title: M_12153 BALB\c NeuT+ 24 weeks

city: Milan

first: Matteo

last: Milani

state: Milan

address: Via Amadeo, 42

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: To assess the expression levels of microRNAs Illumina mouseWG-6 v2.0 microarrays designed on miRBase 19.0 from Agilent Technologies were used.

scan_protocol: Microarrays from Agilent were scanned with an Agilent SureScan scanner, and raw data were collected using Agilent’s Feature Extraction software v10.7.

data_processing: Raw data were preprocessed using an optimized version of the MA algorithm implemented in the AgiMicroRna package (Lopez-Romero 2011). For circulating microRNAs data were log2-transformed only, as standard normalization strategies are not suitable for circulating microRNA data.

source_name: Plasma

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

extract_protocol: Total RNA was extracted from plasma samples using the commercial column-based system Qiagen miRNeasy® Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: MMTV-NeuT transgenic females, and age-matched non transgenic siblings, were sacrified at 6, 12 and 24 weeks of age.

tag: gender

value: female

value: BALB\c NeuT+

tag: age (weeks)

tag: tumor grade

tag: tumor burden

tag: hemolyzed

value: y

tag: batch


title: Non-cancer control, rectus abdominis muscle biopsy 1

status: Public on Dec 03 2019

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with mucinous cystadenoma.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: rectus abdominis muscle biopsy

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Biopsies from the rectus abdominis muscle were harvested from patients at the beginning of surgery, and a portion to be used for RNA isolation was immediately snap-frozen in liquid nitrogen followed by storage at -80⁰C.  Muscles were minced and homogenized in TRIzol for RNA extraction.

tag: diagnosis

value: mucinous cystadenoma

tag: Sex

value: F

tag: tnm

tag: bw loss in 6 months prior to surgery

tag: age

tag: neoadjuvant therapy (y/n)

tag: survival post-surgery (or days elapsed since surgery, if still alive at time of censor)

value: n.d. (not determined)

tag: tissue

value: rectus abdominis muscle


title: M_12158 BALB\c NeuT+ 24 weeks

organism: Mus musculus

tag: genotype


title: 861_DP

type: SRA

city: Cambridge

first: Rebecca

middle: H

last: Herbst

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute of MIT and Harvard

library_source: transcriptomic

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options. Estimated counts from rsem were upper-quartile normalized where the 75th percentile was set to 1000.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample; Supplementary data file includes normalized counts.

molecule: polyA RNA

source_name: Sorted CD103+KLRG1+ Tregs

extract_protocol:
Cells were directly sorted into TCL buffer. Whole transcriptome amplication was performed with Smartseq v2 protocol.
RNA libraries were prepared for sequencing with the Illumina Nextera kit according to the manufacturer's instructions.

tag: strain

value: LSL-KrasG12D, p53fl/fl, Foxp3RFP


title: EPI2C12

city: Great Chesterford

first: Nicolas

last: Gambardella

state: Essex

address: Lewis House, Great Chesterford Court

country: United Kingdom

institute: aSciStance Ltd

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim Galore version: 0.4.1 (a wrapper for Cutadapt 1.8.1 with parameters  -f fastq -e 0.1 -q 20 -O 1 and FastQC)
Reads were mapped to GRCh38 whole genome using HiSAT2 v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Counts were produced using SeqMonk 0.34. All reads overlapping an exon were counted, all reads from all exons of all isoforms added, counting each one once.
Counts Per Million reads (CPM) were calculated dividing reads from all exons of all isoforms by the size of the library in reads, multiplied by 1 million.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma Separated Value file containing Counts Per Million reads. Rows are genes (rownames are Gene Symbols) and columns are cells.

source_name: engineered epicardial cell

extract_protocol:
Total RNA was extracted from cultures using RNeasy mini from Qiagen. DNA contamination was removed from the samples using DNA-free™ DNA Removal Kit from Ambion (Thermofisher).
cDNA synthesis and Illumina libraries were performed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit from TAKARA.

tag: cell type

value: hPSC-derived epicardium

tag: es line


title: Hottip-Tg-ST-HSC-ATAC-seq-1

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

library_source: genomic

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end).
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIP-seq, HiC-seq and CHIRP-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1).
Genome coverage tracks were created using deepTools version 3.0.
Chromatin structure HiC-seq was calculated and displayed with HOMER, Juicer and Juicebox software.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples, and peaks annotation for ATAC-seq, ChIP-seq and CHIRP-seq.

molecule: genomic DNA

source_name: Lin- Sca1+ Kit+ cd135- cd34+ Bone marrow cells

growth_protocol: Total bone marrow cells were isolated from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers. Human MOLM13 leukemia cells were cultured at RMPI1640 and 10% FBS media.

extract_protocol:
RNA samples extracted with Trizol and treated with DNase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3, H3K79me2 and MLL antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745; Anti-H3K27me3, Millipore, Cat No. 07-449; Anti-H3K79me2, Abcam, Cat No. ab3594.; Anti-MLL, Millipore, #05-765). ATAC-seq samples derived according to Nextera Tn5 Transposase kits. CHIRP-seq library constructs with the Illumina TruSeq CHIP DNA library kit. HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ChIP-seq and CHIRP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK, HSC cells from transgenic mice and MOLM13 AML cells without any treatment.

tag: cell types

value: Mouse-derived Bone marrow cells

tag: tissue origin

value: Bone marrow

tag: cell subtype

value: Lin- Sca1+ Kit+ cd135- cd34+

tag: genotype/variation

value: Hottip-Tg


title: EPI2C11


title: Positive_4

city: Zurich

first: Kurt

last: Tobler

address: Winterthurerstrasse 266a

department: Veterinary Virology

country: Switzerland

institute: University of Zurich

data_processing:
Base-calling and quality value calculations were performed using the Illumina data processing pipeline (version 1.8.2)
Sequence alignment of the resulting high-quality reads to the Equine (build: EquCab2) and viral genome (EcPV2_GB: EU503122.1) and quantification of gene level expression was carried out using “RSEM” (Version 1.2.5)
Differentially expressed genes were idenitfied by count based negative binomial model implemented in the software package “edgeR” (R version: 3.0.2, edgeR version: 3.4.2) The normalization factor was calculated by trimmed mean of M values (TMM) method.
Supplementary_files_format_and_content: quantification of gene level expression

organism: Equus caballus

source_name: penile tissue

extract_protocol:
Tissue samples were immersed in RNA later for strorage. For extraction, samples were treated with bashing beads and RNA was extracted with Direct-zol Miniprep kit
The SureSelect SS RNA Library Prep was used for library preparation. Briefly, total RNA samples (1 µg) were ribosome depleted and then reverse-transcribed into double-stranded cDNA with Actinomycin added during first-strand synthesis. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters. The adapters contain the index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The TruSeq SR Cluster Kit v3-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq 2000 in single read mode with read length of 100 base pairs using the TruSeq SBS Kit v3-HS (Illumina, Inc, California, USA)

tag: disease

value: squamous cell carcinomas

tag: number


title: M_17016 BALB\c NeuT+ 6 weeks

tag: gender

tag: age (weeks)

tag: tumor grade

value: no

tag: tumor burden

tag: hemolyzed

tag: batch


title: WT-ST-HSC-ATAC-seq-2

value: WT


title: EPI2C10


title: EPI2C4


title: WT-ST-HSC-ATAC-seq-1


title: EPI2C1


title: M_15652 BALB\c NeuT- 12 weeks

value: BALB\c NeuT-

value: normal


title: Positive_3


title: Hottip-Tg-LT-ATAC-RNA-seq-2

source_name: Lin- Sca1+ Kit+ cd135- cd34- Bone marrow cells

value: Lin- Sca1+ Kit+ cd135- cd34-


title: EPI2B9


title: Positive_2


title: M_15657 BALB\c NeuT- 12 weeks

value: female

value: y


title: E13_red_Replicate 1 [94731]

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

data_processing:
All libraries were sequenced 3x (technical replicates) to increase read depth. Raw reads were delivered as unaligned BAM files and technical replicates were combined using samtools (v1.8) and converted to fastq format using bamToFastq (bedtools suite v2.26.0) for alignment. Reads within transcripts were counted using STAR_2.5.0c with an index prepared from GRCm38 and Gencode M16 gene annotation. Note that for optimal representation of the long non-coding RNA Meg3 the spliced ENSMUST00000143836.7 transcript was modified to represent a single exon transcript. Parameters used for STAR alignment: --outFilterMultimapNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --quantMode GeneCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Read counts in transcripts as reported by STAR as tab delimited text

growth_protocol: Mouse protocols were reviewed by institutional preclinical core facility (PCF) at IST Austria and all breeding and experimentation was performed under a license approved by the Austrian Federal Ministry of Science and Research in accordance with the Austrian and EU animal laws. Mice were maintained and housed in animal facilities with a 12-hour day/night cycle and adequate food/water conditions according to IST Austria institutional regulations. Mouse lines with chromosome 7 MADM cassettes: MADM-7-GT JAX stock # 021457, MADM-7-TG JAX stock # 021458, Emx1-Cre: JAX stock # 005628. All MADM-based analyses were carried out in a mixed C57BL/6J, CD1 genetic background.

extract_protocol:
sorted cells were directly processed without RNA extraction
Smart-Seq2 (VBCF GmbH Vienna)

treatment_protocol: Pregnant females were sacrificed and E13/E16 embryos were collected. Neocortex area was dissected. Single individuals were used as replicates. Single cell suspensions were prepared by using Papain containing L-cysteine and EDTA (vial 2, Worthington), DNase I (vial 3, Worthington), Ovomucoid protease inhibitor (vial 4, Worthington), EBSS (Thermo Fisher Scientific), DMEM/F12 (Thermo Fisher Scientific), FBS and HS. All vials from Worthington kit were reconstituted according to the manufacturer’s instructions using EBSS. The dissected brain area was directly placed into Papain-DNase solution (20units/ml papain and 1000 units DNase). Enzymatic digestion was performed for 30min at 37°C in a shaking water bath. Next, solution 2 (EBSS containing 0.67mg Ovomucoid protease inhibitor and 166.7 U/ml DNase I) was added, the whole suspension was thoroughly mixed and centrifuged for 5min at 1000rpm at RT. Supernatant was removed and cell pellet was resuspended in solution 2. Trituration with p1000 pipette was performed to mechanically dissolve any remaining tissue parts. DMEM/F12 was added to the cell suspension as a washing solution, followed by a centrifugation step of 5min with 1500rpm at RT. Cells were resuspended in media (DMEM/F12 containing 10% FBS and 10% HS) and kept on ice until sorted. Right before sorting, cell suspension was filtered using a 40µm cell strainer. FACS was performed on a BD FACS Aria III using 100 nozzle and keeping sample and collection devices (0.8ml PCR tubes) at 4°C. Duplet exclusion was performed to ensure sorting of true single cells. Cells were sorted into 4µl lysis buffer (0.2% Triton X-100, 2U/µl RNase Inhibitor [Clonetech]). Immediately after sorting was completed samples were transferred into a 96 well plate (Bio-Rad) that was kept on dry ice. GFP+, tdT+ and GFP+/tdT+ cells (200-400 cells) were collected.

