title: D12P1

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

data_processing:
Raw data were filtered with the SOAPnuke software
Clean reads were compared to the reference genome (GCF_000001405.37_GRCh38.p11) with HISAT
Clean reads were compared to the reference gene sequences with Bowtie2
Gene expression levels were calculated with RSEM
Differentially expressed genes (DEGs) analyzed with the DEGseq software
Genome_build: GCF_000001405.37_GRCh38.p11
Supplementary_files_format_and_content: TXT files include FPKM values for each sample

source_name: Cardiac

growth_protocol: Cardiac differentiation was induced according to a published protocols (Burridge, Matsa et al. 2014) with modifications.

extract_protocol:
Total RNA were extracted with Trizol
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Toxicants at 60 µM concentrations were added to the medium starting from day 0 until the end of the differentiation process.

value: Human embryonic stem cell cardiac differentiation day 12 sample

value: 60 microM PFOS


title: D12P2

status: Public on Feb 16 2020

type: SRA

address: 双清路18号林业大学北门

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: developmental stage

tag: treatment


title: MKN_74_control

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
MKN74
processed data file: cpm_normalized_log2.xlsx

data_processing:
ChIP-seq: Base calling performed using CASAVA version 1.7
ChIP-seq: mapped to hg19 whole genome using bowtie2 v.2.1.0
ChIP-seq: Enrichment levels were called using homer v.4.9.1. ONECUT2 ChIP-seq was prossed with homer transcription factor option.
RNA-seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: mapped to hg19 whole genome using STAR v2.5.1.
RNA-seq: Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using homer.
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

extract_protocol:
The RNA sequencing library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA). and For ChIP-seq, Cells were fixed using 1% formaldehyde, lysed and sonicated using a Bioruptor (Diagenode Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols. For ChIP-seq, immunoprecipitation was performed with anti-ONECUT2(proteintech, catalog no. 21916-1-AP). 250-400 bp genomic libraries were generated from the input and immunoprecipitated DNA and sequenced using Illumina NextSeq_500 to generate 75 bp single-end reads.

tag: cell type

value: gastric cancer cell line


title: LSD1_2

city: ALLSTON

first: Donglim

last: Park

state: MA

address: 4 Price Rd, Apt11

department: Medical oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using the BWA aligner
peaks were called using using the default parameters of MACS2 relative to the input samples.
Genome_build: hg19
Supplementary_files_format_and_content: .narrwPeak.bed and .xls peak files were generated using MACS2.

molecule: genomic DNA

growth_protocol: MCC cell lines were grown in RPMI supplemented with 10% FBS and antibiotics.

extract_protocol:
The ChIP method was modified from protocols described in Schmidt et al.(Schmidt et al., 2009). MKL-1 cells were cross-linked using dual cross-linking with disuccinimidyl glutarate (DSG) and formaldehyde. After cross-linking, cells were lysed using SimpleChIP buffer A and B (Cell signaling) and DNA was processed with the Micrococcal nuclease (New England Biolabs Inc.) for 30 minutes at 37°C followed by sonicating for 20s pulses 5 times at 4°C.
30 ng of DNA from ChIP experiments or input DNA were prepared for sequencing with NEBNext ChIP-seq Library Prep Reagent Set for Illumina (New England BioLabs). Amplified libraries were cleaned up using AMPure XP beads (Beckman Coulter) and checked on a Bioanalyzer (Agilent) to confirm a narrow distribution with a peak size around 275 bp. Diluted libraries were used for 50 cycles single-end sequencing on NextSeq 550 systems  (Illumina) at the Molecular Biology Core Facilities (MBCF) at Dana-Farber Cancer Institute following the manufacturer’s protocol.

tag: tumor type

value: Merkel cell carcinoma

value: MCC tumor derived cell line

tag: chip antibody

value: LSD1 (abcam; rabbit; ab17721)


title: AGS_ONECUT2

description:
AGS_OC2_over
processed data file: cpm_normalized_log2.xlsx

source_name: AGS

value: AGS


title: E11 Prdm16cKO B

city: New York

first: Qiangqiang

last: Zhang

state: NY

address: 430 East 67th St

institute: Memorial Sloan-Kettering Cancer Center

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E11mutB__E11cKO

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Chui_et_al_Processed_Data_Files.xls: Excel file containing normalized counts.

organism: Mus musculus

source_name: ventricular zone embryonic cortical tissue

extract_protocol:
Ventricular tissue were isolated from three pairs of wild-type (WT) and Prdm16 cKO (conditional knockout) mutant E11.5, E13.5, E15.5, and E17.5 embryos. RNA was isolated using Qiagen RNeasy Micro Kit (QIAGEN).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 125-150ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102). Samples were barcoded and ran on the HiSeq 4000 platform, using the HiSeq 3000/4000 SBS Kit (Illumina).

tag: strain

tag: genotype

value: Prdm16 conditional knockout

value: Embryonic day 11.5

tag: tissue

value: Ventricular zone embryonic cortical tissue


title: D12F2

address: 双清路18号林业大学北门

value: 60 microM F-53B


title: E11 wildtype A

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E11contA__E11wildtype

value: Wildtype


title: AGS_control

description:
AGS
processed data file: cpm_normalized_log2.xlsx


title: LSD1_1


title: WT ESC-3

city: Hong Kong

first: Wuming

last: Wang

address: Sha Tin

institute: The Chinese University of Hong Kong

data_processing:
The raw reads were cleaned using internal software SOAPnuke (Version v1.5.2, Website: https://github.com/BGI-flexlab/SOAPnuke) by removing adapter sequences, reads in which unknown bases are more than 10%, and low quality reads.
The clean reads were stored in FASTAQ format.
We used HISAT (Version v2.0.4, Website: http://www.ccb.jhu.edu/software/hisat) to do the mapping step, and calculated gene expression with a software package called RSEM (Version v1.2.12, Website: http://deweylab.biostat.wisc.edu/ RSEM).
FPKM method was used in calculated expression level, and the calculated gene expression can be directly used for comparing the difference of gene expression among sample.
Genome_build: HG19
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: embryonic stem cells

growth_protocol: Mouse ESCs were cultured in DMEM/F12 containing GlutaMAX and sodium pyruvate (Life Technologies, 10565) with 15% fetal bovine serum (Hyclone, SH30071), nonessential amino acid solution (Life Technologies, 11140), -mercaptoethanol (Life Technologies, 31350) with 1 × 103 units/ml LIF (Millipore, ESG1106), 1 uM PD0325901 (Sigma, PZ0162), and 2.5 uM CHIR99021 (Sigma, SML1046). The mouse ESCs were grown on gelatin-coated plates and the medium was replaced every other day. The ESC cultures were passaged every 2 days.

extract_protocol:
ESCs and embryoid bodies were collected, and RNA was harvested using Trizol reagent. The quality of the isolated RNA was determined with Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). The RNA was converted into a template molecules library for sequencing on the BGISEQ-500.
Briefly, total RNA samples were ribo-depleted and then fragmented. The fragmented samples were reversed transcribed to cDNA, end-repaired and 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified, and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. Denature the PCR products by heat, and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: The Pten-/- ESCs and Pten-A3 mutant ESCs were generated by the CRISPR-Cas9 system. ESCs were cultured in 6-well plates and transfected with donor plasmid and constructs containing Cas9 and target sequences using lipofectamine 3000, and these were then subjected to cell sorting of GFP-positive cells after transfection for 48 h. The enriched gene-modified cell populations were cultured in 60-mm dishes for 4-5 days, and each cell clone was passaged into 24-well plates. Finally, the Pten−/− and Pten-A3 mutant cell lines were identified by sequencing, and the cells were stored in liquid nitrogen.

value: embryonic stem cells

value: wild type


title: ML-2-ctrl

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
The raw sequencing reads were filtered for adapter and low quality sequences using cutadapt (Martin, 2011) and custom scripts. Low quality reads were defined as sequencing reads with more than 5% unknown bases (‘N’) and reads with more than 50% of the bases.
Alignment, expression estimation and tests for differential expression were processed by RSEM 1.2.31 (Li and Dewey, 2011) and EBSeq Version 1.10.0 (Leng et al, 2013). Resulting values were indicated by Transcript Per Million (TPM).
Genome_build: Human genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Acute myeloid leukemia cells

extract_protocol:
Total RNA from different samples were extracted (Rnaeasy mini kit, Qiagen), and used for construction of sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GFP overexpression


title: D12F1

address: 双清路18号林业大学北门


title: Not immuno-precipitated input control of hapX mutant

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using tophat2 with '--very-sensitive' option.
Peak calling and comparison was performed by macs2 v2.2.1 using modified parameter (callpeak -m 3 30 -B -q 0.01 --nomodel --keep-dup all).
Differential peak calling was performed by macs2 v2.2.1 using default parameter and q-value < 0.05.
Resulting peaks were annotated by annotatePeaks in homer v4.8 and homemade scripts.
Genome_build: C. neoformans var. grubii H99 (GCA_000149245.3)
Supplementary_files_format_and_content: The peaks showing differences between wild type and mutant were selected and confirmed by manual curation. Annotated peaks were listed as a xlsx format for each mutant.

organism: Cryptococcus neoformans H99

growth_protocol: C. neoformans cells were cultured in YNB + BPS with or without 100 μM of FeCl3 at 30˚C for 6 hours.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Library was constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645, NEB, UK) following manufacturer's instructions.

tag: culture condition

value: YNB low iron medium

value: HapX-Flag

value: Anti-FLAG antibody (Abcam, #ab1162)


title: hiPSCs-CECs-4

city: Baltimore

first: S. Amer

last: Riazuddin

state: Maryland

address: 600 N. Wolfe St

institute: Johns Hopkins University School of Medicine

data_processing:
The base calls were assigned through the Illumina Real Time Analysis (RTA) software (version 1.17.20) and base call files were converted from a binary format (BCL) to flat file format (qseq.txt) using Illumina BCL Converter software (Ver. 1.9.4).   Qseq.txt files were de-multiplexed to single sample FASTQ files using de-multiplexer software written at Center for Inherited Disease Research (CIDR), Johns Hopkins University as part of CIDRSeqSuite (Ver. 7.1.0; unpublished).
The raw RNA-Seq reads (FASTQ) were processed and analyzed using Lasergene Genomics Suite (DNASTAR, Madison, WI, USA). The paired-end reads were assembled with SeqMan NGen (Ver. 12), using default parameters. The human reference genome (GRCh38.p11) was used for the mapping of RNA-Seq reads. The ArrayStar (Ver, 12; DNASTAR) was used for normalization, differential gene expression and statistical analysis of mapped paired-end reads using the default parameters. The expression data quantification and normalization were calculated using the RPKM value for each gene; the RPKM corresponds to reads per kilobase per million mapped reads
In parallel, we created expression profile to examine the genes differential expression in iPSCs-derived CECs compared with hESCs-derived CECs using Spotfire DecisionSite with Functional Genomics (TIBCO Spotfire, Boston, MA). All transcripts’ log2-fold changes between hESCs- and iPSCs-derived CECs were analyzed to determine the standard deviation (s.d.) from their mean of 0, which represents no change. We chose a ≥ 2 s.d., the cutoff value for differentially expressed genes.
Genome_build: Human reference genome (GRCh38.p11)
Supplementary_files_format_and_content: Excel spread sheets including gene expression values (RPKM) for each Sample

source_name: Human iPSCs-derived CECs

growth_protocol: Both, hESCs and iPSCs were seeded on 35 mm Matrigel-coated plates on day 0 using cell dissociation buffer. The hESCs and iPSCs were grown for four days in mTeSR1 medium (StemCell Technologies). On day 4, mTeSR1 media was replaced with dual Smad inhibitors media containing 500 ng/ml human recombinant Noggin, and 10 µM SB431542 in a basal media of 80% DMEM-F12, 20% knockout serum replacement, 1% non-essential amino acids, 1 mM L-glutamine, 0.1mM beta-mercaptoethanol, and 8 ng/ml basic fibroblast growth factor. On day 6, dual Smad inhibitors media was replaced by Cornea media containing 0.1X B27 supplement, 10 ng/ml human recombinant PDGF-BB, and 10 ng/ml recombinant human Dkk-2 in basal media. On day 7, the differentiating CECs were transferred to new Matrigel-coated plates (35 mm) and were grown in Cornea media for 13 additional days.

