title: TT16-9022-AN16-8942 [US-10017345]

description:
US-10017345
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: HMLER2_HDAC1_siRNA_CC12

status: Public on Feb 24 2020

type: SRA

city: Miami

first: Corrado

last: Caslini

state: FL

address: 1501 NW 10th Avenue

country: USA

institute: University of Miami

description:
processed data files:
DESeq2_HMLER2_siHDAC1_vs_siNT.txt
HMLER2_siHDAC1_vs_siNT.txt
CC12

library_source: transcriptomic

data_processing:
Base calling and data filtering  was performed on BaseSpace Illumina platform.
RNA-seq fastq files were uploaded to the Galaxy web platform and we used the public server at galaxy.org to analyze the data. RNA-seq data sets were paired and aligned using HISAT2 (version 2.1.0) to reference version NCBIv37/hs19 of the human genome; transcript assembly, quantification and merging was done with StringTie (version 1.3.4).
Number of reads per transcript was counted using featureCounts (version 1.6.3) and differential expression analysis was performed using DESeq2 (version 2.11.40.2).
A cutoff of 0.6<log2<-0.6, p<0.05 was applied for the identification of genes with significant differential expression.
Genome_build: hs19
Supplementary_files_format_and_content: Tab-delimited text files from DESeq2 differential expression analysis (DESeq2*.txt) and files with normalized counts
DESeq2_BPLER2_siHDAC7_vs_siNT.txt: differential measurements
BPLER2_siHDAC7_vs_siNT.txt: normalized counts
DESeq2_BPLER2_siHDAC1_vs_siNT.txt: differential measurements
BPLER2_siHDAC1_vs_siNT.txt: normalized counts
DESeq2_HMLER2_siHDAC7_vs_siNT.txt: differential measurements
HMLER2_siHDAC7_vs_siNT.txt: normalized counts
DESeq2_HMLER2_siHDAC1_vs_siNT.txt: differential measurements
HMLER2_siHDAC1_vs_siNT.txt: normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: non-stem breast cancer cells

growth_protocol: BPLER and HMLER cells were described before (Cancer Cell 12, 160-170, 2007). Both cell types and BPLER culture medium (BMI-T) are available from the Live Tissue Culture Service Center, University if Miami (contact LTCC@med.miami.edu).

extract_protocol:
Total RNA preparations were obtained with RNAzol® RT (Sigma) and cleaned with Turbo DNA-Free Kit (Ambion).
DNase I-treated total RNA preparations were qualitatively validated by Eukaryote Total RNA 6000 Nano analysis on 2100 Bioanalyzer (Agilent) and libraries were prepared using the KAPA RNA HyperPrep kit according to manufacturer instructions (KAPA).

treatment_protocol: BPLER and HMLER cells were plated in 10cm petri dish at 7.0x10e5 cell/plate respectively in BMI-T and MEGM (Lonza) medium 24h before transfection. Cells were transfected with pools, 50 nM each, of HDAC1 and HDAC7 specific double-stranded RNAs and non-specific (NS) siRNAs as control using Lipofectamine RNAiMAX (Invitrogen) in OptiMEM (GIBCO, Life Technologies) added directly to the medium. The cells were harvested 72h later for total RNA extraction.

tag: cell line

tag: cell type

value: Breast primary epithelial cells

tag: transforming gene

value: hTERT; SV40-LT/st; hRASV12

tag: sirna


title: TT13-2572-AN13-0006 [US-10017306]

city: West Point

first: Alexei

middle: A

last: Podtelezhnikov

state: PA

address: 770 Sumneytown Pike

department: Non-clinical Drug Safety

institute: Merck & Co., Inc.

description:
US-10017306
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

data_processing:
Genome alignment and gene quantitation was performed using OmicSoft Array Studio
Cleaned reads were aligned to the Rnor_6.0 genome reference using the OmicSoft Aligner with a maximum of 2 allowed mismatches
Gene level counts were determined by the RNA-Seq by expectation maximization algorithm as implemented in OmicSoft Array Studio and using Ensembl.R94 gene models
FPKM normalization was applied to RNA-Seq counts followed by log-transformation with smoothing, i.e., log10(FPKM+0.01)
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Count, FPKM

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was purified from frozen liver samples using the MagMAX™ Express Magnetic Particle Processor (Applied Biosystems, # 4400074)
Total RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA HT Sample Preparation Kit (Illumina, #RS-122-2103)

tag: study

tag: strain

value: Han Wistar

tag: Sex

value: M

tag: agent

value: 0.9percent (w/v) Sodium Chloride for Injection

tag: treatment

value: -control-

tag: dose(mkd)

tag: days of administration

tag: rin


title: TT11-2512-AN11-0006 [US-1420969]

description:
US-1420969
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: TT13-2572-AN13-0005 [US-10017305]

description:
US-10017305
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: F


title: ATF3-null Nutlin Replicate 3 RNAseq

city: Albany

first: Morgan

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

data_processing:
PolyA+ RNAseq raw data were aligned to the human hg19 genome using STAR. Transcript counts were generated using STAR in quant-mode using the UCSC RefSeq transcriptome assembly for hg19. Raw read counts across treatments and biological replicates were processed for differential gene expression using DESeq2.
MPRA RNAseq data were analyzed using fastx-toolkit (hannonlab.cshl.edu) modules fastx-splitter and fastx-collapser.
CCNG1 amplicon ChIP data were analyzed using the fastx-toolkit (hannonlab.cshl.edu) modules fastx-collapser in order to extract count values per unique sequencing read.
Genome_build: hg19 Homo sapiens
Supplementary_files_format_and_content: PolyA+ RNAseq processed data contain raw read counts per RefSeq/UCSC gene in the hg19 assembly. MPRA RNAseq processed files contain raw MPRA expression counts for each barcode found in the original MPRA library across all 6 conditions (HCT116 WT or p53-/- cells treated with either DMSO or Nutlin, plus Genomic DNA barcode counts). CCNG1 amplicon ChIP processed data contains read counts for each sequence found over 2000 times in the genomic DNA input experiment for the Nutlin ChIP and Input conditions.

molecule: polyA RNA

source_name: Colon carcinoma cells

growth_protocol: HCT116 WT, p53-/-, and ATF3-/- colon carcinoma cells were grown at 37˚C in a humidified, water-jacketed incubator with 5% carbon dioxide. Cells were grown in McCoy's 5A medium supplemented with 10% fetal bovine serum.

extract_protocol:
For HCT116 WT, p53-/-, and ATF3-/- colon carcinoma RNA-seq experiments, total RNA was isolated using standard methods (Omega Biotek). PolyA+ RNA was isolated from 2 micrograms of total RNA using polydT beads supplied with the BioO Stranded RNAseq kit.
Illlumina-compatible RNA-seq libraries were created from fragmented polyA+ RNA using the BioO NextFlex Stranded RNAseq Kit as per manufacturer's instructions. Illumina-compatible, dual barcodes; 75bp single-end reads

treatment_protocol: Either DMSO or 5 micromolar Nutlin-3A were added to fresh, pre-warmed complete McCoy's 5A medium at t=0 and cells were incubated for 6 hours before harvest.

tag: genotype

tag: drug treatment

value: 5 micromolar Nutlin-3A

value: colon carcinoma

tag: antibody


title: HMLER2_HDAC1_siRNA_CC06

description:
processed data files:
DESeq2_HMLER2_siHDAC1_vs_siNT.txt
HMLER2_siHDAC1_vs_siNT.txt
CC06


title: TT13-2572-AN13-0010 [US-10017310]

description:
US-10017310
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: SesameOil

value: bardoxolone


title: TT11-2512-AN11-0004 [US-1420966]

description:
US-1420966
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2512-AN11-0004 [US-1468494]

description:
US-1468494
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2512-AN11-0002 [US-1468450]

description:
US-1468450
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2572-AN13-0003 [US-10017304]

description:
US-10017304
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2572-AN13-0004 [US-10017303]

description:
US-10017303
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: HMLER2_NT_siRNA_CC10

description:
processed data files:
DESeq2_HMLER2_siHDAC7_vs_siNT.txt,DESeq2_HMLER2_siHDAC1_vs_siNT.txt
HMLER2_siHDAC7_vs_siNT.txt,HMLER2_siHDAC1_vs_siNT.txt
CC10

value: Non-targeting (NT)


title: TT16-9022-AN16-8939 [US-10017342]

description:
US-10017342
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 99percent Corn Oil, 1percent Acetone


title: HMLER2_HDAC7_siRNA_CC11R

description:
processed data files:
DESeq2_HMLER2_siHDAC7_vs_siNT.txt
HMLER2_siHDAC7_vs_siNT.txt
CC11R


title: TT13-2572-AN13-0008 [US-10017309]

description:
US-10017309
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: HMLER2_HDAC7_siRNA_CC11

description:
processed data files:
DESeq2_HMLER2_siHDAC7_vs_siNT.txt
HMLER2_siHDAC7_vs_siNT.txt
CC11


title: TT13-1509-AN13-0028 [TT13-1509_13-0028]

description:
TT13-1509_13-0028
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.4percent (w/v) Hydroxypropyl Methylcellulose in Deionized Water

value: PCN


title: ATF3-null DMSO Replicate 1 RNAseq

value: DMSO


title: TT13-1509-AN13-0026 [TT13-1509_13-0026]

description:
TT13-1509_13-0026
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2572-AN13-0001 [US-10017301]

description:
US-10017301
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2509-AN11-0072 [US-1468484]

description:
US-1468484
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: amoxicillin


title: BPLER2_HDAC1_siRNA_CC09

description:
processed data files:
DESeq2_BPLER2_siHDAC1_vs_siNT.txt
BPLER2_siHDAC1_vs_siNT.txt
CC09

source_name: stem-like breast cancer cells

value: Breast primary epithelial cells

value: hTERT; SV40-LT/st; hRASV12


title: DENV-WT-Aag2

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

country: China

institute: Wuhan University

description: small RNA

data_processing:
Libraries of small RNAs from cell culture were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s instructions. The libraries were sequenced by Illumina HiSeq 2000 at RiboBio. The sequencing reads were mapped to the human genome (release hg19) or mosquito genome (AaeGL5.0) by using Bowite 2.2.5 and the cellular miRNA expression level was determined on the basis of the number of reads that was identical to the annotated miRNA sequences in miRBase version 18, only allowing −2 or +2 nt to be templated by the corresponding genomic sequence at the 3′ end. Viral small RNA (vsRNA) reads which cannot be mapped to human genome were then mapped to DENV2 genome with 100% identity. The subsequent analysis of length and location of these vsRNAs were calculated using in-house Perl scripts. Pairs of complementary 22-nt vsRNAs in each library in different distance categories were computed using principles as previously described (Li et al., 2016; Li et al., 2013).
Genome_build: hg19, AaeGL5.0
Supplementary_files_format_and_content: *_reads.txt: Tab-delimited text files include read sequences and counts.

