title: HEK293T TNIP2 196-346 Pulldown 2

city: Kansas City

first: Gaye

middle: L

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

description: HEK293T TNIP2 196-346 Pulldown 2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and mapped to hg19 whole genome using tophat version 2.0.14
Read counts for each gene were calculated with Rsubread 1.16.1, normalized counts were obtained using DESeq2 1.6.3
FPKM values were calculated with DESeq2 1.6.3
Genome_build: hg19

source_name: Halo purified RNA

growth_protocol: HEK293 cells were cultured in DMEM + FBS + 10% pen/strep

extract_protocol:
Total RNA was prepared from either 100 µl of the whole cell extract or from 90 µl of the Halo purified samples using RNeasy® Mini kits (Qiagen). Ribosomal RNA was removed using the Ribo-Zero kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with plasmids expressing either Halo-tag (control) or Halo-TNIP2 196-346

value: Halo -TNIP2 196-346 transfected cells


title: HEK293T TNIP2 196-346 Pulldown 1

status: Public on Oct 24 2016

type: SRA

country: USA

description: HEK293T TNIP2 196-346 Pulldown 1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: genotype/variation


title: HEK293T TNIP2 196-346 Pulldown 3

description: HEK293T TNIP2 196-346 Pulldown 3


title: HEK293T TNIP2 196-346 Input 2

description: HEK293T TNIP2 196-346 Input 2

source_name: total RNA


title: HEK293T TNIP2 196-346 Input 3

description: HEK293T TNIP2 196-346 Input 3


title: Mouse Uterus OMLPS 21

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

data_processing:
Illumina CASAVA pipeline version 1.8.2 was used for basecalling.
Sequencing reads were aligned to the reference genome (mm10) employing Subread, and summarized at the gene level using featureCounts, with Entrez gene annotation.
Differentially expressed genes were identified from gene-level counts employing edgeR.
Coexpression network analysis was performed on VST transformed counts (varianceStabilizingTransformation, DESeq2 package).
Genome_build: mm10
Supplementary_files_format_and_content: Data are provided as raw gene-level counts, and DESeq2 VST transformed counts

organism: Mus musculus

source_name: Uterus

extract_protocol:
Total RNA was extracted employing TRIzol followed by RNeasy
Libraries were prepared according to Illumina's TruSeq Stranded mRNA Protocol (RS-122-2101) at the Australian Genome Research Facility. Libraries were sequenced on the HiSeq 2500 with 50 bp single reads following the manufactures protocols.

tag: strain

value: Balb/c

tag: tissue

value: Uterus

tag: treatment

value: OM85 pretreat plus LPS challenge

tag: age

value: Gestational day 17.5


title: Mouse Uterus LPS 18

value: LPS challenge


title: Mouse Uterus OM 9

value: OM85 pretreatment


title: HEK293T TNIP2 196-346 Input 1

description: HEK293T TNIP2 196-346 Input 1


title: Mouse Uterus OM 8


title: Mouse Uterus LPS 14


title: Mouse Uterus Control 6

value: sham control


title: HEK293T Control Pulldown 2

description: HEK293T Control Pulldown 2

value: Halo tag transfected cells


title: HEK293T Control Pulldown 1

description: HEK293T Control Pulldown 1


title: Mouse Uterus OM 7


title: Mouse Uterus Control 4


title: HEK293T Control Input 1

description: HEK293T Control Input 1


title: HEK293T Control Input 3

description: HEK293T Control Input 3


title: Mouse Uterus Control 3


title: HEK293T Control Input 2

description: HEK293T Control Input 2


title: FACS sorted brain mural cells 2

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: FACS sorted brain mural cells 2

data_processing:
The reads were aligned to the Ensembl mouse gene assembly (NCBIM37) using Tophat2 software (version 2.0.4).
The duplicated reads were removed using the picard tool (version 1.92).
FPKM sumaary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each sample

source_name: brain

extract_protocol:
We isolated double positive cells from the brain of Pdgfrb-eGFP/NG2-DsRed transgenic mice using FACS. Cells were lysed, RNA extracted and sequenced with next-generation sequencing (NGS). For comparison, we also determined the transcriptome of brain microvascular fragments (containing both endothelial cells and mural cells) isolated by mechanical tissue disintegration, collagenase digestion and immune-panning using anti-CD31 antibodies coupled to magnetic beads.
RNA integrity and concentration of the FACS sorted cells and the isolated microvasculature was checked with the Agilent RNA 6000 pico kit and an Agilent 2100 Bioanalyzer (Agilent Biotechnologies). For conversion of the RNA to a cDNA library for Illumina sequencing, the SMARTer® Stranded Total RNA Sample Prep Kit - Low Input Mammalian kit from Clontech was used according to the manufacturer’s protocol. The total RNA was depleted from rRNA and tRNA’s with the RiboGone- Mammalian kit (Clontech) prior to library construction.

value: NG2-DsRed/Pdgfrb-eGFP mice (Gensat.org. Line name:Tg(Pdgfrb-eGFP)JN169Gsat/Mmucd).

value: brain


title: Mouse Uterus Control 5


title: Mouse Uterus Control 1


title: FACS sorted brain mural cells 3

description: FACS sorted brain mural cells 3


title: FACS sorted brain mural cells 1

description: FACS sorted brain mural cells 1


title: Col s+h-2R

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

data_processing:
Used Tophat and Bowtie for read alignment onto Arabidopsis reference genome and Cufflinks for obtaining the FPKMs and assessment of significance of fold change
Genome_build: TAIR9
Supplementary_files_format_and_content: Tab-delimited file (opens in Excel); FPKMs for Control, Salt, Heat, and Salt-Heat combination stress

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Plants were grown on soil mixture under controlled conditions: 21oC, 12-h light cycle, 100 mmol m-2s-1, and relative humidity of 70%

extract_protocol:
Total RNA was extracted by using Trizol reagent and purified using Qiagen RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All treatments were perfomed in parallel. Salt stress was imposed on 12-d-old plants by applying 150mM NaCl for 13 days. Twenty five-d-old plants grown in the presense or absense of salt stress were subjected to heat stress (44oC) for 1h.

value: leaves

tag: ecotype

value: Twenty-five-day-old plants

value: Treated with salt and heat combination


title: Col s+h-1R


title: Mouse Uterus OM 10


title: Mouse Uterus Control 2


title: Brain microvascular fragments 2

description: Brain microvascular fragments 2


title: Brain microvascular fragments 3

description: Brain microvascular fragments 3


title: Col s+h-3R


title: NRPE1_RIPseq_ago4_rep2

city: Ann Arbor

first: Andrzej

middle: T

last: Wierzbicki

state: Michigan

address: 830 N. University

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description: processed data file: PolV_transcripts_rep2.txt

data_processing:
Reads were mapped to the Arabidopsis genome (TAIR10) using SOAPsplice 1.10 (Huang et al., 2011, PMCID: PMC3268599), allowing a maximum gap size within a read of 10300bp.mapped to the same chromosome and were at most 3kb apart.
Reads belonging to the same pair were joined after mapping and only kept if reads from the same pair had mapped to the same chromosome and were at most 3kb apart.
Pol V transcript calling used data from two independent biological replicates of RIP-seq. Data from both repeats were first combined to determine the ends of Pol V-associated RNAs. Then, read counts from both repeats were considered separately to filter the transcript list using a combination of arbitrary criteria and statistical testing using the negative binomial test. The filtering criteria included a minimum of 8 reads in Col-0, a minimum 4-fold enrichment between Col-0 and nrpe1, a p value of 0.05 and an FDR of 0.05. AGO4-bound transcript were called using AGO4 RIP-seq Col-0/ago4 and considered Pol V-dependent if AGO4 RIP-seq Col-0/nrpe1 >= 4 or considered Pol V-independent if AGO4 RIP-seq nrpe1/ago4 >= 4.
Genome_build: TAIR10
Supplementary_files_format_and_content: PV_Transcripts.txt: Tab-delimited text file includes coordinates of Pol V transcripts called using Pol V (NRPE1) RIP-seq rep. 1 and 2 (see header for more information).
Supplementary_files_format_and_content: AGO4_TRANSCRIPTS.txt: Tab-delimited text file includes coordinates of AGO4-bound transcripts called using AGO4 RIP-seq (see header for more information).

growth_protocol: Plants were grown in soil in long-day conditions. For all experiments, approximately 2.5 weeks old seedlings were used.

extract_protocol:
RNA-immunoprecipitation was performed as described in Rowley et al., 2013 (PMID:23707621) using NF-pellet paint instead of Glycoblue. Experiments were performed with protein A agarose beads coated with salmon sperm DNA (for anti-NRPE1) or  Dynabeads protein A (anti-AGO4), respectively. After immuno-precipitation, samples were digested with Turbo DNase
Illumina TruSeq Stranded mRNA Sample Prep Kit, replacing the heat fragmentation with an incubation step on ice for 5 minutes

treatment_protocol: Tissue were fixed with 0.5% formaldehyde as described in Rowley et al., 2013 (PMID:23707621)

tag: ecotype background

value: ago4-1 (introgressed into the Col-0 background; PMID 12522258)

value: approx. 2.5 weeks old

value: aerial part of seedlings grown on soil

tag: rip antibody

tag: molecule subtype

value: nuclear RNA


title: Col h-3R

value: Treated with 44oC heat stress for 2h


title: HEK293T Control Pulldown 3

description: HEK293T Control Pulldown 3


title: NRPE1_RIPseq_Col-0_rep2

value: wild-type


title: NRPE1_RIPseq_idn2_rep2


title: WT-3

city: Singapore

first: Lina

last: Yao

address: 5 Science Drive 2

department: Department of Microbiology and Immunology

country: Singapore

institute: National University of Singapore

description: RNA was collectd on day 6

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
Two methods were used to analyze the HISEQ data.
1. Sequenced reads were trimmed for adaptor sequences, low-quality sequences, and then mapped to the in-house Dunaliella tertiolecta transcriptome database Dt_v10 based on BLASTX against Chlamydomonas reinhardtii. Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated in Partek® Flow® software (version 4.0, Partek Inc., St. Louis, MO, USA). Subsequently, the different expressed transcripts were imported into Partek® Genomics Suite® software (version 6.6, Partek Inc., St. Louis, MO, USA) for gene annotation and KEGG pathway analysis. ‘Additional_file_1_1’ was the full set of output data. Contigs that could be successfully annotated, and with FDR <= 0.05 and fold-change of mutant / WT >= 2 or <= -2 were used as the criteria to filter the significant differential expressed genes, as shown in ‘Additional_file_1_2’.
2. Transcript level comparison was also performed using RSEM with default settings. The count data from RSEM was imported in the Ebseq pipeline for differential expression analysis. The output count data are shown in ‘Additional_file_2_1’. We further filtered out contigs with FDR<=0.05 (‘Additional_file_2_2’) using RSEM software. Subsequently, we used Trinity de novo assembly for G11_7 and WT sampels to bulid up the transcriptome database (‘Dt-G11_7.fa’), and then BLASTX against reference protein sequences from all plants and bacterial proteins from NCBI. The corresponding annotation file is shown in ‘Dt-G11_annotation’. Contigs that could be successfully annotated, and with FDR <= 0.05 are shown in ‘Additional_file_2_3’. The National Supercomputing Centre (NSCC) was used for running the aforementioned software, which greatly benefits from the abundant computing resources.
genome build: Dt_v10 (GEO accession no. GSE70876), Dt-G11_7.fa
processed data files format and content: tab-delimited text files include gene annotation and differential expression analysis, text file of transcriptome database.
Additional_file_1_1: Differential gene expression analysis result from Partek Flow software.
Additional_file_1_2: Contigs that could be successfully annotated, and with FDR <= 0.05 and fold-change of mutant / WT >= 2 or <= -2 (Partek pipeline).
Additional_file_2_1: Count data from RSEM pipeline.
Additional_file_2_2: Differential gene expression results with FDR <= 0.05 (RSEM-Ebseq pipeline).
Additional_file_2_3: Contigs that cound be successfully annotated, and with FDR <= 0.05.
Dt-G11_7.fa: This FASTA file obtained from Trinity de novo assembly for G11_7 and WT sampels.
Dt-G11_annotation: Annotation file for Dt-G11_7

organism: Dunaliella tertiolecta UTEX 'LB 999'

source_name: Wild type

growth_protocol: Dunaliella tertiolecta strain UTEX LB-999 was obtained from the UTEX Culture Collection of Algae (University of Texas at Austin, TX). The cells were grown in flasks in sterile ATCC-1174 DA liquid medium (American Type Culture Collection at Manassas, Virginia) containing 0.5M NaCl incubated on a rotary shaker at 25°C, under 12 h light/12 h dark with light intensity of 30 μmol photons•m-2•s-1.

