title: ESC-PGA3

status: Public on Feb 16 2019

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

institute: Radboud University Nijmegen, RIMLS

description: RNA-Seq

data_processing:
FASTQ files were mapped using GSNAP version 2012-07-20 (Wu and Nacu, 2010). To avoid bias in the mapping of either the B6- or the DBA2-derived reads, the alternative alleles of polymorphic sites between the B6 and DBA2 genome were included in the reference during mapping (GSNAP SNP-tolerant mapping; flag –v). Only sequence tags aligning to a single position in the genome were included for further analysis.
In light of the difference in sequencing length between the samples, we only used the first 35 bp of the forward read for RPKM quantification, data visualization and PCA/ clustering analysis (in case of paired-end reads, we only included the forward read if the distance between read pairs was <10kb to exclude aspecifically mapped reads but to include reads covering introns). To obtain RNA-seq gene expression values (RPKM), we converted the GSNAP output to Browser Extensible Data (BED) files which were used as input for Genomatix (ElDorado 08–2011) selecting RefSeq genes (NCBI m37 genome assembly; MM9). For viewing, profiles were normalized based on the total number of reads and converted to Wiggle (WIG) files.
ChIP-Seq enriched regions (“peaks”) were determined on tag-normalized BED files using MACS version 1.4.2 at p-value 10-6 for H3K4me3 (Zhang et al., 2008) or, for H3K27me3, using a minimum threshold of 24 overlapping tags, merging enriched regions within 1500bp. Peaksets of either H3K4me3 or H3K27me3 were merged for all samples and quantified using the tag-normalized BED files by determining the number of reads present within the enriched regions for each of the profiles. WIG files were generated for visualisation
Genome_build: mm9
Supplementary_files_format_and_content: Wig files can be directly uploaded to the UCSC genome browser.

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: Derivation and maintenance of B6D2F1 ESC and EpiSC lines is described in Kobolak et al. (2010) and Maruotti et al. (2010), respectively. B6D2F1 ESCs were cultured on mouse embryonic fibroblast (MEF) feeder cells in media containing fetal calf serum (FCS). B6D2F1 EpiSCs were maintained feeder-free in defined medium complemented with 20 ng/ml Activin A and 12 ng/ml fibroblast growth factor 2 (FGF2). In order to get rid of the MEFs for RNA-Seq or ChIP-Seq, ESCs were replated on 6cm feeder-free culture dishes and incubated at 37°C. After 30 min, floating ESCs were harvested, washed with 1XPBS and collected.

extract_protocol:
RNA was harvested (i) for the ESCs using the RNeasy Plus Mini Kit (QIAGEN) including gDNA eliminator treatment according to instructions of the manufacturer; and (ii) for the EpiSCs using Trizol (Invitrogen) according to the manufacturer’s recommendations. Total RNA (100 μg) was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN). mRNA (100–200 ng) was fragmented by hydrolysis (5× fragmentation buffer: 200mM Tris acetate, pH8.2, 500 mM potassium acetate and 150 mM magnesium acetate) at 94 °C for 90 s and purified (RNAeasy Minelute Kit; QIAGEN). cDNA was synthesized using 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). Double-stranded cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer’s recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN). ChIP-Seq was performed according to Marks et al. (2012). For RNA-Seq of ESCs and EpiSCs, cDNA was prepared for sequencing by end repair of 20 ng double-stranded cDNA as measured by Qubit (Invitrogen).
ChIP-Seq was performed according to Marks et al. (2012). For RNA-Seq of ESCs and EpiSCs, cDNA was prepared for sequencing by end repair of 20 ng double-stranded cDNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Quality control of the adaptor-containing DNA libraries was performed by quantitative PCR and by running the products on an Automated Electrophoresis System (Experion, BioRad). Cluster generation and sequencing was performed using the Illumina Genome Analyzer IIx, Hi-Seq 2000 or NextSeq 500 platforms according to standard Illumina protocols. Generation of FASTQ files and demultiplexing was performed using Illumina CASAVA. All sequencing analyses were conducted based on the M. musculus NCBI m37 genome assembly (MM9; assembly July 2007).

tag: cell type

value: ESCs

tag: strain background

tag: Sex


title: 3413-ARH-22

status: Public on Feb 18 2019

type: SRA

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

country: USA

institute: Vanderbilt University

library_source: transcriptomic

data_processing:
alignment with STAR v 2.5.1b, controlling for unannotated, non-canonical and rare junctions
read count generation during STAR alignment using –quantmode GeneCounts option that works like HTSeq-Count in default mode
Genome_build: GRCh38.84
Supplementary_files_format_and_content: txt files, raw read counts output from STAR alignment using option -–quantmode GeneCounts

molecule: polyA RNA

organism: Homo sapiens

source_name: pulmonary artery

extract_protocol:
RNA was extracted from mice kidneys with a Qiagen RNEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: PAH


title: EpiSC-NT2 (cumulus donor)

city: Nijmegen

department: Molecular Biology

country: Netherlands

description: RNA-Seq

organism: Mus musculus

source_name: EpiStem Cells (EpiSC)

value: EpiSCs

value: female


title: EpiSC-NT3 (cumulus donor)

description: RNA-Seq


title: ESC-PGA2

description: RNA-Seq


title: ESC-NT1 (MEF donor)

description: RNA-Seq

value: male


title: ESC-NT2 (cumulus donor)

description:
RNA-Seq
female largely X0

tag: sex chromosomes

value: largely X0


title: Copper supplementation 3

description: blood pooled from three individuals

data_processing:
alignment with STAR v 2.5.1b, controlling for unannotated, non-canonical and rare junctions
read count generation during STAR alignment using –quantmode GeneCounts option that works like HTSeq-Count in default mode
Genome_build: Bos taurus genome build UMD3.1
Supplementary_files_format_and_content: txt files, raw read counts output from STAR alignment using option -–quantmode GeneCounts

organism: Bos taurus

source_name: Blood

extract_protocol:
RNA was harvested using a Qiagen RNEasy kit with 1 ug of total RNA used for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for stranded libraries

tag: copper levels in blood (avg for 3 individuals)


title: ESC1

description: RNA-Seq


title: ESC-NT3 (cumulus donor)

description: RNA-Seq


title: ESC2

description: RNA-Seq


title: ESC-PGA1

description: RNA-Seq


title: 12: Nontargeting

city: Reno

first: William

middle: T

last: Gerthoffer

state: Nevada

address: 1440 N Virginia St

department: Pharmacology

institute: University of Nevada, Reno

data_processing:
Sequencing adapters were trimmed and bases identifified with Illumina Casava 1.9 base calling software
Sequencing reads were trimmed with Trimmomatic (leading, 3; trailing, 3; sliding window 4, 20; minlen, 30) on Globus Genomics cloud implementation of Galaxy NGS tools
Trimmed reads were mapped to the mouse mm10 reference genome with RNA STAR, Galaxy tool v 2.5, default options
Gene-level expression was measured using featureCounts (Galaxy tool v 1.4.5.p5), pe, unstranded
Differential expression was assessed with Deseq2 (Galaxy tool v2.1.39), parametric fit
Genome_build: mm10
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text file includes normalized counts calculated using Deseq2 to discover differentially expressed genes.

molecule: total RNA

source_name: Nontargeting oligo treated

extract_protocol:
Lung lobes stored in RNALater solution were weighed (~25-30 mgs) and minced into 2-3 mm pieces. Total RNA was extracted with QIAzol Lysis Reagent (Qiagen, 1023537) using Zirconia beads (Biospec,11079110ZX) and a Mini-Bead Beater16™.  Total RNA, including microRNA, was isolated using a Qiagen miRNEasy kit (#217004). Three methods were used to determine RNA concentration and RNA quality -  spectrophotometry of total RNA (NanoDrop 1000), gel filtration of RNA integrity (RNA 6000 Nano Kit, Agilent 2100 Bioanalyzer), and fluorescent dye binding (Quant-iT RiboGreen Kit, Invitrogen55).  RNA quality determined by A260/280 ranged from 1.8 to 2.2, A260/230 >2 and RIN values ranged from 6.9 to 8.6.
Initial RNA quantification was performed with a Qubit RNA assay kit, followed by RIN determination with an Agilent 2100 Bioanalyzer. cDNA libraries were prepared using 2 micrograms of RNA in TruSeq RNA sample preparation kits. Final quantification was performed with a Kapa Library Quant kit. Nonstranded cDNA libraries were sequenced using an Illunina HiSeq 2500 instrument (HiSeq v4 reagents) at read depth of 10M reads/sample for unsensitized and nontargeting and 15M reads for HDM and antimiR-145 treated samples.

tag: strain

value: BALB/c AnNHsd

tag: tissue

value: lung, left lobe

tag: age

value: 70 days


title: 15: Nontargeting


title: 14: Nontargeting


title: 11: Nontargeting


title: 6: AM145

source_name: AntimiR-145 treated


title: 7: AM145


title: 5: AM145


title: 3: AM145


title: 4: AM145


title: Rosa males

description: flash frozen kidney from 3 mice pooled

source_name: Kidney

tag: bmpr2 mutationtype

value: Rosa

tag: treatment

value: Control

tag: gender


title: 1: AM145


title: 2: AM145


title: 29: HDM

source_name: HDM sensitized


title: 27: HDM


title: 28: HDM


title: 30: HDM


title: 10: AM145


title: 23: HDM


title: 13: Nontargeting


title: 24: HDM


title: 8: AM145


title: 20: Unsensitized

source_name: Unsensitized


title: 21: HDM


title: 26: HDM


title: 25: HDM


title: 18:Unsensitized


title: 16: Unsensitized


title: 17: Unsensitized


title: 19: Unsensitized


title: ESC3_H3K27me3

description: ChIP-Seq H3K27me3

library_source: genomic

molecule: genomic DNA


title: ESC-NT4 (cumulus donor)_H3K4me3

description:
ChIP-Seq H3K4me3
female largely X0


title: ESC-PGA4_H3K4me3

description: ChIP-Seq H3K4me3


title: ESC-NT4 (cumulus donor)_H3K27me3

description:
ChIP-Seq H3K27me3
female largely X0


title: 22: HDM


title: EpiSC-PGA2

description: RNA-Seq


title: ESC-PGA4_H3K27me3

description: ChIP-Seq H3K27me3


title: EpiSC-PGA1

description: RNA-Seq


title: ESC3_H3K4me3

description: ChIP-Seq H3K4me3


title: EpiSC3

description: RNA-Seq


title: EpiSC1

description: RNA-Seq


title: EpiSC2

description: RNA-Seq


title: EpiSC-NT1 (cumulus donor)

description: RNA-Seq


title: 01-075-V5

status: Public on Feb 15 2019

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
reads were mapped to hg19 Refseq annotation using Bowtie 2 version 2.2.2 as part of Tophat 2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: PBMCs

extract_protocol:
PBMCs were isolated from fresh whole blood using Ficoll (Ficoll-Paque Plus, GE Healthcre) and total RNA was extracted from 10e7 PBMCs using TRIzol reagent (Life Technologies).  Messenger RNA was isolated with Oligotex mRNA mini kit (Qiagen)
Scriptseq RNA-seq library preparation kit (Epicentre) was used to generate the RNA-seq libraries according to the manufacturer's protocol.

tag: individual

value: patient 01-075

tag: disease state

value: Lyme disease

tag: time

value: 6 months following treatment completion (V5)

value: PBMC


title: 01-094-V5

value: patient 01-094


title: 01-009-V5

value: patient 01-009


title: 01-075-V2

value: 3 weeks later, immediately following completion of a standard course of antibiotics (V2)


title: 01-003-V5

value: patient 01-003


title: 01-009-V2


title: 01-017-V5

value: patient 01-017


title: 01-016-V5

value: patient 01-016


title: 01-004-V5

value: patient 01-004


title: 01-004-V2


title: 01-009-V1

value: acute Lyme pre-treatment (V1)


title: 01-004-V1


title: 01-003-V2


title: 01-003-V1


title: 01-094-V1


title: 9: AM145

value: BALB/c AnNHsd


title: 01-016-V2


title: 01-075-V1


title: 01-017-V1


title: tet1plusmb30

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
We used TopHat (version 2.0.9) to align reads to mouse genome (mm10) and Cufflinks (version 2.1.1) to get FPKMs and find differentially expressed genes with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: hippocampus

extract_protocol:
Whole hippocampi were removed, flash frozen on dry ice, and RNA was isolated using Trizol reagent (ThermoFisher). RNA libraries were prepared and sequenced using the Illumina HiSeq 2000 machine as per manufacturer’s protocols (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Electroconvulsive shock (ECS) was administered via alligator clamps applied bilaterally to the ears of the mouse using a stimulator (Digitimer) and waveform generator (Agilent Trueform 33500 series). The following optimized parameters were used to generate a tonic-clonic seizure: 100 Hz, 0.2-ms pulse width, 18 mA stimulation for 1.15 seconds. Seizures typically lasted less than 1 min and mice typically recovered in 30-90 seconds by self-righting. Hippocampi from Tet1Δe4-/- and Tet1+/+ mice (ECS) were harvested 1.5-2 hours after stimulation, a timeframe when activity-dependent genes are known to be upregulated.