extract_protocol:
The differentiated CECs were harvested on day 20 (D20) for total RNA isolation and next-genration RNA sequencing.
Total RNA was subjected to RNA-Seq library preparation using NEBNext Ultra II RNA Library Prep Kit for Illumina. Approximately, 1.0 µg of high-quality total RNA (≥ 8.0 RIN Score) was used for polyadenylated RNA selection using oligo dT beads, followed by the fragmentation of selected polyadenylated RNA. The fragmented RNA was used as a template for cDNA synthesis by reverse transcriptase with random primers. The cDNA was further converted into double-stranded DNA that was end-repaired to incorporate the specific index adapters for multiplexing, followed by a purification step and amplification for 15 cycles. The quality and functionality of the final amplified libraries were examined on an Agilent 2100 Bioanalyzer (Agilent) and quantitative PCR (qPCR) according to the manufacturer’s instructions.

value: iPSCs-derived CECs


title: Elute_Expt.1_4

city: Redwood City

first: Yuping

last: Chen

state: CA

address: 309 Oak Ave

institute: Stanford University

data_processing:
Step 1: Aligned with Bowtie2 to Candida albicans genome and output unalignable reads for alignment to Saccharomyces cerevisiae genome
Step 2: Aligned the output reads from Step 1
Step 3: rRNA reads were removed with custom perl scripts
Step 4: RPKM values were measured using SeqMonk
Step 5: Linear regression and slopes of RPKM vs time or size were calculated with custom R script
Genome_build: saccharomyces_cerevisae_R64-1-1_20110208 (obtained from the SGD (S288C R64-1-1), corresponding to R64-1-1 on Ensembl, GCA_000146045.2)
Supplementary_files_format_and_content: .xlsx; slopes

organism: Saccharomyces cerevisiae

growth_protocol: YEP supplemented with 1% Ethanol

extract_protocol:
Hot acid phenol total RNA extraction
Ovation Universal RNA-Seq System (NuGEN)

treatment_protocol: Supplemented with known amount of Candida albicans strain BWP17 grown over-night in YEPD supplemented with 80 microgram/ml uridine before RNA extraction

tag: genotype/variation

tag: size (fl)

value: Elutriation followed by addition of 1NM-PP1


title: MKN74_OC2over_ONECUT2

value: gastric cancer cell line

value: ONECUT2 overexpression

value: anti-ONECUT2 (proteintech, catalog no. 21916-1-AP)


title: hiPSCs-CECs-2


title: D12D2

address: 双清路18号林业大学北门

value: Human embryonic stem cell cardiac differentiation day 12 sample

value: DMSO


title: Not immuno-precipitated input control of cir1 mutant


title: MKN74_OC2over_input


title: Not immuno-precipitated input control of hapX mutant that treated iron

value: YNB low iron medium + 100 μM of FeCl3


title: hiPSCs-CECs-3


title: D12D1

address: 双清路18号林业大学北门


title: Not immuno-precipitated input control of cir1 mutant that treated iron


title: MKN74_control_input


title: MKN74_control_ONECUT2


title: hiPSCs-CECs-1


title: hESCs-CECs-4

source_name: Human ESCs-derived CECs

value: hESCs-derived CECs


title: ML-2-FST317

value: FST317 overexpression


title: D8P1

address: 双清路18号林业大学北门

value: Human embryonic stem cell cardiac differentiation day 8 sample

value: 60 microM PFOS


title: D8P2

address: 双清路18号林业大学北门


title: D8F2

address: 双清路18号林业大学北门

value: 60 microM F-53B


title: AGS_OC2over_ONECUT2

value: AGS


title: hESCs-CECs-3


title: AGS_OC2over_input


title: hESCs-CECs-2


title: hapX mutant that treated iron


title: hapX mutant

value: YNB low iron medium


title: AGS_control_ONECUT2


title: D8F1

address: 双清路18号林业大学北门


title: D8D2

address: 双清路18号林业大学北门


title: cir1 mutant


title: hESCs-CECs-1


title: cir1 mutant that treated iron


title: AGS_control_input


title: D8D1

address: 双清路18号林业大学北门


title: ATOH1_1

source_name: MKL-1 MCC Cells

value: MCC tumor derived cell line


title: neuroblastoma sample 183

status: Public on Feb 15 2020

type: genomic

city: Genova

first: Annalisa

last: Pezzolo

address: Via Gerolamo Gaslini, 3

country: Italy

institute: IRCCS Istituto Gaslini

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505C, each hybridization produced a pair of 16-bit images, which were processed using the Agilent Feature Extraction 10.5 Software

data_processing: The data were analyzed using the Agilent Genomic Workbench 7.0.40 software, the altered chromosomal regions and breakpoints events were detected using ADM-1 (threshold 10) with 0.5 Mb window size. Losses were defined as loci with log2 ratio ≤-0.5, gain as loci with log2 ratio ≥0.5, amplifications as loci with log2 ratio ≥2 and loci with log2 ratio ≥3.5 were considered as high level of amplifications.

source_name: neuroblastoma tumor

label_protocol: Genomic DNA was labeled following Agilent protocol (G4410-90010_CGH_Enzymatic_Protocol_v6.2.1). Yield was assessed with a nanodrop system. Tumor DNA was labeled with cyanine-5 (Cy5), and reference DNA (Agilent's Human Reference DNA) was labeled with cyanine-3 (Cy3).

extract_protocol: DNA from frozen neuroblastoma primary tumors was extracted using the QiaAmp DNA MINI kit (Qiagen). Its quality was assessed by agarose gel electrophoresis. Tumor samples were obtained before treatment at the time of diagnosis

value: neuroblastoma tumor

source_name: Agilent Human Reference DNA

value: Agilent Human Reference DNA


title: neuroblastoma sample 185


title: neuroblastoma sample 166


title: neuroblastoma sample 167


title: neuroblastoma sample 155


title: neuroblastoma sample 169


title: neuroblastoma sample 184


title: neuroblastoma sample 150


title: neuroblastoma sample 165


title: neuroblastoma sample 145


title: neuroblastoma sample 168


title: neuroblastoma sample 156


title: neuroblastoma sample 148


title: neuroblastoma sample 153


title: neuroblastoma sample 157


title: neuroblastoma sample 151


title: neuroblastoma sample 177


title: neuroblastoma sample 182


title: neuroblastoma sample 90


title: neuroblastoma sample 159


title: neuroblastoma sample 149


title: neuroblastoma sample 212


title: neuroblastoma sample 158


title: BT183

type: RNA

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

description: MAS5.0 normalized data

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: Biotin

source_name: ETMR cell line

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

value: ETMR tumor cell line


title: neuroblastoma sample 164


title: neuroblastoma sample 154


title: neuroblastoma sample 163


title: neuroblastoma sample 152


title: neuroblastoma sample 147


title: neuroblastoma sample 144


title: neuroblastoma sample 138


title: neuroblastoma sample 140


title: neuroblastoma sample 132


title: neuroblastoma sample 115


title: neuroblastoma sample 128


title: neuroblastoma sample 141


title: neuroblastoma sample 108


title: neuroblastoma sample 105


title: neuroblastoma sample 124


title: neuroblastoma sample 133


title: neuroblastoma sample 106


title: neuroblastoma sample 111


title: neuroblastoma sample 110


title: neuroblastoma sample 119


title: neuroblastoma sample 104


title: neuroblastoma sample 125


title: neuroblastoma sample 134


title: neuroblastoma sample 114


title: neuroblastoma sample 130


title: neuroblastoma sample 103


title: neuroblastoma sample 113


title: neuroblastoma sample 136


title: neuroblastoma sample 129


title: neuroblastoma sample 121


title: neuroblastoma sample 142


title: neuroblastoma sample 122


title: neuroblastoma sample 117


title: neuroblastoma sample 126


title: neuroblastoma sample 112


title: neuroblastoma sample 99


title: neuroblastoma sample 98


title: neuroblastoma sample 102


title: βCat-GOF: 1369-3

city: Boston

first: David

last: Breault

address: 300 Longwood Ave.

department: Endocrinology

institute: Boston Childrens Hospital

data_processing:
alignment with STAR to mm10 (version: 2.4.1d)
counting with featureCounts (version: 1.4.4)
count normalization with DESeq2 (version: 1.6.3)
Supplementary_files_format_and_content: combined.counts.csv: text files with the output of featureCounts generated using BAM files output by STAR
Supplementary_files_format_and_content: norm_counts.csv: normalized counts from DESeq2 (median of ratios method)

source_name: adrenals

growth_protocol: All animals were maintained on a mixed sv129-C57Bl/6 genetic background, with ad lib access to food and water, under a 12-hour light / 12-hour dark cycle.

extract_protocol:
Total RNA was isolated from whole adrenals trimmed of adherent fat and homogenized in TRI Reagent (Sigma) using a Direct-zol RNA miniprep kit (Zymo Research), following the manufacturer’s protocol.
Illumina TruSeq mRNA prep kit

value: adrenals

value: bigenic ASCre/+ ::Ctnnb1fl(ex3)/+

tag: age

value: 10-11 week old

tag: gender

value: female


title: βCat-GOF: 1369-8


title: βCat-GOF: 1387-8


title: Wt_Ctr: 1367-7

value: ASCre/+


title: βCat-GOF: 1369-2


title: βCat-GOF: 1369-2ear


title: βCat-GOF: 1369-4


title: Wt_Ctr: 1367-10


title: Wt_Ctr: 1367-5


title: neuroblastoma sample 91


title: Wt_Ctr: 1367-1-2


title: neuroblastoma sample 96


title: Mouse_liver_KAS-Input.rep2

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
Library strategy: KAS-seq
Low-quality and adapter-containing reads were trimmed from KAS-seq raw data using trim-galore package under single-end mode, reads shorter than 50 bp were removed.
Trimmed reads were aligned to reference genome (mm10) using bowtie2 (v2.3.3.1) under default parameters. Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9).
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the KAS-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
We used MACS2 to call all reported KAS-seq peaks in this manuscript. Based on the KAS-seq profile on UCSC genome browser, most KAS-seq peaks on gene body are very broad. Therefore, MACS2 was run using broad peaks-call mode under default parameters, except for --broad-cutoff 0.1 and –qvalue 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: KAS-seq tag density files(bigWig)&Peaks files(bed)

source_name: mouse liver tissue

extract_protocol:
N3-kethoxal labeling genomic DNA(gDNA) in mouse tissue was isolated. 1 µg genomic DNA was then suspended in 95 µL DNA elution buffer supplemented with 5 µL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma, 760749), and incubated at 37 ˚C for 1.5 h with gentle shake. 5 µL RNase A (Thermo, 12091039) was added into the reaction mixture followed by an incubation at 37 ˚C for 5 min. Biotinylated gDNA was then recovered by DNA Clean & Concentrator-5 kit (Zymo). gDNA was suspended into 100 µL water and subjected to sonication by using Bioruptor Pico at 30s-on/30s-off setting for 30 cycles. 5% of the fragmented DNA was saved as input, and the rest 95% was used to enrich biotin-tagged DNA by incubating with 10 µL pre-washed Dynabeads MyOne Streptavidin C1 (Thermo, 65001) at room temperature for 15 min. The beads were washed and DNA was eluted by heating the beads in 15 µL H2O at 95 ˚C for 10 min.
Eluted DNA and its corresponding input were used for library construction by using Accel-NGS Methyl-seq DNA library kit (Swift, 30024).

