title: Chr4-cl KO B6 kidney #T2597 (4 weeks)

source_name: Kidney

value: 4 weeks

value: Kidney


title: Chr4-cl WT B6 blood #T00525 (20 weeks)

status: Public on Jun 27 2019

type: SRA

city: Bethesda

first: Gernot

last: Wolf

state: Maryland

address: 6 Center Drive

department: NICHD

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse reference genome using Tophat (--I 200000 --g 1)
Mapped reads were converted to bigwig files with DeepTools (--normalizeUsing RPKM --ignoreDuplicates).
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files

molecule: total RNA

organism: Mus musculus

source_name: Blood

growth_protocol: ES cells were grown in DMEM supplemented with 20% FCS and LIF or in 2i media as indicated in the sample information.

extract_protocol:
Total RNA from ES cells was purified and depleted from genomic DNA using the RNeasy Plus minikit (Qiagen). Tissues were lysed using TRIzol reagent and RNA was purified after Isopropanol precipitation with RNeasy columns (Qiagen)
RNA libraries were prepared for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina) or the SureSelect mRNA sequencing kit (Agilent) and polyA enrichment.

tag: age

value: 20 weeks

tag: tissue

value: Blood

tag: strain

tag: genotype/variation

value: Chr4-cl WT

tag: media


title: Chr4-cl KO B6 kidney #T2601 (4 weeks)

value: Chr4-cl KO/KO


title: Chr4-cl WT B6 blood #T00414 (20 weeks)


title: Chr4-cl WT B6 kidney #T2602 (4 weeks)


title: Chr4-cl WT B6 kidney #T2596 (4 weeks)


title: Chr4-cl WT B6 brain #T2602 (4 weeks)

source_name: Brain

value: Brain


title: Chr4-cl WT B6 brain #T2596 (4 weeks)


title: Chr4-cl KO B6 testis #T00835 (4 weeks)

source_name: Testis

value: Testis


title: Chr4-cl KO B6 testis #T00834 (4 weeks)


title: Chr4-cl WT B6 testis #T2602 (4 weeks)


title: Chr4-cl KO B6 liver #T00834 (4 weeks)

source_name: Liver

value: Liver


title: Chr4-cl KO B6 testis #T2601 (4 weeks)


title: Chr4-cl KO B6 brain #T2601 (4 weeks)


title: Chr4-cl KO B6 liver #T2601 (4 weeks)


title: Chr4-cl KO B6 liver #T2597 (4 weeks)


title: Chr4-cl WT B6 testis #T00833 (4 weeks)


title: Chr4-cl WT B6 liver #T2602 (4 weeks)


title: Chr4-cl WT B6 liver #T2596 (4 weeks)


title: Input Chr2-cl KO B6 ES cells #D10

library_source: genomic

data_processing:
Reads were mapped using Bowtie or Bowtie2, as indicated in the sample information.
Mapped reads were converted to bigwig files with DeepTools (--normalizeUsing RPGC --ignoreDuplicates).
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig coverage files

molecule: genomic DNA

source_name: B6 ES cells

growth_protocol: ES cells were grown on feeder MEFs in standard ES cell media containing 20% FCS and LIF or in 2i media as indicated in the sample information.

extract_protocol:
Native chromatin was purified and immunoprecipitated as described previously (Karimi et al., 2011). Cross-linked ChIP was performed as described previously (references are given in the sample information).
Illumina Truseq (Chr2-cl WT and KO ES cells) or DNA SMART kit (Takara) (all other samples)

value: Chr4-cl KO

tag: cell type

value: ES cells

tag: culture media

tag: chip antibody

value: n/a (Input)

tag: ChIP

value: ChIP (Ecco et al. 2016)

tag: mapping


title: Input Chr2-cl WT B6 ES cells #H7


title: KAP1 Chr2-cl WT B6 ES cells #E6

value: KAP1 (Tronolab, rabbit polyclonal S23470)


title: Input Chr2-cl WT B6 ES cells #E6


title: Input Chr2-cl WT B6 ES cells #A8


title: Input Chr2-cl KO B6 ES cells #G11


title: KAP1 Chr2-cl WT B6 ES cells #A8


title: KAP1 Chr2-cl WT B6 ES cells #H7


title: H3K9me3 Chr2-cl KO B6 ES cells #G11

value: H3K9me3 (Diagenode, C15410056)


title: H3K9me3 Chr2-cl KO B6 ES cells #B10


title: H3K9me3 Chr2-cl KO B6 ES cells #D10


title: KAP1 Chr2-cl KO B6 ES cells #B10


title: Input Chr2-cl KO B6 ES cells #B10


title: Chr4-cl WT B6 liver #T00833 (4 weeks)


title: KAP1 Chr2-cl KO B6 ES cells #G11


title: Chr4-cl KO B6 brain #T2597 (4 weeks)


title: H3K9me3 Chr2-cl WT B6 ES cells #E6


title: H3K9me3 Chr2-cl WT B6 ES cells #H7


title: H3K9me3 Chr13.2-cl KO B6 ES cells #80

value: 20% FCS

value: H3K9me3 (Active Motif #39161)

value: Native ChIP

value: Bowtie (-5 3 --best)


title: H3K9me3 Chr2-cl WT B6 ES cells #A8


title: H3K9me3 Chr13.1-cl KO B6 ES cells #65


title: H3K9me3 Chr13.1-cl WT B6 ES cells #10


title: H3K9me3 Chr13.2-cl KO B6 ES cells #90


title: H3K9me3 Chr13.1-cl KO B6 ES cells #14


title: H3K9me3 Chr10-cl KO B6 ES cells #76


title: H3K9me3 Chr10-cl KO B6 ES cells #34


title: H3K9me3 Chr13.1-cl WT B6 ES cells #7


title: KAP1 Chr2-cl KO B6 ES cells #D10


title: H3K9me3 Chr10-cl WT B6 ES cells #46


title: QXT46

data_processing:
Library strategy: gDNA capture-seq
R1 and R2 reads were mapped to the mm9 genome separately, each both in under settings that only allows non-duplicated, uniquely mappable reads (Bowtie -m 1 --best --strata; samtools rmdup -s) and under settings that allows multimapping and duplicated reads (Bowtie --best).
Of the multimapping reads, only reads that overlap (min. 50% of read) with RLTRETN, MMETn-int, ETnERV-int, ETnERV2-int or ETnERV3-int repeats were kept.
Non-duplicated and uniquely mappable reads whose paired read partners were overlapping ETn repeats were then clustered (as bed files) using bedtools (bedtools merge -i -n -d 1000) to receive a list of all potential annotated and non-annotated new ETn insertions.
Genome_build: mm9
Supplementary_files_format_and_content: bed files with clustered ETn-paired reads

source_name: ear

extract_protocol:
Genomic DNA was purified from Proteinase K digested lysates using the gDNA Clean & Concentrator kit (Zymo)
Libraries were constructed and enriched using the SureSelectQXT Target Enrichment kit (Agilent) and custom RNA capture probes complementary to ETn LTRs.

value: ear

tag: mouse id

tag: Sex

value: F

tag: genotype

value: Chr4-cl KO/KO (F2)

tag: ancestry


title: QXT48

value: M


title: QXT50

value: Chr4-cl KO/WT


title: QXT16

value: Chr4-cl KO/KO (F4)


title: QXT14


title: QXT15


title: QXT7

source_name: blood

value: blood


title: QXT3

value: Chr4-cl WT


title: QXT8


title: QXT2

source_name: tail

value: tail

value: Chr4-cl KO/KO (F3)


title: QXT19

source_name: ES cells

value: ES cells


title: QXT20


title: QXT49


title: QXT47


title: QXT4


title: QXT13


title: QXT1


title: WT BM

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

data_processing:
CellRanger v2.0.2 Pipeline:
cellranger mkfastq : sample demultiplexing and fastq conversion by bcl2fastq v2.17
cellranger mkgtf & mkref : filtered  Ensembl GRCm38.84 annotation file  (for protein_coding, lincRNA and antisense genes) and built reference folder
cellranger count  : alignment by STAR v2.5.1b and quantification against GRCm38.84 transcriptome. Produced BAM files (provided as Raw files) containing all aligned and unaligned reads, with each record annotated for respective barcode, UMI and gene assignment. Also produced gene-barcode matrices (submitted as Processed data files, described below).
Read alignments to exonic loci (at least 50% intersection) are prioritized over non-exonic loci, and are considered confidently mapped with MAPQ set to 255. Only confidently mapped reads with matching strand to annotated transcripts are considered for UMI counting. For further details, see the CellRanger algorithms overview: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms/overview
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Filtered gene-barcode matrices generated by cellranger count, in Market Exchange format, describing UMI counts per detected gene per detected cell for each sample. For further details on interpreting, loading and processing these matrices, see official documentation here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

molecule: polyA RNA

source_name: Bone Marrow

growth_protocol: All mice were maintained and treated in accordance with NIAID and Animal Care and Use Committee guidelines. They were housed under specific pathogen free conditions.

extract_protocol:
Single cell capture were prepared using the Chromium platform and Chromium Single Cell 3′ v1 chemistry multiplex Kit (10x Genomics, Catalog # 120232 and #120233) following manufacturer’s described protocols
RNA-Seq libraries were prepared using the Chromium platform and Chromium Single Cell 3′ v1 chemistry multiplex Kit (10x Genomics, Catalog # 120232 and #120233) following manufacturer’s described protocols
Single cell RNA-Seq. Libraries were sequenced in a Illumina HiSeq2500 Rapid Mode (HiSeq® Rapid PE Cluster Kit V2 and HiSeq® Rapid SBS Kit V2 (50 cycles, 2 kits)) with 10 pM pool libraries using the following read length: 98 bp Read 1, 14 bp i7 Index, 8 bp i5 Index and 10 bp Read 2.

treatment_protocol: iLIN28B mice were were fed with sterile food pellets ad libitum containing 200 mg of doxycycline per kg of diet (Bio Serv) for 4 weeks. Littermates bearing rtTA*M2 but not tetO-LIN28B were also treated with Dox and used as WT controls alongside iLIN28B in experiments.

tag: gender

value: Female

value: 8 weeks

value: CLP (Lin-Sca-1intc-Kitint CD127+)

tag: phenotype

value: Untreated


title: WT BM +Dox

value: WT littermate control (dox-induced)


title: H3K9me3 Chr10-cl WT B6 ES cells #25

value: 20% FCS

value: H3K9me3 (Active Motif #39161)

value: Native ChIP

value: Bowtie (-5 3 --best)


title: iLIN28B +Dox

value: LIN28B+ (dox-induced)


title: FL

source_name: Fetal Liver

value: Male/female

value: 16.5 days


title: h_Mecp2_KD3_40

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence using Trimmomatic v0.33 with arguments -threads 10 input.1.fastq.gz input.2.fastq.gz output.1.trimmed.fastq.gz output.1U.trimmed.fastq.gz output.2.trimmed.fastq.gz output.2U.trimmed.fastq.gz ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:30
Trimmed and high quality reads were aligned using STAR v2.4.2a on index created using hg19 genome assembly and Ensembl 74 annotation. Software parameters are as follows STAR --runThreadN 10 --runMode alignReads --genomeDir hg19 --genomeLoad LoadAndKeep --readFilesCommand zcat --outFilterIntronMoti fs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 80000000000 --outFileNamePrefix output.STAR. --readFilesIn output.1.trimmed.fastq.gz output.2.trimmed.fastq.gz
Normalized bigwig tracks were generated using Bedtools genomeCoverageBed program with parameters genomeCoverageBed -ibam input.bam -split -bg -g hg19.fa.fai -scale no_mapped_reads > output.bg and then bedgraph files were converted to bigwig files using UCSC tools bedGraphToBigWig utility
SubRead v1.5.0 package was use to assign read pairs to genes and generate count tables. The following parameters were used: featureCounts -T 10 -p -s 1 –primary -t exon -g gene_id -a annotation.gtf -o counts.tsv input.bam
Sequenced reads were quasi-mapped and gene expression was quantified using sailfish v0.10.0 using Gencode v19 annotation as index. The following parameters were used: sailfish quant -i gencode.v19.index -o outdir -p 12 -1 input.1.fastq.gz -2 input.2.fastq.gz –enforceLibCompat -g gencode.v19.index.genes –numBootstraps 20 –biasCorrect -l IU
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

organism: Homo sapiens

source_name: LUHMES-derived neurons

growth_protocol: LUHMES cells were cultured and differentiated according to published protocol (Shah et al., 2016).

extract_protocol:
Total RNA was isolated from all generated cell lines at day 9 of differentiation using either an RNeasy Mini kit or an AllPrep DNA/RNA Mini kit (Qiagen). Genomic DNA contamination was removed with a DNA-free kit (Ambion) and remaining DNA-free RNA was tested for purity using PCR for GAPDH genomic locus. Total RNA was tested on 2100 Bioanalyzer (Agilent Technologies) to ensure a RIN quality higher than 9 and quantified using Nanodrop.
Equal amounts of total RNA (1 µg to 2.5 µg) were taken forward for library preparation and ERCC RNA Spike-in control mixes (Ambion) were added according to manufacturer guide. Ribosomal RNA was depleted using the Ribo-Zero Gold rRNA Removal module (Epicentre, Illumina) and isolated mRNA was tested for purity on 2100 Bioanalyzer (Agilent Technologies). mRNA was quantified with Qubit and equal amounts used for cDNA synthesis and 3’ terminal tagging using ScriptSeq v2 RNA-seq library preparation kit (Epicentre, Illumina). The library was PCR amplified to add adaptors and barcodes.
ScriptSeq v2 RNA-seq library preparation kit

treatment_protocol: Cells were modified using CRISPR system for KO and infected with lentiviruses carrying MeCP2 for OE.