extract_protocol:
Total RNA of G11_7, WT was extracted on day 6 from D. tertiolecta cells using an RNeasy® Plant Mini Kit (Qiagen, Valencia, CA, USA), according to manufacturer’s protocol. RNA quality was verified using Agilent RNA 6000 Nano Kit in Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.) and gel electrophoresis.
The libraries were sequenced using Illumina HiSEQ 4000 High Sequencers and prepared for sequencing using standard Illumina protocols.

treatment_protocol: G11_7 mutant was generated from random insertional mutagenesis after neutral lipid screening, and subsequent two rounds of fluorescence-activated cell sorting.

tag: time point

value: day 6

value: Wild type


title: Brain microvascular fragments 1

description: Brain microvascular fragments 1


title: Col h-2R

value: Treated with 44oC heat stress for 1h


title: Col h-1R


title: NRPE1_RIPseq_nrpe1_rep1

description: processed data file: PolV_transcripts_rep1.txt


title: G11_7-3

description: RNA was collectd on day 6


title: Col s-1R

value: Treated with 150mM NaCl for 15days


title: NRPE1_RIPseq_Col-0_rep1


title: WT-2

description: RNA was collectd on day 6


title: G11_7-2

description: RNA was collectd on day 6


title: AGO4_RIPseq_ago4

description: processed data file: AGO4-bound_transcripts.txt

value: anti-AGO4 (Wierzbicki et al., 2009; doi:10.1038/ng.365)


title: Col c-3R

value: Control


title: Col c-2R


title: WT-1

description: RNA was collectd on day 6


title: NRPE1_RIPseq_nrpe1_rep2


title: AGO4_RIPseq_nrpe1


title: G11_7-1

description: RNA was collectd on day 6


title: AGO4_RIPseq_Col-0


title: Col c-1R


title: p_ctrl_t1_5

status: Public on Oct 23 2016

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

description: CEL-Seq

data_processing:
The left end reads were barcode split with FASTX-Toolbox and the right end reads were used for mapping to mm10 genome (UCSC) with TopHat 2.1.0.
The reads that aligned to exonic regions of all UCSC annotated genes were counted with FeatureCounts 1.4.3-p1.
The raw read counts per gene were imported in edgeR 3.10.5 (R 3.2.2) and a MDS plot was made to detect outlier samples, and mouse #17 was removed for further analysis.
Only the genes with at least 1 count per million reads in at least three samples were kept for analysis.
To find differentially expressed genes between CD69+ and CD69- DMSO treated cells, edgeR’s GLM likelihood ratio test was used taking variation into account caused by: library number, mouse, and time point. To find differential genes between CD69+ GSI treated cells at day 2 and CD69- GSI treated cells at day 2; and between CD69+ GSI treated cells at day 2 and CD69+ DMSO treated cells at day 2, the GLM likelihood ratio test was used taking variation caused by: library number, and mouse into account. FDR correction for multiple testing was used and adjusted p-values < 0.05 were considered significant.
Genome_build: mm10

source_name: CD69+ memory T cells (lung)

extract_protocol:
RNA was isolated from 200-1500 cells. Samples were precipitated in 0.3M Sodium Acetate (Sigma), 2 ug Glycogen (Thermo Scientific) and 70% EtOH overnight at -20C. After washing in 70% EtOH, RNA pellets were dissolved in primer mix and incubated for 2 minutes at 70 °C.
CEL-seq approach was used as earlier described in PMID: 22939981, which uses poly-T primers attached by a unique 8 nt barcode for each sample, followed by the Illumina 5' adaptor sequence and a T7 reverse transcription promotor. Samples were linear amplified and pooled into 7 libraries which were sequenced over 4 lanes on a Illumina HIseq2500. Paired-end 50 bp reads were generated, the left reads were used for barcode identification and the right reads for alignment.

value: lung

tag: cell type

value: CD69+ memory T cells

tag: mouse

value: DMSO

tag: time

tag: library


title: p_ctrl_t2_4

description: CEL-Seq


title: p_GSI_t1_5

description: CEL-Seq

value: GSI


title: p_GSI_t2_4

description: CEL-Seq


title: p_ctrl_t1_4

description: CEL-Seq


title: p_GSI_t2_3

description: CEL-Seq


title: Col s-3R

value: leaves

value: Twenty-five-day-old plants


title: p_ctrl_t1_3

description: CEL-Seq


title: p_GSI_t1_3

description: CEL-Seq


title: p_GSI_t1_4

description: CEL-Seq


title: Col s-2R


title: p_ctrl_t2_3

description: CEL-Seq


title: p_GSI_t1_2

description: CEL-Seq


title: p_GSI_t2_1

description: CEL-Seq


title: p_ctrl_t1_2

description: CEL-Seq


title: p_ctrl_t2_2

description: CEL-Seq


title: m_ctrl_t2_4

description: CEL-Seq

source_name: CD69- memory T cells (lung)

value: CD69- memory T cells


title: m_ctrl_t1_4

description: CEL-Seq


title: m_GSI_t2_3

description: CEL-Seq


title: m_GSI_t1_5

description: CEL-Seq


title: m_ctrl_t1_3

description: CEL-Seq


title: m_GSI_t2_4

description: CEL-Seq


title: p_ctrl_t1_1

description: CEL-Seq


title: m_GSI_t2_2

description: CEL-Seq


title: m_GSI_t1_2

description: CEL-Seq


title: m_ctrl_t1_1

description: CEL-Seq


title: m_ctrl_t1_2

description: CEL-Seq


title: m_GSI_t1_1

description: CEL-Seq


title: p_GSI_t2_2

description: CEL-Seq


title: m_ctrl_t2_3

description: CEL-Seq


title: m_ctrl_t2_1

description: CEL-Seq


title: p_GSI_t1_1

description: CEL-Seq


title: m_ctrl_t2_2

description: CEL-Seq


title: m_ctrl_t1_5

description: CEL-Seq


title: p_ctrl_t2_1

description: CEL-Seq


title: THY1+HE- TAC2

city: los angeles

first: Sara

last: Ranjbarvaziri

state: California

address: 650 Charles E young

department: Cardiology

institute: ucla

data_processing:
The raw reads were generated by HiSeq 2500 sequencing control software. Illumina Casava1.8 software was used for basecalling and fastq file generation.
Fastq files were input into NextGene software (version 2.3.3). Low quality sequences were removed. Sequence data was then mapped to mm10 whole genome.
The subsequent statistical analyses were performed using Partek genomics Suite 6.6. Thresholds for selecting significant genes were set at >= 1.5-fold and p<0.05. Genes that met both criteria simultaneously were considered as significant changes.
Global functional analyses, network analyses and canonical pathway analyses were performed using Ingenuity Pathway Analysis (Ingenuity® Systems, www.ingenuity.com).
Genome_build: mm10
Supplementary_files_format_and_content: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated in NextGene (version 2.3.3).

source_name: THY1+HE- sorted cells

extract_protocol:
Thy1+HE- cells were double sorted directly into RNA Later solution (Ambion). Total RNA were extracted using RNeasy miniElute cleanup kit (Qiagen) according to manufacturer’s instructions.
The cDNA library was generated using the reagents provided in the Illumina ® TruSeq™ RNA Sample Preparation v2 Kit (Illumina).
The clustering was performed on a cBot cluster generation system using an Illumina HiSeq single read cluster generation kit (Illumina) according to the manufacturer's instructions. The amplified cDNA library was sequenced on an Illumina HiSeq 2500 for estimating transcript abundance (1X50 reads and >12 million reads/sample).

treatment_protocol: Thy1+HE- cells were isolated from sham- and TAC-operated hearts 7 days after operation

value: TAC

tag: organ

value: heart

tag: day

value: 7 days post surgery


title: THY1+HE- TAC1


title: THY1+HE- TAC3


title: m_GSI_t1_4

description: CEL-Seq


title: m_GSI_t1_3

description: CEL-Seq


title: THY1+HE- Sham1

value: sham


title: ZIKV rep2

city: MIAMI

first: Fan

last: Lai

state: FL

address: 1501 NW 10th Ave, BRB 731G

institute: University of Miami

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 mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Trizol
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: infection status

value: ZIKV infected


title: THY1+HE- Sham3


title: Mock rep2

value: not infected


title: ZIKV rep1


title: THY1+HE- Sham2


title: A125PrF [BS-Seq]

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

country: China

institute: Sun Yat-sen University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Paired-end HiSeq2000 sequencing reads were aligned by BSmooth bisulfite alignment pipeline (version 0.7.1) as previously described in detail. Briefly, reads were aligned by Bowtie2 (version 2.0.1) against human genome (hg19) as well as the lambda phage genome.
After alignment, methylation measurements for each CpG were extracted from aligned reads. We filtered out measurements with mapping quality < 20 or nucleotide base quality on cytosine position < 10 and we also removed measurements from the 5’ most 10 nucleotides of both mates.
bsseq package in BSmooth was used to identify small and large differentially methylated regions (DMRs).
Genome_build: hg19
Supplementary_files_format_and_content: text file, methylated read count and total read count at each CpG site and each sample

molecule: genomic DNA

source_name: Patient A125

growth_protocol: Unless otherwise stated, cells were grown to 70% (A38-Lg) or 100% (A38-Per) confluence in DMEM with 10% Fetal Bovine Serum (FBS)

extract_protocol:
DNA was extracted with MasterPure kits
Whole genome bisulfite sequencing libraries were generated using TruSeq DNA Sample preparation protocol (Illumina) with modifications. Bisulfate conversion was done after gel size selection using EZ DNA Methylation-Gold Kit (Zymo Research). To amplify bisulfate converted library Kapa Hifi Uracil+ (Kapa Biosystems) polymerase was used.

value: Primary Tumor


title: A124PrF [BS-Seq]

source_name: Patient A124


title: A125PrS [BS-Seq]


title: A125Lv2 [BS-Seq]

value: liver metastasis


title: A124Per [BS-Seq]

value: peritoneal metastasis


title: A125Lv1 [BS-Seq]


title: 38-Lg_1_INP_batch2

description: Input for 38-Lg_1_K36me3

data_processing:
Basecalls performed using CASAVA version 1.8.2
For 46 bp paired-end Illumina HiSeq2000 sequencing data, reads were aligned against human genome (hg19) using BWA with default parameters. After alignment, duplicate reads were removed and only uniquely aligned reads were kept for further analysis. For 48 bp single-end Solid sequencing data, reads were aligned using Bowtie with default parameters and only uniquely aligned reads were kept for further analysis.
For narrow histone modification peaks including H3K4Me3, H3K9Ac, H3K16Ac and H3K27ac, MACS2 were used for peak calling with default parameters. While for broad histone modifications peaks in including H3K36Me3, H3K27me3, H3K9Me2/3, and yH2AX, peak calling were performed using RSEG which is based on hidden Markov model (HMM) and specifically designed for identifying broad histone peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bed files, called peaks by MACS2 and called domains by RSEG

source_name: Patient A38

extract_protocol:
For ChIP-seq, Input and IP DNA were extracted with Phenol:Chloroform.
Libraries were prepared from 10-20 ng of IP ChIP DNA and 100-150 ng of input DNA according to Illumina’s instructions along with the ChIP-seq DNA Sample Prep Kit (IP-102-1001). Briefly, samples were checked for quality and concentration from 150-250 bp on a bioanalyzer. DNA was end-repaired using Klenow polymerase in 58 μL of reaction buffer. For IP DNA, Klenow was diluted 1:5. Samples were incubated at 20°C for 30 minutes and subsequently purified on QIAquick PCR purification columns. A-tails were then added to the DNA with Klenow and dATP in NEB buffer 2 at 37°C for 30 minutes and cleaned with Qiagen MiniElute PCR purification columns. Sequencing adapters were then ligated onto the DNA for 15 minutes at room temperature followed by cleaning with MiniElute columns. Samples were then run on 2% agarose gels and DNA from 216-366 bp (DNA plus adapters) were cut from the gel and purified with a Qiagen QIAquickGel Extraction kit. Concentrations were then checked on a bioanalyzer and 8 ng were PCR amplified with Phusion polymerase (Fisher) for 15 cycles (10 sec 98°C, 30 sec 65°C, 30 sec 72°C) followed by 5 minutes at 72°C. Samples were then cleaned with Ampure kits (Illumina) and washed with 80% ethanol. DNA samples were resuspended at the end of the cleanup into 17.5 μL buffer EB (Qiagen) and subjected to next generation sequencing on Illumina HiSeq platform according to manufacturers instructions.

