title: RMM227

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

data_processing:
Transcripts Per Million (TPM) were calculated using RSEM, Bo Li and Colin N Dewey, BMC Bioinformatics, 2011
Genome_build: mm4
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: Lung cells

extract_protocol: Single cell cDNA libraries were using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1. Use of 10 µM TSO; 2. Use of 250 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x51 cycles on an Illumina HiSeq 2000 system (Illumina, San Diego, CA, USA) (188 samples/lane).

value: Interstitial Macrophages


title: RMM229

status: Public on Jan 26 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type


title: RMM226


title: RMM225


title: RMM224


title: RMM230


title: RMM228


title: RMM223


title: RMM222


title: RMM221


title: Uninjured control replicate 3A

city: St Louis

first: Dan

last: Carlin

state: MO

address: 660 S Euclid Ave / Campus Box 8108

department: Neuroscience

country: USA

institute: Washington University in St Louis

data_processing:
Samples were QC’d using FastQC and not trimmed
Reads were aligned to mm10 using STAR-align with default settings  Reads aligned to mm10 using STAR-align with default settings
Reads aligned to genes were counted using Htseq-counts with default settings
Technical replicates were collapsed in DESeq2
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Counts files generated from HTseq-count

source_name: Uninjured control

extract_protocol:
3 days post-injury mice were sacrificed. L4 dorsal root ganglia contralateral to injury were isolated, dissociated with papain and collagenase and passed through 70 um filter. Cells were FACS sorted for GFP-positive cells into Clontech lysis buffer with 5% RiboLock Rnase Inhibitor (Thermo Fisher).
Library preparation was performed with ~100 cells collected by flow cytometry in 10 ul of Clontech’s reaction buffer using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech) per manufacturer’s protocol. Three technical replicates of 100 cells each (A-C) were obtained for each biological replicate (1-4). cDNA was amplified for 13 cycles. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty cycle 20%, cycles/burst 50, time 120 seconds at room temperature. cDNA was blunt ended, had an A base added to the 3’ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

treatment_protocol: Sciatic nerve of mice was crushed with forceps.

tag: strain background

value: mixed:C57BL/6 and AJ

tag: age

value: 8-9 weeks

tag: Sex

value: female

tag: genotype

value: Nav1.8-Cre; Tsc2 flox/+; Rosa26-ZsGreen

tag: tissue

value: L4 dorsal root ganglia contralateral to sciatic nerve crush

value: Nav1.8-positive dorsal root ganglia neurons

tag: sorted fraction

value: 100 FACS-sorted GFP-positive cells


title: oocyte_KO2

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
Sequencing adapters were trimmed using Cutadapt and low quality reads were pre-filtered by FASTX-Toolkit before mapping.  The quality of reads after filtering was examined using fastQC.
All filtered reads were aligned to mouse reference genome (GRCm38/mm10) by STAR with default parameters.
Individual mapped reads were quantified to annotation model to calculate gene counts. Differentially expression analysis between Mfn1-/- or WT groups were performed using using DESeq 2 package.
Differentially expressed genes between Mfn1-/- and WT groups were determined using false discovery rate (FDR) of < 0.05, Foldchange > 2 and minimal of 5 reads as cutoffs.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: counts

source_name: Secondary follicle-enclosed oocytes

extract_protocol:
cDNA synthesis and amplification was performed using 5 oocytes per sample and Smart-Seq2 protocol.
Sequencing libraries were constructed using the amplified cDNA and Nextera® XT DNA Library Preparation Kit (Illumina, San Diego, CA) and indexed using Nextera® XT Index Kit (Illumina). Library quality was confirmed using DNA 1000 kit on Tapestation 2200 (Aglilent Technologies), and the libraries were then sequenced on Illumina’s Hiseq 2500 platform with 75bp pair-end reads.

treatment_protocol: Secondary follicles were collected from 8-week-old Mfn1-/- and WT mice by digesting the ovaries with 1.5 mg/mL collagenase type V (Sigma, St. Louis, MO) for 1 h at 37°C in M2 medium (Sigma, St. Louis, MO) [7]. Secondary follicle-enclosed oocytes (referred as the oocytes) and granulosa cells were collected by further digesting the harvested secondary follicle with Accutase solution (Sigma, St. Louis, MO) for 15min.

tag: strain


title: oocyte_KO3


title: oocyte_KO1


title: RMM220


title: RMM219


title: RMM218


title: ERplus2

city: Utrecht

first: Ana

last: Lourenço

address: Uppsalalaan 8

country: Netherlands

institute: UMC Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly) using TopHat v2.0.9 as previously described (Trapnell et al., 2012). Only uniquely mapped reads were selected for further analysis.
guide transcripts were assembled using CuffLinks v2.2.1. Reads were quartile normalized using the –library-norm-method quartile option.
Differential gene analysis was performed using CuffDiff.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing  average differential gene expression FPKM normalized values

molecule: polyA RNA

organism: Homo sapiens

source_name: Immortalized human mammary epithelial cells

extract_protocol:
total RNA-isolation with RNAeasy kit (Qiagen)
TruSeq stranded ribo-zero kit (Illumina)
Samples were sequenced on the NextSeq 500 (Illumina), SE75

treatment_protocol: Upon lentiviral transduction HMLEs were grown and expanded under puromycin selection before RNA-isolation (0.5 µg/mL)

tag: construct

value: ER

tag: treatment

value: plus 4OH-tamoxifen


title: oocyte_WT4


title: ERmin1

value: Immortalized human mammary epithelial cells

value: minus 4OH-tamoxifen


title: RMM216


title: RMM215


title: RMM214


title: RMM217


title: RMM213


title: oocyte_WT2


title: oocyte_WT3


title: oocyte_WT1


title: RMM211


title: RMM210


title: RMM208


title: RMM209


title: RMM207


title: HS_SC_R2: psp1 mutant rep2

city: Burjassot

first: Roc

last: Ros

state: valencia

address: Vicent Andres Estelles

department: Biologia Vegetal

country: Spain

institute: Universitat de Valencia

description: phosphoserine phosphatase mutant

data_processing:
Single end reads in fastq format were mapped against the TAIR10 Arabidopsis transcriptome (www.arabidopsis.org) using kallisto (v0.43.0 with default parameters except l=200 and s=30), (Bray et al., 2016
Data was combined in R (v3.3.2) and analyzed
Principal component analysis was carried out with prcomp (scale=T).
Differential expression was assessed with edgeR in classic mode (Robinson et al., 2010) followed by Benjamini Hochberg correction (Benjamini and Hochberg, 1995).
Enrichment analysis were conducted using topGO (R package version 2.22.0) with Fisher’s Exact Test (Fisher, 1922) followed by Benjamini Yekutieli correction (Benjamini and Yekutieli, 2001).

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Wild type and psp1 mutant plants were sterilized and sown on 0.8% agar plates containing one-fifth-strength Murashige and Skoog medium with Gamborg vitamins, buffered with 0.9 g/l MES (adjusted to pH 5.7 with Tris). After four days of stratification at 4°C, plates were vertically placed in a growth chamber at 20-22ºC under a 16 h day/8 h night photoperiod, 100 μmol m−2 s−1.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA II kit (Macherey-Nagel)
Using 3-15 μg of RNA as starting material, a mRNA enrichment was performed with the MicroPoly(A) Purist kit (AMBION). To prepare the RNA-Seq library, the SOLID Total RNA-seq kit (Life Technologies) was used. After obtaining the library, an equimolar mixture of it was used to perform an emulsion PCR using the automatic system of EZ Beads (Life Technologies). Then, the bead enrichment was performed, followed by its deposition in the sequencing wells. The sequencing step was performed using a SOLID 5500XL equipment of 75 nucleotides using the Exact Call Chemistry. Single end reads in fastq format were mapped against the TAIR10 Arabidopsis transcriptome (www.arabidopsis.org) using kallisto (v0.43.0 with default parameters except l=200 and s=30), (Bray et al., 2016). Data was combined in R (v3.3.2) and analyzed. Principal component analysis was carried out with prcomp (scale=T). Differential expression was assessed with edgeR in classic mode (Robinson et al., 2010) followed by Benjamini Hochberg correction (Benjamini and Hochberg, 1995). Enrichment analysis were conducted using topGO (R package version 2.22.0) with Fisher’s Exact Test (Fisher, 1922) followed by Benjamini Yekutieli correction (Benjamini and Yekutieli, 2001). The level of significance was fixed at 0.01 (1%) after correction.

treatment_protocol: Three independent biological replicates of aerial part and roots of each sample were harvested at the end of the night period for the analysis

value: roots

tag: ecotype

value: Columbia

tag: genotype/variation

value: psp1 mutant


title: HS_SC_R3: psp1 mutant rep3

description: phosphoserine phosphatase mutant


title: RMM204


title: RMM206


title: RMM202


title: HS_SC_PA3: psp1 mutant rep3

description: phosphoserine phosphatase mutant

source_name: Aerial part

value: Aerial part


title: HS_SC_R1: psp1 mutant rep1

description: phosphoserine phosphatase mutant


title: RMM201


title: RMM199


title: HS_SC_PA2: psp1 mutant rep2

description: phosphoserine phosphatase mutant


title: HS_SC_PA1: psp1 mutant rep1

description: phosphoserine phosphatase mutant


title: RMM203


title: RMM198


title: WT_SC_R3: WT rep3

description: Wild type plant

value: wild type


title: RMM200

value: Interstitial Macrophages


title: RMM212


title: RMM196


title: WT_SC_R2: WT rep2

description: Wild type plant


title: RMM194


title: WT_SC_R1: WT rep1

description: Wild type plant


title: RMM193


title: RMM192


title: RMM195


title: WT_SC_PA3: WT rep3

description: Wild type plant


title: RMM191


title: WT_SC_PA2: WT rep2

description: Wild type plant


title: RMM190


title: WT_SC_PA1: WT rep1

description: Wild type plant


title: RMM188


title: RMM186


title: RMM185


title: RMM187


title: 102278-11

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

institute: Erasmus MC

description:
Demultiplex_ID: Merged_102278-11
processed data file: Nkseq_processed_GEO.txt

data_processing:
The trimmed fastQ files were aligned to build human_g1k_v37 Ensembl Release 75 reference genome using STAR/2.5.1b-foss-2015b [Dobin A et al. 2012] with default settings. Before gene quantification picard/2.2.2-foss-2015b-Java-1.8.0_74 [Picard] was used to sort the aligned reads. Dropseq Drop-seq_tools/1.12-Java-1.7.0_80 [Macosko et al. 2015] was used for flagging individual cells and UMI's. The gene level quantification was performed again by using Dropseq filtering readcount on unique UMI's. Ensembl version 75 was used as gene annotation database.
Genome_build: human_g1k_v37 Ensembl Release 75
Supplementary_files_format_and_content: Nkseq_processed_GEO.txt: Tab-delimited text file contains FPKM values.

source_name: PBMC

growth_protocol: Not applicable.

extract_protocol:
Total RNA was isolated from purified NK cells using the PicoPure® RNA Isolation Kit (Arcturus). To assess the quantity of the samples, the concentration of the RNA was determined using the Nanodrop ND1000 spectrophotometer. The quality and integrity of the RNA samples were analyzed on a RNA 6000 Lab-on-a-Chip using the Bioanalyzer 2100 (Agilent Technologies). mRNA was isolated from total RNA using the poly-T-oligo-attached magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed.
The sequence libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) according to the manufacturer's protocol. The quality and yield after sample preparation were measured with a DNA 1000 Lab-on-a-Chip. The size of the resulting products had a peak around 300 basepairs on a DNA 1000 chip.