value: LUHMES-derived neurons

tag: cell line name

tag: differentiation

tag: developmental stage

tag: mecp2 expression level


title: h_Mecp2_KD2_55

tag: tissue


title: WGBS: BS_diff63_ctr_d9_3

data_processing:
Trim reads with trimmomatic v0.32
Align reads with Bismark v0.19
Deduplicate reads (Bismark)
Extract Methylation values (Bismark)
Genome_build: hg19
Supplementary_files_format_and_content: Bismark .cov format

source_name: BS-seq control

extract_protocol:
Briefly, genomic DNA was isolated using DNeasy Blood and Tissue kit (Qiagen) according to manufacturer’s procedure. The bisulfite reaction was performed using EZ DNA Methylation Gold kit on 100 ng of gDNA according to manufacturer protocol. Genomic DNA was mixed with 0.5% of unmethylated lambda DNA (Promega) for assessment of efficiency of bisulfite reaction. For TAB-seq, the TAB reaction was performed according to published protocol and genomic DNA was sonicated for 30 cycles of 30 sec ON and 30 sec OFF on low power using a Bioruptor (Diagenode). Ox-BS was prepared by CEGX company using TrueMethyl kit workflow.
For WGBS, random primed DNA synthesis and tagging was performed on converted gDNA. Finally, DNA was PCR amplified to generate a library for high-throughput sequencing. For TAB-seq, DNA was end-repaired and the ends where 3’ adenylated in order to facilitate adapter ligation. Size selection was performed using Agencourt AMPure XP (Beckman Coulter) beads and, after adapter ligation and size selection, DNA was bisulfite treated using EpiTect Bisulfite kit (Qiagen) and PCR amplified using custom primers
WGBS of wildtype LUHMES-derived neurons at day 9 was performed by whole genome bisulfite sequencing using an Epignome Methyl-seq kit (Epicentre, Illumina).

tag: div

value: Day 9

tag: passage

value: LUHMES cell line

value: differentiation 63


title: WGBS: BS_diff61_ctr_d9_2

tag: cell type

value: differentiation 61


title: WGBS: BS_diff60_ctr_d9_1

value: differentiation 60


title: h_Mecp2_KD2_41


title: h_KD_scrambled_control_41

value: SC


title: h_KD_scrambled_control_55


title: h_KD_scrambled_control_40


title: h_Mecp2_overexpressed_40

value: OE 3x


title: h_Mecp2_KD3_55


title: h_control_non-infected_55

value: WT


title: h_Mecp2_overexpressed_55


title: h_control_non-infected_41


title: WGBS: BS_OXBS_diff63


title: WGBS: BS_OXBS_diff61


title: Brca1Tumor_24

type: RNA

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Gene expression data for Trp53/Brca1-null mammary tumor #24 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured

data_processing:
The raw CEL files were imported and processed with genepattern AffySTExpressionFileCreator tool from Broad institiute.
Expression data was generated by AffySTExpressionFileCreator tool using the Robust Multi-array Average (RMA) algorithm as provided by the 'oligo' package in Bioconductor.

label: biotin

source_name: Trp53/Brca1-null mammary tumor #24 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre adenovirus

label_protocol: Labeling, hybridization and scan were performed by the Dana-Farber Cancer Institute Molecular Biology Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

growth_protocol: Wild-type luminal mammary epithelial cells were sorted from Rosa26-Stop-YFP female mice after Ad-K8-Cre injection; Trp53/Brca1-null mammary tumors were collected from Trp53L/L;Brca1L/L female mice after Ad-K8-Cre injection.

extract_protocol: RNeasy kit (Qiagen, #73504) was used on wild-type luminal mammary epithelial cells or Trp53/Brca1-null mammary tumors according to manufacturer's protocol

treatment_protocol: Wild-type luminal mammary epithelial cells were obtained from Rosa26-Stop-YFP female mice 10-14 days after intraductal injection of Ad-K8-Cre; Trp53/Brca1-null mammary tumors were obtained from Trp53L/L;Brca1L/L females several months after intraductal injection of Ad-K8-Cre.

value: mammary gland

value: mammary tumor


title: Brca1Tumor_25

description: Gene expression data for Trp53/Brca1-null mammary tumor #25 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre

source_name: Trp53/Brca1-null mammary tumor #25 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre adenovirus


title: K8wt_4

description: Gene expression data for wild-type YFP+ luminal mammary epithelial cells sorted from Rosa26-Stop-YFP female mouse #4 10-14 days after intraductal injection of Ad-K8-Cre

source_name: Wild-type YFP+ K8+ luminal mammary epithelial cells sorted from Ad-K8-Cre-injected Rosa26-Stop-YFP female mouse 4

value: luminal mammary epithelial cells

value: wildtype


title: K8wt_1

description: Gene expression data for wild-type YFP+ luminal mammary epithelial cells sorted from Rosa26-Stop-YFP female mouse #1 10-14 days after intraductal injection of Ad-K8-Cre

data_processing: The raw CEL files were imported and processed with genepattern AffySTExpressionFileCreator tool from Broad institiute. Expression data was generated by AffySTExpressionFileCreator tool using the Robust Multi-array Average (RMA) algorithm as provided by the 'oligo' package in Bioconductor.

source_name: Wild-type YFP+ K8+ luminal mammary epithelial cells sorted from Ad-K8-Cre-injected Rosa26-Stop-YFP female mouse 1


title: K8wt_2

description: Gene expression data for wild-type YFP+ luminal mammary epithelial cells sorted from Rosa26-Stop-YFP female mouse #2 10-14 days after intraductal injection of Ad-K8-Cre

source_name: Wild-type YFP+ K8+ luminal mammary epithelial cells sorted from Ad-K8-Cre-injected Rosa26-Stop-YFP female mouse 2


title: Brca1Tumor_23

description: Gene expression data for Trp53/Brca1-null mammary tumor #23 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre

source_name: Trp53/Brca1-null mammary tumor #23 developed in a Trp53L/L;Brca1L/L female mouse injected with Ad-K8-Cre adenovirus


title: WGBS: BS_OXBS_diff60


title: OXBS-Seq: OXBS_OXBS_diff63

source_name: oxBS control


title: h_Mecp2_overexpressed_41


title: OXBS-Seq: OXBS_OXBS_diff61


title: h_control_non-infected_40


title: h_Mecp2_KD2_40


title: h_Mecp2_KD3_41


title: WGBS: BS_TAB_diff60_ctr_d9_2


title: WGBS: BS_TAB_diff63_ctr_d9_4


title: WGBS: BS_TAB_diff60_ctr_d9_1


title: TAB-seq: TAB_TAB_diff60_ctr_d9_3

source_name: TAB-seq control


title: TAB-seq: TAB_TAB_diff61_ctr_d9_3


title: OXBS-Seq: OXBS_OXBS_diff60


title: WGBS: BS_TAB_diff61_ctr_d9_2


title: input_Control_HepG2_batch6

city: Wuhan

first: Rui

last: Xiao

state: Hubei

address: Medical Research Institute, Wuhan University

department: Medical Research Institute

country: China

institute: Wuhan University

description: input DNA control (SE)

data_processing:
ChIP-seq data were processed in accordance with ENCODE uniform transcription factor ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/).
Briefly, ChIP-seq reads were aligned to the GRCh37 human genome using BWA;
PCR duplicates and reads of low quality were filtered;
Peak-calling was performed with SPP and IDR with 0.02 IDR threshhold;
Signal tracks were generated with MACS2 and bigWig applications from UCSC genome browser (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Peak files were narrowPeak files generated by SPP; column information of narrowPeak file is explicated at the link (https://genome-euro.ucsc.edu/FAQ/FAQformat.html#format12).

growth_protocol: ENCODE cell culture protocols

extract_protocol:
Nuclei were isolated and sonicated and lysates were cleared-up and applied for purification of RBP-DNA complexes with antibodies.
Libraries were constructed according to the instruction of the Illumina Preparing Samples for ChIP Sequencing.

tag: cell line

value: Hepatocellular carcinoma


title: input_Control_HepG2_batch5

description: input DNA control (SE)


title: input_Control_HepG2_batch8

description: input DNA control (SE)


title: input_Control_HepG2_batch3

description: input DNA control (SE)


title: CCAR2_ChIP-seq_HepG2

description: ChIP-seq data (SE)

tag: chip antibody

value: CCAR2 (Zen BioScience Cat# 200093)


title: input_Control_HepG2_batch10

description: input DNA control (SE)


title: input_Control_HepG2_batch11

description: input DNA control (SE)


title: input_Control_HepG2_batch12

description: input DNA control (SE)


title: SAFB2_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: SAFB2 (Bethyl Cat# A301-112A)


title: POLR2G_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: POLR2G (GeneTex Cat# GTX108874)


title: PRPF4_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: PRPF4 (MBL Cat# RN093PW)


title: PCBP2_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: PCBP2 (MBL Cat# RN025P)


title: PTBP1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: PTBP1 (MBL Cat# RN011P)


title: TAF15_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: TAF15 (Abcam Cat# ab134916)


title: FIP1L1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: FIP1L1 (Abclonal Cat# #A5016)


title: HNRNPK_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: HNRNPK (MBL Cat# RN019P)


title: SRSF7_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: SRSF7 (MBL Cat# RN079PW)


title: TAB-seq: TAB_TAB_diff63_ctr_d9_6

value: LUHMES-derived neurons

value: Day 9

value: LUHMES cell line

value: differentiation 63


title: SRSF9_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: SRSF9 (MBL Cat# RN081PW)


title: SRSF3_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: SRSF3 (MBL Cat# RN080PW)


title: input_Control_HepG2_batch7

description: input DNA control (SE)

value: Hepatocellular carcinoma


title: SRSF4_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: SRSF4 (Bethyl Cat# A303-670A)


title: MF.microglia.Il34wt.HB.2

city: New York

first: Christie

last: Chang

state: New York

address: 1470 Madison Avenue, 5-301

institute: Icahn School of Medicine at Mount Sinai

data_processing:
2 x 25bp reads were used with no further trimming
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.3
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM12)
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values

source_name: Cerebellum

extract_protocol:
Primary microglia were FACS sorted according to the Immgen standardized protocol for ULI sequencing. RNA was lysed in RLT buffer and extracted according to the protocol provided by the RNeasy Mini Kit (Qiagen, USA).
Nextera XT DNA Library Preparation Kit (Illumina) and Illumina Nextseq-500 system were used for library preparation and sequencing, respectively.

value: Cerebellum

tag: age

value: 9 weeks

value: primary microglia


title: MF.microglia.Il34wt.HB.1


title: MF.microglia.Il34wt.FB.1

source_name: Forebrain

value: Forebrain


title: MF.microglia.Il34wt.FB.3


title: MF.microglia.Il34ko.HB.2


title: MF.microglia.Il34wt.FB.2


title: MF.microglia.Il34ko.FB.2


title: MF.microglia.Il34ko.FB.1


title: FUS_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: FUS (Bethyl Cat# A300-294A)


title: MF.microglia.Csf1wt.FB.1

value: post natal day 8


title: MF.microglia.Csf1ko.HB.3


title: MF.microglia.Csf1wt.HB.3


title: MF.microglia.Csf1wt.HB.2


title: MF.microglia.Csf1ko.HB.1


title: MF.microglia.Csf1ko.HB.2


title: MF.microglia.Csf1ko.FB.3


title: MF.microglia.Csf1wt.FB.


title: MG.Csf1wt.Cerebrum.3


title: MF.microglia.Csf1ko.FB.2


title: MF.microglia.Csf1ko.FB.1


title: MF.microglia.Il34ko.HB.1


title: MF.microglia.Il34ko.FB.3


title: MG.Csf1wt.Cerebrum.2


title: MG.Csf1wt.Cerebellum.3


title: MG.Csf1wt.Cerebrum.1


title: MG.Csf1wt.Cerebellum.2


title: MG.Csf1wt.Cerebellum.1


title: MG.Csf1ko.Cerebrum.4


title: MF.microglia.Csf1wt.FB.2


title: MG.Csf1ko.Cerebrum.3


title: MF.microglia.Csf1wt.HB.1


title: MG.Csf1ko.Cerebrum.2


title: MG.Csf1ko.Cerebrum.1


title: fb_il34_2

data_processing:
Sequencing was performed using the Illumina NextSeq-500 system.
Transcript abundances were quantified with the Ensembl GRCm38 Mouse cDNA and ncRNA reference using Kallisto version 0.43.0.
Transcript abundances were summarized to gene level using tximport.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV files include TPM values

extract_protocol:
Primary human STG and cerebellar microglia were purified using a Percoll gradient and positive selection using CD11b-conjugated magnetic beads (Miltenyi). RNA was lysed in RLT buffer and extracted using protocol provided by Rneasy Mini Kit (Qiagen).
cDNA synthesis and library preparation was performed using the SMART-Seq v4 Ultra Low Input RNA Kit and Low Input Library Prep Kit v2 (Clontech), respectively

value: WT

tag: treatment

tag: time point

value: 24 hours

value: primary murine microglia


title: MG.Csf1ko.Cerebellum.4

tag: genotype


title: MG.Csf1ko.Cerebellum.1


title: fb_csf1_3

value: CSF-1 (20 ng/ml)


title: fb_csf1_2


title: fb_csf1_1


title: fb_il34_1


title: cer_csf1_3


title: MG.Csf1ko.Cerebellum.3


title: cer_csf1_2


title: cer_csf1_1


title: cer_il34_2


title: C57BL/6 monocytes spinal cord EAE fast #2

last: Jordan

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

description: FACS Aria sorted

data_processing:
Transcript abundances were quantified using the Ensembl GRCm38 cDNA reference using Kallisto version 0.44.0.
Transcript abundances were summarized to gene level using tximport
Expression matrices were filtered for only transcripts with greater than 5 TPM in all replicates of at least one condition
Genome_build: Ensembl GRCm38 cDNA reference
Supplementary_files_format_and_content: CSV

source_name: monocytes

growth_protocol: mice were used at the age of 8-12 weeks

extract_protocol:
Rneasy Mini Kit (Qiagen)
Low Input Library Prep Kit v2 (Clontech)

treatment_protocol: food 4hrs: food and water ad libitum; fast 4hrs: food was removed from cage for the indicated time and bedding was changed, water ad libitum; EAE food: food and water ad libitum; EAE fast: intermittent fast in 24hr cycles for 4 weeks (food removed or added every morning between 8am and 9am, bedding changed), water ad libitum

value: monocytes

tag: strain

tag: organ of origin

value: spinal cord

value: fast

value: wild type

value: EAE


title: C57BL/6 monocytes spinal cord EAE food #4

description: FACS Aria sorted

value: food

tag: phenotype


title: C57BL/6 monocytes spinal cord EAE fast #3

description: FACS Aria sorted


title: C57BL/6 monocytes spinal cord EAE fast #1

description: FACS Aria sorted


title: C57BL/6 monocytes spinal cord EAE food #2

description: FACS Aria sorted


title: C57BL/6 monocytes spinal cord EAE food #1

description: FACS Aria sorted


title: C57BL/6 monocytes fast 4hrs #3

description: FACS Aria sorted

value: bone marrow


title: fb_il34_3


title: C57BL/6 monocytes fast 4hrs #1

description: FACS Aria sorted


title: C57BL/6 monocytes food 4hrs #3

description: FACS Aria sorted


title: C57BL/6 monocytes food 4hrs #1

description: FACS Aria sorted


title: cer_il34_3

value: Cerebellum


title: Brca1_tumor2

description:
mRNA
Single cell RNA-Seq

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines (10X Genomics).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary_files_format_and_content: matrix.mtx: Filtered gene-barcode matrix file (demultiplexed).

