title: 3037_CD8_ZK_IFNgpos

value: subject 3037


title: 2692_CD8_ZK_IFNgpos

status: Public on Jan 23 2019

type: SRA

city: La JOLLA

first: Alba

last: Grifoni

state: CALIFORNIA

address: 9420 Athena Circle

country: USA

institute: La Jolla Insitute for allergy and immunology

library_source: transcriptomic

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

molecule: polyA RNA

organism: Homo sapiens

source_name: Cryopreserved PBMC

growth_protocol: Cells were isolated post thawing of cryopreserved PBMC samples and lysed after 3 hrs of stimulaton and  IFN-gamma capture assay.

extract_protocol:
Cryopreserved PBMC were thawed, stimulated with ZIKA pool of peptides or anti-CD3/CD28 stimulation or with no stimuli. After 3 hr of stimulation cells were stained with antibodies and IFNg capture assay, 200 cells of CD8 T cells were sorted using BD Aria 3 or BD Aria Fusion cell sorter for each condition, multiple of 200  cells were collected when possible.  CD8 responding and non responding  cells were defined with the expression of the followiing antibodies CD3+CD8+IFNg+ and CD3+CD8+IFNg- respectively.
Microscaled cDNA amplification of purified total RNA (1 to 5 ng) following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: Cells were pulsed for 3 hrs with no stimuli or ZIKV pool of peptides or anti-CD3/CD28 beads.

tag: individual

value: subject 2692

tag: stimulation

tag: cell type

value: CD8 T cells

tag: cell subset

value: CD3+CD8+IFNg+ T cells


title: 3027_CD8_ZK_IFNgpos

value: subject 3027


title: 2894_CD8_antiCD3_IFNgpos

value: subject 2894

value: CD3+CD8+ T cells


title: 3054_CD8_ZK_IFNgneg

value: subject 3054


title: 3053_CD8_ZK_IFNgneg

value: subject 3053


title: 3030_CD8_ZK_IFNgneg

value: subject 3030


title: 3028_CD8_ZK_IFNgpos

value: subject 3028


title: 2653_CD8_ZK_IFNgneg

value: subject 2653


title: 2894_CD8_ZK_IFNgneg


title: 3052_CD8_ZK_IFNgneg

value: subject 3052


title: 3043_CD8_ZK_IFNgneg

value: subject 3043


title: 3037_CD8_ZK_IFNgneg


title: 3039_CD8_ZK_IFNgneg

value: subject 3039


title: 3045_CD8_ZK_IFNgneg

value: subject 3045


title: 3038_CD8_ZK_IFNgneg

value: subject 3038


title: 3028_CD8_ZK_IFNgneg


title: 2692_CD8_ZK_IFNgneg


title: 3031_CD8_ZK_IFNgneg

value: subject 3031


title: 3027_CD8_ZK_IFNgneg


title: 2653_CD8_unstimulated

value: IFNgneg


title: 3054_CD8_unstimulated

value: CD8 T cells


title: 2894_CD8_unstimulated


title: 3053_CD8_unstimulated


title: 3052_CD8_unstimulated


title: Glioblastoma_AGO2RIP_B13_totalRNA

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B13_AGO2_T_S71_L005_R1_001
total RNA seq

data_processing:
Adaptors were trimmed using Cutadapt and qualtiy of reads were checked using FASTQC
Data was aligned either to the human (hg38) or to the mouse (mm10) genome using StarAligner 2.5.0a.
For analysis of small RNAs 1 mismatch per 22nt were allowed, for mRNA analyses default setting were used.
For the analyses of small RNAs deriving from transposable elements, we uniquely aligned the data to the human genome (hg38) using StarAligner 2.5.0a (0 mismatches). For the analysis of transposable elements in total RNA samples data was uniquely aligned, allowing for 2 mismatches in 50bp (--outFilterMismatchNoverLmax 0.04).
mRNA and non-coding RNAs were quantified using the subread package FeatureCoutns (primary reads) using annotation files from Ensembl and iGenomes NCBI annotations. Transposable elements were quantified using the RepeatMasker Track from UCSC.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: featC.3UTR.txt.gz [Tab-delimited table with quantification of reads mapping to 3UTR annotation of Ensembl. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.linc.txt.gz [Tab-delimited table with quantification of reads mapping to lncRNA annotation of NCBI igenomes. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.refseq.txt.gz [Tab-delimited table with quantification of reads mapping to igenomes NCBI annotation. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.RNR.txt.gz [Tab-delimited table with quantification of reads mapping to RNR from NCBI annotation. Column 1-7 contains transcriptID,chr,start,end,strand and length. All other columns shows read numbers in each sample, identified in header]
featC.repeatsONLYminOverlap.txt.gz [Tab-delimited table with quantification of reads mapping to repeats from UCSC genome browser RepeatMasker track annotations. Column 1: RepName, Column2: Total length of all elements of the given element subfamily. Column 3-: each column correspond to one sample, identified in header]
featC.repeatsONLYminOverlap2024.txt.gz [Tab-delimited table with quantification of 20-24 nt long reads mapping to repeats from UCSC genome browser RepeatMasker track annotation. Column 1: RepName, Column2: Total length of all elements of the given element subfamily. ]
featC.piRNA2024minOverlap.txt.gz [Tab-delimited table with quantification of 20-24 nt long reads mapping to piRNAs from piRNAbank annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.piRNAminOverlap.txt.gz [Tab-delimited table with quantification of reads mapping to piRNAs from piRNAbank annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.miRbaseminoverlap.txt.gz [Tab-delimited table with quantification of reads mapping to miRNAs from miRbase annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.miRbase2024_minoverlap.txt.gz [Tab-delimited table with quantification of 20-24nt long reads mapping to miRNAs from miRbase annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.hg38tRNA_minO.txt.gz [Tab-delimited table with quantification of reads mapping to tRNAs from UCSC genome browser RepeatMasker track annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.small.hg38tRNAminO.txt.gz [Tab-delimited table with quantification of 20-24nt  reads mapping to tRNAs from UCSC genome browser RepeatMasker track annotations. Column 1-6 contains transcriptID,chr,start,end,strand and transcript length. Column 7-All other columns shows read numbers in each sample, identified in header]
featC.3UTRCells.txt.gz [Tab-delimited table with quantification of reads mapping to 3UTR annotation of Ensembl. Column 1 contains transcriptID. Column 2: reads of RIP and input samples]
Bigwigs

molecule: total RNA

source_name: brain

extract_protocol:
Brain biopsies were lysed using TissueLyser LT and Immunoprecipitation was conducted using antibodies against AGO2. RNA extraction was done using the miRNAeasey mico kit.
NuGen Ovation RNAseq V2 kit, followed by the Ovation® Ultralow V2 Library or Ovation® Rapid Library Systems

tag: tissue

value: Glioblastoma

tag: rip antibody

tag: ago protein


title: 3047_CD8_unstimulated

value: subject 3047


title: Glioblastoma_AGO2IN_B11_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B11_AGO2IN_T_S68_L005_R1_001
total RNA seq

value: AGO2 IN


title: HumanCortex_AGO2RIP_B14_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B14_AGO2_T_S73_L005_R1_001
total RNA seq

value: cortex


title: 3043_CD8_unstimulated

value: CD3+CD8+ T cells


title: Glioblastoma_AGO1IN_B10_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B10AGO1IN
small RNA seq

extract_protocol:
Brain biopsies were lysed using TissueLyser LT and Immunoprecipitation was conducted using antibodies against AGO2. RNA extraction was done using the miRNAeasey mico kit.
NEBNext Multiplex Small RNA Library Prep Set for Illumina

value: AGO1 IN


title: HumanCortex_AGO2RIP_B14_smallRNA

description:
small RNA
featC.repeatsONLYminOverlap.txt.gz,  featC.repeatsONLYminOverlap2024.txt.gz [Repeats]
featC.piRNAminOverlap.txt.gz,  featC.piRNA2024minOverlap.txt.gz [piRNA]
featC.miRbaseminoverlap.txt.gz, featC.miRbase2024_minoverlap.txt.gz [miRbase]
featC.hg38tRNA_minO.txt.gz, featC.small.hg38tRNAminO.txt.gz [tRNA]
B14_AGO2_S_S19_L005_R1_001
small RNA seq


title: 3038_CD8_unstimulated


title: 3039_CD8_unstimulated


title: GL261 cell line RNA-seq

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

data_processing:
DeFuse (Galaxy Tool Version 1.6.1), Minnesota Supercomputing Institute implementation, run against the raw fastq files
Trinity run against the raw fastq files
transcriptsToOrfs (Galaxy Tool Version 0.0.2), Minnesota Supercomputing Institute implementation, run against the Trinity output
DeFuse Trinity comparison tool (Galaxy Tool Version 0.6.1), Minnesota Supercomputing Institute implementation, run against output from deFuse, Trinity, and transcriptsToOrfs

organism: Mus musculus

source_name: Glioma

growth_protocol: DMEM with 10% FBS and 1% Pen/Strep

extract_protocol: RNA-sequencing data were used to detect fusions capable of producing proteins containing neoantigens.

tag: strain

tag: cell line


title: Glioblastoma_AGO2IN_B13_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B13_AGO2IN_T_S72_L005_R1_001
total RNA seq


title: 3028_CD8_unstimulated


title: 3027_CD8_unstimulated

value: subject 3027


title: 3037_CD8_unstimulated

value: subject 3037


title: 3031_CD8_unstimulated


title: Mutant, rep2

city: Freiburg

first: Andreas

middle: S.

last: Richter

address: Stuebeweg 51

department: Bioinformatics Unit

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Processed data file: zebrafish_diff_expr_genes_DESeq2.tsv.gz
Processed data file: zebrafish_exon_skipping_rMATS.tsv.gz

data_processing:
Basecalling was performed with Illumina RTA version 1.18.64.
Mouse reads were aligned to GRCm38 genome assembly using TopHat 2.0.13 with the following settings: transcriptome alignment to GENCODE release M4 gene annotation first, library type fr-firststrand, fragment length mean and standard deviation set to sample-specific values. The fragment length metrics was determined by mapping a 1 million read pair subsample to the mouse transcriptome using Bowtie 2.2.3. Zebrafish reads were aligned with the same strategy to Zv9 genome assembly and Ensembl 78 gene annotation.
The numbers of sequenced fragments per annotated gene (based on GENCODE M4 mouse or Ensembl 78 zebrafish annotation, respectively) were quantified with featureCounts version 1.4.5-p1. Fragments were only counted if both ends aligned to the same chromosome with a minimum mapping quality of 10 and in agreement with the strand orientation of the annotated gene.
Differential gene expression analysis for mouse was performed with the Bioconductor package edgeR version 3.12.0 using the quasi-likelihood (QL) method, robustified against potential outlier genes. Weakly expressed genes with less than 0.2 counts-per-million (CPM) in at least 3 samples were filtered out. The FDR threshold was 1%. Differentially expressed genes in zebrafish were called using the Bioconductor package DESeq2 version 1.6.3 at 5% FDR. As the mutant and wild-type fish were different mixtures of genetic backgrounds, the linear regression formula used was modified accordingly ("~background+condition").
Differential alternative splicing events were analysed with rMATS 3.0.9. Aligned reads were filtered to include only reads overlapping with annotated transcripts in the same strand orientation based on GENCODE M4 mouse or Ensembl 78 zebrafish annotation, respectively. Fragment size mean and standard deviation were set to sample-specific values as described for the read alignment step. Alternative splicing events supported by reads spanning splice junctions were reported.
Genome_build: Zv9
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include significant differentially expressed genes as reported by edgeR and DESeq2 for mouse and zebrafish, respectively. Tab-delimited text files include exon skipping events generated by rMATS.