treatment_protocol: Not applicable.

value: CD3-CD56+ NK cells

tag: gender

value: Male

tag: diagnosis

value: Chronic HBV

tag: hbv clinical phase

value: Immune Tolerant


title: RMM184


title: 102278-09

description:
Demultiplex_ID: Merged_102278-09
processed data file: Nkseq_processed_GEO.txt


title: RMM183


title: RMM197


title: RMM181


title: RMM182


title: RMM180


title: 102415-08

description:
Demultiplex_ID: Merged_102415-08
processed data file: Nkseq_processed_GEO.txt

value: Female


title: RMM179


title: CPP1-w-alpha_R2

city: Montréal

first: Raha

last: Parvizi Omran

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology Department

country: Canada

institute: Concordia University

description:
M00833_0555_annotated.tpm
CPP1-w-alpha_R2 TPM

data_processing:
Each RNA-seq data file was postprocessed to correct read sequences (Song L, Florea L. 2015), trim adapters (Song L, Florea L. 2015), and remove rRNA reads (Song L, Florea L. 2015).    Expression ratios of mutants versus controls in each experiment were calculated to identify changes in gene expression
The C. albicans_SC5314_Assembly22 ORF/gene coding sequences (SC5314_V22) were downloaded from the CGD website (Skrzypek MS, Binkley J, Binkley G, Miyasato SR, Simison M, Sherlock G. 2017)
A PERL script was written to create a gene/open reading frame ID and description file. The reads were then mapped to the SC5314_V22 sequences (Skrzypek MS, Binkley J, Binkley G, Miyasato SR, Simison M, Sherlock G. 2017) to produce raw counts and TPM (transcripts per million) values.
Raw counts and TPM values were annotated with gene descriptions using a PERL script and imported to an Excel spreadsheet for further analysis
Expression ratios of mutants versus controls in each experiment were calculated to identify changes in gene expression
Supplementary_files_format_and_content: [M00833_0555_annotated.tpm.tsv]  The file reports the transcripts per million (TPM) values.
Supplementary_files_format_and_content: [Normalized TPM RNAseq.xlsx]  The M00833_0555_annotated.tpm file has been arranged and normalized over housekeeping gene then the expression ratios of mutants versus control in each experiment were calculated to identify changes in gene expression.

organism: Candida albicans

source_name: Yeast cells

growth_protocol: SC-Glucose medium at room tempreture. Cells with 3 hours of  α-pheromone (1μg/ml) treatment were collected at  OD600=0.8 - 1

extract_protocol:
Total RNA were extracted following the QIAGEN RNeasy minikit   protocol with the cells were disrupted with bead beater shaking for 25 times for 20   seconds with 1 min cooling on ice between treatments.
RNA libraries were prepared for sequencing using standard Illumina's mRNASeq stranded library prepraration kit.

value: CPP1  deletion


title: 102278-07

description:
Demultiplex_ID: Merged_102278-07
processed data file: Nkseq_processed_GEO.txt


title: RMM177


title: 102278-20

description:
Demultiplex_ID: Merged_102278-20
processed data file: Nkseq_processed_GEO.txt

value: Immune Control


title: CPP1-w-alpha_R1

description:
M00833_0555_annotated.tpm
CPP1-w-alpha_R1 TPM


title: RMM178


title: CPP1_R2

description:
M00833_0555_annotated.tpm
CPP1_R2 TPM

growth_protocol: SC-Glucose medium at room tempreture.Cells were collected at OD600=0.8 - 1


title: 102278-19

description:
Demultiplex_ID: Merged_102278-19
processed data file: Nkseq_processed_GEO.txt


title: RMM205


title: RMM189


title: RMM726

data_processing:
Run featureCounts on every bam file using Gencode annotation, to assign mapped sequencing reads to Ensembl gene IDs.
Join together all the counts outputs of featureCounts into a unique matrix of raw counts.
Perform TMM (trimmed mean of M-values) scale normalization on the DGEList.
Calculate RPKM (Reads Per Kilobase of transcript per Million mapped reads) of TMM-normalized counts.
Genome_build: mm7
Supplementary_files_format_and_content: Tab-delimited text files include log2 RPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermofisher, KIT0204) according to manufacturer’s protocol.
cDNA libraries were prepared using 2ng of total RNA and 1ul of a 1:50,000 dilution of Ambion ERCC RNA Spike-in Controls (Thermofisher, 4456740) using the SMARTSeq v2 protocol described in Nature Protocols volume 9, pages 171-181 (Picelli et al., 2014) with the following modifications: 1. Use of 20mM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Nextera XT kit (Illumina, FC-131). 31 samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (20-24 samples/lane)

value: Heart4 Lyve1-


title: RMM724

value: Heart1 Lyve1-


title: RMM725

value: Heart3 Lyve1-


title: CPP1CEK2-w-alpha_R2

description:
M00833_0555_annotated.tpm
CPP1CEK2-w-alpha_R2 TPM

value: CPP1 CEK2 deletion


title: RMM723

value: Heart2 Lyve1-


title: RMM722

value: Heart1 Lyve1+


title: 102278-02

description:
Demultiplex_ID: Merged_102278-02
processed data file: Nkseq_processed_GEO.txt


title: RMM721

value: Heart2 Lyve1+


title: 102415-09

description:
Demultiplex_ID: Merged_102415-09
processed data file: Nkseq_processed_GEO.txt


title: CPP1CEK2_R2

description:
M00833_0555_annotated.tpm
CPP1CEK2_R2 TPM


title: RMM719

source_name: Skin

value: Skin1 Lyve1-


title: RMM720

value: Heart3 Lyve1+


title: RMM718

value: Skin3 Lyve1-


title: CPP1CEK2_R1

description:
M00833_0555_annotated.tpm
CPP1CEK2_R1 TPM


title: RMM716

value: Skin3 Lyve1+


title: 102278-10

description:
Demultiplex_ID: Merged_102278-10
processed data file: Nkseq_processed_GEO.txt

value: CD3-CD56+ NK cells


title: CPP1CEK1-w-alpha_R2

description:
M00833_0555_annotated.tpm
CPP1CEK1-w-alpha_R2 TPM

value: CPP1 CEK1 deletion


title: RMM715

value: Skin1 Lyve1+


title: RMM717

value: Skin2 Lyve1-


title: 102278-03

description:
Demultiplex_ID: Merged_102278-03
processed data file: Nkseq_processed_GEO.txt

value: Male

value: Chronic HBV


title: 102415-05

description:
Demultiplex_ID: Merged_102415-05
processed data file: Nkseq_processed_GEO.txt

value: Immune Active


title: RMM713

value: Skin2 Lyve1+


title: CPP1_R1

description:
M00833_0555_annotated.tpm
CPP1_R1 TPM

value: CPP1  deletion


title: RMM714

value: Skin4 Lyve1+


title: RMM104

source_name: Fat

value: Fat3 Lyve1-


title: 102415-12

description:
Demultiplex_ID: Merged_102415-12
processed data file: Nkseq_processed_GEO.txt

value: Immune Control


title: RMM103

value: Fat2 Lyve1-


title: CPP1CEK1_R2

description:
M00833_0555_annotated.tpm
CPP1CEK1_R2 TPM


title: CPP1CEK2-w-alpha_R1

description:
M00833_0555_annotated.tpm
CPP1CEK2-w-alpha_R1 TPM

value: CPP1 CEK2 deletion


title: RMM102

value: Fat1 Lyve1-


title: CPP1CEK1_R1

description:
M00833_0555_annotated.tpm
CPP1CEK1_R1 TPM


title: 102415-07

description:
Demultiplex_ID: Merged_102415-07
processed data file: Nkseq_processed_GEO.txt

value: Female


title: CEk2-w-alpha_R2

description:
M00833_0555_annotated.tpm
CEk2-w-alpha_R2 TPM

value: CEk2 deletion


title: RMM100

value: Fat2 Lyve1+


title: RMM099

value: Fat1 Lyve1+


title: 102278-08

description:
Demultiplex_ID: Merged_102278-08
processed data file: Nkseq_processed_GEO.txt

value: CD3-CD56+ NK cells


title: CEk2-w-alpha_R1

description:
M00833_0555_annotated.tpm
CEk2-w-alpha_R1 TPM


title: 102415-10

description:
Demultiplex_ID: Merged_102415-10
processed data file: Nkseq_processed_GEO.txt


title: RMM098

source_name: Lung

value: Lung3 mono


title: RMM096

value: Lung1 mono


title: 102415-01

description:
Demultiplex_ID: Merged_102415-01
processed data file: Nkseq_processed_GEO.txt

value: Healthy


title: RMM094

value: Lung2 AM


title: RMM095

value: Lung3 AM


title: CPP1CEK1-w-alpha_R1

description:
M00833_0555_annotated.tpm
CPP1CEK1-w-alpha_R1 TPM

value: CPP1 CEK1 deletion


title: CEk2_R2

description:
M00833_0555_annotated.tpm
CEk2_R2 TPM


title: 102415-04

description:
Demultiplex_ID: Merged_102415-04
processed data file: Nkseq_processed_GEO.txt

value: Male


title: CEk2_R1

description:
M00833_0555_annotated.tpm
CEk2_R1 TPM


title: RMM093

value: Lung1 AM


title: 102415-06

description:
Demultiplex_ID: Merged_102415-06
processed data file: Nkseq_processed_GEO.txt

value: Chronic HBV

value: Immune Active


title: RMM091

value: Lung2 Lyve1-


title: 102415-03

description:
Demultiplex_ID: Merged_102415-03
processed data file: Nkseq_processed_GEO.txt


title: RMM090

value: Lung1 Lyve1-


title: RMM101

value: Fat3 Lyve1+


title: 102415-02

description:
Demultiplex_ID: Merged_102415-02
processed data file: Nkseq_processed_GEO.txt


title: RMM089

value: Lung3 Lyve1+


title: 0 mM K+, replicate 2

city: Boston

first: Shumin

last: Tan

state: MA

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

data_processing:
Illumina bcl2fastq was used for demultiplexing and conversion of reads to FASTQ file format.
Trimmomatic (v0.33) was used with a 4 bp sliding window to trim adapter sequences and low quality bases. Sequence was removed when the sliding window identified read quality below 15 or read length less than 36 bp.
Bowtie (v1.1.1) was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession #: AE000516) to produce SAM files.
HTseq (v0.6.1) was used to determine the number of aligned reads that map to each gene feature in the M. tuberculosis genome.
edgeR (v3.2) was used to normalize data.
R was used for differential gene expression and statistical analyses.
Genome_build: M. tuberculosis CDC1551 genome (GCA_000008585.1) (NCBI accession AE000516).
Supplementary_files_format_and_content: The file contains gene expression analysis (including normalized counts) from 2 biological replicates for each condition.