tag: genotype/variation


title: tet1minusma4


title: tet1minusma3


title: tet1plusma11


title: tet1plusfa4


title: tet1minusma1


title: 01-017-V2


title: H7-sample.24h.2

status: Public on Feb 14 2019

city: Santa Ana

first: Camden

last: Jansen

state: California

address: 10631 Rockhurst Ave

institute: UCI

data_processing:
Library strategy: ATAC-seq
Single-cell libraries were mapped with Bowtie to the mm10 reference genome using the following parameters (bowtie -S -p 2 --trim3 10 -X 2000). Duplicate fragments were removed using Picard (http://picard.sourceforge.net) as previously performed (Buenrostro, 2015). We considered single-cell libraries that recovered > 5k fragments after mapping and duplication removal. Bulk ATAC-seq replicates were mapped to the mm10 reference genome using the following parameters (bowtie -S --trim3 10 -p 32 -m 3 -k 1 -v 2 --best -X 2000). Peak calling was performed on bulk replicates using HOMER with the following parameters (findPeaks <tags> -o <output> -localSize 50000 -size 150 -minDist 50 –fragLength 0). The intersection of peaks in three biological replicates was performed. A consolidated list of peaks was generated from the union of peaks from 0 and 24 hour time-points. Fragment counts for single-cell and bulk samples were estimated from the consolidated peak and compiled into a single experimental data matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Scaled RPM matrix for single-cells was generated and used in our main analysis.

source_name: mouse B3 cell

growth_protocol: ERt2-Ikaros inducible B3 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% FBS

extract_protocol:
Single-cell ATAC-seq was performed using the Fluidigm C1 system as previously shown in (Buenrostro, 2015). Briefly, cells were collected for each time-point at a concentration of 500 cells/μl in a total of 30-50 μl. Additionally, 3 biological replicates of ~50,000 cells were collected for each measured time-point to generate bulk ATAC-seq measurements. Bulk ATAC-seq was performed as previously described (Buenrostro, 2014). Our C1 single-cell capture efficiency was ~70-80% for our pre-B system. Each individual C1 capture site was visually inspected to ensure single-cell capture.
In brief, amplified transposed DNA was collected from all captured single-cells and dual-indexing library preparation was performed. After PCR amplification of single-cell libraries, all subsequent libraries were pooled and purified using a single MinElute PCR purification (Qiagen). The pooled library was run on a Bioanalyzer and normalized using Kappa library quantification kit prior to sequencing.
A single pooled library was sequenced as 40bp paired-end dual indexed reads using the high-output (75 cycle) kit on the NextSeq 500 from Illumina. Two C1 runs were performed for 0 and 24-hour single-cell ATAC-seq experiments.

treatment_protocol: Briefly, cells were induced with 20mM of 4-hydroxytamoxifen (4OHT), over the course of 24 hours. Prior to performing single-cell experiments, cells were washed twice with cold 1X PBS. An additional dose of 4OHT was administered at ~12h for collection of 24 hour samples.

tag: time-point (hours)

tag: single-cell data

value: yes

tag: pooled data

value: no

tag: fluidigm c1 experiment


title: H8-sample.24h.2


title: H4-sample.24h.2


title: 01-016-V1

tag: cell type


title: H11-sample.24h.2


title: H10-sample.24h.2


title: H3-sample.24h.2


title: G7-sample.24h.2


title: G8-sample.24h.2


title: G4-sample.24h.2


title: G3-sample.24h.2


title: H2-sample.24h.2


title: G9-sample.24h.2


title: G2-sample.24h.2


title: G12-sample.24h.2


title: F9-sample.24h.2


title: G5-sample.24h.2


title: G10-sample.24h.2


title: G6-sample.24h.2


title: F7-sample.24h.2


title: G1-sample.24h.2


title: F8-sample.24h.2


title: F6-sample.24h.2


title: F4-sample.24h.2


title: F5-sample.24h.2


title: F2-sample.24h.2


title: F10-sample.24h.2


title: F1-sample.24h.2


title: H1-sample.24h.2


title: E9-sample.24h.2


title: E6-sample.24h.2


title: E3-sample.24h.2


title: E2-sample.24h.2


title: D3-sample.24h.2


title: D8-sample.24h.2


title: E12-sample.24h.2


title: E1-sample.24h.2


title: D12-sample.24h.2


title: D1-sample.24h.2


title: C3-sample.24h.2


title: D10-sample.24h.2


title: C6-sample.24h.2


title: C7-sample.24h.2


title: D11-sample.24h.2


title: C9-sample.24h.2


title: C5-sample.24h.2


title: C4-sample.24h.2


title: C10-sample.24h.2


title: C11-sample.24h.2


title: C12-sample.24h.2


title: E4-sample.24h.2


title: B9-sample.24h.2


title: B8-sample.24h.2


title: B6-sample.24h.2


title: B5-sample.24h.2


title: B2-sample.24h.2


title: E10-sample.24h.2


title: B1-sample.24h.2


title: C8-sample.24h.2


title: D6-sample.24h.2


title: D2-sample.24h.2


title: A9-sample.24h.2


title: A8-sample.24h.2


title: B12-sample.24h.2


title: B11-sample.24h.2


title: A6-sample.24h.2


title: C2-sample.24h.2


title: A5-sample.24h.2


title: A2-sample.24h.2


title: 50k-24h-R3-sample.24h.2


title: A12-sample.24h.2


title: C1-sample.24h.2


title: 50k-24h-R1-sample.24h.2


title: A3-sample.24h.2


title: H9-24h-sample


title: H5-24h-sample


title: H3-24h-sample


title: H1-24h-sample


title: H4-24h-sample


title: G8-24h-sample


title: H2-24h-sample


title: H12-24h-sample


title: B10-sample.24h.2


title: H10-24h-sample


title: G6-24h-sample


title: G5-24h-sample


title: G2-24h-sample


title: G4-24h-sample


title: A7-sample.24h.2


title: 50k-24h-R2-sample.24h.2


title: G1-24h-sample


title: F8-24h-sample


title: G12-24h-sample


title: F6-24h-sample


title: F2-24h-sample


title: F5-24h-sample


title: H8-24h-sample


title: F3-24h-sample


title: F4-24h-sample


title: F12-24h-sample


title: E7-24h-sample


title: E8-24h-sample


title: E6-24h-sample


title: E5-24h-sample


title: E4-24h-sample


title: E9-24h-sample


title: G11-24h-sample


title: D9-24h-sample


title: D4-24h-sample


title: E11-24h-sample


title: E10-24h-sample


title: D7-24h-sample


title: E1-24h-sample


title: D2-24h-sample


title: D12-24h-sample


title: E12-24h-sample


title: D5-24h-sample


title: E2-24h-sample


title: F1-24h-sample


title: D3-24h-sample


title: C8-24h-sample


title: D11-24h-sample


title: C9-24h-sample


title: F10-24h-sample


title: C4-24h-sample


title: C5-24h-sample


title: C7-24h-sample


title: C3-24h-sample


title: C6-24h-sample


title: C2-24h-sample


title: B7-24h-sample


title: C12-24h-sample


title: C10-24h-sample


title: B6-24h-sample


title: B4-24h-sample


title: B3-24h-sample


title: A9-24h-sample


title: B2-24h-sample


title: A5-24h-sample


title: B11-24h-sample


title: B1-24h-sample


title: A2-24h-sample


title: A7-24h-sample


title: B10-24h-sample


title: A10-24h-sample


title: A1-24h-sample


title: A6-24h-sample


title: A8-24h-sample


title: A3-24h-sample


title: H8-sample.0h.2


title: H1-sample.0h.2


title: H11-sample.0h.2


title: C1-24h-sample


title: H3-sample.0h.2


title: H4-sample.0h.2


title: G9-sample.0h.2


title: G3-sample.0h.2


title: G8-sample.0h.2


title: G2-sample.0h.2


title: G12-sample.0h.2


title: G11-sample.0h.2


title: A4-24h-sample


title: G10-sample.0h.2


title: F9-sample.0h.2


title: A12-24h-sample


title: H9-sample.0h.2


title: H12-sample.0h.2


title: F8-sample.0h.2


title: E12-sample.0h.2


title: F2-sample.0h.2


title: E7-sample.0h.2


title: F10-sample.0h.2


title: F1-sample.0h.2


title: E11-sample.0h.2


title: E10-sample.0h.2


title: D9-sample.0h.2


title: E2-sample.0h.2


title: D6-sample.0h.2


title: D8-sample.0h.2


title: E5-sample.0h.2


title: D4-sample.0h.2


title: F7-sample.0h.2


title: D5-sample.0h.2


title: F3-sample.0h.2


title: C7-sample.0h.2


title: G6-sample.0h.2


title: D11-sample.0h.2


title: D10-sample.0h.2


title: C12-sample.0h.2


title: C5-sample.0h.2


title: C1-sample.0h.2


title: C11-sample.0h.2


title: C3-sample.0h.2


title: C4-sample.0h.2


title: C9-sample.0h.2


title: C10-sample.0h.2


title: B7-sample.0h.2


title: B6-sample.0h.2


title: B4-sample.0h.2


title: B2-sample.0h.2


title: B10-sample.0h.2


title: B11-sample.0h.2


title: D1-sample.0h.2


title: B1-sample.0h.2


title: A5-sample.0h.2


title: B12-sample.0h.2


title: A8-sample.0h.2


title: A6-sample.0h.2


title: A12-sample.0h.2


title: A1-sample.0h.2


title: A4-sample.0h.2


title: H8-0h-sample.0h


title: F4-sample.0h.2


title: H7-0h-sample.0h


title: H5-0h-sample.0h


title: H2-0h-sample.0h


title: H4-0h-sample.0h


title: G5-0h-sample.0h


title: G4-0h-sample.0h


title: H1-0h-sample.0h


title: G3-0h-sample.0h


title: G6-0h-sample.0h


title: B9-sample.0h.2


title: B3-sample.0h.2


title: A9-sample.0h.2


title: F6-0h-sample.0h


title: F5-0h-sample.0h


title: F3-0h-sample.0h


title: F7-0h-sample.0h


title: F9-0h-sample.0h


title: F1-0h-sample.0h


title: D7-0h-sample.0h


title: E10-0h-sample.0h


title: E11-0h-sample.0h


title: D6-0h-sample.0h


title: E3-0h-sample.0h


title: D1-0h-sample.0h


title: D8-0h-sample.0h


title: E2-0h-sample.0h


title: D10-0h-sample.0h


title: C9-0h-sample.0h


title: G2-0h-sample.0h


title: C7-0h-sample.0h


title: C4-0h-sample.0h


title: C8-0h-sample.0h


title: E4-0h-sample.0h


title: F11-0h-sample.0h


title: B9-0h-sample.0h


title: B3-0h-sample.0h


title: B8-0h-sample.0h


title: C1-0h-sample.0h


title: B5-0h-sample.0h


title: B2-0h-sample.0h


title: B4-0h-sample.0h


title: A4-0h-sample.0h


title: A5-0h-sample.0h


title: B10-0h-sample.0h


title: C10-0h-sample.0h


title: A3-0h-sample.0h


title: A6-0h-sample.0h


title: A1-0h-sample.0h


title: A2-0h-sample.0h


title: 50k-Rep1-0h-sample.0h


title: H9-24h.2

data_processing:
Single-cell RNA-seq libraries were mapped with Tophat (Trapnell et al., 2009) to the mouse Ensembl gene annotations and mm10 reference genome. Single-cell libraries with a mapping rate less than 50% and less than 450,000 mapped reads were excluded from any downstream analysis, for all subsequent analysis. Cufflinks (Trapnell et al., 2010) version 2.2.1 was used to quantify expression from single-cell libraries using Cuffquant. Gene expression measurements for each single-cell library were merged and normalized into a single data matrix using Cuffnorm.
Genome_build: mm10
Log-transformed FPKMs are available for cells (124) and time-points (0h and 24h) that were used in the development of an integrative computational analysis using self organizing maps (SOMs).