treatment_protocol: For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min at 37 degrees. Isolated chromatin was sonicated to avg length of 200-600bp.

tag: protocol

tag: antibody

value: N/A:Input DNA


title: Mock rep1

tag: tissue


title: m_GSI_t2_1

description: CEL-Seq

value: lung

tag: treatment


title: 38-Per_2_INP_K9me2

description: Input for 38-Per_2_K9me2


title: 38-Per_1_INP_K9me2

description: Input for 38-Per_1_K9me2


title: 38-Lg_1_INP_batch1

description: Input for 38-Lg_1_K27ac, 38-Lg_1_K9ac and 38-Lg_1_K9me3


title: 38-Per_2_INP_batch2

description: Input for 38-Per_2_K27ac


title: 38-Lg_2_INP


title: 38-Lg_2_K9me3

value: Abcam ab8898


title: 38-Per_2_INP_batch1

description: Input for 38-Per_2_K9ac, 38-Per_2_K4me3, 38-Per_2_K36me3 and 38-Per_2_K9me3


title: 38-Per_1_INP


title: 38-Lg_2_INP_K9me2

description: Input for 38-Lg_2_K9me2


title: 38-Lg_1_INP_K9me2

description: Input for 38-Lg_1_K9me2


title: 38-Lg_1_K9me3


title: A124Normal [BS-Seq]

value: Normal Pancreas


title: 38-Lg_2_K27me3

value: Millipore 07-449


title: 38-Lg_1_K9me2

value: Abcam ab1220


title: 38-Per_1_K9me3


title: 38-Per_1_K9me2


title: 38-Per_1_K27me3


title: 38-Lg_2_K9me2


title: 38-Per_2_K9me3


title: 38-Per_1_K4me3

value: Abcam ab8580


title: 38-Per_2_K36me3

value: Abcam ab9050


title: W 6h R1

city: Tübingen

first: Andreas

last: Wachter

address: Auf der Morgenstelle 32

department: Center for Plant Molecular Biology

country: Germany

institute: University of Tübingen

data_processing:
Fastx toolbox v.13 was used for demultiplexing
PALmapper v.0.5 was used to align reads to discover novel splice junctions using the following parameters: -M 3 -G 1 -E 4 -l 15 -L 25 -K 8 -C 35 -I 25000 -NI 2 -SA 100 -CT 10 -a -S -seed-hit-cancel-threshold 10000  -report-map-read -report-spliced-read  -report-map-region -report-splice-sites 0.9 -filter-max-mismatches 0 -filter-max-gaps 0 -filter -splice-region 5 -qpalma-use-map-max-len 2000 -f bamp -threads 2 -polytrim 40 -qpalma-prb-offset-fix -include-unmapped-reads -min-spliced-segment-len 12 -junction-remapping-coverage 3 -fixtrimleft 4 -fixtrimright 4 -no-gap-end 10 -qpalma-indel-penalty 10
PALmapper v.0.5 was used to align reads,  using the newly discovered splice junctions with the following parameters: -M 4 -G 1 -E 4 -l 15 -L 25 -K 8 -C 35 -I 25000 -NI 2 -SA 100 -CT 50 -a -S -seed-hit-cancel-threshold 10000  -report-map-read -report-spliced-read  -report-map-region -report-splice-sites 0.9 -filter-max-mismatches 0 -filter-max-gaps 0 -filter-splice-region 5 -qpalma-use-map-max-len 1000 -f bamn -threads 2 -polytrim 40 -qpalma-prb-offset-fix -min-spliced-segment-len 15 -junction-remapping-coverage 5 -junction-remapping-min-spliced-segment-len 15 -fixtrimleft 4 -fixtrimright 4 -qpalma-indel-penalty 1
Alignment post-processing was performed as follows:
Gene expression was quantified using rDiff v.1.0 with the default parameters
Genome_build: TAIR 10
Supplementary_files_format_and_content: Raw counts for gene expression in tab-delimited file.

source_name: etiolated seedling

growth_protocol: Arabidopsis thaliana Col-0 seeds were surface sterilized in 3.75% NaOCl and 0.01% Triton X-100 and plated on 1/2 MS medium containing 0.8% phytoagar (Duchefa) and 2% sucrose. They were stratified for at least 2 days at 4°C, then germination was induced in white light for 2h. Seedlings were grown at approximately 20°C for 6 days in darkness.

extract_protocol:
Total RNA was isolated using the EURx GeneMATRIX Universal RNA Purification kit with on-column Dnase digest according to the manufacturer's instructions.
Libraries were prepared using the Illumina TruSeqTM sample prep kit v2, Box A, following the protocol according to the guide version September 2012, starting from 4 µg total RNA. The PCR enrichment was done in 34 µL using only half the template available, and followed by an agarose gel purification step and extraction from the gel using the Qiagen MinElute gel extraction kit. Adapters used for multiplexing were 012 and 006 for duplexing, and 012, 006,  019, and 005 for quadruplexing

treatment_protocol: Etiolated seedlings were exposed to continuous white, red, or blue light for 1 or 6 h, or sampled at the onset of the time series, or kept in darkness for the 6 h time course.

tag: age

value: 6 days

value: exposed to white light for 6 h

tag: library multiplexing

value: duplexed


title: W 6hD R2

tag: ecotype

value: quadruplexed


title: 38-Lg_2_K9ac

value: Millipore 07-352


title: W 0h R2


title: 38-Per_2_K9ac


title: W 6hD R1


title: 38-Lg_1_K9ac


title: W 0h R1


title: R 6h R1

value: exposed to red light for 6 h


title: 38-Per_1_K9ac


title: 38-Per_2_K9me2


title: 38-Lg_1_K36me3


title: R 6h R2


title: W 6h R2


title: 38-Lg_1_K27ac

value: Abcam ab4729


title: R 1h R2

value: exposed to red light for 1 h


title: R 1h R1


title: 38-Per_1_K27ac


title: R 6hD R2


title: 38-Per_2_K27ac


title: R 0h R1


title: 38-Lg_2_K27ac


title: 38-Lg_SFM_rep2 [RNA-Seq]

data_processing:
Basecalls performed using CASAVA version 1.8.2
Paired-end HiSeq2000 sequencing reads were aligned against human genome (hg19) by OSA (version 2.0.1) with default parameters. After alignment, only uniquely aligned reads were kept for further analysis.
Reads count for each gene of all samples were estimated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and then were used to identify differentially expressed (DE) genes using DESeq package. Genes with adjusted p-value < 0.01 and fold-change > 2 between A38-41 and A38-5 were considered as DE genes.
Genome_build: hg19
Supplementary_files_format_and_content: text file, raw read counts of each gene for all samples

extract_protocol:
For RNA-seq, RNA was extracted with Trizol reagent.
RNA-Seq libraries were generated using TruSeq Stranded mRNA protacol (Illumina). 2ug of total RNA was used for library generation and 6 minutes of fragmentation. For enrichment of cDNA fragments 11 PCR cycles were used.

value: 70% (A38-Lg) serum free media


title: R 6hD R1


title: 38-Lg_SFM_rep1 [RNA-Seq]


title: R 0h R2


title: 38-Lg_rep2 [RNA-Seq]


title: 38-Per_SFM_rep2 [RNA-Seq]

value: 100% (A38-Per) serum free media


title: 38-Lg_2_INP_solid_batch2

description: Input for 38-Lg_2_K36me3_solid

value: N/A:Input DNA


title: 38-Lg_2_INP_solid_batch1

description: Input for 38-Lg_2_K4me3_solid and 38-Lg_2_K27me3_solid


title: B 6h R1

value: exposed to blue light for 6 h


title: 38-Lg_rep1 [RNA-Seq]


title: 38-Per_1_INP_solid

description: Input for 38-Per_1_K4me3_solid, 38-Per_1_K36me3_solid and 38-Per_1_K27me3_solid


title: B 6h R2


title: B 1h R2

value: exposed to blue light for 1 h


title: 38-Per_SFM_rep1 [RNA-Seq]


title: 38-Lg_2_K4me3


title: 38-Per_rep2 [RNA-Seq]


title: B 1h R1


title: B 0h R2


title: 38-Lg_2_K27me3_solid

value: Millipore 07-449


title: B 6hD R2


title: 38-Lg_rep2 [BS-Seq]


title: 38-Lg_rep1 [BS-Seq]


title: MELAS with m.A3243G mutation [sequencing]

city: Jinan

first: Wei

last: Wang

state: Shandong

address: West Wenhua Road

department: Department of Neurology

institute: Qilu Hospital, Shandong University

description: Muscle pool from 20 MELAS patients with m.A3243G mutation.

data_processing:
A proprietary pipeline script, mRNA Database (http://www.gencodegenes.org/releases/21.html) and lncRNA Database (http://www.gencodegenes.org/releases/21.html) were used for sequencing data analysis. A public software package, CleaveLand3.0, was used for analyzing sequencing data.
Genome_build: GENCODE release 21 (GRCh38)
Supplementary_files_format_and_content: Control without myopathy.txt: Tab-delimited text file includes RPKMs.
Supplementary_files_format_and_content: MELAS with m.A3243G mutation.txt: Tab-delimited text file includes RPKMs.

source_name: Frozen muscle, MELAS

growth_protocol: Muscle biopsies were obtained from patients with myopathy. The samples were stored at -80 °C until used.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analyzed using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >8.0. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manufacturer's instructions of the Ribo-Zero rRNA Removal kit (Epidemiology version) (Epicentre, an Illumina company, Madison, WI).
Following purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the RNA-Seq sample preparation kit (Illumina, San Diego, USA). The average insert size for the single-end libraries was 50 bp. We then performed the single-end sequencing (50 bp) on an Illumina HiSeq 2500 at the LC-BIO (Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Muscle biopsies from the same group were defrosted and pooled in one EP tube.

tag: disease status

value: Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS)

tag: genotype/variation

value: m.A3243G mutation

value: muscle biopsies


title: B 6hD R1

value: 6 days


title: 38-Per_rep1 [RNA-Seq]


title: 38-Per_1_K27me3_solid


title: R143_S4WT20h

status: Public on Oct 22 2016

city: La Jolla

first: Katja

last: Lamia

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

data_processing:
Base-calling perfermed using Genome Analyzer Pipeline Software
Reads trimming using cutadapt (version 1.3)
Tophat (version 2.0.13) and Bowtie2 were used to align the trimmed reads to mouse genome (mm10)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file: raw counts and RPKM values

source_name: mouse embryonic fibroblast

extract_protocol:
RNA was extracted using Trizol reagent.
RNAseq libraries were prepared using 500ng total RNA using the ribo zero (Epicentre) to remove rRNA and the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following manufacturer’s protocol.

tag: genotype

value: wildtype

value: mouse embryonic fibroblast

tag: hours after dexamethasone treatment


title: 38-Per_rep2 [BS-Seq]


title: R143_S4WT4h


title: R143_S4WT8h


title: 38-Lg_2_K36me3_solid

value: Abcam ab9050


title: R143_S4WT16h


title: R143_S4KO8h

value: Cry2 knockout


title: 38-Per_1_K36me3_solid


title: 38-Lg_2_K4me3_solid

value: Abcam ab8580


title: B 0h R1

value: quadruplexed


title: R143_S4KO20h


title: R143_S4WT0h


title: 38-Per_1_K4me3_solid


title: R143_S4WT12h


title: 38-Per_rep1 [BS-Seq]


title: R143_S4KO4h


title: R143_S4KO16h


title: R143_S4KO0h


title: R143_S3WT8h


title: R143_S3WT4h


title: R143_S3WT20h


title: R143_S3WT12h


title: Control without myopathy [sequencing]

description: Muscle pool from 20 healthy controls.