tag: age

tag: color

value: red

tag: tissue

value: cortex

tag: cre

tag: madm

value: Chr. 7

tag: replicate

value: Replicate 1


title: M_15656 BALB\c NeuT+ 12 weeks

tag: genotype

value: BALB\c NeuT+

value: early ca


title: Hottip-Tg-LT-ATAC-RNA-seq-1

tag: cell types

value: Mouse-derived Bone marrow cells

tag: tissue origin

value: Bone marrow

tag: cell subtype


title: Hottip-Tg-ST-HSC-ATAC-seq-2

value: Lin- Sca1+ Kit+ cd135- cd34+

tag: genotype/variation

value: Hottip-Tg


title: Positive_1

tag: disease

value: squamous cell carcinomas

tag: number


title: Positive_5


title: WT-LT-HSC-ATAC-seq-2

value: WT


title: TS6hr_RNA_rep2

city: Charlestown

first: Katia

last: Georgopoulos

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) or hg19 (human genome) assembly using the genome mappers Bowtie2 for ATACseq and STAR for RNAseq and ChIPseq.
For RNA-seq, read normalization, RPKM and differential gene expression, were performed using the HOMER scripts analyzeRepeats.pl and getDiffExpression.pl with implementation of DESeq2 through R.
Peak calling for ATAC-seq was perfomed using MACS2 call peaks  with --keep-dup all --nomodel --shift 37 --extsize 73.
Peak calling for ChIP-seq was performed using the Homer findPeaks algorithm.
Genome_build: mm10, hg19

source_name: adult epidermis

extract_protocol:
Dorsal epidermis was separated from the dermis by digestion with 0.25% trypsin overnight at 4C to obtain a single cell suspension. ITGA6+, CD45-, CD34- cells were sorted with FACS Aria.
Trueseq stranded mRNA sample prep kit (Illumina)

tag: strain

value: keratinocytes


title: M_17011 BALB\c NeuT- 6 weeks

tag: gender

value: BALB\c NeuT-

tag: age (weeks)

tag: tumor grade

value: no

tag: tumor burden


title: Negative_2

value: healthy


title: WT-LT-HSC-ATAC-seq-1

value: Lin- Sca1+ Kit+ cd135- cd34-


title: EPI2B6

tag: cell type

value: hPSC-derived epicardium

tag: es line


title: Negative_1


title: EPI2B5


title: Hottip-Tg-ST-HSC-RNA-seq-2


title: Individual_sgRNA-Cas9_Disruption

city: New Haven

first: James

last: Noonan

state: CT

address: 333 Cedar St

institute: Yale University

description: not applicable

data_processing:
For each sample, fastq reads were trimmed to only contain the variable 20nt sgRNA sequence targeting Cas9 for genetic disruption.  #cutadapt version 1.16  cutadapt -j 20 -l 20 -g GACGAAACACCG  --trimmed-only <input>
Model-based analysis of CRISPR knock-out (MaGeCK) was utilized to generate read counts for all sgRNAs included in each sample.  #mageck v0.5.8  mageck count --norm-method none --list-seq <sgRNAs_sublibrary> --fastq <trimmed_fastq_all_reps_timepoints> --trim-5 0
Model-based analysis of CRISPR knock-out (MaGeCK) was utilized to estimate the biological effects of genetic disruption for each sgRNA in the sample at each timepoint across replicates.  #mageck v0.5.8  mageck mle --threads 10 --update-efficiency --permutation-round 10 --norm-method control --control-sgrna lib/NTC_sgRNA_ID.txt --count-table results/count/<sublibrary_count_matrix> --design-matrix designmatrix.txt
Supplementary_files_format_and_content: Normalized summary file contains estimates of the biological effects relative to non-targeting controls (NTCs) following genetic disruption.  Biological effects are jointly modeled for across two replicates for sgRNAs targeting a single conserved region or targeting a single gene.  Summary files include estimates for 4, 8, or 12 cell divisions and measures of statistical significance.

source_name: H9-derived neural stem cells

growth_protocol: H9-derived human neural stem cells were cultured in Knockout DMEM/F-12 (Life Technologies, c/n 12660012) supplemented with EGF (Connstem, E1000-100UG) and FGF (ConnStem, F1001-10UG), GlutaMax-I (Life Technologies, c/n 35050-061) and StemPro neural supplement (Life Technologies, A1050801) as recommended by the manufacturer.  In addition, cells were cultured on Matrigel–coated (Corning, c/n 354230) flasks seeded at ~50,000 cells per square centimeter.  The doubling time of H9-derived human neural stem cells is approximately 48 hours.

extract_protocol:
Genomic DNA was isolated from ~50 milliion cells per sub-library, per transduction replicate at each timepoint.  Frozen cell pellets were thawed and genomic DNA was isolated using the standard protocol (Qiagen Blood and Cell Culture Maxi Kit, c/n 13362).
Each sgRNA subpool library readout was performed using two steps of PCR as described in Chen et al. Cell (2015).  Second PCR round products were purified using column-based cleanup (NEB Monarch PCR and DNA Cleanup Kit, c/n T1030S).  Libraries of each time point for each sub-library were internally controlled by uniquely barcoding and combining for sequencing on the same channel(s) of a sequencing run.  Diluted libraries were spiked in with whole-exome libraries and sequenced on HiSeq4000 instruments (Illumina).

treatment_protocol: Target cells in 25 cm tissue culture flasks at 250,000 cells per cm2 were transduced in low volume media containing 8ug/mL polybrene, 24 hours after infection virus was removed and cells were passaged to normal density of 50,000 cells per cm2.  For lentiviral titer, varying amounts of concentrated virus were added to 25 cm tissue culture flasks and inoculated for 24 hours.  Cells were then passaged to normal seeding density and infection rate was determined 48 hours later by flow cytometry for GFP expression.  For high-throughput screening, each sub-library was transduced by plating 50 million cells across eight 25 cm flasks and adding the appropriate volume of lentivirus to each flask.  Initial multiplicity-of-infection was ~0.3-0.4 to achieve >1000-fold library coverage and infection was monitored after 24 hours by flow cytometry for GFP expression over the course of the experiment (at 4, 8, and 12 cell divisions).  Cells were harvested at each passage and stored as a cell pellet at -20C for genomic DNA extraction.

tag: timepoint

value: not applicable


title: WT-ST-HSC-RNA-seq-2


title: EPI2B3


title: EPI2B8


title: M_13716 BALB\c NeuT- 24 weeks

value: female

value: normal

tag: hemolyzed

tag: batch


title: M_12476 BALB\c NeuT+ 12 weeks

tag: genotype

value: BALB\c NeuT+

value: y


title: M_14205 BALB\c NeuT- 6 weeks


title: M_12149 BALB\c NeuT- 12 weeks


title: EPI2B12


title: 14d Rap1_ChIPSeq biological repeat 2

city: Stellenbosch

first: Hugh

last: Patterton

address: Merriman Street

department: Center for Bioinformatics and Computational Biology

country: South Africa

institute: Stellenbosch University

data_processing:
Read files were filtered with Trim_Galore with default setting
Filtered reads were aligned to Saccharomyces cerevisiae genome release 64-2 with Bowtie2 using default settings
Peaks were identified in the aligned files using MACS2 with default settings
Generated "Treatment" and "Input" bedgraph files were  converted to wiggle format and normalized to the same number of total counts using the "normalize_wiggle" and "convert_bedgraph_to_wiggle" Python programs available at http://www.github.com/hpatterton
Genome_build: S288C_reference_genome_R64-2-1
Supplementary_files_format_and_content: wiggle

organism: Saccharomyces cerevisiae

source_name: 14 d culture

growth_protocol: Yeast cells were cultured in YPD at 30 degrees for the times indicated

extract_protocol:
Cells were lysed with 300 ml acid washed glass beads (425-600 mm) by vigorous agitation for 30 s in a BeadRuptor2 followed by 30 s on ice, repeated 7 times. Sufficient lysis (90%) was confirmed by light microscopy. The lysate was subsequently sonicated at 4°C to obtain an average DNA fragment length of 300 bp. Samples were centrifuged and the supernatant, containing sheared chromatin, recovered.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultures (50 ml) were cross-linked in 1% (v/v) formaldehyde for 20 m, 25°C, and the reaction quenched with glycine (125 mM), 5 m, 25°C. The cells were washed once in 50 ml PBS (pH 7.4), and resuspended in lysis buffer (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1mM EDTA, 1% (v/v) Triton-X-100 and Complete-mini EDTA free protease inhibitor cocktail [Roche]).