tag: ip method

value: Wild type

value: liver


title: Wt_Ctr: 1367-5-2


title: Wt_Ctr: 1367-1


title: neuroblastoma sample 93


title: Mouse_liver_KAS-IP.rep2

value: N3-kethoxal biotin IP


title: neuroblastoma sample 72


title: neuroblastoma sample 74


title: neuroblastoma sample 77


title: neuroblastoma sample 76


title: neuroblastoma sample 82


title: Mouse_liver_KAS-IP.rep1


title: neuroblastoma sample 71


title: neuroblastoma sample 84


title: mESC_KAS-Input.rep2

data_processing:
Low-quality and adapter-containing reads were trimmed from KAS-seq raw data using trim-galore package under single-end mode, reads shorter than 50 bp were removed.
Trimmed reads were aligned to reference genome (hg19 for HEK293T cells or mm10 for mESC) using bowtie2 (v2.3.3.1) under default parameters. Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9).
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the KAS-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
We used MACS2 to call all reported KAS-seq peaks in this manuscript. Based on the KAS-seq profile on UCSC genome browser, most KAS-seq peaks on gene body are very broad. Therefore, MACS2 was run using broad peaks-call mode under default parameters, except for --broad-cutoff 0.1 and –qvalue 0.01.
hg19&mm10
KAS-seq tag density files(bigWig)&Peaks files(bed)

source_name: mouse embryonic stem cells

growth_protocol: Murine embryonic stem (ES) cells  were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1 mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1% (v/v) nonessential amino acid stock (100×, Gibco), 1% penicillin/streptomycin stock (100×, Gibco), and 1,000 U/mL LIF (Millipore).

extract_protocol:
Cells were harvested and genomic DNA (gDNA) was isolated from cells by PureLink genomic DNA mini kit. 1 µg genomic DNA was then suspended in 95 µL DNA elution buffer supplemented with 5 µL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma, 760749), and incubated at 37 ˚C for 1.5 h with gentle shake. 5 µL RNase A (Thermo, 12091039) was added into the reaction mixture followed by an incubation at 37 ˚C for 5 min. Biotinylated gDNA was then recovered by DNA Clean & Concentrator-5 kit (Zymo). gDNA was suspended into 100 µL water and subjected to sonication by using Bioruptor Pico at 30s-on/30s-off setting for 30 cycles. 5% of the fragmented DNA was saved as input, and the rest 95% was used to enrich biotin-tagged DNA by incubating with 10 µL pre-washed Dynabeads MyOne Streptavidin C1 (Thermo, 65001) at room temperature for 15 min. The beads were washed and DNA was eluted by heating the beads in 15 µL H2O at 95 ˚C for 10 min.
Eluted DNA and its corresponding input were used for library construction by using Accel-NGS Methyl-seq DNA library kit (Swift, 30024).

treatment_protocol: Cells were incubated in completed culture medium containing 1‰ N3-kethoxal and for 5-10 min at 37 ˚C, 5% CO2.


title: mESC_KAS-Input.rep1


title: neuroblastoma sample 89


title: mESC_KAS-IP.rep1

tag: ip method or chip antibody


title: neuroblastoma sample 80


title: Input DNA_Seq

city: Detroit

first: Fei

state: Michigan

address: 259 Mack Ave.

department: Pharmaceutical Sciences

institute: Wayne State University

data_processing:
The 75-nt sequence reads were generated using Illumina NextSeq 500 platform.
The reads were mapped to the genome hg19 using the BWA algorithm with default settings.
The 75-nt reads were extended in silico (using Active Motif software) at their 3 ́- ends to a length of 200 bp fragments. The densities of fragments along the genome were determinated by dividing the genome into 32-nt bins and then counting the number of fragments in each bin. This signal maps were stored in bigWig files.
The peaks are called using SICER algorithm (version 1.1).
Normalized method is Drosophila spike-in adjustment
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files include fragment densities.

source_name: Bronchial epithelial cells

growth_protocol: Cells were grown in DMEM medium (Sigma #D5796) supplemented with 5% FBS, 1% L-Glutamamin, 1% Pen/strep Penicillin-Streptomycin (10,000 U/mL), and 2ug/ml Blasticidin.

extract_protocol:
Eight million WT and KO BEAS-2B cells were fixed and subjected to immunoprecipitation using ChIP-grade antibodies against H3K4me3 (Active Motif Cat# 39159), H3K9me3 (Active Motif Cat# 39161), H3K27me3 (Active Motif cat #39155) and H3R8me2a (Active Motif cat #39651). ChIP and input/control DNA were prepared for sequencing using Illumina NextSeq 500.
Libraries were generated using Next Gen DNA library kit (active motif #53216)

treatment_protocol: Mdig KO cells and WT were generated by CRISPR-Cas9. KO cells do not expression mdig/mina53 (Invitrogen # 397300), where WT cells have normal mdig protein expression.

value: lung, bronchus

tag: disease

value: Normal

value: WT


title: H3R8me2a_WT_ChIPSeq

tag: cell line

value: H3R8me2a (Active Motif cat #39651)


title: H3R8me2a_KO_ChIPSeq

value: mdig/mina53 KO


title: mESC_KAS-IP.rep2


title: neuroblastoma sample 75


title: neuroblastoma sample 64


title: neuroblastoma sample 66


title: neuroblastoma sample 69


title: neuroblastoma sample 57


title: neuroblastoma sample 60


title: neuroblastoma sample 62


title: neuroblastoma sample 59


title: neuroblastoma sample 58


title: neuroblastoma sample 70


title: H3K9me3_KO_ChIPSeq

value: H3K9me3 (Active Motif Cat# 39161),


title: H3K27me3_KO_ChIPSeq

value: H3K27me3 (Active Motif cat #39155)


title: H3K9me3_WT_ChIPSeq

value: H3K9me3 (Active Motif Cat# 39161)


title: H3K4me3_WT_ChIPSeq

value: H3K4me3 (Active Motif Cat# 39159)


title: H3K4me3_KO_ChIPSeq


title: H3K27me3_WT_ChIPSeq


title: GOSmock_rep2

city: Loughborough

first: Ian

middle: Frank

last: Connerton

state: Leicestershire

address: College Road, Sutton Bonington

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

description: polyA RNA enriched library

data_processing:
We used an Illumina NextSeq 500 system with 2x75 bp read length. Base-calling was performed with BaseSpace during sequencing with the Real-Time Analysis (RTA) software version 2.4.11, Workflow and Analysis Software were both version 1.37.0 generating Illumina 1.9 Phred33 quality scores encoding.
Illumina sequencing instrument generated per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using Illumina bcl2fastq Conversion Software v1.37.0.
Quality and adapter trimming was performed with the CLC Genomics Workbench 12.03 software package using the 'Trim Sequences' tool with standard parameters.
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 12.03 using the 'Map Reads to Reference' tool with standard parameters.
Mapping sequencing reads, counting and distributing the reads across genes and transcripts were computed using RNA-Seq analysis module of CLC Genomics Workbench 12.03. Briefly, genes and transcripts (with annotated splice variants) were extracted from the reference genome Hg38 (version GRCh38), using a gene and a mRNA track respectively. Next, paired reads were mapped against all the transcripts plus the entire gene. From this mapping, the paired reads are categorized and assigned to the genes and expression values for each gene and each transcript were calculated.
Counting of the mapped paired reads generated the following expression values: Total counts (total number of reads mapped to the transcript) and counts normalized for sequencing-depth CPM (mapped paired reads Counts Per Million), RPKM (Reads Per Kilobase of exon model per Million mapped reads), TPM (Transcripts Per Million). Statistical comparisons generated were: Max group means (maximum of the group average RPKM), -log2 fold change (logarithmic fold change), Fold change (signed fold change), P-value (standard p-value), FDR p-value (false discovery rate corrected p-value), Bonferroni (Bonferroni corrected p-value).
Genome_build: Hg38 (version GRCh38)
Supplementary_files_format_and_content: Expression Table GOS-FOS-1_2_3.txt is tab-delimited text file that contains gene annotations (Uniprot, Ensembl), expression values in Total counts, CPM, RPKM, TPM, fold change values, P-value,  FDR corrected p-value, Bonferroni corrected p-value for each annotated gene. Undefined values are reported as NaN (not a number), p-values<1E-16 are represented as 0.000.

source_name: ATCC® HTB-37™ Caco-2 passage 18

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM), seeded at a density of 10^5 cells onto 1.12 cm^2 Transwell® permeable support with a 0.4 μm tissue culture treated polyester membrane placed in a 12-well plate and maintained in a humidified atmosphere of 95 % air and 5 % CO2 at 37 °C for 18 days. Fresh culture medium containing DMEM (D6546, Sigma, Gillingham, UK), sterile Fetal Bovine Serum 10 % v/v (F9665 , Sigma, Gillingham, UK), L-glutamine 2mM (G7513, Sigma, Gillingham, UK), MEM non-essential amino acid solution supplement 1x (M7145, Sigma, Gillingham, UK), penicillin 100 U/ml and streptomycin 100 µg/ml (P0781, Sigma, Gillingham, UK) was replenished every 2 to 3 days.

extract_protocol:
Cells were gently washed in situ twice with ice cold sterile PBS followed by addition of 500 μl of TRIzol™ reagent (ThermoFisher Scientific, Paisley, UK) for harvesting by directly scraping the cells from the culture surface. Harvested cells were treated for total RNA extraction according to TRIzol™ reagent manufacturer’s protocol. Purified RNAs were quality-assessed using Agilent TapeStation 2200 and  were subsequently aliquoted to limit freeze-thaw cycles and stored in −80°C.
Library was prepared according to Illumina protocol. Briefly, mRNA was purified from 1 μg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490; New England Biolabs, Ipswich, UK). Indexed sequencing libraries were prepared using the NEBNext Ultra directional RNA Library Preparation Kit for Illumina (E7760; New England Biolabs, Ipswich, UK) and NEBNext Multiplex Oligos for Illumina, Index Primers Sets 1 and 2 (E7335 and E7500; New England Biolabs, Ipswich, UK). Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (Q32854; ThermoFisher Scientific, Paisley, UK). Library fragment-length distributions were analysed using the Agilent TapeStation 4200 and the Agilent High Sensitivity D1000 ScreenTape Assay (5067-5584 and 5067-5585; Agilent, Stockport, UK). For sequencing, libraries were pooled in equimolar amounts and final library quantification performed using the KAPA Library Quantification Kit for Illumina.