organism: Danio rerio

source_name: whole embryo, Tnpo3 mutant

extract_protocol:
Total RNA was extracted from purified mouse thymocytes using RNeasy Mini kit (Qiagen), including a DNaseI treatment step. For the analysis of mutant zebrafish, RNA was extracted from 4 dpf embryos using Tri-Reagent (Sigma), treated with DNaseI and re-extracted with Tri-Reagent. RNA quality was determined using the 2100 Bioanalyzer instrument (Agilent) and RNA concentration was determined using Qbit 2.0 Fluorometer (Life Technologies).
RNA libraries were prepared for sequencing using the TruSeq Stranded Total RNA kit with Ribo-Zero Human/Mouse/Rat (RS-122-2203, Illumina).

tag: genotype/variation

tag: strain/background

value: mixed background B

value: whole embryo

tag: age

value: 4 dpf

tag: surface phenotype


title: 2692_CD8_unstimulated

value: subject 2692


title: 3030_CD8_unstimulated

value: subject 3030


title: Mutant, rep3


title: 24023_tumor_prostate_WGBS

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

library_source: genomic

data_processing:
Bisulphite reads were aligned to the human genome using version 1.2 of an internally developed pipeline, publicly available for download from http://github.com/astatham/Bisulphite_tools.
Adaptor sequences and poor quality bases were removed using Trimgalore (version 0.2.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode with default parameters.
Bismark v0.8.326 was used to align reads to hg19 using the parameters “-p 4 –bowtie2 –X 1000 –unmapped –ambiguous –gzip –bam”
PCR duplicates were removed using Picard v1.91 (http://broadinstitute.github.io/picard)
Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using bismark_methylation_extractor with the parameters “-p –no_overlap –ignore_r2 4 –comprehensive –merge_non_CpG –bedgraph –counts –report –gzip –buffer_size 20G”
Genome_build: hg19
Supplementary_files_format_and_content: bw; Clinical_PCa_samples_WGBS_bigTable.tsv

molecule: genomic DNA

source_name: prostate biopsy DNA from a single donor

growth_protocol: Five 2 mm core biopsies were taken from 1) each of the dominant nodule in areas of >90% cancer cell density, and 2) adjacent benign prostate tissue.

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA kit (Qiagen, USA)
EpiGnome Methyl-Seq kit (Epicentre)
post-bisulphite adapter tagging

treatment_protocol: no treatment

tag: sample id

value: prostate tumor


title: 3045_CD8_unstimulated

value: subject 3045


title: 448C_tumor_prostate_WGBS


title: Wild-type, rep3

source_name: whole embryo, wild-type

value: mixed background A


title: Glioblastoma_AGO2RIP_B11_totalRNA

description:
featC.3UTR.txt.gz [3utr]
featC.linc.txt.gz [linc]
featC.refseq.txt.gz [refseq]
featC.RNR.txt.gz [RNR]
B11_AGO2_T_S67_L005_R1_001
total RNA seq


title: Wild-type, rep2


title: 294C_tumor_prostate_WGBS


title: Wild-type, rep1


title: LLC1 cell line RNA-seq

source_name: Lewis Lung carcinoma


title: 3640_tumor_prostate_WGBS


title: 204C_tumor_prostate_WGBS


title: 1579C_tumor_prostate_WGBS


title: 3047_CD8_ZK_IFNgneg

value: CD8 T cells


title: 408C_tumor_prostate_WGBS


title: 1601C_tumor_prostate_WGBS


title: 3131_tumor_prostate_WGBS


title: 3131_benign_prostate_WGBS

value: adjacent benign normal prostate


title: 514C_tumor_prostate_WGBS


title: Mutant, rep1


title: 24023_benign_prostate_WGBS


title: 3640_benign_prostate_WGBS


title: LNCaP H3K9me3 ChIP-seq

city: Darlinghurst

first: Qian

last: Du

address: 384 Victoria St

institute: Garvan Institute of Medical Research

data_processing:
Peaks were called with Peak Ranger version 1.16 using default parameters.
Broad domains were called with Enriched Domain Detecter (https://github.com/CollasLab/edd) using default parameters.
ChIP-seq reads were aligned to hg19 using bowtie v1.1.0 allowing up to 3 mismatches, discarding ambiguous and clonal reads.
See individual sample.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated using Peak Ranger or Enriched Domain Detector.

source_name: LNCaP prostate cancer cell

growth_protocol: Cell lines were cultured according to manufacturer's instructions.

extract_protocol:
Cells were cross-linked for 10 min in media containing 1% formaldehyde before quenching with 1.25mM glycine. Cell pellets were collected and resuspended in cell lysis buffer (1% Igepal, 85mM KCL, 5mM PIPES pH 8) to a concentration of 1mL per 10^7 cells, incubated on ice for 15 mins, and dounced 20x. Nuclear pellets were collected at 430xg for 5min at 4C and resuspended in nuclear lysis buffer (50mM Tris pH8, 10mM EDTA, 1% SDS, protease inhibitors), 20uL per 10^6 cells, and incubated on ice for 30 min. Lysates were sonicated to fragment lengths of 200 to 500bp. The sonicated lysate was spun at 16,100g for 10 mins at 4°C and aliquoted. The chromatin was diluted 5x in IP dilution buffer (50mM Tris pH 7.4, 1mM EDTA, 150mM NaCl, 1% Igepal, 0.25% Na Deoxychlorate and protease inhibitors). 5ug of chromatin in 250uL total volume is used per ChIP. Preloaded magnetic beads (Dynabeads M280 Streptavidin, Invitrogen #11205D) with anti-H3K9me3 (Diagenode, C15500003) or control-antibody were made by washing 68uL of beads with TBS/0.5% BSA 2x, followed by incubating with antibodies (1.8ug diluted in 105uL TBS/0.5% BSA) for 1 hr at 4C on a rotator. Excess streptavidin biotin-binding sites were blocked with 2x washes of 200uL of 5uM biotin (Sigma Aldrich, B4501) in TBS/0.5% BSA, rotating for 10 min at 4C. Beads were washed 2x with IP dilution buffer, then the chromatin added and incubated O/N at 4C on a rotator. The antibody/protein complexes were collected, washed several times and eluted in 1% SDS and 50mM NaHCO3. Crosslinks were reversed for 6hr at 65C in elution buffer with 200mM NaCl, treated with 1uL of 10ug/uL RNase A and 1uL of 20mg/mL Proteinase K. DNA was purified, the library was prepared (Illumina TruSeq Chip Library Prep Kit).
Libraries were prepared using the Illumina TruSeq Chip Library Prep Kit. The resulting libraries were sequenced on the Illumina HiSeq 2500 platform configured for 50bp single-end reads.

value: Prostate

value: LNCaP

tag: chip-antibody


title: PrEC Lamin A/C ChIP-seq

data_processing:
Broad domains were called with Enriched Domain Detecter (https://github.com/CollasLab/edd) using default parameters.
ChIP-seq reads were aligned to hg19 using bowtie v1.1.0 allowing up to 3 mismatches, discarding ambiguous and clonal reads.
See individual sample.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated using Peak Ranger or Enriched Domain Detector.

source_name: PrEC normal prostate cell

extract_protocol:
Cells (10^7 per ChIP) were cross-linked in suspension for 10 min in PBS containing 1% formaldehyde before quenching with 1.25mM glycine. Pellets were collected and resuspended in hypertonic buffer (10mM Tris pH 7.5, 5mM NaCl, 1.5mM MgCl2, 0.5mM DTT, 0.5mM PMSF protease inhibitor), incubated on ice for 30 mins, and dounced 50x. MgCl2 was then adjusted to 5mM, NP-40 (IGEPAL) was added to final concentration of 0.1%, incubated on ice for 10 mins, before centrifugation at 2400g for 10 mins. The pellet was resuspended in MNase buffer (20mM Tris pH 7.5, 15mM NaCl, 1mM CaCl2) at 25 million cells/ml, incubated for 5 mins at 37°C, 0.5U MNase was added per 1 million cells and then incubated at 37°C for 5 mins.  Digestion was stopped with 10mM final EDTA in ice for 10 mins. Samples were diluted to 8 million cells/ml with lysis buffer (50mM Tris pH8, 10mM EDTA, 0.5% SDS, 0.5mM PMSF and prostease inhibitors)  before sonication. The sonicated lysate was spun at 16,100g for 10 mins at 4°C and aliquoted. The chromatin was diluted 5x in NP-40 buffer (20mM Tris pH 8, 5mM EDTA, 150mM NaCl, 1% NP-40 and protease inhibitors, SDS 0.1%), pre-cleared with Santa Cruz A/G beads for 1 hr at 4°C, spun at 1000rpm for 1 min at 4°C, before adding antibody 5ug lamin B1 (Abcam, #ab16048) and 10ug lamin A/C (Santa Cruz. #sc7292) for overnight incubation with rotation. ChIP material was collected and washed 3x in 1 ml ice-cold RIPA buffer. Crosslink was reversed and DNA eluted for 6 h on a shaker at 37°C in elution buffer (50mM NaCl, 20mM Tris-HCl, pH 7.5, 5mM EDTA, 1% SDS) containing 0.5μg/ml RNase A and 2μg/ml Proteinase K. DNA was purified, the library was prepared (Illumina TruSeq Chip Library Prep Kit).
Libraries were prepared using the Illumina TruSeq Chip Library Prep Kit. The resulting libraries were sequenced on the Illumina HiSeq 2500 platform configured for 50bp single-end reads.

value: PrEC

value: Lamin A/C (Santa Cruz, #sc7292)


title: LNCaP DNase-seq

data_processing:
Peaks were called with F-seq version 1.84 with parameters p-value cut off: 1.
ChIP-seq reads were aligned to hg19 using bowtie v1.1.0 allowing up to 3 mismatches, discarding ambiguous and clonal reads.
See individual sample.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated using Peak Ranger or Enriched Domain Detector.

