title: MDA-MB231-Myc_Doxycycline_120h_2 [G_180]

city: Groningen

first: Marcel

last: van Vugt

state: Groningen

address: Hanzeplein 1

department: Department of Medical Oncology

country: Netherlands

institute: UMCG

data_processing:
Generated by MOLGENIS Compute; Pipeline version NGS_RNA/3.2.5; August 14, 2017
The reference we always use for the MOLGENIS pipeline toolbox developed in our department: Byelas H. DM, Neerincx P., Dijk van F., Kanterakis A., Deelen P., Swertz M. Scaling bio-analyses from computational clusters to grids University Medical Centre Groningen 2013 [CEUR-WS.org CEUR Workshop Proceedings 993]. Available from: http://ceur-ws.org/Vol-993/paper2.pdf.
NGS: single reads 75 nt. Mean read length is 64 nt, (excluding the  bases used for the barcodes)
Gene expression quantification  The trimmed fastQ files where aligned to build human_g1k_v37 ensembleRelease 75 reference genome using hisat/0.1.5-beta-foss-2015b [1] allowing for 2 mismatches. Before gene quantification SAMtools/1.2-foss-2015b [2] was used to sort the aligned reads.  The gene level quantification was performed by HTSeq/0.6.1p1-foss-2015b [3] using --mode=union--stranded=no and, Ensembl version 75 was used as gene annotation database.
Calculate QC metrics on raw and aligned data  Quality control (QC) metrics are calculated for the raw sequencing data. This is done using  the tool FastQC FastQC/0.11.3-Java-1.7.0_80 [4]. QC metrics are calculated for the aligned reads using Picard-tools picard/1.130-Java-1.7.0_80 [5] CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-Metrics and SAMtools/1.2-foss-2015b flagstat.  These QC metrics form the basis in this final QC report.Used tool versions:  Java/1.7.0_80  FastQC/0.11.3-Java-1.7.0_80  hisat/0.1.5-beta-foss-2015b  SAMtools/1.2-foss-2015b  R/3.2.1-foss-2015b  wkhtmltopdf/0.11.0_rc1-static-amd64  picard/1.130-Java-1.7.0_80  HTSeq/0.6.1p1-foss-2015b  Python/2.7.10-foss-2015b  GATK/3.6-Java-1.8.0_74  multiqc/1.0-foss-2015b-Python-2.7.11  Ghostscript/9.16-foss-2015b    1. Dobin A, Davis C a, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M,  Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15â€“21.  2. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R,  Subgroup 1000 Genome Project Data Processing: The Sequence Alignment/Map format and SAMtools. Bioinforma 2009, 25 (16):2078â€“2079.  3. Anders S, Pyl PT, Huber W: HTSeq â€“ A Python framework to work with high-throughput sequencing data HTSeq â€“ A Python framework to work with high-throughput sequencing data. 2014:0â€“5.  4. Andrews, S. (2010). FastQC a Quality Control Tool for High Throughput Sequence Data [Online].  Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ SAMtools/1.2-foss-2015b  5. Picard Sourceforge Web site. http://picard.sourceforge.net/ picard/1.130-Java-1.7.0_80
Supplementary_files_format_and_content: csv, read count

growth_protocol: hTERT-immortalized human retina epithelial (RPE1), Human embryonic kidney 293 (HEK-293T) and triple-negative breast cancer cell lines MDA-MB-231, BT549, and HCC1806 were obtained from ATCC (#CRL4000, #CRL3216, #HTB26, #HTB122, #CRL2335). RPE1, HEK-293T, and MDA-MB-231 cells were maintained in Dulbecco's Minimum Essential Media (DMEM, Thermofisher), supplemented with 10% (v/v) fetal calf serum (FCS) and 1% penicillin/streptomycin (Gibco). BT-549 and HCC1806 were cultured in Roswell Park Memorial Institute medium (RPMI, Thermofisher), complemented with 10% FCS and 1% penicillin/streptomycin. All cells were grown at 37°C in normoxic conditions (20% O2 and 5% CO2).

extract_protocol:
RNA was isolated using the mirVANA kit (Ambion, AM1561). To determine RNA quality, RNA was separated by electrophoresis on microfluidic sipper chips and detected by fluorescence (LabChip GX, Caliper LifeSciences). RNA Quality Scores (RQS) were based on electropherogram features (total and fast region areas, 28S, and 18S height), and ranged from 0-10. Only samples with RQS scores above 5 were included for analysis.
To generate cDNA libraries suitable for next-generation sequencing (NGS), the QuantSeq RNAseq 3' mRNA kit (Lexogen) was employed. Briefly, the poly-A tail from total RNA was bound to oligo-dT primers to synthesize the first cDNA strand. After RNA removal, a second cDNA strand was synthesized by random priming.
The double-stranded cDNA library was purified, and PCR amplified with Illumina sequencing adapters. The libraries were sequenced with 65 base-pair reads on a NextSeq 500 sequencer (Illumina)..

treatment_protocol: Expression of CDC25A, CCNE1, or MYC in MDA-MB-231, BT549, HCC1806, RPE1-TP53wt, and RPE1-TP53mut cells was induced using 1 µg/mL of doxycycline. Cells were harvested and frozen at -80°C at 48 hours and 120 hours after doxycycline induction.

value: Doxycycline

tag: time point


title: Neural Progenitor Cells Iso-E - HiC_rep3

status: Public on Oct 11 2021

type: SRA

city: Cambridge

first: Hiruy

last: Meharena

state: MA

address: 43 Vassar St

department: The Picower Institute for Learning and Memory

country: USA

institute: Massachusetts Institute of Technology

library_source: genomic

data_processing:
Hi-C - fastq.gz.gz paired-end reads were processed through Juicer as previously described (Rao et al., 2014). In Brief, paired-end read pairs were aligned separately to the human genome (hg19) using BWA, then, duplicates/invalid pairs were removed, and the remaining reads were filtered based on mapping quality score of 30 (Li and Durbin, 2009). Interaction matrices were generated at resolutions of 2.5Mb, 1Mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, and 5kb and normalized interactions matrices were produced at all resolutions using Knight and Ruiz.
ChIP-seq - fastq.gz.gz reads for each replicate were aligned using Bowtie 2.0  (bowtie2 --very-sensitive -k 30) to hg19 (human) and dm6 (drosophila) (Langmead and Salzberg, 2012).  Samtools was used to sort (samtools sort), remove duplicates (samtools markdup), remove mitochondrial reads (samtools view) and index BAM files (samtools index) (Li et al., 2009). Bigwigs were generated from BAM files adjusted to the scale-factor for each sample using the percentage of mapped reads from the drosophila genome (dm6) to total reads over input utilizing deepTools (3.5.0) bamCoverage (Egan et al., 2016; Ramirez et al., 2016). Peak regions were identified using homer (4.11), with the function findPeaks utilizing the reads generated from input samples as background.
ATAC-seq - fastq.gz.gz paired-end reads for each replicate were aligned using Bowtie 2.0  (bowtie2 --very-sensitive -k 30) to hg19 (Langmead and Salzberg, 2012).  Samtools was used to sort (samtools sort), remove duplicates (samtools markdup), remove mitochondrial reads (samtools view), index BAM files (samtools index), and BAM files were shifted by +4bp and -5bp using an in-house algorithm (Li et al., 2009). Accessible chromatin peak calling was performed using Model-based Analysis of ChIP-Seq (macs2 callpeak -f BAMPE -g hs -q 0.05) (Zhang et al., 2008). Differential peaks analysis between the isogenic pairs was performed using Diffbind v1.16.3 (Ross-Innes et al., 2012).
RNA-seq - fastq.gz.gz paired- and single-end reads were aligned using STAR (v.2.6.1a) to GRCh37 reference genome (GENCODE 19) (Dobin et al., 2013). Transcripts were quantified using HTSeq, data was normalized utilizing RUV-seq and differential gene-expression analysis was performed through DESeq2 (Anders et al., 2015; Love et al., 2014; Risso et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: hic files were generated utilizing juicer
Supplementary_files_format_and_content: bigwig files were generated utilizing deepTools

molecule: genomic DNA

organism: Homo sapiens

source_name: Neural Progenitor Cells

growth_protocol: iPSC - Fibroblasts of the derived from individuals with Down syndrome and euploid controls were utilized to generate iPSCs using Sendai virus to overexpress OCT4, SOX2, KLF4, and c-MYC, utilizing the CytoTune-iPS Sendai Reprogramming kit (Thermofisher scientific, A16518) as previously described (Raja et al., 2016). iPSCs were cultured on irradiated mouse embryonic fibroblasts (MEFs, Thermo Fisher Scientific, A34181) in DMEM/F12 media supplemented with knockout serum replacement (KSR, 20% v/v), MEM non-Essential amino acid solution (Sigma-Aldrich M7145), Glutamax (Thermo Fisher Scientific 35050-079), 8 ng/μl recombinant human FGF-basic (FGF2, PeproTech, 100-18B) and 71.5µM 2-mercaptoethanol (Sigma-Aldrich M6250). The quality of cells was monitored daily and differentiated cells were mechanically removed under a light microscope in a biosafety hood. iPSCs were cultured to 80% confluence and non-differentiated colonies were transferred to a feeder-free system and grown on Matrigel hESC-Qualified Matrix coated plates (VWR, 354277) using mTeSR1 medium (Stemcell technologies, 85850). iPSCs for RNA-seq, ATAC-seq, and Hi-C grown under feeder-free conditions.    NPC - iPSCs were grown to 80% confluence on feeder-free conditions in mTeSR1 medium. iPSCs were then dissociated into single cell suspension using ReLeSR™ (Stemcell Technology, 05872) following the manufacturers guidelines. 3 million cells were then transferred into a single well of AggreWell™800 (Stemcell Technology, 34811) to form 300 embryoid bodies of 10,000 iPSCs each in NPC-differentiation medium [1:1 of DMEM/F12 Glutamax and Neurobasal (Life Technologies 10565-042 and Thermo Fisher Scientific 21103049), N-2 Supplement (Invitrogen,17502-048), B-27 Serum-Free Supplement (Gibco, 12587010), 2.5µg/l insulin (Thermo Fisher Scientific, 41400045), Glutamax (Thermo Fisher Scientific, 35050-079), MEM non-Essential amino acid solution (Sigma-Aldrich, M7145), 71.5µM 2-mercaptoethanol, Pen/strep (Gemini Bio-Products, 400-109), Dorsomorphin (PeproTech, 8666430) and SB431542 (Tocris,1614)]. Half NPC-induction medium replacement was performed daily for 5 days and on day 6 EBs were washed and transferred onto Matrigel coated plates. Complete NPC-induction medium replacement was performed daily for 7 days, and on day 12 STEMdiff™ Neural Rosette Selection Reagent (Stemcell technologies, 05832) was utilized to isolate NPC-rosettes and re-plated on onto fresh Matrigel coated plates in NPC-induction medium. Complete NPC-induction medium replacement was performed for 7 days and on day 20 NPCs were transferred onto fresh Matrigel coated plates in NPC-expansion medium [1:1 of DMEM/F12 Glutamax and Neurobasal (Life Technologies 10565-042 and Thermo Fisher Scientific 21103049), N-2 Supplement (Invitrogen,17502-048), B-27 Serum-Free Supplement (Gibco, 12587010), 2.5µg/l insulin (Thermo Fisher Scientific, 41400045), Glutamax (Thermo Fisher Scientific, 35050-079), MEM non-Essential amino acid solution (Sigma-Aldrich, M7145), 71.5µM 2-mercaptoethanol, Pen/strep (Gemini Bio-Products, 400-109) and 8 ng/μl recombinant human FGF-basic (FGF2, PeproTech, 100-18B)]. NPCs were passaged ones a week and NPCs for RNA-seq, ATAC-seq, ChIP-seq and Hi-C were used between passage 3-5.