organism: Aedes aegypti

source_name: Aedes aegypti Aag-2 cells

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina).

tag: infection

value: Dengue virus serotype 2

tag: genotype/variation

value: DENV-WT


title: DENV-K135A-Aag2

description: small RNA

tag: cell line


title: HMLER2_NT_siRNA_CC04

description:
processed data files:
DESeq2_HMLER2_siHDAC7_vs_siNT.txt,DESeq2_HMLER2_siHDAC1_vs_siNT.txt
HMLER2_siHDAC7_vs_siNT.txt,HMLER2_siHDAC1_vs_siNT.txt
CC04

tag: cell type


title: TT11-2512-AN11-0002 [US-1421092]

description:
US-1421092
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: M

value: -control-


title: TT13-1509-AN13-0008 [TT13-1509_13-0008]

description:
TT13-1509_13-0008
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar


title: BPLER2_HDAC1_siRNA_CC03

description:
processed data files:
DESeq2_BPLER2_siHDAC1_vs_siNT.txt
BPLER2_siHDAC1_vs_siNT.txt
CC03

tag: transforming gene


title: TT11-2509-AN11-0070 [US-1468470]

description:
US-1468470
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: TT11-2509-AN11-0066 [US-1468451]

description:
US-1468451
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-1509-AN13-0004 [TT13-1509_13-0004]

description:
TT13-1509_13-0004
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2572-AN13-0002 [US-10017302]

description:
US-10017302
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: SesameOil


title: TT13-1509-AN13-0024 [TT13-1509_13-0024]

description:
TT13-1509_13-0024
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: BPLER2_HDAC1_siRNA_CC09R

description:
processed data files:
DESeq2_BPLER2_siHDAC1_vs_siNT.txt
BPLER2_siHDAC1_vs_siNT.txt
CC09R

tag: sirna


title: TT13-2572-AN13-0011 [US-10017311]

description:
US-10017311
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: study

value: F

value: bardoxolone


title: TT13-1509-AN13-0006 [TT13-1509_13-0006]

description:
TT13-1509_13-0006
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: strain


title: TT11-2509-AN11-0040 [US-1468445]

description:
US-1468445
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: Sex

value: naproxen


title: BPLER2_HDAC7_siRNA_CC08

description:
processed data files:
DESeq2_BPLER2_siHDAC7_vs_siNT.txt
BPLER2_siHDAC7_vs_siNT.txt
CC08


title: TT13-1509-AN13-0002 [TT13-1509_13-0002]

description:
TT13-1509_13-0002
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: agent

value: 0.4percent (w/v) Hydroxypropyl Methylcellulose in Deionized Water


title: dcl2/dcl4 methylC-seq

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

library_source: genomic

data_processing:
Data were mapped to the TAIR10 reference genome.
MethylC-seq analyses were performed as described in Schmtiz et. al., PMID: 23739894.
Genome_build: TAIR10
Supplementary_files_format_and_content: allC files reporting methylation of each cytosine in the genome is provided for methylC-seq data.

molecule: genomic DNA

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under 16-hour day conditions at 22ºC in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds.

extract_protocol:
DNA was isolated using fractional precipitation followed by phenol-chloroform extraction and RNase A treatment.
1 ug of DNA was used to prepare libraries as previously described in Urich et. al., PMID: 25692984.
Multiplexed libraries were sequenced on NextSeq 500.

tag: ecotype background

value: Columbia

tag: tissue


title: TT13-1509-AN13-0022 [TT13-1509_13-0022]

description:
TT13-1509_13-0022
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: treatment

value: PCN

tag: dose(mkd)

tag: days of administration


title: BPLER2_HDAC7_siRNA_CC08R

description:
processed data files:
DESeq2_BPLER2_siHDAC7_vs_siNT.txt
BPLER2_siHDAC7_vs_siNT.txt
CC08R


title: dcl3 methylC-seq - replicate B

description: Replicate A is available in GSE79746.

source_name: inflorescence (stage 1-12) immature flower buds.


title: TT11-2509-AN11-0034 [US-1468458]

description:
US-1468458
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: rin


title: TT11-2509-AN11-0006 [US-1468489]

description:
US-1468489
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2509-AN11-0008 [US-1468449]

description:
US-1468449
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: dcl1 sRNA

description: total small RNA

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
ShortStack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.

source_name: inflorescence (stage 1-12) immature flower buds

extract_protocol:
Inflorescence small RNA was isolated with TRIzol reagent (Invitrogen) and concentrated using the mirVana microRNA Isolation Kit (Ambion).
For AGO1-IP samples, AGO1 was immunoprecipitated from inflorescence tissue using Agrisera anti-AGO1 primary antibody. RNA was isolated from AGO1-IP or mock-IP samples using TRIzol reagent.
Size-enriched small RNAs were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina).
Multiplexed libraries were sequenced on HiSeq2500 or HiSeq4000.

tag: ecotype


title: BPLER2_NT_siRNA_CC07R

description:
processed data files:
DESeq2_BPLER2_siHDAC7_vs_siNT.txt, DESeq2_BPLER2_siHDAC1_vs_siNT.txt
BPLER2_siHDAC7_vs_siNT.txt, BPLER2_siHDAC1_vs_siNT.txt
CC07R

value: Non-targeting (NT)


title: TT11-2509-AN11-0004 [US-1468491]

description:
US-1468491
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: BPLER2_HDAC7_siRNA_CC02

description:
processed data files:
DESeq2_BPLER2_siHDAC7_vs_siNT.txt
BPLER2_siHDAC7_vs_siNT.txt
CC02

value: Breast primary epithelial cells


title: TT11-2509-AN11-0002 [US-1468455]

description:
US-1468455
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: BPLER2_NT_siRNA_CC07

description:
processed data files:
DESeq2_BPLER2_siHDAC7_vs_siNT.txt, DESeq2_BPLER2_siHDAC1_vs_siNT.txt
BPLER2_siHDAC7_vs_siNT.txt, BPLER2_siHDAC1_vs_siNT.txt
CC07

value: hTERT; SV40-LT/st; hRASV12


title: TT11-2508-AN11-0070 [US-1468419]

description:
US-1468419
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: diphenhydramine


title: rdr1/rdr2/rdr6 sRNA- replicate B

description: total small RNA

value: inflorescence (stage 1-12) immature flower buds


title: TT11-2508-AN11-0066 [US-1468402]

description:
US-1468402
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: TT11-2509-AN11-0068 [US-1468483]

description:
US-1468483
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M

value: amoxicillin


title: TT11-2508-AN11-0038 [US-1468481]

description:
US-1468481
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: diltiazem


title: BPLER_MS275_Input_ChIPSeq

data_processing:
Base calling, data filtering and read alignment performed on BaseSpace Illumina platform.
Broad peak calling was performed using SICER (v.0.1.1) with default parameters. Peak regions were further filtered after SICER peak calling with adjusted p-value (FDR)<0.01 and fold change >2.5.
Identification of super-enhancers was done using ROSE algorithm (Cell 153, 307-319, 2013; Cell 153, 320-334, 2013).
Genome_build: hs19
Supplementary_files_format_and_content: bigWig files were generated from bed files using the Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1)
Supplementary_files_format_and_content: tab-delimited text files include: Stitched enhancer ID; chromosome; stitched enhancer start; stitched enhancer end; number of constituent stitched; size of constituents stitched together; signal(s) of ranking_bam, rank of ranking bam, binary of super-enhancer (1) vs. typical (0). Signal of ranking bam is density times length.

growth_protocol: BPLER2 cells were described before (Cancer Cell 12, 160-170, 2007). Both cells and BPLER culture medium (BMI-T) are available from Live Tissue Culture Service Center, University if Miami  (contact LTCC@med.miami.edu).

extract_protocol:
Lysates from formaldehyde cross-linked cells were clarified from sonicated nuclei and histone-DNA complexes were immunoprecipitated with antibody. Cross-links were reversed and DNA extracted for library construction.
Libraries for paired-end sequencing and alignment were prepared according to NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® according to manufacturer instructions (New England BioLabs).

treatment_protocol: BPLER2 cells were plated in 15cm petri dish at 3.3x10e6 cell/plate in BMI-T medium. The day after, cells were treated with 1 mM (f.c.) MS-275 for 24 hours. After treatment, cells were formaldehyde cross-linked, harvested and processed for chromatin immunoprecipitation (ChIP)-sequencing analysis.