extract_protocol:
Cells (7x10^6 per sample) were scraped, centrifuged and washed with PBS. Cell pellets were resuspended in nuclear extraction buffer (10mM Tris-HCl pH7.4, 12.5mM NaCl, 3mM MgCl, 0.1mM EDTA, 0.5% IGEPAL) and dounced until nuclei were visible under light microscope with 0.4% Trypan Blue staining. DNase1 (Roche, #04716728001) was added to nuclei pellets of LNCaP (24U) and PrEC (12U) and incubated at 37°C for 15 minutes. DNaseI reactions were terminated by the addition of 36mM EDTA and Proteinase K was added before incubating at 55°C overnight. DNA was purified by phenol-chloroform extraction and ethanol precipitation. Samples were separated using electrophoresis on a 1% agarose gel. 100-300bp sections were excised and purified using the QIAquick Gel Extraction kit. Library preparation and sequencing were performed by the USC Epigenome Center.
Libraries were prepared using the Illumina TruSeq Chip Library Prep Kit. The resulting libraries were sequenced on the Illumina HiSeq 2000 or 2500 platform configured for 50bp single-end reads.


title: PrEC Lamin B1 ChIP-seq

value: Lamin B1 (Abcam, #ab16048)


title: LNCaP Lamin B1 ChIP-seq


title: PrEC H3K9me3 ChIP-seq


title: 356C_tumor_prostate_WGBS


title: Hela-tot-PolII_MagohKD_Rep1

status: Public on Jan 22 2019

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

description: cell culture

data_processing:
The data was sequenced on a HiSeq2500 in a rapid run with a readlength of 68 bp single read (HiSeq Rapid SBS/Cluster Kit v2) .   Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Mapping was performed using bowtie2 version 2.2.8 against ensemble release 84 of BDGP6. Parameters “-N 1 --phred 33 --fr --end-to-end --maxins 1000 --minins 0 --very-sensitive)
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts. Reads were extended to fragment length.
Genome_build: hg38
Supplementary_files_format_and_content: UCSC compatible library size normalized bigwig tracks

source_name: Total pol II ChIP for Magoh knockdown

growth_protocol: HeLa cells were cultured in standard RPMI medium supplemented with 10% FBS and 2% Penicillin/Streptomycin. For knockdown experiments ctrl siRNA (against GFP) and Magoh si RNA was transfected using RNAi Max reagent from Invitrogen (Cat No- 13778150). Cells were harvested after 60 hrs post transfection.

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 μl of TE.
NebNext Ultra II according to manufacturer's protocol.

treatment_protocol: cells were fixed with 1% formaldehyde for 10 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4°C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4°C.

tag: chip antibody

value: RBP1 (Diagenode, catalog# 15200004, lot# 001-11)

value: Human Cervical Carcinoma cells

value: HeLa

value: Mago depleted


title: Hela-tot-PolII_controlKD_Rep2

description: cell culture

source_name: Total pol II ChIP for ctrl knockdown

value: control


title: HelaMagohKD_Input

description: cell culture

source_name: Input control for ChIP with Magoh KD


title: HelacontrolKD_Input

description: cell culture

source_name: Input control for ChIP with Ctrl KD


title: PrEC H3K36me3 ChIP-seq

data_processing:
Peaks were called with Peak Ranger version 1.16 using default parameters.
ChIP-seq reads were aligned to hg19 using bowtie v1.1.0 allowing up to 3 mismatches, discarding ambiguous and clonal reads.
See individual sample.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated using Peak Ranger or Enriched Domain Detector.

extract_protocol:
Cells (10^6 per ChIP) were cross-linked in suspension for 10 min in media containing 1% formaldehyde before quenching with 1.25mM glycine. The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1µg/ml aprotinin and 1µg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. Chromatin lysate was sonicated to generate a majority of fragments between 200 and 500bp. 10µg of each antibody was used per ChIP. No antibody controls were also included, and no precipitation was observed by quantitative Real-Time PCR analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by Protein A/G PLUS agarose beads (Santa Cruz, sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1M NaHCO3, treated with proteinase K for 1 hour, followed by DNA purification using phenol/chloroform extraction and ethanol precipitation, and finally resuspended in 30µl H2O. The ChIP DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-seq DNA Sample Prep Kit.
Libraries were prepared using the Illumina TruSeq Chip Library Prep Kit. The resulting libraries were sequenced on the Illumina HiSeq 2000 or 2500 platform configured for 50bp single-end reads.


title: B_polyA-mRNA_controlKD_Rep2

description:
strand specific mRNA Seq
Sample_imb_roignant_2015_13_LacZ_2

data_processing:
The data was sequenced on a HiSeq2500 in a rapid run with a readlength of 71 bp paired end (HiSeq Rapid SBS/Cluster Kit v2)  or on a NextSeq500 with 42bp paired end.    Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4 (HiSeq2500) or blc2fastq v2.19 (NextSeq500)
Mapping was performed suing STAR (v. 2.5.1b) against ensembl release 84 of BDGP6.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Counts per gene were derived using htseq count (v.0.6.1p1)
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalised bigwig tracks and readcounts per gene

organism: Drosophila melanogaster

growth_protocol: Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No -) supplemented with 10% FBS and 2% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted from cells using Trizol reagent, following the manufacturer’s protocol
Libraries of strand-specific RNA-seq were constructed using Illumina TruSeq Kit, following the manufacturer’s protocol

treatment_protocol: For knock down experiments, dsRNA was synthesized overnight at 37 °C using Hi-Scribe T7 transcription kit (NEB, Cat No- E2040). dsRNA was transfected in S2R+ cells by serum starvation for 6 hours. The treatment was repeated three times and cells were harvested 7 days after the first treatment

value: Embryonic

value: knock-downed  for LacZ


title: B_polyA-mRNA_controlKD_Rep1

description:
strand specific mRNA Seq
Sample_imb_roignant_2015_13_LacZ_1


title: MNAse_controlKD_Rep1

description:
wt_mnase_1
Sequencing of mono nucleosomal fragments from Mnase digestion from Ctrl knockdown cells
cell culture

data_processing:
The data was sequenced on a HiSeq2500 in a high output run with a readlength of  58 bp PE (TruSeq SBS Kit v3) .   Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Libraries were demultiplexed using 6 bp front tags. After sorting the tags were trimmed + the added T were trimmed (7 bp in total)
Mapping was performed using bowtie2 version 2.2.8 against ensemble release 84 of BDGP6. Parameters “-N 1 --phred 33 --fr --end-to-end --maxins 1000 --minins 0 --very-sensitive)
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalized bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalized bigwig tracks

growth_protocol: Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 _l of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol.  Custom adaptors with front tag were used in the protocol.

treatment_protocol: 1. S2R+ cells were fixed with 1% formaldehyde for 3 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4¡C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4¡C.  2. MNase: S2R+ cells were fixed with 1% formaldehyde for 10 min at room temperature. Cells were harvested and 20 million nuclei were spun at 3,500 g at 4°C for 10 min. Nuclear Pellet was resuspended in 300 μl of MNase digestion buffer (0.5 mM spermidine, 0.075% NP40, 50 mM NaCl, 10mM Tris-HCl, pH 7.5, 5mM MgCl2, 1mM CaCl2, 1mM β‐mercaptoethanol and complete protease inhibitors). Reaction was spun at 3,200g, 4°C for 10 min and resuspended in 50 μl of MNase digestion buffer and digested with 30U of MNase at 37°C for 10 min at 300 rpm in mixing block. The MNase digestion reaction was quenched with EDTA at 10 mM final concentration. After 10 min on ice, the neclei were washed once with 1 ml of RIPA buffer (140 mM NaCl and complete protease inhibitors). Pellet was resuspended in 300 μl of RIPA buffer (140mM) and sonicated (3 cycles,medium intensity, 30 s on/off intervals) and centrifuged at 18,000g, 4°C for 10 min

tag: assay

value: Micrococcal Nuclease protection assay

value: S2R+ Cells


title: MNAse_controlKD_Rep2

description:
wt_mnase_3
Sequencing of mono nucleosomal fragments from Mnase digestion from Ctrl knockdown cells
cell culture


title: LNCaP Lamin A/C ChIP-seq


title: MNAse_MagoKD_Rep1

description:
mago_mnase_1
Sequencingof mono nucleosomal fragments from Mnase digestion from Mago knockdown cells
cell culture

source_name: Sequencing of mono nucleosomal fragments from Mnase digestion from Mago knockdown cells


title: MNAse_MagoKD_Rep2

description:
mago_mnase_3
Sequencing of mono nucleosomal fragments from Mnase digestion from Mago knockdown cells
cell culture


title: LNCaP H3K36me3 ChIP-seq


title: polyA-mRNA_RnpS1KD_Rep1

description:
strand specific mRNA Seq
Cells were knock downed for RnpS1, replicate 1
cell culture

data_processing:
The data was sequenced on a HiSeq2500 in a rapid run with a readlength of 71 bp paired end (HiSeq Rapid SBS/Cluster Kit v2) .    Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Mapping was performed suing STAR (v. 2.5.1b) against ensembl release 84 of BDGP6.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Counts per gene were derived using htseq count (v.0.6.1p1)
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalized bigwig tracks and readcounts per gene

source_name: Cells were knock downed for RnpS1

value: RnpS1 depleted


title: polyA-mRNA_controlKD_Rep1

description:
strand specific mRNA Seq
Cells were knock downed for Ctrl, replicate 1
cell culture

source_name: Cells were knock downed for Ctrl


title: polyA-mRNA_controlKD_Rep2

description:
strand specific mRNA Seq
Cells were knock downed for Ctrl, replicate 2
cell culture


title: polyA-mRNA_Cdk9-MagoDKD_Rep2

description:
strand specific mRNA Seq
Cells were knock downed for Mago and Cdk9, replicate 2
cell culture

value: Mago and Cdk9 depleted


title: polyA-mRNA_Y14KD_Rep1

description:
strand specific mRNA Seq
Cells were knock downed for Y14, replicate 1
cell culture

source_name: Cells were knock downed for Y14

value: Y14 depleted


title: polyA-mRNA_RnpS1KD_Rep2

description:
strand specific mRNA Seq
Cells were knock downed for RnpS1, replicate 2
cell culture


title: Hela-tot-PolII_MagohKD_Rep2

description: cell culture


title: Hela-tot-PolII_controlKD_Rep1

description: cell culture


title: polyA-mRNA_MagoKD_Rep1

description:
strand specific mRNA Seq
Cells were knock downed for Mago, replicate 1
cell culture

source_name: Cells were knock downed for Mago


title: polyA-mRNA_MagoKD_Rep2

description:
strand specific mRNA Seq
Cells were knock downed for Mago, replicate 2
cell culture


title: polyA-mRNA_Cdk9-MagoDKD_Rep1

description:
strand specific mRNA Seq
Cells were knock downed for Mago and Cdk9, replicate 1
cell culture


title: polyA-mRNA_eIF4AIII_Rep1

description:
strand specific mRNA Seq
Cells were knock downed for elF4AIII, replicate 1
cell culture

source_name: Cells were knock downed for elF4AIII

value: elF4AIII depleted


title: PrEC DNase-seq

value: Prostate


title: polyA-mRNA_Cdk9KD_Rep1

description:
strand specific mRNA Seq
Cells were knock downed for Cdk9, replicate 1
cell culture

source_name: Cells were knock downed for Cdk9

value: Cdk9 depleted


title: HA_RnpS1_RNAseT1_Rep2

description:
ChIP Seq with RnpS1 HA tagged Cells, with Rnase T1 Rep2
cell culture

data_processing:
The data was sequenced on a HiSeq2500 in a rapid run with a readlength of 68 bp single read (HiSeq Rapid SBS/Cluster Kit v2) .   Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Mapping was performed using bowtie2 version 2.2.8 against ensemble release 84 of BDGP6. Parameters “-N 1 --phred 33 --fr --end-to-end --maxins 1000 --minins 0 --very-sensitive)
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalized bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalized bigwig tracks