source_name: Cells from the tumor mass

extract_protocol:
YFP+ premalignant mammary epithelial cells or mammary tumor cells from Trp53L/L;Brca1L/L;R26Y mice post Ad-K8-Cre injection (at the indicated time points) were sorted into Dulbecco’s PBS + 0.04% BSA and retained on ice reagent.
Barcoded single cell RNA-seq libraries were generated as per the manufacturer’s instructions of 10× Chromium Single Cell 3’ v2 reagent kit (10× Genomics, Pleasanton, CA, USA).

tag: strain/background

value: Mixed genetic background

tag: genotype/variation

tag: gender

value: Female

value: Sorted DAPI- live cells from the tumor mass

tag: condition

value: Tumor #2 emerged in the mammary gland after Ad-K8-Cre intraductal injection


title: C57BL/6 monocytes food 4hrs #4

description: FACS Aria sorted


title: C57BL/6 monocytes fast 4hrs #2

description: FACS Aria sorted


title: C57BL/6 monocytes spinal cord EAE food #3

description: FACS Aria sorted


title: Brca1_2weeks

description:
mRNA
Single cell RNA-Seq

source_name: Mammary epithelial cells

value: Sorted YFP+ mammary epithelial cells

value: ~Two weeks after Ad-K8-Cre intraductal injection


title: cer_il34_1

tag: tissue

value: WT

value: 24 hours


title: RIP-seq_SM33 input

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

description: RNA, ribo-depleted

data_processing:
RNA-IP reads were aligned to a version of the mm9 genome with ERCC.fa sequences doped in using Star (version 2.6.0a) (Dobin A et al. Bioinformatics 2013). All mm9 genome annotations were obtained from the UCSC genome browser (Casper J et al. Nucleic Acids Research 2018). Samtools was used to filter aligned reads for q>30 (Li et al., 2009). Reads were counted within UCSC known gene annotations using featureCounts to determine the read count per transcript (Liao et al., 2014).
For normalization, counts per ERCC spike-in transcript were generated for each dataset using featureCounts on the ERCC92.gtf file. The upper quartile values from the set of ERCC spike-in transcripts quantified for each dataset were used to normalize all datasets relative to their respective total RNA input dataset (either SM33 or TSC input).
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were generated from mm9 alignments, after filtering for mapping quality of greater than or equal to 30. There are two WIG files for each dataset, one containing reads aligning to the negative strand and the other containing reads aligning to the positive strand. Both files were scaled relative to input using normalization factors calculated from ERCC spike-ins.

source_name: Male SM33 embryonic stem cells

growth_protocol: TSCs were cultured under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006). To deplete MEF feeder cells from TSCs prior to RNA isolation or crosslinking, TSCs were pre-plated for 40 minutes and cultured for three days in 70% MEF-conditioned TSC media supplemented with Fgf4 (25ng/ml; Invitrogen) and Heparin (1mg/ml; Sigma). This was done once for harvesting chromatin and twice before RNA isolation. ESCs were cultured in media consisting of DMEM high glucose plus sodium pyruvate, 0.1 mM non-essential AA, 0.1 mM MTG, 2 mM L-glutamine, 1000 U/ml LIF (ESG1107, Millipore Sigma, St. Louis, MO) and 15% ES-qualified FBS. ESCs were maintained on gamma-irradiated feeders from CD1 embryos, plated approximately 1.5 million feeders per 10-cm plate. At the passage prior to harvesting cells for ChIP, ESCs were pre-plated for 40 minutes and cultured for two days in 70% MEF-conditioned media supplemented as above.

extract_protocol:
TSCs and SM33 ESCs were fixed in 0.3% methanol-free formaldehyde for 30 min at 4 °C. Whole cell lysates were sonicated and RNA was immunoprecipitated using the specified antibody and isolated using Trizol (Invitrogen).
Libraries were prepared using the Kapa Ribo-zero kit following the manufacturer’s instructions, pooled, and sequenced using single-end 75-bp reads on an Illumina Nextseq 500.

treatment_protocol: Cells were treated with 1µg/ml of doxycycline (Sigma) for 24 hours prior to RNA isolation.

tag: parent of origin

value: C57BL/6 x 129SV-Jae

tag: passage number

tag: antibody

value: Inducible promoter driving Xist at endogenous locus


title: RIP-seq_SM33 IgG

value: IgG (Invitrogen, 02-6502)


title: C57BL/6 monocytes fast 4hrs #4

description: FACS Aria sorted

tag: cell type

value: monocytes

value: fast


title: C57BL/6 monocytes food 4hrs #2

description: FACS Aria sorted

value: wild type


title: RIP-seq_SM33 HNRNPK

value: HNRNPK (Abcam, ab39975)


title: Brca1_5months

description:
mRNA
Single cell RNA-Seq

source_name: Mammary epithelial cells and CD45+ leukocytes

value: Sorted YFP+ mammary epithelial cells and CD45+ leukocytes

value: ~Five months after Ad-K8-Cre intraductal injection


title: C57BL/6 monocytes spinal cord EAE fast #4

description: FACS Aria sorted

value: spinal cord

value: EAE


title: RIP-seq_TSC input

description: RNA, ribo-depleted

source_name: F1 C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father

value: wildtype


title: RIP-seq_TSC CTCF

value: gift from V. Lobanenkov


title: RIP-seq_TSC HNRNPK

value: HNRNPK (Santa Cruz, sc28380)


title: HNRNPK knockdown H3K27me3 rep2

data_processing:
ChIP sequencing reads were aligned using bowtie2, using default parameters. All mm9 genome annotations were obtained from the UCSC genome browser (Casper J et al. Nucleic Acids Research 2018). Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/). Only reads that had a mapping quality greater than or equal to 30 were used.
hiddenDomains 3.0 (Starmer J, Magnuson T. BMC Bioinformatics 2016) was used to call peaks from H3K27me3 ChIP-Seq data, using input DNA sequenced from formaldehyde crosslinked TSCs or ESCs as a control. Default parameters plus max.read.count=10 were used in the main hiddenDomains.R script, and neighboring enriched bins were merged to generate the final set of H3K27me3 peaks. MACS2 (Zhang Y et al. Genome Biology 2008) was used to call peaks from all other ChIP-Seq datasets, with the same input used in hiddenDomains and parameters –broad –broad-cutoff 0.01.
CAST/EiJ pseudogenome creation and allele-specific read retention was performed as in (Calabrese et al. G3 2015; Calabrese et al. Cell 2012).
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were generated from mm9 alignments, after filtering for mapping quality of greater than or equal to 30. Where indicated, the WIG file includes reads pooled from the two replicates.

growth_protocol: TSCs were cultured under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006). To deplete MEF feeder cells from TSCs prior to RNA isolation or crosslinking, TSCs were pre-plated for 40 minutes and cultured for three days in 70% MEF-conditioned TSC media supplemented with Fgf4 (25ng/ml; Invitrogen) and Heparin (1mg/ml; Sigma). This was done once for harvesting chromatin and twice before RNA isolation. For cortical neurons, embryonic day 13.5 (E13.5) to E16.5 mouse cortices were dissected and trypsinized with TrypLE express at 37 °C for 10 min. Dissociated neurons were cultured with Neurobasal medium with 5% fetal bovine serum, GlutaMAX (Invitrogen), B27 (Invitrogen) and Antibiotic-Antimycotic (Invitrogen) and changed into Neurobasal medium supplemented with 4.84 µg ml−1 uridine 5′-triphosphate (Sigma), 2.46 μg ml−1 5-fluoro-2′-deoxyuridine (Sigma,), GlutaMAX (Invitrogen), B27 (Invitrogen), and Antibiotic-Antimycotic (Invitrogen) at DIV1 and DIV3. Neurons were fixed in 10cm plates at DIV5. ESCs were cultured in media consisting of DMEM high glucose plus sodium pyruvate, 0.1 mM non-essential AA, 0.1 mM MTG, 2 mM L-glutamine, 1000 U/ml LIF (ESG1107, Millipore Sigma, St. Louis, MO) and 15% ES-qualified FBS. ESCs were maintained on gamma-irradiated feeders from CD1 embryos, plated approximately 1.5 million feeders per 10-cm plate. At the passage prior to harvesting cells for ChIP, ESCs were pre-plated for 40 minutes and cultured for two days in 70% MEF-conditioned media supplemented as above.

extract_protocol:
For all ChIPs except EZH2, cells were crosslinked in 0.6% formaldehyde. For Ezh2 ChIPs, cells were crosslinked in 1.5mM EGS (ethylene glycol bis(succinimidyl succinate); ThermoFisher Pierce) in PBS for 30 minutes and then in 0.6% formaldehyde. Whole cell lysates were sonicated and chromatin extracts were immunoprecipitated using the specified antibody.
Purified immunoprecipitated DNA was prepared for sequencing on the Illumina platform using Next Reagents (NEB).

treatment_protocol: Cells were treated with 1µg/ml of doxycycline (Sigma) for four days prior to crosslinking for H3K27me3 ChIP.

value: HNRNPK knockdown, polyclonal

tag: chip antibody

value: H3K27me3 (Abcam ab6002)


title: Cas9 noguide H3K27me3 rep1

value: CRISPR/Cas9 no guide RNA, polyclonal


title: HNRNPK knockdown rep2

description:
RNA, ribo-depleted
rna_hk_r2neg.wig.gz
rna_hk_r2pos.wig.gz

data_processing:
RNA sequence reads were aligned to genomic sequence using Star (version 2.6.0a) (Dobin A et al. Bioinformatics 2013). All mm9 genome annotations were obtained from the UCSC genome browser (Casper J et al. Nucleic Acids Research 2018). Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/). Only reads that had a mapping quality greater than or equal to 30 were used.
CAST/EiJ pseudogenome creation and allele-specific read retention was performed as in (Calabrese et al. G3 2015; Calabrese et al. Cell 2012).
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were generated from mm9 alignments, after filtering for mapping quality of greater than or equal to 30. Where indicated, the WIG file includes reads pooled from the two replicates. There are two WIG files for each dataset, one containing reads aligning to the negative strand and the other containing reads aligning to the positive strand.

growth_protocol: TSCs were cultured under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006). To deplete MEF feeder cells from TSCs prior to RNA isolation or crosslinking, TSCs were pre-plated for 40 minutes and cultured for three days in 70% MEF-conditioned TSC media supplemented with Fgf4 (25ng/ml; Invitrogen) and Heparin (1mg/ml; Sigma). This was done once for harvesting chromatin and twice before RNA isolation.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen).
RNA-Seq libraries were prepared using Stranded mRNA-Seq Kits (Kapa Biosciences) and RNA HyperPrep Kits with RiboErase (Kapa Biosciences).

