2

source_name: PRDX2 siRNA-transfected HT29 cells


title: H2A.Z_In_arp8_4h_Rep1

description:
Processed data file (IP/Input): H2A.Z_arp8_4h.bedgraph
'IP/Input' bedgraph files include ChIP signals normalized to their corresponding input DNA; 'Input only' bedgraph files include data solely of input DNA, independent of ChIP.

source_name: ∆arp8, DSB, 4h, input

value: double-strand break (DSB)

tag: chip antibody


title: 5month old GAA Knock-out_3

tag: tissue


title: 5month old GAA Knock-out_4


title: ctrl1


title: ATCC52813 + endosymbionts, rep2


title: 5month old GAA Knock-out_2


title: cre1


title: bos_taurus_091125_lane_6

status: Public on May 12 2017

city: Urbana

first: Don

middle: Leigh

last: Armstrong

state: IL

address: 1206 W Gregory Drive

department: Institute for Genomic Biology

institute: University of Illinois at Urbana Champaign

data_processing:
Reads failing QC were removed using fastQC, aligned using STAR, and quantified using Cufflinks against appropriate ENSEMBL reference genomes
Genome_build: ENSEMBL v80
Supplementary_files_format_and_content: gene FPKM values from cufflinks

organism: Bos taurus

source_name: placenta

extract_protocol:
The villous portion of the tissue was homogenized in Trizol resulting in the isolation of total RNA following the manufacturer's instructions (Life Technologies, Grand Island, NY). The RNA was further purified using Qiagen’s RNeasy Midi Kit in conjunction with the RNase-Free DNase Set following the manufacturer’s protocol to remove any contaminating DNA from the sample (Valencia, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta


title: bonobo_101116_lane_6

organism: Pan paniscus


title: ateles_fusciceps_R223_L4

data_processing:
Reads failing QC were removed using fastQC, aligned using STAR, and quantified using Cufflinks against appropriate ENSEMBL reference genomes
Genome_build: ENSEMBL v80
Supplementary_files_format_and_content: gene FPKM values from cufflinks and assembled transcriptome (using trinity) in fasta format.

organism: Ateles fusciceps


title: M3149 E2

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

data_processing:
Derived sequences were analyzed by applying a custom computational pipeline consisting of the open-source gSNAP, Cufflinks, and R for sequence alignment and ascertainment of differential gene expression (CITES). In short, reads generated were mapped to the mouse genome (Mm9) by gSNAP, expression (FPKM) derived by Cufflinks, and differential expression analyzed with ANOVA in R.
Genome_build: Mm9
Supplementary_files_format_and_content: .csv text file that includes calculated expression values for each sample, along with calcualted Q and p values between control and mutant samples

source_name: E15.5 Cranial base tissue

extract_protocol:
Embryonic cranial base samples were dissected out of E15.5 control or Memo1-mutant embryos.  Following isolation, tissue was stored in RNAlater at 4C overnight, then at -20C.  Following genotype identification, samples were removed from RNAlater, and total mRNA extracted using the Norgen Biotek Total RNA Purification Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Memo1 mutant (ENU allele)


title: PRDX2 siRNA-transfected HT29 cells_rep1

description: PRDX2 siRNA-transfected HT29 cells replicate1


title: M3159 E4


title: M3150 E3

value: Control


title: M3159 E3


title: M3159 E5


title: TET1_FL_2 RNA-Seq

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: Column 9 in processed file

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in fastq files to hg19 and generating BAM files
ht-seq-count  with default settings to generate counts of each gene
Cuffdiff to generate FPKM and fold change of each condition compared to control, we filtered for genes that had 0 reads across all samples
Genome_build: hg19
Supplementary_files_format_and_content: The processed file is plain text format. The first 9 columns are the FPKMs of the individual samples.

source_name: HEK293T embryonic kidney cell line

growth_protocol: HEK293T cells were cultured in DMEM medium with 10% fetal bovine serum

extract_protocol:
RNA was isolated using Rneasy Plus Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: Cells were transfected with pIRES expression plasmids using Lipofectamine 2000.  RNA was isolated 4 days post transfection.

tag: cell type

value: embryonic kidney cell line

value: The 293T cell line is a highly transfectable derivative of human embryonic kidney 293 cells, and contains the SV40 T-antigen

tag: source

value: fetus


title: TET1_FL_3 RNA-Seq

description: Column 10 in processed file


title: Osr2+/- lower molar

city: Cincinnati

first: Rulang

last: Jiang

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.Implanted in tophat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: molar mesechyme

extract_protocol: E14.5 mouse embryo heads were frozen in OCT in liquid nitrogen, micro-dissect the molar mesenchyme by LCM after frozen section. Micro-dissected tissues were frozen at −80°C, total RNA was extracted by using RNeasy micro kit from Qiagen.cDNA was made by the NuGEN Ovation RNA-Seq v2 Assay.

value: mixed background

value: molar mesechyme

tag: age

value: embryonic day 14.5

value: Control Osr2+/-


title: Osr2-/- lower molar

value: mutant Osr2-/-


title: armadillo_R1410_GTGAAA_L007

organism: Dasypus novemcinctus


title: M3150 E4


title: Sample 9_mdx+GTx-026

first: Daniel

middle: Lee

last: Johnson

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

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

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

value: mdx

tag: treated with

value: gastrocnemious


title: Sample 8_mdx+GTx-026


title: TET1_FL_1 RNA-Seq

description: Column 8 in processed file


title: 5month old GAA Knock-out_1

value: gastrocnemius muscle

value: 5 month old

tag: genotype

value: GAA knock-out


title: Sample 5_mdx+vehicle

value: vehicle


title: TET1_ALT_3 RNA-Seq

description: Column 4 in processed file


title: Control siRNA-transfected HT29 cells_rep1

description: Control siRNA-transfected HT29 cells replicate1

value: Control siRNA


title: Sample 6_mdx+vehicle


title: TET1_ALT_2 RNA-Seq

description: Column 3 in processed file


title: Sample 7_mdx+GTx-026


title: Sample 3_wildtype +Vehicle

source_name: wildtype +Vehicle_gastrocnemious

value: wildtype


title: TET1_ALT_1 RNA-Seq

description: Column 2 in processed file


title: Sample 1_wildtype +Vehicle


title: Sample 2_wildtype +Vehicle


title: mouse_101116_lane_7

value: placenta


title: Empty Vector_2 RNA-Seq

description: Column 6 in processed file

value: embryonic kidney cell line


title: Sample 4_mdx+vehicle


title: Empty Vector_1 RNA-Seq

description: Column 5 in processed file

value: The 293T cell line is a highly transfectable derivative of human embryonic kidney 293 cells, and contains the SV40 T-antigen


title: canis_familiaris_101116_lane_8

organism: Canis lupus familiaris


title: TET1_FL_3 Dream

description: minimum sequencing depth 20 reads per CpG site

data_processing:
Sequencing reads were mapped to SmaI sites in the human genome (hg19) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor based on observed vs expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated plain text file

extract_protocol:
DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA).
Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB).
Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

treatment_protocol: Cells were transfected with pIRES expression plasmids using Lipofectamine 2000.  Genomic DNA was isolated 4 days post transfection.