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 µl of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA II library preperation kit, following manufacturer's protocol

treatment_protocol: S2R+ cells were fixed with 1% formaldehyde for 3 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC),   and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4°C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4°C.

value: anti-HA (F-7) (Santa Cruz, catalog# sc-7392, lot# I0916)


title: HA_RnpS1_RNAseT1_Rep1

description:
ChIP Seq with RnpS1 HA tagged Cells, with Rnase T1 Rep1
cell culture


title: HA_RnpS1_Rep2

description:
ChIP Seq with RnpS1 HA tagged Cells Rep2
cell culture

source_name: ChIP Seq with RnpS1 HA tagged Cells


title: Input_HA_RnpS1

description:
ChIP Seq of Input DNA
cell culture

source_name: ChIP Seq of Input DNA


title: HA_RnpS1_Rep1

description:
ChIP Seq with RnpS1 HA tagged Cells Rep1
cell culture


title: HAMago_MagoKD_Rep2

description:
ChIP Seq with Mago HA tagged Cells with Mago KD Rep2
cell culture

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 µl of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA II library preparation kit, following manufacturer's protocol

treatment_protocol: S2R+ cells were fixed with 1% formaldehyde for 3 min at room temperature,   and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC),   and lysed by sonication.   The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4°C.   Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4°C.


title: polyA-mRNA_Y14KD_Rep2

description:
strand specific mRNA Seq
Cells were knock downed for Y14, replicate 2
cell culture


title: HAMago_MagoKD_Rep1

description:
ChIP Seq with Mago HA tagged Cells with Mago KD Rep1
cell culture


title: HA_Mago_RNAseT1_Rep2

description:
ChIP Seq with Mago HA tagged Cells, with Rnase T1 Rep2
cell culture


title: HA_Mago_Rep1

description:
ChIP Seq with Mago HA tagged Cells Rep1
cell culture

source_name: ChIP Seq with Mago HA tagged Cells


title: HA_Mago_Rep2

description:
ChIP Seq with Mago HA tagged Cells Rep2
cell culture


title: HA_Ctrl_RNAseT1_Rep1

description:
ChIP Seq with Ctrl HA tagged Cells, with Rnase T1 Rep1
cell culture


title: HA_Mago_RNAseT1_Rep1

description:
ChIP Seq with Mago HA tagged Cells, with Rnase T1 Rep1
cell culture


title: HA_Ctrl_RNAseT1_Rep2

description:
ChIP Seq with Ctrl HA tagged Cells, with Rnase T1 Rep2
cell culture


title: polyA-mRNA_eIF4AIII_Rep2

description:
strand specific mRNA Seq
Cells were knock downed for elF4AIII, replicate 2
cell culture


title: HA_Ctrl_Rep1

description:
ChIP Seq with Ctrl HA tagged Cells Rep1
cell culture

source_name: ChIP Seq with Ctrl HA tagged Cells


title: HA_Ctrl_Rep2

description:
ChIP Seq with Ctrl HA tagged Cells Rep2
cell culture


title: polyA-mRNA_Cdk9KD_Rep2

description:
strand specific mRNA Seq
Cells were knock downed for Cdk9, replicate 2
cell culture


title: Input_HA_Mago

description:
Input for Mago HA overexpression
cell culture

source_name: Input for Mago HA overexpression


title: 4SU-MagoKD_t2_Rep2

description: DRB treated sample with 2 minutes without DRB, Mago knock down Rep2

data_processing:
The data was sequenced on a HiSeq2500 in a rapid run with a readlength of 68 bp single read (HiSeq Rapid SBS/Cluster Kit v2) .    Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Mapping was performed suing STAR (v. 2.5.1b) against ensembl release 84 of BDGP6.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: BDGP6
Supplementary_files_format_and_content: bigwig

source_name: cell culture

extract_protocol:
5,6-dichlorobenzimidazole 1-_-d-ribofuranoside (DRB) from Sigma (D1916) was used at a final concentration of 300_M, dissolved in water, for 5 hours. 4-thiouridine (4sU) was purchased from Sigma (T4509) and used at a final concentration of 100 _M. Control and Mago KD was performed as described before. All the samples were labeled for 8 minutes with 4-thiouridine, and transcription was allowed to proceed after DRB removal for 0, 2, 8 and 16 minutes along with one non-DRB treated control.A total of 100 to 130 ug RNA was used for the biotinylation reaction. 4sU-labeled RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce), dissolved in dimethylformamide (DMF) at a concentration of 1 mg/mL. Biotinylation was done in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) and 0.2 mg/mL Biotin-HPDP for 2 h with rotation at room temperature. Two rounds of chloroform extractions removed unbound Biotin-HPDP. RNA was precipitated at 20,000 g for 20 min at 4¡C with a 1:10 volume of 5M NaCl and an equal volume of isopropanol. The pellet was washed with 75% ethanol and precipitated again at 20,000 g for 10 min at 4¡C. The pellet was left to dry, followed by resuspension in 100 _L RNase-free water. Biotinylated RNA was captured using Dynabeads MyOne Streptavidin T1 beads (Invitrogen). Biotinylated RNA was incubated with 50 _L Dynabeads with rotation for 15 min at 25¡C. Beads were magnetically fixed and washed with 1_ Dynabeads washing buffer. RNA-4sU was eluted with 100 _L of freshly prepared 100 mM dithiothreitol (DTT), and cleaned on RNeasy MinElute Spin columns (Qiagen).
Enriched nascent RNAs were converted to cDNA libraries with Drosophila Ovation Kit (Nugen) with integrated ribosomal depletion workflow

treatment_protocol: dsRNA was transfected in S2R+ cells by serum starvation for 6 hours. The treatment was repeated three times and cells were harvested 7 days after the first treatment.

tag: pulldown

value: Biotin enrichment

tag: treatment


title: 4SU-MagoKD_t8_Rep2

description: DRB treated sample with 8 minutes without DRB, Mago knock down Rep2

tag: cell type


title: 4SU-MagoKD_t0_Rep2

description: DRB treated sample without release, Mago knock down Rep2


title: 4SU-MagoKD_NT_Rep2

description: Non DRB treated Mago Knock down Sample, Rep2

value: Non DRB treated Mago Knock down Sample


title: 4SU-MagoKD_t16_Rep2

description: DRB treated sample with 16 minutes without DRB, Mago knock down Rep2


title: 4SU-controlKD_t8_Rep2

description: DRB treated sample with 8 minutes without DRB, Ctrl knock down Rep2


title: 4SU-controlKD_t16_Rep2

description: DRB treated sample with 16 minutes without DRB, Ctrl knock down Rep2


title: 4SU-controlKD_t2_Rep2

description: DRB treated sample with 2 minutes without DRB, Ctrl knock down Rep2


title: 4SU-controlKD_t0_Rep2

description: DRB treated sample without release, Ctrl knock down Rep2


title: 4SU-MagoKD_t16_Rep1

description: DRB treated sample with 16 minutes without DRB, Mago knock down


title: 4SU-controlKD_NT_Rep2

description: Non DRB treated Ctrl Sample, Rep2

value: Non DRB treated Ctrl Sample


title: 4SU-MagoKD_t8_Rep1

description: DRB treated sample with 8 minutes without DRB, Mago knock down


title: 4SU-MagoKD_t0_Rep1

description: DRB treated sample without release, Mago knock down


title: 4SU-MagoKD_NT_Rep1

description: Non DRB treated Mago Knock down Sample


title: 4SU-controlKD_t16_Rep1

description: DRB treated sample with 16 minutes without DRB, Ctrl knock down


title: 4SU-controlKD_t2_Rep1

description: DRB treated sample with 2 minutes without DRB, Ctrl knock down


title: 4SU-controlKD_NT_Rep1

description: Non DRB treated Ctrl Sample


title: 4SU-controlKD_t8_Rep1

description: DRB treated sample with 8 minutes without DRB, Ctrl knock down


title: polyA-mRNA_BtzKD_Rep1

description:
strand specific mRNA Seq
Btz_KD_1_S5

value: knock-downed  for Btz


title: polyA-mRNA_BtzKD_Rep2

description:
strand specific mRNA Seq
Btz_KD_2_S6


title: B_tot-PolII_RnpS1KD_Rep2

description: imb_roignant_2017_18_JA_ChIP_RnpS1_PolII_2

data_processing:
Samples were sequencing on an Illumian NextSeq500 and demultiplexed using bcl2fastq v2.19. The libraries contain a Yeast spike in.
Mapping was done using bowtie2 (v. 2.2.8) against BDGP6 fo the Drosophila genome
Bigwig tracks were produced using bedTools (v.2.25) and bedGraphToBigwig
Genome_build: BDGP6
Supplementary_files_format_and_content: sequencing depth normalised bigwig tracks

source_name: ChIP Seq of Pol II in RnpS1 KD

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 _l of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol
NebNext UltraII

treatment_protocol: S2R+ cells were fixed with 1% formaldehyde for 10 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4¡C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4¡C.