value: Yeast cells

tag: chip antibody

value: Rap1 (Abcam, ab103520)


title: 14d Input DNA biological repeat 2


title: M_15653 BALB\c NeuT- 12 weeks


title: Hottip-Tg-LT-HSC-RNA-seq-2

tag: cell types

value: Mouse-derived Bone marrow cells

tag: tissue origin

value: Bone marrow


title: Negative_3


title: EPI2B7


title: 14d Rap1_ChIPSeq biological repeat 1


title: EPI2B11


title: M_12475 BALB\c NeuT+ 12 weeks

value: early ca


title: M_14204 BALB\c NeuT+ 6 weeks

value: ripetizione in corso


title: M_12152 BALB\c NeuT- 24 weeks


title: Hottip-Tg-LT-HSC-RNA-seq-1

tag: cell subtype

tag: genotype/variation

value: Hottip-Tg


title: 14d Input DNA biological repeat 1


title: Hottip-Tg-ST-HSC-RNA-seq-1

value: Lin- Sca1+ Kit+ cd135- cd34+


title: EPI2B10


title: WT-LT-HSC-RNA-seq-2

value: WT


title: M_13710 BALB\c NeuT- 24 weeks

value: BALB\c NeuT-


title: 16h Rap1_ChIPSeq biological repeat 2

source_name: 16 h culture


title: EPI2B2


title: EPI2B1


title: WT-LT-HSC-RNA-seq-1

value: Lin- Sca1+ Kit+ cd135- cd34-


title: WT-ST-HSC-RNA-seq-1


title: 16h Input DNA biological repeat 2


title: EPI2A9

value: hPSC-derived epicardium


title: M_CI71 BALB\c NeuT- 6 weeks

value: no


title: 16h Rap1_ChIPSeq biological repeat 1


title: EPI2A8


title: EPI2A7


title: 16h Input DNA biological repeat 1


title: EPI2A6


title: EPI2A5


title: RNA-Seq_heatshock rep1

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description: Replica 1

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed from low quality and/or short sequences by trimmomatic v. 0.36 using the following options: LEADING:18 TRAILING:18 SLIDINGWINDOW:4:22 MINLEN:20
Trimmed reads were mapped to hg19p13 by STAR aligner 2.6.1c with hg19 ENSEMBLE genome map v.87 ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz. Alignment options were the following:  --outSAMtype BAM SortedByCoordinate --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM
Wig files with unique mappings from each replica and strand were converted to bigWig by wigToBigWig tool from UCSC Kent Utilities http://hgdownload.soe.ucsc.edu/admin/exe/ and then averaged by wiggletools 1.2 with the following options: wiggletools write_bg rnaseq.str1.mean.bedGraph mean rnaseq.rep1.str1.bw rnaseq.rep2.str1.bw. The files with mean expression signal for each strand were then converted to bigWig by bedGraphToBigWig tool from UCSC Kent utilities.
Trimmed reads were quantified to hg19p13 with ENSEMBLE genome map v.87 by RSEM 1.3.1 using the following options: rsem-calculate-expression --star --output-genome-bam --calc-ci --num-threads 10 --ci-memory 4096 --star-gzipped-read-file. This operation was performed for both replicas separately and both replicas simultaneously.
Genome_build: Homo Sapiens hg19/GRCh37.p13 genome with included to chr14 from address 1 Human ribosomal DNA U13369. ENSEMBL annotation v.87 in GTF format for GRCh37/hg19 H.sapiens genome
Supplementary_files_format_and_content: bigWig files contain normalized (RPM, reads per million) expression signal genomewide for each strand. Results files contain quantified expression values in TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase Million) for each gene.

source_name: cultured cells

growth_protocol: HEK293T cells were grown in DMEM with 10% FBS in a humidified incubator at 37°C and 5% CO2 to 80% confluency.

extract_protocol:
Total RNA was extracted from cell lysed with Trisol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA Quality was checked with  BioAnalyser and  RNA 6000 Nano Kit(Agilent). Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion).
Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length.

treatment_protocol: RNA-Seq procedure was used for analysis of expression in HEK293T cells. Heat shock treatment was performed for 20 min at 43°C. Then heat-shock treated cells were incubated for 6 h at 37°C. Then cells of each replicate were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample.

tag: cell line

tag: tissue

value: kidney

value: wild type


title: RNA-Seq_heatshock rep2

description: Replica 2


title: M_15659 BALB\c NeuT+ 12 weeks

tag: gender

value: female

value: BALB\c NeuT+

value: severe dys


title: M_14197 BALB\c NeuT- 6 weeks

tag: age (weeks)

value: mild/moderate dys

value: y


title: EPI2A4


title: M_17010 BALB\c NeuT- 6 weeks

tag: tumor grade


title: M_14202 BALB\c NeuT+ 6 weeks

tag: tumor burden


title: HEK293T RNA-Seq rep1

description: Replica 1

source_name: HEK293T human cells


title: M_12478 BALB\c NeuT+ 12 weeks

value: early carcinoma


title: EPI2A3

tag: cell type


title: EPI2A2

tag: es line


title: M_12148 BALB\c NeuT- 12 weeks

value: normal


title: 4C-rDNA-old primers rep2

description: Replica 2

data_processing:
Library strategy: 4C-seq
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.16 using the following options: --trim-n --times=4 --minimum-length 20 -q 26 --untrimmed-output=4C_notail.fastq.gz -g GCCTAAGCCTGCTGAGAACTTTC -g CAGCATTCTGTAGGGAGATCAAATC -a GAAAGTTCTCAGCAGGCTTAGGC -a GATTTGATCTCCCTACAGAATGCTG
Untrimmed sequences from the file 4C_notail.fastq.gz were trimmed for the following adaptor sequences by cutatapt v. 1.16 using the following options --trim-n --times=4 --trimmed-only --minimum-length 20 -q 26 -g TCTTTGAAAAAAATCCCAGAAGTGGT -g AAGTCCAGAAATCAACTCGCCAGT -a ACTGGCGAGTTGATTTCTGGACTT -a ACCACTTCTGGGATTTTTTTCAAAGA. Then outputs of previous and current adaptor removal steps were concatenated in one file 4C_trimmed.fastq.gz for furher processing
Trimmed reads were mapped to hg19p13 by bwa 0.7.12-r1039 using the mem algorithm. All non-aligned reads were removed from resulting alignment file by samtools 1.6: -b -S -F 4 -@ 10 allalign.sam > aligned.bam
Mapping and alignment results were converted to resulting tables using samtools 1.6 and ad hoc Perl scripts.
Each replica results table was converted to bedGraph file for further processing using reads amount as data value. Intersection file was built by bedtools v. 2.27.1 with the following command line: bedtools intersect -a 4C_hg19_old_rep1.bedGraph -b 4C_hg19_old_rep2.bedGraph -wb. Ad hoc Perl script was used to convert bedtools output file back to bedGraph file with summing up in the overlapped regions.
Genome_build: Homo Sapiens hg19/GRCh37.p13 genome with included to chr14 from address 1 Human ribosomal DNA U13369
Supplementary_files_format_and_content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence. bedGraph files for each replica and intersection are supplied too.

extract_protocol:
DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978).  Cross-linking  To suspension containing about 20x106 HEK293T cells in 40 ml of DMEM formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C.  Lysis   The pellet of cells was resuspended at °C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C.  Digestion with EcoRI  The nuclei pellet was resuspended in 756 l of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C.   Ligation  To inactivate the restriction enzyme, 35l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5l of BSA (5 mg/ml), 80l of 100 mM ATP, and 5241l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.    DNA purification  For isolation of DNA 50l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE.   Digestion with FaeI  About 15 g of DNA was digested in 250l solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100l of 0.1xTE.   Ligation  For circularization 15g of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50l of 0.1xTE.   PCR and library preparation  One or two rounds of PCR were used as described below. There are about 300-400 copies of rDNA. That is why a single round of PCR (with up to 35 cycles) was found to be sufficient. DNA concentration was titrated and finally about 30 ng of DNA was used for PCR with primers   5’ TCTTTGAAAAAAATCCCAGAAGTGGT 3’ and 5’ AAGTCCAGAAATCAACTCGCCAGT 3’ (for PCR-1), and 5’ GCCTAAGCCTGCTGAGAACTTTC 3’ and 5’ CAGCATTCTGTAGGGAGATCAAATC 3’ (for PCR-2). After separation in 2% agarose gels two DNA fractions (200-400 bp and higher 400 bp) were eluted using QIAqiuck gel extraction kit (Quigen). The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina) using adapter AR006 for 200-400 bp DNA fraction and adapter R007 for DNA fraction higher 400 bp. The samples were sequenced using MiSeq (Illumina).
One or two rounds of nested PCR were used as described below. There are about 300-400 copies of rDNA. That is why a single round of PCR (with up to 30 cycles) was found to be sufficient. DNA concentration was titrated and finally about 30 ng of DNA was used for PCR with primers ("old primers")   5’ TCTTTGAAAAAAATCCCAGAAGTGGT 3’ and 5’ AAGTCCAGAAATCAACTCGCCAGT 3’ (for PCR-1), and 5’ GCCTAAGCCTGCTGAGAACTTTC 3’ and 5’ CAGCATTCTGTAGGGAGATCAAATC 3’ (for PCR-2). PCR products were purified using QIAqiuckPCR purification kit kit (Quigen). The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina). The samples were sequenced using HiSeq 1500 (Illumina) following the manufacturer's protocols.

tag: strain


title: 4C-rDNA-old primers rep1

description: Replica 1


title: EPI2A12


title: M_17015 BALB\c NeuT+ 6 weeks

tag: hemolyzed


title: M_13707 BALB\c NeuT- 24 weeks

tag: batch


title: EPI2A11


title: EPI2A10


title: M_17014 BALB\c NeuT+ 6 weeks

tag: genotype


title: EPI2A1


title: M_13708 BALB\c NeuT+ 24 weeks


title: HEK293T RNA-Seq rep2

description: Replica 2


title: prg-1(n4357) Mutant Gravid Adults mRNA 25C, Rep 2

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
prg-1_wholeAnimals_2_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx

data_processing:
trimming and filtering: Adapters and low-quality bases were removed using Trimmomatic v. 0.35.
alignment: Trimmed reads were mapped to the C. elegans genome (Wormbase release WS230) and transposon consensus sequences (repbase) using Star v. 2.5.0a.
additional processing: Reads from specific features were counted using samtools v. 1.6 (transposon consensus sequences) or RSEM v. 1.3.0 (all other features). Differential expression analysis was done using DESeq2 v. 1.18.1.
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230
Supplementary_files_format_and_content: Normalized abundance table in Excel format

organism: Caenorhabditis elegans

growth_protocol: Animals were grown on NGM plates containing the E. coli strain OP50.

extract_protocol:
sample collection: Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
RNA was depleted of rRNA using RiboZero and enriched for >200nt sizes with Zymo RNA clean and concentrator-5. Libraries were then prepared according to the NEBNext® Ultra™ II Directional RNA kit protocol. Size selection and library purification was done using AMPure XP beads.

