title: ME_24h3

city: Hangzhou

first: Suo

middle: jing

last: qi

state: Zhejiang

address: 866 Yuhangtang Rd

department: college of life sciences

institute: Zhejiang university

data_processing:
A cDNA library constructed by technology from the pooled RNA from scutellum of hordeum vulgare was sequenced run with Illumina sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced.
We aligned reads of samples to the reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package–edgeR.
Genome_build: Hordeum_vulgare.IBSC_v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Hordeum vulgare

source_name: mature embryo scutellum

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

treatment_protocol: After removing the embryonic axis, immature embryos (IME) and mature embryos (ME) were placed, with the scutellum facing upwards, in the callus induction medium [63] in a growth chamber at 24C in the dark for callus induction.

value: Golden promise

tag: tisssue

value: embryo

value: mature embryos are derived from  barley mature seeds

tag: time point


title: BAT7

status: Public on Jan 22 2022

type: SRA

city: Nashville

first: Masoud

last: Ghamari-Langroudi

state: TN

address: 8435 MRB #IV, 2215 Garland ave

country: USA

institute: Vanderbilt University

description:
BAT7
BAT_SFN

library_source: transcriptomic

data_processing:
1. Data Quality Control: filtering reads containing adapter or with low quality.
2. Statistics Analysis of Data Production and Quality.
3. Mapping Reads to Reference Genome.
4. Gene Expression Quantification.
5. Correlation analysis (for biological replicates only).
6. Differential Expression Analysis (two or more groups of samples).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: FPKM_all_samples.xlsx
Supplementary_files_format_and_content: Differentially_Expressed_Genes_SFN_effects_all_tissues.xlsx

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA samples from each tissue were prepared with Trizol.
mRNA library preparation (poly A enrichment).

treatment_protocol: Male 12-week-old C57/BJ wild type mice were fed with high fat diet for 16-20 weeks. Around 28 weeks of age, mice were treated with daily ip injections of either SFN (5 mg/kg) or vehicle for one week.

tag: strain

tag: tissue

value: Brown Adipose Tissue

tag: Sex

value: Male

tag: genotype

value: wild type

tag: body weight

value: diet-induced obesity

tag: treatment

value: Sulforaphane

tag: mouse id


title: BAT6

description:
BAT6
BAT_SFN


title: BAT9

description:
BAT9
BAT_SFN


title: MSC_3

city: Odense

first: Eduardo

last: Fernandez-Rebollo

address: Campusvej 55

department: Functional Genomics and Metabolism

country: Denmark

institute: University of Southern Denmark

description:
Sample_3
Bone marrow isolated mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

data_processing:
Pair-end reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and low-quality reads were removed using TrimGalore.
Reads were mapped to the GRCh38 assembly of the human genome using Tophat2, version 2.0.10, and reassembled with Cufflinks.
Differential gene expression was analyzed using the DESeq2 package, version 1.10.1.
Significance of transcriptomic changes was estimated using the R limma package with an adjusted paired p-value <0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM_iMSC_manuscript.txt: Tab-delimited text file includes FPKM.

organism: Homo sapiens

source_name: bone marrow derived mesenchymal stromal cells

growth_protocol: MSCs and iMSCs were cultured in basal medium consisting of Dulbecco’s Modified Eagle Medium (DMEM, 1g/L glucose; PAA, Pasching, Austria) with 1% penicillin/streptomycin (PAA) and 1% L-glutamine, and supplemented with 10% human platelet lysate (HPL). Induced pluripotent stem cells were reprogrammed from the same MSC donors that were used for experiments with primary MSCs. Reprogramming was performed with episomal plasmids. iPSCs were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm²) in StemMACS iPS-Brew XFe96 (all Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). iPSCs were re-differentiated toward iMSCs under MSC culture conditions as described by Frobel et al., 2014. After one week, differentiated iPSCs were maintained on 0.1% gelatine-coated TCP or HPL-gel and passaged every further week using trypsin-EDTA 0.25% (Gibco/Thermo Fisher Scientific).

extract_protocol:
RNA was isolated from the samples using the NucleoSpin RNA extraction kit (Macherey-Nagel, Düren, Germany).
Library preparation was performed with the Illumina TruSeq Stranded Total RNA Sample Preparation Kit, with a total input amount of 1 µg, following the standard protocol with ribosomal depletion (Illumina Ribo-Zero Gold rRNA removal kit) and the NextSeq 500/550 High Output Kit v2 (carried out by the Core Genomics-facility IZKF, RWTH Aachen University).