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: Mtb strain CDC1551 wild-type was grown to an OD600 of 0.6 (mid-log phase) in standing vented T-75 flasks in 20 ml of media originally seeded at an OD600 of 0.05.

extract_protocol:
RNA was extracted as previously described by Rohde, Abramovitch, and Russell (Cell Host and Microbe 2:352-364, 2007). In brief, RNA was stabilized with guanidine-thiocyanate lysis buffer prior to a freeze-thaw step. Once thawed, bacteria were lysed with 5 µg/ml lysozyme, followed by hot Trizol and physical disruption through silica bead agitation in a Beadbeater.  A chloroform extraction was used to further isolate the RNA before purification with an RNAeasy kit (Qiagen). DNA was degraded with Turbo DNAfree DNAse (Ambion). RNA quality was assessed with an Aligent Bioanalyzer before removal of rRNA with a Ribo-Zero rRNA removal kit (bacterial) (Ilumina).
The cDNA library was constructed with the Illumina Tru-Seq Stranded kit. The polyA enrichment procedure was skipped.

treatment_protocol: Mtb at mid-log phase were subcultured in 10 ml of media to an OD600 of 0.3 in standing vented T-25 flasks containing either standard 7H9, pH 7 media, or K+-free 7H9, pH 7 media. Exposure was for 4 hours in a humidified, 37C, 5% CO2 incubator before RNA was extracted.

value: wild-type

tag: exposure condition

value: K+-free 7H9, pH 7


title: CEK1-w-alpha_R2

description:
M00833_0555_annotated.tpm
CEK1-w-alpha_R2 TPM

value: CEk1 deletion


title: CEK1-w-alpha_R1

description:
M00833_0555_annotated.tpm
CEK1-w-alpha_R1 TPM


title: 0 mM K+, replicate 1


title: control, replicate 2


title: RMM088

value: Lung2 Lyve1+


title: RMM097

value: Lung2 mono


title: 102278-06

description:
Demultiplex_ID: Merged_102278-06
processed data file: Nkseq_processed_GEO.txt

value: CD3-CD56+ NK cells

value: Healthy


title: RMM087

value: Lung1 Lyve1+


title: control, replicate 1


title: CEK1_R1

description:
M00833_0555_annotated.tpm
CEK1_R1 TPM


title: 102278-13

description:
Demultiplex_ID: Merged_102278-13
processed data file: Nkseq_processed_GEO.txt


title: CEk1CEk2-w-alpha_R2

description:
M00833_0555_annotated.tpm
CEk1CEk2-w-alpha_R2 TPM

growth_protocol: SC-Glucose medium at room tempreture. Cells with 3 hours of  α-pheromone (1μg/ml) treatment were collected at  OD600=0.8 -1

value: CEk1 CEk2 deletion


title: CEk1CEk2-w-alpha_R1

description:
M00833_0555_annotated.tpm
CEk1CEk2-w-alpha_R1 TPM


title: ztf-11_03

city: Stanford

first: Kang

last: Shen

state: CA

address: 385 Serra Mall, Herrin lab 144

institute: Stanford University

description: Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing dsRNA against ztf-11. 3 of 4 biological replicates.

data_processing:
Raw reads were trimmed of adaptor sequences using fastx (http://hannonlab.cshl.edu/fastx_toolkit/)
Mapped using Tophat2 and featureCounts.
Differential expression analysis was performed using DeSeq2
Genome_build: ce10
Supplementary_files_format_and_content: Excel spreadsheet file containing DESeq2 output results

organism: Caenorhabditis elegans

source_name: Embryo

growth_protocol: Standard C. elegans growing protocols

extract_protocol:
Embryos were isolated using bleaching and then incubated in M9 for three hours. Egg shells were disturbed with chymotrypsin/chitinase treatment. Embryonic cells were then homogenized by qiaShredder columns (Qiagen) following manufacturer's instructions. RNA was extracted using RNeasy micro plus kit (Qiagen) followng manufacturer's instructions.
mRNA libraries were prepared by Stanford Genome Sequencing Center using TruSeq Stranded mRNA Library Preparation kit (Illumina).

treatment_protocol: Knockdown by feeding RNAi. In brief, synchronized L1 animals were grown on a lawn of bacterial clone expressing dsRNA against ztf-11 or control for 64 hours in 20℃. Each bacterial lawn were innoculated onto 10cm NGM plates containing IPTG (1mM) 3 days prior to each experiment.

value: mixed

tag: developmental stage

value: embryo


title: ztf-11_02

description: Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing dsRNA against ztf-11. 2 of 4 biological replicates.


title: ztf-11_04

description: Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing dsRNA against ztf-11. 4 of 4 biological replicates.


title: CEk1CEk2_R2

description:
M00833_0555_annotated.tpm
CEk1CEk2_R2 TPM


title: 102415-15

description:
Demultiplex_ID: Merged_102415-15
processed data file: Nkseq_processed_GEO.txt

tag: cell type

value: Male

value: HCV


title: 102278-16

description:
Demultiplex_ID: Merged_102278-16
processed data file: Nkseq_processed_GEO.txt


title: ztf-11_01

description: Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing dsRNA against ztf-11. 1 of 4 biological replicates.


title: 102415-14

description:
Demultiplex_ID: Merged_102415-14
processed data file: Nkseq_processed_GEO.txt


title: CEk1CEk2_R1

description:
M00833_0555_annotated.tpm
CEk1CEk2_R1 TPM


title: CEK1_R2

description:
M00833_0555_annotated.tpm
CEK1_R2 TPM


title: CAI4-w-alpha_R2

description:
M00833_0555_annotated.tpm
CAI4-w-alpha_R2 TPM

growth_protocol: SC-Glucose medium at room tempreture. Cells with 3 hours of  α-pheromone (1μg/ml) treatment were collected at OD600=0.8 - 2

value: Wild type


title: 102278-12

description:
Demultiplex_ID: Merged_102278-12
processed data file: Nkseq_processed_GEO.txt


title: L4440_04

description: Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing control feeding vector (L4440). 4 of 4 biological replicates.

value: treated with feeding RNAi clone expressing control vector (L4440)


title: 102278-15

description:
Demultiplex_ID: Merged_102278-15
processed data file: Nkseq_processed_GEO.txt


title: L4440_03

description: Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing control feeding vector (L4440). 3 of 4 biological replicates.


title: L4440_02

description: Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing control feeding vector (L4440). 2 of 4 biological replicates.


title: CAI4-w-alpha_R1

description:
M00833_0555_annotated.tpm
CAI4-w-alpha_R1 TPM

growth_protocol: SC-Glucose medium at room tempreture. Cells with 3 hours of  α-pheromone (1μg/ml) treatment were collected at OD600=0.8 - 1


title: CAI4_R2

description:
M00833_0555_annotated.tpm
CAI4_R2 TPM


title: 102278-14

description:
Demultiplex_ID: Merged_102278-14
processed data file: Nkseq_processed_GEO.txt


title: 102415-16

description:
Demultiplex_ID: Merged_102415-16
processed data file: Nkseq_processed_GEO.txt


title: 102278-18

description:
Demultiplex_ID: Merged_102278-18
processed data file: Nkseq_processed_GEO.txt


title: L4440_01

description: Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing control feeding vector (L4440). 1 of 4 biological replicates.


title: CAI4_R1

description:
M00833_0555_annotated.tpm
CAI4_R1 TPM


title: U251-Capture Hi-C replicate 2

status: Public on Jan 25 2019

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

country: China

institute: Nankai University

description: Capture Hi-C of WT glioma cell line

library_source: genomic

data_processing:
Clean reads of RNA-seq were mapped to hg19 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture Hi-C were cut into two pieces in the DpnII sites
All the reads were mapped to hg19 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: hg19
Supplementary_files_format_and_content: Text files include genes counts values, Capture Hi-C signal peaks for each Sample

molecule: genomic DNA

source_name: Capture Hi-C of WT glioma cell line

growth_protocol: U251 cell line was cultured in DMEM supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Cells were fixed in formalin for 10min and DNA was isolated and digested with Dpn II then sheared to 200-300bp fragments by sonication. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs), using Illumina X Ten.
RNA,  Capture Hi-C libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TMZ-treated groups were 1mM TMZ treated for 72h,and DMSO-treated groups were control groups for the same conditions

tag: cell line

value: glioma

value: WT


title: WGS variants of K562

city: Seoul

first: Hyeon

middle: Joo

last: Lee

state: - Please choose -

address: 222 Wangsimni-ro, Seongdong-gu

department: Department of Life Science

country: South Korea

institute: Hanyang University

description: WGS variants of K562

data_processing:
Basecalls performed using CASAVA version 1.8.2
The RNA-seq data for clone 10 was mapped to the human reference genome (hg19) using Bowtie version 1.0.0 (Trapnell et al., 2009) with unique-mapping parameter "-m 1".
To measure expression level, we estimated both reads per million reads (RPM) values on the GENCODE annotation version 19.
After whole genome sequencing (WGS) of the parental cells was performed, the reads were mapped using BWA version 0.7.10-r789, duplicates were marked with Picard version 1.96, realigned based on the presence of an insertion or deletion, and the quality scores recalibrated using GATK version 3.4.
The variants were called using GATK HaplotypeCaller version 3.4.
Genome_build: hg19
Supplementary_files_format_and_content: The variants called using GATK HaplotypeCaller version 3.4.

source_name: WGS variants of K562

growth_protocol: K562, a human erythromyeloblastoid leukemia cell line, was purchased from American Type Culture Collection (Manassas, VA) and cultured in Roswell Park Memorial Institute medium (RPMI; Invitrogen, Carlsbad, CA) supplemented with 100 units ml-1 penicillin, 100 µg ml-1 streptomycin, and 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Libraries were prepared according to illumina's instruction accompanying the Truseq stranded mRNA prep kit. Briefly, The polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads and then fragmented into small pieces. The cleaved RNA fragments were primed into random hexamers into first strand cDNA using reverse transcriptase and random primers. The RNA template removed and a replacement strand synthesized, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library.
Paired-end strand-specific RNA-seq

treatment_protocol: Cells were transfected with plasmid mixtures of Cas9-puro, U6-sgRNA encoding sgRNAs at a weight ratio of 1:1:1 using Neon (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. One day after transfection, puromycin (Cat no. A11138-03, Invitrogen, Carlsbad, CA) was added to the culture media at a final concentration of 2.5 µgml-1 for two days. Three days after transfection, cells were analyzed.


title: non-CD44+CD24- MCF-7 cells

type: RNA

city: Nanjing

first: Liang

last: Jin

address: 24 Tongjiaxiang Avenue

institute: China Pharmaceutical University

description: Gene expression of lncRNAs and mRNAs in BCSCs MCF-7 cells.

hyb_protocol: For hybridization,  RNase H was added to the 2nd-Cycle cDNA from above and Incubated for 45 min at 37 °C, then 5 min at 95 °C, then for at least 2 min at 4 °C. After hybridization, microarrays were washed by using GeneChip® Hybridization, Wash, and Stain Kit.

scan_protocol: After washing, slides were scanned with the Affymetrix DNA Microarray Scanner

data_processing: After washing, GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) that installed in GeneChip® Scanner 3000.

source_name: non-CD44+CD24- MCF-7 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671 or equivalent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,   Valencia, CA).

extract_protocol: The total RNA was extracted from cells using TRIzol reagent (Invitrogen, CA, USA). The quantity of RNA was assessed by NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was tested by standard denaturing agarose gel electrophoresis.

treatment_protocol: We used flow cytometry sorting to obtain CD44+CD24- MCF-7 cells and non-CD44+CD24- MCF-7 cells.