tag: age

value: gravid adults (54h, 25 C)

value: Whole worms

tag: molecule subtype

value: Total RNA (rRNA-depleted, >200 nt)


title: prg-1(n4357) Mutant Gravid Adults mRNA 25C, Rep 1

description:
prg-1_wholeAnimals_1_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx


title: M_17007 BALB\c NeuT- 6 weeks


title: prg-1(n4357) Mutant Gravid Adults mRNA 25C, Rep 3

description:
prg-1_wholeAnimals_3_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx


title: M_14200 BALB\c NeuT- 6 weeks


title: mut-16(pk710) Mutant Gravid Adults mRNA 25C, Rep 3

description:
mut-16_wholeAnimals_3_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx


title: EPI1H8


title: EPI1H7


title: mut-16(pk710) Mutant Gravid Adults mRNA 25C, Rep 2

description:
mut-16_wholeAnimals_2_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx


title: M_14198 BALB\c NeuT+ 6 weeks


title: mut-16(pk710) Mutant Gravid Adults mRNA 25C, Rep 1

description:
mut-16_wholeAnimals_1_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx


title: M_CI70 BALB\c NeuT- 6 weeks


title: Wild Type Gravid Adults mRNA 25C, Rep 3

description:
wt_wholeAnimals_3_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx

source_name: Wild Type Gravid Adults mRNA 25C


title: M_13711 BALB\c NeuT+ 24 weeks


title: EPI1H6


title: EPI1H5


title: M_13706 BALB\c NeuT- 24 weeks


title: Wild Type Gravid Adults mRNA 25C, Rep 1

description:
wt_wholeAnimals_1_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx


title: Wild Type Gravid Adults mRNA 25C, Rep 2

description:
wt_wholeAnimals_2_mRNA_25C
processed data file: wt_vs_mutant_wholeAnimals_transposons_25C.xlsx


title: M_CI72 BALB\c NeuT- 6 weeks


title: M_12477 BALB\c NeuT- 12 weeks


title: EPI1H4


title: M_15658 BALB\c NeuT+ 12 weeks


title: prg-1(n4357) Mutant Gravid Adults mRNA 20C, Rep 3

description:
prg-1_wholeAnimals_3_mRNA
processed data file: wt_vs_mutant_wholeAnimals_transposons_20C.xlsx

value: gravid adults (68-70h, 20 C)


title: prg-1(n4357) Mutant Gravid Adults mRNA 20C, Rep 2

description:
prg-1_wholeAnimals_2_mRNA
processed data file: wt_vs_mutant_wholeAnimals_transposons_20C.xlsx


title: EPI1H9


title: EPI1H12


title: prg-1(n4357) Mutant Gravid Adults mRNA 20C, Rep 1

description:
prg-1_wholeAnimals_1_mRNA
processed data file: wt_vs_mutant_wholeAnimals_transposons_20C.xlsx


title: mut-16(pk710) Mutant Gravid Adults mRNA 20C, Rep 3

description:
mut-16_wholeAnimals_3_mRNA
processed data file: wt_vs_mutant_wholeAnimals_transposons_20C.xlsx


title: S_nbB_3 [STAT_nbB3]

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

institute: Imperial College

data_processing:
Basecalls performed using CASAVA 1.8.4
Paired-end 100bp reads were quality trimmed using trimgalore (standard parameters).
Trimmed reads were mapped to non mRNA species' index using Bowtie2 (--un-conc) and unmapped reads were extracted.
Surviving paired end reads were then mapped to the E. coli NC_000913.3 genome using Bowtie2 (--no-discordant --no-mixed).
Raw count matrices were computed using the summarisedOverlaps function (mode="Union",singleEnd=F,ignore.strand=F,fragments=T) from the GenomicAlignments R package and then the differential expression analysis was performed with the R package DESeq2.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: cvs file containing gene information, basMean, log2FoldChange and padj for each condition.

organism: Escherichia coli

source_name: Expressing non binding HMfB_17 hrs after induction

growth_protocol: Escherichia coli cells were obtained from DSMZ (https://www.dsmz.de/) and grown at 37C in LB medium under constant agitation (180rpm).

extract_protocol:
Induced cells were harvested at the precise time point, centrifuge to remove the medium and the pellet snap frozen in liquid nitrogen. Protoplasts were obtained by incubating the pellet in Y1 buffer () for 1 hours at 37C. Total mRNA was extracted using RNeasy Mini Kit. Illumina Ribo-zero rRNA removal reagent was used to deplete the samples of rRNA before library preparation.
For the RNA samples paired-end reads were prepared using TruSeq Stranded RNA LT Kit

treatment_protocol: Expression of HMf histones was triggered by Rhamnose induction to a final working concentration of 15mM. The cells were harvested in late exponential and stationary phase, which means 2 hours and 17 hours after induction, respectively.

value: Expressing non binding HMfB

tag: timepoint

value: 17 hours after induction

value: Total RNA depleted for ribosomal RNA


title: S_nbB_5 [STAT_nbB5]


title: S_nbB_6 [STAT_nbB6]


title: EPI1H10

value: hPSC-derived epicardium


title: S_nbB_2 [STAT_nbB2]


title: mut-16(pk710) Mutant Gravid Adults mRNA 20C, Rep 2

description:
mut-16_wholeAnimals_2_mRNA
processed data file: wt_vs_mutant_wholeAnimals_transposons_20C.xlsx


title: EPI1G9


title: EPI1G8


title: S_nbB_1 [STAT_nbB1]


title: S_nbA_5 [STAT_nbA5]

source_name: Expressing non binding HMfA_17 hrs after induction

value: Expressing non binding HMfA


title: Wild Type Gravid Adults mRNA 20C, Rep 3

description:
wt_wholeAnimals_3_mRNA
processed data file: wt_gonads_vs_wholeAnimals_mRNAs.xlsx

source_name: Wild Type Gravid Adults mRNA 20C


title: mut-16(pk710) Mutant Gravid Adults mRNA 20C, Rep 1

description:
mut-16_wholeAnimals_1_mRNA
processed data file: wt_vs_mutant_wholeAnimals_transposons_20C.xlsx


title: EPI1G7


title: Wild Type Gravid Adults mRNA 20C, Rep 2

description:
wt_wholeAnimals_2_mRNA
processed data file: wt_gonads_vs_wholeAnimals_mRNAs.xlsx


title: S_nbA_4 [STAT_nbA4]


title: EPI1G6


title: S_nbA_3 [STAT_nbA3]


title: Wild Type Gravid Adults mRNA 20C, Rep 1

description:
wt_wholeAnimals_1_mRNA
processed data file: wt_gonads_vs_wholeAnimals_mRNAs.xlsx


title: EPI1H3


title: Wild Type Gravid Adults sRNA 20C, Rep 3

description:
wt_wholeAnimals_3_sRNA
processed data file: wt_gonads_vs_wholeAnimals_sRNAs.xlsx

data_processing:
trimming and filtering: Reads were parsed from adapter sequeces and filtered for quality (>1 base with Q<30) using CASHX v. 2.3.
alignment: Parsed reads were aligned to the C. elegans genome (WS230) using CASHX v. 2.3 and to transposon consensus sequences (repbase) using Bowtie2 v. 2.3.4.1.
additional processing: Reads from specific features were counted using using samtools v. 1.6 (transposon consensus sequences) or CASHX v. 2.3 (all other features). miRNA annotations were based on miRBase release 20. WAGO class 22G-RNA annotation was based on (Phillips et al 2012). CSR-1 class 22G-RNA annotation was based on (Claycomb et al 2009). piRNA annotation was based on WormBase release WS230. Differential expression analysis was done using DESeq2 v. 1.18.1.
Base calling and fastq file generation was done using Illumina software.
Genome_build: WS230
Supplementary_files_format_and_content: Normalized abundance table in Excel format

source_name: Wild Type Gravid Adults sRNA 20C

extract_protocol:
sample collection: Whole worms were flash frozen in liquid nitrogen prior to Trizol/chloroform extraction
Small RNAs (~16-30-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with RNA polyphosphatase to facilitate capture of 22G-RNAs. Libraries were then prepared according to the NEBNext® Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels.

value: Small RNAs (polyphosphatase treated, 16-30 nt)


title: S_nbA_2 [STAT_nbA2]


title: EPI1G5


title: EPI1H11


title: EPI1G4


title: EPI1G3


title: EPI1G12


title: E_nbB_2 [EXP_nbB2]

source_name: Expressing non binding HMfB_2 hrs after induction

value: 2 hours after induction


title: Wild Type Gravid Adults sRNA 20C, Rep 1

description:
wt_wholeAnimals_1_sRNA
processed data file: wt_gonads_vs_wholeAnimals_sRNAs.xlsx


title: E_nbB_4 [EXP_nbB4]


title: EPI1G2


title: S_nbA_1 [STAT_nbA1]


title: E_nbB_1 [EXP_nbB1]


title: EPI1G1


title: Wild Type Gravid Adults sRNA 20C, Rep 2

description:
wt_wholeAnimals_2_sRNA
processed data file: wt_gonads_vs_wholeAnimals_sRNAs.xlsx


title: E_nbB_3 [EXP_nbB3]


title: EPI1F9


title: E_nbB_5 [EXP_nbB5]


title: EPI1G10


title: E_nbA_6 [EXP_nbA5]

source_name: Expressing non binding HMfA_2 hrs after induction


title: EPI1G11

source_name: engineered epicardial cell


title: mut-16(pk710) Mutant Dissected Gonads sRNA 20C, Rep 3

description:
mut-16_gonads_3_sRNA
processed data file: wt_vs_mutant_gonads_sRNAs.xlsx

extract_protocol:
sample collection: Dissected gonads were collected in Trizol on ice over the course of 8-10 hours, then stored at -80 C. The Trizol containing the gonad tissue underwent 2 freeze/thaw cycles using liquid nitrogen prior to Trizol/chloroform extraction.
Small RNAs (~16-30-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with RNA polyphosphatase to facilitate capture of 22G-RNAs. Libraries were then prepared according to the NEBNext® Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels.

value: Dissected gonads


title: E_nbA_2 [EXP_nbA2]


title: Wild Type Dissected Gonads sRNA 20C, Rep 3

description:
wt_gonads_3_sRNA
processed data file: wt_gonads_vs_wholeAnimals_sRNAs.xlsx

source_name: Wild Type Dissected Gonads sRNA 20C


title: prg-1(n4357) Mutant Dissected Goands sRNA 20C, Rep 1

description:
prg-1_gonads_1_sRNA
processed data file: wt_vs_mutant_gonads_sRNAs.xlsx


title: prg-1(n4357) Mutant Dissected Goands sRNA 20C, Rep 3

description:
prg-1_gonads_3_sRNA
processed data file: wt_vs_mutant_gonads_sRNAs.xlsx


title: EPI1F6


title: prg-1(n4357) Mutant Dissected Goands sRNA 20C, Rep 2

description:
prg-1_gonads_2_sRNA
processed data file: wt_vs_mutant_gonads_sRNAs.xlsx


title: mut-16(pk710) Mutant Dissected Gonads sRNA 20C, Rep 2

description:
mut-16_gonads_2_sRNA
processed data file: wt_vs_mutant_gonads_sRNAs.xlsx


title: EPI1F8


title: mut-16(pk710) Mutant Dissected Gonads sRNA 20C, Rep 1

description:
mut-16_gonads_1_sRNA
processed data file: wt_vs_mutant_gonads_sRNAs.xlsx


title: E_nbA_3 [EXP_nbA3]


title: RORα liver-specific KO

city: Seoul

first: Hyeon-Ji

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: liver

growth_protocol: Six-week-old male RORα f/f and RORα-LKO mice were fed an HFD for 12 weeks