source_name: mouse B3 cells

extract_protocol:
Single cells were isolated using the Fluidigm C1 System. Single cell C1 runs were completed using the smallest IFC (5-10 um) based on the estimated size of B3 cells. Briefly, cells were collected for 0,2,6,12,18 and 24 hour time-points at a concentration of 400 cells/μl in a total of 50 μl. To optimize cell capture rates on the C1, buoyancy estimates were optimized prior to each run. Each individual C1 capture site was visually inspected to ensure single-cell capture and cell viability. After visualization, the IFC was loaded with Clontech SMARTer kit lysis, RT, and PCR amplification reagents.
cDNA was normalized across all libraries from 0.1-0.3 ng/μl and libraries were constructed using Illumina’s Nextera XT library prep kit per Fluidigm’s protocol. Constructed libraries were multiplexed and purified using AMPure beads. The final multiplexed single-cell library was analyzed on an Agilent 2100 Bioanalyzer for fragment distribution and quantified using Kapa Biosystem’s universal library quantification kit.
The library was normalized to 2 nM and sequenced as 75bp paired-end dual indexed reads using Illumina’s NextSeq 500 system at a depth of ~1.0-2.0 million reads per library.

value: mouse B3 cells


title: H11-24h.2


title: H10-24h.2


title: H8-24h.2


title: B12-0h-sample.0h


title: H6-24h.2


title: H7-24h.2


title: H5-24h.2


title: H2-24h.2


title: H1-24h.2


title: H3-24h.2


title: G10-24h.2


title: G11-24h.2


title: G6-24h.2


title: G7-24h.2


title: 50k-Rep2-0h-sample.0h


title: G12-24h.2


title: G2-24h.2


title: G5-24h.2


title: G4-24h.2


title: F10-24h.2


title: G1-24h.2


title: F12-24h.2


title: F11-24h.2


title: 50k-Rep3-0h-sample.0h


title: F9-24h.2


title: F6-24h.2


title: F7-24h.2


title: F4-24h.2


title: F1-24h.2


title: F2-24h.2


title: E11-24h.2


title: E8-24h.2


title: E10-24h.2


title: G8-24h.2


title: E9-24h.2


title: E6-24h.2


title: E5-24h.2


title: E4-24h.2


title: E3-24h.2


title: E1-24h.2


title: E2-24h.2


title: D7-24h.2


title: D9-24h.2


title: D5-24h.2


title: D11-24h.2


title: C12-24h.2


title: C8-24h.2


title: D4-24h.2


title: C9-24h.2


title: C6-24h.2


title: D3-24h.2


title: C1-24h.2


title: C2-24h.2


title: C4-24h.2


title: C7-24h.2


title: C3-24h.2


title: B11-24h.2


title: B10-24h.2


title: B5-24h.2


title: B9-24h.2


title: B3-24h.2


title: E7-24h.2


title: B7-24h.2


title: A10-24h.2


title: A9-24h.2


title: B1-24h.2


title: B4-24h.2


title: D10-24h.2


title: A12-24h.2


title: A7-24h.2


title: A2-24h.2


title: H12-24h


title: A6-24h.2


title: A5-24h.2


title: H11-24h


title: H9-24h


title: A1-24h.2


title: H3-24h


title: H8-24h


title: H6-24h


title: G10-24h


title: H2-24h


title: G11-24h


title: H1-24h


title: H4-24h


title: G6-24h


title: G7-24h


title: G9-24h


title: G8-24h


title: G4-24h


title: G5-24h


title: G2-24h


title: G1-24h


title: F6-24h


title: F12-24h


title: F5-24h


title: F4-24h


title: F2-24h


title: F3-24h


title: F1-24h


title: B8-24h.2


title: E11-24h


title: E8-24h


title: E7-24h


title: E10-24h


title: E9-24h


title: E5-24h


title: E6-24h


title: E4-24h


title: E1-24h


title: D12-24h


title: F9-24h


title: D10-24h


title: D11-24h


title: D9-24h


title: D6-24h


title: D5-24h


title: D4-24h


title: E12-24h


title: C12-24h


title: D3-24h


title: D1-24h


title: C6-24h


title: C9-24h


title: C5-24h


title: D2-24h


title: E3-24h


title: C1-24h


title: C2-24h


title: E2-24h


title: B9-24h


title: B8-24h


title: D8-24h


title: B5-24h


title: B7-24h


title: B2-24h


title: A10-24h


title: A9-24h


title: B1-24h


title: A8-24h


title: A6-24h


title: C8-24h


title: A5-24h


title: A1-24h


title: H12-18h.2


title: B10-24h


title: B6-24h


title: H11-18h.2


title: H7-18h.2


title: H9-18h.2


title: H4-18h.2


title: H10-18h.2


title: H8-18h.2


title: H3-18h.2


title: H6-18h.2


title: B3-24h


title: H1-18h.2


title: B4-24h


title: A12-24h


title: C3-24h


title: G11-18h.2


title: G7-18h.2


title: G8-18h.2


title: A7-24h


title: G3-18h.2


title: G5-18h.2


title: G6-18h.2


title: G2-18h.2


title: G1-18h.2


title: F12-18h.2


title: F11-18h.2


title: F10-18h.2


title: F8-18h.2


title: F9-18h.2


title: H2-18h.2


title: F6-18h.2


title: F2-18h.2


title: F4-18h.2


title: F1-18h.2


title: G9-18h.2


title: E12-18h.2


title: E6-18h.2


title: E5-18h.2


title: E7-18h.2


title: E11-18h.2


title: D11-18h.2


title: E4-18h.2


title: E2-18h.2


title: E1-18h.2


title: D8-18h.2


title: D6-18h.2


title: D7-18h.2


title: D1-18h.2


title: D2-18h.2


title: D4-18h.2


title: D10-18h.2


title: C11-18h.2


title: C10-18h.2


title: C9-18h.2


title: C7-18h.2


title: B11-18h.2


title: B9-18h.2


title: C2-18h.2


title: C1-18h.2


title: B12-18h.2


title: B8-18h.2


title: C4-18h.2


title: B3-18h.2


title: B4-18h.2


title: B5-18h.2


title: B1-18h.2


title: B6-18h.2


title: A11-18h.2


title: A12-18h.2


title: A9-18h.2


title: A10-18h.2


title: C12-18h.2


title: A3-18h.2


title: A6-18h.2


title: C6-18h.2


title: H8-18h


title: H10-18h


title: C8-18h.2


title: H7-18h


title: A5-18h.2


title: B7-18h.2


title: H6-18h


title: B2-18h.2


title: E10-18h.2


title: G11-18h


title: G5-18h


title: G12-18h


title: G6-18h


title: A8-18h.2


title: G8-18h


title: H3-18h


title: G3-18h


title: G10-18h


title: G7-18h


title: G9-18h


title: G4-18h


title: F9-18h


title: F12-18h


title: G2-18h


title: F11-18h


title: G1-18h


title: F4-18h


title: F7-18h


title: F5-18h


title: F6-18h


title: F3-18h


title: E10-18h


title: E9-18h


title: H4-18h


title: E12-18h


title: E8-18h


title: E7-18h


title: E6-18h


title: E1-18h


title: E3-18h


title: D12-18h


title: D10-18h


title: D5-18h


title: D11-18h


title: E4-18h


title: D1-18h


title: D8-18h


title: D6-18h


title: C11-18h


title: C10-18h


title: D3-18h


title: C9-18h


title: C7-18h


title: C8-18h


title: C2-18h


title: C5-18h


title: C3-18h


title: C1-18h


title: B9-18h


title: B10-18h


title: B6-18h


title: B5-18h


title: B4-18h


title: B3-18h


title: B2-18h


title: B8-18h


title: A10-18h


title: A9-18h


title: D4-18h


title: A8-18h


title: A4-18h


title: H9-12h


title: A11-18h


title: H8-12h


title: A1-18h


title: H2-12h


title: A3-18h


title: H7-12h


title: H11-12h


title: G3-12h


title: H3-12h


title: G8-12h


title: G6-12h


title: G11-12h


title: H1-12h


title: F12-12h


title: G2-12h


title: A2-18h


title: F9-12h


title: F6-12h


title: F4-12h


title: F1-12h


title: F5-12h


title: E12-12h


title: F2-12h


title: H6-12h


title: E11-12h


title: E6-12h


title: E5-12h


title: E7-12h


title: E3-12h


title: E1-12h


title: D12-12h


title: F7-12h


title: F3-12h


title: D9-12h


title: D4-12h


title: D10-12h


title: C11-12h


title: D7-12h


title: C6-12h


title: D1-12h


title: D5-12h


title: C4-12h


title: D11-12h


title: C12-12h


title: D8-12h


title: B8-12h


title: C7-12h


title: D2-12h


title: C2-12h


title: A12-12h


title: C1-12h


title: B6-12h


title: B12-12h


title: B10-12h


title: B7-12h


title: A11-12h


title: A8-12h


title: B9-12h


title: B5-12h


title: A7-12h


title: B4-12h


title: A5-12h


title: H11-6h


title: H10-6h


title: B3-12h


title: B1-12h


title: H7-6h


title: A1-12h


title: A4-12h


title: H12-6h


title: G10-6h


title: H4-6h


title: G8-6h


title: G7-6h


title: G3-6h


title: A10-12h


title: F10-6h


title: F12-6h


title: G12-6h


title: H2-6h


title: G9-6h


title: F5-6h


title: F2-6h


title: F4-6h


title: F3-6h


title: F1-6h


title: E9-6h


title: E11-6h


title: G6-6h


title: H8-6h


title: E8-6h


title: E6-6h


title: E5-6h


title: E4-6h


title: H9-6h


title: E3-6h


title: E2-6h


title: D12-6h


title: E1-6h


title: F9-6h


title: H1-6h


title: D9-6h


title: D11-6h


title: D6-6h


title: D1-6h


title: D5-6h


title: C12-6h


title: D7-6h


title: D3-6h


title: C9-6h


title: C3-6h


title: C4-6h


title: B12-6h


title: B7-6h


title: B5-6h


title: F8-6h


title: C8-6h


title: C7-6h


title: C10-6h


title: B9-6h


title: C1-6h


title: B11-6h


title: A10-6h


title: A9-6h


title: B1-6h


title: A8-6h


title: B3-6h


title: H12-2h


title: A6-6h


title: H9-2h


title: A2-6h


title: H10-2h


title: A1-6h


title: H11-2h


title: H7-2h


title: C2-6h


title: H5-2h


title: B4-6h


title: G12-2h


title: G6-2h


title: G5-2h


title: G4-2h


title: G8-2h


title: G10-2h


title: G9-2h


title: G2-2h


title: F5-2h


title: H6-2h


title: G1-2h


title: F11-2h


title: F3-2h


title: G3-2h


title: F9-2h


title: E7-2h


title: E6-2h


title: F8-2h


title: F7-2h


title: F2-2h


title: F1-2h


title: F10-2h


title: H4-2h


title: E11-2h


title: E10-2h


title: H1-2h


title: E12-2h


title: D4-2h


title: D2-2h


title: E8-2h


title: E5-2h


title: E3-2h


title: C3-2h


title: D11-2h


title: D12-2h


title: E2-2h


title: D9-2h


title: B6-2h


title: D8-2h


title: D3-2h


title: D1-2h


title: C9-2h


title: C11-2h


title: E4-2h


title: A5-2h


title: B9-2h


title: C4-2h


title: B5-2h


title: H5-0h


title: H4-0h


title: B2-2h


title: F4-2h


title: H1-0h


title: A4-2h


title: A1-2h


title: A11-2h


title: H10-0h


title: A2-2h


title: G11-0h


title: D7-2h


title: C5-2h


title: H9-0h


title: H8-0h


title: C2-2h


title: H3-0h


title: H6-0h


title: G10-0h


title: G8-0h


title: C1-2h


title: G4-0h


title: G5-0h


title: G7-0h


title: H2-0h


title: G12-0h


title: G9-0h


title: G6-0h


title: H7-0h


title: F10-0h


title: F9-0h


title: G2-0h


title: F6-0h


title: F12-0h


title: G1-0h


title: F1-0h


title: F4-0h


title: G3-0h


title: F3-0h


title: F5-0h


title: F2-0h


title: F7-0h


title: E9-0h


title: E12-0h


title: E6-0h


title: E4-0h


title: D6-0h


title: E10-0h


title: F11-0h


title: E2-0h


title: E3-0h


title: C9-0h


title: D1-0h


title: D11-0h


title: D8-0h


title: D3-0h


title: C7-0h


title: D10-0h


title: D5-0h


title: D2-0h


title: C11-0h


title: C4-0h


title: E7-0h


title: C6-0h


title: E1-0h


title: B11-0h


title: B10-0h


title: C1-0h


title: C2-0h


title: B9-0h


title: B1-0h


title: A12-0h


title: B2-0h


title: F8-0h


title: B7-0h


title: A6-0h


title: B5-0h


title: A5-0h


title: C10-0h


title: C3-0h


title: A11-0h


title: A10-0h


title: A7-0h


title: BEZ-235 & SAHA 3

city: Ghent

first: Shana

last: Claeys

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics Ghent

data_processing:
Illumina FASTQ software was used for basecalling.
Sequencing reads were aligned to the Hg38 genome using STAR (Dobin et al, Bioinformatics, 2013).
Count values were calculated using RSEM (Li et al, BCM Bioinformatics, 2011).
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text file include counts for each sample

source_name: neuroblastoma

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum, 1% glutamin, 1% kanamycin, 1% penicilin/streptomycin and HEPES (25mM).

extract_protocol:
Total RNA was harvested with the miRNeasy micro kit (Qiagen) with Dnase treatment on-column.
Library prep was performed with the TruSeq Stranded mRNA Library Prep Kit LT (Illumina), following manufacturer’s instructions. To assess the quality of the library, BioAnalyzer (Agilent) was used and concentrations were checked by performing qPCR with the Kapa Library Quantification Kit (Kapa Biosystems).

treatment_protocol: NB-1 cells were treated with sterile DMSO, 0.5 μM BEZ-235, 0.5 μM SAHA or the combination for 48h. This was performed for 3 biological replicates.

tag: cell line

value: 0.5 μM BEZ + 0.5 μM SAHA


title: BEZ-235 & SAHA 2


title: BEZ-235 2

value: 0.5 μM BEZ + 0 μM SAHA


title: B3-0h


title: A8-0h


title: D12-0h


title: A9-0h


title: DMSO 2

value: 0 μM BEZ + 0 μM SAHA


title: BEZ-235 & SAHA 1


title: SAHA 3

value: 0 μM BEZ + 0.5 μM SAHA


title: SAHA 2


title: BEZ-235 3


title: DMSO 3


title: SAHA 1


title: B4-0h


title: rPmt1KoVOE_rep1 [RNA-seq]

status: Public on Feb 13 2019

city: Berlin

first: Ann

middle: E.