value: Human breast cancer cells

tag: cell subtype

value: breast cancer stem cells (non-CD44+CD24-)


title: SATB1-P6

city: Beijing

first: Yang

last: Wang

address: Xishiku Street

institute: Peking University First Hospital

data_processing:
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAPaligner/SOAP2.
Gene expression levels were calculated by reads per kilobase transcriptome per million mapped reads（RPKM）method.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: skin lesion

extract_protocol:
Lesional skin biopsies were obtained from 7 patients with CD30+LPDs (4 SATB1+, 3 SATB1-), from which total RNA samples were extracted and purified.
According to the TruSeq RNA Sample Prep Kit v2 (Illumina, San Francisco, CA), RNA libraries were prepared as follows. Firstly, 200ng total RNA samples extracted from 7 CD30+LPDs skin lesions were purified by oligo-dT beads, then poly (A)-containing mRNA were fragmented into small pieces with Elute, Prime, Fragment Mix. Then double-strand cDNA was synthesized by First Strand Master Mix, Super Script II (Thermo Fisher Scientific, Waltham, MA) reverse transcription and Second Strand Master Mix. In the next, the purified fragmented cDNA was combined with End Repair Mix and added with A-Tailing Mix. Adaptor ligation was made as well. After several rounds of PCR, the final library was constructed. Then the library was qualified through Agilent 2100 bioanalyzer instrument (Agilent Technologies, Santa Clara, CA) and Quantitative real-time polymerase chain reaction. The qualified library was sequenced on an Illumina HiSeqTM 2000 platform using paired-end reads. 10G raw data for each sample were obtained. The reads were aligned to the hg19 genome with SOAPaligner/SOAP2 (Li et al., 2009).

value: skin

tag: tumor

tag: molecular classification


title: SATB1+P4

tag: tissue


title: SATB1+P3


title: Breast tumor tissue3

description: Gene expression of lncRNAs and mRNAs in breast cancer tissue.

scan_protocol: After washing, GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) that installed in GeneChip® Scanner 3000.

data_processing: Data was extracted using Affymetrix GeneChip Command Console (version4.0, Affymetrix).  Normalization was performed using the Expression Console.

source_name: Breast tumor tissue3

extract_protocol: The total RNA was extracted from fresh tissues using TRIzol reagent (Invitrogen, CA, USA). The quantity of RNA was assessed by NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was tested by standard denaturing agarose gel electrophoresis. RNA from the 3 paired tissues was used for microarray analysis by Affymetrix Human OE LncRNA Microarray.

treatment_protocol: None of the patients received radiotherapy and chemotherapy before the surgery.

value: breast tissue

tag: disease state

value: tumor

value: Female


title: SATB1-P7


title: SATB1-P5


title: Adjacent normal tissue3

source_name: Adjacent normal tissue3

value: adjacent normal


title: Adjacent normal tissue1

source_name: Adjacent normal tissue1


title: CD44+CD24- MCF-7 cells

description: Gene expression of lncRNAs and mRNAs in non-BCSCs MCF-7 cells.

source_name: CD44+CD24- MCF-7 cells

value: non-BCSCs (CD44+CD24-)


title: Breast tumor tissue2

source_name: Breast tumor tissue2


title: Adjacent normal tissue2

source_name: Adjacent normal tissue2


title: sample1_BDM_None_24h

city: Berlin

first: Brian

last: Caffrey

state: Germany

address: Ihnestrasse 63-73

department: Computational Molecular Biology

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
3’ adapters were clipped from the reads
reads shorter than 18 nucleotides (nt) were discarded
reads with identical sequence were collapsed
mapped to the human genome, hg19 assembly, using bowtie v1 and only alignments with zero mismatches in the first 18 nt were kept. Up to two mismatches were allowed after 18 nt.
Only reads which aligned to less than five multiple positions were kept for further analysis
Raw read counts for both the mature and the star strand of each miRNA were determined with the ‘Quantifier’ module of miRDeep2, based on miRbase annotation v20 (104).
miRNA raw read counts for all 12 libraries were quantile-normalized and differential expression analysis between all pairwise conditions was performed with the Limma R package.
miRNAs with an absolute log2 fold change higher or equal than 0.65 (corresponding to a linear fold change of 1.5) and adjusted p-value lower or equal than 0.2 (Benjamin-Hochberg correction) in at least one comparison were considered significantly regulated.
Genome_build: hg19
Supplementary_files_format_and_content: plain text of either raw or normalized counts

growth_protocol: Legionella pneumophila strain Corby wild type was routinely grown on buffered charcoal-yeast extract (BCYE) agar plates at 37 °C for three days.

extract_protocol:
RNA was extracted from cells by phenol-chloroform precipitation
Samples with sufficient RNA quality were used for Illumina library preparation according to the manufacturer´s instructions. Briefly, 3’ and 5’ adapters were ligated to 1 µg total RNA with T4 RNA ligase (Epicentre). Following the reverse transcription of the RNA into cDNA, PCR amplification was performed. To distinguish the prepared samples, different index primers were added. Afterwards, samples with unique indices were pooled into two libraries and cDNA was loaded on a PAA-gel. The fraction with a size of 145 – 160 bp was cut from the gel to enrich for small RNAs. This fraction contained the cDNA transcribed from mature miRNAs generated from 22 nt RNA fragments. Following elution of the cDNA, the final libraries were concentrated by ethanol precipitation. Finally, prepared libraries were validated by a Bioanalyzer run and sent for sequencing.

treatment_protocol: The miRNome of L.p.-infected BDMs was determined by Illumina TruSeq small RNA sequencing. BDMs of three different donors were infected with L. pneumophila at an MOI of 0.25 for 24 h and 48 h or left untreated as control. RNA quality was examined on a Bioanalyzer 2100 (Agilent). Samples with sufficient RNA quality (RIN > 8) were used for Illumina library preparation according to the manufacturer´s instructions (Illumina, USA).

value: Blood derived macrophages(BDM)

tag: infection

tag: molarity of infection

tag: time point (hrs)


title: sample7_BDM_None_48h


title: sample6_BDM_L. pneumophila corby_24h

source_name: BDM_L. pneumophila corby_24h

value: Legionella pneumophila corby


title: sample11_BDM_None_48h


title: sample8_BDM_L. pneumophila corby_48h

source_name: BDM_L. pneumophila corby_48h


title: sample5_BDM_None_24h


title: sample12_BDM_L. pneumophila corby_48h


title: sample4_BDM_L. pneumophila corby_48h


title: sample10_BDM_L. pneumophila corby_24h


title: Breast tumor tissue1

source_name: Breast tumor tissue1


title: SATB1+P1


title: SATB1+P2


title: U251-Capture Hi-C replicate 1

description: Capture Hi-C of WT glioma cell line

tag: genotype


title: sample9_BDM_None_24h


title: sample2_BDM_L. pneumophila corby_24h


title: sample3_BDM_None_48h


title: WT, biological rep. 1 (nup84∆, control)

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

description: Gene expression data from mid-log yeast cells in YPD medium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were normalized by RMA (Robust Microarray Average) to allow direct comparison between expression values in different experiments. Statistical analysis was performed by LIMMA (Linear Models for Microarray Analysis) using the program affylmGUI. Genes showing at least 1.5-fold expression change compared to wild-type strain with a p-value FDR < 0.01, were considered as altered. Expression values were obtained with the anti-log of RMA values

label: biotin

organism: Saccharomyces cerevisiae

source_name: Total RNA from W303 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Each strain was grown to mid-log phase in liquid YPD medium

extract_protocol: Total RNA was isolated with the Rneasy Midi kit (QIAGEN)

tag: strain

value: W303-1A bar1-delta

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3-1 bar1-delta-HphMX


title: nup84∆, biological rep. 1

source_name: Total RNA from W303 nup84-delta cells

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3-1 bar1-delta-HphMX nup84::KanMX


title: nup84∆, biological rep. 3


title: WT, biological rep. 2  (nup84∆, control)


title: Mes_rep4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

description:
raw data file:
251486833508_0004.gpr

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the Axon 4100A scanner Molecular Devices,  San Jose, USA) at 10 µm/pixel resolution and analyzed with GenePix Pro 5.1.0.19

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Organ homogenate, embryonic lung E12.5

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

extract_protocol: QIAgen RNeasy kit

value: embryonic lung

value: mesenchyme


title: nup84∆, biological rep. 2


title: Epi_rep4

description:
raw data file:
251486833508_0004.gpr

value: epithelium


title: E_rep3

description: Rosa26rtTAtet(O)solubleR2b + 6h DOX

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

source_name: Rosa26rtTAtet(O)solubleR2b + 6h DOX

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Loss of function: Lungs from Rosa26rtTAtet(O)solubleR2b mice were treated with doxycycline for 6 hours (3 samples) and 9 hours (3 samples). Gain of function: Lungs from Rosa26rtTAtet(O)fgf10 mice were treated with doxycycline for 9 hours (3 samples). Control samples (wild-type) were untreated.

value: lungs

tag: group

value: Loss of function

tag: time

value: 6h DOX


title: Epi_rep1

description:
raw data file:
251486833508_0001.gpr


title: WT, biological rep. 3  (nup84∆, control)


title: C_rep2

description: Rosa26rtTAtet(O)solubleR2b + 9h DOX

source_name: Rosa26rtTAtet(O)solubleR2b + 9h DOX

value: 9h DOX


title: B_rep1

description: control (wild-type)

source_name: control (wild-type)

value: control


title: SKMEL2: E, biological rep 3

first: Ryan

middle: P

last: Kuzmickas

address: 77 Avenue Louis Pasteur, NRB458B

department: Genetics

institute: Brigham and Women's Hospital

description:
E, biological rep 3
gene expression data after E (24hr)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA-normalized with Affymetrix Transcriptome Analysis Console (TAC) software

source_name: gene expression data after E (24hr)

label_protocol: standard Affymetrix protocol

growth_protocol: SKMEL2 cells were cultured in RPMI supplemented with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol: RNA was isolated from SKMEL2 cells 24 hours after treatment with indicated drugs. Prior to RNA extraction ERCC spike-in control mix was added to Trizol and RNA isolation was performed using the Qiagen Rneasy kit (74201).

treatment_protocol: SKMEL2 cells were treated for 24 hours with vehicle (DMSO), dabrafenib(100nM)+trametinib(10nM) (MAPKi), entinostat(1µM) (HDACi) or all 3 agents

tag: treatment

value: entinostat (24hr)

value: melanoma cell line


title: SKMEL2: DTE, biological rep 3

description:
DTE, biological rep 3
gene expression data after DTE (24hr)

source_name: gene expression data after DTE (24hr)

value: dabrafenib+trametinib+entinostat (24hr)


title: SKMEL2: DTE, biological rep 2

description:
DTE, biological rep 2
gene expression data after DTE (24hr)


title: B_rep3

description: control (wild-type)


title: E_rep1

description: Rosa26rtTAtet(O)solubleR2b + 6h DOX


title: SKMEL2: DTE, biological rep 1

description:
DTE, biological rep 1
gene expression data after DTE (24hr)


title: Mes_rep1

description:
raw data file:
251486833508_0001.gpr


title: Mes_rep2

description:
raw data file:
251486833508_0002.gpr


title: A_rep3

value: Gain of function


title: C_rep1

description: Rosa26rtTAtet(O)solubleR2b + 9h DOX


title: A_rep1


title: A_rep2


title: E_rep2

description: Rosa26rtTAtet(O)solubleR2b + 6h DOX


title: C_rep3

description: Rosa26rtTAtet(O)solubleR2b + 9h DOX


title: B_rep2

description: control (wild-type)


title: Epi_rep2

description:
raw data file:
251486833508_0002.gpr


title: Mes_rep3

description:
raw data file:
251486833508_0003.gpr


title: Epi_rep3

description:
raw data file:
251486833508_0003.gpr


title: Hs695T: DTE, biological rep 3

growth_protocol: Hs695T cells were cultured in RPMI supplemented with 10% FBS

extract_protocol: RNA was isolated from Hs695T cells 24 hours after treatment with indicated drugs. Prior to RNA extraction ERCC spike-in control mix was added to Trizol and RNA isolation was performed using the Qiagen Rneasy kit (74201).