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN mRNA-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: liver

value: RORalpha f/f:Alb-Cre


title: EPI1F5


title: E_nbA_5 [EXP_nbA4]


title: EPI1F3


title: E_nbA_1 [EXP_nbA1]


title: Wild Type Dissected Gonads sRNA 20C, Rep 1

description:
wt_gonads_1_sRNA
processed data file: wt_gonads_vs_wholeAnimals_sRNAs.xlsx


title: RORα f/f

value: RORalpha f/f


title: EPI1F2


title: S_EV_6 [STAT_EV6]

source_name: Transformed with Empty Vector_17 hrs after induction

value: Transformed with Empty Vector


title: Wild Type Dissected Gonads sRNA 20C, Rep 2

description:
wt_gonads_2_sRNA
processed data file: wt_gonads_vs_wholeAnimals_sRNAs.xlsx


title: S_EV_5 [STAT_EV5]


title: EPI1F12


title: B2_K16_1d_control.wig

description: biological repeat 2 of H4K16Q after 1 d culture

source_name: 1d culture

extract_protocol:
Cells were lysed with 300 ml acid washed glass beads (425-600 mm) by vigorous agitation for 30 s in a BeadRuptor2 followed by 30 s on ice, repeated 7 times. Sufficient lysis (90%) was confirmed by light microscopy. The lysate was subsequently sonicated at 4°C to obtain an average DNA fragment length of 300 bp. Samples were centrifuged and the supernatant, containing sheared chromatin, recovered.
Sequencing library was prepared with a NEXTflex DNA Sequencing kit (PerkinElmer) according to the manufacturer’s protocol.

value: Yeast cells

value: JDY86 H4K16Q

tag: chip antibody


title: prg-1(n4357) Mutant Dissected Gonads mRNA 20C, Rep 3

description:
prg-1_gonads_3_mRNA
processed data file: wt_vs_mutant_gonads_mRNAs.xlsx

extract_protocol:
sample collection: Dissected gonads were collected in Trizol on ice over the course of 8-10 hours, then stored at -80 C. The Trizol containing the gonad tissue underwent 2 freeze/thaw cycles using liquid nitrogen prior to Trizol/chloroform extraction.
RNA was depleted of rRNA using RiboZero and enriched for >200nt sizes with Zymo RNA clean and concentrator-5. Libraries were then prepared according to the NEBNext® Ultra™ II Directional RNA kit protocol. Size selection and library purification was done using AMPure XP beads.

tag: genotype/variation


title: B2_WT_1d_control.wig

description: biological repeat 2 of WT after 1 d culture

value: JDY86 WT


title: B2_WT_1d_treatment.wig


title: S_EV_4 [STAT_EV4]


title: prg-1(n4357) Mutant Dissected Gonads mRNA 20C, Rep 1

description:
prg-1_gonads_1_mRNA
processed data file: wt_vs_mutant_gonads_mRNAs.xlsx

value: Total RNA (rRNA-depleted, >200 nt)


title: S_EV_3 [STAT_EV3]


title: EPI1F11


title: EPI1F10


title: B2_K16_1d_treatment.wig


title: EPI1F1


title: S_EV_2 [STAT_EV2]


title: B2_H18_6d_control.wig

description: biological repeat 2 of H4H18A after 6 d culture

source_name: 6d culture

value: JDY86 H4H18A


title: S_B_6 [STAT_B6]

source_name: Expressing HMfB_17 hrs after induction

value: Expressing HMfB


title: prg-1(n4357) Mutant Dissected Gonads mRNA 20C, Rep 2

description:
prg-1_gonads_2_mRNA
processed data file: wt_vs_mutant_gonads_mRNAs.xlsx

value: gravid adults (68-70h, 20 C)


title: B2_H18_6d_treatment.wig


title: mut-16(pk710) Mutant Dissected Gonads mRNA 20C, Rep 1

description:
mut-16_gonads_1_mRNA
processed data file: wt_vs_mutant_gonads_mRNAs.xlsx


title: EPI1E9


title: Wild Type Dissected Gonads mRNA 20C, Rep 3

description:
wt_gonads_3_mRNA
processed data file: wt_gonads_vs_wholeAnimals_mRNAs.xlsx

source_name: Wild Type Dissected Gonads mRNA 20C


title: S_B_4 [STAT_B4]

value: 17 hours after induction

value: Total RNA depleted for ribosomal RNA


title: Wild Type Dissected Gonads mRNA 20C, Rep 2

description:
wt_gonads_2_mRNA
processed data file: wt_gonads_vs_wholeAnimals_mRNAs.xlsx


title: S_B_3 [STAT_B3]


title: EPI1E7

value: hPSC-derived epicardium


title: EPI1E8


title: S_B_2 [STAT_B2]


title: EPI1E5


title: B2_E50_6d_control.wig

description: biological repeat 2 of H3E50A after 6 d culture

value: JDY86 H3E50A


title: B2_E50_6d_treatment.wig


title: B2_H18_1d_treatment.wig

description: biological repeat 2 of H4H18A after 1 d culture


title: Wild Type Dissected Gonads mRNA 20C, Rep 1

description:
wt_gonads_1_mRNA
processed data file: wt_gonads_vs_wholeAnimals_mRNAs.xlsx


title: S_A_5 [STAT_A5]

source_name: Expressing HMfA_17 hrs after induction

value: Expressing HMfA


title: S_B_1 [STAT_B1]


title: EPI1E4


title: B2_E50_1d_control.wig

description: biological repeat 2 of H3E50A after 1 d culture


title: 202226400157_R07C01

type: genomic

city: Los Angeles

first: Daniel

last: Nachun

state: CA

address: 695 Charles E Young Dr S

institute: UCLA

description: jejunum mucosa

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k or MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
Data from 450k and EPIC IDAT files were read in separately with RnBeads and combined, only keeping the probes shared by the two platforms.  Probes were filtered to remove those outside CpG contexts, in SNP, on the sex chromosomes, if they missing values, or if their standard deviation was below 0.005, indicating low variability.  The greedy cut algorithm was used to remove probes with poor detection score p-values.  After filtering of probes, data were normalized using BMIQ with the ENMix oob background correction method.
BMIQ and ENMix oob normalized beta values

label: Cy5 and Cy3

source_name: jejunum

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using standard phenol-chloroform extraction with ethanol precipitation

value: mucosa

tag: Sex

value: male


title: EPI1E3

extract_protocol:
Total RNA was extracted from cultures using RNeasy mini from Qiagen. DNA contamination was removed from the samples using DNA-free™ DNA Removal Kit from Ambion (Thermofisher).
cDNA synthesis and Illumina libraries were performed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit from TAKARA.


title: 202226400157_R06C01

description: duodenum spheroid

source_name: duodenum

value: spheroid

value: female


title: B2_E50_1d_treatment.wig


title: EPI1E12


title: B1_WT_6d_control.wig

description: biological repeat 1 of WT after 6 d culture


title: S_A_3 [STAT_A3]


title: 202226400157_R05C01

description: jejunum mucosa


title: B2_H18_1d_control.wig


title: EPI1E11


title: S_A_2 [STAT_A2]


title: 202226400157_R04C01

description: colon mucosa

source_name: colon


title: B1_WT_6d_treatment.wig


title: B1_WT_1d_control.wig

description: biological repeat 1 of WT after 1 d culture


title: 202226400157_R08C01

description: duodenum spheroid


title: S_A_1 [STAT_A1]


title: EPI1E10


title: E_EV_4 [EXP_EV4]

source_name: Transformed with Empty Vector_2 hrs after induction

value: Transformed with Empty Vector

value: 2 hours after induction


title: EPI1D9


title: EPI1E1


title: S_A_4 [STAT_A4]


title: B1_WT_1d_treatment.wig

value: Yeast cells


title: 202226400157_R02C01

description: colon spheroid


title: 202226400015_R08C01

description: colon spheroid


title: EPI1D7


title: 202226400157_R01C01

description: colon crypt

value: crypt


title: B1_K16_6d_control.wig

description: biological repeat 1 of H4K16Q after 6 d culture

value: JDY86 H4K16Q


title: EPI1D8


title: E_EV_3 [EXP_EV3]


title: 202226400157_R03C01

description: colon crypt


title: B1_K16_1d_treatment.wig

description: biological repeat 1 of H4K16Q after 1 d culture


title: mut-16(pk710) Mutant Dissected Gonads mRNA 20C, Rep 3

description:
mut-16_gonads_3_mRNA
processed data file: wt_vs_mutant_gonads_mRNAs.xlsx

tag: tissue

value: Dissected gonads

value: Total RNA (rRNA-depleted, >200 nt)


title: 202226400015_R05C01

description: jejunum mucosa


title: E_EV_2 [EXP_EV2]


title: E_EV_1 [EXP_EV1]


title: 202226400015_R06C01

description: duodenum mucosa


title: B1_H18_6d_treatment.wig

description: biological repeat 1 of H4H18A after 6 d culture

value: JDY86 H4H18A


title: B1_K16_1d_control.wig


title: B1_K16_6d_treatment.wig


title: 202226400015_R04C01

description: duodenum spheroid


title: E_B_5 [EXP_B5]

source_name: Expressing HMfB_2 hrs after induction

value: Expressing HMfB


title: EPI1D5


title: E_B_4 [EXP_B4]

value: Total RNA depleted for ribosomal RNA


title: E_EV_5 [EXP_EV5]


title: E_B_6 [EXP_B6]


title: EPI1D2

value: hPSC-derived epicardium


title: E_B_3 [EXP_B3]


title: EPI1D4


title: EPI1D3


title: B1_H18_1d_control.wig

description: biological repeat 1 of H4H18A after 1 d culture


title: 202226400015_R03C01

description: jejunum crypt


title: B1_E50_6d_control.wig

description: biological repeat 1 of H3E50A after 6 d culture

value: JDY86 H3E50A


title: EPI1D12


title: B1_H18_1d_treatment.wig


title: 202226400015_R02C01

description: duodenum diff. spheroid

value: diff. spheroid


title: EPI1D1


title: 202226400101_R07C01

description: jejunum crypt


title: EPI1D11


title: E_B_1 [EXP_B1]


title: EPI1C9


title: 202226400015_R01C01

description: colon crypt


title: B1_H18_6d_control.wig


title: E_A_3 [EXP_A3]

source_name: Expressing HMfA_2 hrs after induction

value: Expressing HMfA


title: E_A_6 [EXP_A6]


title: E_A_5 [EXP_A5]