treatment_protocol:
Cells were treated with 1µg/ml of doxycycline (Sigma) for four days prior to RNA isolation.
see SAMPLES


title: RIP-seq_TSC IgG


title: Cas9 noguide rep2

description:
RNA, ribo-depleted
rna_ntg_r2neg.wig.gz
rna_ntg_r2pos.wig.gz


title: Cas9 noguide rep1

description:
RNA, ribo-depleted
rna_ntg_r1neg.wig.gz
rna_ntg_r1pos.wig.gz


title: HNRNPK knockdown H3K27me3 rep1


title: HNRNPK knockdown rep1

description:
RNA, ribo-depleted
rna_hk_r1neg.wig.gz
rna_hk_r1pos.wig.gz


title: Cas9 noguide H3K27me3 rep2


title: NonCGI deletion B6 H3K27me3

value: Non-CGI ~2600 bp deletion on chr17, clonal


title: CGI deletion A13 H3K27me3

value: Slc22a3 CGI deletion, clonal


title: NonCGI deletion B11 H3K27me3


title: AB6393

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: [AB*.txt] tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: [metadata.txt] file associating each single cell with its amplification batch and index sorting readouts

source_name: White adipose tissue

growth_protocol: 8-week old mice, housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were euthanized and nd perfused immediately through the left ventricle of the heart with 20 ml of phosphate-buffered saline (PBS) to remove circulating leukocytes from the tissue. The epididymal (visceral) adipose tissue (EAT) was readily located and excised right above the epididymis. The subcutanous adipose tissue (SAT) was obtained from the inguinal fat depot. The tissue was placed in a 50 ml tube with 10 ml DMEM without phenol red at room temperature, cut into tiny bits with scissors, incubated with collagenase II at 37°C for 20 min. while gently agitating, filtered through a 100-μm cell strainer, and spun down at 500g for 10 min with low acceleration/brake, beginning at room temperature and cooling to 4°C. Cells were resuspended in 500 μl RBC lysis solution (Sigma) and incubated on ice for 2-5 min. (depending on the initial amount of tissue) and washed. The resulting cell suspension was incubated with anti-CD45 or a cocktail of antibodies for selected markers.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. Briefly, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014};

treatment_protocol:
[treatment protocol (1)] At age 8-9 weeks, for some mice the normal chow was replaced with a high fat diet (HFD; irradiated Rodent Diet With 60 kcal% Fat, D12492i Research Diets Inc., New Brunswick, NJ).
[treatment protocol (2)] Founding Trem2-/- knock-out (KO) breeder mice were crossed with wild-type (WT) mice at the Weizmann Institute animal facility to produce second-generation cohorts of WT and KO littermates. F1 offspring was bred to produce homozygous WT or KO, some of which were also set to feed on HFD. Heterozygous F2 mice were not used for experiments.

value: Trem2 wild-type C57BL/6 Littermates

tag: treatment (diet)

value: Normal chow

tag: mouse age (weeks)

tag: time point (weeks)

tag: tissue subtype

value: total immune cells

tag: selection marker

tag: replicate id


title: AB6402

tag: strain

value: Trem2 knock-out C57BL/6

value: High-fat diet

value: epididymal (visceral) adipose tissue (EAT)


title: AB6400


title: AB6386


title: AB6394


title: AB6399


title: AB6396


title: AB6397


title: AB6388


title: AB6390


title: AB6389


title: AB6392


title: AB6398


title: AB6387


title: AB6391


title: AB6384


title: AB6382


title: AB6380


title: AB6383


title: AB5961


title: CGI deletion A12 H3K27me3


title: AB6395


title: AB5962


title: AB6381


title: AB5959


title: AB5958


title: AB5957


title: AB6401


title: AB5960


title: AB6385


title: AB5956


title: AB5953


title: AB5954


title: AB5952


title: AB5951


title: AB5950


title: AB5947


title: AB5945


title: AB5949


title: AB5940


title: AB5948


title: AB5936


title: AB5941


title: AB5946


title: AB5955


title: AB5935


title: AB5934


title: AB5933


title: AB5931


title: AB5928


title: AB5929


title: AB5930


title: AB5927


title: AB5944


title: AB5942


title: AB5943


title: AB5938


title: AB5939


title: AB5937


title: AB5926


title: AB5924


title: AB5922


title: AB5923


title: AB3684

value: Db/+ wild-type C57BL/6 Littermates


title: AB5919


title: AB5921


title: AB3683


title: AB3686


title: AB3685


title: AB3682

value: Db/Db C57BL/6


title: AB3681


title: AB5932


title: AB3680


title: AB3678


title: AB3679


title: AB3677


title: AB3676


title: AB3674


title: AB3675


title: AB3672


title: AB3671


title: AB3673


title: AB5925


title: AB3670


title: AB3132


title: AB3130


title: AB3131


title: AB5920


title: AB3129


title: AB3128


title: AB2930


title: AB2931


title: AB3127


title: AB2927


title: AB2921


title: AB2924


title: AB2923


title: AB2925


title: AB2922


title: AB2926


title: AB2857


title: AB2929


title: AB2856


title: AB2920


title: AB2855


title: AB2590


title: AB2589


title: AB2588


title: AB2587


title: AB2928


title: AB2585


title: AB2586


title: AB2583


title: AB2584


title: AB2582


title: AB2580


title: AB2579


title: AB2581


title: AB2577


title: AB2578


title: AB2576


title: AB2575


title: AB2854


title: AB2452


title: AB2454


title: AB2453


title: AB2448


title: AB2445


title: AB2449


title: AB2455


title: AB2456


title: AB2395


title: AB2401


title: AB2446


title: AB2400


title: AB2402


title: AB2447


title: AB2394


title: AB2393


title: AB2391


title: AB2392


title: AB2388


title: AB2390


title: AB2368


title: AB2389


title: AB2367


title: AB2366


title: AB2364


title: AB2365


title: AB2207


title: p53Brca1_1M_3

data_processing:
Visualization Pipeline for RNAseq (Viper) analysis tool developed by Center for Functional Cancer Epigenetics (CFCE) at Dana-Farber Cancer Institute was used to generate standard outputs.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include normalized FPKM matrices for each Sample .

extract_protocol:
YFP+ mammary epithelial cells were sorted from female mice with the corresponding genotypes 1 month after intraductal injection of Ad-K8-Cre, and RNA was harvested from the sorted cells using Trizol reagent.
RNA libraries were prepared for sequencing using Low Input mRNA Library (Clontech SMARTer) v4 kit

value: mixed genetic background

value: Sorted YFP+ mammary epithelial cells

value: 1 month after Ad-K8-Cre intraductal injection

tag: genotype


title: AB2208


title: p53Brca1_1M_2


title: p53_1M_3


title: p53_1M_2


title: WT_1M_2

value: wild-type


title: p53_1M_1


title: WT_1M_3


title: WT_1M_1


title: KRAB noguide rep1

value: CAST/EiJ mother X C57BL/6J father

tag: genotype/variation

value: CRISPR-I no guide RNA


title: VP160 noguide rep2

value: CRISPR-a no guide RNA


title: KRAB Airn rep2

value: CRISPR-I Airn-targeting guide RNA


title: KRAB noguide rep2


title: VP160 Airn rep2

value: CRISPR-a Airn-targeting guide RNA


title: KKO4 rep2

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
K4neg.wig
K4pos.wig

treatment_protocol: see SAMPLES

value: Kcnq1ot1 truncation


title: VP160 Airn rep1


title: VP160 noguide rep1


title: KKO4 rep1


title: KKO3 rep2

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
K3neg.wig
K3pos.wig


title: KKO2 rep1

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
K2neg.wig
K2pos.wig


title: AKO10 rep2

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
A10neg.wig
A10pos.wig

value: Airn truncation


title: AKO24 rep2

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
A24neg.wig
A24pos.wig


title: AKO2 rep2

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
A2neg.wig
A2pos.wig


title: KKO2 rep2


title: AKO24 rep1


title: KKO3 rep1


title: AKO2 rep1


title: p53Brca1_1M_1


title: WT 2016 rep1

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
62_2016polyAneg.wig
62_2016polyApos.wig

value: wildtype


title: AKO10 rep1


title: WT 2015 rep2

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
62_2015polyAneg.wig
62_2015polyApos.wig


title: WT 2016 rep2


title: KRAB Airn rep1


title: ESC Rosa26 input

source_name: Embryonic stem cells

value: Full length Xist inserted at Rosa26 locus


title: ESC Rosa26 RING1B 72hr

treatment_protocol:
Cells were treated with 1µg/ml of doxycycline (Sigma) for 72 hours prior to crosslinking.
see SAMPLES

value: RING1B (Cell Signaling #5694)


title: ESC Rosa26 RING1B 0hr


title: ESC Rosa26 RING1B 12hr

treatment_protocol:
Cells were treated with 1µg/ml of doxycycline (Sigma) for 12 hours prior to crosslinking.
see SAMPLES


title: ESC Rosa26 H3K27me3 12hr

value: H3K27me3 (Abcam ab6002)


title: TSC B/C SMC1

source_name: F1 B/C trophoblast stem cells

value: C57BL/6J mother X CAST/EiJ father

value: SMC1 (Bethyl A300-055A)


title: TSC C/B SMC1


title: TSC VP160 Airn RING1B rep2

treatment_protocol:
Cells were treated with 1µg/ml of doxycycline (Sigma) for four days prior to crosslinking for RING1B ChIP.
see SAMPLES


title: TSC VP160 noguide RING1B


title: TSC KKO2 RING1B


title: TSC VP160 Airn RING1B rep1


title: TSC KKO3 RING1B


title: TSC AKO24 RING1B


title: TSC C/B EZH2

value: EZH2 (Cell Signaling #5246)


title: TSC KRAB noguide H3K27me3 rep1

treatment_protocol:
Cells were treated with 1µg/ml of doxycycline (Sigma) for four days prior to crosslinking for H3K27me3 ChIP.
see SAMPLES


title: TSC B/C EZH2


title: TSC VP160 noguide H3K27me3 rep2


title: TSC input


title: TSC KRAB noguide H3K27me3 rep2


title: TSC KRAB Airn H3K27me3 rep1


title: TSC VP160 Airn H3K27me3 rep2


title: TSC VP160 noguide H3K27me3 rep1


title: TSC VP160 Airn H3K27me3 rep1


title: ESC Rosa26 H3K27me3 72hr


title: TSC KRAB Airn H3K27me3 rep2


title: WT 2015 rep1


title: ESC Rosa26 H3K27me3 0hr


title: TSC C/B H2AK119ub rep2


title: Neuron B/C H3K27me3 rep2

source_name: F1 B/C cortical neurons


title: Neuron B/C H3K27me3 rep1


title: Neuron C/B H3K27me3 rep1

source_name: F1 C/B cortical neurons


title: Neuron C/B H3K27me3 rep2


title: TSC KKO3 H3K27me3


title: TSC AKO10 H3K27me3


title: TSC C/B WT H3K27me3 rep2


title: TSC B/C WT H3K27me3 rep3

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
k27_101.wig


title: TSC B/C WT H3K27me3 rep4


title: TSC C/B H2AK119ub rep1


title: BM CLP

data_processing:
Base-calling was performed with bcl2fastq v2.17
Reads were aligned to the mm10 (GRCm38) mouse reference genome using STAR v2.5.2 with default mapping parameters
Bigwigs coverage tracks were library-size normalized by reads per million (RPM)
Transcript expression values were normalized to fragments per kilo base of transcript per million mapped reads (FPKM) by RSEM v1.2.30 against the Ensembl GRCm38.p5 annotation
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Normalized bigwig files and a comma-delimited table of FPKM expression values

source_name: BM, CLP

extract_protocol:
Fetal livers were harvested from E14.5 embryos and mechanically disrupted  to obtain single-cell suspension. For BM cell isolation, femurs and tibias were cut from both ends and the BM was flushed into a 15 ml centrifuge tube with 5% FBS. RNA was isolated from FACS-sorted cells using the NucleoSpin RNA XS kit (Clontech Laboratories, Inc ) per manufacturer’s instructions.
Low-input RNA-seq library preparation was Performed per manufacturer’s instructions using the SMARTer Stranded Total RNA-Seq – Pico Input Mammalian kit (Clontech).

tag: age

value: 6-8 weeks

value: Bone Marrow

value: CLP


title: FL CLP

source_name: FL, CLP

value: Fetal Liver


title: FL LSK

source_name: FL, LSK

value: LSK


title: TSC AKO10 RING1B

value: CAST/EiJ mother X C57BL/6J father


title: TSC KKO2 H3K27me3


title: BM LSK

source_name: BM, LSK


title: VJ_C_M_S33_L002

city: Antwerpen

first: Nicolas

last: De Neuter

address: Middelheimlaan 1

country: Belgium

institute: University of Antwerp

description: 180302_NB501809_0264_AHJGHCBGX5_readcounts.txt

data_processing:
trimming of low quality bases: name: Trimmomatic, version: 0.36, parameters: -phred33 HEADCROP:20 SLIDINGWINDOW:4:15 MINLEN:30
removal of polyA tails: custom Perl script, removes polyA tails at the end of reads if the read ends with 7 or more As; also removes reads with length <= 20
read mapping: name: HISAT2, version: 2.0.4, parameters: -x GRCh38_noalt_h2, outputs SAM files
read counting: custom Python script, uses the Python library HTSeq to count how many reads map to each gene. Uses GCF_000001405.31_GRCh38.p5_genomic.gff as an annotation source.  One output file containing counts is created for each SAM file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Format: tsv (tab-separated file); Content: raw read counts for each gene and sample/lane combination (genes as rows and sample/lane as columns). For example, sample 1 (AZT11_C_S34) was sequenced on four lanes from a single flow cell and resulted in the following files, each resulting in a separate column: AZT_16_C_S2_L001_R1_001.fastq.gz, AZT_16_C_S2_L002_R1_001.fastq.gz, AZT_16_C_S2_L003_R1_001.fastq.gz, AZT_16_C_S2_L004_R1_001.fastq.gz. One file is provided per sequencing run.