treatment_protocol: After 18 days of culture, a confluent monolayer was obtained with a TEER exceeding 400 Ωcm2 as measured by an EVOM voltohmmeter (World Precision Instruments, Sarasota, FL, USA). Independently, replicates of cells from passages ranging 22 to 26 were gently washed 3 times (at hourly intervals) with non-supplemented (serum-free, antibiotics-free) DMEM culture medium and finally replenished from apical and basolateral side of the Transwell® inserts with  2% (v/v) oligosaccharides-containing media or mock-treatment media for 24h exposure before being harvested for total RNA extraction.

value: Colon

value: Epithelial cells

tag: passage


title: GOSmock_rep1

description: polyA RNA enriched library


title: GOSmock_rep3

description: polyA RNA enriched library


title: GOS_rep3

description: polyA RNA enriched library


title: FOSmock_rep3

description: polyA RNA enriched library


title: GOS_rep1

description: polyA RNA enriched library


title: neuroblastoma sample 35

value: neuroblastoma tumor

value: Agilent Human Reference DNA


title: FOSmock_rep1

description: polyA RNA enriched library


title: neuroblastoma sample 56


title: neuroblastoma sample 55


title: FOSmock_rep2

description: polyA RNA enriched library


title: neuroblastoma sample 26


title: FOS_rep3

description: polyA RNA enriched library


title: neuroblastoma sample 61


title: GOS_rep2

description: polyA RNA enriched library


title: neuroblastoma sample 22


title: FOS_rep1

description: polyA RNA enriched library


title: FOS_rep2

description: polyA RNA enriched library


title: neuroblastoma sample 28


title: neuroblastoma sample 20


title: neuroblastoma sample 17


title: neuroblastoma sample 25


title: neuroblastoma sample 21


title: neuroblastoma sample 24


title: neuroblastoma sample 16


title: neuroblastoma sample 15


title: neuroblastoma sample 13


title: KI740_Gro_BJ5ta

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
GRO_BJ5ta_PE740-742_hg19_nm.bw
GRO_BJ5ta_PE740-742_hg19_np.bw

data_processing:
Library strategy: GRO-seq
GRO-seq reads were aligned to the hg19 human reference genome using Bowtie 2 with  -X 2000 --no-mixed --no-discordant parameters. Reads with MAPQ score greater than 20 were used in downstream analyses.
We computed “normalized GRO-seq base coverage,” which was the sum of GRO-seq fragment per-base coverage normalized to gene lengths and sequencing depths.
Genome_build: hg19
Supplementary_files_format_and_content: *.bw: bigWig file for length-normalized depth-normalized genome-wide perbase fragment coverage.

growth_protocol: Cells were cultured in high-glucose DMEM (Gibco, 11965-092) containing 9% fetal bovine serum (FBS) and penicillin-streptomycin.

extract_protocol:
RNAs were purified from the reaction by Trizol LS (Invitrogen 10296028) followed by isopropanol precipitation. RNAs were treated with TurboDNase (Ambion AM18907) and fragmented by Fragmentation Buffer (Ambion AM8740). BrU-incorporated RNA fragments were immunoprecipitated with mouse monoclonal anti-BrdU antibody 3D4 (BD Biosciences 555627).
Immunoprecipitated RNAs were used to construct DNA sequencing libraries using NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs E7760).

treatment_protocol: Nuclei isolated from trypsinized cells are resuspended in Nuclear Storage buffer (50 mM Tris pH 8.0, 0.1 mM EDTA, 5 mM MgCl2, 40% glycerol, RNase inhibitor). An equal volume of 2x NRO buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 0.5 mM ATP, 0.5 mM GTP, 0.5 mM BrUTP, 2 µM CTP) was added to the nuclear suspension and incubated for 4 min at 30ºC for nuclear run-on reaction. The reaction was supplemented with Sarkosyl (0.5% final concentration) and further incubated for 4 min at 30ºC.

tag: lmna genotype

tag: transgene

value: No

tag: cell sorting

value: No sorting


title: neuroblastoma sample 27


title: neuroblastoma sample 19


title: KI742_Gro_BJ5ta

value: Wild type


title: HEK293_RNA-seq.rep2

data_processing:
Low-quality and adapter-containing reads were trimmed using trim-galore package under paired-end mode, any reads shorter than 50 bp were removed.
The remaining trimmed sequences were mapped to the reference genome (hg19) with hisat2 under default settings.
The expression level of each gene was quantified with normalized FPKM with FPKM_count.pl in RSeQC software.
Expressed genes were defined using the FPKM cutoff over 0.5.
hg19
FPKM of expressed genes(xls)

source_name: HEK293 cells

growth_protocol: HEK293T cells were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and grown at 37 ˚C with 5% CO2

extract_protocol:
Total RNA were extracted from cells by using Trizol reagent (Thermo, 15596026). Total RNA were subjected to polyA selection by using Dynabeads mRNA purification kit (Thermo, 61006).
20 ng polyA RNA were used for library construction by using SMARTer Stranded RNA-seq kit (Takara, 634839).


title: HEK293_RNA-seq.rep1


title: neuroblastoma sample 12


title: HEK293_Trip_KAS-IP.rep1

value: N3-kethoxal biotin IP

tag: treatment

value: Treated for 2h under 1µM triptolide (Sigma, T3652)


title: HEK293_Trip_KAS-Input.rep1


title: HEK293_Trip_KAS-IP.rep2


title: HEK293_Trip_KAS-Input.rep2


title: HEK293_DRB_KAS-Input.rep2

value: Treated for 2h under 100µM DRB (Sigma, D1916)


title: HEK293_DRB_KAS-IP.rep2


title: HEK293_DRB_KAS-IP.rep1


title: HEK293_DRB_KAS-Input.rep1


title: HEK293_Ctrl_KAS-IP.rep2

value: Treated for 2h under DMSO (Sigma, 760749)


title: neuroblastoma sample 9


title: neuroblastoma sample 211


title: HEK293_Ctrl_KAS-Input.rep2


title: AB3976: Patient_4_TEP_Rep3

city: Bethesda

first: Luigi

last: Notarangelo

state: MD

address: 10 center drive, 10CRC, 5W3840

department: NIAID

institute: NIH

data_processing:
bcl conversion and de-multiplexing was performed with bcl2fastq
Read alignment was performed with STAR v2.6.0. The genome index was generated with a version of the GRCh38 build obtained from GENCODE. The transcript annotation file was also obtained from GENCODE (v28 primary assembly annotation)
Read counting was performed with featureCounts (part of the subread package, v1.6.2). Key parameters:  -T 16 -O -t exon -g gene_name -a gencode.v28.primary_assembly.annotation.gtf
The ouptut of featureCounts (raw read counts) was converted to a matrix (RawReadCounts.txt) with R v3.5.1
Genome_build: GRCh38
Supplementary_files_format_and_content: RawReadCounts.txt: A tab-delimited text file with 56871 rows and 28 columns. The first row is a header row with sample IDs. The first column has gene symbols. The values are raw (un-normalized) read counts generated by featureCounts.

source_name: Thymic epithelial progenitor cells

growth_protocol: Primary skin fibroblasts from Patient 1, Patient 4, and a healthy control (BJ fibroblast line, ATCC) were reprogrammed to iPSCs by infection with the non-integrating CytoTune Sendai viral vector kit (Thermo Fisher Scientific) .

extract_protocol:
RNeasy kit (QIAGEN, Hilden, Germany)
TruSeq Stranded mRNA Library Prep Kit for NeoPrep (NeoPrep) for Control_1 and Patient_1, or NEBNext Ultra II Directional with poly-A selection (NEBNext) for Control_2 and Patient_4

treatment_protocol: For differentiation, iPSCs were transferred to plates coated with Corning Matrigel hESC-qualified Matrix. After 4-5 passages, the cells were plated on Matrigel-coated 24-well plates at a density of 2.5 x 10^5 cells/cm^2. Between day 1 and day 5 (d1-d5), iPSC differentiation was carried out in RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 1% penicillin/streptomycin, 1% L-glutamine, and increasing concentrations of KSR (0% on d1, 0.2% on d2–d3, and 2% on d4-d5). In the period d6-d14, cells were differentiated in DMEM/F12 with 1% penicillin/streptomycin, 1% L-glutamine, 0.5% v/v B-27 supplement (Thermo Fisher Scientific, Waltham, MA). During this period, the following factors were added to the culture: activin A, 100 ng/ml (d1–d5); Wnt3a, 25 ng/ml (d1) or 50 ng/ml (d8–d14); all-trans retinoic acid (RA), 0.25 µM (d6–d8) or 0.1 µM (d9–d14); BMP4, 50 ng/ml (d6–d14); LY364947, 5 mM (d6–d9); FGF8b, 50 ng/ml (d8–d14); and KAAD-cyclopamine, 0.5 mM (d8–d14). Supplements and factors were from Thermo Fisher Scientific, Waltham, MA (B27, KSR); R&D Systems, Minneapolis, MN (activin A, Wnt3a, BMP4, and FGF8b); and, Millipore-Sigma, St. Louis, MO (RA, KAAD-cyclopamine, LY364947).