tag: expression plasmid


title: opossum_091125_lane_7

organism: Monodelphis domestica


title: TET1_ALT_3 Dream


title: Rad18-deficient, 0 min, input

city: Tokyo

first: Yasukazu

last: Daigaku

address: 3-8-31 Ariake Koto-ku

department: Cancer institute

country: Japan

institute: Japanese Foundation for Cancer Research

description:
rad18-delta-0min-input
BrdU-IP-seq-cdc25-18-gr25pc.wig
BrdU-IP-seq-cdc25-18-gr50pc.wig
BrdU-IP-seq-cdc25-18-gr75pc.wig

data_processing:
Sequence pair-end reads were mapped to the S. pombe reference genome using bowtie2 with 50bp-triming of 3'-side of R1 and R2 reads.
Pairs of sequence reads which were properly aligned were selected based on 0x2 bit of the flag paramer of each pair.
Pairs of sequence read mapping to a single genomic location: 300-bp bin  were summed.
Normalized numbers were generated by dividing the sequence pair counts at each bin by the total number of reads.
Replication progression was calculated (see the original paper) for each 300 bp region of the genome (termed local replication rate) when the whole genome was either 25, 50 or 75% replicated.
Genome_build: ASM294v2.23
Supplementary_files_format_and_content: Wig files, datasets of local replicarion rates across the genome

organism: Schizosaccharomyces pombe

source_name: Genomic DNA from rad18-deleted cells 0 min after cdc25 G2 arrest and release

growth_protocol: Cells were synchronized in G2 phase by cdc25 block and sampled

extract_protocol: Genomic DNA was sonicated and denatured (mock treated). The yielded single-stranded DNA was converted to double strands, which were used for Illumina library preparation using NEBNext® Ultra™ DNA Library Prep Kit.

value: h- smt-0 leu1-32 ade6-704  leu1::[leu1-adh:hENT1] his7+ adh1::hsv-TK cdc25-22 rhp18::KanMX6

tag: protocol

value: cdc25 G2 arrest and release

tag: time (after release)

value: 0 min

tag: chip  antibody

value: input


title: Rad18-deficient,160 min, IP

description:
rad18-delta-160min-IP
BrdU-IP-seq-cdc25-18-gr25pc.wig
BrdU-IP-seq-cdc25-18-gr50pc.wig
BrdU-IP-seq-cdc25-18-gr75pc.wig

source_name: Genomic DNA from rad18-deleted cells 160 min after cdc25 G2 arrest and release

growth_protocol: Cells were synchronized in G2 phase by cdc25 block, released into meduim containing 0.5 micro-M of BrdU and sampled at 160 min after release

extract_protocol: Genomic DNA was subjected to immunoprecipitation with anti-BrdU antibody. The yielded single-stranded DNA was converted to double strands, which were used for Illumina library preparation using NEBNext® Ultra™ DNA Library Prep Kit.

tag: strain

tag: genotype/variation

value: 160 min

value: anti-BrdU antibody (BD biosciences, catalog# 347580)


title: TET1_FL_2 Dream


title: TET1_FL_1 Dream


title: TET1_ALT_2 Dream


title: TET1_ALT_1 Dream


title: Rad18-deficient,90 min, IP

description:
rad18-delta-90min-IP
BrdU-IP-seq-cdc25-18-gr25pc.wig
BrdU-IP-seq-cdc25-18-gr50pc.wig
BrdU-IP-seq-cdc25-18-gr75pc.wig

source_name: Genomic DNA from rad18-deleted cells 90 min after cdc25 G2 arrest and release

growth_protocol: Cells were synchronized in G2 phase by cdc25 block, released into meduim containing 0.5 micro-M of BrdU and sampled at 90 min after release

value: 90 min


title: Rad18-deficient,85 min, IP

description:
rad18-delta-85min-IP
BrdU-IP-seq-cdc25-18-gr25pc.wig
BrdU-IP-seq-cdc25-18-gr50pc.wig
BrdU-IP-seq-cdc25-18-gr75pc.wig

source_name: Genomic DNA from rad18-deleted cells 85 min after cdc25 G2 arrest and release

growth_protocol: Cells were synchronized in G2 phase by cdc25 block, released into meduim containing 0.5 micro-M of BrdU and sampled at 85 min after release

value: 85 min


title: Empty Vector_3 Dream


title: Rad18-deficient,80 min, IP

description:
rad18-delta-80min-IP
BrdU-IP-seq-cdc25-18-gr25pc.wig
BrdU-IP-seq-cdc25-18-gr50pc.wig
BrdU-IP-seq-cdc25-18-gr75pc.wig

source_name: Genomic DNA from rad18-deleted cells 80 min after cdc25 G2 arrest and release

growth_protocol: Cells were synchronized in G2 phase by cdc25 block, released into meduim containing 0.5 micro-M of BrdU and sampled at 80 min after release

value: 80 min


title: Empty Vector_2 Dream


title: Empty Vector_1 Dream


title: Rad18-proficient, 0 min, input

description:
rad18-plus-0min-input
BrdU-IP-seq-cdc25-wt-gr25pc.wig
BrdU-IP-seq-cdc25-wt-gr50pc.wig
BrdU-IP-seq-cdc25-wt-gr75pc.wig

source_name: Genomic DNA from rad18+ cells 0 min after cdc25 G2 arrest and release

value: h- smt-0 leu1-32 ade6-704  leu1::[leu1-adh:hENT1] his7+ adh1::hsv-TK cdc25-22


title: Rad18-deficient,70 min, IP

description:
rad18-delta-70min-IP
BrdU-IP-seq-cdc25-18-gr25pc.wig
BrdU-IP-seq-cdc25-18-gr50pc.wig
BrdU-IP-seq-cdc25-18-gr75pc.wig

source_name: Genomic DNA from rad18-deleted cells 70 min after cdc25 G2 arrest and release

growth_protocol: Cells were synchronized in G2 phase by cdc25 block, released into meduim containing 0.5 micro-M of BrdU and sampled at 70 min after release