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

description:
processed data file:
combinedRNAseqCounts.txt

data_processing:
After quality and adapter trimming (AGATCGGAAGAGCACACGTCT), reads were aligned to fission yeast tRNA (CCA-appended sequences from gtrnadb.ucsc.edu and www.pombase.org), rRNA (www.arb-silva.de, www.pombase.org) and mitochondrial tRNA and rRNA sequences (www.arb-silva.de, www.pombase.org) using Bowtie allowing 2 mismatches, discarding any mapped reads from further analysis.
The remaining reads were aligned with Bowtie against cDNA sequences from www.pombase.org, allowing 2 mismatches and using 23nt as seed region.
Reads of length 26-29 nt whose 5' end map from 15 nt downstream of the CDS start of a gene and 3' end map from 5 nt upstream of the CDS stop were assigned to that gene.
Codon occupancy was calculated as the codon proportions in the A-site (read start +15-16nt) divided by averaged codon proportions in the 3 codon sites up and dowstream of the ribosome.
For RNA-seq, processing was done similarly except that reads were kept at any mapping position and if read length was at least 25 nt.
Genome_build: ASM294v2
Supplementary_files_format_and_content: tab-delimited text files containing codon occupancy, footprint counts assigned to each CDS for all samples, and RNA-seq read counts assigned to each mRNA for all samples.

organism: Schizosaccharomyces pombe

source_name: AEP100_AEP8 + REP4X-pmt1

growth_protocol: Strains AEP1 and AEP8 were grown in full medium (YES) with 0.03 µM queuine, where indicated. Strains AEP99 and AEP100 were grown in minimal medium (EMM). Cultures were inoculated at an OD600 of 0.2 and grown to an optical density of 1.0.

extract_protocol:
Ribosome footprinting was performed essentially as described (Duncan and Mata, 2014; Ingolia et al., 2011). S. pombe cultures were grown at 30°C to an OD600 of 1.0, 150 µg/ml cycloheximide was added to the medium and cells were incubated for further 15 min at 30°C. Cells were harvested and flash-frozen immediately in liquid nitrogen. 15 OD of each sample was lysed by adding 100 µl lysis buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 200µg/ml cycloheximide, 1% triton, protease inhibitor) and 1 g chilled glass beads (0.5 mm diameter). Samples were homogenized using a FastPrep-24 (MP Biomedicals) at level 6 for 13 seconds and subsequently diluted with 400 µl lysis buffer. Two centrifugation steps (1: 5 min, 4°C, 16000xg; 2: 15 min, 4°C, 16000xg) removed glass beads and cellular debris, respectively. For footprint isolation, 400 µl of the supernatants were digested with 4 U DNase I (ThermoScientific) and 800 U of RNase I (Ambion), for 45 minutes at room temperature with gentle shaking. 800 U of RNasin ribonuclease inhibitor (Promega) was added to quench the reaction. The samples were run on a 17.5 - 50% sucrose gradient to isolate monosomes. Footprint monosome RNAs were end-repaired with T4 polynucleotide kinase (TaKaRa), and size selected (28-31 nucleotides) on a 15% polyacrylamide Tris-borate-EDTA-urea gel. Total RNA was extracted from 100 µl lysate using TRIzol (Invitrogen) according to the manufacturers instructions.
Small RNA-seq: Small RNA libraries were constructed according to the protocol using NEB NEXT Small RNA library Prep Set for Illumina (Multiplex Compatible) E7330, and size-selected (120-170 base pairs) before sequencing. RNAseq: After quantification of total RNA and quality assessment on an Advanced Analytical Fragment Analyzer using the DNF-472 High Sensitivity RNA Analysis Kit (all Advanced Analytical Tech. Inc; Ankeny Iowa, U.S.A.), the mRNA was isolated from high quality total RNA extracts by using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490). Illumina-compatible RNA-libraries were constructed by using the NEBNext Ultra RNALibrary Prep Kit for Illumina (E7530) as well as the NEBNext Multiplex Oligos for Illumina (E7335) following the distributors instruction manuals. Multiplexed RNA libraries were mixed in equilibrium according to their Qubit (Life Technologies) measurements, fragment distribution profiles on the Advanced Anayltical Fragment Analyzer and quantification of library 5'-and 3'- ends by Real Time PCR. For each library, 30 Mio clusters were sequenced in a 1x 75 base mode on a Illumina NextSeq500 instrument according to the manufacturer’s protocol and using the NextSeq 500/550 High Output Sequencing Kit v2 (75 cycles) (Product Code: FC-404-2005).

value: AEP8 + REP4X-pmt1

tag: growth medium

value: EMM


title: rPmt1KoV_rep2 [RNA-seq]

source_name: AEP99_AEP8 + REP4X

tag: strain

value: AEP8 + REP4X


title: rPmt1KoVOE_rep3 [RNA-seq]


title: rPmt1Ko_rep2 [RNA-seq]

value: pmt1 knockout

value: YES


title: rPmt1Ko_rep3 [RNA-seq]


title: rwtq_rep2 [RNA-seq]

value: wt

value: YES + 0.03 µM queuine


title: rPmt1Koq_rep1 [RNA-seq]


title: rPmt1KoV_rep1 [RNA-seq]


title: rwtq_rep1 [RNA-seq]


title: rPmt1Koq_rep2 [RNA-seq]


title: rPmt1KoV_rep3 [RNA-seq]


title: C5-0h

tag: tissue


title: BEZ-235 1


title: rPmt1Ko_rep1 [RNA-seq]


title: rwtq_rep3 [RNA-seq]


title: ASC + Ishikawa cells Rep2

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

description:
processed data file:
ishi_gene_exp.txt

data_processing:
Raw fastq is mapped to human genome by TopHat using default parameters
Cufflinks produces assembled transfrags for each replicate
Cuffmerge merges the assembly files
CuffDiff is used to detect differentially expressed genes between each two of cell population
R package CummeRbund is used to to generate the expression plots
Genome_build: HG19
Supplementary_files_format_and_content: em_gene_exp.txt is the list of all differentially expressed genes of ASC + endometrial cells vs Control - endometrial cells. ishi_gene_exp.txt is the list of all differentially expressed genes of ASC+Ishikawa cells vs Control-Ishikawa cells.

source_name: Ishikawa cancer cells_cultured_with_ASC

growth_protocol: Routine cell media for endometrial epithelial cells and adipose stromal cells used, respectively. ASCs were seeded on a matrigel-layered insert of a Boyden chamber during co-culture.

extract_protocol:
RNA extracted using Rneasy Plus kit (Life Technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adipose stromal cells (ASCs) with catalog number AG17929  were obtained from the Coriell Institute (Camden, NJ) . The cells were obtained from fat tissue during subject's abdomen and waist ante-mortem elective cosmetic tumescent liposuction. ASCs were seeded on a matrigel-layered insert of a Boyden chamber. In the bottom well, endometrial cells were seeded for co-culture experiment. Control wells contained the matrigel-layered insert without ASCs. Co-cultures were carried out for three weeks, followed by lysis of endometrial cells for RNA isolation.

value: Ishikawa

value: Established endometrial cancer cell line


title: ASC + Ishikawa cells Rep1

description:
processed data file:
ishi_gene_exp.txt


title: rwt_rep3 [RNA-seq]


title: rwt_rep1 [RNA-seq]


title: rwt_rep2 [RNA-seq]


title: A1-0h


title: DMSO 1


title: Control -Ishikawa cells Rep2

description:
processed data file:
ishi_gene_exp.txt

source_name: Ishikawa cancer cells_control


title: ASC + endometrial cells Rep1

description:
processed data file:
em_gene_exp.txt

value: immortalized endometrial epithelial cell line


title: rPmt1Koq_rep3 [RNA-seq]


title: rPmt1KoVOE_rep2 [RNA-seq]


title: INS-1 S487D 1

city: Shenzhen

first: Bowen

last: Xing

state: Guangdong

address: Nanhai Street 3688

country: China

institute: Shenzhen University

data_processing:
base-calling：bcl2fastq(v2.17)
data filtrting step1：cutadapt（v1.8.1）
data filtrting step2：remove N bases(our program)
data filtrting step3：FASTQ quality filter：fastq_quality_filter（v0.0.13）
alignment genome:tophat(v2.0.13)
quantify gene count:gfold(V1.1.2)
Genome_build: NCBI rn6(GCF_000001895.5_Rnor_6.0)
Supplementary_files_format_and_content: abundance measurements

organism: Rattus norvegicus

source_name: INS-1 S487D

growth_protocol: INS-1 cells overexpressing menin S487A or S487D mutant were established by transduction with pMX-puro-Flag-Menin derived retroviruses, and cultured in RPMI1640 medium supplemented with 10% FBS, 10 mM HEPES buffer, 2 mM glutamine, 1 mM sodium pyruvate, 50 μM beta-mercaptoethanol and 1% Pen/Strep

extract_protocol:
RNA was harvested using Trizol reagent.The purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RINe above 7.0. mRNAs were isolated from Total RNA and fragmented to approximately 200bp. Subsequently, the collected mRNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of TruSeq® RNA LT/HT Sample Prep Kit (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rat insulinoma cells; Insulin secreting beta cell derived line

tag: passages

value: overexpressing menin S487D mutant


title: adipocyte_KD_rep3

city: New York

first: Chenyi

last: Xue

institute: Columbia University

data_processing:
Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) read was uniquely mapped, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp
Differential expression was tested by Cuffdiff with options "-u ". Annotation included mRNAs from RefSeq and stringent set of lincRNAs from Cabili et al. 2011.
Genome_build: hg19
Supplementary_files_format_and_content: DIFF files were obtained from Cuffdiff output.
Supplementary_files_format_and_content: adipocyte_ctrl_shR.diff  contains differential expression result for control v.s. linc-AQPEP KD. Annotation included mRNAs from RefSeq and stringent set of lincRNAs from Cabili et al. 2011. sample_1 = control, sample_2 = KD

source_name: adipocyte

growth_protocol: Primary human adipose stromal cells (ASCs) were extracted from freshly isolated subcutaneous adipose tissue and expanded in DMEM/F-12 medium supplemented with 10% fetal bovine serum and human EGF and FGF. For adipocyte differentiation, confluent ASC (passage 5-10) were incubated in differentiation media containing insulin (1.7 μM), dexamethasone (250 nM), isobutylmethylxanthine (500 μM), PPARγ agonist GW347845 (2 μM), panthothenate (4 mg/L) and biotin (8 mg/L). After 7 days, cells were incubated with medium supplemented with insulin (1.7 μM), dexamethasone (250 nM), panthothenate (4 mg/L) and biotin (8 mg/L) for additional 7 days.

extract_protocol:
RNA samples were extracted using Trizol  (Invitrogen) according to the manufacturer's instructions. Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA)
With a minimum of 1 µg input RNA, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the TruSeq Stranded RNA Library Prep Kit (Illumina, San Diego, CA). Fragments of ~350 bp were selected by gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using Illumina’s HiSeq 2000.

treatment_protocol: ASC-adipocytes were transduced on day 8 post adipogenic induction with either control shRNA or linc-ADAL shRNA in a 6-well plate scale.