source_name: Frozen muscle, control

value: healthy

value: control


title: R143_S3WT0h


title: R143_S3KO8h


title: R143_S3KO4h


title: R143_S3KO16h


title: R143_S3KO20h


title: R143_S3KO12h


title: R143_S2WT20h


title: R143_S2WT4h


title: R143_S3KO0h


title: R143_S2WT12h


title: R143_S2KO8h


title: R143_S2WT8h


title: R143_S2WT16h


title: R143_S2WT0h


title: R143_S1WT8h


title: R143_S4KO12h


title: R143_S2KO20h


title: R143_S2KO4h


title: R143_S2KO16h


title: R143_S2KO12h


title: R143_S2KO0h


title: R143_S1WT20h


title: R143_S1WT0h


title: R143_S3WT16h


title: R143_S1WT16h


title: R143_S1KO4h


title: R143_S1KO20h


title: R143_S1KO8h


title: R143_S1WT4h


title: R143_S1WT12h


title: R143_S1KO12h


title: RNA-seq Celf1 +/+ PN3 rep2

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

description: mixed 129v/BL6 strain

data_processing:
TopHat 2.02 is used to align reads to reference genome.
Fragments Per Kilobase per Megabase of library size (FPKM) were calculated using RSEM 1.2.4
Genome_build: mm9

source_name: cardiac ventricle

growth_protocol: Mice were maintained in standard conditions

extract_protocol:
RNeasy fibrous tissue mini kit was used for RNA isolation (QIAGEN #74704)
Illumina TruSeq RNA protocols.
Paired end 100 cycles run was used to sequence the flow cell on a HiSeq2000 Sequencing system.

treatment_protocol: In all the cases blood and atria were carefully removed and ventricles were flash frozen in liquid nitrogen and kept at -80°C until RNA isolation step.

value: cardiac ventricle

tag: gender

value: male

value: Celf1 +/+


title: RNA-seq Celf1 -/-  PN3 rep2

description: mixed 129v/BL6 strain

value: Celf1 -/-


title: R143_S1KO0h


title: RNA-seq Celf1 +/+ PN3 rep1

description: mixed 129v/BL6 strain


title: RNA-seq Celf1 +/+ PN38

description: mixed 129v/BL6 strain


title: RNA-seq Celf1 -/-  PN3 rep1

description: mixed 129v/BL6 strain


title: TMR_40HT

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (2x100bp, paired-end)

data_processing:
Image processing, base calling, quality scoring (Phred), FASTQ file generation, and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina; San Diego, CA).
The FASTQ-formatted sequence data was analyzed using a standard TopHat-Cufflinks workflow (Trapnell et al., 2012). In brief, sequence reads were mapped to the reference human genome assembly (Feb. 2009, GRCh37/hg19) with TopHat software (Trapnell et al., 2009). Subsequently, the Cufflinks package (Trapnell et al., 2010) was applied for transcript assembly, quantification of normalized gene and isoform expression in FPKM (fragments per kilobase of transcript per million mapped fragments), and testing for differential expression (Cuffdiff).
Processed data are Cufflinks output files (tracking) and contain Gene IDs, locus, and FPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene ID, locus, and FPKM values for each gene and were prepared from the Cufflinks output files (tracking).

source_name: TMR cells cultured in the presence of 4-hydroxytamoxifen (1 uM).

growth_protocol: MCF-7 cells (ATCC HTB-22) were cultured in complete medium (DMEM, 10% FBS, Pen-Strep). The tamoxifen resistant (TMR) sublines were generated by maintaining the parental MCF-7 cells in phenol red-free medium supplemented with 10% charcoal/dextran stripped fetal bovine serum containing 1 µM 4-hydroxytamoxifen (Sigma) for over 8 months. The cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from MCF-7 parental and TMR cells treated with or without 4-hydroxytamoxifen for 24 hours.
RNA-Sequencing (RNA-Seq) libraries were prepared from 1 μg total RNA using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. Briefly, poly-adenylated mRNA was purified from total RNA and rRNA removed by two rounds of binding to magnetic poly-T beads.  This was followed by RNA fragmentation by incubation in the presence of divalent cations at 94ºC for 5 minutes.  Double-stranded cDNA was generated by random-primed first-strand synthesis with SuperScript II reverse transcriptase and subsequent second strand synthesis with RNase H and DNA Polymerase I.  The cDNA was then blunt-ended with T4 and Klenow DNA polymerases to remove 3′-overhangs and fill in 5′-overhangs, phosphorylated with T4 PNK, and then 3′-A tailed by incubation with Klenow Fragment (3´→5´ exo–) and dATP.  Illumina paired-end (PE) adapters were ligated, followed by purification wit AMPure XP beads.  The library was enriched by high-fidelity PCR amplification (15 cycles) with Phusion DNA Polymerase (Finnzymes Oy) and adapter-specific primers.

treatment_protocol: MCF7 and TMR cells were seeded into 6-well tissue culture plates. The following day, media was replaced by phenol red-free DMEM medium supplemented with 10% charcoal/dextran-treated fetal bovine serum and the cells were allowed to grow for two days. then, cells were treated with 4-hydroxytamoxifen or vehicle for another 24 hours.

tag: cell line

value: TamR subline

tag: cell line description

value: Tamoxifen-resistant cell line

tag: agent


title: ns_pi4

city: Philadelphia

first: Tamas

last: Dolinay

state: PA

address: 220 S. 33rd St., Towne building, Room 390

department: Bioengineering

institute: University of Pennsylvania

description: library strategy: Quant-Seq

data_processing:
fastq files from 20 sequenced samples. N=5 biological replicates were used for 4 experimental conditions
STAR was used to align reads to the rn6 reference genome
HTSeq was used to obtain raw read counts per gene
DESeq2 was used to perform differential expression analysis
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include raw read count values per gene for each sample that passed QC (Rat_Stretch_HTSeq_count.txt) and gene-based differential expression results for pairs of samples that passed QC under mechanical stretch and PERK inhibitor (PI) treatment (DESeq2_output_from_HTSeq_counts_controlling_for_rat.txt)

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Unstretched monolayers pretreated with 1microM GSK2606414 PERK kinase inhibitor for 18 hours

growth_protocol: Primary type II pneumocytes were grown fibronectin-coated silastic membranes. After 4 days of culturing the cells transform to AEC-I cells and form monolayers.

extract_protocol:
Total RNA was extracted from 20  rat AEC-I samples and DNase treated before library preparation for next generation sequencing. We pooled samples from 4 technical replicates of monolayers prepared from the same animal to provide sufficient  genomic material for RNA extraction.
500ng  of total RNA was used to generate libraries with  Lexogen's QuantSeq 3'mRNA-Seq library prep kit for Illumina, FWD (Cat #015.24).  The QuantSeq kit generates one fragment per transcript and sequences obtained are close to the 3'end of polyadenylated RNA.  The quality of purified libraries was checked  by Agilent Bioanalyzer using High Sensitivity DNA kit  and quantified by KAPA library Quantification kit_Illumina (Cat # KK4835).  Finally, equimolar concentrations of all libraries were pooled and subsequently next generation sequencing was performed on the NextSeq500 instrument (75 bp single read) using NextSeq(tm) 500 Mid Output Kit (cat#FC-404-2001).

treatment_protocol: Prepared monolayers were randominzed into 4 conditions: 1. Unstretched membranes  treated with 0.01% DMSO for 24 hours (NS). These monolayers served as controls. 2. Unstretched monolayers pretreated with 1microM GSK2606414 (PI) compound for 24 hours (NSPI). 3. Monolayers stretched with 25% surface area change for 6 hours after 18 hours  of 0.01% DMSO treatment (S). 4.Monolayers stretched with 25% surface area change for 6 hours after 18 hours of 1microM PI treatment (SPI).

tag: cell type

value: alveolar type-I-like epithelial (AEC-I) cells

tag: source

value: primary isolated cells

tag: strain

value: Sprague-Dawley


title: ns_pi5

description: library strategy: Quant-Seq


title: TMR

source_name: TMR cells cultured in medium with vehicle control.

value: vehicle control


title: s_pi5

description: library strategy: Quant-Seq

source_name: Stretched monolayers pretreated with  1micro M GSK2606414 for 18 hours


title: ns_pi1

description: library strategy: Quant-Seq


title: s_pi3

description: library strategy: Quant-Seq


title: s_pi4

description: library strategy: Quant-Seq


title: s_pi2

description: library strategy: Quant-Seq


title: MCF7_40HT

source_name: MCF-7 cells cultured in the presence of 4-hydroxytamoxifen (1 uM).

value: MCF-7 breast adenocarcinoma cell line

value: Parental cell line


title: ns3

description: library strategy: Quant-Seq

source_name: unstretched monolayers


title: s_pi1

description: library strategy: Quant-Seq


title: ns4

description: library strategy: Quant-Seq


title: ns2

description: library strategy: Quant-Seq


title: ns5

description: library strategy: Quant-Seq


title: R143_S1KO16h

value: Cry2 knockout

value: mouse embryonic fibroblast


title: ns1

description: library strategy: Quant-Seq


title: s5

description: library strategy: Quant-Seq

source_name: Monolayers exposed to 25% surface area change with cutom built biaxial cyclic (15/min) stetcher for 6 hours


title: s4

description: library strategy: Quant-Seq


title: ns_pi3

description: library strategy: Quant-Seq


title: ns_pi2

description: library strategy: Quant-Seq


title: s2

description: library strategy: Quant-Seq


title: s1

description: library strategy: Quant-Seq


title: ZikV_PR_Input_1_MeRIP

status: Public on Oct 21 2016

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zurich

description: processed data file: ZikV_PR_peaks

data_processing:
library strategy: MeRIP-seq
Basecalls performed using CASAVA version 1.8.2
PAR-CLIP: Bowtie v1 alignment to human genome hg19
PAR-CLIP: Unaligned reads from step 1 aligned to CA JFH HCV with 2 mismatches
PAR-CLIP: PARalyzer v1.1 was applied to step 2 with cluster minimum read depth of 3 reads
PAR-CLIP: Background reads (GFP-FL PAR-CLIP) were subtracted from the YTHDF sets topologically
MeRIP-seq: STAR version 2.5.0 alignment to combined hg19 and viral genomes
MeRIP-seq: Reads aligning to viral genomes were extracted for peak calling
MeRIP-seq: the MeRIPPeR peak caller was applied with a minimum peak width of 100
MeRIP-seq: peaks called in two separate replicates for each viral strain were intersected for final calls
Genome_build: hg19
Supplementary_files_format_and_content: PAR-CLIP: csv files include PARalyzer output showing YTHDF protein binding clusters on the HCV RNA genome, MeRIP: bed files include peaks called by MeRIPPeR

growth_protocol: 2 10cm plates of Huh7 cells

extract_protocol:
24 hrs, TRIZOL
Illumina Tru-seq PolyA RNA

treatment_protocol: ZIKV (PRVABC59 - MOI 2)

value: liver cell line

tag: viral strain

value: ZIKV (PRVABC59)


title: ZikV_PR_IP_2_MeRIP

description: processed data file: ZikV_PR_peaks


title: ZikV_PR_Input_2_MeRIP

description: processed data file: ZikV_PR_peaks


title: ZikV_PR_IP_1_MeRIP

description: processed data file: ZikV_PR_peaks


title: ZikV_Dakar_IP_2_MeRIP

description: processed data file: ZikV_Dakar_peaks

treatment_protocol: ZIKV-DAKAR-41525 (MOI 2)


title: s3

description: library strategy: Quant-Seq


title: ZikV_Dakar_Input_2_MeRIP

description: processed data file: ZikV_Dakar_peaks


title: YFV_IP_2_MeRIP

description: processed data file: YFV_peaks

treatment_protocol: YFV-17D (MOI 2)


title: ZikV_Dakar_IP_1_MeRIP

description: processed data file: ZikV_Dakar_peaks


title: ZikV_Dakar_Input_1_MeRIP

description: processed data file: ZikV_Dakar_peaks


title: YFV_IP_1_MeRIP

description: processed data file: YFV_peaks


title: YFV_Input_2_MeRIP

description: processed data file: YFV_peaks


title: MCF7

source_name: MCF-7 cells cultured in medium with vehicle control.