value: 70 min


title: Rad18-proficient,160 min, IP

description:
rad18-plus-160min-IP
BrdU-IP-seq-cdc25-wt-gr25pc.wig
BrdU-IP-seq-cdc25-wt-gr50pc.wig
BrdU-IP-seq-cdc25-wt-gr75pc.wig

source_name: Genomic DNA from rad18+ cells 160 min after cdc25 G2 arrest and release


title: Rad18-deficient,75 min, IP

description:
rad18-delta-75min-IP
BrdU-IP-seq-cdc25-18-gr25pc.wig
BrdU-IP-seq-cdc25-18-gr50pc.wig
BrdU-IP-seq-cdc25-18-gr75pc.wig

source_name: Genomic DNA from rad18-deleted cells 75 min after cdc25 G2 arrest and release

growth_protocol: Cells were synchronized in G2 phase by cdc25 block, released into meduim containing 0.5 micro-M of BrdU and sampled at 75 min after release

value: 75 min


title: Rad18-proficient,90 min, IP

description:
rad18-plus-90min-IP
BrdU-IP-seq-cdc25-wt-gr25pc.wig
BrdU-IP-seq-cdc25-wt-gr50pc.wig
BrdU-IP-seq-cdc25-wt-gr75pc.wig

source_name: Genomic DNA from rad18+ cells 90 min after cdc25 G2 arrest and release


title: Empty Vector_3 RNA-Seq

description: Column 7 in processed file

value: fetus


title: Day 30 human embryonic stem cell-derived cardiomyocytes. Circadian 48 hour time course

city: Utrecht

first: Pieterjan

last: Dierickx

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
D30_T4_T48
CEL-Seq
Processed data file: D30_T4_T48.txt

data_processing:
Paired-end reads obtained by CEL-Seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: D0_T48.txt: Tab-delimited text file for sequencing libraries of timepoint T48 of the D0 timecourse, listing all genes (rows) and the number of sequenced reads for all samples. Column name indicates the timepoint followed by a number indicating one of the triplicates. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: D15_T4_T48.txt: Tab-delimited text file for sequencing libraries of the D15 timecourse, listing all genes (rows) and the number of sequenced reads for all samples. Column name indicates the timepoint of the experiment followed by a number indicating one of the triplicates. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. These are the combined counts from both libraries that were sequenced in order to obtain this timecourse (library1, which contains barcodes 4-20, and library2, which contains barcodes 21-39).
Supplementary_files_format_and_content: D30_T4_till_T48_TN.txt: Tab-delimited text file for sequencing libraries of the D30 timecourse, listing all genes (rows) and the number of sequenced reads for all samples. Column name indicates the timepoint of the experiment followed by a number indicating one of the triplicates. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Embryonic stem (ES) cell-derived cardiomyocytes, day 30, circadian timepoints ZT4-ZT48

growth_protocol: Human embryonic stem (ES) cells were grown in Essential8 medium (Gibco). The ES cell line is described in: "NKX2-5(eGFP/w) hESCs for isolation of human cardiac progenitors and cardiomyocytes." Elliott et al., Nature Methods, 2011 (doi: 10.1038/nmeth.1740).

extract_protocol:
Cells were lysed with TRIzol (Life Technologies) and total RNA was isolated according to the manufacturer's instructions.
RNA was processed using the previously described CEL-Seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired-end sequencing.

treatment_protocol:
Human embryonic stem (ES) cells were differentiated towards cardiomyocytes following the published protocol (van den Berg et al., 2015, doi: 10.1007/7651_2014_178).
Three different circadian time-courses were performed for 48 hrs in total in the same manner for undifferentiated ES cells, and D15 and D30 ES cell-derived cardiomyocytes. For the circadian samples of the undifferentiated ES cells, we only performed CEL-Seq on (circadian) timepoint 48 (hrs), while for D15 and D30 ES cell-derived cardiomyocytes, CEL-Seq was performed on the whole circadian time-course (T4-T48).

value: Embryonic stem cell-derived cardiomyocytes

tag: day


title: Day 15 human embryonic stem cell-derived cardiomyocytes. Circadian 48 hour time course part 2

description:
D15_T4_T48_library2
CEL-Seq
Processed data file: D15_T4_T48.txt

source_name: Embryonic stem (ES) cell-derived cardiomyocytes, day 15, circadian timepoints ZT4-ZT48


title: Rad18-proficient,70 min, IP

description:
rad18-plus-70min-IP
BrdU-IP-seq-cdc25-wt-gr25pc.wig
BrdU-IP-seq-cdc25-wt-gr50pc.wig
BrdU-IP-seq-cdc25-wt-gr75pc.wig

source_name: Genomic DNA from rad18+ cells 70 min after cdc25 G2 arrest and release


title: Day 0 human embryonic stem cells. Timepoint 48 (3 replicates)

description:
D0_T48
CEL-Seq
Processed data file: D0_T48.txt

source_name: Undifferentiated embryonic stem (ES) cells, day 0, circadian timepoint ZT48

value: Undifferentiated embryonic stem cells


title: Rad18-proficient,85 min, IP

description:
rad18-plus-85min-IP
BrdU-IP-seq-cdc25-wt-gr25pc.wig
BrdU-IP-seq-cdc25-wt-gr50pc.wig
BrdU-IP-seq-cdc25-wt-gr75pc.wig

source_name: Genomic DNA from rad18+ cells 85 min after cdc25 G2 arrest and release


title: Day 15 human embryonic stem cell-derived cardiomyocytes. Circadian 48 hour time course part 1

description:
D15_T4_T48_library1
CEL-Seq
Processed data file: D15_T4_T48.txt


title: Rad18-proficient,80 min, IP

description:
rad18-plus-80min-IP
BrdU-IP-seq-cdc25-wt-gr25pc.wig
BrdU-IP-seq-cdc25-wt-gr50pc.wig
BrdU-IP-seq-cdc25-wt-gr75pc.wig

source_name: Genomic DNA from rad18+ cells 80 min after cdc25 G2 arrest and release


title: elephant_091125_lane_5

organism: Loxodonta africana

source_name: placenta

value: placenta


title: Rad18-proficient,75 min, IP

description:
rad18-plus-75min-IP
BrdU-IP-seq-cdc25-wt-gr25pc.wig
BrdU-IP-seq-cdc25-wt-gr50pc.wig
BrdU-IP-seq-cdc25-wt-gr75pc.wig

source_name: Genomic DNA from rad18+ cells 75 min after cdc25 G2 arrest and release


title: Col-0_4ºC

status: Public on May 11 2017

city: Madrid

first: Julio

last: Salinas

address: Ramiro de Maeztu, 9

department: Departamento de Biologia Medioambiental

country: Spain

institute: Centro de Investigaciones Biologicas

description: Arabidopsis thaliana L.