tag: cell type

value: iPSCs derived thymic epithelial progenitor cells

tag: donor type

value: Patient

tag: library prep

value: NEBNext


title: neuroblastoma sample 208

tag: tissue


title: neuroblastoma sample 14


title: AB3975: Patient_4_TEP_Rep2


title: neuroblastoma sample 206


title: neuroblastoma sample 210


title: HEK293_Ctrl_KAS-IP.rep1

tag: genotype


title: neuroblastoma sample 86


title: AB3974: Patient_4_TEP_Rep1


title: neuroblastoma sample 53


title: neuroblastoma sample 88


title: AB3965: Control_2_TEP_Rep1

value: Control


title: neuroblastoma sample 202


title: neuroblastoma sample 203


title: AB3966: Control_2_TEP_Rep2


title: neuroblastoma sample 209


title: neuroblastoma sample 65


title: neuroblastoma sample 67


title: HEK293_Ctrl_KAS-Input.rep1


title: AB3939: Patient_4_iPS_Rep2

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: neuroblastoma sample 205


title: neuroblastoma sample 118


title: neuroblastoma sample 204


title: neuroblastoma sample 50


title: neuroblastoma sample 51


title: neuroblastoma sample 47


title: Mouse_liver_KAS-Input.rep1

value: liver


title: AB3931: Control_2_iPS_Rep3


title: neuroblastoma sample 46


title: AB3938: Patient_4_iPS_Rep1


title: AB3930: Control_2_iPS_Rep2


title: neuroblastoma sample 52


title: AB2638: Patient_1_TEP_Rep2

value: NeoPrep


title: AB3929: Control_2_iPS_Rep1


title: AB2637: Patient_1_TEP_Rep1


title: AB2635: Control_1_TEP_Rep2


title: AB2636: Control_1_TEP_Rep3


title: AB2634: Control_1_TEP_Rep1


title: neuroblastoma sample 44


title: neuroblastoma sample 43


title: neuroblastoma sample 214


title: neuroblastoma sample 201


title: neuroblastoma sample 48


title: AB2630: Control_1_DE_Rep3

source_name: Definitive endoderm

value: iPSCs derived definitive endoderm cells


title: neuroblastoma sample 196

value: neuroblastoma tumor


title: AB2639: Patient_1_TEP_Rep3


title: AB2627: Patient_1_iPS_Rep3


title: neuroblastoma sample 213

value: Agilent Human Reference DNA


title: AB2628: Control_1_DE_Rep1


title: neuroblastoma sample 199


title: neuroblastoma sample 197


title: AB2625: Patient_1_iPS_Rep1


title: AB2624: Control_1_iPS_Rep3


title: neuroblastoma sample 194


title: AB2629: Control_1_DE_Rep2


title: neuroblastoma sample 200


title: neuroblastoma sample 198


title: AB2623: Control_1_iPS_Rep2


title: neuroblastoma sample 195


title: AB2626: Patient_1_iPS_Rep2


title: AB2622: Control_1_iPS_Rep1


title: KI542_ATAC_BJ5ta

data_processing:
For alignment, the first 38 nt from the both 5′ ends of the 41-nt paired-end reads were used. The rationale of this trimming is that the minimum size of DNA fragments that can be flanked by Tn5 transposition events has been estimated to be 38 bp, and therefore, a 41-nt read could contain a part of read-through adaptors, which may affect disproportionally mapping of these small fragments. Our bowtie2 mapping parameters were, therefore, [-X 2000 --no-mixed --no-discordant --trim3 3].
The center of the active Tn5 dimer is located +4-5 bases offset from the 5′-end of the transposition sites. To represent the Tn5 loading center by reads, the 5′-end of the plus-strand and minus-strand reads were shifted 4 nt and 5 nt in the 5′-to-3′ direction, respectively, and the shifted end (1 nt) was extended +/–100 nt.
To generate background datasets that capture local bias of read coverage, the shifted read ends were extended +/–5,000 nt and used to construct local lambda background file. This local lambda file and the Tn5 density file were used as inputs for MACS2 “bdgcomp” and “bdgpeakcall” to generate the fold-enrichment file for Tn5 density over background (bigWig).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig for coverage-normalized fold enrichment scores.

extract_protocol:
One hundred thousand trypsinized cells were incubated with ATAC hypotonic buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2) at 4ºC for 10 min during 500 g centrifugation. Cells were incubated in Tagmentation mix (Tagmentation DNA buffer Illumina 15027866; Tagmentation DNA enzyme Illumina 15027865) at 37ºC for 30 min.
Purified DNA was used to construct high-throughput sequencing libraries using NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs M0541).

value: No


title: KI540_ATAC_BJ5ta

value: No sorting


title: AB3940: Patient_4_iPS_Rep3


title: neuroblastoma sample 193


title: neuroblastoma sample 188


title: neuroblastoma sample 187


title: neuroblastoma sample 189


title: neuroblastoma sample 180


title: neuroblastoma sample 190


title: neuroblastoma sample 207


title: neuroblastoma sample 45


title: neuroblastoma sample 192


title: neuroblastoma sample 181


title: neuroblastoma sample 186


title: AB3967: Control_2_TEP_Rep3


title: 28-z CAR-transduced T cells, rep 3

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

description: 28z anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep3

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 2.0 ST array for 16-18 hr at 45°C.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Scanner #4)

data_processing: Raw intensity files were processed using Affymetrix Expression Console (version 1.4.1). Processed using RMA algorithm.

label: biotin

source_name: 28-z CAR-transduced human CD8+ T cells, biological replicate #3

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate.

growth_protocol: Human CD8+ T cells were cultured in vitro (RPMI supplemented with 10% human AB serum).

extract_protocol: Stimulated T cells were collected 4 days later and CAR+ CD8+ T cells were isolated by flow cytometry. The expression of CAR genes was detected by protein L staining. RNA was isolated from the purified CAR-T cells with the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: CD8+ T cells were retrovirally transduced with individual anti-CD19 CAR genes (28-z, 28-BB-z and 28-IL2RB-z (YXXQ)) and were stimulated with K562 cells expressing CD19.

value: CD8+ T cells

tag: car gene

tag: donor


title: neuroblastoma sample 175


title: 28-IL2RB-z (YXXQ) CAR-transduced T cells, rep 3

description: 28IL2RBz(YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep3

source_name: 28-IL2RB-z (YXXQ) CAR-transduced human CD8+ T cells, biological replicate #3

value: 28-IL2RB-z (YXXQ)


title: 28-IL2RB-z (YXXQ) CAR-transduced T cells, rep 1

description: 28IL2RBz(YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep1

source_name: 28-IL2RB-z (YXXQ) CAR-transduced human CD8+ T cells, biological replicate #1


title: 28-z CAR-transduced T cells, rep 1

description: 28z anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep1

source_name: 28-z CAR-transduced human CD8+ T cells, biological replicate #1


title: 28-IL2RB-z (YXXQ) CAR-transduced T cells, rep 2

description: 28IL2RBz(YXXQ) anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep2

source_name: 28-IL2RB-z (YXXQ) CAR-transduced human CD8+ T cells, biological replicate #2


title: 28-BB-z CAR-transduced T cells, rep 2

description: 28BBz anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep2

source_name: 28-BB-z CAR-transduced human CD8+ T cells, biological replicate #2


title: 28-BB-z CAR-transduced T cells, rep 3

description: 28BBz anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep3

source_name: 28-BB-z CAR-transduced human CD8+ T cells, biological replicate #3


title: 28-z CAR-transduced T cells, rep 2

description: 28z anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep2

source_name: 28-z CAR-transduced human CD8+ T cells, biological replicate #2


title: neuroblastoma sample 191

source_name: neuroblastoma tumor

source_name: Agilent Human Reference DNA


title: neuroblastoma sample 176


title: neuroblastoma sample 174


title: 28-BB-z CAR-transduced T cells, rep 1

description: 28BBz anti-CD19 CAR-transduced CD8+ T cells stimulated by CD19, rep1

source_name: 28-BB-z CAR-transduced human CD8+ T cells, biological replicate #1


title: neuroblastoma sample 1


title: neuroblastoma sample 171


title: neuroblastoma sample 178


title: neuroblastoma sample 8


title: perturbseq_ieps

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

description: Cells were encapsulted and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

molecule: polyA RNA

source_name: Induced endoderm progenitors derived from mouse embryonic fibroblasts

extract_protocol:
Cells were encapsulted and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry)
10x Genomics Chromium single cell preparation

tag: strain


title: neuroblastoma sample 173


title: neuroblastoma sample 172


title: neuroblastoma sample 123


title: neuroblastoma sample 179


title: neuroblastoma sample 162


title: neuroblastoma sample 170


title: neuroblastoma sample 161


title: neuroblastoma sample 146


title: neuroblastoma sample 143


title: neuroblastoma sample 95


title: neuroblastoma sample 68


title: neuroblastoma sample 4


title: neuroblastoma sample 94


title: neuroblastoma sample 78


title: neuroblastoma sample 116


title: neuroblastoma sample 160


title: neuroblastoma sample 109


title: neuroblastoma sample 10


title: neuroblastoma sample 11


title: neuroblastoma sample 85


title: neuroblastoma sample 107


title: neuroblastoma sample 79


title: neuroblastoma sample 2


title: neuroblastoma sample 131


title: neuroblastoma sample 100


title: neuroblastoma sample 135


title: neuroblastoma sample 97


title: neuroblastoma sample 101


title: neuroblastoma sample 81


title: neuroblastoma sample 120


title: neuroblastoma sample 137


title: KI835_Input_LCDD

description: KI835_Input_LCDD_312724_hg19_BT2q20x200n.bw

data_processing:
ChIP-seq reads were mapped to the hg19 human reference genome using Bowtie2 with the default “--sensitive” parameter. Reads with MAPQ score greater than 20 were used in downstream analyses.
Reads from biological replicates of ChIP and corresponding input samples were used as input files for MACS2. In MACS2, duplicate reads were removed first, and then significantly enriched peak regions were called, and input-normalized perbase coverage of 200 nt-extended reads was computed (“fold enrichment bedgraph”).
Genome_build: hg19

source_name: LMNA-null with transgene LMNC-S22D-S392D cc1499-6

growth_protocol: Cells were cultured in high-glucose DMEM (Gibco, 11965-092) containing 9% fetal bovine serum (FBS) and penicillin-streptomycin. Progeria-patient primary skin fibroblasts AG11498 (Coriell Cell Repository) and primary skin fibroblasts from a healthy donor GM07492 (Coriell Cell Repository) were grown in MEM Alpha (Life Technologies, 12561-056) with 9% FBS and penicillin-streptomycin.

extract_protocol:
Cells in culture dishes were crosslinked in 1% formaldehyde for 15 min and the reaction was quenched by 125 mM glycine. Cross-linked cells were washed with LB1 (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and then with LB2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 10 mM Tris-HCl pH 8.0). Chromatin was extracted by sonication in LB3-Triton (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroyl sarcosine, 1% Triton). LB1, LB2, and LB3-Triton used during extraction were supplmented with 1x protease inhibitor cocktail (Calbiochem 539131) and 100 nM phosphatase inhibitor Nodularin (Enzo ALX-350-061).  One million cells were used in a single 200-µL ChIP reaction. Antibodies used in ChIP are: rabbit monoclonal anti-phospho-Ser22-LMNA antibody D2B2E (Cell Signaling 13448S, Lot # 1; 5 µL per IP); mouse monoclonal anti-unphospho-Ser22-LMNA antibody E1 (Santa Cruz Biotechnology sc-376248, Lot # H2812; 10 µL per IP); mouse monoclonal anti-acetyl-Lys27 histone H3 antibody (Wako MABI0309, Lot # 14007; 2 µL per IP); mouse monoclonal anti-trimethyl-Lys4 histone H3 antibody (Wako MABI14004, Lot # 14004; 2 µL per IP); mouse monoclonal anti-Ty1 antibody (Diagenode C15200054, Lot # 005; 1 µL per IP).
Immunoprecipitated DNA was reverse-crosslinked and used to construct high-throughput sequencing libraries using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370).

value: LMNA null

value: Lamin C-S22D/S392D

tag: antibody

value: Input


title: neuroblastoma sample 127


title: neuroblastoma sample 73


title: neuroblastoma sample 92


title: KI834_Input_LCAA

description: KI834_Input_LCAA_312723_hg19_BT2q20x200n.bw

source_name: LMNA-null with transgene LMNC-S22A-S392A cc1499-5

value: Lamin C-S22A/S392A


title: neuroblastoma sample 63


title: KI833_Input_LCWT

description: KI833_Input_LCWT_312722_hg19_BT2q20x200n.bw

source_name: LMNA-null with transgene LMNC cc1499-4

value: Lamin C


title: neuroblastoma sample 42


title: neuroblastoma sample 83


title: KI831_Input_LAAA

description: KI831_Input_LAAA_312720_hg19_BT2q20x200n.bw

source_name: LMNA-null with transgene LMNA-S22A-S392A cc1499-2

value: Lamin A-S22A/S392A


title: KI832_Input_LADD

description: KI832_Input_LADD_312721_hg19_BT2q20x200n.bw

source_name: LMNA-null with transgene LMNA-S22D-S392D cc1499-3

value: Lamin A-S22D/S392D


title: KI828_Ab190380_LCAA

description: Ab190380_LCAA_macs2hg19_t816t822t828c834_fe_k1sort.bw

value: anti-full-length-LMNA (Abcam ab190380)


title: KI826_Ab190380_LADD

description: Ab190380_LADD_macs2hg19_t814t820t826c832_fe_k1sort.bw


title: KI827_Ab190380_LCWT

description: Ab190380_LCWT_macs2hg19_t815t821t827c833_fe_k1sort.bw


title: neuroblastoma sample 87


title: KI830_Input_LAWT

description: KI830_Input_LAWT_312719_hg19_BT2q20x200n.bw

source_name: LMNA-null with transgene LMNA cc1499-1

value: Lamin A


title: KI829_Ab190380_LCDD

description: Ab190380_LCDD_macs2hg19_t817t823t829c835_fe_k1sort.bw


title: neuroblastoma sample 6


title: KI825_Ab190380_LAAA

description: Ab190380_LAAA_macs2hg19_t813t819t825c831_fe_k1sort.bw


title: genomic DNA from HCC827GR_hydroxymethylation

city: Leuven

first: Diether

last: Lambrechts

address: Herestraat 49

department: Human Genetics

country: Belgium

institute: KU Leuven

description: Zhang et al., 2016

hyb_protocol: TAB-seq processed DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K or EPIC Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data processing was done using Bioconductor’s minfi package in R. Briefly, raw intensity files were read into R. Samples were normalized using Subset-quantile Within Array Normalization (SWAN).