treatment_protocol: Hs695T cells were treated for 24 hours with vehicle (DMSO), dabrafenib(100nM)+trametinib(10nM) (MAPKi), entinostat(1µM) (HDACi) or all 3 agents


title: Hs695T: DTE, biological rep 2


title: Hs695T: E, biological rep 1

description:
E, biological rep 1
gene expression data after E (24hr)


title: Hs695T: E, biological rep 2

description:
E, biological rep 2
gene expression data after E (24hr)


title: SKMEL2: DT, biological rep 2

description:
DT, biological rep 2
gene expression data after DT (24hr)

source_name: gene expression data after DT (24hr)

value: dabrafenib+trametinib (24hr)


title: SKMEL2: E, biological rep 2


title: Hs695T: DMSO, biological rep 2

description:
DMSO, biological rep 2
gene expression data after DMSO (24hr)

source_name: gene expression data after DMSO (24hr)

value: DMSO (24hr)


title: Hs695T: DT, biological rep 1

description:
DT, biological rep 1
gene expression data after DT (24hr)


title: Hs695T: E, biological rep 3


title: SKMEL2: DMSO, biological rep 1

description:
DMSO, biological rep 1
gene expression data after DMSO (24hr)


title: Hs695T: DTE, biological rep 1


title: Hs695T: DMSO, biological rep 3

description:
DMSO, biological rep 3
gene expression data after DMSO (24hr)


title: SKMEL2: DT, biological rep 3

description:
DT, biological rep 3
gene expression data after DT (24hr)


title: A2058: DTE, biological rep 1

growth_protocol: A2058 cells were cultured in DMEM supplemented with 10% FBS, 1% Penicillin/Streptomycin

extract_protocol: RNA was isolated from A2058 cells 24 hours after treatment with indicated drugs. Prior to RNA extraction ERCC spike-in control mix was added to Trizol and RNA isolation was performed using the Qiagen Rneasy kit (74201).

treatment_protocol: A2058 cells were treated for 24 hours with vehicle (DMSO), dabrafenib(100nM)+trametinib(10nM) (MAPKi), entinostat(1µM) (HDACi) or all 3 agents


title: SKMEL2: DMSO, biological rep 3


title: A2058: DTE, biological rep 2


title: SKMEL2: DT, biological rep 1


title: A2058: E, biological rep 3


title: A2058: E, biological rep 2


title: Hs695T: DT, biological rep 3


title: A2058: DTE, biological rep 3


title: SKMEL2: E, biological rep 1


title: A2058: E, biological rep 1


title: Hs695T: DMSO, biological rep 1


title: A2058: DT, biological rep 1


title: A2058: DT, biological rep 3


title: A2058: DMSO, biological rep 3


title: SKMEL2: DMSO, biological rep 2


title: A2058: DT, biological rep 2


title: Hs695T: DT, biological rep 2


title: bc.del.D12.L (repli-seq)

city: Tallahassee

first: David

middle: M

last: Gilbert

address: 319 Stadium Drive

department: Biology

institute: Florida State University

data_processing:
Reads are mapped to mm10 using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools
Log2 ratio of early to late coverage is calculated in 5kb windows
Log 2 ratio data were IQR normalized to 4.59
Genome_build: mm10
Supplementary_files_format_and_content: All .txt datasets are normalized to RPM for both early and late fractions before taking log2 ratios, and then Loess smoothed

growth_protocol: Mouse ESCs were maintained on 1% gelatin coated dishes. 46C was grown in GMEM supplemented with 10% FBS and LIF; hybrid cells (Cas/129 and V6.5) in DMEM supplemented with 2i plus LIF.

extract_protocol:
Genome-wide RT profiles were constructed as previously described. Briefly, cells were pulse labeled with BrdU for 2 hours and separated into early and late S-phase fractions by Propidium iodide staining and flow cytometry. BrdU-substituted DNA from 40k early and late S-phase cells was immunoprecipitated by anti-BrdU antibody (Becton Dickinson 347580)
Sequencing libraries were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

treatment_protocol: CRISPR-mediated deletion or inversions

value: mESC

tag: hybrid cells

tag: s phase fraction

value: Late S fraction

tag: protocol


title: Trim.E9.L (repli-seq)

description: Rex1-TRIM_RT_chr8_IQRnorm_mm10_9-1-18.txt

tag: cell type


title: RexTrim.D8.L (repli-seq)


title: Trim.E9.E (repli-seq)

value: Early S fraction


title: Trim.D9.E (repli-seq)


title: RexTrim.D8.E (repli-seq)


title: TMZ_HOTAIR-KO2 replicate 1

description: RNA-seq of TMZ-treated HOTAIR regulatory element KO glioma cell line

extract_protocol:
Total RNA was extracted using the Eastep® Super Total RNA Extraction Kit following the manufacturer’s instruction. Then, ribosomal RNA was deleted from 5 μg of total extracted RNA using the Ribo-Zero Gold Kit, using Illumina HiSeq-4000.
RNA,  Capture Hi-C libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: glioma

value: HOTAIR regulatory element KO


title: bc.del.D12.E (repli-seq)


title: Trim.D9.L (repli-seq)


title: RexTrim.D3.L (repli-seq)


title: DMSO_HOTAIR-KO2 replicate 1

description: RNA-seq of DMSO-treated HOTAIR regulatory element KO glioma cell line


title: Rex1.E3.E (repli-seq)


title: TMZ_HOTAIR-KO1 replicate 2

source_name: RNA-seq of TMZ-treated HOTAIR regulatory element KO glioma cell line


title: Rex1.D1.L (repli-seq)


title: DMSO_HOTAIR-KO2 replicate 2

source_name: RNA-seq of DMSO-treated HOTAIR regulatory element KO glioma cell line


title: RexTrim.D3.E (repli-seq)


title: a.G5.E (repli-seq)


title: TMZ_HOTAIR-KO1 replicate 1


title: DMSO_HOTAIR-KO1 replicate 1


title: A2058: DMSO, biological rep 2


title: A2058: DMSO, biological rep 1


title: Rex1.D1.E (repli-seq)


title: a.G5.L (repli-seq)


title: HE23W_2_LVRV

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

description: single cell RNA seq of 48 heart tissue cells

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to human reference genome (hg19) using TopHat (v 2.0.12) -pass mapping steps.
Genome_build: hg19
Supplementary_files_format_and_content: TPM.txt files include the TPM values of RefSeq genes

source_name: 23W post-gestation human embryos

extract_protocol: Single cell was randomly picked with mouth pipette, then washed by 1mg/ml HSA() and transferred into prepared lysis buffer. The cells can store at -80℃ or do it immediately. We used a modified SMART-seq2 protocol to lysis for release all RNA, reverse transcription for capture the cDNA of mRNA and pre-amplification for increase yields of cDNAs. The resulting cDNAs from single cells were barcoded, and then pooled together with different barcode. Followed by 4 cycles, the index of sequence with biotin modified was added at 3’ end.

value: Heart

value: Heart tissue cells


title: TMZ_HOTAIR-KO2 replicate 2


title: ac.H8.L (repli-seq)


title: Rex1.E3.L (repli-seq)


title: HE17W_3_TV

description: single cell RNA seq of 32 heart tissue cells

source_name: 17W post-gestation human embryos


title: HE22W_2_AOPO

source_name: 22W post-gestation human embryos


title: HE17W_3_BVLV


title: HE17W_3_AV


title: HE17W_3_PV


title: DMSO_HOTAIR-KO1 replicate 2


title: HE9W_1_LV

source_name: 9W post-gestation human embryos


title: HE9W_1_RA


title: 4k.b.c.G12 [Bru-seq]

description:
Nascent RNA
processed data file: RPKM-9-7-18.txt

data_processing:
Library strategy: Bru-seq
Reads are mapped to mm10 using bowtie2.
Allele-specific analysis was performed using harp (http://github.com/dvera/harp).
RPM-normalized read densities were calculated with bedtools2 (Quinlan and Hall, 2010) genomecov, using a scaling factor of 1000000/(number of parsed reads in library).
Genome_build: mm10
Supplementary_files_format_and_content: *bed: bed files
Supplementary_files_format_and_content: RPKM-9-7-18.txt: Tab-delimited text file

extract_protocol:
Trizol
Nascent RNA was pulled down using anti-BrdU antibodies conjugated magnetic beads. Strand specific cDNA libraries were constructed using 300ng Bru-labeled RNA and sequenced on Illumina HiSeq 2500 with 100bp single end.

treatment_protocol: Cells was pulse labeled with 2 mM bromouridine (Bru) for 30 minutes.


title: b.del.D10 [Bru-seq]


title: ac.del.E4 [Bru-seq]


title: HE6W_2_RV

description: single cell RNA seq of 96 heart tissue cells

source_name: 6W post-gestation human embryos


title: HE6W_2_RA


title: HE9W_1_RV


title: HE22W_2_LARA


title: a.del.53 [Bru-seq]


title: c.del.A12 [Bru-seq]


title: ab.del.D12 [Bru-seq]


title: HE6W_2_LV


title: 245kdel.F9 [Bru-seq]


title: 100kdel.C3 [Bru-seq]


title: ac.H8.E (repli-seq)


title: HE6W_2_LA


title: HE5W_1_RV

source_name: 5W post-gestation human embryos


title: VavKO_2

city: Suita

first: Hiroyasu

last: Kidoya

state: Osaka

address: 3-1 Yamadaoka

department: Research Institute for Microbial Diseases

country: Japan

institute: Osaka university

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode(for sample 1-3,6-8) and a 150-base paired-end mode(for sample 4,5,9,10).
Illumina Casava1.8.2 software used for basecalling and demultiplexing.
RNA-seq reads were trimmed and algined to mouse transcriptome (UCSC gene) and genome (mm10) references respectively using  Burrows-Wheeler Aligner.
After transcript coordinate was converted to genomic positions, an optimal mapping result was selected either from transcript or genome mapping by comparing the minimal edit distance to the reference.
Local realignment was performed within in-house short reads aligner with smaller k-mer size (k=11).
The transcripts per kilobase million (TPM) was calculated using Salmon software ver.0.9.1.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-delimited text file include TPM values for each sample.

source_name: mouse bone marrow HSC

extract_protocol:
Total RNA was extracted from cells using RNeasy-plus mini kits (Qiagen) according to the manufacturer's instructions.
Library preparation was performed using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa) and Nextera XT(Illumina) according to the manufacturer’s instructions.