data_processing:
The original image data produced by the sequencer (Illumina HiSeq 2000) was transferred into sequences, which were defined as "raw reads" (or "raw data") and saved as ".fastq" files.
Raw data was cleaned removing adaptor sequences, reads with a percentage of unknown Ns greater than 5% and low-quality reads (reads with >50% bases with quality index <5). Clean reads were saved as ".fastq" files.
Reads were mapped to reference Arabidopsis genome TAIR10 release using SOAP2 software (Li et al., 2009). No more than five mismatches per read were allowed.
The gene expression level was calculated using the RPKM method (Mortazavi et al., 2008) using uniquely mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include gene identifiers, the number of uniquely mapped clean reads, length, coverage and the corresponding estimation of expression level (RPKM) for each gene model.

organism: Arabidopsis thaliana

source_name: leaves from two-week-old plants, WT, 4ºC

growth_protocol: Plants were grown under long-day photoperiods (photon flux of 90 µmol m-2 s-1). For cold treatments, plants were grown on soil. For high salt treatments, plants were grown on 0.5X GM medium plates.

extract_protocol:
Leaf tissue was collected, immediately frozen on liquid nitrogen and stored at -80ºC. For total RNA extraction, frozen tissue was homogenized to a fine powder and total RNA was extracted using TRIzol® Reagent (Life Technologies), treated with DNaseI (Roche) and further cleaned with RNeasy Plant Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For cold treatment, plants were exposed to 4ºC for 24h under long-day photoperiods (photon flux of 40 µmol m-2 s-1). For high salt treatments, plants were transferred from 0.5X GM medium to 150 mM NaCl-containing plates for 10h under long-day photoperiods (photon flux of 90 µmol m-2 s-1).

tag: ecotype/background

value: WT

value: leaves

value: two weeks

tag: treatment


title: lsm8-1_4ºC

description: Arabidopsis thaliana L.

source_name: leaves from two-week-old plants, lsm8-1, 4ºC


title: lsm8-1_GM

description: Arabidopsis thaliana L.

source_name: leaves from two-week-old plants, lsm8-1, GM

value: GM


title: Col-0_GM

description: Arabidopsis thaliana L.

source_name: leaves from two-week-old plants, WT, GM


title: lsm8-1_20ºC

description: Arabidopsis thaliana L.

source_name: leaves from two-week-old plants, lsm8-1, 20ºC


title: AtWT_COBL9GFP1

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description: processed data file: AtWTCOBL9GFP_FPKM.xlsx

data_processing:
Illumina Casava1.7.0 was used for basecalling of Sample 8955 and Casava 1.8.2 was used for all the other samples.
The first 15bp of each read were trimmed.
Reads were mapped using Tophat v2.0.3 for Arabidopsis samples and Tophat v2.0.9 for rice samples. Default settings with --segment length 17 parameter were used to map the reads to the reference annotation (already mentioned in the sample information above).
FPKM values were calculated by Cufflinks2 v2.1.1 with multiread correction (-u -G).
Raw reads were counted by HTSeq v0.6.1 with setting -m intersection-strict -s no -f bam and analyzed by edgeR to identify the differentially expressed genes between Atrhd6_WERGFP and AtWT_WERGFP. For the DE analysis, first, low expressed genes were filtered (counts per million > 1 for at least three out of total six samples were kept). Second, raw counts were normalized using the default timmed mean of M-values and the variation was modeled using a tag-wise dispersion. Last, the raw P values were corrected for multiple testing by Benjamini-Hochberg method and a FDR q-value <= 0.01 and fold-change >=2 was used to find the significantly differentially expressed genes.
Genome_build: See sample information above.
Supplementary_files_format_and_content: Excel file that contains the normalized cpm and DE result for the analysis between Atrhd6_WERGFP and AtWT_WERGFP. Excel files that contain the FPKM value generated by Cufflinks for the gene expression profiling of the AtWT_COLB9GFP and the OsWT_EXPA30GFP.

growth_protocol: Seeds were surface sterilized and germinated on agarose-solidified MS media under constant light at 22C.

extract_protocol:
RNA was extracted using Qiagen RNAeasy Plant Micro Kit.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: Root tips of seedlings plated 4-5 days were pooled and digested using cell wall degrading enzymes. Fluorescence-activated cell sorting was used to specifically collect the cells that expressed GFP.

tag: variety

value: Columbia

value: Ensembl Plant Release 19, TAIR10

value: 4-5 days after plating


title: AtWT_COBL9GFP3


title: lsm8-1_NaCl

description: Arabidopsis thaliana L.

source_name: leaves from two-week-old plants, lsm8-1, NaCl

value: NaCl


title: AtWT_COBL9GFP2


title: AtWT_WERGFP3

description: processed data file: Atrhd6WERGFP_vs_AtWTWERGRP_DE_result.xlsx

source_name: wild-type WER::GFP

value: wild-type WER::GFP


title: Atrhd6_WERGFP2

source_name: rhd6 WER::GFP

value: rhd6 WER::GFP


title: Col-0_20ºC

description: Arabidopsis thaliana L.

source_name: leaves from two-week-old plants, WT, 20ºC


title: 12-703-4 (PDGFB; p53KO; H3.3K27M)

city: New York

first: Oren

middle: Josh

last: Becher

address: 1468 Madison Avenue, A21-02

department: Pediatrics

institute: Mount Sinai

description: PDGF-B; H3.3K27M; p53 loss

data_processing:
Read pairs were aligned to mouse genome (mm9) by Expression Analysis
The number of read-pairs per gene was determined based upon the NCBIM37 gene annotation from ENSEMBLE database
Genes that did not have at least 10 read-pairs in any single library were excluded from further analysis
Normalization and differential expression analysis was carried out using the DESeq bioconductor package (default parameters)
Genome_build: mm9
Supplementary_files_format_and_content: EXCEL, differentially expressed genes between PDGF-B; H3.3K27M; p53 loss and PDGF-B; p53 loss

source_name: brainstem glioma

extract_protocol:
tumors were isolated and snap frozen.  Total RNA was isolated by Expression Analysis (EA), RNA quality was assessed at EA, and Illumina RNAseq was performed at EA.
RNA libraries were prepared for sequencing at Expression Analysis using standard Illumina protocols

tag: genetic strain

value: Nestin tv-a; p53 floxed mouse

tag: mouse strain


title: AtWT_WERGFP2


title: 12-623-12 (PDGFB; p53KO; H3.3K27M)