extract_protocol:
RNA was extracted utilizing RNeasy Plus Mini Kit (Qiagen).
In situ Hi-C - Hi-C libraries were generated from 2 million iPSCs and NPCs using the Arima Hi-C kit (Arima Genomics, San Diego) following to the manufacturer’s instructions without any modifications. Briefly, the Arima Hi-C kit consists of 6 steps: (i) cells were crosslinked with 1% formaldehyde, (ii) DNA was digested using the Arima restriction enzyme cocktail within intact permeabilized nuclei, (iii) ends were filled and biotinylated, (iv) blunt ends were ligated, (v) ligated fragments were purified, sheared and a biotin pull down was performed using streptavidin, and (vi) adapters were ligated, barcoded and amplified using the Kappa Hyperprep Kit (Roche, KK8502).    ChIP-seq - Library preparation consists of 8 steps: (i) cells were crosslinked with 1% formaldehyde, (ii) chromatin was sheared (Covaris E220 Focused-ultrasonicator) after lysing cells, (iii) digested chromatin was incubated with 2ug of LMNB1 antibody (Abcam, ab8982), samples were also incubated without any antibody for input and Spike-in chromatin was incubated with Spike-in antibody (Active motif). (iv) same amount of Spike-in chromatin/antibody was added to each sample. (V) antibody-bound DNA/protein complexes and input samples were captured and washed using Protein G magnetic beads. (vi) cross-links were reversed and protein was digested using proteinase K. (vii) DNA was purified utilizing QIAquick PCR Purification Kit (Qiagen, 28104) (viii) libraries were prepared utilizing the Kappa Hyperprep Kit (Roche, KK8502).    ATAC-seq - Libraries were prepared as previously described (Buenrostro et al., 2015).    RNA-seq - 150 ng of RNA was used to prepare libraries using the Kapa mRNA hyperprep kit for standard RNA libraries (Roche, KK8540) on a TecanEvo 150s (Tecan).

treatment_protocol: NPCs were treated daily for 5 days with vehicle (DMSO) or a combination of 400nM of dasatinib and 15uM of quercetin

tag: cell type

value: Neural Progenitor Cells

tag: strain

value: Control

tag: chip antibody

tag: treatment

value: untreated

tag: cell line


title: MDA-MB231-Empty_NO Dox_120h_2 [G_173]

library_source: transcriptomic

molecule: polyA RNA

source_name: MDA-MB231-Empty_NO Dox_120h

tag: genotype/variation

value: NO Dox


title: MDA-MB231-CyclinE_Doxycycline_120h_2 [G_178]


title: MDA-MB231-Empty_Hydroxyurea_120h_2 [G_172]

value: Hydroxyurea


title: pluripotent NCRM1 cells replicate 2

city: Milan

first: Fabio

last: Marchiano

address: Via Alessandro Manzoni 56

country: Italy

institute: Humanitas

data_processing:
STAR (v2.7.3a) for reads mapping
featureCounts (v2.0.1) for reads count
DESeq2 (v 1.22.2) for gene expression analysis
Genome_build: ENSEMBL GRCh38 release 77
Supplementary_files_format_and_content: raw count matrix and excel tables containing the results of the differential expression analysis + normalized counts

molecule: total RNA

source_name: iPSC cell culture

extract_protocol:
RNA was isolated using NucleoSpin RNA kit (Macherey and Nagel, 740955) with on-column DNA digestion following the manufacturer’s protocol.
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples received were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: iPSC

tag: age + media

value: day 0


title: pluripotent NCRM1 cells replicate 3


title: pluripotent NCRM1 cells replicate 1


title: MDA-MB231-Myc_NO Dox_48h_2 [G_170]

source_name: MDA-MB231-Myc_NO Dox_48h


title: human fetal brown adipose tissue day 122

source_name: primary tissue

value: primary tissue

value: day 122


title: Neural Progenitor Cells Iso-E - HiC_rep2


title: skeletal muscle differentiation at day 15 (KCTiP) rep 3

value: day 15


title: Neural Progenitor Cells Iso-T - HiC_rep2

value: Down syndrome


title: brown adipocyte differentiation on day +40 replicate 2

value: day +40


title: skeletal muscle differentiation at day 15 (KCTiP) rep 2


title: human fetal brown adipose tissue day 115

value: day  115


title: MDA-MB231-Myc_NO Dox_120h_2 [G_179]

source_name: MDA-MB231-Myc_NO Dox_120h


title: Induced pluripotent stem cell Iso-T - HiC_rep2

source_name: Induced Pluripotent Stem Cells

value: Induced Pluripotent Stem Cells


title: MDA-MB231-Cdc25a_NO Dox_120h_2 [G_175]

source_name: MDA-MB231-Cdc25a_NO Dox_120h


title: MDA-MB231-CyclinE_NO Dox_120h_2 [G_177]

source_name: MDA-MB231-CyclinE_NO Dox_120h


title: skeletal muscle differentiation at day 15 (KCTiP) rep 1


title: Induced pluripotent stem cell Iso-T - HiC_rep1


title: MDA-MB231-Empty_Doxycycline _120h_2 [G_174]

source_name: MDA-MB231-Empty_Doxycycline _120h


title: MDA-MB231-Myc_NO Dox_120h_1 [G_161]


title: MDA-MB231-Empty_Hydroxyurea_48h_2 [G_163]


title: MDA-MB231-Cdc25a_Doxycycline_120h_2 [G_176]


title: MDA-MB231-Empty_Hydroxyurea_120h_1 [G_154]


title: MDA-MB231-Myc_NO Dox_48h_1 [G_152]


title: MDA-MB231-CyclinE_Doxycycline_48h_1 [G_151]


title: MDA-MB231-CyclinE_NO Dox_48h_1 [G_150]

source_name: MDA-MB231-CyclinE_NO Dox_48h


title: MDA-MB231-Myc_Doxycycline_48h_2 [G_171]


title: MDA-MB231-Cdc25a_Doxycycline_48h_1 [G_149]


title: MDA-MB231-CyclinE_NO Dox_120h_1 [G_159]


title: MDA-MB231-Empty_Doxycycline _48h_2 [G_165]

source_name: MDA-MB231-Empty_Doxycycline _48h


title: MDA-MB231-Cdc25a_NO Dox_48h_2 [G_166]

source_name: MDA-MB231-Cdc25a_NO Dox_48h


title: MDA-MB231-Empty_Hydroxyurea_48h_1 [G_145]


title: MDA-MB231-Cdc25a_NO Dox_120h_1 [G_157]


title: MDA-MB231-Empty_NO Dox_120h_1 [G_155]


title: MDA-MB231-Myc_Doxycycline_120h_1 [G_162]


title: MDA-MB231-Cdc25a_Doxycycline_120h_1 [G_158]


title: MDA-MB231-Cdc25a_Doxycycline_48h_2 [G_167]


title: GC_B_Doc_4_ATAC-seq

city: Melbourne

first: Andrea

last: Di Pietro

state: VIC

address: 305 Grattan Street

department: Cancer Immunology program

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie2 with the default settings.
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are normalized to reads per million (rpm) using R/Bioconductor and tab delimited text file containing rpm normalized data for all peaks and all samples as well as peak annotations and locations.

organism: Mus musculus

source_name: Germinal Center B cells

extract_protocol:
Fresh cell pellets were lysed and genomic DNA tagmented.
Tagmented DNA library was built using the Illumina Library Quantification Kit for BioRad iCycler (KAPA Biosystems)

treatment_protocol: C57BL/6 mice were either treated with LCMV WE or Docile for 14 days. Germinal Center B cells were sort-purified from total splenocytes.

tag: tissue

value: Germinal Center B cells

value: LCMV Docile

tag: assay

value: ATAC-Seq


title: MDA-MB231-Empty_NO Dox_48h_2 [G_164]

source_name: MDA-MB231-Empty_NO Dox_48h


title: MDA-MB231-CyclinE_Doxycycline_120h_1 [G_160]

value: Doxycycline


title: HCC1806-CyclinE_NO Dox_120h_2 [G_141]

source_name: HCC1806-CyclinE_NO Dox_120h


title: MDA-MB231-CyclinE_NO Dox_48h_2 [G_168]


title: MDA-MB231-Cdc25a_NO Dox_48h_1 [G_148]


title: GC_B_Doc_3_ATAC-seq


title: MDA-MB231-Empty_NO Dox_48h_1 [G_146]


title: HCC1806-Empty_Doxycycline _120h_2 [G_138]

source_name: HCC1806-Empty_Doxycycline _120h


title: MDA-MB231-CyclinE_Doxycycline_48h_2 [G_169]


title: GC_B_WE_4_ATAC-seq

value: LCMV WE


title: MDA-MB231-Myc_Doxycycline_48h_1 [G_153]


title: MDA-MB231-Empty_Doxycycline _120h_1 [G_156]


title: HCC1806-Myc_NO Dox_120h_2 [G_143]

source_name: HCC1806-Myc_NO Dox_120h


title: HCC1806-Empty_Hydroxyurea_120h_2 [G_136]


title: HCC1806-CyclinE_Doxycycline_120h_2 [G_142]


title: HCC1806-Myc_Doxycycline_48h_2 [G_135]


title: GC_B_WE_3_ATAC-seq


title: HCC1806-Cdc25a_Doxycycline_120h_2 [G_140]


title: HCC1806-Myc_Doxycycline_120h_2 [G_144]


title: HCC1806-CyclinE_NO Dox_48h_2 [G_132]

source_name: HCC1806-CyclinE_NO Dox_48h


title: HCC1806-Cdc25a_Doxycycline_48h_2 [G_131]


title: MDA-MB231-Empty_Doxycycline _48h_1 [G_147]


title: HCC1806-Cdc25a_NO Dox_48h_2 [G_130]

source_name: HCC1806-Cdc25a_NO Dox_48h


title: HCC1806-Empty_NO Dox_120h_2 [G_137]

source_name: HCC1806-Empty_NO Dox_120h


title: HCC1806-Cdc25a_NO Dox_120h_2 [G_139]

source_name: HCC1806-Cdc25a_NO Dox_120h


title: GC_B_Doc_1_ATAC-seq


title: HCC1806-Empty_NO Dox_48h_2 [G_128]

source_name: HCC1806-Empty_NO Dox_48h


title: YH6_ATGTCA_R1

city: Cincinnati

first: Yuhang

last: Zhang

state: OH

address: 231 Albert Sabin Way

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: cancer-associated fibroblast

growth_protocol: Fibroblasts were maintained in DMEM medium supplemented with 10% FBS 1X P/S.

extract_protocol:
Total RNA was extracted using PureLink RNA Mini Kit (Invitrogen 12183018A) following standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cancer-associated fibroblast

tag: genotype

value: beta-catenin -/-


title: GC_B_Doc_2_ATAC-seq


title: YH8_GTGAAA_R1

source_name: normal fibroblast

value: normal fibroblast

value: wild type


title: YH2_TTAGGC_R1


title: HCC1806-Myc_NO Dox_48h_2 [G_134]

source_name: HCC1806-Myc_NO Dox_48h

value: NO Dox


title: GC_B_WE_2_ATAC-seq


title: GC_B_WE_1_ATAC-seq


title: YH1_CGATGT_R1


title: HCC1806-CyclinE_Doxycycline_48h_2 [G_133]


title: HCC1806-Cdc25a_NO Dox_120h_1 [G_121]


title: HCC1806-Empty_NO Dox_120h_1 [G_119]


title: HCC1806-Empty_Doxycycline _120h_1 [G_120]


title: HCC1806-Empty_Doxycycline _48h_2 [G_129]

source_name: HCC1806-Empty_Doxycycline _48h


title: HCC1806-Empty_Hydroxyurea_120h_1 [G_118]

value: Hydroxyurea


title: YH9_GAGTGG_R1


title: YH4_AGTCAA_R1


title: YH7_CCGTCC_R1


title: HCC1806-Empty_Hydroxyurea_48h_2 [G_127]


title: HCC1806-Myc_Doxycycline_120h_1 [G_126]


title: YH5_AGTTCC_R1


title: HCC1806-CyclinE_Doxycycline_48h_1 [G_115]


title: Sorafenib-resistant_3

type: RNA

city: Suzhou

first: Yanmin

last: Xu

address: Suzhou industrial park, 199 renai road

department: Pathology Center and Department of Pathology

country: China

institute: Soochow University

description: Gene expression data from Sorafenib-resistant HCC xenografts

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

label: biotin

source_name: Sorafenib-resistant HCC xenografts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Sorefenib-resistant HCC cells lines were maintained in the continuous presence of 10 μM sorafenib, supplemented every 72 h.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Acquired resistance developed after long-term exposure to sorafenib over 6 months; for in vivo gavage experiments, prepared 60 mg/kg or 100 mg/kg solution for oral gavage and all animals were administered via gavage for at least 2 weeks,  the body weight loses >20%.