value: a stem-like breast cancer (BrCa) cell model

value: TERT; SV40-LT/st; HRASV12

value: MS-275 (Entinostat)

tag: chip antibody


title: BPLER_DMSO_Input_ChIPSeq

value: DMSO


title: BPLER_MS275_H3K27ac_ChIPSeq

value: H3K27ac - ChIP grade (Abcam, ab4729)


title: 100_TB small RNA

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

description: variety: 5BB

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC Program and CLC Genomic Workbench 11
Trimming of raw reads was performed using the CLC Genomic Workbench 11
Removing redundant reads using the CLC Genomic Workbench 11
Supplementary_files_format_and_content: trimmed redundant list, each read with its number of repeats

organism: Vitis vinifera

source_name: samples derived from rootstock nursery

extract_protocol:
CTAB method (Gambino, 2008: https://doi.org/10.1002/pca.1078 )
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

tag: cultivar

tag: locale

value: Beled

value: pooled RNA from leaf, shoot tip


title: BPLER_DMSO_H3K27ac_ChIPSeq

tag: cell line

tag: cell type


title: AI.Treated.98B

type: RNA

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

label: biotin

source_name: breast tumour

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: mRNA from baseline (B) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

value: female

tag: timepoint

value: baseline (B)

value: Negative

value: LumA

tag: accession

tag: reanalysis


title: TT11-2508-AN11-0034 [US-1468420]

description:
US-1468420
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: study

tag: strain

tag: Sex

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: AI.Treated.157B


title: AI.Treated.119B [reanalysis]

value: AI.Treated.119B [reanalysis]


title: AI.Treated.112B [reanalysis]

value: AI.Treated.112B [reanalysis]


title: AI.Treated.145B


title: AI.Treated.118B [reanalysis]

value: AI.Treated.118B [reanalysis]


title: TT11-2508-AN11-0040 [US-1468439]

description:
US-1468439
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: M

tag: agent


title: TT11-2508-AN11-0008 [US-1468443]

description:
US-1468443
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: treatment

value: -control-


title: AI.Treated.135B [reanalysis]

value: AI.Treated.135B [reanalysis]


title: AI.Treated.100B

value: Normal


title: AI.Treated.110B


title: AI.Treated.94B [reanalysis]

value: AI.Treated.94B [reanalysis]


title: AI.Treated.27B [reanalysis]

value: AI.Treated.27B [reanalysis]


title: AI.Treated.74B [reanalysis]

value: AI.Treated.74B [reanalysis]


title: AI.Treated.184B


title: AI.Treated.104B [reanalysis]

value: AI.Treated.104B [reanalysis]


title: AI.Treated.127B [reanalysis]

value: female

value: AI.Treated.127B [reanalysis]


title: 99_AS small RNA

description: variety: 5C, S.O.4, Ruggeri

value: 5C, S.O.4, Ruggeri

value: Abasár

tag: tissue

value: pooled RNA from leaf, shoot tip, tendril


title: 97_TC2 small RNA

description: variety: 5C, Ruggeri

value: 5C, Ruggeri

value: Tarcal

value: pooled RNA from leaf, shoot tip, flower, tendril


title: TT11-2508-AN11-0036 [US-1468493]

description:
US-1468493
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: 0.5percent (w/v) Methylcellulose in Deionized Water

value: diltiazem

tag: dose(mkd)

tag: days of administration


title: 98_LB small RNA

description: variety: Fercal, S.O.4, 5BB, Borner, 5C, Georgikon

value: Legyesbénye


title: TT11-2508-AN11-0006 [US-1468406]

description:
US-1468406
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M

value: -control-

tag: rin


title: 95_AD small RNA

description: variety: 5C, 5BB, 125AA, Fercal

value: 5C, 5BB, 125AA, Fercal

value: Aldebrő


title: 96_TC small RNA

description: variety: variety collection

value: cultivar collection


title: TT11-2508-AN11-0004 [US-1468414]

description:
US-1468414
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2508-AN11-0002 [US-1468418]

description:
US-1468418
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: AI.Treated.168B [reanalysis]

value: female

value: baseline (B)

value: Negative

value: LumA

value: AI.Treated.168B [reanalysis]


title: 93_KSZ small RNA

description: variety: 5C, Fercal, S.O.4, 125AA, Paulsen, 5C, Ruggeri, Richter

value: Kővágószőlős

value: pooled RNA from leaf, shoot tip, tendril


title: TT11-2503-AN11-0080 [US-1470466]

description:
US-1470466
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Hydroxypropyl Methylcellulose/0.1percent Polysorbate 80

value: lapatinib


title: 94_SZ small RNA

description: variety: 5BB, Fercal

value: 5BB, Fercal

value: Szekszárd


title: TT11-2503-AN11-0078 [US-1421090]

description:
US-1421090
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: 90_MR small RNA

description: variety: 5C, Gerorgikon, Berlandieri, Fercal

value: 5C, Gerorgikon, Berlandieri, Fercal

value: Mogyorósi Raposka


title: 91_V small RNA

description: variety: 5BB, 5C

value: 5BB, 5C

value: Villány

value: pooled RNA from leaf, shoot tip, tendril samples


title: TT11-2503-AN11-0076 [US-1420981]

description:
US-1420981
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: 92_P small RNA

description: variety: variety collection

value: cultivar collection

value: Pécs

value: pooled RNA from leaf, shoot tip, flower, tendril


title: AI.Treated.65B

value: female

value: baseline (B)

value: Negative

value: LumA


title: AI.Treated.102B


title: AI.Treated.152B

value: LumB


title: TT11-2503-AN11-0078 [US-1470520]

description:
US-1470520
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Hydroxypropyl Methylcellulose/0.1percent Polysorbate 80

value: lapatinib


title: AI.Treated.80B [reanalysis]

value: AI.Treated.80B [reanalysis]


title: AI.Treated.92B [reanalysis]

value: AI.Treated.92B [reanalysis]


title: AI.Treated.76B [reanalysis]

value: AI.Treated.76B [reanalysis]


title: AI.Treated.143B [reanalysis]

value: AI.Treated.143B [reanalysis]


title: AI.Treated.172B [reanalysis]

value: AI.Treated.172B [reanalysis]


title: AI.Treated.142B [reanalysis]

value: AI.Treated.142B [reanalysis]


title: AI.Treated.49B [reanalysis]

value: AI.Treated.49B [reanalysis]


title: AI.Treated.4B

value: Positive


title: AI.Treated.62B [reanalysis]

value: AI.Treated.62B [reanalysis]


title: AI.Treated.67B [reanalysis]

value: AI.Treated.67B [reanalysis]


title: AI.Treated.147B [reanalysis]

value: female

value: AI.Treated.147B [reanalysis]


title: AI.Treated.37B [reanalysis]

value: baseline (B)

value: Negative

value: AI.Treated.37B [reanalysis]


title: AI.Treated.178B [reanalysis]

value: LumA

value: AI.Treated.178B [reanalysis]


title: TT11-2503-AN11-0076 [US-1470463]

description:
US-1470463
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: M

value: 0.5percent (w/v) Hydroxypropyl Methylcellulose/0.1percent Polysorbate 80

value: lapatinib


title: TT11-2503-AN11-0074 [US-1420990]

description:
US-1420990
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2503-AN11-0074 [US-1470512]

description:
US-1470512
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: 85_NG small RNA

description: variety: 5BB, Fercal, S.O.4

value: 5BB, Fercal, S.O.4

value: Nemesgulács

value: pooled RNA from leaf, shoot tip, tendril


title: 89_ZG small RNA

description: variety: 5BB, Fercal

value: 5BB, Fercal

value: Zalaszentgrót


title: 86_MT small RNA

description: variety: Fercal

value: Fercal

value: Mogyorósi-Hegy Tapolca


title: AI.Treated.180B [reanalysis]

value: female

value: LumB

value: AI.Treated.180B [reanalysis]


title: AI.Treated.149B [reanalysis]

value: baseline (B)

value: Negative

value: Normal

value: AI.Treated.149B [reanalysis]


title: TT11-2503-AN11-0080 [US-1420951]

description:
US-1420951
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: M


title: AI.Treated.113B

value: LumA


title: AI.Treated.84B [reanalysis]

value: AI.Treated.84B [reanalysis]


title: 88_ZE small RNA

description: variety: Ruggeri, Georgikon, 125AA, 5BB, Fercal, S.O.4, 5C

value: Zalaegerszeg


title: AI.Treated.115B [reanalysis]

value: AI.Treated.115B [reanalysis]


title: TT11-2503-AN11-0048 [US-1470519]

description:
US-1470519
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water

value: flucloxacillin


title: 84_BH small RNA

description: variety: Fercal, S.O.4

value: Fercal, S.O.4

value: Becsehely

value: pooled RNA from leaf, shoot tip, tendril


title: 87_FH small RNA

description: variety: 5C/420A, Fercal

value: 5C/420A, Fercal

value: Figyeháza


title: 83_BB small RNA

description: variety: 5C, 125AA, Fercal

value: 5C, 125AA, Fercal

value: Balatonboglár


title: TT11-2503-AN11-0044 [US-1470524]

description:
US-1470524
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2503-AN11-0042 [US-1470508]

description:
US-1470508
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: AI.Treated.88B [reanalysis]

value: female

value: baseline (B)

value: Negative

value: AI.Treated.88B [reanalysis]


title: 82_BSZ small RNA

description: variety: Fercal, S.O.4

value: Balatonszárszó

value: pooled RNA from leaf, shoot tip, flower, tendril


title: AI.Treated.71B [reanalysis]

value: LumA

value: AI.Treated.71B [reanalysis]


title: TT11-2503-AN11-0016 [US-1420945]

description:
US-1420945
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: M

value: 0.5percent (w/v) Hydroxypropyl Methylcellulose/0.1percent Polysorbate 80

value: -control-


title: AI.Treated.60B


title: AI.Treated.31B [reanalysis]

value: AI.Treated.31B [reanalysis]


title: AI.Treated.171B


title: TT11-2503-AN11-0046 [US-1470505]

description:
US-1470505
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water

value: flucloxacillin


title: AI.Treated.108B [reanalysis]

value: LumB

value: AI.Treated.108B [reanalysis]


title: AI.Treated.78B [reanalysis]

value: female

value: AI.Treated.78B [reanalysis]


title: AI.Treated.87B [reanalysis]

value: baseline (B)

value: Negative

value: AI.Treated.87B [reanalysis]


title: TT11-2503-AN11-0016 [US-1470437]

description:
US-1470437
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: AI.Treated.117B


title: TT11-2503-AN11-0014 [US-1420968]

description:
US-1420968
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: AI.Treated.167B [reanalysis]

value: AI.Treated.167B [reanalysis]


title: AI.Treated.146B [reanalysis]

value: LumA

value: AI.Treated.146B [reanalysis]


title: AI.Treated.125B [reanalysis]

value: AI.Treated.125B [reanalysis]


title: AI.Treated.58B [reanalysis]

value: AI.Treated.58B [reanalysis]


title: AI.Treated.137B [reanalysis]

value: AI.Treated.137B [reanalysis]


title: AI.Treated.86B


title: TT11-2503-AN11-0014 [US-1470461]

description:
US-1470461
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: M

value: 0.5percent (w/v) Hydroxypropyl Methylcellulose/0.1percent Polysorbate 80

value: -control-


title: AI.Treated.43B [reanalysis]

value: AI.Treated.43B [reanalysis]


title: TT11-2503-AN11-0012 [US-1420949]

description:
US-1420949
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: L.KLGE_003

city: Oxford

first: Cristina

last: Di Genua

address: Headley Way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
Sequenced were trimmed using Trim Galore
Reads were mapped to mm10 murine reference genome using Bowtie2
SAMtools was used to convert sam files to bam files
Duplicates were removed using MarkDuplicates function from the Picard tools package
Bam files were subsampled and merged using SAMtools
Peaks were called using MACS2
Regions of chromatin accessibility were quantified as peak counts using the featureCounts function from the Subread package
Peaks were annotated using Homer
Genome_build: mm10
Supplementary_files_format_and_content: csv file include peak counts for each sample