treatment_protocol: Bone marrow cells were stained with antibodies against cell surface markers (lineage markers, Sca-1 and  cKit, CD34 and Flt3, Biolegend) and HSCs (Lin- ScaI+ cKit+ CD34- Flt3- cells) were sorted with FACS AriaII (BD).

value: bone marrow HSC

tag: age

value: eight-week

tag: genotype/variation

value: Vav1-iCre; Reg1flox/flox


title: VavKO_3

tag: tissue


title: VavKO_1


title: VavReg1_KO_LT-HSC1

value: HSCs (Lin- ScaI+ cKit+ CD34- Flt3- cells)


title: HE5W_1_RA2


title: Control_LT-HSC2


title: Control_LT-HSC1


title: HE9W_1_LA


title: VavReg1_KO_LT-HSC2


title: HE5W_1_RA1


title: HE5W_1_LV


title: Control_3


title: HE5W_1_LA


title: 10X E10.5 mandible

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v2.0.0 using default parameters to obtain the gene expression matrices
Genome_build: mm10
Supplementary_files_format_and_content: mtx matrix files

source_name: mandible

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: mandible

tag: developmental stage


title: Control_2


title: HE25W_TV_BV

source_name: 25W post-gestation human embryos


title: HE23W_2_TV


title: HE24W_RV

description: single cell RNA seq of 88 heart tissue cells

source_name: 24W post-gestation human embryos


title: HE25W_EP_ED


title: HE25W_AV_EP


title: HE25W_BV_PV


title: HE24W_RA


title: HE24W_LV


title: HE24W_LA


title: HE23W_2_PO


title: HE23W_2_IS


title: HE23W_2_BV


title: HE23W_2_AV


title: HE23W_2_AO


title: HE22W_RV4


title: HE22W_TV


title: HE22W_RA4


title: HE22W_PV


title: HE22W_RA3


title: Control_1


title: HE22W_LV4


title: Late KPC

city: Houston

first: Abdel

middle: Nasser

last: Hosein

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description: Late KPC

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 2.1.1 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 2.1.1 was used with default setting to generate mapped bam files and then to generate filtered feature count (gene-by-cell) matrices
Genome_build: GRCm38
Supplementary_files_format_and_content: Filtered feature-barcode matrices in MEX format, that is, genes-by-cells matrix market file with cell barcode and gene name tab-delimited text files.

source_name: Late invasive mouse pancreatic cancer  (KPC model)

growth_protocol: Mice were caged under standard conditions prior to sacrifice

extract_protocol: Single-cell suspensions were loaded on 10x Genomics Chromium single-cell Controller with 3' library and gel bead kit v2 according to manufacture's recommendations. Meeting 10x Genomics' recommendation, sequenced R1=27cycles, R2=99cycles, i7=8cycles.

treatment_protocol: Mice were untreated

value: Mixed background:C57BL/6 +FVB

tag: age at sacrifice

value: 6 months


title: HE22W_RV3


title: Late KPfC

description: Late KPfC

source_name: Late invasive mouse pancreatic cancer  (KPfC model)

value: 60 days


title: HE22W_PO


title: Late KIC

description: Late KIC

source_name: Late invasive mouse pancreatic cancer (KIC model)


title: Normal Pancreas

description: Normal Pancreas

source_name: Normal mouse pancreas

value: Normal mouse pancreas


title: HE22W_IS


title: HE22W_AP

description: single cell RNA seq of 47 heart tissue cells


title: HE22W_LA3


title: HE22W_BV


title: HE22W_BT

description: single cell RNA seq of 49 heart tissue cells


title: HE22W_AV


title: Early KIC

description: Early KIC

source_name: Early invasive mouse pancreatic cancer (KIC model)

value: 40 days


title: HE20W_RV

source_name: 20W post-gestation human embryos


title: HE20W_RA


title: HE20W_LV


title: Blood Tfh rep 2

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

data_processing:
Basecalling was performed using Illumina Software
Reads were aligned to the mouse genome mm10 using CLC Genomics software suite
Reads per million were generated for each sample
Genome_build: mm10
Supplementary_files_format_and_content: Tab-deliminated file

source_name: Tfh

extract_protocol:
Tissues were surgically removed and mashed through 70micron strainers, cells were sorted on an Aria cell sorter and RNA was extracted using RLT buffer
RNA libraries were constructed using previously published protocols using Illumina adaptors (Sage Nature Immunology 2016)

value: Blood

value: Tfh


title: LN Tcon rep 3

source_name: Tcon

value: Lymph Node

value: Tcon


title: Spl Tfh rep 3

value: Spleen


title: HE22W_AO

value: Heart


title: Blood Tcon rep 3


title: LN Tfh rep 3


title: HE22W_LA4

value: Heart tissue cells


title: HE20W_LA


title: Blood Tfh rep 3


title: HE22W_LV3


title: Spl Tfh rep 2


title: HE17W_2_RV

source_name: 17W post-gestation human embryos


title: Spl Tcon rep 2


title: HE17W_2_RA


title: LN Tfh rep 2


title: Blood Tcon rep 2


title: Blood Tfh rep 1


title: LN Tcon rep 2


title: Blood Tcon rep 1


title: HE17W_2_LA


title: HE17W_1_RV


title: HE17W_2_LV


title: HE23W_2_LARA

source_name: 23W post-gestation human embryos


title: HE17W_1_RA


title: HE17W_1_LV


title: Spl Tcon rep 1


title: HE17W_1_LA


title: LN Tfh rep 1


title: LN Tcon rep 1


title: Blood Treg rep 3

source_name: Treg

value: Treg


title: Spl Tfh rep 1


title: HE15W_RV

source_name: 15W post-gestation human embryos


title: Spl Tfr rep 3

source_name: Tfr

value: Tfr


title: HE13W_2_RV

description: single cell RNA seq of 40 heart tissue cells

source_name: 13W post-gestation human embryos


title: HE15W_LA


title: HE15W_LV


title: HE13W_2_RA


title: HE13W_2_LA


title: HE13W_2_LV


title: HE15W_RA


title: Spl Treg rep 3


title: Blood Tfr rep 2


title: HE13W_1_RV


title: Blood Tfr rep 3


title: LN Treg rep 3


title: Spl Tfr rep 2


title: HE13W_1_LV

description: single cell RNA seq of 50 heart tissue cells


title: Spl Treg rep 2


title: HE13W_1_RA


title: HE23W_2_PV


title: HE13W_1_LA


title: HE10W_RV

source_name: 10W post-gestation human embryos


title: LN Treg rep 2


title: LN Tfr rep 2


title: Blood Tfr rep 1


title: HE10W_RA


title: Spl Tcon rep 3


title: LN Tfr rep 3


title: HE7W_3_RV

description: single cell RNA seq of 43 heart tissue cells

source_name: 7W post-gestation human embryos


title: Blood Treg rep 1


title: Spl Tfr rep 1


title: Spl Treg rep 1


title: HE7W_3_RA


title: HE10W_LV


title: LN Treg rep 1


title: LN Tfr rep 1


title: Blood Treg rep 2


title: Tfh rep 2

extract_protocol:
Cells were sorted based on FoxP3-GFP and CD45.1 expression
RNA libraries were constructed using previously published protocols using Illumina adaptors (Sage Nature Immunology 2016)

treatment_protocol: In Vitro Suppression Assay

tag: culture

value: Sorted from In Vitro Suppression Assay

tag: foxp3 status

value: Negative


title: Fox - Tfr rep 3

source_name: Fox - Tfr


title: Tfh rep 3


title: HE7W_2_LV


title: HE7W_3_LA


title: HE7W_2_RA


title: HE7W_3_LV


title: HE7W_2_LA2


title: Fox - Tfr rep 2


title: HE7W_2_LA1


title: HE7W_2_RV


title: Tfh rep 1


title: HE7W_1_LV


title: Fox - Tfr rep 1


title: HE7W_1_RA


title: HE10W_LA


title: Fox + Tfr rep 1

source_name: Fox + Tfr

value: Positive


title: HE6W_LV

source_name: 6W post-gestation human embryos


title: F/F Treg rep 3

source_name: F/F Treg

extract_protocol:
Lymph nodes were mashed through 70micron filters and cells were sorted
RNA libraries were constructed using previously published protocols using Illumina adaptors (Sage Nature Immunology 2016)

treatment_protocol: Ex Vivo Sorting

value: lymph node

tag: genotype

value: F/F


title: F/+ Tfr rep 3

source_name: F/+ Tfr


title: F/F Tfr rep 3

source_name: F/F Tfr


title: HE7W_1_LA


title: Fox + Tfr rep 3


title: Fox + Tfr rep 2


title: F/+ Treg rep 3

source_name: F/+ Treg


title: F/+ Tcon rep 3

source_name: F/+ Tcon


title: HE6W_LA


title: F/F Treg rep 2


title: F/+ Tfr rep 2


title: F/F Treg rep 1


title: F/+ Treg rep 2


title: F/F Tfr rep 1


title: F/+ Tfr rep 1


title: F/+ Tcon rep 2


title: HE7W_1_RV


title: F/F Tcon rep 1

source_name: F/F Tcon


title: HE6W_RV


title: F/+ Tcon rep 1


title: F/+ Treg rep 1


title: 145k.del.G5 [Capture Hi-C]

data_processing:
Reads were trimmed by Trim Galore! (https://github.com/FelixKrueger/TrimGalore).
Mapped to mm10 using HiCUP v0.5.9 (Wingett et al., 2015).
Allele parsed using SNPsplit v0.3.0 (Krueger and Andrews, 2016).
Capture Hi-C heatmaps were plotted in R using interaction matrix for 10kb windows.
Genome_build: mm10
Supplementary_files_format_and_content: *mat: Tab-delimited text

growth_protocol: Mouse ESCs were maintained on 1% gelatin coated dishes. Hybrid cells (Cas/129) were grown in DMEM supplemented with 2i plus LIF. ESC to NPC differentiation was carried out as previously described (Abranches et al., 2009). mESCs were plated on 0.1% gelatin-coated dishes in serum-free ESGRO Complete Clonal Grade medium (Millipore Inc.) at high density. After 24 hours, cells were passaged to RHB-A media (Stem Cell Science Inc.) at the density of 1x10^4cells/cm2 and maintained for 12 days with media changed every other day.

extract_protocol: Capture Hi-C enriching 45488946-50879849 on chromosome 16 was performed as previously described (Dryden et al., 2014). Hi-C libraries from 25 million cells were constructed with 4 base cutter MboI, and target enrichment was performed using Agilent SureSelect RNA oligo system with custom designed capture probes (50bp RNA targeting Mbo1 fragments containing at least 1 SNP). Capture Hi-C libraries were then sequenced on Illumina NextSeq 550 with 150bp pair end.