value: adipose

tag: shRNA treatment

value: linc-ADAL KD


title: INS-1 S487D 3


title: INS-1 S487D 2


title: INS-1 S487A 1

source_name: INS-1 S487A

value: overexpressing menin S487A mutant


title: INS-1 S487A 2


title: Control -Ishikawa cells Rep1

description:
processed data file:
ishi_gene_exp.txt


title: Stage 1 sample 1 from Jersey cattle

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

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 Capra hircus  whole genome using bowtie v2 with default parameters
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: Assembly: UMD3.1 (GCA_000003055.3) – Cow
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Stage

source_name: milk epithelial cells

growth_protocol: Milk epithelial cells were extracted from milk

extract_protocol:
RNA was extracted by TriZol method. RNA was quantified by spectrophotometer (ThermoFisher, USA) and the quality and integrity was assessed by Bioanalyzer (Agilent, USA). The RIN values ranged from 6.5 -9.3.
Library construction by Illumina Truseq stranded mRNA sample preparation kit.

treatment_protocol: Cells were stored at -80°C

tag: stage of lactation

value: 1st stage (March)

tag: lactation number

value: 2nd time lactating

value: milk epithelial cells

tag: breed

value: Jersey cattle


title: Stage 2 sample 2 from Jersey cattle

value: 2nd stage (July)

value: 3rd time lactating


title: Stage 2 sample 1 from Jersey cattle


title: Stage 1 sample 2 from Jersey cattle


title: ASC + endometrial cells Rep2

description:
processed data file:
em_gene_exp.txt


title: 4M M5 AD

city: Tallahassee

first: Joseph

middle: Ligon

last: Bundy

state: FL

address: 1115 W Call St

department: Department of Biomedical Sciences

institute: Florida State University

data_processing:
Sequences from Illumina adapters were trimmed using Trimmomatic (version 0.32) using the TruSeq3-SE.fa adapter sequence file provided with the program. A minimum length of 50 bases (MINLEN:50) was chosen as a cutoff for each read and 2 seed mismatches were allowed. All reads between 50 and 100 bases were included in further analyses.
The trimmed sequencing reads were aligned to the mouse genome (genome release GRCm38) using Tophat (2.0.13, --read-mismatches and --read-edit-dist set to 3). A General Transfer Format (GTF) file was used with Tophat (--GTF option) for the purpose of gene annotation (Mus_musculus.GRCm38.68.gtf).
Following mapping reads were futher processed (filtered, sorted and indexed) with Samtools and only reads that mapped to a single gene were used for further analysis.
The uniquely mapped reads were used to generate counts for each annotated gene using easyRNASeq (from Bioconductor version 3.0.2, geneModels summarization)
Differential expression analysis of count tables for female and male mice of various ages was performed using the default settings of DESeq2 (1.8.1, Benjamini-Hochberg FDR correction).
Cufflinks (2.1.1, --no-effective-length-correction, --max-bundle-length 10000000 --GTF Mus_musculus.GRCm38.68.gtf) was used to generate FPKM (fragments per kilobase per million reads) normalized values.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Microsoft Excel Worksheet (.xlsx). Contains unnormalized counts generated by easyRNASeq and normalized FPKM values generated by Cufflinks. The raw counts were used by DESeq2 for differential expression analysis.
Supplementary_files_format_and_content: Supplemental_file_1_genelists.xlsx: Multi-tab Excel file containing summary statistics from various pairwise comparisons of gene expression performed by DESeq2.
Supplementary_files_format_and_content: Supplemental_file_2_QPCR_validation.xlsx: Multi-tab Excel file containing a report of a qRTPCR experiment performed on a subset of these samples for validation purposes.

source_name: Hippocampus

growth_protocol: 2 month old Male 5XFAD mice and female C57BL/6J mice were ordered from The Jackson Laboratory (Bar Harbor, ME). Hemizygous male transgenics and female WT animals were crossed yielding both transgenic and wild-type animals. Animals were group housed and kept on a 12 hour light-dark cycle. Food and water were provided ad libitum.

extract_protocol:
The hippocampus (from both sides of the brain) was dissected and rapidly frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted from the entire hippocampus from each animal using TRI Reagent (Sigma-Aldrich) according to manufacturer’s directions.
RNA from the dissected hippocampal tissue was extracted using a miRNeasy minikit (Qiagen, catalog #217004) with MaXtract high density columns (Qiagen, catalog #129056). A set of synthetic RNA standards were then added to 5 μg of RNA from each sample as spike-ins to assess the performance of each library (ERCC ExFold RNA Spike-In Mixes Ambion, catalog #4456739). mRNA was purified with a NEBNext mRNA magnetic isolation module (NEB, catalog #E7490L).  cDNA libraries were generated from 50 ng of isolated mRNA using a NEBnext Ultra mRNA library preparation kit for Illumina sequencers (NEB, catalog #E7530L), and a unique 6-nucleotide index was incorporated to each library (NEB, catalog #E7335S, E7500S). The concentration of each cDNA library was estimated with qPCR using Illumina sequencing primers (KAPA Biosystems catalog # KK4835), and average fragment length was determined with a bioanalzyer high sensitivity DNA chip (Agilent Technologies, catalog #5076-4626).  12nM of each cDNA library was pooled into one of three cDNA library pools. Each of the three cDNA pools underwent additional quality control analysis via bioanalyzer and KAPA-PCR. 10pM of each cDNA library pool was sequenced on an Illumina HiSeq 2500

tag: Sex

value: Male

tag: age

value: 4 Month

value: Hippocampus


title: Control -endometrial cells Rep1

description:
processed data file:
em_gene_exp.txt


title: Control -endometrial cells Rep2

description:
processed data file:
em_gene_exp.txt


title: 4M M1 AD


title: 4M F3 AD

value: Female


title: adipocyte_KD_rep2


title: adipocyte_control_rep3

value: control


title: adipocyte_KD_rep1


title: D9-0h

value: mouse B3 cells


title: adipocyte_control_rep1


title: adipocyte_control_rep2


title: 2M M5 AD

value: 2 Month


title: Stage 3 sample 3 from Jersey cattle

value: 3rd stage (December)


title: 2M M4 AD


title: C8-0h


title: 4M M2 AD


title: Stage 3 sample 2 from Jersey cattle


title: 4M F1 AD


title: 4M M4 AD


title: 4M F2 AD


title: 1M M4 AD

value: 1 Month


title: 4M F5 AD


title: 1M M1 AD


title: 1M F5 AD


title: 1M F1 AD


title: Stage 1 sample 3 from Jersey cattle


title: 2M M3 AD


title: 2M M1 AD


title: 2M F5 AD


title: 2M M2 AD


title: fPmt1KoV_rep3 [small RNA-seq]

description:
processed data file:
CodonOccupancy.txt
combinedFootprintCounts.txt

tag: genotype/variation

value: AEP8 + REP4X

value: EMM


title: fPmt1KoV_rep1 [small RNA-seq]


title: 2M F4 AD


title: 2M F2 AD


title: 2M F1 AD


title: fPmt1Koq_rep2 [small RNA-seq]

value: pmt1 knockout

value: YES + 0.03 µM queuine


title: 1M M5 AD


title: fPmt1Ko_rep3 [small RNA-seq]

value: YES


title: INS-1 S487A 3

value: Rat insulinoma cells; Insulin secreting beta cell derived line

value: overexpressing menin S487A mutant


title: fPmt1Ko_rep2 [small RNA-seq]


title: fwtq_rep1 [small RNA-seq]

value: wt


title: 4M F4 AD


title: 4M M3 AD

value: Male


title: 1M M2 AD


title: 1M M3 AD


title: 1M F4 AD


title: 2M F3 AD


title: Stage 3 sample 1 from Jersey cattle

value: 2nd time lactating

value: milk epithelial cells

value: Jersey cattle


title: 1M F3 AD

value: Female

value: Hippocampus


title: 1M F2 AD


title: fPmt1KoVOE_rep3 [small RNA-seq]

value: AEP8 + REP4X-pmt1


title: fwt_rep3 [small RNA-seq]


title: fPmt1KoVOE_rep2 [small RNA-seq]


title: fPmt1KoVOE_rep1 [small RNA-seq]


title: Stage 3 sample 3 from Kashmiri cattle

organism: Bos indicus

value: 3rd stage (December)

value: Kashmiri cattle


title: fPmt1Koq_rep3 [small RNA-seq]


title: fPmt1KoV_rep2 [small RNA-seq]

value: AEP8 + REP4X


title: fPmt1Ko_rep1 [small RNA-seq]


title: fwtq_rep3 [small RNA-seq]


title: fwtq_rep2 [small RNA-seq]


title: BCR-ABL STAT5 rep1

status: Public on Feb 12 2019

city: Kyoto

first: Hideyo

last: Hirai

state: Kyoto

address: 54 Kawahara-cho, Sakyo-ku

country: Japan

institute: Kyoto University Hospital

data_processing:
Base calls were performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 (ver2.1.0).
Peak call was performed using MACS2 ( ver2.1.0), and the significant enriched regions were determined using whole cell lysate as input (FDR = 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files represent the peak calls generated using MACS2

source_name: hepatopoietic stem cells

growth_protocol: EML cells were maintained in Iscove Modified Dulbecco’s Medium (IMDM) (Gibco) supplemented with 20 % heat-inactivated horse serum (Gibco) and 10% BHK-MKL conditioned medium as a source of SCF.

extract_protocol:
EML cells were fixed with fixation buffer (11.1% formaldehyde in culture medium) followed by adding 1.5 M Glycine for neutralization. Fixed cells were lysed with buffer containing sodium dodecyl sulfate and sonicated using Bioruptor (Cosmo Bio, Tokyo, Japan). The sheared chromatin samples were subjected to immunoprecipitation using protein G magnet beads (Dynabeads Protein G, Thermo Fisher Scientific) Antibodies used for ChIP were as follows; normal rabbit IgG (sc-2027X, Santa Cruz Biotechnology), anti-STAT5 (sc-835X, Santa Cruz Biotechnology), anti-STAT5a antibody (sc-1081X, Santa Cruz Biotechnology), normal mouse IgG (sc-2025, Santa Cruz Biotechnology), anti-STAT1 antibody (sc-592X, Santa Cruz Biotechnology), anti-H3K27Ac antibody (308-34843, Wako). Immunoprecipitated chromatins were purified using PCR Purification Kit (Qiagen).
Purified immunoprecipitated chromatins were subjected to a library preparation for next-generation sequencing using TruSeq ChIP Sample Prep Kit (illumina, San Diego, CA, USA), according to the manufacturer’s instruction.

treatment_protocol: EML cells were retrovirally transduced with GFP alone  (MIG)  or BCR-ABL and GFP (BCR-ABL), then GFP positive cells were purified using FACSAria cell sorter.

value: hepatopoietic stem cells

tag: condition

value: retrovirally transduced with BCR-ABL and GFP (BCR-ABL)

tag: chip antibody

value: anti-STAT5 (sc-835X, Santa Cruz Biotechnology, lot# A0915)


title: fwt_rep2 [small RNA-seq]

value: YES


title: fwt_rep1 [small RNA-seq]


title: fPmt1Koq_rep1 [small RNA-seq]

value: pmt1 knockout

value: YES + 0.03 µM queuine


title: Stage 2 sample 3 from Kashmiri cattle

value: 2nd stage (July)


title: Stage 2 sample 1 from Kashmiri cattle


title: Stage 1 sample 3 from Kashmiri cattle

value: 1st stage (March)

value: 3rd time lactating


title: RKM-012-09

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina Casava1.8.2 software used for basecalling and demultiplexing.
Reads were mapped to hg19 genome assembly with the STAR (v2.4.0f1) aligner args: --outFilterMultimapNmax 1 --outFilterType BySJout --outSJfilterReads Unique --sjdbGTFfile refGene.gtf --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Per sample annotated transcript models were quantitated with Cufflinks (v2.1.1) args: -G refGene.gtf
Sample transcript models were merged with Cuffmerge (v2.1.1)
FPKM (Fragments per kilobase of exon per million reads mapped) abundance estimates and differential expression was caluclated with Cuffdiff (v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows).