source_name: Whole blood

extract_protocol:
Paxgene blood RNA extraction (pre-analytix): RNA extraction from blood, collected in Paxgene blood RNA tubes (Pre-analytix)
Lexogen QuantSeq 3mRNA library preparation FWD kit

tag: infected with/healthy control

value: Haemophilus influenzae

value: whole blood

tag: library name


title: VJ_B_M_S31_L001

value: Enterovirus

tag: tissue


title: VJ_B_M_S31_L003


title: VJ_A_M_S29_L003


title: VJ_C_M_S33_L001


title: VJ_B_C_S32_L003

value: Control


title: VJ_B_M_S31_L004


title: VJ_A_M_S29_L001


title: VJ_A_M_S29_L002


title: VJ_B_C_S32_L004


title: VJ_C_M_S33_L003


title: VJ_C_M_S33_L004


title: VJ_B_C_S32_L001


title: VJ_B_C_S32_L002


title: VJ_C_C_S34_L004


title: VJ_C_C_S34_L001


title: VJ_A_C_S30_L002


title: VJ_A_C_S30_L004


title: VJ_A_C_S30_L003


title: VJ_A_C_S30_L001


title: UZG_1_S40_L004

value: Varicella


title: VJ_C_C_S34_L002


title: UZG_1_S40_L003


title: UZG_1_S40_L002


title: VJ_C_C_S34_L003


title: UZB_9_S13_L004

description: 180321_NB501809_0276_AHJJ3LBGX5_readcounts.txt


title: UZG_1_S40_L001


title: TSC AKO24 H3K27me3

tag: parent of origin

tag: passage number

value: Airn truncation


title: VJ_B_M_S31_L002


title: VJ_A_M_S29_L004


title: UZB_5_S12_L004

value: Neuroborreliose bact. Borrelia burgdorferi


title: UZB_5_S12_L001


title: UZB_3_S10_L004


title: UZB_4_S11_L004


title: UZB_5_S12_L003


title: UZB_9_S13_L003


title: UZB_9_S13_L001


title: UZB_1_S9_L003


title: UZB_4_S11_L003


title: UZB_9_S13_L002


title: UZB_1_S9_L004


title: UZB_13_S39_L004

value: Herpes simplex type I


title: UZB_3_S10_L003


title: UZB_1_S9_L002


title: UZB_13_S39_L002


title: UZB_1_S9_L001


title: UZB_12_S38_L004

value: Neisseria meningitidis


title: UZB_12_S38_L003


title: UZB_4_S11_L001


title: UZB_13_S39_L001


title: UZB_3_S10_L002


title: UZB_12_S38_L001


title: UZB_12_S38_L002


title: UZB_13_S39_L003


title: UZB_5_S12_L002


title: UZB_11_S37_L004

value: Streptococcus pneumoniae


title: UZB_11_S37_L002


title: UZB_4_S11_L002


title: UZB_11_S37_L003


title: UZB_3_S10_L001


title: UZB_11_S37_L001


title: UZA_6_S4_L003


title: UZA_4_M_S11_L003


title: UZA_4_M_S11_L001


title: UZA_6_S4_L002


title: UZA_4_M_S11_L004


title: UZA_6_S4_L004


title: UZA_4_C_S12_L004


title: UZA_4_C_S12_L001


title: UZA_4_C_S12_L002


title: UZA_4_M_S11_L002


title: UZA_3_M_S9_L003


title: UZA_3_M_S9_L002


title: UZA_4_C_S12_L003


title: UZA_3_M_S9_L001


title: UZA_3_C_S10_L004


title: UZA_3_C_S10_L001


title: UZA_3_C_S10_L003


title: UZA_3_C_S10_L002


title: R_UZA_25_S37_L003

value: antiphospholipid syndrome


title: R_UZA_25_S37_L002


title: R_UZA_21_S36_L004

value: pyelonefritis


title: R_UZA_21_S36_L002


title: R_UZA_21_S36_L003


title: R_UZA_21_S36_L001


title: St_Luc_1_S36_L004


title: St_Luc_1_S36_L002


title: UZA_3_M_S9_L004


title: St_Luc_1_S36_L001


title: ELI8M_S17_L002

description: 180214_NB501809_0255_AHJFNMBGX5_readcounts.txt


title: ELI8M_S17_L003


title: UZA_6_S4_L001


title: ELI8M_S17_L001


title: ELI8C_S18_L004


title: ELI8C_S18_L001


title: ELI7M_S15_L004


title: ELI7M_S15_L003


title: ELI8C_S18_L002


title: ELI7M_S15_L002


title: ELI7C_S16_L004


title: R_UZA_25_S37_L004


title: ELI7M_S15_L001


title: R_UZA_25_S37_L001


title: ELI7C_S16_L001


title: ELI6M_S13_L004


title: ELI6M_S13_L003


title: ELI7C_S16_L002


title: ELI6M_S13_L002


title: ELI6C_S14_L004


title: ELI6C_S14_L003


title: ELI8M_S17_L004


title: ELI6C_S14_L002


title: ELI6M_S13_L001


title: ELI5M_S11_L003


title: ELI5M_S11_L002


title: St_Luc_1_S36_L003


title: ELI6C_S14_L001


title: ELI5C_S12_L003


title: ELI5M_S11_L004


title: ELI5C_S12_L002


title: ELI2M_S9_L003


title: ELI5C_S12_L004


title: ELI7C_S16_L003


title: ELI5C_S12_L001


title: ELI2M_S9_L002


title: ELI8C_S18_L003


title: ELI2C_S10_L004


title: ELI2C_S10_L001


title: ELI1M_S7_L001


title: ELI2M_S9_L004


title: ELI2C_S10_L002


title: ELI2M_S9_L001


title: ELI2C_S10_L003


title: ELI1C_S8_L004


title: ELI1C_S8_L003


title: ELI1C_S8_L002


title: ELI1C_S8_L001


title: ELI5M_S11_L001


title: STA_6_S3_L003


title: STA_6_S3_L001


title: STA_5_S2_L002


title: STA_5_S2_L001


title: STA_6_S3_L004


title: STA_2_S35_L004

value: Neisseria meningititis B


title: STA_2_S35_L003


title: STA_2_S35_L002


title: STA_2_S35_L001


title: STA_1_S1_L004


title: STA_1_S1_L002


title: STA_1_S1_L001


title: ELI1M_S7_L004


title: R_UZG_9_S30_L004

value: systemic onset juvenile arthritis


title: R_UZG_9_S30_L002


title: R_UZG_9_S30_L003


title: STA_5_S2_L004


title: R_UZG_8_S29_L004


title: R_UZG_8_S29_L003


title: R_UZG_8_S29_L002


title: ELI1M_S7_L002


title: R_UZG_7_S28_L004

value: juvenile idiopathic arthritis


title: R_UZG_7_S28_L003


title: R_UZG_7_S28_L002


title: STA_6_S3_L002


title: STA_5_S2_L003


title: R_UZG_7_S28_L001


title: R_UZG_6_S27_L004

value: chronic recurrent multifocal osteomyelitis


title: R_UZG_6_S27_L003


title: R_UZG_6_S27_L001


title: R_UZG_6_S27_L002


title: STA_1_S1_L003


title: R_UZG_5_S26_L004


title: R_UZG_5_S26_L002


title: R_UZG_4_S25_L004


title: R_UZG_4_S25_L002


title: R_UZG_9_S30_L001


title: R_UZG_4_S25_L003


title: R_UZG_5_S26_L001


title: R_UZG-2_S33_L004

value: early onset sarcoidose


title: R_UZG-2_S33_L003


title: R_UZG_4_S25_L001


title: R_UZG-2_S33_L002


title: R_UZG_1_S24_L004


title: R_UZG_1_S24_L003


title: R_UZG-2_S33_L001


title: R_UZG_8_S29_L001


title: R_UZG_1_S24_L002


title: R_UZG_1_S24_L001


title: NIK_9_S8_L004


title: NIK_9_S8_L003


title: NIK_9_S8_L002


title: ELI1M_S7_L003


title: NIK8M_S5_L004


title: NIK8M_S5_L003


title: NIK_9_S8_L001


title: NIK8M_S5_L002


title: NIK8C_S6_L004


title: R_UZG_5_S26_L003


title: NIK8C_S6_L003


title: NIK8C_S6_L002


title: NIK7M_S3_L001


title: NIK7C_S4_L003


title: NIK8C_S6_L001


title: NIK7C_S4_L002


title: NIK7M_S3_L004


title: NIK7M_S3_L002


title: NIK7C_S4_L001


title: NIK_6_S6_L004


title: NIK7C_S4_L004


title: NIK8M_S5_L001


title: NIK_6_S6_L003


title: NIK_6_S6_L001


title: NIK7M_S3_L003


title: NIK_6b_S7_L004


title: NIK_6b_S7_L003


title: NIK_6b_S7_L002


title: NIK_4_S5_L003


title: NIK_6b_S7_L001


title: NIK_4_S5_L002


title: NIK_4_S5_L004


title: NIK3M_S1_L003


title: NIK3M_S1_L004


title: NIK3M_S1_L002


title: NIK3C_S2_L004


title: NIK3M_S1_L001


title: NIK3C_S2_L003


title: NIK3C_S2_L001


title: DIN_6_M_S23_L002


title: DIN_6_M_S23_L001


title: DIN_6_M_S23_L004


title: DIN_6_C_S24_L004


title: DIN_6_M_S23_L003


title: NIK3C_S2_L002


title: DIN_6_C_S24_L003


title: NIK_6_S6_L002


title: DIN_6_C_S24_L001


title: DIN_5_M_S21_L003


title: DIN_5_C_S22_L004


title: DIN_5_M_S21_L004


title: DIN_6_C_S24_L002


title: DIN_5_M_S21_L001


title: DIN_5_C_S22_L003


title: DIN_5_C_S22_L002


title: DIN_5_C_S22_L001


title: DIN_5_M_S21_L002


title: NIK_4_S5_L001


title: DIN_4_M_S19_L003


title: DIN_4_M_S19_L004


title: DIN_4_M_S19_L002


title: DIN_4_C_S20_L004


title: DIN_4_C_S20_L002


title: DIN_4_C_S20_L001


title: DIN_3_M_S17_L002


title: DIN_3_M_S17_L003


title: DIN_4_C_S20_L003


title: DIN_4_M_S19_L001


title: DIN_3_M_S17_L001


title: DIN_3_C_S18_L004


title: DIN_3_C_S18_L001


title: DIN_3_C_S18_L002


title: DIN_2_M_S15_L004


title: DIN_2_M_S15_L003


title: DIN_2_M_S15_L001


title: DIN_3_C_S18_L003


title: DIN_2_C_S16_L004


title: DIN_3_M_S17_L004


title: DIN_2_C_S16_L002


title: DIN_1_M_S13_L004


title: DIN_1_M_S13_L003


title: DIN_1_M_S13_L002


title: DIN_2_M_S15_L002


title: DIN_2_C_S16_L001


title: DIN_1_M_S13_L001


title: DIN_1_C_S14_L002


title: DIN_1_C_S14_L003


title: DIN_1_C_S14_L001


title: DIN_14_M_S27_L004


title: DIN_14_M_S27_L003


title: DIN_14_M_S27_L002


title: DIN_14_C_S28_L003


title: DIN_14_C_S28_L002


title: DIN_14_C_S28_L004


title: DIN_14_M_S27_L001


title: DIN_14_C_S28_L001


title: DIN_12_M_S25_L003


title: DIN_12_M_S25_L002


title: DIN_2_C_S16_L003


title: DIN_12_M_S25_L001


title: DIN_1_C_S14_L004


title: R_BEN-019_S23_L004

value: mixed connective tissue disease


title: R_BEN-019_S23_L003

value: whole blood


title: DIN_12_C_S26_L003


title: R_BEN-020_S39_L002

value: familial mediterreanan fever


title: R_BEN-020_S39_L001


title: DIN_12_C_S26_L001

value: Control


title: DIN_12_C_S26_L004


title: DIN_12_C_S26_L002


title: R_BEN-019_S23_L002


title: R_BEN-019_S23_L001


title: R_BEN-018_S22_L004

value: connective tissue disease


title: R_BEN-018_S22_L003


title: R_BEN-018_S22_L002


title: R_BEN-016_S21_L004

value: autoinflammatory disease


title: R_BEN-018_S22_L001


title: R_BEN-016_S21_L002


title: R_BEN-016_S21_L003


title: R_BEN-015_S20_L004


title: R_BEN-015_S20_L002


title: DIN_12_M_S25_L004

value: Enterovirus


title: R_BEN-015_S20_L003


title: R_BEN-016_S21_L001


title: R_BEN-020_S39_L004


title: R_BEN-014_S32_L004

value: unknown


title: R_BEN-014_S32_L003


title: R_BEN-020_S39_L003


title: R_BEN-014_S32_L001


title: R_BEN-014_S32_L002


title: R_BEN-012_S19_L004


title: R_BEN-012_S19_L003


title: R_BEN-012_S19_L002


title: R_BEN-011_S18_L002


title: R_BEN-011_S18_L001


title: R_BEN-010_S35_L003

value: Behcet or familial mediterreanan fever


title: R_BEN-010_S35_L004


title: R_BEN-008_S31_L004


title: R_BEN-008_S31_L003


title: R_BEN-008_S31_L002


title: R_BEN-008_S31_L001


title: R_BEN-011_S18_L004


title: R_BEN-015_S20_L001


title: R_BEN-006A_S17_L003

value: juvenile dermatomyositis


title: R_BEN-006A_S17_L004


title: R_BEN-006C_S34_L001


title: R_BEN-006C_S34_L002


title: R_BEN-006C_S34_L004


title: R_BEN-006A_S17_L001


title: R_BEN-006C_S34_L003


title: R_BEN-006A_S17_L002


title: R_BEN-005_S38_L004


title: R_BEN-005_S38_L002


title: R_BEN-005_S38_L003


title: R_BEN-005_S38_L001


title: R_BEN-003_S16_L004


title: R_BEN-003_S16_L003


title: R_BEN-012_S19_L001


title: R_BEN-010_S35_L002


title: R_BEN-010_S35_L001


title: R_BEN-002_S15_L003


title: R_BEN-002_S15_L002


title: R_BEN-002_S15_L004


title: R_BEN-003_S16_L001


title: R_BEN-002_S15_L001


title: R_BEN-001A_S14_L003

value: aicardi goutiere syndrome


title: R_BEN-001A_S14_L004


title: R_BEN-001A_S14_L001


title: R_BEN-001A_S14_L002


title: R_BEN-003_S16_L002


title: AZT9M_S31_L003


title: AZT9M_S31_L002


title: AZT9M_S31_L001


title: AZT9C_S32_L003


title: AZT9M_S31_L004


title: AZT9C_S32_L001


title: AZT7M_S29_L002


title: AZT7M_S29_L001


title: AZT7C_S30_L004


title: AZT9C_S32_L002


title: AZT7M_S29_L003


title: AZT7C_S30_L003


title: R_BEN-011_S18_L003


title: AZT7C_S30_L001


title: AZT6M_S27_L003


title: AZT7C_S30_L002


title: AZT6M_S27_L002


title: AZT6M_S27_L004


title: AZT6C_S28_L002


title: AZT6C_S28_L003


title: AZT6M_S27_L001


title: AZT6C_S28_L001


title: AZT5M_S25_L004


title: AZT6C_S28_L004


title: AZT5M_S25_L003


title: AZT5M_S25_L001


title: AZT5M_S25_L002


title: AZT7M_S29_L004


title: AZT9C_S32_L004


title: AZT5C_S26_L001


title: AZT5C_S26_L003


title: AZT5C_S26_L002


title: AZT3M_S23_L004


title: AZT3M_S23_L003


title: AZT5C_S26_L004


title: AZT3C_S24_L001


title: AZT3C_S24_L003


title: AZT3C_S24_L004


title: AZT3M_S23_L002


title: AZT3C_S24_L002


title: AZT2M_S21_L003


title: AZT2M_S21_L002


title: AZT2M_S21_L001


title: AZT2C_S22_L004


title: AZT_20_M_S7_L004


title: AZT2C_S22_L001