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Cells were sorted into lysis buffer containing TD tagmentation buffer (Illumina), 1% digitonin, 10% Tween 20 and PBS. After cells were sorted into the lysis buffer the Tn5 transposase was then added and immediately incubated at 30C for 30mins with an agitation at 300rpm. Samples were then purified using a Qiagen MinElute Kit .
Samples were then PCR amplified and indexed using NEBNext High-Fidelity 2x PCR master mix and P7 and P5 primers containing Nextera adaptor sequences.
Samples were sequenced on Illumina NextSeq 500 Instrument

treatment_protocol: 500 CD45.2+LKFcgRII/III+CD55- cells were isolated by fluorescent activated cell sorting for each sample

value: Bone marrow

tag: tumor stage

value: Leukemia

tag: genotype

value: KLG-E


title: AI.Treated.72B

value: female

value: baseline (B)


title: AI.Treated.141B

value: Negative


title: L.KLGE_002


title: TT11-2503-AN11-0010 [US-1420953]

description:
US-1420953
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: AI.Treated.63B [reanalysis]

value: AI.Treated.63B [reanalysis]


title: TT11-2503-AN11-0012 [US-1470458]

description:
US-1470458
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2503-AN11-0008 [US-1470528]

description:
US-1470528
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: AI.Treated.154B [reanalysis]

value: LumB

value: AI.Treated.154B [reanalysis]


title: AI.Treated.28B [reanalysis]

value: LumA

value: AI.Treated.28B [reanalysis]


title: L.KLGE_001


title: TT11-2503-AN11-0010 [US-1470455]

description:
US-1470455
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: AI.Treated.32B [reanalysis]

value: AI.Treated.32B [reanalysis]


title: L.KLGM_002

value: KLG-M


title: L.KLGM_003


title: TT11-2503-AN11-0006 [US-1470460]

description:
US-1470460
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M

value: -control-


title: AI.Treated.90B [reanalysis]

value: AI.Treated.90B [reanalysis]


title: TT11-2503-AN11-0002 [US-1470436]

description:
US-1470436
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: AI.Treated.52B [reanalysis]

value: AI.Treated.52B [reanalysis]


title: AI.Treated.47B [reanalysis]

value: AI.Treated.47B [reanalysis]


title: AI.Treated.61B

value: female


title: AI.Treated.150B

value: baseline (B)


title: AI.Treated.121B [reanalysis]

value: Negative

value: AI.Treated.121B [reanalysis]


title: AI.Treated.162B


title: TT11-2503-AN11-0004 [US-1470453]

description:
US-1470453
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: AI.Treated.107B [reanalysis]

value: AI.Treated.107B [reanalysis]


title: L.KL_001

value: Bone marrow

value: Leukemia

value: KL


title: L.KLGM_001


title: TT11-2502-AN11-0048 [US-1470961]

description:
US-1470961
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: lumiracoxib


title: AI.Treated.93B [reanalysis]

value: LumA

value: AI.Treated.93B [reanalysis]


title: L.KL_003


title: AI.Treated.153B [reanalysis]

value: AI.Treated.153B [reanalysis]


title: L.KL_002


title: AI.Treated.126B [reanalysis]

value: LumB

value: AI.Treated.126B [reanalysis]


title: AI.Treated.23B [reanalysis]

value: Positive

value: AI.Treated.23B [reanalysis]


title: TT11-2502-AN11-0042 [US-1470890]

description:
US-1470890
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: AI.Treated.77B [reanalysis]

value: female

value: baseline (B)

value: Negative

value: AI.Treated.77B [reanalysis]


title: TT11-2502-AN11-0046 [US-1470888]

description:
US-1470888
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: AI.Treated.183B [reanalysis]

value: AI.Treated.183B [reanalysis]


title: AI.Treated.36B [reanalysis]

value: AI.Treated.36B [reanalysis]


title: AI.Treated.176B [reanalysis]

value: AI.Treated.176B [reanalysis]


title: TT11-2502-AN11-0008 [US-1470898]

description:
US-1470898
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: -control-


title: AI.Treated.7B [reanalysis]

value: LumA

value: AI.Treated.7B [reanalysis]


title: AI.Treated.111B [reanalysis]

value: AI.Treated.111B [reanalysis]


title: KLG_001

value: Bone marrow

value: Pre-leukemia

value: KLG


title: KLG_003


title: KLG_002


title: AI.Treated.41B


title: TT11-2502-AN11-0004 [US-1470899]

description:
US-1470899
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: TT11-2502-AN11-0002 [US-1470937]

description:
US-1470937
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: KL_002

value: KL


title: KL_001


title: TT11-2502-AN11-0006 [US-1470886]

description:
US-1470886
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: AI.Treated.95B [reanalysis]

value: female

value: baseline (B)

value: AI.Treated.95B [reanalysis]


title: TT10-2505-AN10-0039 [US-1420948]

description:
US-1420948
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: F

value: 100percent PEG 400

value: almorexant


title: 7-day old mutant tendon

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
cellranger-1.2.0 with default parameters was used to anzlye the 10X Single-cell RNA-seq.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression for each cell was recored by three files: the sparse matrix of read counts, the row information for gene symbols and columns for cell barcode ids

source_name: Mouse tendon cells

extract_protocol:
Tendons from P7 mutant and wild-type (as a control) pups were harvested and enzymatically digested. The released cells cells were then centrifuged, resuspended in alpha-MEM with 5% FBS and subjected to scRNA-seq processing/analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: Tendon

value: mutant


title: TT10-2505-AN10-0037 [US-1421053]

description:
US-1421053
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: AI.Treated.129B

value: Negative

value: LumA


title: AI.Treated.138B [reanalysis]

value: AI.Treated.138B [reanalysis]


title: AI.Treated.9B [reanalysis]

value: Positive

value: AI.Treated.9B [reanalysis]


title: AI.Treated.48B [reanalysis]

value: AI.Treated.48B [reanalysis]


title: AI.Treated.169B [reanalysis]

value: AI.Treated.169B [reanalysis]


title: AI.Treated.59B [reanalysis]

value: AI.Treated.59B [reanalysis]


title: AI.Treated.75B [reanalysis]

value: female

value: AI.Treated.75B [reanalysis]


title: 7-day old wild-type tendon

value: wild type


title: TT10-2505-AN10-0037 [US-1468433]

description:
US-1468433
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: F


title: miR7_SCR_s2: LNA-scramble treated mouse enteroids scRNA-seq

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

data_processing:
Sequencing was demultiplexed, aligned to the genome, and quality checked using 10X Genomics Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data contains barcodes, gene list, and counts matrix.

source_name: small intestine

extract_protocol: Libraries were prepped according to 10X Genomics Chromium Single Cell 3' kits (v2 chemistry)

value: Enteroids formed from jejunal crypts


title: TT10-2505-AN10-0035 [US-1421079]

description:
US-1421079
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 100percent PEG 400

value: almorexant


title: TT10-2505-AN10-0035 [US-1468466]

description:
US-1468466
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: miR7_LNA7_s2: LNA-7 treated mouse enteroids scRNA-seq


title: AI.Treated.116B [reanalysis]

value: baseline (B)

value: AI.Treated.116B [reanalysis]


title: TT10-2505-AN10-0033 [US-1421064]

description:
US-1421064
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: RNASeq_ATRXKD_Rep2

city: Philadelphia

first: Kavitha

last: Sarma

address: 3601 Spruce St

institute: The Wistar Institute

data_processing:
Alignment (CUT&RUN): Bowtie2
peak calling was done using MACS2 --broadPeak mode from aligned .bam files with default options
Alignment (RNA-Seq): STAR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files compaitble with UCSC genome browser or IGV.  Broadpeak files were used from MACS output. TPM output for RNA-Seq alignment

growth_protocol: Mouse embryonic fibroblast cells were grown in DMEM-high glucose medium supplemented with 10% calf serum, 3% HEPES, 1% glutamine, 1% non-essential amino acids and 1% penicillin-streptomycin at 37 °C.

extract_protocol:
DNA was collected from the supernatant after treatment with CUT&RUN using the indicated antibodies (Skene & Henikoff eLife 2017).
Total RNA was collected and PolyA RNA was slectively enriched using NEB # E7490S
DNA was end-repaired using End-It Repair Kit, tailed with an A using Klenow exo minus, and ligated to adapters (NEB #E7600S) with T4 DNA ligase. Fragments > 150 bp were size-selected with AMpure beads (Beckman Coulter) and subjected to ligation-mediated PCR amplification with barcoded adapters (NEB #E7600S) for Illumina sequencing using Q5 DNA polymerase. All enzymes except Q5 (NEB) were from Enzymatics (a Qiagen company).
Libraries prepared using the Ultra II directional RNA library prep kit for illumina (NEB #E7760S).