source_name: Left ventricle (heart)

extract_protocol:
Hearts were removed, left ventricle isolated and preserved in RNALater, then frozen at -80C. Tissue was homogenized with beads in Qiazol and RNA isolated using RNAeasy Mini kit.
Libraries were prepared using the Illumina TruSeq mRNA protocol. Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

treatment_protocol: RNALater

tag: surgery

value: Sham

value: Male


title: RKM-012-07


title: RKM-012-10


title: Stage 1 sample 1 from Kashmiri cattle

value: milk epithelial cells


title: Stage 3 sample 1 from Kashmiri cattle


title: RKM-012-06


title: BCR-ABL STAT5 rep2


title: RKM-012-03

value: CKD


title: Stage 2 sample 2 from Kashmiri cattle

value: 2nd time lactating


title: Stage 3 sample 2 from Kashmiri cattle

value: 3rd stage (December)


title: MIG STAT5 rep2

value: retrovirally transduced with GFP alone  (MIG)


title: RKM-012-01


title: MIG STAT5 rep1


title: RKM-012-08


title: BCR-ABL whole cell lysate


title: HFOB 2

city: Aurora

first: Malgorzata

last: Skaznik-Wikiel

state: Colorado

address: 12700 East 19th Avenue

department: Obstetrics and Gynecology

institute: University of Colorado School of Medicine

data_processing:
Base calling was conducted using the asecalling software RTA version 2.7.3
Adaptor trimming and trimming based on read quality (sliding window function with a quality cutoff of 20 and minimum length of 50 bp) was performed with Trimmomatic (Galaxy version 0.32.3).
Sample reads were aligned to the mm10 reference genome with TopHat (Galaxy version 2.1.0)
Cufflinks (Galaxy version 2.2.1.0) was used to assemble transcripts and Cuffmerge (Galaxy version 0.0.6) was used to merge transcripts into a final transcript assembly.
Cuffdiff (Galaxy version 2.2.1.3) was used to assess differentially expressed genes between the groups.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files with the FPKM values for each group.

source_name: Ovary

extract_protocol:
Ovaries were removed and flash frozen in liquid nitrogen, RNA was extracted with Qiagens Rneasy mini kit (#74104) following manufacture protocols.
Libraries were prepared with Illumina TruSEQ mRNA stranded library construction kit. Barcode sequences are as follows, sample 1 - ACAGTG, sample 2 - GCCAAT, sample 3 - CTTGTA, sample 4 - GTGAAA, sample 5 - CGATGT, sample 6 - TGACCA, sample 7 - CAGATC, sample 8 - CCGTCC, sample 9 - ATGTCA

treatment_protocol: HFLN and HFOB mice were fed a 60% fat diet for 10 weeks, control were fed a 16% fat standard chow.

value: 15 weeks

value: Ovary

tag: diet

value: 60% HFD

tag: sample group

value: obese after HFD


title: RKM-012-04


title: RKM-012-02


title: MIG whole cell lysate

tag: cell type

value: hepatopoietic stem cells


title: RKM-012-05


title: HFOB 3


title: HFLN 1

value: lean after HFD


title: Control 3

value: standard chow

value: control


title: Control 1


title: Control 2


title: Stage 1 sample 2 from Kashmiri cattle

value: 1st stage (March)

value: Kashmiri cattle


title: HFOB 1


title: Dina_rep2(RNAseq)

status: Public on Feb 11 2019

first: Scott

last: Hiebert

address: Vanderbilt University, 2220 pierce Avenue, 512 PRB

department: Biochemistry

data_processing:
Base calling, filtering and demultiplexing was done by Illumina CASAVA 1.8.2 with default settings
Raw reads were trimmed to remove adapters and low quality reads using Trimmomatic (version0.32) with parameters IllUMINACLIP:adapter.txt:2:30:7TRAILING:15
Reverse complement of trimmed reads were generated using fastx_reverse_complement (version 0.0.13) with default settings.
For resequenced samples, the sequencing reads from DMSO_1hr and THZ1_1hr were pooled from both the runs and merged them for the dowstream PROseq analysis
The reverse complement sequences were then aligned to human genome hg19 using bowtie2 (version 2.2.4) with default settings.
RNSeq raw reads were aligned to hg19 using TopHat (version 2.0.10) with default settings
Genome_build: hg19
Supplementary_files_format_and_content: For PROseq genome coverage was normalized and calculated for each strand separately and reported in bedGraph format. For RNAseq a DIFF file with gene expression information is reported containing gene names, chromosomal coordinates, log2 transformed values of fold change along with test statistic.

source_name: t(8;21)-containing acute myeloid leukemia cell line

growth_protocol: RPMI 1640 supplimented with 10% Fetal Plex and 2mM L-Glutamine

extract_protocol:
Nuclei were isolated by dounce homogenization of treated cells in isotonic buffer containing 0.1% triton-X 100. Nuclear run-on assay was performed with ATP,UTP,GTP and biotin-11-CTP. Nuclei were lyzed in Trizol and nuclear RNA was extracted and fragmented and biotinylated RNA was purified with streptavidin magnetic beads, followed by 3' adapter ligation, 5' repair and adapter ligation, RT and PCR amplification.
PROseq

tag: cell line

value: Kasumi-1 cells

tag: treatment

value: 25nM Dina-1hr


title: PHA_rep2(RNAseq)

value: 5uM PHA-1hr


title: PHA_rep1(RNAseq)


title: Dina_rep1(RNAseq)


title: HFLN 2

tag: strain

tag: tissue


title: DMSO_rep1(RNAseq)


title: Palbo_rep2(RNAseq)

value: 5uM Palbo-1hr


title: PHA_rep1(PROseq)


title: THZ1_rep2(RNAseq)

value: 400nM THZ1-1hr


title: FVP_rep2(RNAseq)

value: 400nM FVP-1hr


title: THZ1_rep2(PROseq)


title: THZ1_rep1(RNAseq)


title: Dina_rep1(PROseq)


title: THZ1_rep1(PROseq)


title: FVP_rep1(RNAseq)


title: DMSO_rep1(PROseq)


title: DMSO_rep2(RNAseq)


title: PHA_rep2(PROseq)


title: Palbo_rep1(RNAseq)


title: HFLN 3


title: Dina_rep2(PROseq)


title: siNT-Hypoxia 72h rep 3

city: Woolloongabba

first: Iman

last: Azimi

state: Queensland

address: 20 Cornwall St

country: Australia

institute: The University of Queensland

data_processing:
Sequencing: NextSeq 500, NextSeq Control Software v1.3.0.23, RTA v2.1.3
Mapping software: STAR v2.3.0e_r291
Gene counts: HTSeq-0.6.1
Genome_build: UCSC hg19
Supplementary_files_format_and_content: gene counts: per-gene counts generated using htseq_count

source_name: siNT-Hypoxia 72h

growth_protocol: The MDA-MB-468 cell line was obtained from The Brisbane Breast Bank, UQCCR, Brisbane, QLD, Australia and maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with high glucose (Sigma-Aldrich, St Louise, MO, USA), supplemented with 4 mM L-glutamine 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was isolated and purified using an RNeasy Plus Mini Kit (74134; Qiagen). mRNA integrity was assessed on a Agilent 2100 Bioanalyzer, and were of high quality (RNA integrity numbers [RIN] of 8.7-9.2).
TruSEQ Stranded Total RNA

treatment_protocol: Cells were seeded at 6000 (for 48 h hypoxia) and 3500 (for 72 h hypoxia) per well in 96-well plates. Post seeding (24 h), cells were transfected with siRNA for 48 h. DharmaFECT4 Transfection Reagent (0.1 µL per well) and Dharmacon ON-TARGETplus SMARTpool siRNAs (Thermo Scientific, Waltham, MA, USA) were used for silencing ORAI3 (L-015896-00). Non-targeting siRNA (siNT; D-001810-10) was used as control treatment. Cells were then serum starved (0.5% FBS) for 24 h and exposed to hypoxic conditions (1% O2) for 48 h or 72 h.

value: basal-like breast cancer cells

tag: transfected with

value: Non-targeting siRNA (siNT)

tag: exposed to

value: hypoxic conditions (1% O2) for 72hrs


title: Palbo_rep1(PROseq)

city: Nashville


title: FVP_rep2(PROseq)


title: Palbo_rep2(PROseq)


title: FVP_rep1(PROseq)


title: siORAI3-Hypoxia 72h rep 2

source_name: siORAI3-Hypoxia 72h

value: siRNAs silencing ORAI3 (siORAI3)


title: siNT-Hypoxia 72h rep 2


title: siORAI3-Hypoxia 72h rep 3


title: siNT-Hypoxia 72h rep 1


title: siORAI3-Hypoxia 48h rep 3

source_name: siORAI3-Hypoxia 48h

value: hypoxic conditions (1% O2) for 48hrs


title: SMD32316PL4_8G

city: Oxford

first: Alba

last: Rodriguez-Meira

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
RNA-Seq:Short reads (76-bp) were trimmed for Nextera adaptors and aligned to the human genome using STAR
RNA-Seq: primary alignments mapping to a set of RefSeq annotated transcripts were quantified using FeatureCounts
RNA-Seq: Expression values were quantified as read per kilobase of transcript length per million mapped reads (RPKM)
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: RPKM values

source_name: Bone Marrow

extract_protocol:
cDNA libraries were synthetized from single cells using TARGET-seq method
Illumina sequencing libraries were prepared using the Illumina Nextera XT DNA kit, using one forth of the standard volume recommended by Illumina
Samples were sequenced on Illumina NextSeq Instrument

treatment_protocol: HSPC (defined as Lineage-CD34+ cells) were isolated by Fluorescent Activated Cell Sorting from patients or normal donors

tag: method

value: TARGET-seq

tag: donor

tag: timepoint

value: baseline

value: patient

tag: diagnosis

value: MDS/MPN overlap

tag: batch

tag: plate

tag: lineage

tag: mutation


title: siNT-Hypoxia 48h rep 3

source_name: siNT-Hypoxia 48h


title: SMD32316PL4_8D


title: siORAI3-Hypoxia 72h rep 1


title: siORAI3-Hypoxia 48h rep 1


title: siNT-Hypoxia 48h rep 2


title: SMD32316PL4_9F


title: DMSO_rep2(PROseq)