title: YFV_Input_1_MeRIP

description: processed data file: YFV_peaks


title: WNV_Input_2_MeRIP

description: processed data file: WNV_peaks

extract_protocol:
48hrs, TRIZOL
Illumina Tru-seq PolyA RNA

treatment_protocol: WNV-TX (MOI 5)

value: WNV-TX 2002 HC


title: WNV_IP_2_MeRIP

description: processed data file: WNV_peaks


title: WNV_IP_1_MeRIP

description: processed data file: WNV_peaks


title: WNV_Input_1_MeRIP

description: processed data file: WNV_peaks


title: DenV_IP_2_MeRIP

description: processed data file: DenV_peaks

treatment_protocol: DENV (MOI 2)

value: DENV-NGC


title: HCV_Input_2_MeRIP

description: processed data file: HCV_peaks

extract_protocol:
72 hrs, TRIZOL
Illumina Tru-seq PolyA RNA

treatment_protocol: HCV JFH-1 (culture adapted - MOI 0.3)

value: HCV JFH-1 (culture adapted)


title: HCV_IP_1_MeRIP

description: processed data file: HCV_peaks


title: DenV_IP_1_MeRIP

description: processed data file: DenV_peaks


title: DenV_Input_1_MeRIP

description: processed data file: DenV_peaks


title: HCV_Input_1_MeRIP

description: processed data file: HCV_peaks


title: siSCR-Galactose media-rep1

city: Freiburg

first: Aindrila

last: Chatterjee

state: BW

address: Stübeweg 51

institute: Max Planck Institute of Immunbiology and Epigenetics

description:
DESeq2.counts_normalized_GalMOFKD.tsv
HUMAN_Gal_siSCR_1

data_processing:
reads where mapped using the STAR aligner (v2.4.2a) and counted for Ensembl transcripts (release 77 for Human and release 78 for Mouse) using featureCounts (v1.4.6-p2). Differential gene expression levels were determined using DESeq2 (v1.8.2). Genes were considered significantly different at a cut-off false discovery rate value of 0.05. Gene set enrichment analysis have been done using the GSEA software (v.2.2.1) using curated gene sets from Reactome, KEGG and HALLMARK.
For the mouse samples, the featureCount has been performed on the protein coding genes only.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Normalized counts from DESeq2

source_name: siSCR-Galactose media, Hela cells

extract_protocol:
total RNA was isolated using Trizol reagent as described in methods.
mRNA was enriched with Oligo dT magnetic beads, Poly A+, (RIN>8). Sequencing Library was prepared using TruSeq stranded mRNA sample preparation kit (RS-122-2101).

value: HeLa cervical cancer cell line

value: control

tag: media adaptation

value: galactose


title: siSCR-Galactose media-rep3

description:
DESeq2.counts_normalized_GalMOFKD.tsv
HUMAN_Gal_siSCR_3


title: siMOF-Glucose media-rep2

description:
DESeq2.counts_normalized_GluMOFKD.tsv
HUMAN_Gluc_siMOF_2

source_name: siMOF-Glucose media, Hela cells

value: MOF KD

value: glucose


title: siMOF-Galactose media-rep1

description:
DESeq2.counts_normalized_GalMOFKD.tsv
HUMAN_Gal_siMOF_2

source_name: siMOF-Galactose media, Hela cells


title: siMOF-Glucose media-rep3

description:
DESeq2.counts_normalized_GluMOFKD.tsv
HUMAN_Gluc_siMOF_3


title: siMOF-Galactose media-rep2

description:
DESeq2.counts_normalized_GalMOFKD.tsv
HUMAN_Gal_siMOF_3


title: siSCR-Galactose media-rep2

description:
DESeq2.counts_normalized_GalMOFKD.tsv
HUMAN_Gal_siSCR_2


title: siSCR-Glucose media-rep2

description:
DESeq2.counts_normalized_GluMOFKD.tsv
HUMAN_Gluc_siSCR_2

source_name: siSCR-Glucose media, Hela cells


title: siMOF-Glucose media-rep1

description:
DESeq2.counts_normalized_GluMOFKD.tsv
HUMAN_Gluc_siMOF_1


title: siSCR-Glucose media-rep1

description:
DESeq2.counts_normalized_GluMOFKD.tsv
HUMAN_Gluc_siSCR_1


title: dCA rep1

first: Guangshan

address: No 27 ShanDa nan road

department: School of life science

institute: Shandong university

data_processing:
Base-calling using Illumina Casava 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence.
Reads were mapped to Penicillium oxalicum 114-2 coding sequences using SOAPaligner/SOAP2 v2.21 with parameters -m 0 -x 10000 -s 28 -l 32 -v 3 -p 3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Penicillium oxalicum 114-2 sequences (NCBI accession: PRJNA60877)
Supplementary_files_format_and_content: One matrix table includes unique reads numbers, coverage and RPKM values for each genes. Samples were named according to the names of raw files.

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: All strains were grown in Vogel’s medium with indicated carbon sources at 30 degrees C, 200 rpm.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were filtered by filter paper.

tag: strain phenotype

value: deletion CA

tag: carbon source

value: 2% (wt/vol) cellulose

tag: time

value: first precultured in 2% glucose for 22 h and then transferred to no-carbon medium for 2 h, and then transferred to 2% cellulose for 4 h


title: dPoClrC rep3

value: deletion PoClrC


title: dPoClrC rep2


title: dCA rep3


title: dCA rep2


title: HCV_IP_2_MeRIP

description: processed data file: HCV_peaks


title: dPoflbC rep2

value: deletion PoflbC


title: DenV_Input_2_MeRIP

description: processed data file: DenV_peaks


title: dPoflbC rep3


title: Week 10 replicate 6 FVB/N mammary basal epithelial cells [W10_6B]

city: Bronx

first: Cristina

last: Montagna

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

data_processing:
Reads were aligned against the reference mouse genome using GSNAP version 2012-07-20
Assignment of reads to genes was performed by htseq-cout (v0.5.3p3), a component of the HTSeq package
Raw data were normalized using the edgeR package available through Bioconductor.
To avoid skewing of the data we removed genes with an extremely high number of reads (> 2X10^6 reads) and low variability across the samples (as assessed by ANOVA). Low expressed genes across the samples (genes that have less than 1CPM across 3 samples) were also removed. The normalization and filtering methods used left a total of 17,606 unique genes for subsequent analyses.
Thorugh (princpal component analysis) PCA and clustering analysis, one sample (P14_2B) was deemed an outlier and subsequently removed from the dataset.
Genome_build: NCBI Build 37.1 mouse genome
Supplementary_files_format_and_content: Processed data represent EdgeR normalized (counts per million) expression data across 17,606 genes (rows) in the 46 samples finally analyzed (columns).

source_name: Week 10_FVB/N_basal mammary epithelial cells

growth_protocol: Luminal and basal mammary epithelial cells from mice at 8 different developmental timepoints (early and late adult, early and late pregnancy, early and late lactation, early and late involution) were FACS sorted into HBSS with 1% FCS and immediately pelleted.

extract_protocol:
Pelleted cells were immediately homogenized in lysis buffer and extraction was performed following the QIAGEN AllPrep® DNA/RNA Micro Kit
RNA was treated with Rnase-free recombinant DNaseI following the Roche protocol. RNA was purified with the RNeasy MinElute Cleanup Kit (QIAGEN). The final concentration of RNA was determined by Quant-iT Ribogreen RNA Assay Kit (invitrogen) and measured using NanoDrop 3300 Fluorospectrometer. RNA quality analyzed with the Agilent RNA 6000 Pico Assay on the Agilent 2100 Bioanalyzer. 5ng of RNA was amplified using the Ovation RNA-Seq System V2 (NuGEN Technologies) resulting in double stranded cDNA. Samples were sonicated to around 300bp and libraries were made following Illumina library preparation protocol. Sampels were sequenced on the Illumina HiSeq (2000) Sequencing System by multiplexing 6 samples per lane across 8 lanes.

value: FVB/N

tag: cell subtype

value: FACS sorted basal mammary epithelial cells

tag: developmental time point

value: Week 10

tag: developmental stage

value: Non-pregnant

tag: condition

tag: sequencing lane

tag: sort date

tag: rna amplification batch


title: Week 10 replicate 6 FVB/N mammary luminal epithelial cells [W10_6L]

source_name: Week 10_FVB/N_luminal mammary epithelial cells

value: FACS sorted luminal mammary epithelial cells


title: Week 10 replicate 5 FVB/N mammary luminal epithelial cells [W10_5L]


title: Week 10 replicate 3 FVB/N mammary luminal epithelial cells [W10_3L]


title: Week 10 replicate 3 FVB/N mammary basal epithelial cells [W10_3B]


title: Jun_d1BC_plus_dox

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Base-calling (CASAVA)
Demultiplexing (bcl2fastq)
ChIP-seq reads were aligned to the mm10genome assembly using Bowtie 1.00 to sorted BAM via stdoutput using --all --best --strata --v 2 -m 1 -S | samtools view -S - -b | samtools sort -
Tag shift (macs14)
Wig coverage track generation (macs14)
Peak detection (macs14)
Genome_build: mm10
Supplementary_files_format_and_content: Variable step 10bp wig files depincting ChIP-Seq coverage

source_name: d1 blast culture Flk1+ IVD cells

growth_protocol: ESCs were cultured for one day on gelatinised plates in DMEM ESC medium and for another day on gelatinised plated in IMDM ESC medium in the presence of LIF. Subsequently, cells were differentiated as embryoid bodies (EBs) in 15cm bacterial-grade dishes at 1.25x106 cells per 50 ml for 3.75 days in IMDM differentiation medium without LIF. EBs were then dispersed to single cells by TrypLE Express treatment and Flk1pos cells were purified using MACS technology. Purified Flk1pos cells were cultured in gelatinised T150 tissue culture-grade flask at 1.2x106 cells per flask in blast culture medium (IMDM supplemented with 10% FCS, 100 units per ml penicillin and 100 μg ml−1 streptomycin, 1 mM glutamine, 0.45 mM MTG, 0.18 mg ml−1 Human transferrin (Roche 10652202001) 25 μg ml−1 ascorbic acid, 20% D4T conditioned media, 5 μg l−1 recombinant mouse Vascular Endothelial Growth Factor (Peprotech: 450-32), 10 μg l−1 mIL-6 (Peprotech: 216–16)).

extract_protocol:
Chromatin was prepared and immunoprecipitation was carried out as previously described (Lichtinger et al) for the antibodies, H3K27ac (ab4729) and H3K4me2 (Millipore 07-030). For all other antibodies, JunB (sc-46), Runx1 (ab23980), Ets1 (sc-111), and BRD4 (Bethyl laboratories), chromatin was prepared as follows. Cells were resuspended in PBS at 3.3x106 cells/ml and cross-linked with 0.83mg/ml disuccinimidyl glutarate (DSG) for 45 minutes at room temperature with rotation. Cells were washed four times with PBS and further crosslinked in PBS at 2x106 cells/ml with 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, cells were washed twice in PBS and incubated with Buffer A at 4oC for 10 minutes followed by buffer B at 4oC for 10 minutes. Double cross-linked chromatin was then used for immunoprecipitation as previously described (Lichtinger et al).
Libraries were prepared from approximately 10ng DNA from ChIP samples, according to manufacturer's instructions (Illumina).  Samples were sequenced using 50bp single end reads

treatment_protocol: cells were treated with 1µg/ml doxycycline for the duration indicated in each experiment.