treatment_protocol: Stable CRISPR RBR deletion clones were obtained after transfecting MEFs with gRNAs and Cas9 containing plasmid and puromycin selection for 2 days to kill untransfected cells.  Colonies were picked and screened by PCR and western

value: mouse embryonic fibroblast cells (MEFs)

tag: genotype/variation

value: ATRX shRNA

tag: experiment type

value: RNA-Seq


title: RNASeq_ATRXKD_Rep1

tag: cell type


title: AI.Treated.35B [reanalysis]

tag: timepoint

value: Negative

value: LumB

tag: accession

value: AI.Treated.35B [reanalysis]


title: AI.Treated.81B [reanalysis]

value: LumA

tag: reanalysis

value: AI.Treated.81B [reanalysis]


title: AI.Treated.160B [reanalysis]

value: female

value: AI.Treated.160B [reanalysis]


title: AI.Treated.15B [reanalysis]

value: Positive

value: AI.Treated.15B [reanalysis]


title: AI.Treated.17B [reanalysis]

value: AI.Treated.17B [reanalysis]


title: AI.Treated.73B [reanalysis]

value: Normal

value: AI.Treated.73B [reanalysis]


title: AI.Treated.151B [reanalysis]

value: baseline (B)

value: AI.Treated.151B [reanalysis]


title: AI.Treated.144B [reanalysis]

value: AI.Treated.144B [reanalysis]


title: TT10-2505-AN10-0007 [US-1420979]

description:
US-1420979
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: study

tag: strain

value: Sprague Dawley

value: F

value: 100percent PEG 400

value: -control-


title: TT10-2505-AN10-0033 [US-1468492]

description:
US-1468492
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: Sex

tag: agent

value: almorexant


title: RNASeq_△RBR_Rep1

value: mouse embryonic fibroblast cells (MEFs)

value: CRISPR deletion of RBR in endogenous ATRX

value: RNA-Seq


title: TT10-2505-AN10-0007 [US-1468460]

description:
US-1468460
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: treatment


title: RNASeq_△RBR_Rep2


title: RNASeq_WT_Rep2


title: AI.Treated.68B [reanalysis]

value: female

value: Negative

value: LumA

value: AI.Treated.68B [reanalysis]


title: AI.Treated.132B [reanalysis]

value: AI.Treated.132B [reanalysis]


title: TT10-2505-AN10-0005 [US-1421076]

description:
US-1421076
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: dose(mkd)


title: RNASeq_WT_Rep1


title: TT10-2505-AN10-0003 [US-1420941]

description:
US-1420941
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: days of administration


title: TT10-2505-AN10-0001 [US-1420985]

description:
US-1420985
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: rin


title: IgGC&R_△RBR_Rep2

value: CUT&RUN

tag: antibody

value: IgG


title: AI.Treated.124B [reanalysis]

value: baseline (B)

value: Normal

value: AI.Treated.124B [reanalysis]


title: IgGC&R_WT_Rep2


title: raw_ctl_D3-3

city: Dallas

first: Igor

middle: M

last: Dozmorov

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase 22.0
Supplementary_files_format_and_content: excel,expression profiles

source_name: THP-1 uninfected

growth_protocol: Infected cell culture was used

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: Cells were either uninfected or infected for 3 days or 6 days

tag: cell line

value: macrophage; ATCC TIB-202

value: none; uninfected

tag: molecule subtype

value: small RNA


title: raw_ctl_D3-2


title: AI.Treated.45B [reanalysis]

value: AI.Treated.45B [reanalysis]


title: AI.Treated.128B [reanalysis]

value: AI.Treated.128B [reanalysis]


title: AI.Treated.177B [reanalysis]

value: AI.Treated.177B [reanalysis]


title: AI.Treated.156B

value: LumB


title: raw_ctl_D3-1


title: AI.Treated.166B [reanalysis]

value: female

value: AI.Treated.166B [reanalysis]


title: AI.Treated.50B [reanalysis]

value: Negative

value: LumA

value: AI.Treated.50B [reanalysis]


title: H3K27me3C&R_ATRXKD_Rep2

value: mouse embryonic fibroblast cells (MEFs)

tag: genotype/variation

value: ATRX shRNA

value: CUT&RUN

value: H3K27me3 (Active motif #61017)


title: AI.Treated.64B [reanalysis]

value: baseline (B)

value: AI.Treated.64B [reanalysis]


title: AI.Treated.182B


title: AI.Treated.106B


title: AI.Treated.44B [reanalysis]

value: AI.Treated.44B [reanalysis]


title: AI.Treated.83B


title: AI.Treated.69B [reanalysis]

value: AI.Treated.69B [reanalysis]


title: AI.Treated.114B


title: IgGC&R_△RBR_Rep1

value: CRISPR deletion of RBR in endogenous ATRX

tag: experiment type

value: IgG


title: AI.Treated.85B [reanalysis]

value: AI.Treated.85B [reanalysis]


title: AI.Treated.158B

value: LumB


title: AI.Treated.53B [reanalysis]

value: female

value: AI.Treated.53B [reanalysis]


title: AI.Treated.120B [reanalysis]

value: Negative

value: AI.Treated.120B [reanalysis]


title: H3K27me3C&R_ATRXKD_Rep1

tag: cell type


title: EZH2C&R_ATRXKD_Rep2

value: EZH2 (Cell signaling #5246)


title: EZH2C&R_ATRXKD_Rep1

value: mouse embryonic fibroblast cells (MEFs)


title: OVER NRAV rep2 [NO5]

city: Shijiazhuang

first: Jian

last: Li

address: 361 Zhongshan East Road

institute: Hebei Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: OVER NRAV_A549

growth_protocol: A549 cells were grown in RPMI1640 supplemented with 10% (vol/vol) FBS (Gibco) and antibiotics (penicillin and streptomycin) (Solarbio) in a humidified 5% CO2 atmosphere at 37℃.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Cat#217004, Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded in six-well plates. Plasmids or siRNAs were transfected into cells with Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions

value: adenocarcinoma of type II alveolar cells

tag: passages

value: NIRAV overexpression


title: OVER NRAV rep3 [NO6]


title: siNC [NO7]

value: siNC


title: siNRAV [NO8]

value: siNIRAV


title: OVER NRAV rep1 [NO4]

value: NIRAV overexpression II


title: EV rep3 [NO3]

value: emtpy vector


title: AI.Treated.16B [reanalysis]

tag: timepoint

value: baseline (B)

value: Positive

tag: accession

value: AI.Treated.16B [reanalysis]


title: H3K27me3C&R_WT_Rep2

value: CUT&RUN

value: H3K27me3 (Active motif #61017)


title: AI.Treated.130B [reanalysis]

value: female

value: LumB

tag: reanalysis

value: AI.Treated.130B [reanalysis]


title: EV rep2  [NO2]


title: AI.Treated.159B [reanalysis]

value: Negative

value: AI.Treated.159B [reanalysis]


title: AI.Treated.22B [reanalysis]

value: AI.Treated.22B [reanalysis]


title: H3K27me3C&R_△RBR_Rep1

value: mouse embryonic fibroblast cells (MEFs)

value: CRISPR deletion of RBR in endogenous ATRX


title: AI.Treated.34B [reanalysis]

value: LumA

value: AI.Treated.34B [reanalysis]


title: AI.Treated.19B [reanalysis]

value: AI.Treated.19B [reanalysis]


title: AI.Treated.101B


title: H3K27me3C&R_WT_Rep1


title: H3K27me3C&R_△RBR_Rep2


title: EV rep1  [NO1]

value: adenocarcinoma of type II alveolar cells

value: emtpy vector


title: AI.Treated.40B [reanalysis]

value: baseline (B)

value: AI.Treated.40B [reanalysis]


title: plated_control_6

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

data_processing:
All sequencing data were generated by the Washington University Genome Technology Access Center (GTAC)
Bulk RNA sequencing files were generated by Illumina sequencer and processed by GTAC
Singe Cell RNA sequencing files were processed by Cell Ranger 2.1.1
Genome_build: h_sapien Ensembl_R76
Supplementary_files_format_and_content: Bulk RNA sequencing data presented in counts as tab-delimited txt file. Single cell RNA sequencing data presented as matrix files.

source_name: Pacreatic Progenitors

growth_protocol: Cells were grown in bioreactor as described (Velazco-Cruz et al., Stem cell reports 12) or grown using the planar protocol as described in the submitted manuscript.

extract_protocol:
Single Cell RNA Seq: Cells processed during Stage 5 using Chromium Single Cell 3’ Library and Gel Bead  Kit v2 (10x Genomics, 120237). Bulk RNA Seq: Cells processed during Stage 6 where RNA was extracted with the RNeasy Mini Kit (Qiagen, 74016), including a DNase treatment 728 (Qiagen, 79254) during extraction.
Library construction for single cell was constructed using 10X Chromium Protocol. RNA. Library construction for bulk RNA serquencing was prepared using standard Illumina protocols.

treatment_protocol: Singe Cell RNA Seq: Cells treated with 0.5uM Latrunculin A or 5uM Nocodazole during all of Stage 4 of differentiation. Bulk RNA Seq: Cells left untreated or treated with 0.5uM Latrunculin during Stage 4 or 1uM for the first 24 hours of Stage 5.

tag: protocol

value: 6 well tissue culture plastic plate

value: ES-Derived Endocrine Cells

tag: Stage

value: Stage 6

tag: kit used

value: RNeasy Mini Kit (Qiagen, 74016)


title: plated_control_4


title: plated_control_5


title: noRA+Dox rep2

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

data_processing:
Reads were mapped to GRCh38 using STAR
Mapped reads were quantified using STAR option “quantMode TranscriptomeSAM” that allowed counting of reads aligned to each gene
Normalization and differential gene expression were done using Bioconductor/R package DESeq2 (version 1.14.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma delimited file with the raw and normalized counts for each gene

source_name: SH-SY5Y cells

growth_protocol: Cells were conditioned in DMEM containing 0.1 % serum and RA (1 or 5 μM) or an equivalent amount of the DMSO (0.1%) solvent

extract_protocol:
Total RNA was extracted from confluent 10 cm dishes of conditioning the cells using RNeasy Plus mini kit (Qiagen, Eldan Petach-Tikva, Israel) according to manufacturer's instructions
Libraries were prepared using TruSeq stranded total RNA Kit from 300 ng of total RNA. Illumina HiSeq3000 was used to generate paired-end sequencing with a read length of 150 bp raw data.