value: mESC


title: 100k.del.C3 [Capture Hi-C]


title: HE6W_RA


title: c.del.B11 [Capture Hi-C]


title: 18k.del.E12 [Capture Hi-C]


title: F/F Tfr rep 2


title: ChIP TEAD1-HA

city: Lausanne

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

description: Overexpression of TEAD1-HA

data_processing:
Reads were aligned to the mouse reference genome mm10 using STAR 2.5.3a with settings ‘-- alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’
Duplicate reads were removed with Picard and reads not mapping to chromosomes 1-19, X, or Y were removed
Peaks were called with MACS 2.1.1.20160309 with settings ‘-f BAMPE -g mm’. Peaks overlapping peaks called for input (non-immunoprecipitated chromatin) from NIH- 3T3 cells and ENCODE blacklisted peaks were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated with deepTools 2.4.2 with settings '--normalizeUsingRPKM'

growth_protocol: NIH-3T3 cells were routinely cultured at 37°C and 5% CO2 in DMEM, supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were grown in 100 mm cell culture dishes up to a confluence of 90% and split 1:6 every 3-4 days.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature and quenched with 200 mM Tris-HCl pH 8.0, washed with PBS, spun down, and stored at -80°C. The cell pellet was resuspended and in 1.5 ml LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100), incubated 10 min at 4°C, spun down, and resuspended in 1.5 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) incubated 10 min at 4°C. The pellet was spun down, rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS), and finally resuspended in 0.9 ml SDS shearing buffer. All buffers contain contain 1:100 diluted Protease Inhibitor Cocktail in DMSO (Sigma). The suspension was transferred to a milliTUBE 1 ml AFA fiber and sonicated on a E220 focused ultrasonicator (Covaris) using the following settings: 20 min, 200 cycles, 5% duty, 140W, and input sample aliquots were taken. To pull down HA-bound DNA, sonicated chromatin was incubated with anti-HA.11 antibody 16B12 (BioLegend) overnight at 4°C. 2.5 ml Protein G Dynabeads (Thermo Fischer) per one million cells were added to the chromatin and incubated 3 hours at 4°C. The chromatin was washed several times at 4°C with 5 min incubation between each wash and 2 min magnetization to collect beads; twice with Low Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with High Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with LiCl Wash Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM PMSF), and finally with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1 mM PMSF). Beads were finally resuspended in Elution buffer (TE buffer with 1% SDS and 150 mM NaCl), treated with 400 ng/ml Proteinase K and reverse crosslinked at 65°C 1100 rpm overnight. Input samples were treated with 100 mg/ml RNase A and 400 ng/ml Proteinase K and reverse crosslinked at 65°C 1100 rpm overnight. Sonicated chromatin samples were purified using Qiagen MinElute PCR purification kit.
Libraries were prepared with NEBNext ChIP-seq Library Prep Master Mix kit with insert size selection of 250 bp.

treatment_protocol: NIH-3T3 cells were treated overnight with 500 ng/ml of Doxycycline one day after seeding. ChIP-seq was performed on at least 10 million cells.

value: mouse fibroblasts

tag: chip antibody


title: ChIP ZFP319-HA

description: Overexpression of ZFP319-HA


title: ChIP SOX2-YPET OCT4-HA

description: Overexpression of SOX2-YPET and OCT4-HA


title: ChIP SOX2-HA rep1

description: Overexpression of SOX2-HA


title: ChIP SOX2-HA rep2

description: Overexpression of SOX2-HA


title: ChIP THAP4-HA

description: Overexpression of THAP4-HA


title: ChIP Input

description: WT cells


title: c.del.A12 [Capture Hi-C]


title: ChIP SIX6-HA

description: Overexpression of SIX6-HA


title: ab.del.D12 [Capture Hi-C]


title: ab.del.D10 [Capture Hi-C]


title: ChIP TOX3-HA

description: Overexpression of TOX3-HA


title: abc.del.E2 [Capture Hi-C]


title: abc.del.A6 [Capture Hi-C]


title: ChIP PRR3-HA

description: Overexpression of PRR3-HA


title: ChIP OCT4-HA rep1

description: Overexpression of OCT4-HA


title: ChIP SOX15-HA

description: Overexpression of SOX15-HA


title: 680kinv.C5 [Capture Hi-C]


title: ChIP OCT4-HA rep2

description: Overexpression of OCT4-HA


title: ChIP NANOG-HA

description: Overexpression of NANOG-HA


title: ChIP HLF-HA

description: Overexpression of HLF-HA


title: ChIP FOXA1_SW-HA

description: Overexpression of FOXA1_SW-HA


title: ChIP FOXA1_RR-HA

description: Overexpression of FOXA1_RR-HA


title: bc.del.B3 [Capture Hi-C]


title: ChIP FOXA1-HA rep1

description: Overexpression of FOXA1-HA


title: ChIP FOXA1-HA rep2

description: Overexpression of FOXA1-HA


title: ChIP EBF1-HA

description: Overexpression of EBF1-HA


title: ChIP RHOX11-HA

description: Overexpression of RHOX11-HA


title: ChIP MAX-HA

description: Overexpression of MAX-HA


title: ChIP DLX6-HA

description: Overexpression of DLX6-HA


title: human ACVR1 R206H and H3.1K27M 2

city: New York

first: Oren

middle: Josh

last: Becher

state: NY

address: 1468 Madison Avenue, A21-02

department: Pediatrics

institute: Mount Sinai

description: R206H K27M 2

data_processing:
Paired-end fastq files were clipped using fastq-mcf with the following parameters: --max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25
Paired-end fastq files were imported into Galaxy [1] and aligned to the mm10 genome using RNA-STAR (Galaxy version 2.6.0b-1) with default parameters.
Aligned reads were counted using HTSeq-count with the Ensembl mm10 transcriptome GTF file as the feature file with the following parameters: stranded = no, mode = union, minimum alignment quality = 10, map nonunique or ambiguous reads = none.
[1] Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Gruning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016 Jul 8; 44(W1): W3-W10.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include HTSeq count values for each sample.

source_name: P3-P5 brainstem progenitors

growth_protocol: Brainstem progenitors from postnatal day 3-5 Nestin TVA pups were isolated and cultured in serum-free conditions with EGF and FGF2 as previously described.

extract_protocol:
Standard RNA isolation was performed by Expression Analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were infected with RCAS vectors expressing either ACVR1 WT alone, ACVR1 WT with H3.1K27M, R206H ACVR1 alone, or R206H ACVR1 with H3.1K27M.

tag: strain/background

value: Nestin TVA; p53 floxed

value: Brainstem progenitors

tag: vector expression

value: ACVR1 R206H and H3.1K27M


title: human ACVR1 R206H and H3.1K27M 3

description: R206H K27M 3


title: human ACVR1 R206H and H3.1K27M 1

description: R206H K27M 1


title: human ACVR1 R206H 3

description: R206H 3

value: ACVR1 R206H


title: Primary macrophages 8hr stimulation with LPS

city: GULDFORD

first: RACHEL

last: SIMMONDS

state: Surrey

address: FHMS UNIVERSITY OF SURREY, STAG HILL CAMPUS

country: United Kingdom

institute: University of Surrey

description: 8hrs LPS compared to the common reference (pooled donors)

hyb_protocol: Hybridisation took place in miRCURY LNA™ microRNA Array Hybridization buffer (#208022) and washing was with the miRCURY LNA™ microRNA Array, Wash buffer kit (#208021) following the manufacturer's reccomendations

scan_protocol: not available

data_processing: Background subtraction used Normexp with offset value 1 (convolution model described by Ritchie ME, Bioinformatics 2007: 23  p2700-7 ) Normalisation was by LOWESS regression. Spots where no signal above background was detected were removed

source_name: Cells stimulated with LPS for 8hrs (pooled from 4 donors)

label_protocol: 750ng total RNA was mixed with miRCURY LNA™ microRNA Array Spike-in controls (#208040) and then labelled with the miRCURY LNA™ microRNA Power labeling kit (#208032-A) for dual labelling with Hy3 (samples) and Hy5 (common reference) according to manufacturers recommendations

growth_protocol: Primary human monocytes were isolated by elutriation from plateletphoresis residues (blood cones) and differentiated using 10ng/ml M-CSF for 4 days

extract_protocol: Total RNA extracted using the miRvana kit (Ambion)

treatment_protocol: Cells were plated at 1x10e6 cells/ml. The next day cells were stimulated with 100ng/ml TLR-grade LPS and/or 10ng/ml IL-10 for the indicated time. Cells were washed once with 1xPBS and harvested with the MiRvana extraction/homogenisation buffer

value: Monocyte-derived macrophages

tag: stimulator

value: LPS

tag: time

value: 8 hours

source_name: Common Reference

tag: preparation

value: Equal quantities of RNA from each of the six experimental data points


title: Primary macrophages 4hr stimulation with LPS

description: 4hrs LPS compared to the common reference (pooled donors)

source_name: Cells stimulated with LPS for 4hrs (pooled from 4 donors)

value: 4 hours


title: Primary macrophages 2hr stimulation with LPS

description: 2hrs LPS compared to the common reference (pooled donors)

source_name: Cells stimulated with LPS for 2hrs (pooled from 4 donors)

value: 2 hours


title: ChIP CDX2-HA

description: Overexpression of CDX2-HA


title: Primary macrophages 4hr stimulation with IL-10

description: 4hrs IL-10 compared to the common reference (pooled donors)

source_name: Cells stimulated with IL-10 for 4hrs (pooled from 4 donors)


title: ChIP DLX1-HA

description: Overexpression of DLX1-HA


title: Primary macrophages 8hr stimulation with LPS & IL-10

description: 4hrs LPS & IL-10 compared to the common reference (pooled donors)

source_name: Cells stimulated with LPS & IL-10 for 4hrs (pooled from 4 donors)

value: LPS & IL-10


title: human ACVR1 R206H 2

description: R206H 2


title: ChIP BRACHYURY-HA

description: Overexpression of BRACHYURY-HA


title: 680kinv.B10 [Capture Hi-C]

tag: hybrid cells


title: ChIP BHLHB8-HA rep1

description: Overexpression of BHLHB8-HA

tag: cell type


title: ChIP BHLHB8-HA rep2

description: Overexpression of BHLHB8-HA

tag: cell line


title: Unstimulated primary macrophages (control)

description: unstimulated compared to the common reference (pooled donors)

source_name: Unstimulated cells (pooled from 4 donors)


title: ATAC SOX2 rep1

description: Overexpression of SOX2-HA

data_processing:
Reads were aligned to the mouse reference genome mm10 using STAR 2.5.3a with settings ‘-- alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’
Duplicate reads were removed with Picard and reads not mapping to chromosomes 1-19, X, or Y were removed

Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by merging replicate bam files with SAMtools followed by the deepTools functions bamCoverage (with setting --normalizeUsingRPKM). log2-ratio bigWig files were generated using the deepTools function bamCompare based on merged replicates for each TF overexpression sample over merged replicates for control (rtTA3G). on merged duplicates

extract_protocol:
Cells were pelleted and washed with 1X ice cold PBS at 800g for 5 min. Cells were gently resuspended in 50 μl of ice-cold ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40), and immediately pelleted at 800g for 10 min at 4°C. To transpose open chromatin regions, cells were resuspended in 50 μl of transposition reaction mix containing 0.5 μM of Tn5 transposase (in-house prepared) in TAPS-DMF buffer (10 mM TAPS-NaOH, 5 mM Mgcl2, 10% DMF) and incubated at 37°C for 30 min. The transposed DNA was purified using a DNA purification kit and eluted in 12 μl of water.
A 65 μl PCR reaction was setup with 10 μl of transposed DNA, 0.5 μM of forward primer Ad1_noMX, 0.5 μM of multiplexing reverse primer Ad2.x (Buenrostro et al. 2013), 0.6x SYBR Green I, and 1x PCR Master Mix. The samples were thermocycled at 72°C for 5 minutes, 98°C for 30 s, followed by 12 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The amplified ATAC libraries were purified using a DNA purification kit and size selected using Agencourt AMPure beads (0.55X unbound fraction followed by 1.2X bound fraction).