value: RBP1 (Diagenode Cat No-15200004)


title: Input_HA_Ctrl

description:
Input for Ctrl HA overexpression
cell culture

source_name: Input for Ctrl HA overexpression


title: B_tot-PolII_RnpS1KD_Rep1

description: imb_roignant_2017_18_JA_ChIP_RnpS1_PolII_1


title: Input_HAMago_MagoKD

description:
Input for Mago HA overexpression with Mago knockdown
cell culture


title: B_tot-PolII_MagoKD_Rep2

description: imb_roignant_2017_18_JA_ChIP_Mago_PolII_2

source_name: ChIP Seq of Pol II in Mago KD


title: B_tot-PolII_controlKD_Rep2

description: imb_roignant_2017_18_JA_ChIP_Ctrl_PolII_2

source_name: ChIP Seq of Pol II in Ctrl KD


title: 4SU-MagoKD_t2_Rep1

description: DRB treated sample with 2 minutes without DRB, Mago knock down

value: Mago depleted


title: tot-PolII_Y14KD_Rep2

data_processing:
Samples were sequencing on an Illumian NextSeq500 and demultiplexed using bcl2fastq v2.19
Mapping was done using bowtie2 (v. 2.2.8) against BDGP6 fo the Drosophila genome
Bigwig tracks were produced using bedTools (v.2.25) and bedGraphToBigwig
Genome_build: BDGP6
Supplementary_files_format_and_content: sequencing depth normalised bigwig tracks

source_name: ChIP Seq of Pol II in Y14 KD

value: Embryonic


title: B_tot-PolII_controlKD_Rep1

description: imb_roignant_2017_18_JA_ChIP_Ctrl_PolII_1


title: Input_eIF4AIIIKD

description: imb_roignant_2017_17_JA_ChIP_Input_eif4AIII_S14

source_name: ChIP Seq


title: tot-PolII_Y14KD_Rep1


title: Input_controlKD

description: imb_roignant_2017_17_JA_ChIP_Input_Ctrl_S11


title: Input_MagoKD

description: imb_roignant_2017_17_JA_ChIP_Input_Mago_S12


title: tot-PolII_eIF4AIIIKD_Rep1

description: imb_roignant_2017_17_JA_ChIP_eiF4AIII_1_S7

source_name: ChIP Seq of Pol II in eif4a3 KD


title: Input_Y14KD

description: imb_roignant_2017_17_JA_ChIP_Input_Y14_S13


title: tot-PolII_MagoKD_Rep1


title: tot-PolII_controlKD_Rep1


title: Input_BtzKD

description: imb_roignant_2017_17_JA_ChIP_Input_Btz_S22


title: 4SU-controlKD_t0_Rep1

description: DRB treated sample without release, Ctrl knock down

value: control


title: tot-PolII_BtzKD_Rep1

source_name: ChIP Seq of Pol II in Btz KD


title: tot-PolII_controlKD_Rep2


title: 4SU-frag_controlKD_Rep2

data_processing:
Library strategy: 4SU-seq
The data was sequenced on a NextSeq500 demultiplexing was done with blc2fastq v2.19 (NextSeq500)
Mapping was performed suing STAR (v. 2.5.1b) against ensembl release 84 of BDGP6.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Counts per gene were derived using htseq count (v.0.6.1p1)
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalised bigwig tracks and readcounts per gene

source_name: Nascent RNA seq in Ctrl KD

extract_protocol:
5,6-dichlorobenzimidazole 1-_-d-ribofuranoside (DRB) from Sigma (D1916) was used at a final concentration of 300_M, dissolved in water, for 5 hours. 4-thiouridine (4sU) was purchased from Sigma (T4509) and used at a final concentration of 100 _M. Control and Mago KD was performed as described before. All the samples were labeled for 8 minutes with 4-thiouridine, and transcription was allowed to proceed after DRB removal for 0, 2, 8 and 16 minutes along with one non-DRB treated control.A total of 100 to 130 _g RNA was used for the biotinylation reaction. 4sU-labeled RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce), dissolved in dimethylformamide (DMF) at a concentration of 1 mg/mL. Biotinylation was done in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) and 0.2 mg/mL Biotin-HPDP for 2 h with rotation at room temperature. Two rounds of chloroform extractions removed unbound Biotin-HPDP. RNA was precipitated at 20,000 g for 20 min at 4¡C with a 1:10 volume of 5M NaCl and an equal volume of isopropanol. The pellet was washed with 75% ethanol and precipitated again at 20,000 g for 10 min at 4¡C. The pellet was left to dry, followed by resuspension in 100 _L RNase-free water. Biotinylated RNA was captured using Dynabeads MyOne Streptavidin T1 beads (Invitrogen). Biotinylated RNA was incubated with 50 _L Dynabeads with rotation for 15 min at 25¡C. Beads were magnetically fixed and washed with 1_ Dynabeads washing buffer. RNA-4sU was eluted with 100 _L of freshly prepared 100 mM dithiothreitol (DTT), and cleaned on RNeasy MinElute Spin columns (Qiagen).
Enriched nascent RNAs were converted to cDNA libraries with Drosophila Ovation Kit (Nugen) with integrated ribosomal depletion workflow


title: 4SU-frag_controlKD_Rep1


title: HA_Y14_Rep2

source_name: ChIP Seq of HA tagged Y14

value: F-7 (anti-HA), Santa Cruz


title: HA_Y14_Rep1


title: 4SU-frag_MagoKD_Rep2

source_name: Nascent RNA seq in Mago KD


title: B_tot-PolII_MagoKD_Rep1

description: imb_roignant_2017_18_JA_ChIP_Mago_PolII_1


title: tot-PolII_BtzKD_Rep2


title: 4SU-frag_MagoKD_Rep1


title: Input_HA-Y14

source_name: ChIP Seq of Input Ctrl


title: tot-PolII_MagoKD_Rep2


title: HA_eIF4AIII_Rep2

source_name: ChIP Seq of HA tagged eif4a3


title: Input_HA-control


title: HA_control_Rep2

source_name: ChIP Seq of HA tag alone


title: tot-PolII_eIF4AIIIKD_Rep2

description: imb_roignant_2017_17_JA_ChIP_eiF4AIII_2_S8


title: HA_eIF4AIII_Rep1


title: Mago KD_K4Me3_Rep2

source_name: ChIP Seq of K4Me3 in mago KD

value: Ab8580 (anti H3K4Me3)


title: HA_control_Rep1


title: Mago KD_K4Me3_Rep1


title: wtR1_mRNA_Seq_rep2

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
mRNA-Seq: The reads were aligned to the tomato genome using TopHat2 with "--b2-very-sensitive" option. The ITAG2.4 annotation gff3 file was supplied as the “-G” option to TopHat2.
genome build: tomato genome build 2.50 (SL2.50)
processed data files format and content: For mRA_Seq: The FPKM values were calculated via cuffdiff from Cufflinks suite of tools.

organism: Solanum lycopersicum

source_name: mature leaves

growth_protocol: Tomato plants  were grown in soil in a growth room with the condition of 14/10 h and 25/20 °C for day/night.

extract_protocol:
Total RNA was extracted from wtR1, 2A and 2B by Trizol Reagent (Ambion) using the same leaf material as for the DNA extraction.
The library construct and deep sequencing were then performed at the Core Facility of Genomics in Shanghai Center for Plant Stress Biology.

tag: genotype

value: T1 of the regenerated wild type wtR0

value: mature leaves


title: Control KD_K4Me3_Rep2

source_name: ChIP Seq of K4Me3 in Ctrl KD


title: Control KD_K4Me3_Rep1


title: slmet1-1-T1-B_mRNA_Seq_rep1

extract_protocol:
Total RNA was extracted from wtR1, slmet1-1-T1-A and slmet1-1-T1-B by Trizol Reagent (Ambion) using the same leaf material as for the DNA extraction.
The library construct and deep sequencing were then performed at the Core Facility of Genomics in Shanghai Center for Plant Stress Biology.

value: slmet1 T1 progeny

tag: tissue

tag: note

value: label as "2B" in GSE102273_RNA_Seq_FPKM_table.txt


title: slmet1-1-T1-A_mRNA_Seq_rep1

value: label as "2A" in GSE102273_RNA_Seq_FPKM_table.txt


title: slmet1-1-T1-A_mRNA_Seq_rep2


title: wtR1_mRNA_Seq_rep1


title: slmet1-1-T1-B_mRNA_Seq_rep2


title: wtR1_BS

description: treated with bisulfite

data_processing:
MethylC-Seq:Reads were mapped to SL2.50 using BRAT-BW with parameters -m 2 -i 0 -a 1000. Copy-duplicates were remove using remove-dupl command of BRAT-BW. acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
genome build: tomato genome build 2.50 (SL2.50)
processed data files format and content: For MethylC-Seq: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

extract_protocol:
The mature leaves from tomato plants of different genotypes were taken, and the genomic DNA was extracted by DNeasy Plant Mini Kit (Qiagen).
The bisulfite conversion, libarary construction, and deep sequencing were perfomed by the Core facility of the genomics in Shanghai Center for Plant Stress Biology


title: slmet1-T0-B_BS

description: treated with bisulfite

value: slmet1 T0


title: wtO8_BS

description: treated with bisulfite

value: wild type Ohio8245 inbred line


title: Input_HA-eIF4AIII


title: slmet1-T0-A_BS

description: treated with bisulfite


title: slmet1-1-T1-A_BS

description: treated with bisulfite

value: slmet1-1 T1 progeny A


title: wtR0_BS

description: treated with bisulfite

value: regenerated WT T0


title: slmet1-1-T1-B_BS

description: treated with bisulfite

value: slmet1-1 T1 progeny B


title: C75-109A-1

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

country: China

institute: Shanghai Inst. Plant Phys. & Eco.

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the Fusarium graminearum genome assembly (GCA_000599445.1) using Tophat version 2.1.0
Gene abundance measurements were generationed and normalized  using Cufflink version 2.1.1.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using cuffdiff.
Genome_build: Fusarium graminearum (GCA_000599445.1)
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Fusarium graminearum PH-1

source_name: ∆fg3_54-OE::FGM4 mycelium

growth_protocol: F. graminearum strains were cultivated in YEPD liquid medium at 25°C for 3 days with shaking at 150 rpm.

extract_protocol:
Total RNA was extracted from mycelia using TRIzol reagent and then checked by Agilent Bioanalyzer 2100
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: parent strain

value: Mycelium


title: 65A2

source_name: WT-OE::FGM4 mycelium


title: C75-109A-2


title: 65A1


title: C94-3-2

source_name: ∆fgm4 mycelium


title: C94-3-1


title: PH-1-1

source_name: wild type mycelium


title: P22F3_KICHOW

status: Public on Jan 21 2019

city: London

first: Ines

last: Pineda-Torra

address: 5 University Street

country: United Kingdom

institute: University College London

description: Liver S196A

data_processing:
Sequencing was carried out at a concentration of 1.8pM on a Illumina NextSeq 500, NCS v2.1.2, 43bp paired end protocol.
Basecalling was done using the standard Illumina parameters (RTA 2.4.11)
Reads were demultiplexed using Illumina bcl2fastq v2.17 and then were aligned using STAR v2.5.0b.
Transcript abundance was estimated using Illumina's RnaReadCounter tool and differential expression analysis performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw counts of sequencing reads for each sample

source_name: Liver S196A

extract_protocol:
Livers were dissected and placed immediately in RNAlater stabilization solution (Thermo Fisher). RNA was extracted using Trizol reagent and genomic DNA was eliminated with Buffer GE (Qiagen). mRNA was enriched with oligo dT  paramagnetic beads
Libraries were constructed using the Kapa Stranded mRNA-Seq Kit (Cat#KK8421) with 12 cycles of PCR enrichment.

treatment_protocol: Mice were fed a chow diet (18% Protein, 6.2% Fat, 0% Cholesterol; Harlan Laboratories) ad libitum.