tag: sample type

value: HCC xenografts

value: Sorafenib resistant


title: Parental_3

description: Gene expression data from Parenta HCC xenografts

source_name: Parental HCC xenografts

value: parental


title: Parental_4


title: HCC1806-CyclinE_Doxycycline_120h_1 [G_124]


title: HCC1806-CyclinE_NO Dox_120h_1 [G_123]


title: HCC1806-Cdc25a_NO Dox_48h_1 [G_112]


title: HCC1806-Cdc25a_Doxycycline_120h_1 [G_122]


title: Parental_1


title: HCC1806-Myc_NO Dox_120h_1 [G_125]


title: BT549-Myc_Doxycycline_120h_2 [G_108]


title: 28dpl rep2

city: Detroit

first: Ashley

middle: Catherine

last: Kramer

state: Michigan

address: 540 E Canfield St

department: Ophthalmology, Visual and Anatomical Sciences

institute: Wayne State University School of Medicine

data_processing:
Reads were aligned to the zebrafish genome (Build dR10) using STAR and tabulated for each gene region using htseq-count.  Differential expression analysis was conducted using edgeR.
Genome_build: dR10
Supplementary_files_format_and_content: Excel spreadsheet containing raw counts for all genes in each sample on sheet one, all following sheets in the file contain pairwise comparison data for 6 samples in each timepoint compared to the dark-adapted 0hr control dataset.

organism: Danio rerio

source_name: retina

growth_protocol: Adult (6-9 months) albino (alb) zebrafish were used for all experiments. Unless otherwise noted (See treatment protocol), fish were maintained under a daily light cycle of 14 hours light (250 lux):10 hours dark at 28.5º C and fed a combination of flake food and brine shrimp. The Institutional Animal Care and Use Committee at Wayne State University approved all procedures used in this study (Protocol # 19-02-0970)

extract_protocol:
Retinas were surgically removed from euthanized animals and placed in pre-chilled eppendorf tubes. RNA was immediately isolated using the Direct-zol RNA Microprep kit (Zymo Research, Irvine CA, cat#R2062) according to manufacturer protocol and eluted in 15μL of RNAse-free water. RNA integrity and concentration were assesssed on a Nanodrop.
Sequencing libraries were generated from 250ng of total RNA using Lexogen's Quantseq 3' mRNA-Seq Library Prep Kit (Lexogen, Inc., Greenland, NH). Libraries were sequenced on a NovaSeq 6000 with a minimum of 5 million reads per sample.
3' mRNA-Seq

treatment_protocol: The light lesion protocol used for all samples in rows 34 and below is as follows: Adult zebrafish were dark adapted for 5 days in a dark box. 0hr dark-adapted controls were harvested at the conclusion of this adaptation (rows 28-33). Following dark adaptation, fish were subjected to a 30 minute intense light lesion using a Leica EL6000 halide bulb lightsource (~100,000 lux) before being transfered to a tank setup with 4 x 250W halogen lamps (total ~10,000 lux) directed at the tank for 3 days. All labelled timepoints are after onset of the light treatment. After 72 hours, remaining fish were transferred back onto the normal husbandry system and subjected to normal 14:10hr light:dark cycling for the remainder of the tissue collections.

value: albino

tag: tissue type

value: whole retina

value: 28 days after intense light lesion onset, fish back in normal light:dark conditions after 72hpl collection


title: 28dpl rep4


title: 28dpl rep1


title: Sorafenib-resistant_4


title: Sorafenib-resistant_5


title: 14dpl rep6

value: 14 days after intense light lesion onset, fish back in normal light:dark conditions after 72hpl collection


title: HCC1806-Myc_Doxycycline_48h_1 [G_117]


title: YH3_GATCAG_R1


title: 14dpl rep3


title: BT549-Cdc25a_Doxycycline_120h_2 [G_104]


title: Sorafenib-resistant_2


title: 14dpl rep1


title: HCC1806-CyclinE_NO Dox_48h_1 [G_114]


title: 28dpl rep6


title: HCC1806-Empty_Doxycycline _48h_1 [G_111]


title: BT549-Myc_NO Dox_48h_2 [G_98]

source_name: BT549-Myc_NO Dox_48h


title: 28dpl rep5


title: 10dpl rep3

value: 10 days after intense light lesion onset, fish back in normal light:dark conditions after 72hpl collection


title: HCC1806-Empty_Hydroxyurea_48h_1 [G_109]


title: Huh7-Sorafenib-resistant

description: Gene expression data from Huh7-Sorafenib-resistant cell lines

source_name: Huh7 Sorafenib-resistant HCC cells

value: HCC cell lines


title: Sorafenib-resistant_1


title: 10dpl rep4


title: HCC1806-Myc_NO Dox_48h_1 [G_116]


title: 28dpl rep3


title: Huh7-Parental

description: Gene expression data from Huh7-Parental cell lines

source_name: Huh7-Parental cell lines


title: HCC1806-Empty_NO Dox_48h_1 [G_110]


title: BT549-CyclinE_Doxycycline_120h_2 [G_106]

value: Doxycycline


title: BT549-CyclinE_NO Dox_48h_2 [G_96]

source_name: BT549-CyclinE_NO Dox_48h


title: 5dpl rep6

value: 5 days after intense light lesion onset, fish back in normal light:dark conditions after 72hpl collection


title: 14dpl rep5


title: BT549-CyclinE_Doxycycline_48h_2 [G_97]


title: BT549-CyclinE_NO Dox_120h_2 [G_105]

source_name: BT549-CyclinE_NO Dox_120h


title: 5dpl rep4


title: BT549-Myc_NO Dox_120h_2 [G_107]

source_name: BT549-Myc_NO Dox_120h


title: HCC1806-Cdc25a_Doxycycline_48h_1 [G_113]


title: BT549-Cdc25a_NO Dox_48h_2 [G_94]

source_name: BT549-Cdc25a_NO Dox_48h


title: 5dpl rep3


title: BT549-Cdc25a_NO Dox_120h_2 [G_103]

source_name: BT549-Cdc25a_NO Dox_120h


title: BT549-Empty_NO Dox_48h_2 [G_92]

source_name: BT549-Empty_NO Dox_48h


title: 5dpl rep2


title: BT549-Empty_NO Dox_120h_2 [G_101]

source_name: BT549-Empty_NO Dox_120h


title: 14dpl rep4


title: BT549-Cdc25a_Doxycycline_48h_2 [G_95]


title: 14dpl rep2


title: BT549-Empty_Hydroxyurea_48h_2 [G_91]


title: 72hpl rep6

value: 72 hours after intense light lesion onset


title: BT549-Empty_Doxycycline _120h_2 [G_102]

source_name: BT549-Empty_Doxycycline _120h


title: BT549-Myc_Doxycycline_48h_2 [G_99]


title: 10dpl rep5


title: 72hpl rep4


title: BT549-CyclinE_NO Dox_120h_1 [G_87]


title: 72hpl rep2


title: BT549-Empty_Hydroxyurea_120h_2 [G_100]


title: 5dpl rep1


title: BT549-Empty_Doxycycline _48h_2 [G_93]

source_name: BT549-Empty_Doxycycline _48h


title: BT549-Empty_NO Dox_120h_1 [G_83]


title: 10dpl rep2


title: 36hpl rep4

value: 36 hours after intense light lesion onset


title: 36hpl rep3


title: BT549-Myc_Doxycycline_48h_1 [G_81]


title: BT549-Myc_NO Dox_48h_1 [G_80]


title: BT549-CyclinE_Doxycycline_120h_1 [G_88]


title: 10dpl rep6


title: 36hpl rep2


title: BT549-Cdc25a_NO Dox_120h_1 [G_85]


title: BT549-Empty_Doxycycline _120h_1 [G_84]


title: BT549-Cdc25a_Doxycycline_120h_1 [G_86]


title: BT549-CyclinE_Doxycycline_48h_1 [G_79]


title: BT549-Myc_NO Dox_120h_1 [G_89]


title: BT549-Cdc25a_NO Dox_48h_1 [G_76]


title: 5dpl rep5


title: BT549-Empty_Hydroxyurea_120h_1 [G_82]


title: 10dpl rep1


title: BT549-Empty_Doxycycline _48h_1 [G_75]


title: BT549-Empty_NO Dox_48h_1 [G_74]


title: 24hpl rep2

value: 24 hours after intense light lesion onset


title: BT549-Myc_Doxycycline_120h_1 [G_90]


title: 24hpl rep3


title: 24hpl rep5


title: BT549-Empty_Hydroxyurea_48h_1 [G_73]


title: 72hpl rep5


title: RPE-1-(P53-/-)-CyclinE_Doxycycline_120h_2 [G_70]


title: 72hpl rep1


title: 0hr dark-adapted control rep5

value: housed in dark-box for 5 days


title: 72hpl rep3


title: 24hpl rep6


title: RPE-1-(P53-/-)-CyclinE_NO Dox_120h_2 [G_69]

source_name: RPE-1-(P53-/-)-CyclinE_NO Dox_120h

value: NO Dox


title: 24hpl rep4


title: 0hr dark-adapted control rep4


title: BT549-CyclinE_NO Dox_48h_1 [G_78]


title: 36hpl rep6


title: 0hr dark-adapted control rep3


title: AUTS2_mBrain_ChIPseq [re-analysis]

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

data_processing:
For ChIP-Seq data processing, reads were aligned to the mouse reference genome mm10 and dm6 for spike-in samples, using Bowtie2 (v2.4.1) with default parameters. Reads of quality score less than 30 were removed using samtools (v1.9) and PCR duplicates were removed using picard (v2.18.11). Regions in mm10 genome blacklist was removed using bedtools (v2.27.1) and bigwig files were generated using deepTools (v3.2.1) and parameters: --binSize 50 --normalizeUsing RPKM --ignoreDuplicates  --ignoreForNormalization chrX --extendReads 250 for visualization in IGV. Peaks were called using MACS2 (v2.1.1) with parameters: -g mm --keep-dup 1 --nomodel --extsize 300. Motif discovery was performed using HOMER (v4.10) with default parameters. For visualization of ChIP-seq, uniquely aligned reads were normalized using dm6 spike-in. Heatmaps were performed using the functions computeMatrix followed by plotHeatmap and plotProfile from deepTools (v3.2.1).
For RNA-Seq data processing, reads were aligned to the mouse reference genome mm10 using STAR (v2.6.1d) with parameters: --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 1 --outSAMstrandField intronMotif  --outSAMmapqUnique 60 --twopassMode Basic --outSJfilterReads Unique --outFilterIntronMotifs RemoveNoncanonical. Gene counts were calculated using featureCounts (v1.6.3) with parameters: -p, -s 2, -t exon, and RefSeq mm10 annotation downloaded from GENCODE. The output gene count tables were used as input into DeSeq2 for normalization and differential expression analysis.
For scRNA-Seq data processing, raw non-demultiplexed fastq files were processed using zUMIs (v2.9.4) with STAR (v2.7.3a) to generate expression profiles for both the 5′ ends containing UMIs as well as combined full-length and UMI data. The parameters: find_pattern: ATTGCGCAATG, UMI (12-19), cDNA (23-50) was specified for Read 1. The UMI count table containing both intron and exon reads was used by Seurat for downstream analysis. Cells with more than 3000 genes detected and less than 5% of reads mapping to mitochondrial genome were retained. Data were normalized (scTransform) and used for principal component analysis dimensionality reduction, followed by louvain clustering and UMAP dimensionality reduction. Differential gene expression analysis between defined cell clusters was performed using R package presto.
Genome_build: mm10 and dm6
Supplementary_files_format_and_content: Bigwig files generated by deepTools (v3.2.1) are RPKM normalized track files; Narrowpeak files generated by MACS2 (v2.1.1) are peak files; featurecount.txt files generated by featureCounts (v1.6.3) are gene counts files. RDS files for scRNA-Seq are gene-cell matrix generated by zUMIs (v2.9.4) and Seurat object respectively.

source_name: brain

extract_protocol:
For ChIP-seq in mouse brain, the whole brains were homogenized with a glass douncing homogenizer. The cell homogenate was fixed with 1% paraformaldehyde for eight min at room temperature and quenched with 0.125 M glycine for five min at room temperature, followed by centrifugation through a 29% iodixanol cushion. The nuclei pellet was resuspended and sonicated using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Sepharose, chromatin was incubated with antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with the same BSA-blocked protein G beads.For ChIP-seq in 393T-REx cells, cells were crosslinked with 1% formaldehyde for eight min at room temperature and the nuclei were then isolated. As described above, following sonication and pre-clearing, chromatin IP was performed to isolate associated DNA
For ChIP-seq library construction, 5-10 ng of DNA extracted from the chromatin immunocomplexes. Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 350±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530)

tag: developmental stage

value: Postnatal Day 1

tag: antibody

value: AUTS2 (house made)


title: 24hpl rep1


title: RPE-1-(P53-/-)-Myc_Doxycycline_120h_2 [G_72]


title: 36hpl rep1


title: RPE-1-(P53-/-)-Cdc25a_NO Dox_120h_2 [G_67]


title: BT549-Cdc25a_Doxycycline_48h_1 [G_77]


title: 36hpl rep5


title: RNA_NPC_Day8_CBX7_KO_Rep2

city: Boston

first: Robert

last: Kingston

address: 185 Cambridge Street, 7th Floor

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Adapter sequences were removed from reads usinng Cutadapt v.1.14 with "--minimumLength 30"
Reads were aligned to the mm10 genome using STAR v2.7.0
Reads in gene exons were counted using featureCounts v1.6.3
Gene annotations were obtained from ncbi refseq
EdgeR was used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.4