tag: cell type

value: mesenchymal stromal cells

tag: passage

tag: donor

value: Donor 3

tag: gender

tag: age


title: eW1

description:
eW1
eWAT_Veh

value: epididymal white adipose tissue

value: vehicle


title: eW8

description:
eW8
eWAT_SFN


title: eW4

description:
eW4
eWAT_Veh


title: ME_24h2

country: China


title: BAT5

description:
BAT5
BAT_Veh


title: MSC_2

description:
Sample_2
Bone marrow isolated mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 2

value: Female


title: ME_24h1


title: BAT3

description:
BAT3
BAT_Veh


title: BAT4

description:
BAT4
BAT_Veh


title: MSC_1

description:
Sample_1
Bone marrow isolated mesenchymal stromal cells in early passages.
processed data file: FPKM_iMSCs_manuscript.txt

value: Donor 1


title: BAT2

description:
BAT2
BAT_Veh


title: Donor 2 MCSF/SQLE

city: Los Angeles

first: Tran

middle: Hue

last: Do

state: CA

address: 615 Charles E Young Dr

institute: David Geffen School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
Each read was tagged with a 12bp barcode and 8bp unique molecular identifier (UMI
After alignment, the reads were grouped by the barcodes and deduplicated using the UMIs. The number of UMIs was then counted for each gene in each cell to generate the digital expression matrix (DEM).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) from healthy donors were isolated from peripheral blood using a Ficoll-Paque (GE Healthcare) density gradient. Monocytes were isolated from PBMCs by adherence for 2 hours with RPMI supplemented with 1% fetal calf serum (FCS) or via positive selection with CD14 microbead (Miltenyi Biotec, cat# 130-050-201). Monocytes were seeded at 500,000 cells/well in a 24-well plate and differentiated in M-CSF (50 ng/ml) (R&D Systems, cat. # 216MC025/CF) for 5 day in RPMI with 10% FCS at 37°C. In vitro 5-day M-CSF derived macrophages were then stimulated with either M-CSF (50 ng/ml) (R&D Systems, cat. # 216MC025/) and/or squalene (1 mM) (Thermofisher Scientific, cat.# S3626-100ML). These macrophages were separated from culture plates with trypsin-EDTA and filtered through a 70 μm cell strainer and washed with 1ml of RPMI (Gibco, cat. # 11875093). The macrophages were centrifuged at 300g for 10 mins at 4°C. After discarding the supernatant, the cells were suspended in 1mL of RPMI and counted. Live cells were counted using 0.4% trypan blue (Gibco, cat. # 15250061). If the cell viability was above 90%, we loaded isolated cells onto the Chromium instrument (10X Genomics) as described above. Single cell RNA-seq sequencing, alignment, and analyses are described above.
Isolated cells were loaded into the Chromium instrument (10X Genomics) according to manufacturer’s protocol, sequenced with NovaSeqS2, and analyzed using Seurat.

value: blood

value: mixed sample (non-demultiplexed)


title: ME_0h2

value: Golden promise


title: Donor 2 MCSF


title: ME_0h3

value: embryo


title: ME_0h1

value: mature embryos are derived from  barley mature seeds


title: Donor 1 MCSF


title: PHH-HBV

city: SHANGHAI

first: Wenjing

last: Zai

address: Dongan Road

institute: Fudan University

data_processing:
The sequencing reads from all RNA-seq experiments were trimmed by Cutadapt v3.1 (https://cutadapt.readthedocs.io/en/stable/), then aligned to the human (hg19) reference genome by Hisat2 (https://daehwankimlab.github.io/hisat2/)
The resulting files were sorted by SAMtools (http://samtools.sourceforge.net/) and analyzed for expression using FeatureCounts (http://subread.sourceforge.net/).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Primary human hepatocytes

growth_protocol: 5C-PHH were cultured as described in Xiang C, et al., Science 2019. In brief, Cell were  cultured with 5C medium (Null medium (Williams’ medium E containing B27, Glutamax, and Pen Strep) supplemented with Forskolin (20 μM), SB431542 (10 μM), IWP2 (0.5 μM), DAPT (5 μM), and LDN193189 (0.1 μM))

extract_protocol: RNA libraries were prepared for sequencing using the Illumina mRNA-Seq Prep Kit (Illumina)

treatment_protocol: The day after plating, 5C-PHH were infected with concentrated HBV particles (ayw) collected from HepAD38 supernatant at a multiplicity of infection (MOI) 200, in Null medium containing 4 % PEG8000. For mock- infection groups, cells were treated with Null medium containing 4 % PEG8000. 20 h later, the medium was removed, and cells were rinsed with PBS for three times. Cell were then cultured with 5C medium for indicated time before treatment and harvesting.