description: PDGF-B; H3.3K27M; p53 loss


title: BOW2008A94

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

description: Count_table.txt, CPM_table.txt

data_processing:
Real time Analysis (RTA): HiSeq 2500 - RTA v1.18.64, HCS v2.2.58; HiSeq 4000 - RTA v2.73, HCS v3.3.52
Base-calling: Hiseq 2500 was basecalled with bcl2fastq v1.8.4; HiSeq 4000 was basecalled with bcl2fastq v2.17.1.14
Adapter trimming: RNA-seq reads were trimmed for Nextera and Illumina  adapter sequences using skewer-v0.1.125
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.0-beta with default parameters to a modified reference genome comprising the human genome, Homo sapiens GRCh37 - human_g1k_v37, and fasta sequences for ERCC spike-ins
Mark Duplicates: Duplicate reads were marked using MarkDuplicates.jar implemented in Picard tools v1.92
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 75 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million
Genome_build: GRCh37
Supplementary_files_format_and_content: Count_table.txt: raw read counts for all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: CPM_table.txt:  Counts per million normalized counts all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: Metadata_Table.xlsx: Contains two excel sheets with Sheet 1 = cell metadata with information regarding treatment sequencing batch, imaging, and QC metrics
Supplementary_files_format_and_content: Metadata_Table.xlsx: Sheet2= Contains description of column headers of cell metadata in Sheet 1

source_name: K562 cell line

growth_protocol: K562 cells were maintained (1–10 × 105 cell/ml) in T75 flasks in RPMI 1640 + 2mM Glutamine + 10% Foetal Bovine Serum (FBS)

extract_protocol:
FluidigmC1 RNAseq protocol: cDNA was generated using SMARTer Ultra Low RNA Kit (Clontech)
Nextera XT DNA Library Preparation Kit (Illumina)

treatment_protocol: Hoechst 33342 (2µM final concentration, 20min at RT), propidium iodide (3.75µM final concentration, 20min at RT)

tag: cell type

value: Human immortalised myelogenous leukemia line

tag: passages

value: 90-92 hours

tag: cell line

value: untreated


title: BOW2008A93

description: Count_table.txt, CPM_table.txt


title: Atrhd6_WERGFP1

tag: age


title: AtWT_WERGFP1


title: 11-1204-1 (PDGFB; p53KO; H3.3WT)

description: PDGF-B; p53 loss


title: 11-1114-2 (PDGFB; p53KO; H3.3WT)

description: PDGF-B; p53 loss


title: Col-0_NaCl

description: Arabidopsis thaliana L.

source_name: leaves from two-week-old plants, WT, NaCl

tag: tissue


title: BOW2008A95

description: Count_table.txt, CPM_table.txt


title: BOW2008A96

description: Count_table.txt, CPM_table.txt


title: BOW2008A81

description: Count_table.txt, CPM_table.txt


title: BOW2008A82

description: Count_table.txt, CPM_table.txt


title: 12-623-6 (PDGFB; p53KO; H3.3K27M)

description: PDGF-B; H3.3K27M; p53 loss


title: BOW2008A84

description: Count_table.txt, CPM_table.txt


title: BOW2008A92

description: Count_table.txt, CPM_table.txt


title: Atrhd6_WERGFP3


title: 11-1106-4 (PDGFB; p53KO; H3.3WT)