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells were formed as described in Bibel et al., 2007 (Nature Protocols). In brief, embryonic stem cells were de-MEFed and grown in suspension for 4 days without LIF to form cellular aggregates. After 4 days, retinoic acid was added to a final concentration of 5uM for neural differentiation. NPCs were collected for analysis on days 6 and 8 of differentiation.

extract_protocol:
RNA was isolated from pelleted cells using the PureLink RNA Mini Kit (Invitrogen) according to manufacturer's instructions. Samples were treated with DNase using the TURBO DNA-free Kit (Invitrogen). rRNA was depleted using the NEBNext rRNA Depletion Kit, and cDNA was generated using the NEBNext Ultra II Directional RNA First and Second Strand Synthesis Modules (New England Biolabs).
Libraries were prepared as described in Bowman et al., 2013 (BMC Genomics). In brief, this protocol includes end repair, A-tailing, adapter ligation, and real-time PCR amplification, with SPRI cleanup of samples between each step.

value: J1 cells

value: CBX7 KO

tag: age

value: 8 days


title: RNA_NPC_Day6_CBX7_KO_Rep3

value: 6 days


title: RPE-1-(P53-/-)-Myc_NO Dox_120h_2 [G_71]


title: naïve control rep6

value: albino

value: whole retina

value: no treatment, normal light:dark conditions (14:10hrs)


title: naïve control rep5


title: RNA_NPC_Day8_CBX7_KO_Rep3


title: B6_H3K4me3_ChIPSeq Rep 2 (re-analysis)

city: Bar Harbor

first: Natalie

middle: R

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
H3K4me3 ChIP-seq, wild-type B6 mice
H3K4me3Peaks_B6.bed
H3K4me3_H3K36me3Peaks_B6.bed

data_processing:
Single-end ChIP-Seq reads were trimmed with Trimmomatic and aligned to the mm10 genome assembly using BWA v0.7.9a
ChIP-Seq reads were filtered to remove duplicates and to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph, bed

source_name: spermatocytes

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Nuclei were fixed with 1% formaldehyde, and chromatin was fragmented by Mnase digestion. Cross-links were reversed and chromatin eluted by incubation at 68 degrees Celsius. After high-speed spin soluble chromatin was removed and used for ChIP with anti-H3K4me3.
Libraries were prepared for sequencing using standard Illumina protocols.

value: spermatocytes

value: 14 days post-partum


title: B6_H3K4me3_ChIPSeq Rep 1 (re-analysis)


title: RNA_NPC_Day0_CBX7_KO_Rep2

source_name: Embryonic stem cells

value: 0 days


title: 0hr dark-adapted control rep6

source_name: retina


title: RNA_NPC_Day8_CBX7_KO_Rep1


title: naïve control rep4


title: 0hr dark-adapted control rep2


title: RPE-1-(P53-/-)-Myc_Doxycycline_48h_2 [G_63]

value: Doxycycline


title: RNA_NPC_Day0_CBX7_KO_Rep3


title: RPE-1 (P53-/-)-Empty_NO Dox_120h_2 [G_65]

source_name: RPE-1 (P53-/-)-Empty_NO Dox_120h


title: RNA_NPC_Day6_CBX7_KO_Rep2


title: RNA_NPC_Day6_CBX7_KO_Rep1


title: RNA_NPC_Day8_mCaPS_Rep3


title: naïve control rep2


title: RPE-1-(P53-/-)-Myc_NO Dox_48h_2 [G_62]


title: RNA_NPC_Day0_CBX7_KO_Rep1


title: 0hr dark-adapted control rep1


title: RPE-1-(P53-/-)-Cdc25a_Doxycycline_120h_2 [G_68]


title: RPE-1 (P53-/-)-Empty_Hydroxyurea_120h_2 [G_64]

source_name: RPE-1 (P53-/-)-Empty_Hydroxyurea_120h

value: Hydroxyurea


title: RNA_NPC_Day8_mCaPS_Rep2


title: RNA_NPC_Day6_mCaPS_Rep3


title: RNA_NPC_Day6_mCaPS_Rep1


title: RNA_NPC_Day0_mCaPS_Rep3


title: RPE-1-(P53-/-)-CyclinE_Doxycycline_48h_2 [G_61]


title: RNA_NPC_Day8_CaPS_Rep3


title: RPE-1-(P53-/-)-Cdc25a_NO Dox_48h_2 [G_58]


title: RNA_NPC_Day8_CaPS_Rep2


title: RPE-1 (P53-/-)-Empty_Doxycycline _120h_2 [G_66]

source_name: RPE-1 (P53-/-)-Empty_Doxycycline _120h


title: RPE-1 (P53-/-)-Empty_Doxycycline _48h_2 [G_57]

source_name: RPE-1 (P53-/-)-Empty_Doxycycline _48h


title: naïve control rep3


title: RNA_NPC_Day6_mCaPS_Rep2


title: naïve control rep1


title: RNA_NPC_Day6_CaPS_Rep3


title: RNA_NPC_Day8_CaPS_Rep1


title: RPE-1 (P53-/-)-Empty_NO Dox_48h_2 [G_56]

source_name: RPE-1 (P53-/-)-Empty_NO Dox_48h


title: RNA_NPC_Day6_CaPS_Rep2


title: RNA_NPC_Day8_mCaPS_Rep1


title: RNA_NPC_Day6_CaPS_Rep1


title: RNA_NPC_Day0_mCaPS_Rep1


title: RPE-1-(P53-/-)-Cdc25a_Doxycycline_48h_2 [G_59]


title: RPE-1-(P53-/-)-Myc_Doxycycline_120h_1 [G_54]


title: RNA_NPC_Day0_mCaPS_Rep2


title: RPE-1-(P53-/-)-CyclinE_NO Dox_48h_2 [G_60]

source_name: RPE-1-(P53-/-)-CyclinE_NO Dox_48h


title: RNA_NPC_Day0_CaPS_Rep3


title: Stab2KO LSECs, replicate 1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from Stab2KO LSECs

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: C57BL/6J LSECs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: RNA was extracted from primary murine LSECs immediately after isolation

extract_protocol: RNA was extracted from primary endothelial cells using E.Z.N.A. TM Total-RNA-Kit I (OMEGA Biotec, Norcross, GA, USA).

treatment_protocol: Murine LSECs from different groups were isolated and purified using CD146 (LSEC) MicroBeads. Purity was assessed using FACS. Three mice per genotype were pooled per biological replicate in Microarray analyis.

value: liver sinusoidal endothelial cells (LSECs)


title: RNA_NPC_Day0_CaPS_Rep2


title: Stab1KO LSECs, replicate 1

description: Gene expression data from Stab1KO LSECs


title: RPE-1-(P53-/-)-CyclinE_Doxycycline_120h_1 [G_52]


title: RNA_NPC_Day8_WT_Rep2

value: WT


title: RNA_NPC_Day8_WT_Rep3


title: RNA_NPC_Day6_WT_Rep2


title: RPE-1 (P53-/-)-Empty_Hydroxyurea_48h_2 [G_55]

source_name: RPE-1 (P53-/-)-Empty_Hydroxyurea_48h


title: RPE-1-(P53-/-)-CyclinE_NO Dox_120h_1 [G_51]

value: NO Dox


title: RNA_NPC_Day6_WT_Rep1


title: RNA_NPC_Day6_WT_Rep3


title: RNA_NPC_Day0_WT_Rep3


title: RNA_NPC_Day8_WT_Rep1


title: Stab1KO LSECs, replicate 2

description: Gene expression data from Stab1KO LSECs


title: RNA_NPC_Day0_WT_Rep2


title: RNA_NPC_Day0_CaPS_Rep1


title: RPE-1-(P53-/-)-Cdc25a_Doxycycline_120h_1 [G_50]


title: Stab2KO LSECs, replicate 3

description: Gene expression data from Stab2KO LSECs


title: RNA_EB_Day10_CBX7_KO_Rep2

source_name: Embryoid bodies

growth_protocol: Embryonic stem cells (ESCs) were cultured on 1% gelatin with a feeder layer of MEFs in DMEM supplemented with 15% Hyclone FBS (GE Healthcare), GlutaMax (Invitrogen), penicillin/streptomycin, non-essential amino acids, 1000U/mL LIF, and 2-betamercatoethanol. To form embryoid bodies (EBs), ESCs were de-MEFed and resuspended in differentiation media (IMDM supplemented with 15% HyClone FBS , GlutaMax, and penicillin/streptomycin) at a concentration of 8,400 cells/mL. Drops were set at 50uL per drop on the bottom of a non-adherent tissue culture plate, and plates were storeed upside down. After 4 days, EBs were pooled together and grown in suspension in non-adherent plates, changing media every day. EBs were collected for analysis on days 6 and 10 of differentiation.

value: 10 days


title: RNA_EB_Day10_CBX7_KO_Rep3


title: RPE-1-(P53-/-)-Cdc25a_NO Dox_120h_1 [G_49]


title: Stab1KO LSECs, replicate 3

description: Gene expression data from Stab1KO LSECs


title: RPE-1 (P53-/-)-Empty_Doxycycline _120h_1 [G_48]


title: Stab2KO LSECs, replicate 2

description: Gene expression data from Stab2KO LSECs


title: Wildtype LSECs, replicate 2

description: Gene expression data from Wildtype LSECs

value: Ctrl


title: RNA_NPC_Day0_WT_Rep1

value: J1 cells


title: Sperm-Stress-F2-4

city: Shanghai

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

description: WGBS

data_processing:
The raw data derived from both WGBS and scWGBS were filtered to obtain clean reads. Adaptor-polluted reads, low-quality reads, and reads with over 10% Ns were removed. Clean reads were mapped to the reference genome (mm10, UCSC) by Bismark (ver. 2.2.3), and only uniquely mapped reads were retained. Cytosines were considered to be methylated based on the binomial test followed by adjusting the false discovery rate using the Benjamini-Hochberg method. The methylation level of a single cytosine was calculated as mC/(mC+umC), where mC was the number of methylated reads and umC was the number of the unmethylated reads. Reads from different strand were merged for further analysis.
DMRs were identified using Bioconductor package DSS (v2.14.0) which uses biological replicates and information from CpG sites across the genome to stabilize the estimation of the dispersion parameters59. The core of DSS is a procedure based on Bayesian hierarchical model to estimate and shrink CpG site-specific dispersions, then conduct Wald tests for detecting differential methylation. Only CpGs that were covered at least fivefold were considered for a given comparison.
We first performed statistical tests of differentially methylated loci using DMLtest function (smoothing = TRUE, smoothing.span=500) in DSS; the results were then used to detect differentially methylated cytosines (DMCs) with the parameters: absolute delta beta value (|Δβ|DMC) > 0.1, p.threshold < 0.01 (the threshold for p-value here actually refers to local false discovery rate-FDR).
The DMCs were then merged into blocks if they both showed similar methylation patterns using callDMR function with the parameters: |Δβ|DMR > 0.1, the minimum length for a DMR ≥ 50 bp, the minimum number of CpG sites for DMR ≥ 4 and p.threshold (FDR) < 0.01. Merging nearby CpG sites (refer in particular to not differentially methylated CpG sites) into blocks can cause some regions with methylation difference smaller than theoretical value.
Thus, we further filtered out DMRs with standards: |Δβ|DMR ≥ 0.1 or variated more than 20% (as some of the regions changed from un-methylated/low-methylated to methylated/high-methylated. Although the |Δβ| value was small, their alterations were relatively large when compared to their original status). DMRs-related genes were then annotated using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: txt files about metylated reads and unmethylated reads in each CpG site

source_name: sperm

extract_protocol:
We randomly selected three mice from each generation of both the control group and stress group as three biological replicates. After semen quality assessment, their sperm were pelleted down by centrifugation at 500 g for 5 min and then incubated in somatic cell lysis buffer for 30 min on ice to eliminate contaminated somatic cells. Sperm samples were used only if their purity reached >99.5% and were evaluated by microscopy. Sperm DNA and small RNAs were simultaneously extracted using the All Prep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. It was noteworthy that the dithiothreitol (DTT, 40mM) was used to disturb the disulfide bonds of the sperm during the nucleic acid extraction process.The quality and concentrations of DNA were examined by a NanoDrop2000 (Thermo Fisher Scientific, Waltham, MA, USA).
DNA methylation patterns of the sperm samples were determined by WGBS, which has been widely used to measure the methylation status of whole genome at single-base resolution. The sequencing libraries of 18 sperm DNA samples were constructed using NEBNext Kit (NEB, U.S.) according to the manufacturer’s instructions. In brief, DNA were fragmented into 100–300 bp sections by sonication with a Diagenome sonicator. Then, they were subjected to end-repair, A-tailing and adaptor ligation. After size selection (200-300 bp) of the adaptor-ligated DNA by 2% gel electrophoresis, bisulfite conversion was performed using the EZ DNA methylation Gold Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions. Bisulfite treated DNA was then PCR amplified using ZymoTaq DNA Polymerase with 14-15 cycles. Bisulfite-converted libraries were sequenced with 2× 150 bp paired-end (PE150) reads on an Illumina HiSeq 4000 platform. The spiked-in lambda DNA was used to determine the bisulfite conversation rate.