value: d1 blast culture Flk1+ IVD cells

tag: dox treatment

tag: chip antibody


title: Week 10 replicate 5 FVB/N mammary basal epithelial cells [W10_5B]


title: Pregnancy day 3.5 replicate 6 FVB/N mammary basal epithelial cells [P3_6B]

source_name: Pregnancy day 3.5_FVB/N_basal mammary epithelial cells

value: Pregnancy day 3.5

value: Pregnancy


title: dPoClrC rep1


title: Pregnancy day 3.5 replicate 6 FVB/N mammary luminal epithelial cells [P3_6L]

source_name: Pregnancy day 3.5_FVB/N_luminal mammary epithelial cells


title: Pregnancy day 3.5 replicate 4 FVB/N mammary basal epithelial cells [P3_4B]


title: Jun_d1BC_minus_dox

tag: cell type


title: Pregnancy day 3.5 replicate 4 FVB/N mammary luminal epithelial cells [P3_4L]


title: Pregnancy day 14.5 replicate 5 FVB/N mammary basal epithelial cells [P14_6B]

source_name: Pregnancy day 14.5_FVB/N_basal mammary epithelial cells

value: Pregnancy day 14.5


title: Pregnancy day 3.5 replicate 2 FVB/N mammary basal epithelial cells [P3_2B]


title: Pregnancy day 3.5 replicate 2 FVB/N mammary luminal epithelial cells [P3_2L]


title: TEAD4 HE1 WT

data_processing:
Base-calling (CASAVA)
Demultiplexing (bcl2fastq)
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 1.00 to sorted BAM via stdoutput using --all --best --strata --v 2 -m 1 -S | samtools view -S - -b | samtools sort -
Tag shift (macs14)
Wig coverage track generation (macs14)
Peak detection (macs14)
Genome_build: mm10
Supplementary_files_format_and_content: Variable step 10bp wig files depicting ChIP-Seq coverage

source_name: TEAD4 HE1 WT

growth_protocol: A Flag-tagged dominant negative FOS (dnFOS) construct was PCR-amplified from CMV plasmid (CMV500-8584hep-fosLZ(MO), A-FOS, kindly provided by Charles Vinson (Olive et al, 1997)) and HindIII as well as Not1 sites were introduced. The GFP of the p2lox plasmid (kindly provided by Michael Kyba (Kyba et al, 2002)) was exchanged for Flag-tagged dnFOS. A2lox ESCs (a gift from Michael Kyba (Kyba et al, 2002)) or Bry-GFP ESCs were cultured as described before (Gilmour et al, 2014; Regha et al, 2015). Briefly, cells were grown on mitomycin C-inactivated mouse embryonic feeder cells (MEFs) in DMEM medium supplemented with 15% FCS (Stem Cell Technologies), 1 mM sodium pyruvate, 1 mM glutamine, 100 units per ml penicillin and 100 μg ml−1 streptomycin, 25 mM HEPES buffer, 1 × non-essential amino acids, 0.15 mM MTG and 103 units per ml LIF (ESGRO mLIF, Millipore ESG1107). Medium was changed every day and cells were passaged every 2nd day using TrypLE Express (Thermo Fisher). For transfection with p2lox-dnFOS plasmid, 2.5x106 A2lox ESCs were resuspended in 100 µl PBS (Sigma D8537), 20 µg of each p2lox-dnFOS plasmid and Cre-expressing plasmid were added and cells were electroporated at 240 V, 7 ms settings on a EPI 2500 electroporator (Fischer). Cells were plated quickly on NEO-resistant feeder cells in ESC medium and 1 day later selection was started by adding 300µg/ml G418. Clones were picked after 6 days of selection, assessed for their differentiation ability and transgene expression upon doxycycline addition. ESCs were cultured for one day on gelatinized plates in DMEM ESC medium and for another day on gelatinized plates in IMDM ESC medium in the presence of LIF. Subsequently, cells were differentiated as embryoid bodies (EBs) in 15cm bacterial-grade dishes at 1.25x106 cells per 50 ml for 3.75 days in IMDM differentiation medium without LIF. EBs were then dispersed to single cells by TrypLE Express treatment and Flk1pos cells were purified using MACS technology. Purified Flk1pos cells were cultured in gelatinized T150 tissue culture-grade flask at 1.2x106 cells per flask in blast culture medium (IMDM supplemented with 10% FCS, 100 units per ml penicillin and 100 μg ml−1 streptomycin, 1 mM glutamine, 0.45 mM MTG, 0.18 mg ml−1 Human transferrin (Roche 10652202001) 25 μg ml−1 ascorbic acid, 20% D4T conditioned media, 5 μg l−1 recombinant mouse Vascular Endothelial Growth Factor (Peprotech: 450-32), 10 μg l−1 mIL-6 (Peprotech: 216–16)).

extract_protocol: Chromatin was prepared and immunoprecipitation was carried out as previously described (Lichtinger et al). Cells were resuspended in PBS at 3.3x106 cells/ml and cross-linked with 0.83mg/ml disuccinimidyl glutarate (DSG) for 45 minutes at room temperature with rotation. Cells were washed four times with PBS and further crosslinked in PBS at 2x106 cells/ml with 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, cells were washed twice in PBS and incubated with Buffer A at 4oC for 10 minutes followed by buffer B at 4oC for 10 minutes. Double cross-linked chromatin was then used for immunoprecipitation as previously described (Lichtinger et al). Antibodies used were for the antibodies, Fos (sc-253-X), Jun (sc-1694-X) and TEAD4 (ab58310).

value: WT hemogenic endothelium 1 IVD cells

value: TEAD4 (Abcam, catalog# ab58310)


title: Pregnancy day 14.5 replicate 5 FVB/N mammary luminal epithelial cells [P14_6L]

source_name: Pregnancy day 14.5_FVB/N_luminal mammary epithelial cells


title: Pregnancy day 14.5 replicate 3 FVB/N mammary luminal epithelial cells [P14_3L]


title: Pregnancy day 14.5 replicate 3 FVB/N mammary basal epithelial cells [P14_3B]


title: TEAD4 d1BC plus dox

source_name: TEAD4 d1BC plus dox


title: dPoflbC rep1


title: Pregnancy day 14.5 replicate 2 FVB/N mammary luminal epithelial cells [P14_2L]


title: TEAD4 d1BC minus dox

source_name: TEAD4 d1BC minus dox


title: MOF-KO-rep3

description:
DESeq2.counts_normalized_mouse.tsv
A51_KO

molecule: nuclear RNA

source_name: MOF-KO, P15 mouse cardiomyocyte nuclei

extract_protocol:
Cardiomyocyte nuclei were isolated as previously described (Preißl et al. 2015, Circ Res.). Nuclear RNA was extracted using the RNeasy Micro Kit (Qiagen).
RNA was reverse transcribed and amplified with the Nugen Ovation RNA-seq System V2 (Nugen). The resulting cDNA was fragmented using a Bioruptor (25x 30/90 seconds, low, Diagenode). Sequencing libraries were constructed using the NEBNext Ultra DNA Library Prep Kit (NEB) from 100ng fragmented cDNA with 9-13 PCR cycles.

value: cardiomyocyte

tag: genotype/variation

value: MOF-/-

tag: age

value: post natal day 15


title: Pregnancy day 14.5 replicate 2 FVB/N mammary basal epithelial cells [P14_2B]

tag: strain


title: Lactation day 3 replicate 6 FVB/N mammary basal epithelial cells [L3_6B]

source_name: Lactation day 3_FVB/N_basal mammary epithelial cells

value: Lactation day 3

value: Lactation


title: MOF-KO-rep2

description:
DESeq2.counts_normalized_mouse.tsv
A35_KO


title: Lactation day 3 replicate 4 FVB/N mammary basal epithelial cells [L3_4B]


title: Lactation day 3 replicate 6 FVB/N mammary luminal epithelial cells [L3_6L]

source_name: Lactation day 3_FVB/N_luminal mammary epithelial cells


title: Lactation day 3 replicate 5 FVB/N mammary luminal epithelial cells [L3_5L]


title: Lactation day 3 replicate 4 FVB/N mammary luminal epithelial cells [L3_4L]


title: Cre-Cntrl-rep5

description:
DESeq2.counts_normalized_mouse.tsv
A32_Cntrl

source_name: Cre-Cntrl, P15 mouse cardiomyocyte nuclei

value: WT


title: Cre-Cntrl-rep4

description:
DESeq2.counts_normalized_mouse.tsv
A50_Cntrl


title: Lactation day 10 replicate 6 FVB/N mammary basal epithelial cells [L10_6B]

source_name: Lactation day 10_FVB/N_basal mammary epithelial cells

value: FVB/N

value: Lactation day 10


title: Lactation day 10 replicate 6 FVB/N mammary luminal epithelial cells [L10_6L]

source_name: Lactation day 10_FVB/N_luminal mammary epithelial cells


title: Cre-Cntrl-rep3

description:
DESeq2.counts_normalized_mouse.tsv
A39_Cntrl


title: Lactation day 10 replicate 5 FVB/N mammary basal epithelial cells [L10_5B]

value: FACS sorted basal mammary epithelial cells


title: Lactation day 10 replicate 5 FVB/N mammary luminal epithelial cells [L10_5L]


title: Cre-Cntrl-rep2

description:
DESeq2.counts_normalized_mouse.tsv
A37_Cntrl


title: Lactation day 10 replicate 4 FVB/N mammary luminal epithelial cells [L10_4L]


title: Cre-Cntrl-rep1

description:
DESeq2.counts_normalized_mouse.tsv
A36_Cntrl


title: Involution day 2 replicate 6 FVB/N mammary basal epithelial cells [Id2_6B]

source_name: Involution day 2_FVB/N_basal mammary epithelial cells

value: Involution day 2

value: Involution


title: Involution day 2 replicate 4 FVB/N mammary basal epithelial cells [Id2_4B]


title: Involution day 2 replicate 4 FVB/N mammary luminal epithelial cells [Id2_4L]

source_name: Involution day 2_FVB/N_luminal mammary epithelial cells

value: FACS sorted luminal mammary epithelial cells


title: Involution day 2 replicate 2 FVB/N mammary basal epithelial cells [Id2_2B]


title: Lactation day 3 replicate 5 FVB/N mammary basal epithelial cells [L3_5B]


title: Involution day 2 replicate 2 FVB/N mammary luminal epithelial cells [Id2_2L]


title: Involution week 4 replicate 5 FVB/N mammary basal epithelial cells [Iw4_5B]

source_name: Involution week 4_FVB/N_basal mammary epithelial cells

value: Involution week 4

value: Non-pregnant


title: Involution week 4 replicate 6 FVB/N mammary luminal epithelial cells [Iw4_6L]

source_name: Involution week 4_FVB/N_luminal mammary epithelial cells


title: Involution week 4 replicate 5 FVB/N mammary luminal epithelial cells [Iw4_5L]


title: MOF-KO-rep1

description:
DESeq2.counts_normalized_mouse.tsv
A33_KO


title: Involution week 4 replicate 3 FVB/N mammary basal epithelial cells [Iw4_3B]


title: Month 4 replicate 6 FVB/N mammary basal epithelial cells [Month4_6B]

source_name: Month 4_FVB/N_basal mammary epithelial cells

value: Month 4


title: Involution week 4 replicate 6 FVB/N mammary basal epithelial cells [Iw4_6B]


title: Month 4 replicate 6 FVB/N mammary luminal epithelial cells [Month4_6L]

source_name: Month 4_FVB/N_luminal mammary epithelial cells


title: Month 4 replicate 2 FVB/N mammary luminal epithelial cells [Month4_2L]


title: Month 4 replicate 1 FVB/N mammary basal epithelial cells [Month4_1B]


title: Involution week 4 replicate 3 FVB/N mammary luminal epithelial cells [Iw4_3L]


title: Month 4 replicate 2 FVB/N mammary basal epithelial cells [Month4_2B]


title: Month 4 replicate 1 FVB/N mammary luminal epithelial cells [Month4_1L]


title: Involution day 2 replicate 6 FVB/N mammary luminal epithelial cells [Id2_6L]


title: SMC1B-LAP ChIP-Seq (Input)

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

data_processing:
Reads obtained from SMC3 and SMC1β-LAP ChIP-Seq experiments were aligned to the mouse reference genome (release mm9, July 2007) with Bowtie 2 version 0.12.8 (12). For each read, a maximum of three mismatches in a seed of 56 nucleotides was allowed and only reads with at most three valid alignments were further processed. From reads with multiple alignments, only the best-scoring one was reported. Peak calling was performed with MACS2, using the following set of parameters: 300 bp band width, model fold between 8 and 30 and different q-value cut-offs (0.5, 0.1 and 0.001).
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing peak summit coordinates.

source_name: Spermatocytes

growth_protocol: Animals were bred and maintained under pathogen-free conditions in the Experimental Center of the Medizinisch-Theoretisches Zentrum of the Medical Faculty at the Dresden University of Technology according to approved animal welfare guidelines, permission number 24-9168.24-1/2010-25, granted by the State of Saxony.