title: 202226400101_R08C01

description: jejunum crypt

value: male


title: EPI1C7


title: 202226400101_R06C01

description: duodenum diff. spheroid


title: hKRT_DKD_Exp2_RNA_rep1

source_name: neonatal foreskin

extract_protocol:
Primary human epidermal keratinocytes were incubated for 6 hours with the infection medium containing lentiviral particles derived from shRNA lentiviral constructs for Mi-2β and/or cJUN or control, and then selected for 3-5 days in puromycin.
Trueseq stranded mRNA sample prep kit (Illumina)

tag: cell types

value: keratinocytes

value: DKD


title: hKRT_DKD_Exp2_RNA_rep2


title: EPI1D10


title: EPI1C8


title: hKRT_JUNKD_Exp2_RNA_rep3

value: JUNKD


title: B1_E50_6d_treatment.wig


title: EPI1C6


title: 202226400101_R05C01

description: colon crypt

value: female


title: 202226400101_R04C01

description: duodenum crypt


title: hKRT_JUNKD_Exp2_RNA_rep1


title: hKRT_Mi2KD_Exp2_RNA_rep3


title: 202226400101_R03C01

description: colon mucosa

value: mucosa


title: hKRT_JUNKD_Exp2_RNA_rep2


title: 202226400101_R01C01

description: duodenum spheroid

value: spheroid


title: 202226400101_R02C01

description: colon crypt

value: crypt


title: EPI1C5


title: E_A_2 [EXP_A2]

value: 2 hours after induction


title: hKRT_Mi2KD_Exp2_RNA_rep2


title: E_A_1 [EXP_A1]


title: EPI1C2


title: EPI1C12


title: 202226400132_R08C01

description: jejunum crypt


title: hKRT_Mi2KD_Exp2_RNA_rep1


title: 202226400132_R06C01

description: colon spheroid


title: 202226400132_R07C01

description: colon spheroid


title: hKRT_CTR_Exp2_RNA_rep3

value: CTR


title: 202226400132_R05C01

description: colon crypt


title: hKRT_CTR_Exp2_RNA_rep2


title: EPI1C10


title: EPI1C11


title: EPI1C1


title: EPI1C3


title: Skin fibroblasts, Patient4-replica2

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

hyb_protocol: After cRNA labeling it was dispersed onto the microarray to perform the hybridization at 65°C for 17 h with 10 rpm rotation. Finally, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

scan_protocol: Microarray slides were scanned using G2505C scanner (Agilent Technologies) at 3 µm resolution. Probes features were extracted using the Feature Extraction Software v. 10.7.3.1 with GE_1_Sep09 protocol (Agilent Technologies).

data_processing: Intra-array normalization was directly performed by the Feature Extraction Software. For each sample, we set probe expression to NA (not available) when flag “Positive and Significant” from Feature Extraction Software was ‘FALSE’. To avoid problems in clustering analysis NA was transformes as 0.1. To normalize data, we used quantile inter-arrays normalization (normalizeQuantiles, limma R package). Data for long non-coding RNAs were excluded for the normalization of coding RNAs. The expression of probes with the same ProbeName was averaged.   Microarray data were analysed using the MultiExperiment Viewer (MeV, Ver. 4.8). We used a t-test (from MeV) to identify differentially expressed RNAs between cells derived from AGS patients and WT. P-values were computed using a gene permutation approach and corrected using Bonferroni. We consider a gene differentially expressed when corrected p-value was ≤ 0.05. Differentially expressed genes resulted from each comparison were grouped to identify interesting profiles considering all samples. Gene grouping was performed using the Self Organizing Tree Algorithm (SOTA) implemented in the MultiExperiment Viewer software. Clustering was performed using the Pearson correlation. Genes in specific clusters were classified according to their function using the Reactome database implemented in the WEB-based GEne SeT AnaLysis Toolkit. To calculate FDR corresponding to each pathway it was used the Benjamini and Hochberg correction for multiple tests.

source_name: skin fibroblasts

label_protocol: Fluorescent cRNA to hybridize onto microarray was produced by Low Input Quick Amp Labeling Kit (Agilent) according to manufacturer instructions.

growth_protocol: All fibroblasts were grown in DMEM with 4.5 g/liter glucose, 10% (v/v) fetal calf serum, nonessential amino acids, and antibiotics. Cell cycle distribution in fibroblast cultures was determined by flow cytometry after propidium iodide staining of EtOH 70% fixed resuspended cells, with a BD Biosciences FACSCanto II Flow cytometer.    To identify 20% S-phase enriched cell culture, 0.2 million cells/ 10 cm dish were seeded and collected for FACS analysis starting after 30 hours and every 2-3 hours until two days post seeding.

extract_protocol: TRIzol Reagent (Thermo Fisher Scientific) was used to extract RNA from cell cultures according to the manufacturer’s protocol. Prior to RNA extraction, cell cultures were washed in PBS to remove excess medium then Trizol was added directly on the dish and cells were detached using a cell scraper. RNA quality was tested on UV spectrophotometer and 2100 Agilent Bioanalyzer following the protocol provided by the manufacturer.

treatment_protocol: Untreated samples

tag: condition

value: Aicardi Goutières Syndrome (AGS)

tag: cell line

tag: race

value: Indian

value: skin

value: fibroblast

tag: gender

value: Female

tag: cell cycle stage

value: 20% S phase


title: Skin fibroblasts, Patient3-replica2

value: Arab

tag: cell type

value: Male


title: EPI1B8

source_name: engineered epicardial cell

value: hPSC-derived epicardium

tag: es line


title: Skin fibroblasts, Patient4-replica3


title: Skin fibroblasts, Patient4-replica1


title: 202226400132_R04C01

description: colon crypt

value: male

tag: batch


title: hKTR_Mi2KD_input_rep2

extract_protocol:
Primary human epidermal keratinocytes were incubated for 6 hours with the infection medium containing lentiviral particles derived from shRNA lentiviral constructs for Mi-2β or control, and then selected for 3-5 days in puromycin.
As detailed in Hu et al. Genes Dev (2016)

value: keratinocytes

tag: genotype


title: hKRT_CTR_input_rep4


title: EPI1B9


title: Skin fibroblasts, Patient2-replica2

value: Caucasian


title: Skin fibroblasts, Patient3-replica3


title: Skin fibroblasts, Patient2-replica3


title: 202226400132_R03C01

description: colon mucosa

value: mucosa

tag: age

value: female


title: 202226400132_R02C01

description: duodenum diff. spheroid

value: diff. spheroid


title: hKRT_CTR_Exp2_RNA_rep1


title: hKRT_CTR_input_rep3


title: EPI1B7


title: hKRT_CTR_JunB_ChIP_rep1


title: EPI1B6


title: Skin fibroblasts, Patient2-replica1


title: Skin fibroblasts, Patient3-replica1


title: Skin fibroblasts, Patient1-replica2


title: Control4 RNA-seq

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

description:
Whole transcriptome sequencing
CCM_reads_TPM_normalized.matrix.txt.gz

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version 2.16.0.10 (Illumina). The FASTQ files were adapter and quality trimmed using Trim Galore (version 0.4.1) with default settings
After trimming, FASTQ files were mapped against a reference human genome hg38 with the splice-aware aligner STAR twopassMode Basic (version 2.5.0c) to generate BAM files
Obtained aligned files (BAM format) were subjected to quantification using featureCounts from Subread package. The reads were quantified for Ensembl transcript annotation release GRCh38.93 (corresponds to genome hg38).
Generated matrix file from read quantification was then used for differential expression (DE) analysis. DE analysis was performed using Bioconductor package DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix containing tab-delimited data includes normalized read count values for transcripts in each Sample.

source_name: Normal brain tissue

growth_protocol: Tissue sections were stored in at least 10 volumes of RNAlater-ICE (AM7030; Ambion) at -80°C before total RNA extraction.

extract_protocol:
Total RNA from cells was extracted using RNeasy Micro Kit  according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using NEBNext® Ultra Directional RNA Library Prep Kit for Illumina

treatment_protocol: For RNA extraction, brain tissue specimens were cut off and further slit to smaller pieces. These pieces were transferred into vials containing ceramic beads (Precellys system, CK14L; Peqlab) and RLT lysis buffer from RNeasy Micro Kit (Qiagen)

tag: patient diagnosis

value: normal control

value: brain

tag: lesion

value: Not Applicable


title: Control3 RNA-seq


title: EPI1B5


title: mut-16(pk710) Mutant Dissected Gonads mRNA 20C, Rep 2

description:
mut-16_gonads_2_mRNA
processed data file: wt_vs_mutant_gonads_mRNAs.xlsx

value: gravid adults (68-70h, 20 C)

value: Dissected gonads

tag: molecule subtype

value: Total RNA (rRNA-depleted, >200 nt)


title: Skin fibroblasts, Patient1-replica3

value: Aicardi Goutières Syndrome (AGS)

value: skin

value: fibroblast


title: EPI1B12


title: Control2 RNA-seq


title: EPI1B11


title: 202226400015_R07C01

description: duodenum diff. spheroid


title: Hottip-Tg-ATAC-seq-1

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIP-seq and CHIRP-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ATAC-seq , ChIP-seq and CHIRP-seq.

source_name: Hottip-Tg-ATAC-seq

growth_protocol: Total bone marrow cells were isolated from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers.  Human MOLM13 leukemia cells were culture at RMPI1640 and 10% FBS media.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3 and H3K79me2 antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745;   Anti-H3K27me3, Millipore, Cat No. 07-449;  Anti-H3K79me2, Abcam, Cat No. ab3594.).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.    CHIRP-seq library constructs with the illumina Truth CHIP DNA library kt.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK and MOLM13 cells without any treatment

value: Mouse-derived Bone marrow cells

tag: tissue origin

value: Bone marrow

tag: cell subtype

value: Lin- Sca1+ Kit+ cells

tag: genotype/variation

value: Hottip-Tg


title: WT-LSK-ATAC-seq-1.fastq.gz

source_name: WT-LSK-ATAC-seq

tag: cell types

value: WT


title: 202226400132_R01C01

description: colon crypt

value: crypt

tag: Sex

value: male


title: CCM10 RNA-seq

source_name: CCM pateint's Brainstem

value: Cerebral Cavernous Malformations (CCM)

tag: tissue

value: L/ Medulla oblongata


title: Hottip-Tg-RNA-seq-2

source_name: Hottip-Tg-RNA-seq


title: EPI1B1

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim Galore version: 0.4.1 (a wrapper for Cutadapt 1.8.1 with parameters  -f fastq -e 0.1 -q 20 -O 1 and FastQC)
Reads were mapped to GRCh38 whole genome using HiSAT2 v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Counts were produced using SeqMonk 0.34. All reads overlapping an exon were counted, all reads from all exons of all isoforms added, counting each one once.
Counts Per Million reads (CPM) were calculated dividing reads from all exons of all isoforms by the size of the library in reads, multiplied by 1 million.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma Separated Value file containing Counts Per Million reads. Rows are genes (rownames are Gene Symbols) and columns are cells.