tag: treatment

value: no RA (only DMSO)

tag: dox status

value: Dox (doxycycline)

tag: induced expression

value: alpha-Syn


title: noRA+Dox rep3


title: noRA/noDox rep2

value: no Dox


title: EZH2C&R_△RBR_Rep2

value: mouse embryonic fibroblast cells (MEFs)

value: CUT&RUN

value: EZH2 (Cell signaling #5246)


title: EZH2C&R_WT_Rep2


title: plated_control_3


title: EZH2C&R_△RBR_Rep1

value: CRISPR deletion of RBR in endogenous ATRX


title: AI.Treated.123B [reanalysis]

tag: Sex

value: female

value: Negative

value: LumA

value: AI.Treated.123B [reanalysis]


title: EZH2C&R_WT_Rep1

tag: antibody


title: AI.Treated.131B

value: baseline (B)

value: Basal


title: AI.Treated.164B


title: AI.Treated.66B [reanalysis]

value: AI.Treated.66B [reanalysis]


title: noRA/noDox rep1

tag: cell line


title: AI.Treated.70B [reanalysis]

value: LumB

value: AI.Treated.70B [reanalysis]


title: AI.Treated.148B


title: AI.Treated.89B


title: AI.Treated.139B [reanalysis]

value: AI.Treated.139B [reanalysis]


title: AI.Treated.79B [reanalysis]

value: AI.Treated.79B [reanalysis]


title: ATRXC&R_△RBR_Rep2

value: ATRX (custom-made)


title: noRA/noDox rep3

value: no RA (only DMSO)

value: no Dox


title: plated_control_2

value: 6 well tissue culture plastic plate

value: ES-Derived Endocrine Cells

value: Stage 6

value: RNeasy Mini Kit (Qiagen, 74016)


title: AI.Treated.55B [reanalysis]

value: female

value: Negative

value: AI.Treated.55B [reanalysis]


title: noRA+Dox rep1

value: Dox (doxycycline)

value: alpha-Syn


title: plated_control_1


title: ATRXC&R_WT_Rep2

value: mouse embryonic fibroblast cells (MEFs)

value: CUT&RUN


title: lata_s4_6

tag: agent

value: Latrunculin A


title: ATRXC&R_WT_Rep1


title: RA/noDox rep3

value: RA (retinoic acid)

value: no Dox (doxycycline)


title: AI.Treated.175B [reanalysis]

value: baseline (B)

value: LumB

value: AI.Treated.175B [reanalysis]


title: lata_s4_5


title: RA+Dox rep3


title: AI.Treated.82B [reanalysis]

value: LumA

value: AI.Treated.82B [reanalysis]


title: C-9

data_processing:
Reads were aligned using STAR against the mouse genome assembly (mouse NCBI build38 (mm10) UCSC transcripts)
Gene expression levels were quantified as read counts using the featureCounts function from the Subread package with default parameters
The read counts were used for the identification of global differential gene expression between specified populations and genotypes using the DESeq2 package.
Expression values were quantified as read per kilobase of transcript length per million mapped reads (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

extract_protocol:
Cells were sorted into 4μL of lysis buffer containing; 0.2% Triton X-100, 2.5 uM OligodT, 2.5 mM dTNPs, RNase Inhibitor 20 U and ERCC spike-in 1:4,000,000. cDNA synthesis and PCR amplification were performed based on the published Smart-seq 2 protocol with some modifications.
Illumina sequencing libraries were prepared using the Illumina Nextera XT DNA kit, using one forth of the standard volume recommended by Illumina

treatment_protocol: 100 CD45.2+LKFcgRII/II+CD55-, CD45.1-EGFP-CD71hiTer119-/locKit+, and CD45.2+Mac1+cKitlo were isolated by fluorescent activated cell sorting for each sample

tag: tissue

value: Bone marrow

tag: tumour stage

value: Pre-leukaemia

tag: genotype

value: KL


title: RA/noDox rep2


title: AI.Treated.46B

value: female

value: Negative


title: lata_s4_4

tag: cell type

value: ES-Derived Endocrine Cells

value: Stage 6

value: RNeasy Mini Kit (Qiagen, 74016)


title: C-8


title: RA+Dox rep1

value: Dox (doxycycline)

value: alpha-Syn


title: AI.Treated.20B [reanalysis]

tag: timepoint

value: Positive

value: AI.Treated.20B [reanalysis]


title: RA/noDox rep1

value: RA (retinoic acid)

value: no Dox (doxycycline)


title: C-71

value: Leukaemia

value: KLG-E


title: lata_s4_2

value: Latrunculin A


title: ATRXC&R_△RBR_Rep1

value: mouse embryonic fibroblast cells (MEFs)

tag: genotype/variation

value: CRISPR deletion of RBR in endogenous ATRX

tag: experiment type

value: CUT&RUN

value: ATRX (custom-made)


title: RA+Dox rep2


title: lata_s4_3


title: AI.Treated.5B [reanalysis]

value: female

value: baseline (B)

value: LumB

tag: accession

tag: reanalysis

value: AI.Treated.5B [reanalysis]


title: AI.Treated.11B


title: C-70

value: Bone marrow


title: RNA-Seq_HCT116_siLUCRC

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using STAR version 2.7.0e.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: colorectal cancer

growth_protocol: HCT116 cells were cultured in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using Trizol (Takara) following the manufacturer’s protocol followed by DNase I digestion to remove residual DNA.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq 3000 platform.

tag: sirna

value: siLUCRC


title: lata_s4_1

value: ES-Derived Endocrine Cells

tag: Stage

value: Stage 6

tag: kit used

value: RNeasy Mini Kit (Qiagen, 74016)


title: AI.Treated.6B

value: Positive


title: C-7

value: Pre-leukaemia

value: KL


title: RNA-Seq_HCT116_siCTL

value: siCTL


title: lata_on_s5d1_6

value: Latrunculin A


title: lata_on_s5d1_5


title: lata_on_s5d1_4


title: AI.Treated.134B [reanalysis]

value: Negative

value: LumA

value: AI.Treated.134B [reanalysis]


title: tenocytes, ScxWT-3

city: New York

first: Christopher

middle: L

last: Mendias

address: 535 E 70th St

institute: Hospital for Special Surgery

description:
deseq.txt
counts.txt

data_processing:
Quality assessment and fold change calculations were performed in DESeq2
Sequencing data was quality checked using FastQC, aligned to the reference genome (mm10, UCSC, Santa Cruz, CA, USA) with the STAR software package
Differential expression based on FKPM was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 Output, Raw counts

source_name: Cultured Tail Tendon Fibroblasts

extract_protocol:
RNA was purified with a miRNeasy Micro Kit (Qiagen) supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop 2000 (Thermo Fisher). For each sample, 200ng of RNA was delivered to the Weill Cornell Genomics Core for RNA sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Scx+

tag: 4ht treatment

value: Yes

value: Cultured Tail Tendon Fibroblasts


title: tenocytes, ScxWT-6

description:
deseq.txt
counts.txt


title: tenocytes, ScxWT-5

description:
deseq.txt
counts.txt


title: C-68

value: Leukaemia

value: KLG-M


title: AI.Treated.97B [reanalysis]

tag: Sex

value: female

value: baseline (B)

value: LumB

value: AI.Treated.97B [reanalysis]


title: C-69

value: Bone marrow


title: C-66

value: KLG-E


title: tenocytes, ScxKO-5

description:
deseq.txt
counts.txt

value: Scx-


title: C-67


title: lata_on_s5d1_2

value: ES-Derived Endocrine Cells

value: Stage 6

value: RNeasy Mini Kit (Qiagen, 74016)


title: tenocytes, ScxWT-2

description:
deseq.txt
counts.txt


title: AI.Treated.1B [reanalysis]

value: Positive

value: LumA

value: AI.Treated.1B [reanalysis]


title: AI.Treated.96B [reanalysis]

value: Negative

value: AI.Treated.96B [reanalysis]


title: C-65

value: Leukaemia


title: AI.Treated.179B [reanalysis]

value: AI.Treated.179B [reanalysis]


title: tenocytes, ScxKO-4

description:
deseq.txt
counts.txt

value: Yes

value: Cultured Tail Tendon Fibroblasts


title: C-64

value: KL


title: AI.Treated.2B

value: female

value: baseline (B)

value: LumB


title: lata_on_s5d1_1

value: Latrunculin A


title: biott_5

tag: protocol

value: bioreactor

value: ES-Derived Endocrine Cells


title: C-63

value: Bone marrow

value: KLG-E


title: biott_4

value: Stage 6

value: RNeasy Mini Kit (Qiagen, 74016)


title: lata_on_s5d1_3

tag: agent


title: C-62

tag: tissue


title: biott_3


title: AI.Treated.29B

value: Negative

value: Basal


title: mouse_S66

data_processing:
RNA-Seq:Short reads were aligned to the human genome (GRCh37 assembly (hg19)) and mouse (mm10) using the Cell Rager software.
Read Count : Matrices of read counts were obtained based on the Cell Ranger software
Genome_build: GRCh37 assembly (hg19)
Genome_build: Mouse (mm10)
Supplementary_files_format_and_content: Cell Ranger Market Exchange Format (MEX)

extract_protocol:
cDNA was generated according to the single-cell 10x genomics protocol
Illumina sequencing libraries were constructed according to manufacturer's protocol.

treatment_protocol: Cells were isolated by FACS.

tag: phenotype

tag: age

value: 25 weeks post-transplantation


title: C-61

tag: cell type

tag: tumour stage

value: Leukaemia

tag: genotype

value: KLG-M


title: mouse_S17

value: 22 weeks post-transplantation


title: AI.Treated.161B [reanalysis]

tag: timepoint

value: AI.Treated.161B [reanalysis]


title: AI.Treated.14B [reanalysis]

value: female

value: Positive

tag: accession

value: AI.Treated.14B [reanalysis]


title: AI.Treated.18B [reanalysis]

value: baseline (B)

tag: reanalysis

value: AI.Treated.18B [reanalysis]


title: tenocytes, ScxKO-2

description:
deseq.txt
counts.txt

value: Scx-

value: Yes

value: Cultured Tail Tendon Fibroblasts


title: AI.Treated.10B [reanalysis]

value: LumA

value: AI.Treated.10B [reanalysis]


title: C-60

value: Bone marrow

value: KLG-E


title: AI.Treated.91B [reanalysis]

value: Negative

value: LumB

value: AI.Treated.91B [reanalysis]


title: IgGC&R_WT_Rep1

value: mouse embryonic fibroblast cells (MEFs)

tag: experiment type

value: CUT&RUN

tag: antibody

value: IgG


title: biott_2

value: bioreactor

value: ES-Derived Endocrine Cells

tag: Stage

value: Stage 6

tag: kit used

value: RNeasy Mini Kit (Qiagen, 74016)


title: C-6

value: Pre-leukaemia

value: WT


title: tenocytes, ScxKO-3

description:
deseq.txt
counts.txt

tag: strain

value: Scx-

tag: 4ht treatment

value: Yes

value: Cultured Tail Tendon Fibroblasts


title: biott_1

tag: protocol


title: C-59

value: Bone marrow

value: Leukaemia

value: KLG-M


title: Neural stem cells, siRNA circHIPK2-1

city: Nanjing

first: guangtian

last: wang

address: Dingjiaqiao 87

department: Department of Pharmacology

institute: School of Medicine, Southeast University

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of mouse was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the UCSC (http://genome.ucsc.edu/) C57BL_6NJ mouse reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: neural stem cell

growth_protocol: Adult male C57BL/6J mice (24.0–26.0 g, 8–10 weeks old) were purchased from the Model Animal Research Center of Nanjing University (Nanjing, China) and randomly assigned to experimental groups. All animals were housed under a constant temperature and humidity and a 12-h light/12-h dark cycle, with the lights turned on at 7:00 AM. Food and water were available ad libitum.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012), and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq TM 6000 following the vendor's recommended protocol.