extract_protocol:
Single-cell suspensions of testes were obtained by removal of the tunica albuginea and mashing of the tissue followed by filtration through a 40 µm nylon mesh into PBS to remove cell clumps. For formaldehyde fixation, cells were resuspended at a density of 5 million/ml in DMEM+GlutaMAX containing 10% fetal calf serum (FCS) after additional centrifugation. Formaldehyde was added to a final concentration of 1% (w/v) and cells were crosslinked for 10 min at room temperature under slight agitation. Cells were quenched by addition of glycine to a final concentration of 125 mM for 5 min at room temperature. Crosslinked and non-crosslinked cells were centrifuged and resuspended in FACS buffer (HBSS supplemented with 20 mM HEPES (pH 7.2), 1.2 mM MgSO4, 1.3 mM CaCl2, 6.6 mM sodium pyruvate, 0.05% lactate, glutamine, and 1% fetal calf serum). Cell sorting of GFP-positive cells was performed on an ARIA II (BD Biosciences). Cells were collected into PBS and reanalyzed, counted in a Neubauer chamber, pooled after centrifugation and frozen at -80°C or directly undertaken subsequent ChIP experiments. FlowJo (Tree Star) and FACSDiva softwares were used for cell sorting and data analysis.
As a first step of library preparation, purified DNA molecules of ChIP and input samples were end-repaired with the NEBnext End Repair Module (New England Biolabs) and purified using Agencourt AMPure XP Beads (Beckman Coulter). Blunt-ended fragments were then supplied with a 3’-dA overhang using the NEB- next dA-Tailing Module (New England Biolabs) and purified (see above). Subsequently, adapters (Adaptor-Oligo 1: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’, Adaptor-Oligo 2: 5’-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’) were ligated for large-scale PCR amplification using the 1x NEBnext Quick Ligation Buffer (New England Biolabs using 10x excess of DNA Adaptors, 5 μl Quick T4 DNA Ligase (New England Biolabs) at 50 μl total volume). Size selection of fragments of an adequate size range was performed after separation by agarose gel electrophoresis. After purification, large-scale amplification of library constructs was performed using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with subsequent purification. For quality control and size selection, fragments were run on a 2% agarose E-Gel (Invitrogen) and quantified using the Qubit dsDNA HS Assay Kit (Invitrogen).

tag: construct

value: N-terminally LAP-tagged Smc1b

tag: tissue

value: testes


title: SMC3 ChIP-Seq (Input)


title: SMC3 ChIP-Seq

value: rabbit polyclonal anti-SMC3 (Abcam, ab9263)


title: RNA_Smarca4flfl_Tam rep1

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: mRNA in Smarca4flfl mES cells following tamoxifen treatment

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2
RNA-seq reads were aligned to the mm9 genome assembly using bowtie version 1.1.1, allowing no more than a single mismatch. Duplicate reads were discarded.
Reads within coding regions were counted using htseq, with gene definitions obtained from the refGene table of RefSeq genes in the UCSC Table Browser. The table of all counts was processed using DESeq2, using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file including total numbers of reads overlapping each gene for each sample

source_name: Mouse embryonic stem cells

growth_protocol: Cells are grown in DMEM media supplemented with 15% FBS and LIF.

extract_protocol:
RNA was extracted from cells using QIAzol reagent, and mRNA enriched by poly(dT) capture. RNA was converted to DNA, then size-selected for 200-400 bp DNA fragments before PCR amplification.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Smarca4flfl conditional knockout cell lines were incubated with either ethanol or 0.8 uM 4-hydroxytamoxifen for 48 h. Cells were then harvested 72 h after the start of the treatment.

tag: strain background

value: Mouse embryonic stem cells

tag: passage

value: acute deletion of Smarca4

tag: treated with

value: 0.8 uM 4-hydroxytamoxifen (Tam)


title: RNA_Smarca4flfl_EtOH rep2

description: mRNA in Smarca4flfl mES cells following ethanol treatment

value: ethanol (EtOH)


title: Cbx7_Smarca4V5_WT

description: anti-Cbx7 ChIP in mES cells expressing WT Smarca4V5

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.1.1, allowing no more than a single mismatch. Duplicate reads were discarded.
Peaks were called by comparing ChIP and input samples using MACS 1.4.2 with with default settings.
Peaks with less than 30 reads per million were discarded to ensure high-quality peak calls.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated by extending all read fragments to 200 bp, then calculating the basepair coverage for each replicate using Bedtools, normalizing by the total number of reads within called peaks. For samples with multiple replicates, values in the bigWig files represent coverage calculated in this way averaged across both replicates using bwtool.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with formaldehyde, and protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: For conditional knockout cell lines (Arid1aflfl and Smarca4flfl), cells were incubated with either ethanol or 0.8 uM 4-hydroxytamoxifen for 48 h. Cells were then harvested 72 h after the start of the treatment. Heterozygous Smarca4 mutant cells received no treatment.

value: expressing V5-tagged WT Smarca4 (Smarca4V5)

value: Rabbit anti-Cbx7

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: RNA_Smarca4flfl_EtOH rep1


title: Cbx7_Smarca4flfl_EtOH

description: anti-Cbx7 ChIP in Smarca4flfl mES cells following ethanol treatment

value: Smarca4-CreER (Smarca4flfl)

value: EtOH


title: Cbx7_Smarca4V5_G784E

description: anti-Cbx7 ChIP in mES cells expressing G784E Smarca4V5

value: expressing V5-tagged G784E mutants of Smarca4 (Smarca4V5)


title: Primary neuron-MeDIP Sequencing

city: Beijing

first: J

last: Z

address: 1 Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
The sample was positive control and symboled M001
GSM2350429 was used as an input
All_MeDIP_Signal / DNA Methylation Peak_Annotation.xlsx/M001-IP
Differentially Methylated Regions (Promoter).xlsx / M001 vs M003(hypo); M001 vs M003(hyper)

data_processing:
Illumina Casava software used for basecalling.
The stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8)
Solexa CHASTITY quality filter were used to obtain the clean reads
The clean reads were aligned to mouse genome (UCSC MM10) using BOWTIE software (V2.1.0)
Aligned reads were used for peak calling of the MeDIP regions using MACS V2.
Genome_build: mm10
Supplementary_files_format_and_content: FASTQ format files include the DNA methylation status of gene promoter and the gene body regions in all samples

source_name: Primary neurons

growth_protocol: The primary mouse embryonic fibroblasts (MEFs) were routinely isolated from mouse embryos in fibroblasts medium. The primary neurons were obtained from the 1-day-old pups and cultured in neuronal medium. The induecd neurons were generated from fibroblasts and cultured in neuronal medium.

extract_protocol:
The DNA were extrcted with the genomic DNA extraction Kit
Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit (#FC-102-1002, Illumina)

value: hippocampus-derived primary neurons

tag: passages

value: 3-5 passages

value: ICR


title: 5 dpi iNs-MeDIP Sequencing

description:
The sample was 5 dpi-iduced neurons and symboled M005
GSM2350429 was used as an input
All_MeDIP_Signal / DNA Methylation Peak_Annotation.xlsx/M005-IP
Differentially Methylated Regions (Promoter).xlsx / M005 vs M003(hypo); M001 vs M003 (hyper)

source_name: Induced neurons-5 dpi derived from Mouse embryoic fibroblats

value: MEF-derived induced neurons


title: 3 dpi iNs-MeDIP Sequencing

description:
The sample was 3 dpi-iduced neurons and symboled M004
GSM2350429 was used as an input
All_MeDIP_Signal / DNA Methylation Peak_Annotation.xlsx/M004-IP
Differentially Methylated Regions (Promoter).xlsx / M004 vs M003(hypo); M001 vs M003 (hyper)

source_name: Induced neurons-3 dpi derived from Mouse embryoic fibroblats


title: 1 dpi iNs -MeDIP Sequencing

description:
The sample was 1 dpi-iduced neurons and symboled M002
GSM2350429 was used as an input
All_MeDIP_Signal / DNA Methylation Peak_Annotation.xlsx/M002-IP
Differentially Methylated Regions (Promoter).xlsx / M002 vs M003(hypo); M002 vs M003(hyper)

source_name: Induced neurons-1 dpi derived from Mouse embryoic fibroblats (MEFs)


title: Mix-Input Sequencing

description: The sample was used as an input

data_processing:
Library strategy: hMeDIP-Seq
Illumina Casava software used for basecalling.
The stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8)
Solexa CHASTITY quality filter were used to obtain the clean reads
The clean reads were aligned to mouse genome (UCSC MM10) using BOWTIE software (V2.1.0)
Aligned reads were used for peak calling of the hMeDIP regions using MACS V2.
Genome_build: mm10
Supplementary_files_format_and_content: FASTQ format files include the DNA methylation status of gene promoter and the gene body regions in all samples

source_name: Mouse embryoic fibroblats and iduced neurons

value: mouse E13.5 embryo-derived firoblasts and MEF-derived induced neurons


title: 7 dpi iNs-MeDIP Sequencing

description:
The sample was 7 dpi-iduced neurons and symboled M006
GSM2350429 was used as an input
All_MeDIP_Signal / DNA Methylation Peak_Annotation.xlsx/M006-IP
Differentially Methylated Regions (Promoter).xlsx / M006 vs M003(hypo); M001 vs M003 (hyper)

source_name: Induced neurons-7 dpi derived from Mouse embryoic fibroblats


title: 5 dpi iNs-hMeDIP Sequencing

description:
The sample was 5 dpi-iduced neurons and symboled hM005
All_hMeDIP_Signal / DNA Hydroxymethylation Peak_Annotation.xlsx/hM005-IP
Differentially_Hydroxymethylated / Differentially Hydroxymethylated Regions (Promoter).xlsx / hM005 vs hM003(hypo); hM001 vs hM003 (hyper)


title: MEF-MeDIP Sequencing

description:
The sample was negative control and symboled M003
GSM2350429 was used as an input
All_MeDIP_Signal / DNA Methylation Peak_Annotation.xlsx/M003-IP
Differentially Methylated Regions (Promoter).xlsx

source_name: Mouse embryoic fibroblats

value: mouse E13.5 embryo-derived firoblasts


title: MEF-Input Sequencing

description: The sample was used as an input


title: 1 dpi iNs -hMeDIP Sequencing

description:
The sample was 1 dpi-iduced neurons and symboled hM002
All_hMeDIP_Signal / DNA Hydroxymethylation Peak_Annotation.xlsx/hM002-IP
Differentially_Hydroxymethylated / Differentially Hydroxymethylated Regions (Promoter).xlsx / hM002 vs hM003(hypo); hM002 vs hM003(hyper)


title: 3 dpi iNs-hMeDIP Sequencing

description:
The sample was 3 dpi-iduced neurons and symboled hM004
All_hMeDIP_Signal / DNA Hydroxymethylation Peak_Annotation.xlsx/hM004-IP
Differentially_Hydroxymethylated / Differentially Hydroxymethylated Regions (Promoter).xlsx / hM004 vs hM003(hypo); hM001 vs hM003 (hyper)


title: Primary neuron-hMeDIP Sequencing

description:
The sample was positive control and symboled hM001
All_hMeDIP_Signal / DNA Hydroxymethylation Peak_Annotation.xlsx/hM001-IP
Differentially_Hydroxymethylated / Differentially Hydroxymethylated Regions (Promoter).xlsx / hM001 vs hM003(hypo); hM001 vs hM003(hyper)


title: siSCR-Glucose media-rep3

description:
DESeq2.counts_normalized_GluMOFKD.tsv
HUMAN_Gluc_siSCR_3

source_name: siSCR-Glucose media, Hela cells

tag: cell line

value: HeLa cervical cancer cell line

value: control

tag: media adaptation

value: glucose


title: Two338_4_G4

city: Lausanne

first: Fabienne

last: Maurer

address: Bugnon 27

department: Service of genetic medicine

institute: CHUV

data_processing:
The basecalling software name, version and parameters are OLB-1.9.4/bin/setupBclToQseq.py; --input-dir Data/Intensities/BaseCalls; --output-dir; --use-bases-mask Y*,Y*,Y*
Data filtering steps: remove reads with adaptors; remove reads with unknown nucleotides larger than 5%; remove reads with low quality (more than half of the bases' qualities are less than 5); obtain clean reads
Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, Bioinformatics. 2009 Aug 1;25(15):1966-7. doi: 10.1093/bioinformatics/btp336. PMID: 19497933); mismatches no more than m (m default is 5) bases were allowed in the alignment.
Gene expression levels are measured as RPKM (Mortazavi, Nat Methods. 2008 Jul;5(7):621-8. doi: 10.1038/nmeth.1226. PMID: 18516045)
Gene coverage is the percentage of a gene covered by reads; the value equals to the ratio of the number of bases in a gene covered by unique mapping reads to the number of total bases in that gene.
Differential expression was computed using edgeR (Robinson, Bioinformatics. 2010 Jan 1;26(1):139–40. doi: 10.1093/bioinformatics/btp616. PMID: 19910308)
Genome_build: NCBI genome build 37, mm9
processed data files format and content: The tab-delimited 178_Mouse.Gene.rpkm.xls file includes Ensembl gene IDs, gene names, gene length, read counts (mapped reads), % coverage and RPKM values of 19176 genes in 178 samples
processed data files format and content: The tab-delimited DE_ATE-CTR.tab file summarizes differential expression data as determined between 54 atenolol-treated (ATE) and 53 untreated (CTR) mice; the data consist in log2-transformed fold-change and FDR values computed over 16155 genes.
processed data files format and content: The tab-delimited DE_ISO-CTR.tab file summarizes differential expression data as determined between 53 isoproterenol-treated (ISO) and 53 untreated (CTR) mice; the data consist in log2-transformed fold-change and FDR values computed over 16208 genes

source_name: heart

extract_protocol:
Total RNA was purified from the cardiac ventricles following the recommendations of Ambion for the semi-automated MagMax procedure, then stored at -80°C. RNA quality and integrity (RIN >8.1) were verified on a Bioanalyzer (Agilent).
Library preparation and RNA sequencing were performed by the Beijing Genomics Institute (BGI, Hong Kong, China), following Illumina's protocols for poly(A) selection, library preparation and HiSeq2000 paired-end sequencing (2x 91 bp).