value: hPSC-derived epicardium


title: Skin fibroblasts, Wild-type-replica4

tag: condition

value: control

tag: cell line

tag: race

value: Caucasian

value: Male

value: 20% S phase


title: Hottip-Tg-ATAC-seq-2


title: CCM9 RNA-seq

value: brain

value: L/ Pontine


title: Hottip-Tg-RNA-seq-1


title: Mouse lung adenocarcinoma scRNA-seq [O_45P]

description: 10X 3' Reads

data_processing:
3' RNAseq (10X)
Cellranger mapping to mm10
Genome_build: mm10
Supplementary_files_format_and_content: Cell_meta_info.txt.gz: cell sample annotation table for each cell (row) with the 'cell name, sample-id, tUMI, number-of-genes, cell-id-assigned' information
Supplementary_files_format_and_content: counts.txt.gz: The expression levels for each gene (rows) in each single cell (column) in counts as calculated using cellranger software.

source_name: mouse tissue

extract_protocol:
Dissociated individual cells from lung. Immune cells were then separated by MACS CD45 beads and both fractions were further processed using 3' 10X protocol.
3' RNAseq (10X)

tag: strain

value: Lung

tag: cell-fraction


title: CCM8 RNA-seq

value: R/ Middle cerebellar ped


title: EPI1A9

tag: cell type

tag: es line


title: Mouse lung adenocarcinoma scRNA-seq [O_45N]

description: 10X 3' Reads


title: Skin fibroblasts, Wild-type-replica3

value: skin

value: fibroblast

tag: gender

tag: cell cycle stage


title: Skin fibroblasts, Patient1-replica1

value: Aicardi Goutières Syndrome (AGS)


title: Skin fibroblasts, Wild-type-replica2

value: WT


title: EPI1A8


title: Skin fibroblasts, Wild-type-replica1


title: AML-55-BM-exome-seq

data_processing:
Library strategy: exome-seq
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat, paired end exome-seq reads from mice were aligned to the mm9 genome assembly using BWA,t and ATAC-seq, ChIP-seq, HiC-seq, and CHIRP-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Chromatin structure HiC-seq was calculate and display with HOMER, Juicer and Juicebox software
Genome_build: mm9
Supplementary_files_format_and_content: SNP and indel mutation annotation for exome-seq

source_name: AML-C57BL/6 mice bone marrow

growth_protocol: Total bone marrow cells were isolate from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers.  Human MOLM13 leukemia cells were culture at RMPI1640 and 10% FBS media.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3 and H3K79me2 antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745;   Anti-H3K27me3, Millipore, Cat No. 07-449;  Anti-H3K79me2, Abcam, Cat No. ab3594.; Anti-MLL, Millipore, #05-765).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.    CHIRP-seq library constructs with the illumina Truth CHIP DNA library kt. HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030). Genomic DNA was isolated from mice ear and BM cells including wildtype and Hottip-Tg mice, and genomic exome library was captured and made according to SureSelectXT Mouse All Exon kit (Agilent, Part Number:5190-4641).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq and CHIRP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Genomic DNA was isolated from mice ear and BM cells including wildtype and Hottip-Tg mice, and genomic exome library was captured and made according to SureSelectXT Mouse All Exon kit (Agilent, Part Number:5190-4641), and then 100 bp paired-end sequencing was performed using an Illumina NovaSeq.

treatment_protocol: Immediately extract RNA from LSK, HSC cells from transgenic mice and MOLM13 AML cells without any treatment

value: Mouse-derived bone marrow cells

value: bone marrow


title: WT-LSK-RNA-seq-1

source_name: WT-LSK-RNA-seq

value: Mouse-derived Bone marrow cells

value: Bone marrow

value: Lin- Sca1+ Kit+ cells


title: WT-LSK-ATAC-seq-2.fastq.gz


title: WT-LSK-RNA-seq-2


title: EPI1A7

value: hPSC-derived epicardium


title: CCM7 RNA-seq

tag: patient diagnosis

value: Cerebral Cavernous Malformations (CCM)

tag: lesion

value: R/ Pontine


title: AML-55-ear-exome-seq

source_name: AML-C57BL/6 mice ear skin

value: Mouse-derived ear skin cells

value: ear skin


title: CCM6 RNA-seq

value: brain

value: L/ Pontine


title: Control1 RNA-seq

value: normal control

value: Not Applicable


title: EPI1B10


title: EPI1A4


title: Ewe 2, Fetus 2, Gyrus

city: Bundoora

first: Sebastian

last: Quezada

state: VIC

address: 225-245 Plenty Rd

department: School of Health and Biomedical Sciences

country: Australia

institute: RMIT University

data_processing:
base-calling: Sanger / Illumina 1.9
Mapping: STAR (v 2.4.2a)
Read summarisation: featureCounts from package RSubread (v 1.12.6), using R in RStudio(v 0.98.1103)
Library normalisation and differential expression analysis: edgeR (v 3.4.2)
Differential expression analysis: edgeRun (v 1.0.9)
Genome_build: Fully annotated sheep genome (v 3.1), International Sheep Genome Consortium, downloaded on June 2016.
Supplementary_files_format_and_content: matrix containing counts for all features for all samples including in study, pre-filtering. CSV file.

organism: Ovis aries

source_name: gyral cortical plate cells

growth_protocol: Ontogeny, organisms obtained from external supplier under standard breeding conditions

extract_protocol:
RNA Micro Kit (QIAGEN, Australia)
SPIA libraries:- Nugen Ovation RNA-Seq system V2 (for SPIA amplifications and cDNA generation) using Nugen protocol M01206v5, 2013; followed by Ovation Ultralow System V2 (for rest of library preparation) using Nugen protocol M01379v1, 2014.

treatment_protocol: None. Study is ontogenical

value: Border Leicester/Merino

value: fetal brain cortical plate

tag: developmental stage

value: gestational age 90 days


title: Ewe 2, Fetus 2, Sulcus

source_name: sulcal cortical plate cells


title: AML-51-ear-exome-seq


title: EPI1A5


title: CCM4 RNA-seq

value: R/ Medulla oblongata


title: AML-48-BM-exome-seq

value: Mouse-derived bone marrow cells

value: bone marrow


title: AML-51-BM-exome-seq


title: CCM5 RNA-seq


title: Ewe 2, Fetus 1, Sulcus


title: EPI1A3


title: CCM3 RNA-seq


title: CCM2 RNA-seq

value: R/ Pontomesencephalic


title: Ewe 2, Fetus 1, Gyrus


title: AML-48-ear-exome-seq


title: AML-39-BM-exome-seq


title: Ewe 1, Fetus 2, Gyrus


title: Ewe 1, Fetus 2, Sulcus


title: EPI1A2


title: EPI1A10


title: 947M_3

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

country: Netherlands

institute: University of Groningen

data_processing:
Read trimming (Trimmomatic 0.38)
Alignment into chrimeric genome (STAR 2.6.0a)
Summation (featureCounts, subread 1.6.3)
Genome_build: Mus musculus (release 94) and Streptococcus pneumoniae (prepared in house)
Supplementary_files_format_and_content: tab-delimited text files include raw counts

organism:
Streptococcus pneumoniae
Mus musculus

source_name: Murine lung infected with Streptococcus pneumoniae serotype 3, 6 hpi

growth_protocol: Mouse were kept as usual

extract_protocol:
Total RNA isolation based on phenol-chloroform, gDNA treatment using RNase-free DNase
RNA libraries were prepared for sequencing using standard Illumina protocols with rRNA depletion

treatment_protocol: Streptococcus pneumoniae culture were injected intranasal; lung were harvested six hours after infection

tag: rafr source

value: strain 4559


title: Ewe 1, Fetus 1, Sulcus


title: AML-39-ear-exome-seq


title: EPI1A1

value: hPSC-derived epicardium


title: 947M_2


title: CCM1 RNA-seq

value: Cerebral Cavernous Malformations (CCM)


title: Ewe 1, Fetus 1, Gyrus


title: 947M_1


title: LNCaP-CXCR2 cells

city: Durham

first: Yanjing

last: Li

state: NC

address: 905 S. LaSalle Street GSRB1, 3038

department: Pathology

institute: Duke University

description:
DifferentialExpression-cell line samples
LNCaP-CXCR2

data_processing:
RNA-seq data was processed using the TrimGalore toolkit, which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis
Reads were mapped to the GRCh37v75 version of the human genome and transcriptome (Kersey et al., 2012) using the STAR RNA-seq alignment tool (Dobin et al., 2013)
Gene counts were compiled using the HTSeq tool.  Only genes that had at least 10 reads in any given library were used in subsequent analysis
Normalization and differential expression was carried out using the DESeq2 (Love et al., 2014) Bioconductor (Huber et al., 2015) package with the R statistical programming environment.
Gene set enrichment analysis (Mootha et al., 2003) was performed to identify differentially regulated pathways and gene ontology terms for each of the comparisons performed.
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

source_name: Human prostate cancer cell line_CXCR2 over-expression

extract_protocol:
Fresh prostate tumor samples were obtained from patients with localized prostate adenocarcinoma who received prostatectomy and will be digested into single cells and sorted into Trop2+ CXCR2+ NE, Trop2+ CXCR2- luminal populations. Benign prostate tissue will be digested and sorted into Trop2+CXCR2-CD49f+ basal population. RNA was harvested using Trizol reagent. Illumina TruSeq stranded mRNA Sample Prep Kit was used to isolate mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate cancer

tag: tumor stage

value: hormonal-insensitive primary prostate adenocarcinoma

value: Neuroendocrine cells


title: AML-22-ear-exome-seq

tag: cell types

value: Mouse-derived ear skin cells

value: ear skin


title: WT-130-BM-exome-seq

source_name: WT-C57BL/6 mice bone marrow


title: 947_3

value: strain 9-47


title: Patient 2_Cancer Trop2+CXCR2- luminal

description:
DifferentialExpression-patients' samples
2_CL

source_name: Patients' fresh prostate cancer tissue

value: hormonal-sensitive primary prostate adenocarcinoma

value: Luminal cells


title: LNCaP cells

description:
DifferentialExpression-cell line samples
LNCaP

source_name: Human prostate cancer cell line


title: WT-130-ear-exome-seq

source_name: WT-C57BL/6 mice ear skin


title: 947_2


title: EPI1A12

city: Great Chesterford

first: Nicolas

last: Gambardella

address: Lewis House, Great Chesterford Court

institute: aSciStance Ltd

source_name: engineered epicardial cell


title: 947_1


title: WT-69-BM-exome-seq

city: Hangzhou

first: Huacheng

last: Luo

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences


title: Patient 1_Benign Basal

description:
DifferentialExpression-patients' samples
1_BB

source_name: Patients' fresh prostate tissue

value: benign prostate tissue

value: benign tissue

value: Basal cells


title: WT-69-ear-exome-seq


title: 4559M_3


title: Patient 2_Cancer Trop2+CXCR2+ NE

description:
DifferentialExpression-patients' samples
2_CCX


title: AML-22-BM-exome-seq

value: Mouse-derived bone marrow cells


title: 4559M_1


title: 4559M_2


title: Patient 6953_Cancer Trop2+CXCR2+ NE

description:
DifferentialExpression-patients' samples
6953_CCX


title: CBS-KO-VP-HOTTIP-HiC-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end).
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIP-seq, HiC-seq and CHIRP-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1).
Genome coverage tracks were created using deepTools version 3.0.
Chromatin structure HiC-seq was calculated and displayed with HOMER, Juicer and Juicebox software.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples, and peaks annotation for ATAC-seq, ChIP-seq and CHIRP-seq.