value: sperm

value: untreated offspring-F2 obtained from treated father-F0

value: F1 male x DBA/2J female


title: RNA_EB_Day0_CBX7_KO_Rep2

value: CBX7 KO


title: RNA_EB_Day6_CBX7_KO_Rep2

value: 6 days


title: RNA_EB_Day6_CBX7_KO_Rep3


title: Wildtype LSECs, replicate 3


title: Stabilin-double-deficient LSECs, replicate 3

description: Gene expression data from Stabilin-double-deficient LSECs

value: Stab DKO


title: Wildtype LSECs, replicate 1


title: RPE-1-(P53-/-)-Myc_Doxycycline_48h_1 [G_45]


title: RNA_EB_Day10_mCaPS_Rep3


title: RNA_EB_Day10_CBX7_KO_Rep1


title: Stabilin-double-deficient LSECs, replicate 2


title: RNA_EB_Day10_mCaPS_Rep2


title: RPE-1-(P53-/-)-Myc_NO Dox_120h_1 [G_53]


title: RPE-1 (P53-/-)-Empty_NO Dox_120h_1 [G_47]


title: RNA_EB_Day6_CBX7_KO_Rep1


title: RPE-1 (P53-/-)-Empty_Hydroxyurea_120h_1 [G_46]


title: RNA_EB_Day0_CBX7_KO_Rep3


title: RNA_EB_Day0_CBX7_KO_Rep1


title: Sperm-Stress-F1-11

description: WGBS

value: untreated offspring-F1 obtained from treated father-F0

value: C57BL/6J-Pouf1gfp/gfp x DBA/2J female


title: Sperm-Stress-F2-9

description: WGBS


title: RNA_EB_Day6_mCaPS_Rep1


title: RPE-1-(P53-/-)-Myc_NO Dox_48h_1 [G_44]


title: RNA_EB_Day6_mCaPS_Rep3


title: RNA_EB_Day0_mCaPS_Rep2

value: 0 days


title: RNA_EB_Day10_mCaPS_Rep1


title: RNA_EB_Day10_CaPS_Rep3


title: RNA_EB_Day0_mCaPS_Rep1


title: RNA_EB_Day6_mCaPS_Rep2


title: RPE-1-(P53-/-)-CyclinE_NO Dox_48h_1 [G_42]


title: RNA_EB_Day10_CaPS_Rep2


title: RPE-1 (P53-/-)-Empty_Doxycycline _48h_1 [G_39]

value: Doxycycline


title: RPE-1-(P53-/-)-Cdc25a_Doxycycline_48h_1 [G_41]


title: RPE-1-(P53-/-)-Cdc25a_NO Dox_48h_1 [G_40]


title: Stabilin-double-deficient LSECs, replicate 1


title: Sperm-Stress-F1-10

description: WGBS


title: Sperm-Control-F2-14

description: WGBS

value: untreated offspring-F2


title: RNA_EB_Day0_mCaPS_Rep3


title: Sperm-Stress-F2-8

description: WGBS


title: Sperm-Stress-F1-7

description: WGBS


title: RPE-1 (P53-/-)-Empty_NO Dox_48h_1 [G_38]


title: Sperm-Stress-F0-3

description: WGBS

value: treated father-F0


title: RPE-1-(P53-/-)-CyclinE_Doxycycline_48h_1 [G_43]


title: RNA_EB_Day0_CaPS_Rep2


title: Sperm-Stress-F0-2

description: WGBS


title: RNA_EB_Day6_CaPS_Rep3


title: Sperm-Stress-F0-9

description: WGBS


title: RNA_EB_Day10_WT_Rep3

value: WT


title: RNA_EB_Day0_CaPS_Rep1


title: RPE-1-Myc_Doxycycline_120h_2 [G_36]


title: RNA_EB_Day6_CaPS_Rep1


title: RNA_EB_Day0_CaPS_Rep3


title: RNA_EB_Day10_CaPS_Rep1


title: RPE-1-Myc_NO Dox_120h_2 [G_35]

source_name: RPE-1-Myc_NO Dox_120h

value: NO Dox


title: RPE-1 (P53-/-)-Empty_Hydroxyurea_48h_1 [G_37]

value: Hydroxyurea


title: RNA_EB_Day6_WT_Rep3


title: RNA_EB_Day6_CaPS_Rep2


title: Sperm-Control-F1-12

description: WGBS

value: untreated offspring-F1


title: Sperm-Control-F2-10

description: WGBS


title: RNA_EB_Day6_WT_Rep1

value: J1 cells


title: Sperm-Control-F1-9

description: WGBS

value: sperm


title: Sperm-Control-F2-1

description: WGBS


title: RNA_EB_Day6_WT_Rep2


title: Sperm-Control-F1-3

description: WGBS


title: RNA_EB_Day10_WT_Rep2

value: 10 days


title: RPE-1-CyclinE_Doxycycline_120h_2 [G_34]


title: Sperm-Control-F0-5

description: WGBS

value: untreated father-F0


title: RPE-1-Cdc25a_Doxycycline_120h_2 [G_32]


title: RNA_EB_Day0_WT_Rep3


title: RNA_EB_Day0_WT_Rep2


title: RPE-1-CyclinE_NO Dox_120h_2 [G_33]

source_name: RPE-1-CyclinE_NO Dox_120h


title: Sperm-Control-F0-4

description: WGBS


title: RNA_EB_Day0_WT_Rep1


title: CaPS_EB10_RING1B_CUT&RUN_group2

data_processing:
Library strategy: CUT&RUN
Adapter sequences were removed from reads usinng Cutadapt v.1.14 with "--minimumLength 30"
Reads were aligned to the mm10 and dm6 genomes using Bowtie 2 v.2.3.4.3 with one mismatch permitted per seed, a maximum insert of 2kb, and the "--no-discordant" option specified
PCR duplicates were removed using Samtools v1.9
To normalize ChIP-Seq data, mm10 reads were randomly downsampled using Samtools. The downsampling factor reflected the total number of dm6 reads in the sample, and was corrected with the ratio of dm6:mm10 reads to account for variation in spike-in mixing.
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.4
Supplementary_files_format_and_content: Peak files were generated using Homer v4.10.4. Peaks were filtered to those within 10kb of their associated TSS, and to a minimum tag density that was determined by examination of IGV browser tracks.

extract_protocol:
CUT&RUN was performed as previously described in Skene et al., 2018 (Nat. Protoc.), in native conditions and with modifications for high-calcium/low-salt condititions as described in Meers et al., 2019 (eLife).
Libraries were prepared as described in Bowman et al., 2013 (BMC Genomics). In brief, this protocol includes end repair, A-tailing, adapter ligation, and real-time PCR amplification, with SPRI cleanup of samples between each step.


title: CaPS_EB10_IgG_CUT&RUN_group2


title: RNA_EB_Day10_WT_Rep1


title: Sperm-Control-F0-3

description: WGBS


title: RPE-1-Cdc25a_NO Dox_120h_2 [G_31]

source_name: RPE-1-Cdc25a_NO Dox_120h


title: WT_EB10_RING1B_CUT&RUN_group2


title: WT_EB10_IgG_CUT&RUN_group2


title: RPE-1-Empty_Doxycycline _120h_2 [G_30]

source_name: RPE-1-Empty_Doxycycline _120h


title: 9_RB_10-24-18_S56

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

data_processing:
Data is mapping to genome UCSC mm10 using STAR software
counts data are extract using featureCounts
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Gene counts in txt file

source_name: Bone marrow mononuclear cells

extract_protocol:
Total RNA was extrated and purified with Quiagen Rneasy Plus Micro Kit Cat # 74034
Clontech SMART-Seqv4 Ultra Low Input RNA Kit (Cat#634889), 24rxns; Illumina Nextera XT DNA Lib Kit. Dual Index

treatment_protocol: Primary Shp2 E76K mice were treated with ACP196 (BTKi) and ACP319 (P13K-P110δi) individually and in combination of the both inhibitors for three week along with Vehicle treated group. After treatment period, experimental mice were euthanized, bone marrow mononuclear cells were subjected to RNASeq analysis.

tag: genetic condition

value: Shp2 E76K mice

value: PI3K-P110δ (ACP319) inhibitor treated

value: bone marrow mononuclear cells


title: 8_RB_10-24-18_S55


title: CaPS_ESC_H3K27me3_CUT&RUN_group1

source_name: Embryonic stem cells


title: RPE-1-Empty_NO Dox_120h_2 [G_29]

source_name: RPE-1-Empty_NO Dox_120h

tag: time point


title: 9_RB_10-24-18_S43

tag: cell type


title: WT_NPC8_RING1B_ChIP_group4

data_processing:
Adapter sequences were removed from reads usinng Cutadapt v.1.14 with "--minimumLength 30"
Reads were aligned to the mm10 and dm6 genomes using Bowtie 2 v.2.3.4.3 with one mismatch permitted per seed, a maximum insert of 2kb, and the "--no-discordant" option specified
PCR duplicates were removed using Samtools v1.9
To normalize ChIP-Seq data, mm10 reads were randomly downsampled using Samtools. The downsampling factor reflected the total number of dm6 reads in the sample, and was corrected with the ratio of dm6:mm10 reads to account for variation in spike-in mixing.
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.4
Supplementary_files_format_and_content: Peak files were generated using Homer v4.10.4. Peaks were filtered to those within 10kb of their associated TSS, and to a minimum tag density that was determined by examination of IGV browser tracks.

source_name: Neural progenitor cells

extract_protocol:
Ten to twenty million harvested cells were crosslinked in 1% formaldehyde-PBS for 10 minutes at room temperature. Crosslinking was quenched with glycine, and cells were pelleted by centrifugation at 4°C and washed once in cold PBS. Cells were resuspended in cold lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA pH 8.0, 1% SDS, PIC, 1mM DTT) and incubated for 10 minutes on ice prior to sonication using a QSonica Q800R3 Sonicator. Insoluble chromatin was pelleted by centrifugation, and supernatant was diluted 1:10 with IP Dilution Buffer (20mM Tris-HCl pH 8.1, 150mM NaCl, 2mM EDTA pH 8.0, 0.1% Triton X-100, PIC, 1mM DTT). Sonicated Drosophila chromatin was added at a known ratio to experimental chromatin to serve as a spike-in as previously described (Egan et al., 2016). Triton X-100 was added to a final concentration of 1%, input was collected and diluted to 200mL, and chromatin was added to Protein A Dyanbeads (Invitrogen) that had been previously incubated with experimental and spike-in antibodies. Samples were rotated at 4°C overnight. Beads were washed with IP Dilution Buffer with 1% Triton X-100, followed by Wash Buffer A (50mM HEPES pH 7.9, 500mM NaCl, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, PIC, DTT), followed by Wash Buffer B (20mM Tris-HCl pH 8.0, 250mM LiCl, 1mM EDTA pH 8.0, 0.1% Na-deoxycholate, 1% Igepal, PIC, DTT), followed by a quick TE wash. Beads were incubated at 37°C in 200mL Extraction Buffer (1% SDS, 0.1M NaHCO3) for 15 minutes with shaking. Supernatant was collected, and 12mL 2M TrisHCl, 2mL RNase A (500mg/mL, Roche), and 12mL 5M NaCl were added to ChIP samples and inputs. Crosslinks were reversed overnight at 65°C, followed by 1 hour incubation at 55°C with Proteinase K. DNA was isolated by phenol:chloroform extraction and ethanol precipitation.
Libraries were prepared as described in Bowman et al., 2013 (BMC Genomics). In brief, this protocol includes end repair, A-tailing, adapter ligation, and real-time PCR amplification, with SPRI cleanup of samples between each step.