tag: culture

value: Five chemicals-cultured PHH (5C-PHH)

value: HBV-infected (ayw, MOI 200)

tag: time

value: 2 weeks post infection


title: PHH-Mock

value: Mock-infected


title: PHH-siHBV

value: siHBV-treated (100 nM)


title: Donor 1 MCSF/SQLE


title: si-FLRT2 4

city: Tokyo

first: Yoshiaki

last: Kubota

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Anatomy

country: Japan

institute: Keio University School of Medicine

data_processing:
2 × 150 bp pair-end sequencing was carried out using Illumina Hiseq.
Sequencing data were converted into the fastq format using bcl2fastq software.
The sequence quality was checked by FastQC software, and adapter sequences were eliminated by Trimmomatic.
The counts table was generated by STAR+RSEM analysis to be used to assemble counts.  Differentially expressed genes and isoforms were detected using the DESeq2 module.
Genome_build: mm9
Supplementary_files_format_and_content: CSV

source_name: HUVEC

growth_protocol: Cells were maitained in EGM2 medium (Takara-Bio) at 37°C/20% O2

extract_protocol:
Total RNA was prepared from cultured cells by Rneasy Mini Kit (GIAGEN)
The library for sequencing was prepared using KAPA RNA HyperPrep Kit.

treatment_protocol: Cells were transfected with 40 nmol l−1 siRNA Duplex (QIAGEN, Germantown, MD, USA) using 6 µl ml−1 Lipofectamine™ RNAiMAX (Invitrogen) in OptiMEM. After 4 h, the transfection medium was removed, and complete culture medium was added. Cells were cultured for a further 48 h

tag: sample type

value: cultured cell

tag: transfected


title: IME_48h3

source_name: immature embryo scutellum

tag: tisssue

value: Immature embryos are derived from barley seeds 14 days post-pollination

tag: time point


title: SM2

description:
SM2
SkM_Veh

tag: strain

tag: tissue

value: Skeletal Muscle

value: Male

value: wild type

value: diet-induced obesity


title: IME_48h2


title: BAT1

description:
BAT1
BAT_Veh

value: Brown Adipose Tissue

tag: Sex

tag: genotype

value: vehicle


title: PEF treated with insulin for 72 h_rep2

city: Harbin

first: YingJuan

last: Liang

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequence,then mapped to Sus_scrofa.Sscrofa11.1 whole genome using hisat2 v2.1.0 with parameters -p 8 -k 1 --dta -x -S -1 -2, followed by gene count generation using featureCounts v2.0.2 with parameters -T 5 -p -t exon -g gene_id -a -o.
To estimate the expression levels of all transcripts, RSEM (1.2.28) was used to calculate FPKM. parameters -prepare-reference --gtf  --star -p 8.
Read counts were normalized and compared for differential gene expression using DESeq2 with significance at a false discovery rate-adjusted P<0.05.
Genome_build: Sus_scrofa.Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Sus scrofa

source_name: embryonic fibroblast

extract_protocol:
Total RNA was isolated from the cells at hours 0, 48, and 72 post-insulin treated using RIzol RNA extraction reagent (Thermo Fisher Scientific), following the manufacturer’s protocol. The concentration and purity of total RNA were assessed on Nanodrop 2000 (Thermo Fisher Scientific), and the integrity of total RNA was evaluated with 2% agarose gel electrophoresis and a RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA). rRNA was removed using a Epicenter Ribo-zero rRNA Kit (Epicenter). Sequencing libraries were generated using the NEBNext UltraTM RNA Library Prep Kit for Illumina (number E7530L, New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: fibroblast

tag: treatment

value: treated with insulin for 72 hours


title: PEF treated with insulin for 72 h_rep3

value: embryo

tag: cell type


title: si-FLRT2 3


title: PEF treated with insulin for 72 h_rep1


title: IME_48h1

value: Golden promise


title: si-FLRT2 2


title: IME_24h3


title: PEF treated with insulin for 48 h_rep3

value: treated with insulin for 48 hours


title: PEF treated with insulin for 48 h_rep2


title: si-FLRT2 1


title: PEF treated with insulin for 48 h_rep1


title: si-Cont 3

value: siControl


title: PEF control_rep3

value: untreated


title: IME_24h1


title: IME_0h3


title: si-Cont 2


title: PEF control_rep2


title: PEF control_rep1


title: si-Cont 1


title: IME_0h1


title: si-Cont 4


title: IME_24h2


title: DMSO_treatment_biological_rep1 (GSK-J4/KTP-330 control)

type: RNA

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

description: Gene expression after 24hr in SH-SY5Y treated by MI-773

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.