institute: Vanderbilt University


title: siNT-Hypoxia 48h rep 1


title: SMD32316PL4_8B


title: SMD32316PL4_5G

source_name: Peripheral Blood

value: ET


title: SMD32316PL4_9E


title: SMD32316PL4_5E


title: SMD32316PL4_5F


title: SMD32316PL4_5C


title: SMD32316PL4_4G


title: SMD32316PL4_4B


title: SMD32316PL4_4F


title: siORAI3-Hypoxia 48h rep 2


title: SMD32316PL4_5D


title: SMD32316PL4_3E

value: MF


title: SMD32316PL4_4D


title: SMD32316PL4_12G


title: SMD32316PL4_4E


title: SMD32316PL4_3D


title: SMD32316PL4_9D


title: SMD32316PL4_3C


title: SMD32316PL4_12E


title: SMD32316PL4_12D


title: SMD32316PL4_12B


title: SMD32316PL4_11F


title: SMD32316PL4_11G


title: SMD32316PL4_3F


title: SMD32316PL4_10G


title: SMD32316PL4_10F


title: SMD32316PL4_10B


title: SMD32316PL4_11C


title: SMD32316PL3_5G


title: SMD32316PL4_10D


title: SMD32316PL4_11B


title: SMD32316PL4_10C


title: SMD32316PL3_5C


title: SMD32316PL4_3B


title: SMD32316PL3_5B


title: SMD32316PL3_5D


title: SMD32316PL3_4G


title: SMD32316PL4_12F


title: SMD32316PL3_3G


title: SMD32316PL3_3F


title: SMD32316PL3_4E


title: SMD32316PL3_4C


title: SMD32316PL3_3E


title: SMD32316PL3_4F


title: SMD32316PL3_2G


title: SMD32316PL4_10E


title: SMD32316PL4_11E


title: SMD32316PL3_2F


title: SMD32316PL3_3B


title: SMD32316PL3_2C


title: SMD32316PL3_1F


title: SMD32316PL3_2E


title: SMD32316PL3_1D


title: SMD32316PL3_1E


title: SMD32316PL3_2B


title: SMD32316PL3_2D


title: SMD32316PL3_3D


title: SMD32316PL1_5F


title: SMD32316PL3_1C


title: SMD32316PL1_5E


title: SMD32316PL1_5C


title: SMD32316PL3_1B


title: SMD32316PL3_3C


title: SMD32316PL1_4C


title: SMD32316PL3_4B


title: SMD32316PL1_4D


title: SMD32316PL1_3E


title: SMD32316PL1_2F


title: SMD32316PL1_2D


title: SMD32316PL1_2C


title: SMD32316PL1_4E


title: OX2123PL7_8G

value: normal

value: NORMAL DONOR

value: WT


title: SMD32316PL1_3C


title: OX2123PL7_8B


title: OX2123PL7_8C


title: OX2123PL7_8A


title: OX2123PL7_7F


title: OX2123PL7_8H


title: OX2123PL7_7C


title: OX2123PL7_6F


title: OX2123PL7_7B


title: OX2123PL7_7A


title: OX2123PL7_6G


title: OX2123PL7_6H


title: OX2123PL7_6E


title: OX2123PL7_7G


title: SMD32316PL1_2E


title: OX2123PL7_6C


title: OX2123PL7_8E


title: OX2123PL7_6D


title: OX2123PL6_9G


title: OX2123PL7_6A


title: OX2123PL7_6B


title: OX2123PL6_9F


title: OX2123PL6_9H


title: OX2123PL6_9C


title: OX2123PL7_7H


title: OX2123PL6_8H


title: OX2123PL6_9A


title: SMD32316PL3_1G


title: OX2123PL6_9D


title: OX2123PL6_8G


title: OX2123PL7_7D


title: OX2123PL6_8A


title: OX2123PL6_8F


title: OX2123PL6_8D


title: OX2123PL6_9B


title: OX2123PL7_7E


title: OX2123PL6_7F


title: OX2123PL6_7D


title: OX2123PL6_7E


title: OX2123PL6_7G


title: OX2123PL6_7A


title: OX2123PL6_7B


title: OX2123PL6_7C


title: OX2123PL6_6H


title: OX2123PL6_6G


title: OX2123PL6_6E


title: OX2123PL6_6C


title: OX2123PL6_6D


title: OX2123PL6_5G


title: OX2123PL6_6B


title: OX2123PL6_4H


title: OX2123PL6_5C


title: OX2123PL6_4F


title: OX2123PL6_4C


title: OX2123PL6_3G


title: OX2123PL6_3H


title: SMD32316PL4_11D


title: OX2123PL6_3E


title: OX2123PL6_2G


title: OX2123PL6_2H


title: OX2123PL6_2C


title: OX2123PL6_2D


title: OX2123PL6_3C


title: OX2123PL6_2E


title: OX2123PL6_1H


title: OX2123PL6_1F


title: OX2123PL6_2A


title: OX2123PL6_1B


title: OX2123PL6_1E


title: OX2123PL6_2B


title: OX2123PL6_1G


title: OX2123PL6_4A


title: OX2123PL6_11E


title: OX2123PL6_11G


title: OX2123PL6_11A


title: OX2123PL6_10G


title: OX2123PL6_10H


title: OX2123PL6_11D


title: OX2123PL6_11H


title: OX2123PL6_11C


title: OX2123PL6_10C


title: OX2123PL6_10D


title: OX2123PL6_3F


title: OX2123PL6_10E


title: OX2123PL6_10B


title: OX2123PL6_10A


title: OX2123PL4_9F


title: OX2123PL4_9E


title: OX2123PL4_9D


title: OX2123PL4_9B


title: OX2123PL4_8C


title: OX2123PL4_8B


title: OX2123PL4_8F


title: OX2123PL4_7D


title: OX2123PL4_7C


title: OX2123PL6_10F


title: OX2123PL4_6G


title: OX2123PL4_7B


title: OX2123PL4_5F


title: OX2123PL4_6D


title: OX2123PL4_6F


title: OX2123PL4_6C


title: OX2123PL4_5E


title: OX2123PL4_4B


title: OX2123PL4_4C


title: OX2123PL4_4E


title: OX2123PL4_3F


title: OX2123PL4_3G


title: OX2123PL4_5C


title: OX2123PL4_3E


title: OX2123PL4_2G


title: OX2123PL4_3D


title: OX2123PL4_11E


title: OX2123PL4_3C


title: OX2123PL4_8G


title: OX2123PL4_11C


title: OX2123PL4_11D


title: OX2123PL4_6E


title: OX2123PL4_10B


title: OX2123PL4_10D


title: OX2123PL4_10F


title: OX2123PL4_10C


title: OX2123PL1_5E


title: OX2123PL1_5G


title: OX2123PL1_4G


title: OX2123PL1_4H


title: OX2123PL1_5D


title: OX2123PL1_5C


title: OX2123PL1_5B


title: OX2123PL1_5A


title: OX2123PL4_11G


title: OX2123PL1_4F


title: OX2123PL1_4B


title: OX2123PL1_3F


title: OX2123PL1_4A


title: OX2123PL1_4E


title: OX2123PL1_3D


title: OX2123PL1_3C


title: OX2123PL1_2H


title: OX2123PL1_3A


title: OX2123PL1_2G


title: OX2123PL1_2F


title: OX2123PL1_5F


title: OX2123PL1_2D


title: OX2123PL1_2C


title: OX2123PL1_2A


title: JLMPL6_7E


title: JLMPL6_7D


title: OX2123PL1_2B


title: JLMPL6_7C


title: JLMPL6_7B


title: JLMPL6_7A


title: JLMPL6_6H


title: JLMPL6_6F


title: JLMPL6_6E


title: OX2123PL1_4C


title: JLMPL6_6D


title: OX2123PL1_3E


title: JLMPL6_6G


title: JLMPL6_6A


title: JLMPL6_5H

value: PV


title: JLMPL6_6C


title: JLMPL6_5G


title: JLMPL6_5F


title: JLMPL6_5B


title: JLMPL6_5C


title: JLMPL6_6B


title: OX2123PL1_2E


title: JLMPL6_5E


title: JLMPL6_4H


title: JLMPL6_4E


title: JLMPL6_5A


title: JLMPL6_4G


title: JLMPL6_4D


title: JLMPL6_4B


title: JLMPL6_4C


title: JLMPL6_4A


title: JLMPL6_2G


title: JLMPL6_2F


title: JLMPL6_2B


title: JLMPL6_2D


title: JLMPL6_1H


title: JLMPL6_2E


title: JLMPL6_2C


title: JLMPL6_2A


title: JLMPL6_1G


title: JLMPL6_1E


title: JLMPL6_1F


title: JLMPL6_1A


title: JLMPL6_1B


title: JLMPL6_1D


title: JLMPL5_9E


title: JLMPL5_9D


title: JLMPL5_9G


title: JLMPL5_9A


title: JLMPL5_8G


title: JLMPL5_8H


title: JLMPL5_9B


title: JLMPL6_2H


title: JLMPL5_8F


title: JLMPL5_9C


title: JLMPL5_8E


title: JLMPL5_8B


title: JLMPL5_8D


title: JLMPL5_8C


title: JLMPL5_7G


title: JLMPL5_7H


title: JLMPL5_7A


title: JLMPL5_7E


title: JLMPL5_7B


title: JLMPL5_5C


title: JLMPL5_7D


title: JLMPL6_1C


title: JLMPL5_7F


title: JLMPL5_5B


title: JLMPL5_9F


title: JLMPL5_5A


title: JLMPL5_4G


title: JLMPL5_4F


title: JLMPL5_4E


title: JLMPL5_4C


title: JLMPL5_4B


title: JLMPL5_2H


title: JLMPL5_2F


title: JLMPL5_2G


title: JLMPL5_4D


title: JLMPL5_7C


title: JLMPL5_2D


title: JLMPL5_2C


title: JLMPL5_2E


title: JLMPL5_1G


title: JLMPL5_1H


title: JLMPL5_1F


title: JLMPL5_2A


title: JLMPL5_1C


title: JLMPL5_1E


title: JLMPL5_1D


title: JLMPL5_1B


title: JLMPL5_12D


title: JLMPL5_1A


title: JLMPL5_12B


title: JLMPL5_12H


title: JLMPL5_4H


title: JLMPL5_12A


title: JLMPL5_11H


title: JLMPL5_12G


title: JLMPL5_11D


title: JLMPL5_11E


title: JLMPL5_11B


title: JLMPL5_11C


title: JLMPL5_10H


title: JLMPL5_11A


title: JLMPL5_10E


title: JLMPL5_10B


title: JLMPL5_10G


title: JLMPL5_10C


title: JLMPL5_10D


title: JLMPL5_12F


title: JLMPL5_10F


title: CRKPL2_9F


title: CRKPL2_9H


title: CRKPL2_9G


title: JLMPL5_10A


title: CRKPL2_8E


title: CRKPL2_8H


title: JLMPL5_11G


title: CRKPL2_8G


title: CRKPL2_9E


title: CRKPL2_8B


title: CRKPL2_8C


title: CRKPL2_8D


title: CRKPL2_8F


title: CRKPL2_7H


title: CRKPL2_7G


title: CRKPL2_9B


title: CRKPL2_7F


title: JLMPL5_11F


title: CRKPL2_7D


title: CRKPL2_9C


title: CRKPL2_7A


title: CRKPL2_6H


title: CRKPL2_6F


title: CRKPL2_6E


title: CRKPL2_6C


title: CRKPL2_7C


title: CRKPL2_6A


title: CRKPL2_5H


title: CRKPL2_8A


title: CRKPL2_5F


title: CRKPL2_5G


title: CRKPL2_5D


title: CRKPL2_6G


title: CRKPL2_6B


title: CRKPL2_5E


title: CRKPL2_4H


title: CRKPL2_5B


title: CRKPL2_5A


title: CRKPL2_4G


title: CRKPL2_4E


title: CRKPL2_4F


title: CRKPL2_7E


title: CRKPL2_7B


title: CRKPL2_4C


title: CRKPL2_4A


title: CRKPL2_4B


title: CRKPL2_3B


title: CRKPL2_3D


title: CRKPL2_3C


title: CRKPL2_3A


title: CRKPL2_2G


title: CRKPL2_2H


title: CRKPL2_2D


title: CRKPL2_2F


title: CRKPL2_1G


title: CRKPL2_5C


title: CRKPL2_2A


title: CRKPL2_1E


title: CRKPL2_2B


title: CRKPL2_1F


title: CRKPL2_4D


title: CRKPL2_1C


title: CRKPL2_1B


title: CRKPL2_12C


title: CRKPL2_10G


title: CRKPL2_1D


title: CRKPL2_1H


title: CRKPL2_1A


title: CRKPL2_10F


title: CRKPL2_10D


title: CRKPL2_10C


title: CRKPL2_10E


title: CRKPL1_9D


title: CRKPL2_10A


title: CRKPL2_2E


title: CRKPL1_9E


title: CRKPL1_5E


title: CRKPL1_8C


title: CRKPL1_9C


title: CRKPL1_5F


title: CRKPL1_4F


title: CRKPL1_3F


title: CRKPL2_10H


title: CRKPL2_12A


title: CRKPL1_5D


title: CRKPL1_4C


title: CRKPL1_4E


title: CRKPL1_3C


title: CRKPL1_2C


title: CRKPL1_3D


title: CRKPL1_2E


title: CRKPL1_3E


title: CRKPL1_11E


title: CRKPL1_10F


title: CRKPL1_2F


title: CRKPL1_10D


title: CRKPL1_11C


title: JLMPL5_2B


title: CRKPL1_8F


title: CRKPL1_10C


title: CRKPL1_11D


title: AV12PL3_4H


title: AV12PL3_4F


title: AV12PL3_4G


title: AV12PL3_4E


title: CRKPL1_4D


title: AV12PL3_4B


title: AV12PL3_4D


title: AV12PL3_4A


title: AV12PL3_3H


title: AV12PL3_3G


title: AV12PL3_3D


title: AV12PL3_3C


title: AV12PL3_3E


title: AV12PL3_3F


title: AV12PL3_3B


title: AV12PL3_10C


title: AV12PL3_10F


title: AV12PL3_10G


title: AV12PL3_10E


title: AV12PL3_10D


title: AV12PL3_10H


title: JURKAT_JURKATPL15_4H

extract_protocol:
cDNA libraries were synthetized from single cells using SMART-seq+, mRNA targeting or TARGET-seq method
Illumina sequencing libraries were prepared using the Illumina Nextera XT DNA kit, using one forth of the standard volume recommended by Illumina
Samples were sequenced on Illumina NextSeq Instrument

treatment_protocol: JURKAT, SET2 and HSPCs were isolated by Fluorescent Activated Cell Sorting