description: PDGF-B; p53 loss


title: BOW2008A90

description: Count_table.txt, CPM_table.txt


title: BOW2008A78

description: Count_table.txt, CPM_table.txt


title: BOW2008A77

description: Count_table.txt, CPM_table.txt


title: BOW2008A89

description: Count_table.txt, CPM_table.txt


title: BOW2008A88

description: Count_table.txt, CPM_table.txt


title: BOW2008A91

description: Count_table.txt, CPM_table.txt


title: BOW2008A87

description: Count_table.txt, CPM_table.txt


title: BOW2008A9

description: Count_table.txt, CPM_table.txt


title: BOW2008A76

description: Count_table.txt, CPM_table.txt


title: BOW2008A74

description: Count_table.txt, CPM_table.txt


title: BOW2008A86

description: Count_table.txt, CPM_table.txt


title: BOW2008A80

description: Count_table.txt, CPM_table.txt


title: BOW2008A85

description: Count_table.txt, CPM_table.txt


title: BOW2008A83

description: Count_table.txt, CPM_table.txt


title: BOW2008A8

description: Count_table.txt, CPM_table.txt


title: BOW2008A79

description: Count_table.txt, CPM_table.txt


title: BOW2008A71

description: Count_table.txt, CPM_table.txt


title: BOW2008A70

description: Count_table.txt, CPM_table.txt


title: BOW2008A75

description: Count_table.txt, CPM_table.txt


title: BOW2008A7

description: Count_table.txt, CPM_table.txt


title: BOW2008A68

description: Count_table.txt, CPM_table.txt


title: BOW2008A73

description: Count_table.txt, CPM_table.txt


title: BOW2008A67

description: Count_table.txt, CPM_table.txt


title: BOW2008A72

description: Count_table.txt, CPM_table.txt


title: BOW2008A65

description: Count_table.txt, CPM_table.txt


title: BOW2008A69

description: Count_table.txt, CPM_table.txt


title: BOW2008A57

description: Count_table.txt, CPM_table.txt


title: BOW2008A50

description: Count_table.txt, CPM_table.txt


title: BOW2008A54

description: Count_table.txt, CPM_table.txt


title: BOW2008A55

description: Count_table.txt, CPM_table.txt


title: BOW2008A66

description: Count_table.txt, CPM_table.txt


title: BOW2008A49

description: Count_table.txt, CPM_table.txt


title: BOW2008A64

description: Count_table.txt, CPM_table.txt


title: BOW2008A63

description: Count_table.txt, CPM_table.txt


title: BOW2008A5

description: Count_table.txt, CPM_table.txt


title: BOW2008A46

description: Count_table.txt, CPM_table.txt


title: BOW2008A62

description: Count_table.txt, CPM_table.txt


title: BOW2008A47

description: Count_table.txt, CPM_table.txt


title: BOW2008A53

description: Count_table.txt, CPM_table.txt


title: BOW2008A52

description: Count_table.txt, CPM_table.txt


title: BOW2008A44

description: Count_table.txt, CPM_table.txt


title: BOW2008A60

description: Count_table.txt, CPM_table.txt


title: BOW2008A51

description: Count_table.txt, CPM_table.txt


title: BOW2008A59

description: Count_table.txt, CPM_table.txt


title: BOW2008A48

description: Count_table.txt, CPM_table.txt


title: BOW2008A6

description: Count_table.txt, CPM_table.txt


title: BOW2008A41

description: Count_table.txt, CPM_table.txt


title: BOW2008A58

description: Count_table.txt, CPM_table.txt


title: BOW2008A56

description: Count_table.txt, CPM_table.txt


title: BOW2008A42

description: Count_table.txt, CPM_table.txt


title: BOW2008A61

description: Count_table.txt, CPM_table.txt


title: BOW2008A45

description: Count_table.txt, CPM_table.txt


title: BOW2008A38

description: Count_table.txt, CPM_table.txt


title: BOW2008A40

description: Count_table.txt, CPM_table.txt


title: BOW2008A4

description: Count_table.txt, CPM_table.txt


title: BOW2008A36

description: Count_table.txt, CPM_table.txt


title: BOW2008A35

description: Count_table.txt, CPM_table.txt


title: BOW2008A34

description: Count_table.txt, CPM_table.txt


title: BOW2008A33

description: Count_table.txt, CPM_table.txt


title: BOW2008A37

description: Count_table.txt, CPM_table.txt


title: BOW2008A31

description: Count_table.txt, CPM_table.txt


title: BOW2008A32

description: Count_table.txt, CPM_table.txt


title: BOW2008A3

description: Count_table.txt, CPM_table.txt


title: BOW2008A27

description: Count_table.txt, CPM_table.txt


title: BOW2008A43

description: Count_table.txt, CPM_table.txt


title: BOW2008A26

description: Count_table.txt, CPM_table.txt


title: BOW2008A28

description: Count_table.txt, CPM_table.txt


title: BOW2008A21

description: Count_table.txt, CPM_table.txt


title: BOW2008A22

description: Count_table.txt, CPM_table.txt


title: BOW2008A30

description: Count_table.txt, CPM_table.txt


title: BOW2008A25

description: Count_table.txt, CPM_table.txt


title: BOW2008A24

description: Count_table.txt, CPM_table.txt


title: BOW2008A20

description: Count_table.txt, CPM_table.txt


title: BOW2008A39

description: Count_table.txt, CPM_table.txt


title: BOW2008A2

description: Count_table.txt, CPM_table.txt


title: BOW2008A19

description: Count_table.txt, CPM_table.txt


title: BOW2008A29

description: Count_table.txt, CPM_table.txt


title: BOW2008A17

description: Count_table.txt, CPM_table.txt


title: BOW2008A18

description: Count_table.txt, CPM_table.txt


title: BOW2008A15

description: Count_table.txt, CPM_table.txt


title: BOW2008A14

description: Count_table.txt, CPM_table.txt


title: BOW2008A16

description: Count_table.txt, CPM_table.txt


title: BOW2008A13

description: Count_table.txt, CPM_table.txt


title: BOW2008A12

description: Count_table.txt, CPM_table.txt


title: BOW2008A11

description: Count_table.txt, CPM_table.txt


title: BOW2008A1

description: Count_table.txt, CPM_table.txt


title: BOW2008A10

description: Count_table.txt, CPM_table.txt


title: U2OS ZBTB48 KO clone 5

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4.
Fastq files were mapped with STAR_2.5.1b to the human reference version GRCh38 together with the accompanying gene model v84 from Ensembl.
Secondary alignments were filtered with samtools 1.3.
Counts for every gene were calculated with FeatureCounts v1.4.6-p2 with the gene model v84 from Ensembl.
Counts were normalized and modeled with DESeq2_1.6.3.
Genome_build: GRCh38
Supplementary_files_format_and_content: *tsv: Tab separated file containing counts per gene.

source_name: U2OS cell line, ZBTB48 KO

growth_protocol: HeLa and U2OS cells were cultivated in 4.5 g/l glucose, 4 mM glutamine, 1 mM sodium pyruvate containing Dulbecco's Modified Eagle's Medium (D-MEM) supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco) in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Exponentially growing HeLa and U2OS WT and ZBTB48 KO cells were harvested and RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNaseI digestion according to the manufacturer's instructions. RNA quality was assessed and only samples with a RIN score of 10 were subjected to RNAseq library preparation.
Ribosomal RNA was removed from 1 µg of total RNA using the Ribo-Zero rRNA removal kit (Epicentre). rRNA-depleted RNA was purified with RNA Clean XP beads (Agencourt) and eluted in 8.5 µl of elution buffer. Next, library preparation was continued starting from the elute, prime, fragment step (but skipping the polyA selection steps) of the TruSeq stranded mRNA LT sample prep kit (Illumina) until the end of library preparation. 12 PCR cycles were used for library amplification. Libraries were quantified using the Qubit dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Thermo Fisher) and their profile was checked on a 2100 Bioanalyzer with a DNA 1000 chip (Agilent). Libraries were pooled in equimolar ratio and sequenced on a HiSeq (Illumina). HeLa libraries: 50bp PE in high-output mode plus 7 cycles for the index read; U2OS libraries: SE.

value: ZBTB48 KO


title: BOW2008A23

description: Count_table.txt, CPM_table.txt


title: U2OS ZBTB48 KO clone 2


title: U2OS ZBTB48 KO clone 4


title: U2OS WT rclone 5

source_name: U2OS cell line, WT


title: U2OS ZBTB48 KO clone 1


title: U2OS ZBTB48 KO clone 3


title: U2OS WT clone 4


title: U2OS WT clone 3


title: U2OS WT clone 1


title: HeLa ZBTB48 KO clone 5

source_name: HeLa cell line, ZBTB48 KO

value: HeLa


title: HeLa ZBTB48 KO clone 2


title: HeLa WT clone 5

source_name: HeLa cell line, WT


title: HeLa ZBTB48 KO clone 3


title: HeLa ZBTB48 KO clone 4


title: HeLa WT clone 1


title: HeLa ZBTB48 KO clone 1


title: HeLa WT clone 3


title: HeLa WT clone 2


title: HeLa WT clone 4


title: Hela input WT

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4.
Fastq files were mapped with Bowtie 1.1.2 to the human reference version GRCh38 together with the accompanying gene model.
Secondary alignments were filtered with samtools 1.3.
Peaks were called with Macs 2.1.0.20150420 with parameters -m 5 50 -g hs -bw 200.
Genome_build: GRCh38
Supplementary_files_format_and_content: *tsv: Tab-separated file containing peaks called by macs2 (XLS macs2 format) with the following columns: chr, start, end, length, abs_summit, pileup, -log10(pvalue), fold_enrichment, -log10(qvalue), name.