label: Cy5 and Cy3

source_name: cultured cells

label_protocol: Standard Illumina Protocol

extract_protocol: Cultured cells were washed with DPBS and detached with trypsin-EDTA (0.25%) (Thermofisher). Cell pellets were obtained by centrifugation and were washed once in DPBS. Subsequently, nucleic acids were extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions. All buffers were supplemented with deferoxamine (DFO, 200µM). DNA was dissolved in 80 µL PBS-DFO with RNaseA (200 U, NEB) and incubated for 10 min at 37 ˚C. Next, proteinase K (200 U) was added and the mixture was incubated for 30 min at 56˚C. DNA was purified using the QIAQuick blood and tissue kit (all buffers supplemented with DFO). Elution was performed in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -20˚C until further processing

tag: establishment status

value: Derived in vitro cell line

tag: resistant status

value: resistant

tag: drug

value: gefitinib

tag: illumina platform_id

value: EPIC

value: genomic DNA


title: neuroblastoma sample 40

value: neuroblastoma tumor

value: Agilent Human Reference DNA


title: neuroblastoma sample 41


title: neuroblastoma sample 38


title: genomic DNA from HCC827P_hydroxymethylation

description: Zhang et al., 2016

tag: cell line

value: Established in vitro cell line

value: sensitive


title: neuroblastoma sample 139


title: KI824_Ab190380_LAWT

description: Ab190380_LAWT_macs2hg19_t812t818t824c830_fe_k1sort.bw

tag: lmna genotype

value: LMNA null

tag: transgene

value: No sorting


title: genomic DNA from HCC4006GR_hydroxymethylation

description: Zhang et al., 2016


title: neuroblastoma sample 36


title: genomic DNA from HCC4006P2_hydroxymethylation

description: Zhang et al., 2016


title: KI823_Ab190380_LCDD

value: Lamin C-S22D/S392D

tag: cell sorting


title: genomic DNA from HCC4006ER_hydroxymethylation

description: Jia et al., 2013

value: erlotinib


title: neuroblastoma sample 39


title: neuroblastoma sample 29


title: neuroblastoma sample 31


title: neuroblastoma sample 23


title: neuroblastoma sample 34


title: neuroblastoma sample 33


title: genomic DNA from HCC4006P1_hydroxymethylation

description: Jia et al., 2013


title: A375_POLK_3

first: Nathaniel

middle: R

last: Campbell

institute: Memorial Sloan Kettering Cancer Center

data_processing:
quality control with FASTQC (Babraham Bioinformatics)
trimming with TRIMMOMATIC
reads were aligned to GRCh38 (Ensembl version 90) using STAR with --quantMode GeneCounts
quality control via SeQC
Differential expression was calculated with DESeq2
Genome_build: GRCh38, Ensembl version 90
Supplementary_files_format_and_content: CSV file with raw counts from STAR

source_name: Melanoma

growth_protocol: A375 cells were grown in DMEM supplemented with 2 mM glutamine, 100 IU/ml penicillin, 100 μg/ml streptomycin, and 10% heat-inactivated fetal bovine serum

extract_protocol:
Total RNA from treated cells was extracted using the Quick-RNA Mini-Prep kit (Zymo)
Purified RNA was delivered to GENEWIZ (South Plainfield, NJ) for mRNA preparation with the TruSeq RNA V2 kit (Illumina)

treatment_protocol: Knockout was performed in A375 cells using the Alt-R CRISPR-Cas9 system (IDT)

tag: sgrna

value: POLK

tag: cell type

value: melanoma


title: KI822_Ab190380_LCAA

value: Lamin C-S22A/S392A

value: anti-full-length-LMNA (Abcam ab190380)


title: A375_POLK_2


title: genomic DNA from PancB1Q_hydroxymethylation

description: Lund et al., 2015

value: Derived in vitro cell line


title: genomic DNA from PancVB_hydroxymethylation

description: Lund et al., 2015

value: PancVB


title: genomic DNA from U100

description: Nakagawa et al., 2015

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K or EPIC Beadchips using standard Illumina protocol

data_processing:
Data processing was done using Bioconductor’s minfi package in R. Briefly, raw intensity files were read into R. Samples were normalized using Subset-quantile Within Array Normalization (SWAN).
normalized data matrix includes Average SWAN normalized Beta of CpGs included on both EPIC and 450K arrays and detection P-values

extract_protocol: genomic DNA was extracted and purified from cultured cells using Qiagen DNeasy Kit according to standard instructions

value: resistant

value: olaparib


title: genomic DNA from U10

description: Nakagawa et al., 2015

value: EPIC


title: genomic DNA from UWB1289

description: Nakagawa et al., 2015


title: A375_POLK_1


title: KI820_Ab190380_LADD

value: Lamin A-S22D/S392D


title: KI821_Ab190380_LCWT

value: Lamin C


title: A375_Control_3

value: Non-targeting Control


title: neuroblastoma sample 18

data_processing: The data were analyzed using the Agilent Genomic Workbench 7.0.40 software, the altered chromosomal regions and breakpoints events were detected using ADM-1 (threshold 10) with 0.5 Mb window size. Losses were defined as loci with log2 ratio ≤-0.5, gain as loci with log2 ratio ≥0.5, amplifications as loci with log2 ratio ≥2 and loci with log2 ratio ≥3.5 were considered as high level of amplifications.

extract_protocol: DNA from frozen neuroblastoma primary tumors was extracted using the QiaAmp DNA MINI kit (Qiagen). Its quality was assessed by agarose gel electrophoresis. Tumor samples were obtained before treatment at the time of diagnosis

value: neuroblastoma tumor

value: Agilent Human Reference DNA


title: neuroblastoma sample 3


title: genomic DNA from HCC827GR

description: Zhang et al., 2016

value: gefitinib


title: genomic DNA from HCC4006GR

description: Zhang et al., 2016


title: genomic DNA from HCC827P

description: Zhang et al., 2016

value: Established in vitro cell line

value: sensitive


title: A375_Control_2


title: genomic DNA from HCC4006P2

description: Zhang et al., 2016


title: KI817_Ab190380_LCDD

value: LMNA null

value: Lamin C-S22D/S392D

value: No sorting


title: KI819_Ab190380_LAAA

value: Lamin A-S22A/S392A

value: anti-full-length-LMNA (Abcam ab190380)


title: KI818_Ab190380_LAWT

value: Lamin A


title: A375_Control_1

value: melanoma


title: RR-Tmem-plate1-H3

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

data_processing:
Reads were mapped to the mouse genome mm10 using TopHat v2.0.12 with bowtie v1.1.0
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq Version 2.1.0 (Kalari et al., 2014)
In order to correct for GC bias and gene length differences and obtain similar quantile-by-quantile distributions of gene expression levels across samples, we performed conditional quantile normalization (CQN) on the raw gene counts (Hansen et al., 2012). According to the bimodal distribution of the CQN-normalized and log2-transformed reads per kb per million (RPKM) gene expression values, genes with an average log2 RPKM < 1 across all genotypes were considered not expressed and were excluded from further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text file including CQN-normalized, log2-transformed RPKM values for all samples

source_name: brain

extract_protocol:
Brains from 30 mice were harvested from 8-month-old Tmem106b mice. RNA extraction from the cerebral hemispheres of all 30 brains was performed in one experiment using the RNeasy Plus Mini Kit (#74136; Qiagen) as in our previous study (Nicholson et al., 2018).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: 8 months

tag: Sex

value: Male

tag: cohort

tag: rin


title: RR-Tmem-plate1-H1

tag: genotype

value: Female


title: RR-Tmem-plate1-H2


title: RR-Tmem-plate1-G1


title: RR-Tmem-plate1-G2


title: RR-Tmem-plate1-G3


title: KI816_Ab190380_LCAA

value: Lamin C-S22A/S392A


title: Pat-OE-Gal 1

city: Montreal

first: Isabella

last: Straub

state: QC

address: 3801 University

country: Canada

institute: McGill University

data_processing:
mRNA sequencing via polyA selection
llumina HiSeq, PE 2x150
Data was processed by GENEWIZ

source_name: fibroblasts

growth_protocol: cells were grown for two days in respective media, glucose or galactose before harvesting

extract_protocol:
RNA was prepared from cultured fibroblasts with Quiagen RNA Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: fibroblasts

value: CHCHD10 p.R15L heterozygous+ ectopically expressed CHCHD10 wildtype


title: Pat-OE-Gal 2


title: KI815_Ab190380_LCWT

value: Lamin C

tag: antibody


title: RR-Tmem-plate1-F4


title: Pat-OE-Gal 3


title: RR-Tmem-plate1-F2


title: KI814_Ab190380_LADD

value: Lamin A-S22D/S392D


title: Pat-OE-Glc 3


title: KI813_Ab190380_LAAA


title: RR-Tmem-plate1-E4


title: Pat-OE-Glc 2


title: KI812_Ab190380_LAWT


title: RR-Tmem-plate1-F1


title: Pat-OE-Glc 1


title: RR-Tmem-plate1-E3


title: RR-Tmem-plate1-E2


title: KI805_JUN_GM07492

description: cJun_GM07492_macs2hg19_t609t805c384c482_fe_k1sort.bw

source_name: GM07492 normal fibroblast

value: Wild type

value: No

value: anti-Jun (Santa Cruz H-79 sc-1694)


title: RR-Tmem-plate1-D4


title: RR-Tmem-plate1-E1


title: Patient Galactose 3

value: CHCHD10 p.R15L heterozygous


title: RR-Tmem-plate1-D2


title: RR-Tmem-plate1-D1


title: KI803_K27me3_GM07492

description: K27me3_GM07492_macs2hg19_t802t803c384_fe_k1sort.bw

value: No sorting

value: anti-H3K27me3 (Active Motif MABI0323)


title: RR-Tmem-plate1-F3


title: RR-Tmem-plate1-C3


title: Patient Galactose 2


title: Patient Galactose 1


title: RR-Tmem-plate1-C4


title: KI802_K27me3_GM07492


title: RR-Tmem-plate1-C2


title: Patient Glucose 2


title: KI801_K27me3_AG11498

description: K27me3_AG11498_macs2hg19_t800t801c383_fe_k1sort.bw

source_name: AG11498 HGPS fibroblast

value: LMNA G608G


title: Patient Glucose 3


title: RR-Tmem-plate1-B4


title: RR-Tmem-plate1-B3


title: RR-Tmem-plate1-B2


title: Patient Glucose 1


title: KI800_K27me3_AG11498


title: KI640_E1_AG11498

description: E1_AG11498_macs2hg19_t603t640c539_fe_k1sort.bw

value: anti-pan-N-terminal-LMNA (Santa Cruz E-1 sc-376248)


title: mRNA seq from IGROV-1 / CDDP

data_processing:
Adaptors were removed using FastXClipper
Reads were mapped using Bowtie and TopHat.
Mapped files were sorted using SAMtools.
Counts were extracted using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files, raw counts

growth_protocol: HepG2 cell lines were cultured in William’s E medium with 10% fetal bovine serum (FBS) and 1% pencillin-streptomycin (PS, Life Technology). HCC4006, HCC827, Panc03.27, IGROV-1 and UWB1.289 cell lines and their derivatives were cultured in RPMI 1640 glutaMAX medium supplemented with 10 % FBS and 1% PS. All cells were cultured at 37˚C, in atmospheric oxygen concentration (21%) with 5% CO2. Splitting of cells was performed using trypsin-EDTA. Cell cultures were regularly confirmed to be mycoplasm-free.