treatment_protocol: Embryonic NSCs from C57BL/6J mice were isolated from embryonic day 14 (E14) mouse hippocampus. Embryonic NSCs from the 3rd to 8th passages were used in this study. NSCs were transduced with circCon siRNA or circHIPK2 siRNA lentivirus.

value: hippocampus

value: neural stem cell

tag: transfection

value: siRNA circHIPK2


title: C-58

tag: tissue

value: KL


title: Neural stem cells, siRNA circHIPK2-2


title: lata

tag: agent

value: Latrunculin A

value: ES-Derived Pancreatic Progenitors

value: End of stage 4

value: Gel Bead Kit v2 (10X Genomics, 120237)


title: Neural stem cells, con-3

value: control


title: control


title: pol IV sRNA - replicate B

description:
total small RNA.
Replicate A  in GSE118705.

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
ShortStack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each genome-mapped small-RNA read.

extract_protocol:
Inflorescence small RNA was isolated with TRIzol reagent (Invitrogen) and concentrated using the mirVana microRNA Isolation Kit (Ambion).
For AGO1-IP samples, AGO1 was immunoprecipitated from inflorescence tissue using Agrisera anti-AGO1 primary antibody. RNA was isolated from AGO1-IP or mock-IP samples using TRIzol reagent.
Size-enriched small RNAs were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina).
Multiplexed libraries were sequenced on HiSeq2500 or HiSeq4000.

tag: ecotype background

value: Columbia

tag: genotype/variation

value: inflorescence (stage 1-12) immature flower buds

tag: molecule subtype

value: small RNA


title: Neural stem cells, con-2

tag: cell type


title: Neural stem cells, siRNA circHIPK2-3


title: Neural stem cells, con-1


title: AI.Treated.140B [reanalysis]

tag: Sex

value: female

tag: timepoint

value: baseline (B)

value: Negative

value: LumB

value: AI.Treated.140B [reanalysis]


title: pol IV mock-IP sRNA replicate B

description: IP small RNA

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
ShortStack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.

value: mock

tag: ecotype


title: C-42

value: Bone marrow

tag: tumour stage

value: Leukaemia

tag: genotype

value: KLG-M


title: C-43

value: KL


title: pol IV mock-IP sRNA replicate A

description: IP small RNA

tag: antibody


title: nocodazole

value: nocodazole

value: ES-Derived Pancreatic Progenitors

tag: Stage

tag: kit used


title: AI.Treated.8B [reanalysis]

value: Positive

tag: accession

tag: reanalysis

value: AI.Treated.8B [reanalysis]


title: pol IV AGO1-IP sRNA replicate B

description: IP small RNA

value: Agrisera anti-AGO1 primary antibody

value: Columbia


title: AI.Treated.170B [reanalysis]

value: AI.Treated.170B [reanalysis]


title: AI.Treated.24B [reanalysis]

value: female

value: AI.Treated.24B [reanalysis]


title: AI.Treated.165B [reanalysis]

value: baseline (B)

value: Negative

value: AI.Treated.165B [reanalysis]


title: C-40


title: AI.Treated.30B [reanalysis]

value: LumB

value: AI.Treated.30B [reanalysis]


title: C-41

value: Bone marrow

value: Leukaemia

value: KLG-E


title: pol IV AGO1-IP sRNA replicate A

description: IP small RNA

value: inflorescence (stage 1-12) immature flower buds


title: AI.Treated.3B [reanalysis]

value: AI.Treated.3B [reanalysis]


title: C-5

value: Pre-leukaemia

value: WT


title: C-4


title: 11-MT-Metastatic tumor

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

scan_protocol: GenePix 4000B array scanner, according to the manufacturer's protocol

data_processing: Gene-level analyses was performed. RMA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.5) Copyright ©

source_name: Solid pseudopapillary neoplasm (SPN) of pancreas

label_protocol: Genisphere FlashTag Biotin Labeling Assay according to the manufacturer's protocol

growth_protocol: tissue protocol: Formalin-fixed paraffin-embedded blocks of SPN specimens were obtained from the archives of the Institute of Pathology. Samples were reviewed, and ten micrometer thick sections were cut from the tumor block, and transferred on to glass slides. A single glass slide containing a block sample was stained with hematoxylin and eosin, and tumor margins were marked by the pathologist (EB). Microdissection was performed manually to extract tumoral tissue using a sharp scalpel.

extract_protocol: Total RNA was isolated using miRNeasy Formalin-fixed paraffin-embedded kit (Qiagen, Hilden, Germany), according to manufacturer’s instructions

tag: tissue type

value: MT-Metastatic tumor

tag: sample type

value: Formalin-fixed paraffin-embedded blocks (FFPE Blocks)


title: 12-LT-localized tumor

value: LT-localized tumor


title: wt Col mock-IP sRNA replicate B

description: IP small RNA

value: mock

value: wt Col

tag: tissue

value: Columbia


title: C-39

value: KLG-M


title: AI.Treated.136B [reanalysis]

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

value: female

value: baseline (B)

value: Negative

value: AI.Treated.136B [reanalysis]


title: AI.Treated.33B [reanalysis]

value: LumA

value: AI.Treated.33B [reanalysis]


title: wt Col mock-IP sRNA replicate A

description: IP small RNA

value: inflorescence (stage 1-12) immature flower buds


title: AI.Treated.181B [reanalysis]

value: Basal

value: AI.Treated.181B [reanalysis]


title: 9-Normal

source_name: normal

value: normal


title: 9-MT-Metastatic tumor

value: MT-Metastatic tumor


title: 5-LT-localized tumor

value: Formalin-fixed paraffin-embedded blocks (FFPE Blocks)


title: C-38

value: Bone marrow

value: Leukaemia

value: KLG-E


title: C-37


title: AI.Treated.155B [reanalysis]

value: LumB

value: AI.Treated.155B [reanalysis]


title: wt Col AGO1-IP sRNA replicate B

description: IP small RNA

value: Agrisera anti-AGO1 primary antibody

value: wt Col

value: Columbia


title: wt Col AGO1-IP sRNA replicate A

description: IP small RNA


title: C-36

value: Pre-leukaemia

value: G


title: rdr1/rdr2/rdr6 sRNA - replicate A

description: total small RNA


title: C-35


title: AI.Treated.103B

value: female

value: baseline (B)

value: Negative

value: Normal


title: 4-Normal

value: normal


title: dcl2/dcl3/dcl4 sRNA

description: total small RNA

value: inflorescence (stage 1-12) immature flower buds


title: 4-MT-Metastatic tumor

value: MT-Metastatic tumor

value: Formalin-fixed paraffin-embedded blocks (FFPE Blocks)


title: C-33

value: Bone marrow


title: 7-LT-localized tumor

value: LT-localized tumor


title: C-31


title: AI.Treated.39B [reanalysis]

value: LumA

value: AI.Treated.39B [reanalysis]


title: C-32


title: C-30

value: KL


title: 1-LT-localized tumor


title: C-3

value: KLG


title: C-34


title: C-29


title: AI.Treated.133B [reanalysis]

value: Basal

value: AI.Treated.133B [reanalysis]


title: 2-Normal


title: AI.Treated.109B [reanalysis]

value: AI.Treated.109B [reanalysis]


title: AI.Treated.122B [reanalysis]

value: female

value: LumB

value: AI.Treated.122B [reanalysis]


title: SJCRH30 prexasertib, biological rep2

city: Indianapolis

first: Ricardo

last: Martinez

state: IN

address: 307 E Merrill St

institute: Eli Lilly and Company

description: A pan-cancer transcriptome analysis to identify the molecular mechanism of prexasertib resistance

hyb_protocol: After fragmentation and labeling, DNA target was hybridized on Affymetrix Clariom™S Array, Human (ThermoFisher Scientific-Affymetrix) according to Covance Inc.'s standard protocol.

scan_protocol: CEL. intensity files were generated by GeneChip Command Console Software (AGCC, Thermo Fisher Scientific, Inc).

data_processing: Raw CEL files were imported, log2-transformed, and normalized using GC-content adjusted Signal Space Transformation-Robust Multi-array Average (GC-STT-RMA) algorithm. And final expression results were quantile-normalized for differential expression anlaysis.

source_name: Cell line derived from prexasertib-resistant SJCRH30 xenograft model

label_protocol: Affymetrix  GeneChip WT Plus Reagent Kit (Thermo Fisher Scientific, Inc) was used to generate biotinylated sense-stranded DNA targets according to Covance Inc.'s standard protocol.

extract_protocol: Total RNA was extracted using Direct-zol RNA kit (Zymo Research)according to the manufacturer's instructions.

treatment_protocol: The prexasertib resistant lines were generated through a long-term drug concentration escalation protocol.