tag: strain

value: 16-week old

value: Liver


title: P22F2_KICHOW

description: Liver S196A


title: O12F2_WTCHOW

description: Liver WT

source_name: Liver WT

value: WT


title: O12F1_WTCHOW

description: Liver WT


title: P17NM_KIHFHC

description: Liver S196A rep 3

data_processing:
Sequencing was carried out at a concentration of 1.8pM on a Illumina NextSeq 500, NCS v2.1.2, 43bp paired end protocol.
Basecalling was done using the standard Illumina parameters (RTA 2.4.11)
Reads were demulitplexed using Illumina bcl2fastq v2.17 and then were aligned using STAR v2.5.0b.
Transcript abundance was estimated using Illumina's RnaReadCounter tool and differential expression analysis performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw counts of sequencing reads for each sample

source_name: LXRα-S196A female mice after being fed a High Fat-High Cholesterol diet for 6 weeks

treatment_protocol: Mice were fed a High Fat-High Cholesterol diet (17,2% Cocoa Butter, 2,8% Soybean Oil, 1,25% Cholesterol, 0,5% Sodium Cholate; AIN-76A/Clinton Diet #4, Test Diet Limited, UK) for 6 weeks ad libitum.

tag: gender

value: female


title: P17RKI_HFHC

description: Liver S196A rep 1


title: P17RL_KIHFHC

description: Liver S196A rep 2


title: O10AL_WTHFHC

description: Liver WT rep 3

source_name: wild-type (WT) female mice after being fed a High Fat-High Cholesterol diet for 6 weeks


title: O12F4_WTCHOW

description: Liver WT

tag: genotype/variation


title: O8FNM_WTHFHC

description: Liver WT rep 2


title: Mm_WT_PKHneg_msphr_rna_rep3

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the mus musculs  genome build mm10 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome Mus Musculus index, UCSC mm10 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq2 package (v1.10.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized expression value, log2fold change, pvalue and adjusted pvalue for each gene for each DE analysis

source_name: Mammosphere culture- sorted cells

growth_protocol: cells were isolated from mammary tissue derived from WT or transgenic mice and plated in anchorage independent condition (polyHEMA coated plates) to form mammospheres. Mammospheres were serially passaged in STEM Medium (serum-free mammary epithelial basal medium MEBM, supplemented with 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, 5 μg/ml insulin, 0.5 μg/ml hydrocortisone, 2% B27, 20 ng/ml EGF and βFGF and 4 μg/ml heparin). Mammospheres were disaggregated and RNA extracted.

extract_protocol:
RNA from mammospheres was extracted with Maxwell® 16 LEV simplyRNA cells kit (Promega) and reverse transcribed using random primers and ImProm-II™ reverse transcriptase (Promega), following manufacturer’s instructions.
Libraries of template RNA molecules were prepared from 0.5 to 2 μg high quality input RNA using the Illumina® TruSeq® RNA Sample Preparation Kit v2, following manufacturer’s instructions.

value: FVB/Hsd

value: normal mammary gland

value: 7 weeks old

value: wild type

tag: infection

value: not infected

value: FACS sorted for PKH negative

tag: passage


title: O8FL_WTHFHC

description: Liver WT rep 1

tag: age


title: Mm_WT_PKHneg_msphr_rna_rep2


title: Mm_WT_PKHneg_msphr_rna_rep1


title: Mm_WT_PKHhigh_msphr_rna_rep1

value: FACS sorted for PKH high level


title: Mm_ErbB2_msphr_Nut3_rna_rep2

source_name: Mammosphere culture

value: breast tumor

value: 12-15 weeks old

value: transgenic MMTV-ErbB2

value: Nutlin-3 (2.5 uM for 72h)

value: M6-M7 (72 hours after plating)


title: Mm_p53mm_msphr_rna_rep2

value: Trp53 knockout

value: not treated


title: Mm_ErbB2_msphr_rna_rep5


title: Mm_WT_PKHhigh_msphr_rna_rep2


title: Mm_p53mm_msphr_rna_rep1


title: Mm_ErbB2_msphr_Nut3_rna_rep3


title: Mm_ErbB2_msphr_Nut3_rna_rep1


title: PH-1-2

value: Mycelium


title: Mm_ErbB2_msphr_rna_rep2


title: Mm_ErbB2_msphr_rna_rep3


title: Mm_ErbB2_msphr_rna_rep4


title: Mm_ErbB2_msphr_rna_rep1


title: Mm_WT_msphr_L-MycER_rna_rep2

value: infected with L-pWPI-MycER

value: M3 (72 hours after plating)


title: Mm_WT_msphr_L-MycER_rna_rep3

value: FVB/Hsd


title: Mm_WT_msphr_L-MycER_rna_rep1

value: normal mammary gland


title: Mm_WT_msphr_L-ctrl_rna_rep3

value: 7 weeks old

value: infected with L-pWPI empy vector


title: P22F1_KICHOW

description: Liver S196A

value: 16-week old

value: Liver


title: Mm_WT_msphr_L-ctrl_rna_rep2

value: wild type


title: Mm_NMuNG_L-MycER_ChIPseq_aMyc_rep1

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
ChIP-seq reads were aligned to the mm10 genome assembly using bwa version 0.6.2 with the default parameters
Low-quality and multiple-mapping reads were removed using Samtools with option ‘‘-q 1’
Peaks were called using MACS 1.4.1 with default setting
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were obtained with a combination of bedtools (v2.16.1) sub-commands: aligned reads (bam) were converted in bed with bamToBed and extended to approximately 200 bp with slopbed; then genomeCoverageBed were used to generate the wig file, which in turn is transformed to bigwig with the UCSC Genome Browser utility wigToBigWig.

source_name: immortalized non-transformed mammary cells

growth_protocol: NMuMG cells were routinely passaged in DMEM supplemented with 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, 5 μg/ml insulin

extract_protocol:
Lysates were sonicated and transcription factors-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line name

value: NMuNG

tag: passages

value: Rabbit Polyclonal Anti-c-Myc (N-262), SCB sc-764


title: Mm_NMuNG_L-MycER_ChIPseq_aMyc_rep2

tag: chip antibody


title: Mm_WT_msphr_L-ctrl_rna_rep1


title: Mm_NMuNG_L-Ctrl_Input_ChIPseq


title: Mm_NMuNG_L-MycER_Input_ChIPseq


title: Mm_NMuNG_L-Ctrl_ChIPseq_aMyc_rep2


title: Mm_NMuNG_8hAdri_Input_ChIPseq

value: not infected

value: Adriamycin (0.5 uM for 8h)


title: Mm_NMuNG_8hAdri_ChIPseq_aP53_rep2

value: Rabbit Polyclonal Anti-p53 (CM5), Novocastra NCL-L-p53-CM5p


title: Mm_NMuNG_ChIPseq_aP53_rep2


title: Mm_NMuNG_ChIPseq_aP53_rep1


title: Mm_NMuNG_Input_ChIPseq


title: Mouse miR-741 knock-out by CRISPR cultured spermatogonia stem cells

status: Public on Jan 19 2019

first: Fengjuan

last: Zhang

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description: Total cellular RNA.

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw fastq data was pre-processed using a common procedure. After quality filtering, sequencing reads were clipped from the 3’ adaptor allowing a minimum match of 10nt. Reads unable to match the 3' adaptor sequence or with lengths shorter than 17 bp were discarded.
The useful reads were mapped to the mouse genome by bowtie (bowtie options –v 0 –k 100) (Langmead et al. 2009). The mapped genome sequences were further aligned to known miRNAs, tRNAs, rRNAs, snoRNAs and snRNAs by bowtie. The remaining 25~32 nt sequences were used to identify piRNAs following the method described previously (Inuk Jung et al. 2014) with slight modifications. The clustering parameters were determined as MinReads = 4 and Eps = 2500 bp by running a series of k-dist analysis with different Eps and MinReads in our own data. After clustering all remaining 25~32nt sequences with the determined parameters, all candidate clusters were considered as piRNA clusters without any further scoring and filtering.
Only the reads that exactly matched the 5’ start site of annotated miRNAs and has ≤2 nt deletions or additional sequences derived from pri-miRNAs at the 3’ ends were counted as miRNAs. The count of each miRNAs, piRNAs and tRNA, rRNA, snRNA-derived sequences was normalized to the count of methylated spike-in. The small RNAs were mapped in the following order: miRNA, tRNA, rRNA, snoRNA, snRNA and piRNA.
Genome_build: Mouse mm10 (GRCm38), rabbit oryCun2 (oryCun2.0), rat rn6 (Rnor_6.0), pig susScr3 (Sscrofa10.2).
Supplementary_files_format_and_content: *txt: Tab-delimited text files include useful reads count for each sample; abundance measurements.

source_name: cultured SSCs (spermatogonia stem cells)

growth_protocol: Pre-leptotene and leptotene spermatocytes were isolated from testes of P9 (postnatal day 9) mice; zygotene spermatocytes were isolated from testes of P13 mice; and pachytene spermatocytes and round spermatids were isolated from testes of P25 mice. SSCs were dissociated from a 15-day-old C57BL/6× DBA2 F1 male mouse carrying transgenic actin-EGFP genes. The colonies of SSC were trypsinized and plated on MEF feeder cells in 24-well plate with SF medium.

extract_protocol:
Total cellular RNA was extracted using a TRIzol reagent (Takara).
Approximately 1 µg of total cellular RNA was used to construct a small RNA library according to the Illumina protocol.
High-throughput RNA sequencing was performed using a Hi-Seq 2000 with 50 running circles (Genergy Biotechnology).

treatment_protocol: TALEN or CRISPR plasmids targeting miR-741 were transfected into SSCs with an Amaxa Cell Line Nucleofector Kit L (Lonza). Single SSC colonies were picked and verified by Sanger sequencing.