extract_protocol:
Cell culture medium was removed, cells were washed with DPBS, TRIzol (Life Technologies) was added and cells were processed according to manufacturer’s guidelines.
Up to 4 µg of total RNA was used as an input for the Stranded mRNA-Seq Kit (KAPA). mRNA is captured using magnetic oligo-dT beads: while mRNA is retained, other RNA is washed away in two subsequent washes. mRNA fragments are fragmented and converted to cDNA, with dUTP incorporated in to the second cDNA strands. A-tailing, adapter ligation and enrichment is carried out, to obtain libraries. Enrichment of the libraries is achieved by using KAPA HiFi Hotstart Readymix. The strand marked with dUTP is not amplified, allowing strand specificity.

value: IGROV-1 / CDDP

tag: establishment status

value: Derived in vitro cell line

value: resistant

value: cisplatin

tag: reference

value: Ma et al., 1998


title: RR-Tmem-plate1-D3

value: 8 months

value: Female


title: KI804_JUN_AG11498

description: cJun_AG11498_macs2hg19_t611t804c383c539_fe_k1sort.bw


title: RR-Tmem-plate1-A4

value: Male


title: RR-Tmem-plate1-B1


title: RR-Tmem-plate1-A3


title: RR-Tmem-plate1-A2


title: KI637_E1_GM07492

description: E1_GM07492_macs2hg19_t469t637c482_fe_k1sort.bw


title: KI603_E1_AG11498


title: RR-Tmem-plate1-A1


title: RR-Tmem-plate1-C1


title: mRNA seq from U100

tag: resistant status

tag: drug

value: olaparib

value: Nakagawa et al., 2015


title: tb10_4414_Elf5_reporter_T2_neg_C3

city: Philadelphia

first: Andres

last: Blanco

state: PA

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

data_processing:
fastq files were mapped to the mouse transcriptome (gencode version M14) using salmon
reat counts were summarized to the gene level using tximport
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: summarized counts per gene - not normalized for sequencing depth

source_name: breast tumor

extract_protocol: Tumors were removed and digested with collagenase and hyaluronidase. Tumor cells were sorted with CD45, CD31 and TER119 antibodies to isolate tumor cell enriched population. Based on GFP (Elf5 expression), GFP+ and GFP- cells were further sorted from epithelial enriched population. RNA was harvested using Purelink RNA Mini Kit cat#12183018A and 1 ug of total RNA was used for the construction of sequencing libraries.

tag: strain

tag: genotype/variation


title: KI469_E1_GM07492

tag: lmna genotype

value: Wild type

tag: transgene

value: No


title: tb13_4413_Elf5_reporter_T2_neg_C3


title: mRNA seq from U10

tag: cell line


title: tb09_4414_Elf5_reporter_T2_pos_C3


title: mRNA seq from UWB1289

value: Established in vitro cell line

value: sensitive


title: tb11_4413_Elf5_reporter_T1_neg_C3


title: tb12_4413_Elf5_reporter_T2_pos_C3


title: tb08_4414_Elf5_reporter_T1_neg_C3


title: 4972_WT_C3_T1

source_name: breast tumor_WT

extract_protocol:
Tumors were removed and digested with collagenase and hyaluronidase. Tumor cells were sorted with CD45, CD31 and TER119 antibodies to isolate tumor cell enriched population from either genotype.
RNA was harvested using Purelink RNA Mini Kit cat#12183018A and 1 ug of total RNA was used for the construction of sequencing libraries.

tag: genotyp/variation

value: wild type; Elf5+/+

value: C3-T+ tumors


title: mRNA seq from HCC827GR

value: gefitinib

value: Zhang et al., 2016


title: KI345_K27ac_AG11498

description: K27ac_AG11498_macs2hg19_t345t426c383_fe_k1sort.bw

value: LMNA G608G

tag: cell sorting

value: No sorting


title: 3211_HET_C3_T2

source_name: breast tumor_HET


title: 3211_HET_C3_T1


title: mRNA seq from HCC827P


title: KI383_Input_AG11498

description: KI383_Input_AG11498_Ste08114_hg19_BT2q20x200n.bw


title: 3210_WT_C3_T1


title: mRNA seq from HCC4006GR

value: Derived in vitro cell line

value: resistant


title: mRNA seq from IGROV-1

value: Ma et al., 1998


title: HEK293_Phase_Inhibition_60min_Pol2_Input.rep1

data_processing:
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
hg19
ChIP-seq tag density files(bigWig)

source_name: HEK293 cells

extract_protocol: 5 million cells were used for all ChIP reactions. Crosslinked cells were resuspend in ice-cold lysis buffer (50 mM HEPES, pH=7.9, 5 mM MgCl2, 0.2% Triton X-100, 20% glycerol, 300 mM NaCl) and incubated on ice for 10 min before centrifuged at 500 g for 5 m

treatment_protocol: Cells were crosslinked in 1% formaldehyde diluted in culture medium for 10 min and then quenched with 125 mM glycine for 5 min.

tag: ip method or chip antibody

value: Pol II(8WG16):BioLegend No. 664911

tag: treatment

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 60min


title: HEK293_Phase_Inhibition_60min_Pol2_ChIP-seq.rep2

data_processing:
Trimmed reads were aligned to reference genome using bowtie2 (v2.3.3.1) under default parameters. Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9).
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the ChIP-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
hg19
ChIP-seq tag density files(bigWig)


title: neuroblastoma sample 37

source_name: neuroblastoma tumor

value: neuroblastoma tumor

source_name: Agilent Human Reference DNA

value: Agilent Human Reference DNA


title: mRNA seq from HCC4006P2


title: HEK293_Phase_Inhibition_60min_Pol2_ChIP-seq.rep1

data_processing:
hg19
ChIP-seq tag density files(bigWig)

value: Wild type


title: HEK293_Phase_Inhibition_30min_Pol2_Input.rep2

data_processing:
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the ChIP-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
hg19
ChIP-seq tag density files(bigWig)

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 30min


title: mRNA seq from HCC4006P1_B, repl 2

value: Established in vitro cell line

value: Jia et al., 2013


title: HEK293_Phase_Inhibition_30min_Pol2_Input.rep1

data_processing:
Low-quality and adapter-containing reads were trimmed from ChIP-seq raw data using trim-galore package under single-end mode, reads shorter than 50 bp were removed.
Trimmed reads were aligned to reference genome using bowtie2 (v2.3.3.1) under default parameters. Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9).
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the ChIP-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
hg19
ChIP-seq tag density files(bigWig)


title: HEK293_Phase_Inhibition_30min_Pol2_ChIP-seq.rep2


title: KI420_K9me3_GM07492

description: K9me3_GM07492_macs2hg19_t348t420c384_fe_k1sort.bw

value: No

value: anti-H3K9me3 (Abcam ab8898)


title: HEK293_Phase_Inhibition_15min_Pol2_Input.rep2

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 15min


title: KI539_Input_AG11498

description: KI539_Input_AG11498D_271318_hg19_BT2q20x200n.bw


title: HEK293_Phase_Inhibition_60min_Pol2_Input.rep2


title: HEK293_Phase_Inhibition_5min_Pol2_Input.rep2

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 5min


title: HEK293_Phase_Inhibition_15min_Pol2_ChIP-seq.rep2


title: KI491_D2B2E_AG11498

description: D2B2E_AG11498D_macs2hg19_t491t496c539_fe.bw

value: LMNA G608G

value: anti-phospho-Ser22-LMNA (Cell Signaling D2B2E 13448)


title: mRNA seq from HCC4006P1_A, repl 1

value: sensitive


title: KI424_K9me3_AG11498

description: K9me3_AG11498_macs2hg19_t479t424c383_fe_k1sort.bw

value: No sorting


title: HEK293_Phase_Inhibition_15min_Pol2_Input.rep1


title: mRNA seq from PancB1Q

value: Derived in vitro cell line

value: resistant

value: Lund et al., 2015


title: HEK293_Phase_Inhibition_15min_Pol2_ChIP-seq.rep1

value: Pol II(8WG16):BioLegend No. 664911


title: mRNA seq from PancB1V


title: mRNA seq from HCC4006ER_B, repl 2

value: erlotinib


title: HEK293_Phase_Inhibition_5min_Pol2_Input.rep1

value: Wild type


title: KI348_K9me3_GM07492


title: HEK293_Phase_Inhibition_5min_Pol2_ChIP-seq.rep2


title: HEK293_Phase_Inhibition_5min_Pol2_ChIP-seq.rep1


title: mRNA seq from PancVB

value: PancVB


title: KI609_JUN_GM07492

description: cJun_GM07492_macs2hg19_t609c482_fe_k1sort.bw

value: anti-Jun (Santa Cruz H-79 sc-1694)


title: HEK293_Phase_Inhibition_0min_Pol2_Input.rep2

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 0min


title: KI479_K9me3_AG11498

value: No


title: KI496_D2B2E_AG11498


title: HEK293_Phase_Inhibition_0min_Pol2_Input.rep1


title: mRNA seq from HepG2S3B, repl2

value: sorafenib

value: van Malenstein et al., 2012


title: KI492_D2B2E_GM07492

description: D2B2E_GM07492_macs2hg19_t408t492c482_fe.bw


title: HEK293_Phase_Inhibition_0min_Pol2_ChIP-seq.rep1


title: mRNA seq from HepG2S3A, repl2


title: HEK293_Phase_Inhibition_60min_KAS-IP.rep2

data_processing:
Low-quality and adapter-containing reads were trimmed from KAS-seq raw data using trim-galore package under single-end mode, reads shorter than 50 bp were removed.
Trimmed reads were aligned to reference genome (hg19 for HEK293T cells or mm10 for mESC) using bowtie2 (v2.3.3.1) under default parameters. Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9).
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the KAS-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
We used MACS2 to call all reported KAS-seq peaks in this manuscript. Based on the KAS-seq profile on UCSC genome browser, most KAS-seq peaks on gene body are very broad. Therefore, MACS2 was run using broad peaks-call mode under default parameters, except for --broad-cutoff 0.1 and –qvalue 0.01.
hg19&mm10
KAS-seq tag density files(bigWig)&Peaks files(bed)

extract_protocol:
Cells were harvested and genomic DNA (gDNA) was isolated from cells by PureLink genomic DNA mini kit. 1 µg genomic DNA was then suspended in 95 µL DNA elution buffer supplemented with 5 µL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma, 760749), and incubated at 37 ˚C for 1.5 h with gentle shake. 5 µL RNase A (Thermo, 12091039) was added into the reaction mixture followed by an incubation at 37 ˚C for 5 min. Biotinylated gDNA was then recovered by DNA Clean & Concentrator-5 kit (Zymo). gDNA was suspended into 100 µL water and subjected to sonication by using Bioruptor Pico at 30s-on/30s-off setting for 30 cycles. 5% of the fragmented DNA was saved as input, and the rest 95% was used to enrich biotin-tagged DNA by incubating with 10 µL pre-washed Dynabeads MyOne Streptavidin C1 (Thermo, 65001) at room temperature for 15 min. The beads were washed and DNA was eluted by heating the beads in 15 µL H2O at 95 ˚C for 10 min.
Eluted DNA and its corresponding input were used for library construction by using Accel-NGS Methyl-seq DNA library kit (Swift, 30024).