treatment_protocol: NIH-3T3 cells were treated with 500 ng/ml of Doxycycline 48 hours before the experiment. 50'000 cells were collected.


title: ATAC SOX15 rep2

description: Overexpression of SOX15-HA


title: ChIP DUXBL-HA

description: Overexpression of DUXBL-HA


title: human ACVR1 and H3.1K27M 1

description: ACVR1 WT K27M 1

tag: age

value: ACVR1 WT and H3.1K27M


title: ATAC SIX6 rep2

description: Overexpression of SIX6-HA


title: human ACVR1 1

description: ACVR1 WT 1

tag: genotype/variation

value: ACVR1 WT


title: ATAC rtTA3G control rep4

description: No overexpression


title: ATAC rtTA3G control rep3

description: No overexpression

data_processing:
Reads were aligned to the mouse reference genome mm10 using STAR 2.5.3a with settings ‘-- alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’
Duplicate reads were removed with Picard and reads not mapping to chromosomes 1-19, X, or Y were removed

Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by merging replicate bam files with SAMtools followed by the deepTools functions bamCoverage (with setting --normalizeUsingRPKM). log2-ratio bigWig files were generated using the deepTools function bamCompare based on merged replicates for each TF overexpression sample over merged replicates for control (rtTA3G). on merged replicates


title: ATAC SOX2 rep2

description: Overexpression of SOX2-HA


title: human ACVR1 and H3.1K27M 2

description: ACVR1 WT K27M 2


title: SD11-7

data_processing:
Basecalls performed using CASAVA version 1.8.2
The RNA-seq data for clone 10 was mapped to the human reference genome (hg19) using Bowtie version 1.0.0 (Trapnell et al., 2009) with unique-mapping parameter "-m 1".
To measure expression level, we estimated both reads per million reads (RPM) values on the GENCODE annotation version 19.
After whole genome sequencing (WGS) of the parental cells was performed, the reads were mapped using BWA version 0.7.10-r789, duplicates were marked with Picard version 1.96, realigned based on the presence of an insertion or deletion, and the quality scores recalibrated using GATK version 3.4.
The variants were called using GATK HaplotypeCaller version 3.4.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include transcript name, gene name, coordinates, RPKM values and RPM values

source_name: K563 cells

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Libraries were prepared according to illumina's instruction accompanying the Truseq stranded mRNA prep kit. Briefly, The polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads and then fragmented into small pieces. The cleaved RNA fragments were primed into random hexamers into first strand cDNA using reverse transcriptase and random primers. The RNA template removed and a replacement strand synthesized, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library.
Paired-end strand-specific RNA-seq

treatment_protocol: Cells were transfected with plasmid mixtures of Cas9-puro, U6-sgRNA encoding sgRNAs at a weight ratio of 1:1:1 using Neon (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. One day after transfection, puromycin (Cat no. A11138-03, Invitrogen, Carlsbad, CA) was added to the culture media at a final concentration of 2.5 µgml-1 for two days. Three days after transfection, cells were analyzed.

tag: transfection

value: plasmid mixtures of Cas9-puro and U7-sgRNAs encoding each member of sgRNAs


title: SD2-2

source_name: K562 cells

value: plasmid mixtures of Cas9-puro and U6-sgRNAs encoding each member of sgRNAs


title: ATAC rtTA3G control rep1

description: No overexpression


title: SD5-5


title: ATAC RHOX11 rep2

description: Overexpression of RHOX11-HA


title: ATAC RHOX11 rep1

description: Overexpression of RHOX11-HA


title: ATAC NANOG rep1

description: Overexpression of NANOG-HA


title: ATAC OCT4 rep2

description: Overexpression of OCT4-HA


title: ATAC NANOG rep2

description: Overexpression of NANOG-HA


title: ATAC OCT4 rep1

description: Overexpression of OCT4-HA


title: ATAC rtTA3G control rep2

description: No overexpression


title: RPMI8226_H3K27me3

city: Durham

first: Makoto

last: Nakagawa

state: NC

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

data_processing:
BCL (base call) files obtained with MCS (MiSeq Control Software v2.6.2.1) and RTA (Real Time Analysis v1.18.54.0) were transformed to fastq files using MSR (MiSeq Reporter v2.6.2).
The raw reads were filtered with fastq_quality_filter (parameters: -q 20 -p 50) from the FASTX-Toolkit (v0.0.14), followed by trimming with fastq_quality_trimmer (parameters: -t 20 -l 20).
The filtered and trimmed reads were mapped to human genome hg19 by Bowtie (v1.1.2) with default settings.
MACS2 (v2.1.1.20160309) with default settings was used to call peaks of the mapped reads and to generate bedGraph files.
BedGraph files were converted to bigWig format using the bedGraphToBigWig command.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: multiple myeloma

growth_protocol: RPMI1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Lysates were clarified from sonicated cell and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: peripheral blood

value: B lymphocyte

tag: antibody

value: H3K27me3 (Millipore, 07-449)


title: SD8-6

last: Lee

address: 222 Wangsimni-ro, Seongdong-gu

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Libraries were prepared according to illumina's instruction accompanying the Truseq stranded mRNA prep kit. Briefly, The polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads and then fragmented into small pieces. The cleaved RNA fragments were primed into random hexamers into first strand cDNA using reverse transcriptase and random primers. The RNA template removed and a replacement strand synthesized, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library.

value: human erythromyeloblastoid leukemia cell


title: SD1-29


title: Mock transfected cells 4

description: Mock transfected cells 4


title: SD7-10


title: SD7-27


title: SD3-2


title: SD4-9


title: ATAC SIX6 rep1

description: Overexpression of SIX6-HA

value: mouse fibroblasts


title: SD3-7


title: MM.1S_input

value: B lymphoblast


title: MM.1S_H3K27me3


title: ATAC HLF rep2

description: Overexpression of HLF-HA


title: ATAC HLF rep1

description: Overexpression of HLF-HA


title: SD11-2

source_name: clone containing segmental deletion of Repeat B+C

value: human erythromyeloblastoid leukemia cell line


title: SD10-2

source_name: clone containing segmental deletion of Repeat D


title: RPMI8226_input


title: GSM1827608 MNase_WT

city: Gwangju

first: Wooje

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

institute: Chosun University

description:
processed data file: MNase_seq_OE.bw
processed data file: MNase_Peaks_by_PING.bed

data_processing:
The Input, MeCP2 ChIP-seq, and MNase-seq reads were aligned to the mm9 reference genome using Bowtie 2 with the options --sensitive --score-min L,-1.5,-0.3.
PCR duplicate are removed using samtools rmdup for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bigwig files were generated using the deepTools package.
Supplementary_files_format_and_content: The bed files were generated using the PING program.  For the MNase-seq analysis, “MNase” as the default of the datatype in the postPING() option (alpha2=98; beta2=200000) were used. For MeCP2 ChIP-seq analysis, the combined MeCP2 ChIP-seq data from the two biological replicates were analyzed with “sonicated” in the postPING() option (alpha2=100; beta2=100000).

source_name: Olfactory epithelium

extract_protocol: For MNase digestion, olfactory neuroepithelia were harvested from Mecp2 WT littermate adult mice and resuspended in PIPES buffer (5mM PIPES, 85mM KCl, 0.5% NP-40, pH 8.0) at 4 °C. After disruption with a dounce homogenizer, nuclei were collected by centrifugation. Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA) per microliter volume for 15 min at 37 °C. MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. After digestion with 0.1 µg/µl RNase A (Fermentas, Pittsburgh, PA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY), and pellets were dissolved in H2O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA). MNase-seq libraries were prepared as described (Bioo Scientific, Austin, TX) using 5140-01 NEXTflex DNA Sequencing kit and 514101 NEXTflex DNA Barcodes-6. High throughput sequencing was done with Illumina Hi-Seq 2000.

value: Wild-type, MeCP2(+/y)

value: 8 weeks

value: Olfactory sensory neuron


title: ATAC SOX15 rep1

description: Overexpression of SOX15-HA


title: ATAC FOXA1 rep2

description: Overexpression of FOXA1-HA


title: ATAC FOXA1 rep1

description: Overexpression of FOXA1-HA


title: SD9-42

first: Hyeon

institute: Hanyang University

source_name: clone containing segmental deletion of Repeat A


title: GSM1827605 MeCP2_ChIP_WT_rep2

description:
processed data file: MeCP2_ChIP_OE_merge.bw
processed data file: MeCP2_Peaks_by_PING.bed

extract_protocol: ChIP-seq was done based on methods established previously (Li, Y et al. 2014). Two independent chromatin immunoprecipitation assays were performed using MAGnify chromatin immunoprecipitation kit (Life Technologies, Grand Island, NY). Specifically, main olfactory neuroepithelia (MOE) were dissected from the nasal cavity and dissociated mechanically via trituration in phosphate buffer saline (PBS). Equal number of cells was used for subsequent steps. Protein-DNA complexes were cross linked by incubating dissociated MOE cells with 1% formaldehyde for 5 minutes on a rocker at room temperature. The cross-linking was quenched by adding Glycine. After washing off the media, MOE cells were lysed briefly in SDS containing buffer followed by sonication for 15 minutes with 30 second intervals to shear genomic DNA using a BioruptorTM 300 (Diagenode, Denville, NJ). Sheared DNA was evaluated by 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and selected for sizes ranging between 200 bp and 300 bp. Each sheared genomic DNA preparation was split into two equal portions and incubated with MeCP2 antibody (Diagenode, pAb-052-050) or Rabbit IgG (Millipore, Cat# 12-370) for the negative control. MeCP2-genomic DNA complexes were pulled down and reverse cross-linked by DNase-free Proteinase K and subsequently purified. MeCP2 ChIP-seq and input DNA library were prepared according to manufacturer’s instruction (Bioo Scientific, Austin, TX) using 5143-01 NEXTflex ChIP-Seq kit and 514120 NEXTflex ChIP-Seq Barcodes-6. ChIP and Input DNAs were PCR amplified, cleaned up and sequenced on Illumina Hi-Seq 2000 at QB3 Vincent J. Coates Genomics Sequencing Laboratory in the UC Berkeley.

value: MeCP2 antibody (Diagenode, pAb-052-050)


title: GSM1827604 MeCP2_ChIP_WT_rep1


title: GSM1827607 Input_WT_rep2

description: processed data file: Input_OE_merge.bw


title: GSM1827606 Input_WT_rep1

description: processed data file: Input_OE_merge.bw


title: ATAC DUXBL rep2

description: Overexpression of DUXBL-HA


title: ATAC DUXBL rep1

description: Overexpression of DUXBL-HA


title: ATAC DLX6 rep2

description: Overexpression of DLX6-HA


title: SD9-33


title: SD6-7

source_name: clone containing segmental deletion of 3' splice site of exon 5


title: SD8-7

source_name: clone containing segmental deletion of exon 6


title: ATAC DLX6 rep1

description: Overexpression of DLX6-HA


title: SD5-12

source_name: clone containing segmental deletion of promoter


title: ATAC CDX2 rep2

description: Overexpression of CDX2-HA