tag: strain/background

value: C57BL/6 x DBA2 F1

value: miR-741 knock-out by CRISPR

value: male

value: cultured spermatogonia stem cells

tag: developmental stage

value: postnatal day 15


title: h3_norm3

status: Public on Jan 20 2019

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

data_processing:
We extended the 34-bp reads toward the 3’ end to cover DNA fragments bound by the specific modified histone proteins. The readout was converted to browser extensible data (BED) files for visualization in the UCSC genome browser (http://genome.ucsc.edu).
Genome_build: mm9
Supplementary_files_format_and_content: BED

source_name: Normal liver_H3

extract_protocol:
Small liver pieces were incubated for 10 min at room temperature in 1× phosphate-buffered saline (PBS) containing 1% formaldehyde. The crosslinking reaction was quenched by adding glycine to a final concentration of 0.125 M. After a wash in 1× PBS, liver pieces were homogenized in lysis buffer and incubated for 10 min on ice. Nuclei were pelleted and resuspended in 1× TE buffer. Nuclei were sonicated using a Bioruptor (Diagenode, Liege, Belgium). Chromatin samples were diluted with 2× RIPA buffer to a final 1× concentration. IPs were performed with primary antibody and Dynabeads Protein A complex overnight at 4°C. Immune complexes were washed twice for 10 min in each of the following buffers: 1× RIPA buffer, 1× RIPA + 0.3 M NaCl, LiCl buffer, 1× TE + 0.2% Triton X-100, 1× TE. Then, immune complexes were in 100 μl 1× TE, protease K, and 0.3% sodium dodecyl sulfate (SDS) and incubated at 65°C overnight. Eluted DNA was purified using a QIAGEN PCR purification kit. Buffers were comprised of the following: lysis buffer (10 mM Tris [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1× TE; 10 mM Tris-HCl [pH 7.5], and 1 mM EDTA), 1× RIPA (1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and 10 mM Tris [pH 7.5], 1 mM EDTA), LiCl buffer (0.25 M LiCl, 0.5% NP40, and 0.5% sodium deoxycholate). Every buffer included 1× protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, IN). The following antibodies were used: H3Ace (06-599, Upstate/Millipore, Temecula, CA), H3K36me3 (ab9050, abcam), H3K27me3 (07-449, Upstate/Millipore, Temecula, CA), H3K4me3 (07-473, Upstate/Millipore, Temecula, CA), RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody (abcam, ab5131). RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody (abcam, ab5095), Anti-H3 (millipore 06-755).
Illumina ChIP library prep (Part # 11251892 Rev. A)

tag: phenotype

value: Normal liver

tag: background strain


title: pol2s2p_hbx3

source_name: HBx transgenic liver_pol2s2p

value: HBx transgenic liver


title: h3k4me3_hbx3

source_name: HBx transgenic liverr_H3k4me3


title: pol2s5p_norm3

source_name: Normal liver_pol2s5p


title: h3k36me3_hbx3

source_name: HBx transgenic liver_h3k36me3


title: IY_3b

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo S

institute: Mayo Clinic

data_processing:
Genboree Bioinformatics exceRpt pipeline v2.2.2, using the default parameters. The general steps were listed below.
Trim the adaptor sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and filter out reads that are short after adaptor trimming.
Filter out reads that are mapped (using bowtie2) to UniVec contaminants, 45S, 5S and rRNAs
Map the remaining reads to mm10 genome, miRNA sequence (miRBase v21), piRNA sequences (RNAdb) and tRNA sequences (gtRNAdb), using bowtie. The allowed mismatch is 1 for miRNA and 2 for others.
Count miRNA reads, piRNA reads and tRNA reads.
Normalize raw read counts by log2 (Count Per Million)
Genome_build: mm10
Supplementary_files_format_and_content: Text file separated by tab with column names that have miRNA raw read count information. "UR" column means "number of unique reads", "RC" column means "total number of reads (not necessarily uniquely mapped".

source_name: partial hepatectomy, serum

extract_protocol:
ExoQuick followed by SeraMir Kit (System Biosciences)
NEBNext Small RNA Library

tag: protocol

value: partial hepatectomy

tag: time (hours after partial hepatectomy)

tag: rna source

value: serum


title: pol2s5p_hbx3

source_name: HBx transgenic liver_pol2s5p

tag: tissue


title: h3_hbx3

source_name: HBx transgenic liver_H3


title: Mm_NMuNG_L-Ctrl_ChIPseq_aMyc_rep1

value: infected with L-pWPI empy vector

tag: treatment

value: not treated


title: pol2s2p_norm3

source_name: Normal liver_pol2s2p

value: Liver


title: Mouse wild type cultured spermatogonia stem cells control

description: Total cellular RNA.

value: wild type

tag: gender

tag: cell type


title: IY_8b

tag: strain


title: Mouse miR-741 knock-out by TALEN cultured spermatogonia stem cells

description: Total cellular RNA.

tag: genotype/variation

value: miR-741 knock-out by TALEN


title: Mm_NMuNG_8hAdri_ChIPseq_aP53_rep1

value: NMuNG

tag: infection

value: not infected


title: Mouse wild type mature sperms

description: Total cellular RNA.

source_name: mature sperms

value: mature sperms


title: Mouse wild type round sperms

description: Total cellular RNA.

source_name: round sperms

value: round sperms

value: postnatal day 25


title: Mouse wild type pachytene spermatocytes

description: Total cellular RNA.

source_name: pachytene spermatocytes

value: male

value: pachytene spermatocytes


title: Mouse wild type cultured spermatogonia stem cells

description: Total cellular RNA.

value: cultured spermatogonia stem cells


title: Mouse wild type zygotene spermatocytes

description: Total cellular RNA.

source_name: zygotene spermatocytes

value: zygotene spermatocytes

value: postnatal day 13


title: IY_1b

source_name: no hepatectomy, serum

value: no treatment


title: TTPΔARE RNA-seq_ES538

city: Durham

first: Perry

middle: J

last: Blackshear

address: 101 Alexander Dr.

institute: NIEHS

data_processing:
raw reads were mapped to mm10 RefSeq cDNA sequences using BWA default paired-end read mapping protocol
the reads that were not mapped in-pair were filtered out
total read count of each transcript were reported and normalized by EpiCenter
FPKM data were derived from the normalized read counts
Genome_build: mm10
Supplementary_files_format_and_content: FPKM data

source_name: Spleen

growth_protocol: Living mice; normal growth conditions

extract_protocol:
RNA was isolated from spleens using the GE Healthcare RNA isolation kit. RNA was quantified on Tecan's Infinite 200PRO Nanoquant.
Libraries were prepared according to Illumina's Instructions

value: TTP<delta>ARE

tag: development stage

value: 8-12 weeks

value: spleen


title: WT RNA-seq_ES535

value: WT


title: TTPΔARE RNA-seq_ES536


title: TTPΔARE RNA-seq_ES537


title: TTPΔARE RNA-seq_ES539


title: WT RNA-seq_ES534


title: Rabbit wild type testes postnatal day 110

description: Total cellular RNA mixed with exogenous spike-in.

organism: Oryctolagus cuniculus

source_name: testes postnatal day 110

value: wild type

value: testes

value: postnatal day 110


title: Rabbit wild type testes postnatal day 90

source_name: testes postnatal day 90

value: postnatal day 90


title: WT RNA-seq_ES533


title: Rabbit wild type testes postnatal day 70

source_name: testes postnatal day 70

value: postnatal day 70


title: Mouse wild type leptotene spermatocytes

description: Total cellular RNA.

source_name: leptotene spermatocytes

value: leptotene spermatocytes

value: postnatal day 9


title: Mouse wild type pre-leptotene spermatocytes

description: Total cellular RNA.

source_name: pre-leptotene spermatocytes

value: male

value: pre-leptotene spermatocytes


title: Rabbit wild type testes postnatal day 30

source_name: testes postnatal day 30

value: postnatal day 30


title: Rabbit wild type testes postnatal day 60

source_name: testes postnatal day 60

value: postnatal day 60


title: Rat wild type adult testes

description: Total cellular RNA.

organism: Rattus norvegicus

source_name: adult testes

value: adult


title: Rabbit wild type testes postnatal day 10

source_name: testes postnatal day 10

value: postnatal day 10


title: WT RNA-seq_ES532


title: Pig wild type adult testes

description: Total cellular RNA.

organism: Sus scrofa


title: IGF_153b1 [BS-Seq]

status: Public on Jan 18 2019

city: Glasgow

first: Paul

last: Shiels

address: Level 3, Wolfson Wohl Cancer Research Centre

department: Wolfson Wohl Translational Research Centre

institute: University of Glasgow

description: Post-perfused

data_processing:
Illumina bcl2fastq v2.15.0.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Before the alignment of WGBS reads, the human reference genome (GRCh38) was in silico bisulfite converted. Bismark v0.10.1 and bowtie2 (v2.1.0) was used in the alignment process.
The methylation calls (coverage) for each cytosine loci in CpG context genome-wide was processed using  bismark_methylation_extractor and bismark2bedGraph functions from Bismark module
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited coverage text files include CpG context methylation calls at each cytosine loci genome-wide

source_name: Small needle biopsy

extract_protocol:
Genomic DNA isolated form organic fraction was further purified and concentrated (Zymo Research, US). 100 ng of genomic DNA was bisulfite converted using EZ DNA Methylation-GoldTM Kit (Zymo Research, USA).
Bisulfite converted genomic DNA was further used to generate indexed libraries using EpiGnome™Methyl-Seq kit (Epicentre®Illumina) according to the manufacturer’s instruction. QA and QC was performed for each library.

value: Kidney

tag: functional status/outcome

value: immediate graft function


title: DGF_169b1 [BS-Seq]

description: Post-perfused

value: delayed graft function


title: IGF_168b1 [BS-Seq]

description: Post-perfused


title: Rabbit wild type testes postnatal day 80

source_name: testes postnatal day 80

value: postnatal day 80


title: DGF_150b1 [BS-Seq]

description: Post-perfused


title: IGF_152b1 [BS-Seq]

description: Post-perfused


title: DGF_140b1 [BS-Seq]

description: Post-perfused


title: IGF_74b [BS-Seq]

description: Pre-perfused


title: Rabbit wild type testes postnatal day 180

source_name: testes postnatal day 180

value: wild type

value: postnatal day 180


title: DGF_136b1 [BS-Seq]

description: Post-perfused


title: IGF_74b1 [BS-Seq]

description: Post-perfused


title: IGF_180b [BS-Seq]

description: Pre-perfused


title: DGF_138b1 [BS-Seq]

description: Post-perfused


title: DGF_169b [BS-Seq]

description: Pre-perfused


title: IGF_153b [BS-Seq]

description: Pre-perfused


title: DGF_150b [BS-Seq]

description: Pre-perfused


title: IGF_152b [BS-Seq]

description: Pre-perfused


title: DGF_140b [BS-Seq]

description: Pre-perfused


title: DGF_136b [BS-Seq]

description: Pre-perfused


title: IGF_74b1

description: Post-perfused

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped against the reference human genome (GRCh38 from ensemble) using Tophat v.2.0.131 which depends on bowtie2 v.2.2.3 for sequence alignment with mate inner distance set to 158 bases. The annotation file (GRCh38 release 78 from ensemble) was used (--GTF parameter) to guide mapping of transcript annotations, and other parameters were fixed to defaults.
Mapped fragment counts were summarised (as read counts) at meta-feature level using featureCounts function by ensemble gene-ids using subread v1.4.6
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read counts values per transcript for each sample

extract_protocol:
Small-needle paired renal biopsies immediately after collection were placed in RNA®later (Ambion, USA), processed and stored for further analysis.  Total RNA was isolated using TRI® reagent, on column DNase treated, further purified (Zymo Research)  and  stored at -80°C.  RNA samples with RIN>6 were used for downstream analyses.
400 ng of total RNA and TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit (Illumina) was used to create libraries for downstream NGS. QA and QC was performed for each library.