tag: mouse id number

tag: mouse strain

value: I/LnJ

tag: treatment

value: isoproterenol 10 mg/kg per day

tag: gender

value: male

value: cardiac ventricles


title: Cbx7_Smarca4flfl_Tam

description: anti-Cbx7 ChIP in Smarca4flfl mES cells following tamoxifen treatment

tag: cell type

value: Mouse embryonic stem cells

tag: genotype/variation

value: 0.8 uM 4-hydroxytamoxifen for 48 h

tag: chip antibody

value: Rabbit anti-Cbx7

value: Abcam


title: SMC1B-LAP ChIP-Seq

tag: strain

tag: construct

value: N-terminally LAP-tagged Smc1b

tag: tissue

value: testes

value: goat polyclonal anti-GFP antibody (Antibody Facility, MPI-CBG, Dresden, Germany)


title: Two333_4_E10

value: atenolol 10 mg/kg per day


title: Two320_4_F4


title: RNA_Smarca4flfl_Tam rep2

description: mRNA in Smarca4flfl mES cells following tamoxifen treatment

tag: strain background

tag: passage

value: acute deletion of Smarca4

tag: treated with

value: 0.8 uM 4-hydroxytamoxifen (Tam)


title: Two328_4_G1


title: Two331_4_F7


title: Two301_4_E1


title: Two307_4_F1


title: two235_2_D10

value: BTBRTplus tf/J


title: MEF-hMeDIP Sequencing

description:
The sample was negative control and symboled hM003
All_hMeDIP_Signal / DNA Hydroxymethylation Peak_Annotation.xlsx/hM003-IP
Differentially_Hydroxymethylated / Differentially Hydroxymethylated Regions (Promoter).xlsx

value: mouse E13.5 embryo-derived firoblasts

value: 3-5 passages

value: ICR


title: two221_2_C4

value: control


title: two222_2_C10

value: male


title: 7 dpi iNs-hMeDIP Sequencing

description:
The sample was 7 dpi-iduced neurons and symboled hM006
All_hMeDIP_Signal / DNA Hydroxymethylation Peak_Annotation.xlsx/hM006-IP
Differentially_Hydroxymethylated / Differentially Hydroxymethylated Regions (Promoter).xlsx / hM006 vs hM003(hypo); hM001 vs hM003 (hyper)

value: MEF-derived induced neurons


title: Two317_4_F11

value: I/LnJ

value: isoproterenol 10 mg/kg per day

value: cardiac ventricles


title: Two203_2_C1


title: two209_2_B7


title: Two127_4_H10

value: KK/HlJ


title: Two205_2_B4


title: two039_6_H9

value: SWR/J


title: two103_4_G7


title: Leukaemia_MLL-AF9_RingKO_2

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

description: total RNA extracted with Rneasy Plus Micro Kit Qiagen processed for mRNA library preparation

data_processing:
Sequencing data is aligned to mouse (mm9) genome in a reference guided manner by tophat.
Differentially expressed genes were identified using DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] list of genes with mean read count, fold change, p-value and adjusted p-value.

source_name: MLL-AF9 Leukaemia cells

extract_protocol:
MLL-AF9 leukemic cells were isolated from the bone marrow of the indicated mice, growth in liquid culture, treated with OHT for 72h and collected.
Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 ( RS-122-2001)

value: MLL-AF9 leukemic cells

value: OHT


title: Two037_6_H4


title: Two311_4_E4

value: atenolol 10 mg/kg per day


title: Leukaemia_MLL-AF9_2

extract_protocol:
MLL-AF9 leukemic cells were isolated from the bone marrow of the indicated mice, growth in liquid culture, treated with EtOH for 72h and collected.
Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 ( RS-122-2001)

treatment_protocol: total RNA extracted with Rneasy Plus Micro Kit Qiagen processed for mRNA library preparation

value: EtOH


title: Two033_6_G1


title: two233_2_D4


title: Two032_6_F10


title: Two020_6_G7


title: Leukaemia_MLL-AF9_1


title: Two021_6_G10


title: two215_2_D1


title: Two012_6_F7


title: two226_2_B10


title: Two019_6_H1


title: one938_3_C7


title: two126_4_G10


title: Two001_6_G4


title: one936_3_C4


title: H3K27me3 Leukemia Ring KO

description: Immuno-precipitation of chromatin using a specific antibody against H3K27me3 (Active Motif Cat39155 Lot 07711009).

data_processing:
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie allowing to retain only reads with unique alignment.
Peaks: Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing locus of enriched regions for target of interest

source_name: MLL-AF9 leukemic cells

extract_protocol:
The MLL-AF9 leukemic cells were isolated from the bone marrow of the indicated mice, kept in liquid culture, treated with OHT for 72h and collected.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: MLL-AF9 leukemic cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with H2AK119Ubq or H3K27me3 antibodies, which was further purified using magnetic protein A coupled beads, and recovered DNA was used for high-throughput sequencing.


title: H3K27me3 Leukemia

extract_protocol:
The MLL-AF9 leukemic cells were isolated from the bone marrow of the indicated mice and kept in liquid culture
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: H3K27me3 (Active Motif Cat39155 Lot 07711009)


title: One928_3_B1


title: H2AUbq Leukemia

description: Immuno-precipitation of chromatin using a specific antibody against H2AK119 ubiquitination (Cell signaling D27C4, catalog 8240S and lot2).


title: Leukaemia_MLL-AF9_RingKO_1


title: One924_3_B10


title: One921_3_B7


title: one905_3_A7


title: one837_4_H10

value: LP/J


title: MLL-AF9

data_processing:
Sequencing data is aligned to mouse (mm9) genome in a reference guided manner by tophat.
Differentially expressed genes were identified using DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: list of genes with mean read count, fold change and p-value.

source_name: Lin- HSC

extract_protocol:
The LIN- HSCs were isolated from the bone marrow of the indicated mice using the hematopoietic progenitor enrichment kit (StemCell Technologies), infected, treated with EtOH or OHT for 72h and collected.
total RNA extracted with Rneasy Plus Micro Kit Qiagen processed for mRNA library preparation
Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 ( RS-122-2001 )

value: Ring1b WT Ring1a-/- Cdkn2a-/-

tag: transduced


title: MLL-AF9_OHT

value: Ring1b KO Ring1a-/- Cdkn2a-/-


title: PML-RARa_OHT

value: PML-RARa


title: PML-RARa


title: One831_5_B7


title: one823_5_A4

value: control


title: one825_4_H7

value: male


title: one818_5_B3


title: one835_5_A7


title: HOXA9_OHT


title: one814_4_H4


title: One833_5_B10


title: One925_3_A10


title: one813_5_A1


title: NT-OHT


title: HOXA9


title: NT


title: One714_5_G1

value: NZB/BLNJ


title: One712_5_F10


title: One717_5_F4


title: One903_3_B4


title: One719_5_F7


title: One704_5_E4


title: One722_5_E10


title: One705_5_E7


title: H2AUbq_MLL-AF9

extract_protocol:
The LIN- HSCs were isolated from the bone marrow of the indicated mice using the hematopoietic progenitor enrichment kit (StemCell Technologies), infected and kept in liquid culture
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: LIN- HSCs were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with H2AK119Ubq antibody, which was further purified using magnetic protein A coupled beads, and recovered DNA was used for high-throughput sequencing.

tag: antibody

value: H2AK119 ubiquitination

tag: antibody vendor/catalog/lot

value: Cell signaling D27C4/2

tag: transduction


title: Input

value: Input.


title: H2AUbq_PML-RARa


title: H2AUbq_HOXA9


title: One634_1_H7

tag: mouse id number

value: BALB/cJ

value: cardiac ventricles


title: One633_2_A4

tag: mouse strain


title: One732_5_G4

tag: treatment

value: isoproterenol 10 mg/kg per day


title: One627_2_A10

tag: gender


title: H2AUbq_N


title: One600_1_H10


title: One538_6_A10

value: PL/J


title: One602_1_H1

value: atenolol 10 mg/kg per day


title: One609_2_A7


title: One619_1_H4


title: One523_5_G10


title: One537_6_A7


title: One525_5_H1


title: One518_6_A1


title: One512_6_A4


title: One702_5_F1


title: One506_5_G7


title: One415_1_E1

value: AKR/J


title: One507_5_H10


title: One409_1_D4


title: One411_1_D10


title: One501_5_H4


title: One334_2_F10


title: One336_2_G1


title: One318_2_F1


title: One314_2_F7


title: One303_2_E1


title: One321_2_F4


title: One315_2_E10


title: One325_2_E4


title: One629_2_B1


title: one242_4_C4

value: FVB/NJ


title: one237_4_D10


title: one220_4_D7


title: one217_4_D4


title: one224_4_D1


title: one230_4_C1


title: One142_6_D10

value: SM/J


title: one204_4_C10


title: one203_4_C7


title: One133_6_E10


title: One138_6_F1


title: One141_6_E7


title: One119_6_E4


title: One122_6_D4


title: One139_6_F4


title: One327_2_E7


title: One103_6_E1


title: one039_3_E3


title: one035_3_E7


title: Nine35_5_C7

value: NOD/ShiLtJ


title: one047_3_E10


title: one006_3_C10


title: one041_3_D4


title: Nine28_5_E1


title: one007_3_D1


title: one000_3_D7


title: one026_3_D10


title: Huh7_Flag-YTHDF3_PAR-CLIP

description: processed data file: M6AHCV_Y3-l15-3

data_processing:
library strategy: PAR-CLIP
Basecalls performed using CASAVA version 1.8.2
PAR-CLIP: Bowtie v1 alignment to human genome hg19
PAR-CLIP: Unaligned reads from step 1 aligned to CA JFH HCV with 2 mismatches
PAR-CLIP: PARalyzer v1.1 was applied to step 2 with cluster minimum read depth of 3 reads
PAR-CLIP: Background reads (GFP-FL PAR-CLIP) were subtracted from the YTHDF sets topologically
MeRIP-seq: STAR version 2.5.0 alignment to combined hg19 and viral genomes
MeRIP-seq: Reads aligning to viral genomes were extracted for peak calling
MeRIP-seq: the MeRIPPeR peak caller was applied with a minimum peak width of 100
MeRIP-seq: peaks called in two separate replicates for each viral strain were intersected for final calls
Genome_build: hg19
Supplementary_files_format_and_content: PAR-CLIP: csv files include PARalyzer output showing YTHDF protein binding clusters on the HCV RNA genome, MeRIP: bed files include peaks called by MeRIPPeR

growth_protocol: Total of 2x10^7 cells per cell line were seeded in 30 15 cm plates

extract_protocol:
48 hours post-infection, cells were crosslinked, and pellets were harvested by scraping
Illumina Tru-seq Small RNA

treatment_protocol: Cells were infected with HCV, 3 hrs post-infection, they were treated with 4-thiouridine

tag: cell line

tag: cell type

value: liver cell line

tag: viral strain

value: HCV JFH-1 (culture adapted)


title: One124_6_D7