source_name: HeLa cell line, WT, input

extract_protocol:
Subconfluent HeLa and U2OS cells were washed twice with cold PBS and double cross-linked first with 2 mM DSG (Pierce, predissolved in DMSO) in PBS for 45 min at RT, intermitted by a wash with cold PBS and secondly with 1% formaldehyde in DMEM for 20 min at RT. The formaldehyde was quenched with glycine (0.125 M final concentration) for 5 min at RT, cells were scraped with a plastic scraper and washed once in PBS. For lysis, cells were resuspended in buffer 1 (50 mM Tris-HCl pH 8.0, 250 mM sucrose, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol, 0.5% IGEPAL-630 (Sigma-Aldrich), 0.25% Triton X-100, 0.25% Tween20) for 15 min, pelleted and subsequently resuspended in buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) for 10 min both at 4 ºC. Sonication was performed in 1.5 ml sonication buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.0) with a Branson Digital Sonifier S-450D for 7.5 min (30% amplitude, 10 sec on, 20 sec off).
Library preparation was performed with the NuGEN Ovation Ultralow Library System V2 1-96. Libraries were prepared with a starting amount of 124-6869pg of ChIP DNA and 10-145ng of input DNA were amplified in 13-18 PCR cycles, depending of the starting material used. Libraries were profiled on a 2100 Bioanalyzer (Agilent) and quantified using the Qubit dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Thermo Fisher). Size selection was performed with Lab ChIP XT with XT DNA 700 chips (Perkin Elmer) for the 300-500 bp fragment range according to the manufacturer's instructions. Libraries were pooled in equimolar ratio and sequenced on a HiSeq (Illumina), 50bp SR in high-output mode plus 7 cycles for the index read.

tag: chip antibody


title: U2OS input WT

source_name: U2OS cell line, WT, input


title: HeLa input KO clone2

source_name: HeLa cell line, ZBTB48 KO, input


title: HeLa input KO clone1


title: U2OS WT clone2 ab1

source_name: U2OS cell line, WT, ZBTB48 ChIP

value: ZBTB48 (ab1)


title: U2OS WT clone1 ab1

value: WT


title: U2OS ZBTB48 KO clone1 ab2

source_name: U2OS cell line, ZBTB48 KO, ZBTB48 ChIP

value: ZBTB48 (ab2)


title: U2OS ZBTB48 KO clone2 ab2


title: U2OS ZBTB48 KO clone2 ab1


title: U2OS WT clone 2


title: HeLa WT clone2 ab2

source_name: HeLa cell line, WT, ZBTB48 ChIP


title: HeLa WT clone1 ab2


title: HeLa WT clone2 ab1


title: HeLa WT clone1 ab1


title: HeLa ZBTB48 KO clone2 ab2

source_name: HeLa cell line, ZBTB48 KO, ZBTB48 ChIP


title: HeLa ZBTB48 KO clone1 ab2


title: HeLa ZBTB48 KO clone2 ab1


title: U2OS input KO

source_name: U2OS cell line, ZBTB48 KO, input


title: U2OS WT clone2 ab2


title: Input DNA

city: Groningen

first: Katrin

last: Paeschke

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

institute: University Medical Center Groningen

description: Mms1 is Myc-tagged

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using bowtie (Langmead et al. Genome Biology 2009)
Peaks were called using MACS2 (Zhang et al. Genome biology 2008) using default parameters and options -no model -extsize 180
Genome_build: sacCer3
Supplementary_files_format_and_content: MACS2.0 output file

source_name: whole organism

growth_protocol: yeast cells were growth according to standard protocols

extract_protocol:
yeast lysates were cleared and DNA was sheared to an average length of 200bp. Mms1-Myc was isolated using an antibody directed against Myc.
For genome-wide sequencing, DNA was treated according to manufacturer’s instructions (NEBNext ChIP-seq Library Prep Master Mix Set for Illumina, NEB) and submitted to deep sequencing (Illumina Nextseq500 sequencer).


title: HeLa ZBTB48 KO clone1 ab1


title: Mms1-Myc ChIPseq

description: Mms1 is Myc-tagged

value: Anti-Myc (Clontech, catalog# 631206, lot# 1602362A)


title: U2OS WT clone1 ab2


title: BOW3221A95

description: Count_table.txt, CPM_table.txt

treatment_protocol: CellTracker Green CMFDA "ThermoFisher" (1µM final concentration, 30min at RT), LIVE/DEAD® Fixable Red Dead Cell Stain "ThermoFisher" (per manufacturer protocol)

value: 20-22 hours


title: BOW3221A94

description: Count_table.txt, CPM_table.txt

treatment_protocol: CellTracker Orange CMRA "ThermoFisher" (1µM final concentration, 30min at RT), LIVE/DEAD® Fixable Red Dead Cell Stain "ThermoFisher" (per manufacturer protocol)

value: treated (1 hour with 1 μM Imatinib)