title: AZT2C_S22_L002


title: AZT_20_M_S7_L002


title: AZT_20_C_S8_L004


title: AZT_20_C_S8_L003


title: AZT2C_S22_L003


title: AZT_20_M_S7_L001


title: AZT1M_S19_L003


title: AZT_20_C_S8_L002


title: AZT1M_S19_L004


title: AZT1M_S19_L002


title: AZT3M_S23_L001


title: AZT1M_S19_L001


title: AZT2M_S21_L004


title: AZT1C_S20_L001


title: AZT1C_S20_L004


title: AZT1C_S20_L002


title: AZT_18_M_S5_L002


title: AZT1C_S20_L003


title: AZT_18_M_S5_L004


title: AZT_18_C_S6_L002


title: AZT_18_C_S6_L004


title: AZT_18_C_S6_L001


title: AZT_17_M_S3_L004


title: AZT_18_C_S6_L003


title: AZT_20_M_S7_L003


title: AZT_17_M_S3_L001


title: AZT_18_M_S5_L001


title: AZT_17_C_S4_L004


title: AZT_17_C_S4_L003


title: AZT_20_C_S8_L001


title: AZT_17_M_S3_L003


title: AZT_17_C_S4_L001


title: AZT_17_C_S4_L002


title: AZT_17_M_S3_L002


title: AZT_16_M_S1_L004


title: AZT_16_M_S1_L003


title: AZT_16_C_S2_L004


title: AZT_16_M_S1_L001


title: AZT_16_C_S2_L003


title: AZT_16_C_S2_L002


title: AZT_16_C_S2_L001


title: AZT15M_S39_L001


title: AZT15C_S40_L004


title: AZT15C_S40_L003


title: AZT15C_S40_L001


title: AZT_18_M_S5_L003


title: AZT15C_S40_L002


title: AZT14M_S37_L003


title: AZT14C_S38_L004


title: AZT14C_S38_L003


title: AZT14M_S37_L001


title: AZT14M_S37_L004


title: AZT13M_S35_L004


title: AZT15M_S39_L003


title: AZT13M_S35_L003


title: AZT_16_M_S1_L002


title: AZT11M_S33_L004


title: AZT15M_S39_L002


title: AZT13M_S35_L002


title: AZT13C_S36_L004


title: AZT13C_S36_L003


title: AZT14C_S38_L001


title: AZT13C_S36_L002


title: AZT15M_S39_L004


title: AZT11M_S33_L003


title: AZT13C_S36_L001


title: patient#BP_cerebellum

data_processing:
Sequencing was performed using the Illumina NextSeq-500 system.
Transcript abundances were quantified with the Ensembl GRCh38 cDNA reference using Kallisto version 0.43.0.
Transcript abundances were summarized to gene level using tximport.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files include FPKM values

source_name: Cerebellum

value: Cerebellum

value: 45 years

tag: Sex

value: Female

tag: disease state

value: bipolar disorder

tag: cell type

value: primary microglia


title: patient#BP_STG

source_name: Superior temporal gyrus

value: Superior temporal gyrus


title: Early Time Point Repeat 2

city: New Haven

first: Monkol

last: Lek

state: CT

address: 300 Cedar st

institute: Yale University School of Medicine

description: surrounding region around sgRNA

data_processing:
Reads were aligned to the sgRNA in the GecKO CRISPR library using bowtie2
A custom script was used to determine the raw read counts from the aligned SAM file
For more information please visit https://github.com/leklab/fshd_ko_screen
Supplementary_files_format_and_content: Raw read counts of each sgRNA in the GecKO CRISPR library

source_name: DUX4 inducible myoblast

extract_protocol:
Genomic DNA extraction was performed on both ETP and DUX4 populations,
PCR reactions were performed to amplify sgRNA insert and attach sequencing barcodes.

tag: cell line


title: DUX4 selection Repeat 2

description: surrounding region around sgRNA


title: AZT11C_S34_L004


title: AZT11M_S33_L001


title: AZT14C_S38_L002


title: AZT14M_S37_L002


title: AZT11C_S34_L002


title: Early Time Point Repeat 1

description: surrounding region around sgRNA


title: patient#MA_cerebellum

value: 60 years

value: multisystem atrophy


title: patient#MA_STG


title: AZT13M_S35_L001

value: whole blood


title: DUX4 selection Repeat 1

description: surrounding region around sgRNA


title: AZT11C_S34_L001

value: Control


title: AZT11C_S34_L003


title: MCF7_Abemaciclib_3_24_rep2

first: Peter

last: Sorger

address: 200 Longwood Avenue

department: Department of Systems Biology

institute: Harvard Medical School

data_processing:
Two fastq files from 2 runs of the same sample(except for MCF7, which has only one run) were merged to one using the command "cat" in bash
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bcbio-nextgen software with the following configuration parameters: analysis=RNA-seq genome_build=hg19-ercc  aligner=star quality_format=standard trim_reads=read_through adapters=[truseq, polya] strandedness=firststrand
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated and genes with RPKM of 0 in all of the samples were discarded. RPKM values were log2-transformed with an offset value of 1.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (RPKM values were log2-transformed with an offset value of 1.0.)

source_name: MCF7 breast cancer cell line

growth_protocol: Cells were seeded in 12 well plates, and allowed to adhere for 24 hours

extract_protocol:
RNA was extracted using Applied Biosystems MagMax 96 total RNA isolation kit (AM1830) with DNAse digestion according to the manufacturer’s protocol.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kit (RS-122-2103) from 500 ng of purified total RNA according to the manufacturer’s protocol in a reduced reaction volume.

treatment_protocol: 24 hours after seeding cells CDK4/6 inhibitors were added. Cells were lysed in the plates after 6 or 24 hours.

tag: agent

value: Abemaciclib

tag: dose

value: 3 uM

tag: time

value: 24 hr


title: MCF7_Abemaciclib_0.3_24_rep2


title: MCF7_Control_0_24_rep2

value: 0 uM


title: MCF7_Ribociclib_3_24

value: Ribociclib


title: MCF7_Abemaciclib_1_24_rep2

value: 1 uM


title: MCF7_Abemaciclib_3_24_rep1


title: AZT11M_S33_L002

value: Enterovirus


title: MCF7_Abemaciclib_1_24_rep1


title: MCF7_Abemaciclib_0.3_24_rep1


title: MCF7_Ribociclib_0.3_24


title: MCF7_Palbociclib_0.3_24

value: Palbociclib


title: MCF7_Palbociclib_3_24


title: MCF7_Palbociclib_3_6

value: 6 hr


title: MCF7_Abemaciclib_1_6_rep2


title: MCF7_Control_0_6_rep2


title: MCF7_Ribociclib_0.3_6


title: MCF7_Control_0_24_rep1


title: MCF7_Abemaciclib_3_6_rep2


title: MCF7_Palbociclib_0.3_6


title: MCF7_Ribociclib_3_6


title: MCF7_Abemaciclib_1_6_rep1


title: MCF7_Abemaciclib_0.3_6_rep1


title: MCF7_Control_0_6_rep1


title: T47D_Ribociclib_3_6

source_name: T47D breast cancer cell line


title: T47D_Ribociclib_0.3_6


title: AD_iN cells replicate_2

city: Stanford

first: Samuele

last: Marro

state: California

address: 256 Campus Drive

institute: Stanford University

description: TPM_Marro et al..txt

data_processing:
Paired-end reads were aligned to the human reference sequence NCBI Build (hg38) with STAR (Dobin et al., 2013).
Properly paired reads to the reference were extracted using the samtools function and considered for subsequent analysis.
Expression levels of RefSeq-annotated genes were calculated in units of transcripts per kilobase million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: text file. TPM values

source_name: EGFP sorted cells

growth_protocol: Ngn2-iN and AD-iN cells were generated as described (Yang et al., 2017; Zhang et al., 2013). To generate AM-iN cells, ES cells were treated with Accutase (Innovative Cell Technologies) and plated as dissociated cells in six-well plates (H1 cells: ~5 × 104 cells/well) on day 0. Cells were plated on plates coated with matrigel (BD Biosciences) mTeSR1 containing 2 μM thiazovivin (Bio Vision). At the same time of plating, lentivirus prepared as described above (1.5 μl/well of six-well plate) was added. On day 1, the culture medium was replaced with N2/DMEM/F12/NEAA (Invitrogen) containing doxycycline (2 μg/ml, Clontech) to induce TetO gene expression, and the culture was retained in the medium for ~2 weeks. On day 2 and 3 puromycin was used to selected transduced cells. From day 5 to day 7 AraC (4μM) was added to the media to selected for not dividing cells. On day 6, mouse glial cells were plated on matrigel-coated coverslips (~5 × 104 cells/well of 24-well plate). On day 7, iN cells were dissociated using Accutase and plated on glial cells (~3 × 105 cells/well of 24- well plate)

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
libraries were made using NuGen/NEB protocol.


title: T47D_Palbociclib_3_6


title: AM_iN cells replicate_1

description: TPM_Marro et al..txt


title: AD_iN cells replicate_1

description: TPM_Marro et al..txt


title: AD_iN cells replicate_3

description: TPM_Marro et al..txt


title: AM_iN cells replicate_2

description: TPM_Marro et al..txt


title: T47D_Palbociclib_0.3_6


title: T47D_Abemaciclib_3_6_rep2


title: Ngn2_iN cells replicate_2

description: TPM_Marro et al..txt


title: Ngn2_iN cells replicate_1

description: TPM_Marro et al..txt


title: MCF7_Abemaciclib_3_6_rep1


title: MCF7_Abemaciclib_0.3_6_rep2


title: T47D_Abemaciclib_3_6_rep1


title: T47D_Abemaciclib_0.3_6


title: HS578T_Ribociclib_3_6

source_name: HS578T breast cancer cell line


title: T47D_Control_0_6


title: HS578T_Ribociclib_0.3_6


title: HS578T_Palbociclib_3_6


title: HS578T_Palbociclib_0.3_6


title: HS578T_Control_0_6


title: HS578T_Abemaciclib_3_6_rep2


title: HS578T_Abemaciclib_3_6_rep1


title: HS578T_Abemaciclib_0.3_6


title: HCC1806_Ribociclib_0.3_6

source_name: HCC1806 breast cancer cell line


title: HCC1806_Ribociclib_3_6


title: HCC1806_Palbociclib_3_6


title: HCC1806_Abemaciclib_3_6_rep2


title: HCC1806_Abemaciclib_3_6_rep1


title: HCC1806_Control_0_6


title: HCC1806_Abemaciclib_0.3_6


title: HCC1419_Palbociclib_3_6

source_name: HCC1419 breast cancer cell line


title: HCC1419_Palbociclib_0.3_6


title: HCC1419_Ribociclib_0.3_6


title: HCC1419_Abemaciclib_3_6_rep2


title: HCC1419_Abemaciclib_3_6_rep1


title: BT549_Ribociclib_3_6

source_name: BT549 breast cancer cell line


title: HCC1419_Abemaciclib_0.3_6


title: BT549_Ribociclib_0.3_6


title: BT549_Palbociclib_0.3_6


title: HCC1419_Control_0_6


title: BT549_Palbociclib_3_6


title: BT549_Abemaciclib_3_6_rep1


title: BT549_Control_0_6


title: BT549_Abemaciclib_0.3_6


title: BT20_Palbociclib_0.3_6

source_name: BT20 breast cancer cell line


title: BT20_Ribociclib_3_6


title: BT20_Ribociclib_0.3_6


title: BT20_Abemaciclib_0.3_6


title: BT20_Abemaciclib_3_6_rep1


title: BT20_Abemaciclib_3_6_rep2


title: HCC1806_Palbociclib_0.3_6


title: BT20_Palbociclib_3_6


title: T47D_Ribociclib_3_24


title: BT20_Control_0_6


title: BT549_Abemaciclib_3_6_rep2


title: HCC1419_Ribociclib_3_6


title: T47D_Ribociclib_0.3_24


title: HS578T_Ribociclib_0.3_24


title: HS578T_Palbociclib_0.3_24


title: T47D_Abemaciclib_3_24_rep2


title: T47D_Palbociclib_0.3_24


title: HS578T_Palbociclib_3_24


title: T47D_Abemaciclib_0.3_24


title: T47D_Palbociclib_3_24


title: T47D_Abemaciclib_3_24_rep1


title: HS578T_Ribociclib_3_24


title: HS578T_Abemaciclib_3_24_rep2


title: HS578T_Abemaciclib_0.3_24


title: HS578T_Abemaciclib_3_24_rep1


title: HS578T_Control_0_24


title: T47D_Control_0_24


title: HCC1806_Ribociclib_3_24


title: HCC1806_Palbociclib_0.3_24


title: HCC1806_Abemaciclib_3_24_rep1


title: HCC1806_Abemaciclib_3_24_rep2


title: HCC1806_Palbociclib_3_24


title: HCC1806_Control_0_24


title: HCC1806_Abemaciclib_0.3_24


title: HCC1419_Abemaciclib_3_24_rep2


title: HCC1419_Palbociclib_3_24


title: HCC1419_Ribociclib_0.3_24


title: HCC1419_Abemaciclib_3_24_rep1


title: HCC1419_Abemaciclib_0.3_24


title: HCC1419_Control_0_24


title: HCC1419_Palbociclib_0.3_24


title: BT549_Ribociclib_3_24


title: BT549_Ribociclib_0.3_24


title: BT549_Palbociclib_0.3_24


title: CCAR2_ChIP-seq_K562

description: ChIP-seq data (SE)