value: N3-kethoxal biotin IP

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 60min


title: KI482_Input_GM07492

description: KI482_Input_GM07492_267215_hg19_BT2q20x200n.bw


title: Knockout spermatogonial stem cell replicate 3

city: Beijing

first: Xiwen

last: Lin

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology,CAS

description: Cells were cultured after isolated from KO mouse of 6-7 dpp

data_processing:
The sequencing reads were mapped to the mouse genome (UCSC mm9) by TopHat (v2.0.6).
The expression level of mRNAs was represented by FPKM calculated by Cufflinks (v2.0.2).
Genome_build: UCSC mm9
Supplementary_files_format_and_content: FPKM

source_name: Cultured spermatogonial stem cells

growth_protocol: Spermatogonial stem cells were cultured in medium containing GDNF and bFGF.

extract_protocol:
Total RNA from SSCs was isolated by TRIzol.
The RNA libraries were constructed by NEBNext Ultra Directional RNA Library Prep Kit for Illumina from NEB.
High-throughput sequencing was performed on HiSeq-X10.

treatment_protocol: All cell types contain both wildtype and knockout.

tag: gender

value: Male

tag: development stage

value: 6-7 dpp

value: KO


title: mRNA seq from HepG2S1

value: Derived in vitro cell line


title: HEK293_Phase_Inhibition_60min_KAS-IP.rep1

tag: genotype


title: Knockout spermatogonial stem cell replicate 2


title: Knockout spermatogonial stem cell replicate 1


title: mRNA seq from HepG2B, repl1

value: Established in vitro cell line

value: sensitive


title: mRNA seq from HepG2A, repl1


title: HEK293_Phase_Inhibition_60min_KAS-Input.rep2


title: KI611_JUN_AG11498

description: cJun_AG11498D_macs2hg19_t611c539_fe_k1sort.bw

value: LMNA G608G

value: No sorting

tag: antibody


title: HEK293_Phase_Inhibition_60min_KAS-Input.rep1

value: Wild type


title: KI408_D2B2E_GM07492

value: anti-phospho-Ser22-LMNA (Cell Signaling D2B2E 13448)


title: Wildtype spermatogonial stem cell replicate 3

description: Cells were cultured after isolated from WT mouse of 6-7 dpp

value: WT


title: TG_2

city: Jiangyin

first: Longjuan

last: Qin

state: Jiangsu

address: Sha shan road no. 85

institute: puhebio

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.0.6.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.
RPKM of each gene was aclculated based on the length of the gene and reads count mapped to this gene.
Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Genome_build: mm10

source_name: neuron

growth_protocol: Neuron-derived spinal cord neurons were routinely cultured on complete DMEM medium.

extract_protocol:
Neuron were harvested, frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neuron in NG-group were injured, and Hydrogen incubation on the mechanical injury neurons cells which named TG-group, while IG-group neuron without any processing.

value: ICR

tag: age

value: post natal day 3

tag: tissue

value: spinal cord

value: neurons were injured mechanically, hydrogen incubation(75%)


title: HEK293_Phase_Inhibition_0min_Pol2_ChIP-seq.rep2

value: Pol II(8WG16):BioLegend No. 664911

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 0min


title: HEK293_Phase_Inhibition_30min_KAS-IP.rep2

value: N3-kethoxal biotin IP

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 30min


title: TG_1


title: Wildtype spermatogonial stem cell replicate 2

value: Male

value: 6-7 dpp


title: KI167_JUN_BJ5ta

description: cJun_BJ5ta_macs2hg19_t138t141t167c307c481_fe.bw

data_processing:
ChIP-seq reads were mapped to the hg19 human reference genome using Bowtie2 with the default “--sensitive” parameter. Reads with MAPQ score greater than 20 were used in downstream analyses.
Reads from biological replicates of ChIP and corresponding input samples were used as input files for MACS2. In MACS2, duplicate reads were removed first, and then significantly enriched peak regions were called, and input-normalized perbase coverage of 200 nt-extended reads was computed (“fold enrichment bedgraph”).
Genome_build: hg19

value: No

value: anti-Jun (Santa Cruz H-79 sc-1694)


title: HEK293_Phase_Inhibition_30min_KAS-IP.rep1


title: Wildtype spermatogonial stem cell replicate 1


title: KI141_JUN_BJ5ta


title: HEK293_Phase_Inhibition_30min_KAS-Input.rep2


title: KI426_K27ac_AG11498

value: LMNA G608G


title: KI138_JUN_BJ5ta

value: No sorting


title: NG_1

value: neurons were injured mechanically


title: HEK293_Phase_Inhibition_30min_KAS-Input.rep1

value: Wild type


title: KI436_mRNA_HG16

description:
KI429-452_GencodeBasicV19_ERCC92_PerGeneSymbolTranscript_rpkm.bed
KI429-452_GencodeBasicV19_ERCC92_PerGeneSymbolTranscript_count.bed

data_processing:
RNA-seq reads were aligned to the hg19 human reference genome using Tophat2 with the default parameter. Reads with MAPQ score greater than 50 were used in downstream analyses.
To compute RPKM (Reads Per Kilobase of transcript per Million mapped reads) for each transcribed region, the sum of perbase read coverage in exons was computed, and this was divided by the read length (50), then by the sum of the exon size in kb, and then by the total number of reads in million. In directional RNA-seq datasets, only reads whose direction matches that of the gene model were used to compute RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: *_rpkm.bed: text file (with a header) listing rpkm scores (containing header). *_count.bed: text file (with a header) listing the sum of exon basecounts.

extract_protocol:
For non-FUCCI cells, total RNAs were purified by Trizol (Invitrogen 15596026). After DNase treatment, mRNAs were isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490) and fragmented by Fragmentation Buffer (Ambion AM8740). cDNAs were synthesized using SuperScript II (Invitrogen 18064014) and used to prepare non-directional high-throughput sequencing libraries using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370). For non-FUCCI cells, total RNAs were purified by Trizol LS (Invitrogen 10296028). After DNase treatment, mRNAs were isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490). Fragmentation, cDNA synthesis, and directional library construction were performed using NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs E7760).
For non-FUCCI cells, non-directional high-throughput sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370). For FUCCI cells, directional libraries were prepared using NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs E7760).

treatment_protocol: In the FUCCI4 system, asynchronously cultured BJ-5ta-FUCCI cells were cultured at 50-70% density to prevent G0 entry. Cells were trypsinized and used for FACS in BD FACS Aria II (sorting IDs 2834 and 2847) or BD FACS Aria IIIu (sorting ID 2858). With FACS, mKO2-positive/Clover-negative population was sorted as G1-phase cells, mKO2-negative/Clover-positive population was sorted as G2/M-phase cells, mKO2-negative/Clover-negative population was sorted as EG1-phase cells, and mKO2-positive/Clover-positive/mTurquoise2-positive population was sorted as S-phase cells. Pre-sorting and post-sorting cells were kept in the culture medium on ice. Sorted cells were pelleted and resuspended in Trizol LS (Invitrogen 10296028) for RNA-seq.


title: KI435_mRNA_AG11


title: IG_2

value: control


title: HEK293_Phase_Inhibition_15min_KAS-IP.rep2

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 15min


title: HEK293_Phase_Inhibition_15min_KAS-IP.rep1


title: Wildtype spermatocyte replicate 3

description: Cells were isolated from adult WT mouse

source_name: Isolated spermatocytes

value: Adult

value: WT


title: mRNA seq from HCC4006ER_A, repl 1

tag: establishment status

value: Derived in vitro cell line

tag: resistant status

value: resistant

value: erlotinib

tag: reference

value: Jia et al., 2013


title: KI434_mRNA_GM07


title: Knockout spermatocyte replicate 1

description: Cells were isolated from adult KO mouse

tag: strain

value: KO


title: Wildtype spermatocyte replicate 2

description: Cells were isolated from adult WT mouse

value: Male


title: Wildtype spermatocyte replicate 1

description: Cells were isolated from adult WT mouse


title: HEK293_Phase_Inhibition_15min_KAS-Input.rep1


title: KI433_mRNA_GM08

source_name: GM08398 normal human fibroblast

tag: lmna genotype


title: HEK293_Phase_Inhibition_15min_KAS-Input.rep2


title: RNA4

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

description:
knockdown 2 experiment
RNA4_L6_R1_001

data_processing:
Base calling was performed using the HiSeq Control Software (version 2.2.38 for the RNA1, RNA2, RNA3, RNA4, RNA5,RNA6 samples, and version HD 3.4.0.38 for the other samples)
Alignment to the GRh38 human genome was performed using the hiSat2 aligner (2.1.0)
Abundance quantification of transcripts on input libraries was performed with Salmon (0.8.2)
Genome_build: GRh38
Supplementary_files_format_and_content: Tab-separated raw counts with Ensembl gene ID

source_name: squamous cell carcinoma

growth_protocol: SCC13 cell line were kindly provided by K. Lefort (Departement of Biochemistry, UNIL-Epalinge, Lausanne, Switzerland) and cultured like it previously reported (Lefort K et al. A miR-34a-SIRT6 axis in the squamous cell differentiation network. The EMBO journal 2013;32(16):2248-63).

extract_protocol:
Total RNA (tRNA) was extracted from cultured cells using the RNeasy Mini Kit (Qiagen, Hombrechtikon, Switzerland) according to manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

tag: condition

tag: cell type

tag: shRNA

value: control shRNA SHC2


title: RNA5

description:
knockdown 2 experiment
RNA5_L6_R1_001

value: shRNA-502, named H1


title: RNA6

description:
knockdown 2 experiment
RNA6_L6_R1_001

value: shRNA-358, named H2


title: Knockout spermatocyte replicate 3

description: Cells were isolated from adult KO mouse


title: KI431_mRNA_AG11

value: LMNA G608G

tag: transgene

value: No

tag: cell sorting


title: HEK293_Phase_Inhibition_5min_KAS-IP.rep2

tag: ip method or chip antibody

value: N3-kethoxal biotin IP

tag: treatment

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 5min


title: RNA3

description:
knockdown 1 experiment
RNA3_L6_R1_001


title: Knockout spermatocyte replicate 2

description: Cells were isolated from adult KO mouse

tag: gender

tag: development stage

tag: genotype