value: 8 days


title: WT_ESC_IgG_CUT&RUN_group1


title: 7_RB_10-24-18_S54


title: RPE-1-Empty_Hydroxyurea_120h_2 [G_28]


title: CaPS_NPC8_input_TF_group4


title: 8_RB_10-24-18_S42


title: WT_ESC_H3K27me3_CUT&RUN_group1


title: CaPS_NPC8_RING1B_ChIP_group4


title: CaPS_ESC_IgG_CUT&RUN_group1


title: 7_RB_10-24-18_S41


title: RPE-1-Myc_Doxycycline_48h_2 [G_27]


title: 6_RB_10-30-18_S53

value: BTK (ACP196) inhibitor treated


title: KO_ESC_CBX7_ChIP_group3

value: KO

value: 0 days


title: RPE-1-Myc_NO Dox_48h_2 [G_26]

source_name: RPE-1-Myc_NO Dox_48h


title: KO_ESC_RING1B_ChIP_group3


title: CaPS_NPC8_RING1B_ChIP_group3


title: RPE-1-Cdc25a_Doxycycline_48h_2 [G_23]

value: Doxycycline


title: RPE-1-CyclinE_NO Dox_48h_2 [G_24]

source_name: RPE-1-CyclinE_NO Dox_48h


title: CaPS_NPC6_RING1B_ChIP_group3

value: 6 days


title: 6_RB_10-30-18_S40


title: KO_ESC_input_TF_group3


title: RPE-1-CyclinE_Doxycycline_48h_2 [G_25]


title: CaPS_NPC6_input_TF_group3


title: CaPS_NPC8_input_TF_group3


title: WT_NPC8_input_TF_group4

value: WT


title: RPE-1-Cdc25a_NO Dox_48h_2 [G_22]

source_name: RPE-1-Cdc25a_NO Dox_48h

value: NO Dox


title: CaPS_ESC_CBX7_ChIP_group3


title: CaPS_ESC_input_TF_group3


title: 5_RB_10-24-18_S39


title: RPE-1-Empty_Hydroxyurea_48h_2 [G_19]

value: Hydroxyurea


title: 4_RB_10-24-18_S51


title: WT_NPC8_input_TF_group3


title: CaPS_ESC_RING1B_ChIP_group3


title: RPE-1-Empty_Doxycycline _48h_2 [G_21]

source_name: RPE-1-Empty_Doxycycline _48h


title: 5_RB_10-24-18_S52


title: WT_NPC6_input_TF_group3


title: 3_RB_10-24-18_S37

value: Vehicle treated


title: RPE-1-Myc_NO Dox_120h_1 [G_17]


title: WT_ESC_CBX7_ChIP_group3

value: J1 cells


title: 2_RB_10-24-18_S49


title: WT_ESC_input_TF_group3


title: WT_NPC6_RING1B_ChIP_group3


title: CaPS_ESC_RING1B_ChIP_group2


title: RPE-1-CyclinE_Doxycycline_120h_1 [G_16]


title: 2_RB_10-24-18_S36


title: RPE-1-Myc_Doxycycline_120h_1 [G_18]


title: 12_RB_10-24-18_S59

value: Combo treated


title: NeuN- PacBio REP1

city: New York

first: Sandhya

last: Chandrasekaran

state: NY

address: 1470 Madison Avenue, 9-202, Hess Building

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Hi-C (.hic files):
Quality control was performed using the ‘pre-truncation method’ with HiC-Pro(v2.9).
Libraries were mapped to the Mus musculus reference genome (GRCm38.p5_M13) using bowtie2.2, and combined by matching sex and genotype.
HiC-Pro results were piped to Juicer(v1.14.8) to produce .hic format files using the parser tool ‘hicpro2juicebox’.
Resulting files were then processed into final KR matrix-balanced normalized contact maps with Juicebox.
Genome_build: GRCm38.p5_M13 or mm10
Supplementary_files_format_and_content: .hic files for Juicebox visualization and subcompartment calling
Hi-C (HOMER interactions):
Each read of the paired-end libraries was aligned independently using bwa-mem(v0.7.15), permitting split mapping to the GRCm38.p5_M13 reference annotation.
After mapping, forward and reverse reads were directly supplied to Homer(v4.8) for processing by first, merging the paired-end reads and later, filtering out self-ligation (spikes and continuous) artifacts.
Files were normalized based on sequencing depth and distance between loci, creating a background model necessary for calculating significant pairwise interactions.
Trans- interactions (1Mb resolution) were similarly calculated, but for significant interactions for loci >200Mbp apart (-minDist 200000000) to disregard intra-chromosomal interactions.
Supplementary_files_format_and_content: HOMER interactions (1Mb resolution, p<1e-50)
differential bins file (NeuN+ vs. NeuN-):
Raw .fastq reads were aligned to the Mus musculus reference genome (mm10) using bowtie2.
Only concordant reads were compressed into aligned .bam files, then sorted and indexed using the samtools/0.1.19 suite.
Following PCR duplicate removal, files were converted into .bed files using bedtools(v2.29.2)for further processing.
Differential analysis using diffReps was performed (1kb resolution) at a statistical significance threshold of p<0.001, for NeuN+ (tx) vs. NeuN- (ctrl).
Significantly called regions (spanning a length of 1kb or more) were labeled as NeuN+ enriched or NeuN- enriched according to their log2FoldChange values.
Supplementary_files_format_and_content: differential bins file (NeuN+ vs. NeuN-)
.txt files with BLAST scores for de novo alignments to the IAP-masked genome or IAPEzi:
Bioinformatics processing was performed with SMRT Link v5.1.0, run with default parameters, unless otherwise indicated.
Files were first demultiplexed with lima and circular consensus sequences (CCS) were generated with ccs for filtered sequences with matching paired-end adapters.
CCS reads were then mapped to an IAPEzi consensus sequence (dfam.org) using pbalign.
Passing reads were subsequently mapped to the mouse reference genes using bwa split mapping and filtered based on mapping score (=60).
Reads were then assigned as autosomal IAPEzi or autosomal non-IAPEzi IAP using the GenomicRanges subsetByOverlaps() function (R(v3.6.0)).
The other reads, those not mapping to IAPs denoted in the reference genome, were then blasted against the IAPEzi consensus sequence and IAP masked reference genome in parallel; reads with higher bit scores for the IAPEzi blast than the reference genome were defined as de novo. Full-length de novo insertions were defined as fragments representing >5833bp (0.9*6481).
Supplementary_files_format_and_content: .txt files with BLAST scores for de novo alignments to the IAP-masked genome or IAPEzi
.txt files with transcript alignments to genes and repeats:
Read pairs were aligned to the Mus musculus mouse reference genome (mm10) with Tophat2 short-read aligner.
Reads were counted using HTSeq against the Gencode vM4 Mouse annotation.
Genes were filtered based on the criteria that all replicates in either condition must have at least 5 reads per gene.
On the resulting filtered transcripts, a pairwise differential analysis between Setdb1 conditional mutant vs. control cortex was performed using the voomlimma R package, which converts counts into precision weighted log2 counts per million and determines differentially expressed genes using a linear model.
Significantly differentially expressed genes were identified using a cutoff of Benjamini-Hochberg adjusted p-value less than 0.05.
Discordant pairs were extracted from aligned .bam files using samtools with the following command: samtools view –b –F 2 and reads identifiable with specific flags were quantified and categorized.
Supplementary_files_format_and_content: .txt files with transcript alignments to genes and repeats
RNA-seq:
FastQC was first used for quality control analysis, and trim-galore was used to remove low-quality reads.
Paired-end cleaned data was aligned to reference genome (M. musculus, UCSC mm10) using Tophat2 v2.1.1.
Samtools v1.9 was used to sort and build the alignment files index.
FeatureCounts v1.6.3 from subread package was used to get gene expression level counts by determining the number of reads mapped to gene exons.
Differential analysis was generated by DESeq2.
Significant genes (log2FoldChange > 0.5, Padj < 0.05) were extracted for Gene Ontology Enrichment Analysis by using ShinyGO v0.61 (http://bioinformatics.sdstate.edu/go/).
Deeptools was used to generate normalized bigwig and visualized on IGV.
Supplementary_files_format_and_content: .txt and .xls counts files
peaks files:
FastQC was first used for quality control analysis, and trim-galore was used to remove low-quality reads.
Paired-end cleaned data was then aligned to reference genome (M. musculus, UCSC mm10) using Bowtie2 v2.3.4.3.
Samtools v1.9 was used to sort and build the alignment files index after removing duplications.
MACS2 was used for peak calling (--shift -100 --extsize 200 --nomodel).
Diffbind was used to generated differential change peaks. R packages “ChIPseeker”, “clusterProfiler” “org.Mm.eg.db” and “TxDb.Mmusculus.UCSC.mm10.knownGene” were used for peak annotation.
Significant differential peaks that are located on gene promoters were extracted to generate Gene Ontology Enrichment Analysis by ShinyGO v0.61 (http://bioinformatics.sdstate.edu/go/).
Deeptools was used to generate normalized bigwig and visualized on IGV.
Supplementary_files_format_and_content: .xls peaks files

source_name: NeuN- PacBio

extract_protocol:
Hi-C (Jiang, et. al.): Cortical tissue was prepped for fluorescence activated nuclear sorting (FANS) as follows. Briefly, the dissected tissue was homogenized in a hypotonic lysis solution and fixed in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched with 125 mM glycine. The nuclei were then purified by centrifugation at 4000xg and resuspended in a 1:1 solution of the hypotonic lysis solution and a 1.8M sucrose solution prior to re-centrifugation at 4000xg to isolate out cortical nuclei. The pellet was then resuspended in Dulbecco’s phosphate buffered saline (DPBS) containing 0.1% BSA and 1:1000 anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Samples were incubated for 45 minutes while rotation and protected from light at 4C. DAPI (Invitrogen) was added immediately before sorting to label all nuclei.
ChIP-seq: Cortical tissue was prepped for fluorescence activated nuclear sorting (FANS) as follows. Briefly, the dissected tissue was homogenized in a hypotonic lysis solution and fixed in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched with 125 mM glycine. The nuclei were then purified by centrifugation at 4000xg and resuspended in a 1:1 solution of the hypotonic lysis solution and a 1.8M sucrose solution prior to re-centrifugation at 4000xg to isolate out cortical nuclei. The pellet was then resuspended in Dulbecco’s phosphate buffered saline (DPBS) containing 0.1% BSA and 1:1000 anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Samples were incubated for 45 minutes while rotation and protected from light at 4C. DAPI (Invitrogen) was added immediately before sorting to label all nuclei.
Hi-C (Arima): Cortical tissue was prepped for fluorescence activated nuclear sorting (FANS) as follows. Briefly, the dissected tissue was homogenized in a hypotonic lysis solution and fixed in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched with 125 mM glycine. The nuclei were then purified by centrifugation at 4000xg and resuspended in a 1:1 solution of the hypotonic lysis solution and a 1.8M sucrose solution prior to re-centrifugation at 4000xg to isolate out cortical nuclei. The pellet was then resuspended in Dulbecco’s phosphate buffered saline (DPBS) containing 0.1% BSA and 1:1000 anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Samples were incubated for 45 minutes while rotation and protected from light at 4C. DAPI (Invitrogen) was added immediately before sorting to label all nuclei.
PacBio: Genomic DNA was isolated from FACS-sorted NeuN+ or NeuN- nuclei of adult mouse cerebral cortex using phenol chloroform extraction and was subsequently sheared to ~10kb using g-Tube microcentrifuge tubes (Covaris, 010145).
RNA-Seq (RiboZero): Total RNA was first extracted from the prefrontal mouse cortices (n=12, 6WT/6KO), and prepared with RNeasy Lipid Tissue Mini kit (with on-column DNase1 treatment). The quantity and quality of RNA was checked using a bioanalyzer (Agilent RNA 6000 Nano Kit).
RNA-Seq (QIAseq): Single-cell suspension from adult brain tissues was prepared using Miltenyi’s Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677) and Debris Removal Solution Kit (Miltenyi Biotec, 130-109-398) according to manufacturer instruction with minor modifications. In brief, total brain tissues, except olfactory bulb and cerebellum, were collected quickly and washed with ice cold 1x HBSS. After chopped into small pieces using sharp blade, the brain tissues were transferred into the C-tube containing 1950ul of Enzyme mix 1 and 30ul of Enzyme mix 2 from the kit and incubated on Miltenyi’s gentle MACS Octo Dissociator with Heaters using program 37°C _ABDK_1 for 30 minutes. Afterwards, the digested tissue homogenate gently went through fire polished glass pippette 10 times, and then passed through a 70um cell strainer. Cells were collected via centrifuged at 300g for 10 minutes at 4 °C and resuspended in ice cold 1x HBSS. Debris Removal Solution was then added and overlayed with ice cold 1x HBSS. After centrifugation, three phases in the tube were clearly visualized, from top to bottom: 1x HBSS solution, debris and myelin layer, and single-cell suspension. Discard the top two phases completely, wash the cells in 1x HBSS, centrifuge to collect the cells, and then resuspended the cell pellet in 1 ml of 1x HBSS containing 1% fetal bovine serum. In order to minimize the unwanted microglia activation, single cell suspension was incubated in Fc receptor blocking Reagent (Miltenyi Biotec, 130-092- 575) for 10 min, and then the cell suspension was incubated with CD11b-microbeads (Miltenyi Biotec, 130-093-634) for 10 min at 4 °C in the dark, followed by positive selection with LS separation column (Miltenyi Biotec, 130-042-401). Flow cytometry analysis was performed to check the cell purity. The three different groups of cells (no enrichment, target and non-target cell population) were incubated in CD11b-FITC Monoclonal Antibody (M1/70) (eBioscience, 11-0112-81) at 1:2000 dilution for 30 min at 4 °C in the dark. Stained cells were examined using the Beckman flow cytometer.
ATAC-seq: Single-cell suspension from adult brain tissues was prepared using Miltenyi’s Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677) and Debris Removal Solution Kit (Miltenyi Biotec, 130-109-398) according to manufacturer instruction with minor modifications. In brief, total brain tissues, except olfactory bulb and cerebellum, were collected quickly and washed with ice cold 1x HBSS. After chopped into small pieces using sharp blade, the brain tissues were transferred into the C-tube containing 1950ul of Enzyme mix 1 and 30ul of Enzyme mix 2 from the kit and incubated on Miltenyi’s gentle MACS Octo Dissociator with Heaters using program 37°C _ABDK_1 for 30 minutes. Afterwards, the digested tissue homogenate gently went through fire polished glass pippette 10 times, and then passed through a 70um cell strainer. Cells were collected via centrifuged at 300g for 10 minutes at 4 °C and resuspended in ice cold 1x HBSS. Debris Removal Solution was then added and overlayed with ice cold 1x HBSS. After centrifugation, three phases in the tube were clearly visualized, from top to bottom: 1x HBSS solution, debris and myelin layer, and single-cell suspension. Discard the top two phases completely, wash the cells in 1x HBSS, centrifuge to collect the cells, and then resuspended the cell pellet in 1 ml of 1x HBSS containing 1% fetal bovine serum. In order to minimize the unwanted microglia activation, single cell suspension was incubated in Fc receptor blocking Reagent (Miltenyi Biotec, 130-092- 575) for 10 min, and then the cell suspension was incubated with CD11b-microbeads (Miltenyi Biotec, 130-093-634) for 10 min at 4 °C in the dark, followed by positive selection with LS separation column (Miltenyi Biotec, 130-042-401). Flow cytometry analysis was performed to check the cell purity. The three different groups of cells (no enrichment, target and non-target cell population) were incubated in CD11b-FITC Monoclonal Antibody (M1/70) (eBioscience, 11-0112-81) at 1:2000 dilution for 30 min at 4 °C in the dark. Stained cells were examined using the Beckman flow cytometer.
Hi-C (Jiang, et. al.): Nuclei were digested with 100U MboI, and the restriction fragment ends were labeled using biotinylated nucleotides and re-ligated. After reversal of the cross-linking, ligated DNA was purified and sheared to a length of ~400bp by sonication, and the biotin-tagged ligation junctions were subsequently pulled down with streptavidin beads (Invitrogen, Dynabeads MyOne Streptavidin T1, Catalog No. 65602) and prepared into libraries.
ChIP-seq: Nuclei were pelleted after FANS, resuspended in 300μl of micrococcal nuclease digestion buffer (10mM Tris pH 7.5, 4mM