value: Hepatocellular carcinoma

tag: chip antibody

value: CCAR2 (Zen BioScience Cat# 200093)


title: input_Control_K562_batch1

description: input DNA control (SE)


title: BT549_Palbociclib_3_24


title: XRCC5_ChIP-seq_K562

description: ChIP-seq data (SE)

value: XRCC5 (Zen BioScience Cat# 201004)


title: TARDBP_ChIP-seq_K562

description: ChIP-seq data (SE)

value: TARDBP (Bethyl Cat# A303-223A)


title: SFPQ_ChIP-seq_K562

description: ChIP-seq data (SE)

value: SFPQ (Bethyl Cat# A301-321A)


title: BT549_Abemaciclib_0.3_24


title: BT549_Abemaciclib_3_24_rep1


title: POLR2G_ChIP-seq_K562

description: ChIP-seq data (SE)

value: POLR2G (GeneTex Cat# GTX108874)


title: HCC1806_Ribociclib_0.3_24


title: BT549_Abemaciclib_3_24_rep2


title: HCC1419_Ribociclib_3_24


title: BT20_Ribociclib_3_24


title: NONO_ChIP-seq_K562

description: ChIP-seq data (SE)

value: NONO (Santa Cruz Biotechnology  Cat# sc-166702)


title: BT549_Control_0_24

value: Control


title: GTF2F1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: GTF2F1 (GeneTex Cat# GTX114455)


title: BT20_Ribociclib_0.3_24


title: BT20_Palbociclib_3_24

value: 3 uM


title: SAFB_ChIP-seq_K562

description: ChIP-seq data (SE)

value: SAFB (Zen BioScience Cat# 200580)


title: AGO1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: AGO1 (Cell Signaling Technology Cat# 5053)


title: BT20_Palbociclib_0.3_24

value: 24 hr


title: BT20_Abemaciclib_3_24_rep2

value: Abemaciclib


title: input_Control_K562_batch2

description: input DNA control (SE)


title: BT20_Abemaciclib_3_24_rep1


title: BT20_Abemaciclib_0.3_24


title: RBM25_ChIP-seq_K562

description: ChIP-seq data (SE)

value: RBM25 (Bethyl Cat# A301-068A)


title: RBFOX2_ChIP-seq_K562

description: ChIP-seq data (SE)

value: RBFOX2 (Bethyl Cat# A300-864A)


title: BT20_Control_0_24

value: 0 uM


title: FIP1L1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: Hepatocellular carcinoma

value: FIP1L1 (Abclonal Cat# #A5016)


title: PRPF4_ChIP-seq_K562

description: ChIP-seq data (SE)

value: PRPF4 (MBL Cat# RN093PW)


title: SNRNP70_ChIP-seq_K562

description: ChIP-seq data (SE)

value: SNRNP70 (Santa Cruz Biotechnology Cat# sc-9571)


title: TGCGCG: T47D_Ribociclib_0.3

first: Kartik

last: Subramanian

description:
well: P21
barcode: TGCGCG
T47D_Ribociclib_0.3

data_processing:
barcode and Unique moelcular identifiers (UMIs) were identified for all reads and reads not within one edit distance of a well known barcode were discarded
surviving reads were quasialigned using RapMap.
Reads per well were counted using UMI's, duplicate UMIs were discarded. Mutimapped reads were weighted by  the number of transcirpts they aligned to
Reads counts were collapsed to gene counts by adding all counts for each transcript of a gene.
Genome_build: GRch38
Supplementary_files_format_and_content: .csv file of counts for all gene identifiers that mapped to a mRNA across all 335 samples

growth_protocol: Cells were plated at densitieis ranging from 500 to 2000 cells per well in a 384-well plate and allowed to adhere for 24 hours

extract_protocol:
RNA was extracted using TCL lysis buffer, samples were using universal adapters, barcodes, unique molecular identifiers, and a template switching reverse transcriptase.
Libraries were prepared using Nextera DNA kit (Illumina).
Digitial gene expression (DGE)

treatment_protocol: 24 hours after seeding cells, CDK4/6 inhibitors were added. Cells were lysed in the plates after 6 hours.

value: T47D breast cancer cell line

tag: drug treatment

value: Ribociclib

tag: concentration (um)

tag: time (hours)


title: TGCGGC: T47D_Alvocidib_0.1

description:
well: P22
barcode: TGCGGC
T47D_Alvocidib_0.1

value: Alvocidib


title: TCGCGG: PDXHCI002_Alvocidib_0.1

description:
well: P19
barcode: TCGCGG
PDXHCI002_Alvocidib_0.1

value: PDXHCI002 breast cancer PDX


title: RBM22_ChIP-seq_K562

description: ChIP-seq data (SE)

data_processing:
ChIP-seq data were processed in accordance with ENCODE uniform transcription factor ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/).
Briefly, ChIP-seq reads were aligned to the GRCh37 human genome using BWA;
PCR duplicates and reads of low quality were filtered;
Peak-calling was performed with SPP and IDR with 0.02 IDR threshhold;
Signal tracks were generated with MACS2 and bigWig applications from UCSC genome browser (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Peak files were narrowPeak files generated by SPP; column information of narrowPeak file is explicated at the link (https://genome-euro.ucsc.edu/FAQ/FAQformat.html#format12).

value: RBM22 (Bethyl Cat# A303-923A)


title: SAFB2_ChIP-seq_K562

description: ChIP-seq data (SE)

value: SAFB2 (Bethyl Cat# A301-112A)


title: TCGGCG: T47D_Palbociclib_0.3

description:
well: P20
barcode: TCGGCG
T47D_Palbociclib_0.3

value: Palbociclib


title: FUS_ChIP-seq_K562

description: ChIP-seq data (SE)

value: FUS (Bethyl Cat# A300-294A)


title: TCCCCG: PDXHCI002_Ribociclib_0.3

description:
well: P18
barcode: TCCCCG
PDXHCI002_Ribociclib_0.3


title: PCBP2_ChIP-seq_K562

description: ChIP-seq data (SE)

value: PCBP2 (MBL Cat# RN025P)


title: GTCGGC: MCF7_Alvocidib_0.1

description:
well: P16
barcode: GTCGGC
MCF7_Alvocidib_0.1

value: MCF7 breast cancer cell line


title: RBM39_ChIP-seq_K562

description: ChIP-seq data (SE)

value: RBM39 (Bethyl Cat# A300-291A)


title: PCBP1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: PCBP1 (MBL Cat# RN024P)


title: GTCGCG: MCF7_Ribociclib_0.3

description:
well: P15
barcode: GTCGCG
MCF7_Ribociclib_0.3


title: PTBP1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: PTBP1 (MBL Cat# RN011P)


title: HNRNPUL1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: Hepatocellular carcinoma

value: HNRNPUL1 (Abcam Cat# ab68480)


title: HNRNPLL_ChIP-seq_K562

description: ChIP-seq data (SE)

value: HNRNPLL (Cell Signaling Technology Cat# 4783S)


title: GGTCCC: Hs578T_Alvocidib_0.1

description:
well: P13
barcode: GGTCCC
Hs578T_Alvocidib_0.1

value: Hs578T breast cancer cell line


title: HNRNPL_ChIP-seq_K562

description: ChIP-seq data (SE)

value: HNRNPL (Aviva Cat# ARP40368_P050)


title: HNRNPK_ChIP-seq_K562

description: ChIP-seq data (SE)

value: HNRNPK (MBL Cat# RN019P)


title: GTGGGG: PDXHCI002_Palbociclib_0.3

description:
well: P17
barcode: GTGGGG
PDXHCI002_Palbociclib_0.3


title: GGGGTG: Hs578T_Ribociclib_0.3

description:
well: P12
barcode: GGGGTG
Hs578T_Ribociclib_0.3

value: Ribociclib


title: GGGCGA: HCC1806_Ribociclib_0.3

description:
well: P09
barcode: GGGCGA
HCC1806_Ribociclib_0.3

value: HCC1806 breast cancer cell line


title: GGGCTC: HCC1806_Alvocidib_0.1

description:
well: P10
barcode: GGGCTC
HCC1806_Alvocidib_0.1

value: Alvocidib


title: HNRNPH1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: HNRNPH1 (Aviva Cat# ARP58479_P050)


title: HNRNPC_ChIP-seq_K562

description: ChIP-seq data (SE)

value: HNRNPC (Santa Cruz Biotechnology Cat# sc-10037)


title: TAF15_ChIP-seq_K562

description: ChIP-seq data (SE)

value: TAF15 (Abcam Cat# ab134916)


title: GGGAGG: HCC1806_Palbociclib_0.3

description:
well: P08
barcode: GGGAGG
HCC1806_Palbociclib_0.3

value: Palbociclib


title: U2AF2_ChIP-seq_K562

description: ChIP-seq data (SE)

value: U2AF2 (Bethyl Cat# A303-665A)


title: GGGACC: PDX1258_Alvocidib_0.1

description:
well: P07
barcode: GGGACC
PDX1258_Alvocidib_0.1

value: PDX1258 breast cancer PDX


title: GGCGGA: PDX1258_Ribociclib_0.3

description:
well: P06
barcode: GGCGGA
PDX1258_Ribociclib_0.3


title: U2AF1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: U2AF1 (Bethyl Cat# A302-079A)


title: SRSF9_ChIP-seq_K562

description: ChIP-seq data (SE)

value: SRSF9 (MBL Cat# RN081PW)


title: GGCACG: BT549_Ribociclib_0.3

description:
well: P03
barcode: GGCACG
BT549_Ribociclib_0.3

value: BT549 breast cancer cell line


title: GGCAGC: BT549_Alvocidib_0.1

description:
well: P04
barcode: GGCAGC
BT549_Alvocidib_0.1


title: SRSF3_ChIP-seq_K562

description: ChIP-seq data (SE)

value: Hepatocellular carcinoma

value: SRSF3 (MBL Cat# RN080PW)


title: GGACGC: BT549_Palbociclib_0.3

description:
well: P02
barcode: GGACGC
BT549_Palbociclib_0.3


title: GGTGCG: MCF7_Palbociclib_0.3

description:
well: P14
barcode: GGTGCG
MCF7_Palbociclib_0.3

value: MCF7 breast cancer cell line


title: SRSF1_ChIP-seq_K562

description: ChIP-seq data (SE)

value: SRSF1 (Bethyl Cat#A302-052A)


title: SRSF4_ChIP-seq_K562

description: ChIP-seq data (SE)

value: SRSF4 (Bethyl Cat# A303-670A)


title: SRSF7_ChIP-seq_K562

description: ChIP-seq data (SE)

value: SRSF7 (MBL Cat# RN079PW)


title: TCCGGG: T47D_Palbociclib_0.1

description:
well: O20
barcode: TCCGGG
T47D_Palbociclib_0.1

value: T47D breast cancer cell line


title: input_Control_HepG2_batch17

description: input DNA control (SE)


title: input_Control_HepG2_batch16

description: input DNA control (SE)


title: input_Control_HepG2_batch15

description: input DNA control (SE)


title: TGCCCC: T47D_DMSO_0.0

description:
well: O22
barcode: TGCCCC
T47D_DMSO_0.0

value: DMSO


title: TCCCGC: PDXHCI002_DMSO_0.0

description:
well: O19
barcode: TCCCGC
PDXHCI002_DMSO_0.0

value: PDXHCI002 breast cancer PDX


title: TCGGGC: T47D_Ribociclib_0.1

description:
well: O21
barcode: TCGGGC
T47D_Ribociclib_0.1

value: Ribociclib


title: input_Control_HepG2_batch14

description: input DNA control (SE)


title: GTGGCC: PDXHCI002_Ribociclib_0.1

description:
well: O18
barcode: GTGGCC
PDXHCI002_Ribociclib_0.1


title: GTGCGC: PDXHCI002_Palbociclib_0.1

description:
well: O17
barcode: GTGCGC
PDXHCI002_Palbociclib_0.1


title: GGTGGC: MCF7_Ribociclib_0.1

description:
well: O15
barcode: GGTGGC
MCF7_Ribociclib_0.1


title: TARDBP_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: TARDBP (Bethyl Cat# A303-223A)


title: XRCC5_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: XRCC5 (Zen BioScience Cat# 201004)


title: SFPQ_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: SFPQ (Bethyl Cat# A301-321A)