value: pediatric alveolar rhabdomyosarcoma derived from metastatic site bone marrow

tag: cell line


title: 3-LT-localized tumor


title: SJCRH30 prexasertib, biological rep1


title: AI.Treated.12B [reanalysis]

extract_protocol: mRNA from baseline (B) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

value: baseline (B)

value: Positive

value: AI.Treated.12B [reanalysis]


title: AI.Treated.51B

value: Negative


title: SJCRH30 prexasertib, biological rep3


title: AI.Treated.99B


title: SJCRH30 parental, biological rep3

source_name: Cell line derived from parental, prexasertib sensitive SJCRH30 xenograft model


title: C-26

value: Bone marrow

value: Pre-leukaemia


title: C-27


title: G34 genotype replicate 3 - severe salt stress

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

data_processing:
Base calling, base quality and Phred score relationship performed with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality
In the absence of a reference genome clean reads have been assembled using Trinity software (K 25, Kmer coverage 2). Corset software was used for hierarchical clustering
Seven databases have been applied for gene functional annotation: Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG and GO.
CDS preduction using blast and EST-scan
De novo transcriptome filtered by Corset used as a reference for mapping reads back to transcriptome and quantify the expression level using RSEM.
DESeq used for gene expression difference analysis
Genome_build: FASTA assembled sequences
Supplementary_files_format_and_content: Sample_annotation.xls: annotation result of genes expressed in each sample; FASTA assembled sequences: FASTA file containing sequences of assembled reads;

organism: Arundo donax

source_name: Leaf

growth_protocol: Weekly irrigation with water

extract_protocol:
Total RNA extraction with SpectrumTM Plant Total RNA Extraction kit (Sigma – Aldrich, St. Louis, MO).
All samples passed through three steps before library construction: Nanodrop for preliminary quantitation, agarose gel electrophoresis to tests RNA degradation and potential contamination, Agilent 2100 to checks RNA integrity and quantitation. After the QC procedures, mRNA is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library was ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Libraries are fed into Illumina machines according standard Illumina protocol.

treatment_protocol: Water with no NaCl for CK samples, 250 mM NaCl for S3 samples, 420 mM NaCl for S4 samples

value: Leaf

tag: treatment

value: Sample weekly irrigated with water with 250 mM NaCl


title: AI.Treated.38B [reanalysis]

value: AI.Treated.38B [reanalysis]


title: C-25

value: KL


title: G34 genotype replicate 2 - severe salt stress


title: C-24

value: WT


title: G34 genotype replicate 1 - severe salt stress


title: NCI-H520 prexasertib resistant, biological rep3

source_name: Prexasertib-resistant NCI-H520 cell line with acquired resistance to prexasertib

value: squamous cell lung carcinoma


title: AI.Treated.13B [reanalysis]

source_name: breast tumour

value: AI.Treated.13B [reanalysis]


title: U87_siSETX [3'READS]

city: Bridgewater

first: Wencheng

state: NJ - New Jersey

institute: PTC Therapeutics

description: 3'READS protocol to profile polyA isoforms using sequencing

data_processing:
APA analysis of 3’ READS data was detailed in Di Giammartino et al 2014 (PMID: 25319826).
We first removed 5’ adapter sequences from reads and reads with length < 15 nt after this step were discarded.
We then mapped reads against the hg19 genome sequence using bowtie 2 (version 2.1.0) with the following setting: “--local -5 4”.
Reads with ≥ 2 unaligned Ts at the 5’ end are called poly(A) site supporting (PASS) reads, which were used to identify polyA sites. PolyA sites located within 24 nt from each other were clustered. The polyA site location with the highest read count in a cluster was used to represent the cluster.
PolyA sites mapped to the genome were further assigned to genes, using gene models defined by RefSeq, Ensembl and UCSC Known Gene databases. The 3’ ends of the gene models were extended by 4 kb to include downstream polyA sites. To reduce false polyA sites, we further required 1) the number of PASS reads for a polyA site was ≥ 5% of all PASS reads for the gene; and 2) detected in at least two samples. PolyA sites were separated into different types based on the gene model.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spread sheet "3READS_processed_data.xlsx". Tab "APA-list" contains information of pA isoform abundance and gene expression in siCtrl sample and their changes in siSETX sample (vs. siCtrl). Detailed description is in the "comment" tab of the file.

source_name: U87 cells

extract_protocol:
RNA was purified using the RNeasy kit (Qiagen) followed by on column DNAse treatment (Qiagen).
Total RNA was processed by the 3’ region extraction and deep sequencing (3’READS) method as described in Hoque et al 2013 (PMID: 23241633).

treatment_protocol: 20nM SETX siRNA or control siRNA was transfected in U87 cells with RNAimax (Invitrogen) for 72 hrs.

value: SETX siRNA


title: U87_siCtrl [3'READS]

value: control siRNA


title: C-23

source_name: Bone marrow


title: SJCRH30 parental, biological rep1


title: G34 genotype replicate 3 - no salt stress

value: Sample weekly irigated with water with no NaCl


title: AI.Treated.54B [reanalysis]

value: female

value: LumA

value: AI.Treated.54B [reanalysis]


title: C-22


title: C-21


title: AI.Treated.173B [reanalysis]

value: baseline (B)

value: AI.Treated.173B [reanalysis]


title: G34 genotype replicate 2 - no salt stress


title: Sox9eGFP Low  Chow RNA-seq Rep #4

description:
Sox9-EGFP Low sorted intestine crypt cells from chow diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC243

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9 and dm3 for mouse and fruit fly small RNA-seq, mm10 for mouse RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.

source_name: Intestine

extract_protocol: Clonetech SMARTer Ultra Low Input library preparation kit combined with Nextera XT DNA sample preparation kit

value: small intestine

tag: strain

tag: diet

value: Chow


title: SJCRH30 parental, biological rep2

value: pediatric alveolar rhabdomyosarcoma derived from metastatic site bone marrow


title: NCI-H520 prexasertib resistant, biological rep2


title: AI.Treated.174B [reanalysis]

tag: Sex

value: Negative

value: Basal

value: AI.Treated.174B [reanalysis]


title: NCI-H520 parental, biological rep3

source_name: Parental, prexasertib sensitive NCI-H520 cell line


title: NCI-H520 parental, biological rep2


title: NCI-H520 prexasertib resistant, biological rep1


title: Sox9eGFP Low  HFD RNA-seq Rep #3

description:
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC242

value: HFD


title: G34 genotype replicate 1 - no salt stress

value: Leaf


title: AI.Treated.56B [reanalysis]

tag: timepoint

value: LumB

value: AI.Treated.56B [reanalysis]


title: NCI-H520 parental, biological rep1

value: squamous cell lung carcinoma


title: C-20

value: Bone marrow

tag: cell type

value: Pre-leukaemia

value: WT


title: Sox9eGFP Low  Chow RNA-seq Rep #3

description:
Sox9-EGFP Low sorted intestine crypt cells from chow diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC241


title: C-2

tag: tumour stage

value: KLG


title: Rh41 prexasertib resistant, biological rep5

source_name: Prexasertib-resistant Rh41 cell line

value: pediatric alveolar rhabdomyosarcoma


title: Sox9eGFP Low  Chow RNA-seq Rep #2

description:
Sox9-EGFP Low sorted intestine crypt cells from chow diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC183


title: Sox9eGFP Low HFD RNA-seq Rep #4

description:
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC244


title: C-19

tag: genotype


title: Rh41 prexasertib resistant, biological rep4


title: NS544_HAT2KD_0h_H2AZ_Input_4

city: Planegg-Martinsried

first: T.

middle: Nicolai

last: Siegel

address: Großhaderner Str. 9

department: Department of Physiological Chemistry

country: Germany

institute: Ludwig-Maximilians-Universität

description:
CpB_ws1_ss1_denominator_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

data_processing:
Reads were mapped using Bowtie 2 local
BAM files were sorted and indexed using SAMtools version 1.8
The number of reads was normalised per billion mapped reads and coverage files were generated in the wiggle format using COVERnant version 0.3.0 with the subcommand ratio
Genome_build: HGAP3_Tb427v9; from Zenodo https://doi.org/10.5281/zenodo.823671
Supplementary_files_format_and_content: wiggle format containing coverage tracks

organism: Trypanosoma brucei brucei

source_name: T. brucei 2T1 bloodstream form

growth_protocol: Cells were grown in HMI-11 medium to a density of 0.9 mio cells per ml. For depletion of HAT1 or HAT2, cells were treated with 1 µg/ml Doxycylcin for 48 h.

extract_protocol:
In brief, 2 x 10e8 cells were harvested, crosslinked in 1% formaldehyde, lysed using 200 µM digitonin (final concentration) and chromatin was fragmented using 1 U/µl MNase (Sigma-Aldrich). see Wedel et al. 2017 #1 (DOI: 10.15252/embj.201695323) and Wedel et al. 2017 #2 (10.1016/j.exppara.2017.03.003 ) Immunoprecipitation was performed using Dynabeads M-280 sheep anti-rabbit IgG (Invitrogen) coupled to 10 µg polyclonal affinity-purified H2A.Z rabbit antibody. Bound material was washed and eluted, and cross-links were reversed at 65 °C for ~11 h in the presence of 300 mM NaCl (final concentration).
ChIP-seq libraries were constructed using 35 ng of immunoprecipitated or input DNA for sequencing on an Illumina platform. Following blunt-ending and poly(A)-tailing, Y-shaped adapters (Ford et al., 2014) containing the Illumina Truseq-Adapter-sequences are ligated to each end of a DNA molecule. The library concentrations were determined in duplicates using Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. Q32854) for Qubit 2.0 Fluorometer (Invitrogen, cat. no. Q32866). ChIP-seq libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems, cat. no. KK4824) according to the manufacturer’s instruction and sequenced in paired-end mode with 2 x 76 cycles using an Illumina NextSeq 500 platform.

tag: genotype/variation

tag: time

tag: chip antibody


title: C-17


title: NS545_HAT2KD_48h_H2AZ_Input_3

description:
CpB_ws1_ss1_denominator_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS543_HAT2KD_0h_H2AZ_Input_3

description:
CpB_ws1_ss1_denominator_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: C-18


title: Sox9eGFP Low HFD RNA-seq Rep #1

description:
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC181


title: Rh41 prexasertib resistant, biological rep3


title: NS546_HAT2KD_48h_H2AZ_Input_4

description:
CpB_ws1_ss1_denominator_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: C-15


title: NS541_HAT2KD_48h_H2AZ_ChIP_3

description:
CpB_ws1_ss1_numerator_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS545_HAT2KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS541_HAT2KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

value: polyclonal affinity-purified H2A.Z rabbit antibody (available from T. N. Siegel)


title: Rh41 prexasertib resistant, biological rep1