title: BOW3221A93

description: Count_table.txt, CPM_table.txt


title: BOW3221A89

description: Count_table.txt, CPM_table.txt


title: BOW3221A91

description: Count_table.txt, CPM_table.txt


title: BOW3221A92

description: Count_table.txt, CPM_table.txt


title: BOW3221A9

description: Count_table.txt, CPM_table.txt


title: BOW3221A90

description: Count_table.txt, CPM_table.txt


title: BOW3221A96

description: Count_table.txt, CPM_table.txt


title: BOW3221A86

description: Count_table.txt, CPM_table.txt


title: BOW3221A87

description: Count_table.txt, CPM_table.txt


title: U2OS ZBTB48 KO clone1 ab1


title: BOW3221A84

description: Count_table.txt, CPM_table.txt


title: BOW3221A83

description: Count_table.txt, CPM_table.txt


title: BOW3221A82

description: Count_table.txt, CPM_table.txt


title: BOW3221A80

description: Count_table.txt, CPM_table.txt


title: BOW3221A8

description: Count_table.txt, CPM_table.txt


title: BOW3221A85

description: Count_table.txt, CPM_table.txt


title: BOW3221A81

description: Count_table.txt, CPM_table.txt


title: BOW3221A77

description: Count_table.txt, CPM_table.txt


title: BOW3221A78

description: Count_table.txt, CPM_table.txt


title: BOW3221A79

description: Count_table.txt, CPM_table.txt


title: BOW3221A76

description: Count_table.txt, CPM_table.txt


title: BOW3221A75

description: Count_table.txt, CPM_table.txt


title: BOW3221A74

description: Count_table.txt, CPM_table.txt


title: BOW3221A73

description: Count_table.txt, CPM_table.txt


title: BOW3221A88

description: Count_table.txt, CPM_table.txt


title: BOW3221A71

description: Count_table.txt, CPM_table.txt


title: BOW3221A70

description: Count_table.txt, CPM_table.txt


title: BOW3221A7

description: Count_table.txt, CPM_table.txt


title: BOW3221A72

description: Count_table.txt, CPM_table.txt


title: BOW3221A69

description: Count_table.txt, CPM_table.txt


title: BOW3221A68

description: Count_table.txt, CPM_table.txt


title: BOW3221A65

description: Count_table.txt, CPM_table.txt


title: BOW3221A66

description: Count_table.txt, CPM_table.txt


title: BOW3221A63

description: Count_table.txt, CPM_table.txt


title: BOW3221A64

description: Count_table.txt, CPM_table.txt


title: BOW3221A62

description: Count_table.txt, CPM_table.txt


title: BOW3221A67

description: Count_table.txt, CPM_table.txt


title: BOW3221A6

description: Count_table.txt, CPM_table.txt


title: BOW3221A60

description: Count_table.txt, CPM_table.txt


title: BOW3221A59

description: Count_table.txt, CPM_table.txt


title: BOW3221A57

description: Count_table.txt, CPM_table.txt


title: BOW3221A54

description: Count_table.txt, CPM_table.txt


title: BOW3221A55

description: Count_table.txt, CPM_table.txt


title: BOW3221A56

description: Count_table.txt, CPM_table.txt


title: BOW3221A53

description: Count_table.txt, CPM_table.txt


title: BOW3221A52

description: Count_table.txt, CPM_table.txt


title: BOW3221A50

description: Count_table.txt, CPM_table.txt


title: BOW3221A5

description: Count_table.txt, CPM_table.txt


title: BOW3221A49

description: Count_table.txt, CPM_table.txt


title: BOW3221A47

description: Count_table.txt, CPM_table.txt


title: BOW3221A43

description: Count_table.txt, CPM_table.txt


title: BOW3221A41

description: Count_table.txt, CPM_table.txt


title: BOW3221A48

description: Count_table.txt, CPM_table.txt


title: BOW3221A44

description: Count_table.txt, CPM_table.txt


title: BOW3221A61

description: Count_table.txt, CPM_table.txt


title: BOW3221A46

description: Count_table.txt, CPM_table.txt


title: BOW3221A38

description: Count_table.txt, CPM_table.txt


title: BOW3221A45

description: Count_table.txt, CPM_table.txt


title: BOW3221A4

description: Count_table.txt, CPM_table.txt


title: BOW3221A40

description: Count_table.txt, CPM_table.txt


title: BOW3221A35

description: Count_table.txt, CPM_table.txt


title: BOW3221A37

description: Count_table.txt, CPM_table.txt


title: BOW3221A31

description: Count_table.txt, CPM_table.txt


title: BOW3221A34

description: Count_table.txt, CPM_table.txt


title: BOW3221A33

description: Count_table.txt, CPM_table.txt


title: BOW3221A30

description: Count_table.txt, CPM_table.txt


title: BOW3221A29

description: Count_table.txt, CPM_table.txt


title: BOW3221A3

description: Count_table.txt, CPM_table.txt


title: BOW3221A58

description: Count_table.txt, CPM_table.txt


title: BOW3221A27

description: Count_table.txt, CPM_table.txt


title: BOW3221A28

description: Count_table.txt, CPM_table.txt


title: BOW3221A26

description: Count_table.txt, CPM_table.txt


title: BOW3221A51

description: Count_table.txt, CPM_table.txt


title: BOW3221A25

description: Count_table.txt, CPM_table.txt


title: BOW3221A39

description: Count_table.txt, CPM_table.txt


title: BOW3221A42

description: Count_table.txt, CPM_table.txt


title: BOW3221A24

description: Count_table.txt, CPM_table.txt


title: BOW3221A36

description: Count_table.txt, CPM_table.txt


title: BOW3221A19

description: Count_table.txt, CPM_table.txt


title: BOW3221A2

description: Count_table.txt, CPM_table.txt


title: BOW3221A32

description: Count_table.txt, CPM_table.txt


title: BOW3221A18

description: Count_table.txt, CPM_table.txt


title: BOW3221A20

description: Count_table.txt, CPM_table.txt


title: BOW3221A22

description: Count_table.txt, CPM_table.txt


title: BOW3221A16

description: Count_table.txt, CPM_table.txt


title: BOW3221A17

description: Count_table.txt, CPM_table.txt


title: BATF sgRNA rep1

city: Boston

last: Gewurz

state: Massachusetts

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: tab-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and DESeq2 normalized counts of genes, respectively

source_name: Lymphoblastoid cell lines

growth_protocol: Gm12878 were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal calf serum (FCS) in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
Prior to sample preparation for RNA-seq, dead cells were removed on day 3 after puromycin selection (day 5 after lentiviral transduction of sgRNAs) using Dead Cell Removal Kit (Miltenyi Biotec #130-090-101, San Diego, CA) following the manufacturer’s manual. Total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: GM12878 with stable Streptococcus pyogenes Cas9 were established by lentiviral transduction using the pLentiCas9-Blast(Addgene plasmid #52962) and blasticidin selection. For all transductions, lentiviruses were made by 293T (obtained from ATCC) transfection. To make specific gene knockouts, control or sgRNA oligos against IRF2, IRF4, and BATF were synthesized by Integrated DNA Technologies, Inc. and cloned into the pLentiGuide-Puro vector (Addgene plasmid #52963).  Puromycin selection (3μg/ml) was added 48 hours post transduction. Cells were collected for downstream analysis 3 days after puromycin selection. All sgRNAs were validated for their efficiency of gene knockout by western blot.  Each biological group is performed in triplicates.

value: BATF sgRNA


title: BATF sgRNA rep3


title: IRF4 sgRNA rep2

value: IRF4 sgRNA


title: BOW3221A15

description: Count_table.txt, CPM_table.txt


title: IRF4 sgRNA rep3


title: IRF2 sgRNA rep3

value: IRF2 sgRNA


title: BOW3221A14

description: Count_table.txt, CPM_table.txt


title: IRF2 sgRNA rep2


title: IRF4 sgRNA rep1


title: Control sgRNA rep3

description:
BATF.sgRNA_vs_Control.sgRNA.txt
IRF2.sgRNA_vs_Control.sgRNA.txt
IRF4.sgRNA_vs_Control.sgRNA.txt

value: Control sgRNA


title: BATF sgRNA rep2


title: IRF2 sgRNA rep1


title: BOW3221A13

description: Count_table.txt, CPM_table.txt


title: Control sgRNA rep2


title: BOW3221A11

description: Count_table.txt, CPM_table.txt


title: BOW3221A10

description: Count_table.txt, CPM_table.txt


title: BOW3221A23

description: Count_table.txt, CPM_table.txt


title: Control sgRNA rep1


title: BOW3221A21

description: Count_table.txt, CPM_table.txt


title: BOW3221A1

description: Count_table.txt, CPM_table.txt