title: DGF_97b1

description: Post-perfused


title: DGF_70b1

description: Post-perfused


title: IGF_42b1

description: Post-perfused


title: DGF_181b1

description: Post-perfused


title: IGF_180b1

description: Post-perfused


title: IGF_34b1

description: Post-perfused


title: IGF_168b1

description: Post-perfused


title: DGF_169b1

description: Post-perfused


title: DGF_140b1

description: Post-perfused


title: IGF_151b1

description: Post-perfused


title: IGF_165b1

description: Post-perfused


title: IGF_168b [BS-Seq]

description: Pre-perfused


title: IGF_153b1

description: Post-perfused


title: DGF_156b1

description: Post-perfused


title: IGF_152b1

description: Post-perfused


title: DGF_150b1

description: Post-perfused


title: DGF_138b1

description: Post-perfused


title: IGF_108b1

description: Post-perfused


title: DGF_136b1

description: Post-perfused


title: DGF_128b1

description: Post-perfused


title: IGF_129b1

description: Post-perfused


title: DGF_70b

description: Pre-perfused


title: IGF_74b

description: Pre-perfused


title: DGF_106b1

description: Post-perfused


title: DGF_36b1

description: Post-perfused


title: DGF_138b [BS-Seq]

description: Pre-perfused


title: IGF_39b

description: Pre-perfused


title: IGF_42b

description: Pre-perfused


title: DGF_181b

description: Pre-perfused


title: DGF_36b

description: Pre-perfused


title: IGF_34b

description: Pre-perfused


title: IGF_180b

description: Pre-perfused


title: DGF_169b

description: Pre-perfused


title: IGF_168b

description: Pre-perfused


title: DGF_156b

description: Pre-perfused


title: IGF_152b

description: Pre-perfused


title: IGF_153b

description: Pre-perfused


title: DGF_150b

description: Pre-perfused


title: DGF_97b

description: Pre-perfused


title: DGF_138b

description: Pre-perfused


title: IGF_129b

description: Pre-perfused


title: IGF_165b

description: Pre-perfused


title: DGF_136b

description: Pre-perfused


title: IGF_151b

description: Pre-perfused


title: DGF_140b

description: Pre-perfused


title: IGF_108b

description: Pre-perfused


title: DGF_128b

description: Pre-perfused


title: Microglia_shXbp1_1

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
RNA was sequenced at the Broad Technology Services using the High-throughput eukaryote 3' DGE library.
Rna-seq reads were aligned with BWA Aln (v 0.7.10) against the mm10 transcriptome.
All reads containing bases with quality lower than Q10 were filtered out.
Reads which are aligned must have no more than one mismatch, no more than 20As in a row (poly A tail) and not be aligned to more than 20 different positions in the transcriptome.
Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1.
Uniquely mapped read counts were normalized using TMM normalization and CPM.
Differential genes expression was accessed using Limma (v3.34.1) with p<0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Data matrix text file containing TMM-normalized CPM values

source_name: Flow cytometry sorted microglia

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by trypsinization, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, cells were pelleted, lysed, and RNA was harvested according to the Qiagen RNeasy Mini Kit protocol.
Libraries were processed by the Broad Institute's Broad Technology Labs and the Broad Genomics Platform. Libraries were prepared according to the 3’ Digital Gene Expression (3' DGE) protocol (Soumillon et al., 2014)

treatment_protocol: Induction of EAE in mice intracranially transduced with pLenti-Gfap-GFP-shScramble or pLenti-Gfap-GFP-shXbp1. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: Female

tag: lentivirus

tag: age

tag: disease

value: EAE


title: Monocytes_shXbp1_1

source_name: Flow cytometry sorted monocytes


title: Monocytes_shXbp1_2


title: Microglia_shXbp1_3


title: Microglia_shScrmbl_4

value: shScrmbl


title: Monocytes_shScrmbl_1


title: Microglia_shScrmbl_3


title: Microglia_shScrmbl_2


title: Astrocyte_shXbp1_3

source_name: Flow cytometry sorted astrocytes


title: Astrocyte_shXbp1_4


title: Astrocyte_shXbp1_2


title: Microglia_shScrmbl_1


title: Astrocyte_shScrmbl_4


title: Astrocyte_shScrmbl_3


title: Monocytes_shScrmbl_2


title: Naive_input_Replicate1

data_processing:
Chip-seq reads were aligned using BWA mem (v0.7.8) against the mm10 mouse genome with default settings.
Alignments were filtered with SAMtools (v1.3) to exclude reads with mapping quality <30, not properly aligned, aligned to mitochondrial genome, and aligned to ENCODE blacklist regions.
For peak calling, MACS2 callpeak (V2.1.1) were called on individual replicates for each ChIP (treatment) and Input (control) pair using p<0.01.
Differential peaks were accessed with DiffBind (v 2.5.1) using 800bp peak intervals and were selected with FDR<0.1.
Peaks were annotated using Bedtools (v2.26.0) closest.
Fold enrichment tracks were generated in MACS using bdgcmp to compare treatment against control and were visualized using IGV (v 2.3.59) and Sushi (v1.16.0).
Genome_build: mm10
Supplementary_files_format_and_content: Contains fold enrichment peaks provided by MACS bdgcmp for each ChIP/Input pair.

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by trypsinization, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, chromatin was isolated using the Active Motif ChIP-IT Express Enzymatic shearing kit. Chromatin complexes were IPed with XBP1 antibody (sc-8015X), cross-links were reversed, and DNA was cleaned up for library prep using QIAquick PCR purification kit.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Induction of EAE or Naïve. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: WT

tag: antibody

tag: Sex

value: female

tag: disease state

value: Naïve


title: EAE_input_Replicate3


title: Microglia_shXbp1_2


title: Naive_IP_Replicate1

value: XBP1 antibody (sc-8015X)


title: Naive_IP_Replicate2


title: EAE_IP_Replicate3


title: Astrocyte_shScrmbl_1


title: Astrocyte_shScrmbl_2


title: CXCR4_ZT13_2

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: Ensembl genebuild 76 (mouse assembly GRCm38).
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

source_name: CXCR4f/fxMrp8Cre neutrophils extracted at ZT13

growth_protocol: SPF-kept mice, all donors were male  7-10 weeks of age.

extract_protocol:
Samples were amplified with the Ovation Single Cell kit (NuGen).
cDNA was prepared using the standard Ilumina TrueSeq RNAseq library preparation kit.

treatment_protocol: Freshly extracted blood samples were RBC-lysed and stained for Ly6G (1A8 clone) for sorting.

value: 7-10 weeks

value: CXCR4f/f x Mrp8Cre

tag: time of extraction

value: Blood

value: neutrophils


title: EAE_IP_Replicate2


title: CXCR4_ZT13_1


title: CXCR4_ZT13_3


title: EAE_input_Replicate1


title: shXbp1_Replicate3

data_processing:
Reads were trimmed from 150bp to 50bp with Fastx (v0.0.13) fastx_trimmer.
Reads were aligned against the mm10 mouse genome with Bowtie (v2.3.0) in local mode with maximum fragment size 2000 (-X2000).
Alignments were sorted and filtered with SAMtools (v1.3.) to exclude reads with mapping quality <30, not properly aligned, aligned to the mitochondrial genome and/or aligned to ENCODE blacklist regions.
ATAC-Seq peaks were called for each replicate using MACS2 (v2.1.1).
Differential peaks were determined using DiffBind (v.2.6.1) for 600pb peak intervals and were selected with FDR<0.1.
Peaks were annotated using Bedtools (v2.26.0) closest.
Fold enrichment tracks were generated in MACS using bdgcmp and were visualized using IGV (v 2.3.59) and Sushi (v1.16.0).
Genome_build: mm10
Supplementary_files_format_and_content: Contains fold enrichment peaks provided by MACS2 bdgcmp

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by trypsinization, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, cells were pelleted, washed, and tagmented according to the ATAC-seq protocol (Buenrostro et al., Nature Methods 2013).
Nextera DNA Library Prep Kit


title: EAE_input_Replicate2


title: shXbp1_Replicate2


title: shXbp1_Replicate1


title: shScrmbl_Replicate4

value: pLenti-Gfap-GFP-shScramble


title: BMAL_ZT13_2

source_name: Bmalf/fxMrp8Cre neutrophils extracted at ZT13

value: BMALf/f x Mrp8Cre


title: Astrocyte_shXbp1_1


title: Naive_input_Replicate2


title: CXCR4_2

description: CXCR4f/fxMrp8Cre neutrophils extracted at ZT5

source_name: Neutrophils from blood

value: male

tag: genotype


title: CXCR4_5

tag: tissue


title: CXCR4_4


title: CXCR2_5

description: CXCR2f/fxMrp8Cre neutrophils extracted at ZT5

value: CXCR2f/f x Mrp8Cre


title: shScrmbl_Replicate2


title: shScrmbl_Replicate1


title: BMAL_3

description: Bmalf/fxMrp8Cre neutrophils extracted at ZT5


title: ZT13_9

description: WT neutrophils extracted at ZT13


title: BMAL_ZT13_3


title: CXCR2_4


title: EAE_IP_Replicate1


title: ZT13_2

description: WT neutrophils extracted at ZT13


title: ZT5_5

description: WT neutrophils extracted at ZT5


title: BMAL_4


title: ZT5_9

description: WT neutrophils extracted at ZT5


title: ZT13_8

description: WT neutrophils extracted at ZT13


title: O6_iPS_b4

status: Public on Jan 17 2019

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

institute: tongji university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to hg19 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

source_name: iPS cells

growth_protocol: The fibroblasts were cultured in Knockout DMEM supplemented with 10% fetal bovine serum, 1X nonessential amino acids, 1X GlutaMax, and 1X penicillin/streptomycin. Human iPSCs and ESCs were cultured on the Matrigel-coated plate with MEF-conditioned medium (MEF-CM) or on the CF1 feeder layer with hES medium consisted of DMEM/F12 supplemented with 20% knockout serum replacement, 1% NEAA, 1% GlutaMax, P/S, 100 μM 2-mercaptoethanol (Invitrogen), and 5 ng/ml bFGF. The MEF-CM was harvested after 24 hr incubation of hESC medium onto CF1 feeder cells, supplemented with additional 5 ng/ml bFGF and stored at -80 C until use. The MEF-CM was collected for 6 consecutive days.

extract_protocol:
The sorted TRA1-60+ cells during reprogramming were washed several times in 0.5% BSA-PBS (Sigma) solution and subsequently picked and transferred into lysate buffer by a mouth pipette with 50 cell for each tube.
The amplified cDNA was fragmented using Covaris sonicator (Covaris S220). To generate the sequence libraries, KAPA HyperPlus Library Preparation kit (KAPA KK8510) was used following the manufacturer’s instructions.

treatment_protocol: The reprogramming cells are digest to single cell and isolated by FACS analysis.APC anti-human CD13 , PE anti-human TRA-1-60  were used to obtain CD13- TRA-1-60+ cells for further analysis.

value: iPS cells

tag: time

tag: protocol

value: OCT6SKM reprogramming


title: ZT5_8

description: WT neutrophils extracted at ZT5