tag: strain background

value: cortex


title: NeuN- PacBio REP3


title: NeuN- PacBio REP2


title: WT_ESC_CBX7_ChIP_group2


title: RPE-1-CyclinE_NO Dox_120h_1 [G_15]


title: RPE-1-Empty_NO Dox_48h_2 [G_20]

source_name: RPE-1-Empty_NO Dox_48h


title: NeuN+ PacBio REP5

source_name: NeuN+ PacBio


title: WT_ESC_RING1B_ChIP_group2


title: CaPS_ESC_input_TF_group2


title: NeuN+ PacBio REP4


title: RPE-1-Empty_Doxycycline _120h_1 [G_12]


title: CaPS_ESC_H3K27me3_ChIP_group1


title: 4_RB_10-24-18_S38


title: 11_RB_10-24-18_S45


title: RPE-1-Cdc25a_Doxycycline_120h_1 [G_14]


title: RPE-1-Cdc25a_NO Dox_120h_1 [G_13]


title: CaPS_ESC_CBX7_ChIP_group2


title: 3_RB_10-24-18_S50


title: WT_NPC8_RING1B_ChIP_group3


title: RPE-1-Empty_Hydroxyurea_120h_1 [G_10]


title: 10_RB_10-24-18_S44


title: WT_ESC_input_TF_group2


title: CaPS_ESC_RING1B_ChIP_group1


title: RPE-1-Empty_NO Dox_120h_1 [G_11]


title: GC_B_GC_B_CD23_Doc2_RNA-seq

data_processing:
Alignment ti the mm10 refseq using Subread library
Total read counts using FeatureCounts
Differential expressed genes performing the DeSeq2 tool
Kmeans and Heatmap analysis using kmeans and pheatmap tools
Genome_build: mm10
Supplementary_files_format_and_content: normalised counts

source_name: Germinal Center B cells

extract_protocol:
Snap frozen cell pellets were lysed and total RNA was isolated through the Rneasy Micro purification Kit (QIAGEN)
RNA libraries were prepared for sequencing using MGIEasy RNA Directional Library prep kit

tag: strain

value: Germinal Center B cells

value: LCMV Docile

value: RNA-Seq


title: RPE-1-Myc_Doxycycline_48h_1 [G_9]

data_processing:
Generated by MOLGENIS Compute; Pipeline version NGS_RNA/3.2.5; August 14, 2017
The reference we always use for the MOLGENIS pipeline toolbox developed in our department: Byelas H. DM, Neerincx P., Dijk van F., Kanterakis A., Deelen P., Swertz M. Scaling bio-analyses from computational clusters to grids University Medical Centre Groningen 2013 [CEUR-WS.org CEUR Workshop Proceedings 993]. Available from: http://ceur-ws.org/Vol-993/paper2.pdf.
NGS: single reads 75 nt. Mean read length is 64 nt, (excluding the  bases used for the barcodes)
Gene expression quantification  The trimmed fastQ files where aligned to build human_g1k_v37 ensembleRelease 75 reference genome using hisat/0.1.5-beta-foss-2015b [1] allowing for 2 mismatches. Before gene quantification SAMtools/1.2-foss-2015b [2] was used to sort the aligned reads.  The gene level quantification was performed by HTSeq/0.6.1p1-foss-2015b [3] using --mode=union--stranded=no and, Ensembl version 75 was used as gene annotation database.
Calculate QC metrics on raw and aligned data  Quality control (QC) metrics are calculated for the raw sequencing data. This is done using  the tool FastQC FastQC/0.11.3-Java-1.7.0_80 [4]. QC metrics are calculated for the aligned reads using Picard-tools picard/1.130-Java-1.7.0_80 [5] CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-Metrics and SAMtools/1.2-foss-2015b flagstat.  These QC metrics form the basis in this final QC report.Used tool versions:  Java/1.7.0_80  FastQC/0.11.3-Java-1.7.0_80  hisat/0.1.5-beta-foss-2015b  SAMtools/1.2-foss-2015b  R/3.2.1-foss-2015b  wkhtmltopdf/0.11.0_rc1-static-amd64  picard/1.130-Java-1.7.0_80  HTSeq/0.6.1p1-foss-2015b  Python/2.7.10-foss-2015b  GATK/3.6-Java-1.8.0_74  multiqc/1.0-foss-2015b-Python-2.7.11  Ghostscript/9.16-foss-2015b    1. Dobin A, Davis C a, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M,  Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15â€“21.  2. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R,  Subgroup 1000 Genome Project Data Processing: The Sequence Alignment/Map format and SAMtools. Bioinforma 2009, 25 (16):2078â€“2079.  3. Anders S, Pyl PT, Huber W: HTSeq â€“ A Python framework to work with high-throughput sequencing data HTSeq â€“ A Python framework to work with high-throughput sequencing data. 2014:0â€“5.  4. Andrews, S. (2010). FastQC a Quality Control Tool for High Throughput Sequence Data [Online].  Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ SAMtools/1.2-foss-2015b  5. Picard Sourceforge Web site. http://picard.sourceforge.net/ picard/1.130-Java-1.7.0_80
Supplementary_files_format_and_content: csv, read count

extract_protocol:
RNA was isolated using the mirVANA kit (Ambion, AM1561). To determine RNA quality, RNA was separated by electrophoresis on microfluidic sipper chips and detected by fluorescence (LabChip GX, Caliper LifeSciences). RNA Quality Scores (RQS) were based on electropherogram features (total and fast region areas, 28S, and 18S height), and ranged from 0-10. Only samples with RQS scores above 5 were included for analysis.
To generate cDNA libraries suitable for next-generation sequencing (NGS), the QuantSeq RNAseq 3' mRNA kit (Lexogen) was employed. Briefly, the poly-A tail from total RNA was bound to oligo-dT primers to synthesize the first cDNA strand. After RNA removal, a second cDNA strand was synthesized by random priming.
The double-stranded cDNA library was purified, and PCR amplified with Illumina sequencing adapters. The libraries were sequenced with 65 base-pair reads on a NextSeq 500 sequencer (Illumina)..

tag: treatment


title: 1_RB_10-24-18_S48

value: Shp2 E76K mice

value: bone marrow mononuclear cells


title: WT_ESC_RING1B_ChIP_group3


title: 12_RB_10-24-18_S46


title: NeuN+ PacBio REP3


title: 10_RB_10-24-18_S57


title: NeuN+ PacBio REP2


title: GC_B_GC_B_CD23_WE2_RNA-seq

value: LCMV WE


title: NeuN+ PacBio REP1


title: 11_RB_10-24-18_S58


title: CaPS_ESC_input_histone_group1


title: MN_WT_RNA_rep1

source_name: Differentiated motor neuron

growth_protocol: For motor neuron differentiation, mESCs were differentiated in AK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies. Medium was exchanged on Day 2 of differentiation. Patterning of embryoid bodies was induced by supplementing the media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

extract_protocol:
Cells were lysed in Tripure isolation reagent (sigma) followed by passing through a 20 gauge needle. RNA was purified by chloroform extraction, and precipitated by isopropyl alcohol. Genomic DNA was removed by RNEasy plus Mini Kit.
PolyA+ RNA was isolated from 5 ug total RNA using Dynabeads Oligo(dT)25, fragmented with Mg2+ contained in the 1st strand buffer at 94°C for 15 min, and reverse transcribed using Superscript III and random hexamers to synthesize the first strand. Single strand cDNA was precipitated and dTTP was removed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I and the E. coli ligase, and then purified by MinElute PCR Purification Kit. Double stranded DNA was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 100 bp paired-end reads on the Illumina HiSeq 4000 platform.

value: Differentiated motor neuron

value: wild type


title: MN_WT_RNA_rep2


title: WT_ESC_RING1B_ChIP_group1

value: 0 days


title: RPE-1-Cdc25a_Doxycycline_48h_1 [G_5]

value: Doxycycline


title: RPE-1-Myc_NO Dox_48h_1 [G_8]


title: CaPS_ESC_input_TF_group1


title: WT_ESC_H3K27me3_ChIP_group1

value: WT


title: WT_ESC_input_histone_group1


title: mBrain_RNA_rep2

source_name: brain

growth_protocol: All mice were housed with a 12 hour light-dark cycle. Mixed cohorts of female and male mice were used for all experiments to minimize gender effects. Brain tissue was collected at postnatal Day 1.

extract_protocol:
The whole brains were homogenized in Tripure isolation reagent (sigma) with a glass douncing homogenizer and further lysed by passing through a 20 gauge needle. RNA was purified by chloroform extraction, and precipitated by isopropyl alcohol. Genomic DNA was removed by RNEasy plus Mini Kit.
PolyA+ RNA was isolated from 5 ug total RNA using Dynabeads Oligo(dT)25, fragmented with Mg2+ contained in the 1st strand buffer at 94°C for 15 min, and reverse transcribed using Superscript III and random hexamers to synthesize the first strand. Single strand cDNA was precipitated and dTTP was removed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I and the E. coli ligase, and then purified by MinElute PCR Purification Kit. Double stranded DNA was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 100 bp paired-end reads on the Illumina HiSeq 4000 platform.