value: JURKAT


title: JURKAT_JURKATPL15_4G


title: AV12PL3_10B


title: JURKAT_JURKATPL15_4D


title: AV12PL3_10A


title: JURKAT_JURKATPL15_4E


title: JURKAT_JURKATPL15_4B


title: JURKAT_JURKATPL15_3F


title: JURKAT_JURKATPL15_4A


title: JURKAT_JURKATPL15_3H


title: JURKAT_JURKATPL15_3G


title: AV12PL3_3A


title: JURKAT_JURKATPL15_3D


title: JURKAT_JURKATPL15_3C


title: JURKAT_JURKATPL15_3B


title: JURKAT_JURKATPL15_3E


title: JURKAT_JURKATPL15_2H


title: JURKAT_JURKATPL15_2G


title: JURKAT_JURKATPL15_2F


title: JURKAT_JURKATPL15_2E


title: JURKAT_JURKATPL15_2D


title: JURKAT_JURKATPL15_2C


title: JURKAT_JURKATPL15_11C

source_name: JURKAT_mRNA targeting

value: mRNA targeting


title: JURKAT_JURKATPL15_11G

value: SMART-seq+


title: JURKAT_JURKATPL15_2B


title: JURKAT_JURKATPL15_11H


title: JURKAT_JURKATPL15_11F


title: JURKAT_JURKATPL15_11E


title: JURKAT_JURKATPL15_4C


title: JURKAT_JURKATPL15_11A


title: JURKAT_JURKATPL15_10G


title: JURKAT_JURKATPL15_10H


title: JURKAT_JURKATPL15_10F


title: JURKAT_JURKATPL15_10E


title: JURKAT_JURKATPL15_10C


title: JURKAT_JURKATPL15_10B


title: JURKAT_JURKATPL15_11B


title: JURKAT_JURKATPL15_3A


title: JURKAT_JURKATPL15_10A


title: JURKAT_JURKATPL15_10D


title: JURKAT_JURKATPL15_9C


title: JURKAT_JURKATPL15_9G


title: JURKAT_JURKATPL15_9B


title: SET2_SET2PL4_10F


title: JURKAT_JURKATPL15_9D


title: JURKAT_JURKATPL15_9E


title: JURKAT_JURKATPL15_9A


title: SET2_SET2PL4_10D


title: SET2_SET2PL4_10H


title: SET2_SET2PL4_9G


title: SET2_SET2PL4_10E


title: SET2_SET2PL4_9H


title: SET2_SET2PL4_9F


title: SET2_SET2PL4_9D


title: SET2_SET2PL4_9C


title: SET2_SET2PL4_10C


title: SET2_SET2PL4_10B


title: SET2_SET2PL4_9E


title: SET2_SET2PL4_5G

source_name: SET2_mRNA targeting


title: SET2_SET2PL4_9B


title: SET2_SET2PL4_5F


title: SET2_SET2PL4_5H


title: JURKAT_JURKATPL15_9F


title: SET2_SET2PL4_5B


title: SET2_SET2PL4_5D


title: SET2_SET2PL4_5C


title: SET2_SET2PL4_5E


title: SET2_SET2PL4_4H


title: JURKAT_JURKATPL15_9H


title: SET2_SET2PL4_4D


title: SET2_SET2PL4_4G


title: SET2_SET2PL4_4F


title: SET2_SET2PL4_4C


title: SET2_SET2PL4_3G


title: SET2_SET2PL4_4B


title: SET2_SET2PL4_4A


title: SET2_SET2PL4_3H


title: SET2_SET2PL4_3E


title: SET2_SET2PL4_9A


title: SET2_SET2PL4_3B


title: SET2_SET2PL4_2F


title: SET2_SET2PL4_5A


title: SET2_SET2PL4_2G


title: SET2_SET2PL3_11F


title: SET2_SET2PL4_3D


title: SET2_SET2PL4_3A


title: SET2_SET2PL4_2H


title: SET2_SET2PL4_2C


title: SET2_SET2PL3_11G


title: SET2_SET2PL3_11E


title: SET2_SET2PL4_2A


title: SET2_SET2PL3_11D


title: SET2_SET2PL4_2D


title: SET2_SET2PL4_2E


title: SET2_SET2PL3_11C


title: SET2_SET2PL4_3C


title: SET2_SET2PL4_3F


title: SET2_SET2PL3_10B


title: SET2_SET2PL3_11B


title: SET2_SET2PL3_10C


title: SET2_SET2PL3_10D


title: SET2_SET2PL3_9H


title: SET2_SET2PL3_10A


title: SET2_SET2PL3_9F


title: SET2_SET2PL4_2B


title: SET2_SET2PL3_9E


title: SET2_SET2PL3_8D


title: SET2_SET2PL3_8A


title: SET2_SET2PL3_8B


title: SET2_SET2PL3_3F


title: SET2_SET2PL3_3H


title: SET2_SET2PL3_3G


title: SET2_SET2PL3_3D


title: SET2_SET2PL3_3E


title: SET2_SET2PL3_3C


title: SET2_SET2PL3_2F


title: SET2_SET2PL3_3A


title: SET2_SET2PL3_3B


title: SET2_SET2PL3_2D


title: SET2_SET2PL3_2G


title: SET2_SET2PL3_2H


title: SET2_SET2PL3_2A


title: SET2_SET2PL3_2B


title: SET2_SET2PL3_9G


title: HSPC_JMML2_PL4_5G

source_name: HSPC_mRNA targeting

value: HSPC


title: SET2_SET2PL3_2C


title: HSPC_JMML2_PL4_5H


title: HSPC_JMML2_PL4_5F


title: HSPC_JMML2_PL4_3G


title: HSPC_JMML2_PL4_5B


title: HSPC_JMML2_PL4_5C


title: HSPC_JMML2_PL4_3E


title: HSPC_JMML2_PL4_3F


title: HSPC_JMML2_PL4_3B


title: HSPC_JMML2_PL4_3D


title: HSPC_JMML2_PL4_3A


title: HSPC_JMML2_PL4_5D


title: HSPC_JMML2_PL4_11D


title: HSPC_JMML2_PL4_11G


title: HSPC_JMML2_PL4_11C


title: HSPC_JMML2_PL4_11A


title: HSPC_JMML2_PL4_11B


title: HSPC_JMML2_PL4_10H


title: HSPC_JMML2_PL4_10G


title: HSPC_JMML2_PL4_10F


title: HSPC_JMML2_PL4_10B


title: HSPC_JMML2_PL4_10C


title: HSPC_JMML2_PL4_3H


title: HSPC_JMML2_PL1_5A


title: HSPC_JMML2_PL4_3C


title: HSPC_JMML2_PL1_5C


title: HSPC_JMML2_PL1_5B


title: HSPC_JMML2_PL1_3H


title: HSPC_JMML2_PL1_3G


title: HSPC_JMML2_PL4_10A


title: HSPC_JMML2_PL1_3F


title: HSPC_JMML2_PL1_3B


title: HSPC_JMML2_PL1_3C


title: HSPC_JMML2_PL1_3A


title: HSPC_JMML2_PL1_3D


title: HSPC_JMML2_PL1_3E


title: SET2_CLPL2_9E


title: SET2_CLPL2_9D


title: SET2_CLPL2_9B


title: SET2_CLPL2_9C


title: SET2_CLPL2_8C


title: SET2_CLPL2_4D


title: SET2_CLPL2_4E


title: HSPC_JMML2_PL4_10D


title: HSPC_JMML2_PL4_10E


title: JURKAT_CLPL2_3B


title: JURKAT_CLPL2_3C


title: SET2_CLPL2_4C


title: JURKAT_CLPL2_2C


title: JURKAT_CLPL2_2D


title: JURKAT_CLPL2_10D


title: JURKAT_CLPL2_11B


title: JURKAT_CLPL2_11C


title: JURKAT_CLPL2_11D


title: JURKAT_CLPL2_10C


title: JURKAT_CLPL2_10B


title: JURKAT_CLPL2_2B


title: THZ1_rep2(PROseq)_resequenced

description: Resequenced to increase the sequencing depth for both the replicates DMSO and THZ1 at 1hr treatments. The sequencing reads were pooled and the files were merged prior to aligning to the genome.

value: Kasumi-1 cells

value: 400nM THZ1-1hr


title: THZ1_rep1(PROseq)_resequenced


title: THZ1_2hr_rep2(RNAseq)

value: 400nM THZ1-2hr


title: THZ1_2hr_rep1(RNAseq)


title: DMSO_rep2(PROseq)_resequenced


title: 0hr_rep2(RNAseq)

value: Untreated


title: DMSO_rep1(PROseq)_resequenced


title: THZ1_2hr_rep1(PROseq)


title: THZ1_2hr_rep2(PROseq)


title: THZ1_1hr_rep1(PROseq)


title: SET2_CLPL2_4B

value: TARGET-seq


title: THZ1_1hr_rep2(PROseq)


title: THZ1_30min_rep1(PROseq)

value: 400nM THZ1-30min


title: THZ1_30min_rep2(PROseq)


title: THZ1_15min_rep1(PROseq)

value: 400nM THZ1-15min


title: 0hr_rep2(PROseq)


title: 0hr_rep1(PROseq)


title: GRO-MCF7_2,5-Hexanediol and Estrogen

status: Public on Feb 10 2019

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description:
Treated with 2,5-Hexanediol and Estrogen
Gro-seq in MCF7 Cells Treated with 2,5-Hexanediol and Estrogen

data_processing:
library strategy: GRO-seq
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

source_name: Gro-Seq plus Estrogen

growth_protocol: MCF7, estrogen receptor alpha positive breast cancer cells were cultured in DMEM and 10%FBS under standard condition

extract_protocol:
MCF7 cells after treatment were incubated in swellinig ice-cold buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min. Cells were lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100μl of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
GRO-seq experiments were performed as previously reported (Li et al., 2013). Briefly, MCF7 cells were swollen in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice and then lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol), before being re-suspended in 100µl of freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, re-suspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of Superase.In, 1% sarkosyl, 500µM ATP, GTP, and Br-UTP, 2µM CTP) and incubated for 5 min at 300C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. After base hydrolysis on ice for 40min and followed by treatment with DNase I and antarctic phosphatase, the Br-UTP labeled NRO-RNA was purified by an anti-BrdU argarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 3hr at 4°C while rotating. Then T4 PNK (NEB) was used to repair the end of NRO-RNA. Subsequently, cDNA synthesis was performed as reported(9,33) with few modifications. The RNA fragments were subjected to poly-A tailing reaction by poly-A polymerase (NEB) for 30 min at 37°C. Reverse transcription was then performed using superscript III (Invitrogen) with oNTI223 primer. The cDNA products were separated on a 10% polyacrylamide TBE-urea gel with right product (~100-500bp) being excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (NEB). Re-linearized single strand cDNA were separated by TBE gel and the products of desired size was excised (~120-320bp) for gel extraction. Finally, cDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) with primers oNTI200 and oNTI201 for deep sequencing.

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS. For eRNA knockdown, cells were transfected with LNA targeting specific enhancer RNA and after 24 hours were treated with estrogen for 60 before collecting the samples for ChIP-Seq. Control samples were treated with ICI 182,780, and ER alpha antagonist

value: Human breast cancer cells

tag: genotype/variation

value: wild type

tag: treated with

value: 2, 5-Hexanediol and Estrogen

tag: molecule subtype

value: Nascent RNA


title: GRO-MCF7_1,6-Hexanediol and Estrogen

description:
Treated with 1,6-Hexanediol and Estrogen
Gro-seq in MCF7 Cells Treated with 1,6-Hexanediol and Estrogen

tag: cell line

tag: cell type

value: 1, 6-Hexanediol and Estrogen


title: ATAC-Seq minus Estrogen

description: MCF7 Wild Type cells treated with ICI 182,780

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-Seq reads were aligned to the hg19 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

source_name: ATAC-Seq minus Estrogen

extract_protocol:
MCF7 cells after treatment were trypsinized and washed in PBS. 50,000 cells per sample were used for downstream assay.
ATAC-seq was performed as previously described (Buenrostro et al., 2015). Transposition reaction was performed at 37oC for 30 min using Nextera DNA Library Preparation Kit (Illumina Cat No. 15028212) in 50μl volume (2.5 μl Transposae enzyme, 25 μl 2X TD buffer and 22.5 μl nuclease-free water). The reaction mixture was immediately purified using MinElute PCR purification Kit (Qiagen, Cat No. 28006) and eluted in 10 μl nuclease-free water. The tagmented DNA was then PCR amplified using KAPA Real-Time Library Amplification Kit (Kapa Biosystems, Cat No. KK2701) in a 50 μl reaction (10 μl tagmented DNA, 2.5 μl25 μM PCR primer 1, 2.5 μl 25 μM barcoded PCR primer 2, 25 μl KAPA HiFi HotStart ReadyMix, 10 μl nuclease-free water), using the following program (One cycle at 72oC: 5 min, 98oC: 30sec; 8-12 cycles at 98oC: 10 sec, 63oC: 30 sec and 72oC: 1min). PCR standards, supplied in the kit, were included in separate wells and the reaction was stopped between standard 2 and 3.  The reaction mixture was subjected to size selection (to select fragments ranging 150-800bp) using 1.6 volume of Agencourt AMPure XP magnetic beads (Beckman Coulter, Cat No. A63880), washed once with 80% ethanol, air-dried and eluted in 15 μl of nuclease-free water. The resulting ATAC-seq library was quantified using Qubit Flurometer (Thermo Fisher) and the quality was analyzed by resolving 1 μl on Tapestation (Agilent). Ten nmol of the library was sequenced on HiSeq 4000 sequencer (Illumina). DATA was mapped to hg18 using Bowtie2 with standard settings. Tag directories were created after removing the reads mapped to the mitochondrial chromosome. ATAC-seq peaks were identified using HOMER.

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS were treated with estrogen for 60 before collecting the samples for ATAC-Seq. Control samples were treated with ICI 182,780, and ER alpha antagonist

value: MCF7 WT obtained by clonal selection after transfecting with Cas9 vector

value: ICI 182,780, an estrogen receptor alpha antagonist; Control