title: GGGTGC: MCF7_Palbociclib_0.1

description:
well: O14
barcode: GGGTGC
MCF7_Palbociclib_0.1

value: Palbociclib


title: GGCGCT: PDX1258_Palbociclib_0.3

description:
well: P05
barcode: GGCGCT
PDX1258_Palbociclib_0.3

value: PDX1258 breast cancer PDX


title: input_Control_HepG2_batch13

description: input DNA control (SE)


title: GGGTCG: Hs578T_DMSO_0.0

description:
well: O13
barcode: GGGTCG
Hs578T_DMSO_0.0

value: Hs578T breast cancer cell line


title: GGGGCA: Hs578T_Ribociclib_0.1

description:
well: O12
barcode: GGGGCA
Hs578T_Ribociclib_0.1


title: NONO_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: NONO (Santa Cruz Biotechnology  Cat# sc-166702)


title: GGGGAC: Hs578T_Palbociclib_0.1

description:
well: O11
barcode: GGGGAC
Hs578T_Palbociclib_0.1


title: AGO2_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: Hepatocellular carcinoma


title: AGO1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: AGO1 (Cell Signaling Technology Cat# 5053)


title: RBM39_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: RBM39 (Bethyl Cat# A300-291A)


title: RBM25_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: RBM25 (Bethyl Cat# A301-068A)


title: RBM22_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: RBM22 (Bethyl Cat# A303-923A)


title: RBFOX2_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: RBFOX2 (Bethyl Cat# A300-864A)


title: PCBP1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: PCBP1 (MBL Cat# RN024P)


title: SNRNP70_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: SNRNP70 (Santa Cruz Biotechnology Cat# sc-9571)


title: GTCCCC: MCF7_DMSO_0.0

description:
well: O16
barcode: GTCCCC
MCF7_DMSO_0.0

value: MCF7 breast cancer cell line

value: DMSO


title: HNRNPUL1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: HNRNPUL1 (Abcam Cat# ab68480)


title: GGCGTC: PDX1258_DMSO_0.0

description:
well: O07
barcode: GGCGTC
PDX1258_DMSO_0.0


title: GGCGAG: PDX1258_Ribociclib_0.1

description:
well: O06
barcode: GGCGAG
PDX1258_Ribociclib_0.1

value: Ribociclib


title: GGCTCC: HCC1806_Palbociclib_0.1

description:
well: O08
barcode: GGCTCC
HCC1806_Palbociclib_0.1

value: HCC1806 breast cancer cell line


title: GGAGCC: BT549_Ribociclib_0.1

description:
well: O03
barcode: GGAGCC
BT549_Ribociclib_0.1

value: BT549 breast cancer cell line


title: GGCCAC: PDX1258_Palbociclib_0.1

description:
well: O05
barcode: GGCCAC
PDX1258_Palbociclib_0.1

value: PDX1258 breast cancer PDX

value: Palbociclib


title: GGGCAG: HCC1806_Ribociclib_0.1

description:
well: O09
barcode: GGGCAG
HCC1806_Ribociclib_0.1


title: GGGCCT: HCC1806_DMSO_0.0

description:
well: O10
barcode: GGGCCT
HCC1806_DMSO_0.0


title: GGAGGG: BT549_DMSO_0.0

description:
well: O04
barcode: GGAGGG
BT549_DMSO_0.0


title: HNRNPLL_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: HNRNPLL (Cell Signaling Technology Cat# 4783S)


title: GTF2F1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: Hepatocellular carcinoma

value: GTF2F1 (GeneTex Cat# GTX114455)


title: HNRNPL_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: HNRNPL (Aviva Cat# ARP40368_P050)


title: GCGGCT: T47D_Abemaciclib_1.0

description:
well: N21
barcode: GCGGCT
T47D_Abemaciclib_1.0

value: T47D breast cancer cell line

value: Abemaciclib


title: GCGCGT: T47D_Palbociclib_0.3

description:
well: N20
barcode: GCGCGT
T47D_Palbociclib_0.3


title: HNRNPC_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: HNRNPC (Santa Cruz Biotechnology Cat# sc-10037)


title: GCTGCC: BT549_Palbociclib_0.1

description:
well: O02
barcode: GCTGCC
BT549_Palbociclib_0.1


title: HNRNPH1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: HNRNPH1 (Aviva Cat# ARP58479_P050)


title: GCGACG: PDXHCI002_Abemaciclib_1.0

description:
well: N18
barcode: GCGACG
PDXHCI002_Abemaciclib_1.0

value: PDXHCI002 breast cancer PDX


title: U2AF2_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: U2AF2 (Bethyl Cat# A303-665A)


title: GCCTGC: PDXHCI002_Palbociclib_0.3

description:
well: N17
barcode: GCCTGC
PDXHCI002_Palbociclib_0.3


title: U2AF1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: U2AF1 (Bethyl Cat# A302-079A)


title: SRSF1_ChIP-seq_HepG2

description: ChIP-seq data (SE)

value: SRSF1 (Bethyl Cat#A302-052A)


title: GCCGGT: MCF7_Ribociclib_0.1

description:
well: N16
barcode: GCCGGT
MCF7_Ribociclib_0.1

value: MCF7 breast cancer cell line

value: Ribociclib


title: GCCGCA: MCF7_Abemaciclib_1.0

description:
well: N15
barcode: GCCGCA
MCF7_Abemaciclib_1.0


title: GCCCGA: MCF7_Palbociclib_0.3

description:
well: N14
barcode: GCCCGA
MCF7_Palbociclib_0.3


title: GCGGGA: T47D_Ribociclib_0.1

description:
well: N22
barcode: GCGGGA
T47D_Ribociclib_0.1


title: GCCACC: Hs578T_Abemaciclib_1.0

description:
well: N12
barcode: GCCACC
Hs578T_Abemaciclib_1.0

value: Hs578T breast cancer cell line


title: GCAGGC: Hs578T_Palbociclib_0.3

description:
well: N11
barcode: GCAGGC
Hs578T_Palbociclib_0.3


title: GAGCCC: HCC1806_Palbociclib_0.3

description:
well: N08
barcode: GAGCCC
HCC1806_Palbociclib_0.3

value: HCC1806 breast cancer cell line


title: GAGGGC: HCC1806_Abemaciclib_1.0

description:
well: N09
barcode: GAGGGC
HCC1806_Abemaciclib_1.0


title: GACGGG: PDX1258_Ribociclib_0.1

description:
well: N07
barcode: GACGGG
PDX1258_Ribociclib_0.1

value: PDX1258 breast cancer PDX


title: GACCCG: PDX1258_Abemaciclib_1.0

description:
well: N06
barcode: GACCCG
PDX1258_Abemaciclib_1.0


title: CTGGGC: PDX1258_Palbociclib_0.3

description:
well: N05
barcode: CTGGGC
PDX1258_Palbociclib_0.3

value: Palbociclib


title: GCGCCA: PDXHCI002_Ribociclib_0.1

description:
well: N19
barcode: GCGCCA
PDXHCI002_Ribociclib_0.1


title: CTCGGG: BT549_Ribociclib_0.1

description:
well: N04
barcode: CTCGGG
BT549_Ribociclib_0.1

value: BT549 breast cancer cell line


title: CTCCGC: BT549_Abemaciclib_1.0

description:
well: N03
barcode: CTCCGC
BT549_Abemaciclib_1.0


title: GCCCCT: Hs578T_Ribociclib_0.1

description:
well: N13
barcode: GCCCCT
Hs578T_Ribociclib_0.1


title: GCACCC: HCC1806_Ribociclib_0.1

description:
well: N10
barcode: GCACCC
HCC1806_Ribociclib_0.1


title: XX84 ASC

city: Toulouse

last: Espagnolle

address: Bâtiment INCERE 4 bis, avenue Hubert Curien

country: France

institute: STROMALab, Université de Toulouse, CNRS  ERL5311, EFS, INP-ENVT, Inserm U1031, UPS, Toulouse, France

description: Gene expression data from human cultivated  adipose tissue derived MSC during 21 days

hyb_protocol: hybridization to human U133 plus 2.0 GeneChip microarrays

scan_protocol: GeneChip scanner 3000 and software AGCC

data_processing: Expression signal values and P-values were obtained for each probe set by use of Transcriptome Analysis Console (TAC) Software.(Affymetrix) .

source_name: Healthy donor adipose tissue

label_protocol: Biotinylated cRNA was amplified by the small sample labelling protocol  (two cycle amplification kit, Affymetrix)

growth_protocol: ASC were cultivated with aMEM (minimum essential medium) + 10% FCS (fetal calf serum) + ciprofloxacin during 21 days,

extract_protocol: Use of Rneasy kit (Qiagen). RNA purity and integrity was checked by use of Bioanalyzer 2100 (Agilent).

treatment_protocol: no treatment

tag: disease

value: Healthy donor

value: cultivated adipose tissue derived MSC


title: MI46 ASC

source_name: MM adipose tissue

value: multiple myeloma


title: PP68 ASC


title: MJ44 ASC


title: GCGCTG: T47D_Alvocidib_1.0

description:
well: M21
barcode: GCGCTG
T47D_Alvocidib_1.0

value: T47D breast cancer cell line

value: Alvocidib


title: TG55 ASC


title: GCGAGC: PDXHCI002_Ribociclib_1.0

description:
well: M19
barcode: GCGAGC
PDXHCI002_Ribociclib_1.0


title: GCGGAG: T47D_Ribociclib_1.0

description:
well: M22
barcode: GCGGAG
T47D_Ribociclib_1.0


title: JMW74 ASC


title: MB59 ASC


title: HE59 ASC


title: GCGCAC: T47D_Abemaciclib_1.0

description:
well: M20
barcode: GCGCAC
T47D_Abemaciclib_1.0

value: Abemaciclib


title: GCCTCG: PDXHCI002_Alvocidib_1.0

description:
well: M18
barcode: GCCTCG
PDXHCI002_Alvocidib_1.0

value: PDXHCI002 breast cancer PDX


title: MJB80 ASC


title: CGTGCC: BT549_Palbociclib_0.3

description:
well: N02
barcode: CGTGCC
BT549_Palbociclib_0.3


title: GCCGTG: PDXHCI002_Abemaciclib_1.0

description:
well: M17
barcode: GCCGTG
PDXHCI002_Abemaciclib_1.0


title: SA55 ASC


title: PE46 ASC


title: VG67 ASC


title: GCCGAC: MCF7_Ribociclib_1.0

description:
well: M16
barcode: GCCGAC
MCF7_Ribociclib_1.0


title: GP68 ASC


title: GP56 ASC


title: GCCCTC: MCF7_Alvocidib_1.0

description:
well: M15
barcode: GCCCTC
MCF7_Alvocidib_1.0


title: VC76 ASC


title: GCCCAG: MCF7_Abemaciclib_1.0

description:
well: M14
barcode: GCCCAG
MCF7_Abemaciclib_1.0


title: GCCAGG: Hs578T_Ribociclib_1.0

description:
well: M13
barcode: GCCAGG
Hs578T_Ribociclib_1.0


title: GJL55 ASC


title: FM62 ASC


title: GM49 ASC


title: FJ81 ASC


title: EFM53 ASC


title: 46R_Abemaciclib_150.0

data_processing:
Reads were trimmed and clipped for quality control in cutadapt v1.12
Read quality was checked for each sample using FastQC 0.11.5
High-quality reads were then aligned into BAM files through STAR 2.5.3a using the human assembly GRCh37
BAM files were imported into DEXSeq-COUNT 1.14.2 and raw counts TPM and RPKM were calculated.
Genome_build: GRch37
Supplementary_files_format_and_content: .csv file of counts for all gene identifiers that mapped to a mRNA across all samples

organism:
Homo sapiens
Mus musculus

source_name: mouse engrafted with MCF7 cells

growth_protocol: seven-week-old NU/NU nude mice were supplemented with 8 µg/ml 17ß-estradiol by adding it to their drinking water five days prior to tumor engraftment, and replacing it twice per week. Mice were engrafted with 5 x 106 MCF-7 cells 1:1 in growth factor reduced matrigel subcutaneously in each flank, and allowed to grow to ~300 mm3

extract_protocol:
Animals were sacrificed two hours after receiving the last dose. The tumors were excised and cut in half, one half was fixed in 4% formaldehyde at 4˚C and transferred to 0.1% sodium azide after 48 hours, the other flash frozen, and a thin slice from the center of the tumor was placed in RNAlater at 4˚C (Qiagen, Hilden, Germany), after 48 hours the RNAlater was aspirated, and samples were transferred to -80˚C.
Libraries were prepared using a TruSeq Stranded mRNA sample preparation kit

treatment_protocol: The animals were then randomly assigned to treatment groups, and treated daily for four days with ribociclib (150 mg/kg), palbociclib (150 mg/kg), abemaciclib (25, 75, 100, 125, or 150 mg/kg), or vehicle control (0.5% (w/v)

tag: concentration (mg/kg)


title: DD55 ASC


title: 47L_Palbociclib_150.0


title: GCACGG: Hs578T_Abemaciclib_1.0

description:
well: M11
barcode: GCACGG
Hs578T_Abemaciclib_1.0


title: 45R_Vehicle

value: Vehicle


title: GCAGCG: Hs578T_Alvocidib_1.0

description:
well: M12
barcode: GCAGCG
Hs578T_Alvocidib_1.0


title: DVG52 ASC


title: GAGGCG: HCC1806_Ribociclib_1.0

description:
well: M10
barcode: GAGGCG
HCC1806_Ribociclib_1.0


title: GAGCGG: HCC1806_Alvocidib_1.0

description:
well: M09
barcode: GAGCGG
HCC1806_Alvocidib_1.0


title: 44R_Abemaciclib_125.0


title: 45L_Vehicle