value: Postnatal Day 1


title: 1_RB_10-24-18_S35


title: WT_ESC_input_TF_group1


title: RPE-1-CyclinE_Doxycycline_48h_1 [G_7]


title: CaPS_ESC_CBX7_ChIP_group1


title: STAD_NX.43_P3

city: Tokyo

first: Kuniyo

last: Sueyoshi

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Preventive Medicine, Graduate School of Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Illumina Genome Analyser IIx used for sequencing
Sequenced read were quantified by Salmon (version 0.8.1) software. Briefly, the human whole transcriptome (GENCODE, release 27, GRCh38.p10) and the mouse whole transcriptome (GENCODE, release M15, GRCm38.p5) of protein-coding genes were combined, and a quasi-mapping index of the dual-species was subsequently built with the --type quasi -k 31 preset. The estimation of the transcript abundance was executed by the Salmon quasi-mapping mode with the –l A preset.
The data of transcript-abundance was divided into human transcripts or mouse transcripts, representing cancer-reads or stroma-reads, respectively.
The transcripts of protein coding genes were extracted the whole transcripts. Subsequently the transcript-level read abundance was summarized to the gene-level abundance in Transcript per Million (TPM) value scaled by the library size and the transcript length with the tximport package (version 1.16.1) in R by using summarizeToGene function with the countsFromAbundance = "lengthScaledTPM" preset on the reference to the GRCh38.p10 (GENCODE, release 27) for cancer-reads or the GRCm38.p5 (GENCODE, release M15) for stromal-reads.
Genome_build: GRCh38.p10 for human, GRCm38.p5 for mouse
Supplementary_files_format_and_content: tab-delimited text files include raw transcript-abundance measurements computed by Salmon software for each Sample
Supplementary_files_format_and_content: Matrix table with scaled TPM values for every gene and every sample

organism:
Homo sapiens
Mus musculus

source_name: Patinent derived xenograft

growth_protocol: A total of 43 fresh tumor specimens of 9 distinctive tumor types were surgically resected, sectioned and frozen at −80°C. PDXs were established by the subcutaneous transplantation of the dissolved tissue fragments of 5 mm3 in size into the flank of five- to six-week-old NOD/SCID/γcnull mice (CLEA Japan, Tokyo, Japan). PDX samples were re-transplanted to reproduce the Nth passages (N: 2, 3, ...) of the corresponding PDX.

extract_protocol:
Tumors resected from the mice were frozen and the suspended in trizol reagent (Thermo Fisher Scientific Inc, Waltham, USA), and total RNA was extracted according to the manufacturer’s instruction.
One microgram of total RNA was used as the starting material for a 100-bp paired-end transcriptome-sequencing protocol using an Illumina GAIIx sequencer (Illumina, San Diego, CA, USA). Briefly, PolyA+ RNA was purified from total RNA and fragmented using divalent cations. RNA quality as assessed by RNA integrity number (RIN) using a bioanalyzer (Agilent). Double stranded cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen), and its overhang was converted into blunt end using T4 DNA polymerase. 3’ end of the blunt end was adenylated by Klenow fragment, and PE adapter was ligated. Without size selection, the cDNA library was amplified using PCR. For PCR amplification, 1ul of PCR primer PE 1.0 and 2.0, and 0.5 μL of Phusion DNA polymerase (Finnzymes Oy) were used in a final volume of 50 μL. The PCR condition was as follows: 98 °C for 5 min, then 15 cycles of 98 °C for 10 s, 65 °C for 30 s, and 72 °C for 30 s, followed by 72 °C for 5 min before cooling to 4 °C. PCR primers were removed by QIA quick PCR Purification Kit. Each library was loaded into its own single Illumina flow cell lane, producing 100-mer paired-end reads for each sample.

treatment_protocol: No treatment procedure

tag: primary tumor type (human)

value: stomach adenocarcinoma (STAD)

tag: metastasis site

value: Peritoneal dissemination

tag: originial tumor id

tag: passage of pdx

tag: host mice strain

value: NOD/SCID/γcnull mice


title: RPE-1-Empty_NO Dox_48h_1 [G_2]

tag: genotype/variation

value: NO Dox


title: RPE-1-CyclinE_NO Dox_48h_1 [G_6]


title: SUDLH5_SENP6_RAD21_ChIPSeq

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

data_processing:
Fastq files were mapped to the human genome (hg19) using Bowtie v2.27. and normalized to the sample with the spike in control where applicable.
bedgrpah files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Genome_build: hg19

growth_protocol: Human DLBCL (SU-DHL-5) cells were grown in RPMI supplemented with 20% FCS and 2% glutamine; for spike-in: murine T-Lymphoma(MYC-Tet-OFF) cells were cultured in RPMI supplemented with 10% FCS, 1% penicillin/streptomycin, 1% MEM non-essential amino acids, 1% glutamine, 50 mM beta-mercaptoethanol

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 min. 6% murine T-lymphoma cells were added during cell lysis as exogenous spkie-in for normalization. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using a Branson sonifier or using the Covaris Focused Ultrasonicator M220 for 100 min per ml lysate. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 to 8 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® or NEBNext® Ultra II DNA Library Prep with Sample Purification Beads (New England Biolabs). Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit or Sample Purification Beads. DNA fragments were amplified by 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay.

treatment_protocol: no treatment

value: reconstituted for SENP6

tag: sirna

value: RAD21 (Bethyl Laboratories, A300-080A)


title: MN_ Nrf1KO_ChIP_H3K27ac

description: ChIP DNA

extract_protocol:
Motor neurons differentiated for 6 days were dissociated with 0.05% trypsin, neutralized, fixed with 1% paraformaldehyde for 15 min and quenched with 0.125 M glycine for 5 min at RT, followed by twice wash with PBS. Cell pellets from above steps were lysed in LB1 buffer (50 mM HEPES, pH 7.5 at 4°C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X; 10 min at 4°C), LB2 buffer (10 mM Tris, pH 8 at 4°C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; 10 min at 4°C), and then resuspended in LB3 buffer  (10 mM Tris, pH 7.5 at 4°C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sheared using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Dynabeads, chromatin was incubated with indicated antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G Dynabeads for 2 hr at 4°C. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked at 65°C overnight, digested with protease K and RNaseA and then purified for library construction.
Immunoprecipitated DNA (∼1-30 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 50 bp single-end reads on the Illumina HiSeq 4000 platform.

tag: genotype

value: H3K27ac (Abcam, Cat# ab4729)


title: STAD_NX.42_P8

value: Brain


title: MN_ Nrf1KO_ChIP_H3K27me3

description: ChIP DNA

value: H3K27me3 (Cell Signaling Technology, Cat# 9733)


title: GC_B_GC_B_CD23_Doc1_RNA-seq

tag: tissue

value: Germinal Center B cells

value: LCMV Docile

tag: assay

value: RNA-Seq


title: MN_ Nrf1KO_ChIP_H2AK119ub

description: ChIP DNA

value: Differentiated motor neuron

tag: antibody

value: H2AK119ub1 (Cell Signaling Technology, Cat# 8240)


title: RPE-1-Empty_Doxycycline _48h_1 [G_3]

value: Doxycycline


title: MN_ Nrf1KO_ChIP_Ring1B

description: ChIP DNA

value: Ring1B (Bethyl Laboratories, Cat# A302-869A)


title: CD23_Doc2

data_processing:
Alignment ti the mm10 refseq using Subread library
Total read counts using FeatureCounts
Differential expressed genes performing the DeSeq2 tool
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing: normalised counts, differential expressed genes, p values, FDR, Average expression, FClog


title: WT_ESC_CBX7_ChIP_group1

value: J1 cells

value: WT

tag: age

value: 0 days


title: GC_B_GC_B_CD23_WE1_RNA-seq

value: LCMV WE


title: PAAD_NX.41_P4

value: pancreatic ductal adenocarcinoma (PAAD)

value: Primary

value: NOD/SCID/γcnull mice


title: RPE-1-Empty_Hydroxyurea_48h_1 [G_1]

value: Hydroxyurea

tag: time point


title: Bmi1_Doc1

value: Bmi1 conditional know-out in B cells

tag: cell type


title: CD23_Doc1

tag: strain background


title: STAD_NX.42_P7

value: stomach adenocarcinoma (STAD)

value: Brain


title: CD23_WE1

value: Germinal Center B cells


title: RPE-1-Cdc25a_NO Dox_48h_1 [G_4]

value: NO Dox


title: SUDLH5_Combined_Input

value: empty vector/reconstituted for SENP6


title: E14_ESC_RNA_rep2

source_name: E14 mESC

growth_protocol: E14 mESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021).

value: mESCs

value: wild type


title: Bmi1_WE2


title: mBrain_RNA_rep1

tag: strain

tag: developmental stage

value: Postnatal Day 1


title: STAD_NX.42_P6

tag: primary tumor type (human)


title: Bmi1_Doc2

tag: treatment

value: LCMV Docile


title: PAAD_NX.39_P3

tag: metastasis site

value: Lymph node

tag: originial tumor id


title: E14_ESC_RNA_rep1


title: Bmi1_WE1


title: SUDLH5_EV_RAD21_ChipSeq

value: empty vector

value: RAD21 (Bethyl Laboratories, A300-080A)


title: CD23_WE2

value: LCMV WE


title: MN_WT_ChIP_H3K27me3

description: ChIP DNA

value: Differentiated motor neuron

value: H3K27me3 (Cell Signaling Technology, Cat# 9733)


title: STAD_NX.42_P5

tag: passage of pdx

tag: host mice strain

value: NOD/SCID/γcnull mice


title: MN_WT_ChIP_RYBP

description: ChIP DNA

value: RYBP (Sigma, Cat# PRS2227)


title: PAAD_NX.37_P4

value: pancreatic ductal adenocarcinoma (PAAD)

value: Primary


title: ribo_gir2_4_b1_s2

city: Moscow

first: Sergey

middle: E.

last: Dmitriev

address: Leninskie Gory, 1

country: Russia

institute: Lomonosov Moscow State University

description: Ribosome-bound RNA

data_processing:
Reads were trimmed using cutadapt v. 2.10 with the following parameters for RNA-Seq (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length 20 -q 20) and Ribo-Seq samples (-a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --trimmed-only -q 20).
Additionally for Ribo-Seq, the reads were deduplicated with seqkit rmdup v. 0.10.1, and unique barcodes were then removed with cutadapt v. 2.10 (-q 20 --minimum-length 20 -u -4).
Afterwards, reads were aligned against eukaryotic rRNA sequence set obtained from silva-euk and rfam databases using bowtie2 v. 1.2.3. Only unmapped non-rRNA reads were saved for the further analysis.
Read mapping and counting against the Saccharomyces_cerevisiae.R64-1-1.95 (Ensembl) genome assembly was performed with STAR v. 2.7.9a.
Genome_build: Ensembl Saccharomyces_cerevisiae.R64-1-1.95 (genome-build-accession GCA_000146045.2)
Supplementary_files_format_and_content: Tab-separated text files containing read counts per gene as estimated by STAR.

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: The cells were grown in YPD (2% glucose, 2% peptone, 1% yeast extract) at 30℃ and 220 rpm to exponential growth stage (OD=0.5-0.6).

extract_protocol:
Cell lysates were clarified by two sequential centrifugation steps - 3000g, 5 minutes, 4℃, and 20000g, 10 minutes, 4℃. Part of the cell lysate was used for mRNA isolation using Oligo(dT) beads.  Another part was treated with ribonuclease I for polysome disassembly and applied to a linear 10-50% sucrose gradient in fractionation buffer (20 mM Tris pH 8.0, 140 mM KCl, 15 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide, 1% Triton) and separated on a SW-41 rotor (Beckman) at 35000 rpm, 3 hours, 4℃. Subsequently, ribosome-bound RNA fragments were collected from the monosome fraction. Ribosome-bound RNA was isolated using acidic-phenol extraction.
cDNA libraries for Ribo-Seq and RNA-Seq were constructed in parallel using standard ribosomal profiling library construction protocol (described in Kasari et al., 2019 DOI: 10.1093/nar/gkz600). Importantly, cycloheximide was added to the lysis buffer but not to the growth media.

treatment_protocol: Cells were collected by vacuum filtration, separated from the filter with a plastic scraper and flash frozen in liquid nitrogen in a mortar and ground with a pestle with addition of polysome lysis buffer (20 mM Tris pH 8.0, 140 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide, 1% Triton) with constant addition of liquid nitrogen.

tag: batch

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 gir2::KanMX


title: SUDLH5_SENP6_MYC_ChIPSeq

value: reconstituted for SENP6

tag: sirna

value: MYC (abcam, ab32072)