source_name: MOLM13 leukemia cells

extract_protocol:
RNA samples extracted with Trizol and treated with DNase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3, H3K79me2 and MLL antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745; Anti-H3K27me3, Millipore, Cat No. 07-449; Anti-H3K79me2, Abcam, Cat No. ab3594.; Anti-MLL, Millipore, #05-765). ATAC-seq samples derived according to Nextera Tn5 Transposase kits. CHIRP-seq library constructs with the Illumina TruSeq CHIP DNA library kit. HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ChIP-seq and CHIRP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Human-derived acute myeloid leukemia cells

tag: tissue origin

value: peripheral blood

tag: genotype/variation


title: U87MG, 4 hr, MOI=0.01, replicate 1

city: kunming

first: yongzhong

last: duan

state: Yunnan

address: chongrong west road, chenggong new district

institute: kunming medical university

description: miRNAs expression profile infected by HSV-1 in U87MG cells

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm

source_name: U87MG, 4 hr, MOI=0.01, replicate 1

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat #5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Human neuroblastoma cells SH-SY5Y and human glioblastoma cells U87MG were purchased from American Type Culture Collection (ATCC, VA, USA) and stored in Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences (Kunming, China). The above tow types of cells were cultured in Dulbecco′s modified Eagle′s medium (DMEM, Thermo Fisher Scientific, MA, USA), supplied with 10% (V/V) fetal bovine serum (FBS, Gibco, MA, USA) and penicillin–streptomycin (100 U/mL and 100 μg/mL). The cells were maintained at 37C in a humidified atmosphere containing 5% CO2.

extract_protocol: The total RNA of infected cells was extracted and purified using miRNeasy Mini Kit (QIAGEN, GmbH, Germany) according to the manufacturer’s instructions at the time point of 0, 4 and 10 hpi. The RNA concentration was measured by NanoDrop ND-2000 spectrophotometer (Thermo, MA, USA) and RNA integrity number (RIN) was determined by 2100 Bioanalyzer (Agilent technologies, CA, USA) and agarose gel electrophoresis.

treatment_protocol: SH-SY5Y and U87MG cells were seeded at a density of 3×105 cells/well in 12-well plate overnight to adhere. Cells were washed twice with phosphate buffer saline (PBS) and infected with HSV-1 strains of 17syn+、Kos and Mckrae at an MOI of 0.01, respectively.


title: U87MG, 10 hr, MOI=0.01, replicate 1

source_name: U87MG, 10 hr, MOI=0.01, replicate 1


title: 4559_3

value: strain 4559


title: Patient 7074_Cancer Trop2+CXCR2- luminal

description:
DifferentialExpression-patients' samples
7074_CL

tag: tissue


title: Patient 6953_Benign Basal

description:
DifferentialExpression-patients' samples
6953_BB


title: U87MG, 0 hr, MOI=0.01, replicate 1

source_name: U87MG, 0 hr, MOI=0.01, replicate 1

tag: cell line


title: Brain_Sevoflurane_rep3

city: Beijing

first: Yujie

last: Wang

address: 49 North Garden Road, Haidian District

department: Department of Anesthesiology

institute: Peking Universtity Third Hospital

description: Gene expression data from hipppcampus of  18-month old rat after 4 hours of sevoflurane treatment

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Rat Transcriptome Array Strip (45 oC /24 h), and up to 25 unique probes sequences were hybridized to a single transcript. Following hybridization, each array strip was washed and stained using the Fluidics Station of GeneChip® Scanner 3000 7G system (Affymetrix, Santa Clara, CA).

scan_protocol: The array strips were scanned using the Imaging Station of the GeneChip® Scanner 3000 7G system.

data_processing: Data were analyzed with Microarray Suite 5 (MAS5) and Robust Multi-array Average (RMA) using Affymetrix Expression Console 1.4.1. Affymetrix default analysis settings were used.

organism: Rattus norvegicus

source_name: Rat hippocampus after 4 hours sevoflurane

label_protocol: The obtained cDNA was used for biotin labeling and fragmentation by Affymetrix GeneChip® WT Terminal Labeling and Hybridization.

growth_protocol: Male Sprague-Dawley rats, 18-month old, weighing 550–600 g, were used in the studies. Before sevoflurane anesthesia, the rats were maintained on a standard housing condition with food and water ad libitum for 2 weeks. C6 rat glioma cells were used in the studies. The cells were cultured in F-12K medium (Gibco™, Thermo Fisher Scientific, Waltham, MA, USA) containing 2.5% fetal bovine serum, 15% horse serum, 100 U/ml penicillin, and 100 μg/ml streptomycin. Before treatments, cells were seeded in 6-well plates, with one million cells in 1.5 ml cell culture media per well.

extract_protocol: Total RNAs were isolated from the hippocampi and cells using TRIzol reagent (Invitrogen, Carlsbad, CA), then digested with RNase-Free DNase to remove residual DNAs. The RNA concentrations were analyzed using the Nanodrop 2000 (Thermo Fisher Scientific), then total RNA (2 μg) was reverse-transcribed using the GoScriptTM Reverse Transcription System (Promega).

treatment_protocol: The rats were randomly assigned to the sevoflurane anesthesia or control group. In our study, rats in sevoflurane group received 2.5% sevoflurane in 100% oxygen for 4 hours in an anesthetizing chamber, and the control group received 100% oxygen at an identical flow rate for 4 h in an identical chamber. The rats breathed spontaneously, and sevoflurane and oxygen concentrations were monitored continuously (Datex, Tewksbury, MA, USA). Temperature of the anesthetizing chamber was controlled to maintain rectal temperature of the animals at 37 ± 0.5 °C. Anesthesia was terminated by discontinuing sevoflurane and placing animals in a chamber containing 100% oxygen until 20 minutes after recovery of consciousness. The animals were then returned to individual home cages until sacrifice. Rats were sacrificed by decapitation 3 h after anesthesia. The brain tissues were removed rapidly, and the hippocampus was dissected out and frozen in liquid nitrogen.

tag: age

value: 18-month old

tag: agent

value: 2.5percent  sevoflurane

tag: Sex

value: male

value: Sprague-Dawley


title: Brain_Sevoflurane_rep2

tag: strain


title: HOTTIP-KO-HiC-seq

value: HOTTIP-KO


title: Patient 7074_Cancer Trop2+CXCR2+ NE

description:
DifferentialExpression-patients' samples
7074_CCX

value: prostate cancer

tag: cell type

value: Neuroendocrine cells


title: Brain_Control_rep1

description: Gene expression data from hipppcampus of  18-month old rat

source_name: Rat hippocampus

value: 100percent  oxygen


title: Brain_Control_rep3


title: Brain_Sevoflurane_rep1


title: Brain_Control_rep2


title: 4559_1


title: Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, stressed 1717

status: Public on Dec 02 2019

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, stressed
Ribosomal-bound RNA
1717_Aldh1l1_TRAP_JD130_CPU_stressed_IP_Rep3

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Caudate putamen

growth_protocol: Not applicable

extract_protocol:
The prefrontal cortex, hippocampus, accumbens nucleus and caudate putamen were dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Aldh1l1-TRAP mice were kept together with the CD1 aggressive mouse in a large cage with the Plexiglas divider, that allows visual and olfactory, but no physical contact. The Aldh1l1-TRAP mouse was exposed to direct contact with the CD1 mouse for 10 minutes daily, for ten days. Control mice were kept group housed, 2-3 mice per cage, in the same room but without direct visual contact with the cages included in social defeat paradigm. Mice were kept in a 12-hour light-dark cycle, at room temperature and with water and food provided ad libitum.

tag: animal line

tag: application

value: RNA-seq

tag: sample type

value: Immunopurified (IP)


title: Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, stressed 1716

description:
Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, stressed
Ribosomal-bound RNA
1716_Aldh1l1_TRAP_JD130_CPU_stressed_IP_Rep2


title: CBS-KO-HiC-seq

growth_protocol: Total bone marrow cells were isolated from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers. Human MOLM13 leukemia cells were cultured at RMPI1640 and 10% FBS media.


title: SH-SY5Y, 10 hr, MOI=0.01, replicate 1

description: miRNAs expression profile infected by HSV-1 in SH-SY5Y cells

source_name: SH-SY5Y, 10 hr, MOI=0.01, replicate 1


title: Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, stressed 1715

description:
Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, stressed
Ribosomal-bound RNA
1715_Aldh1l1_TRAP_JD130_CPU_stressed_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, resilient 1714

description:
Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, resilient
Ribosomal-bound RNA
1714_Aldh1l1_TRAP_JD130_CPU_resilient_IP_Rep2


title: Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, control 1711

description:
Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, control
Ribosomal-bound RNA
1711_Aldh1l1_TRAP_JD130_CPU_control_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, resilient 1713

description:
Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, resilient
Ribosomal-bound RNA
1713_Aldh1l1_TRAP_JD130_CPU_resilient_IP_Rep1


title: 4559_2


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, stressed 1709

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, stressed
Ribosomal-bound RNA
1709_Aldh1l1_TRAP_JD130_NAC_stressed_IP_Rep3

source_name: Accumbens nucleus


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, stressed 1710

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, stressed
Ribosomal-bound RNA
1710_Aldh1l1_TRAP_JD130_NAC_stressed_IP_Rep4