source_name: DMSO treatment, biological rep1

growth_protocol: Neuroblastoma SH-SY5Y cells were maintained at 37°C in the MEM or DMEM/F12 medium supplemented with 10-15% fetal bovine serum. GSK-J4 (Cat: S7070 Selleck, USA) or KPT-330 (Cat: S7252 Selleck, USA) was dissolved in DMSO (Cat: D4540 Sigma-Aldrich, USA)

extract_protocol: Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Arraystar Human LncRNA microarray V4.  20,730 coding transcripts and 40,173 LncRNAs and which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.

treatment_protocol: SH-SY5Y cells were treated with 0.5uM GSK-J4 or KTP-330 and control group cells were treated with the same volume of DMSO (DMSO volume < 0.1% cell culture fluid volume and its toxicity＜0.1%(v/v)). 24 hours later. Human Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China.

value: DMSO


title: 5: control - cell tranfected with empty vector

status: Public on Jan 21 2022

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters, reads of phred quality under 20 and reads under 36 read length.
The raw reads were aligned to the EquCab3  genome  as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline. Htseq-count software was used to count the number of aligned reads to specific gene thresholds provided in an Ensembl gtf file version 97.
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Genome_build: Equ Cab3
Supplementary_files_format_and_content: Text files providing raw gene counts

organism: Equus caballus

source_name: in vitro cell culture (skin tissue)

extract_protocol:
The equine fibroblast cell lines were transfected using the nucleofection method with BPV-E4 and BPV-E4^E1 constructs. According to producers protocol, RNA was isolated from cell lines directly from culture dishes with PureLink™ RNA mini kit (Invitrogen, Thermo Scientific, Life Technology, USA). The procedure was maintained with the addition of the DNase treatment step (PureLink™ DNase Set, Invitrogen,Thermo Scientific, Life Technology, USA). The RNA was eluted with DEPC-Treated Water (Life Technologies, Ambion, USA). The quality and quantity of RNA were measured with 2200 TapeStation Automated Electrophoresis System (Agilent Technologies) as well as using nanodrop 2000 spectrophotometer (Thermo Scientific, Life Technology, USA) and agarose gel (2% agarose in TBE buffer) electrophoresis. All samples were sequenced using the NGS approach. According to the attached protocol, the high-quality RNA (RIN value from 9.3 to 9.8) was used for cDNA libraries preparation with theTruSeq RNA Kit v2 kit (Illumina, San Diego, CA, USA). The individual cDNA libraries were ligated with different indexes to pool samples during the NGS sequencing procedure. The quality and quantity of obtained libraries were assessed using Qubit 2.0 (Qubit™ dsDNA BR AssayKit, Invitrogen, Waltham, MA, USA ) and TapeStation 2200 (D100 screencaps, Agilent). Next, the cDNA libraries were sequenced on NextSeq 500 Illumina platform (Illumina, San Diego, CA, USA) and NextSeq 500/550 High Output KIT v 2.5 (75 cycles) according to protocol. The enrichment GeneOntology and over-represented Pathways analyses (KEGG, GO) were performed using David software (v6.8)  based on Equus caballus reference. The significance was shown based on False Discovery Rate (FDR)calculated as p-value after Benjamin multiple testing corrections (Benjamini and Hochberg, 1995). For visualization of gene interaction, String software [https://string-db.org/] was applied with Equus caballus reference.
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.

value: fibroblast cells

tag: genotype/variation

value: tranfected with empty vector


title: 9: cells transfected with BPV-E4

value: transfected with BPV-E4


title: 7: cells transfected with BPV-E4^E1

value: transfected with BPV-E4^E1


title: DMSO_treatment_biological_rep2 (GSK-J4/KTP-330 control)

description: Gene expression after 24hr in SH-SY5Y treated by DMSO

source_name: DMSO treatment, biological rep2

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)


title: 4: cells transfected with BPV-E4


title: 8: cells transfected with BPV-E4^E1


title: 3: cells transfected with BPV-E4


title: 6: control - cell tranfected with empty vector


title: 2: control - cell tranfected with empty vector


title: KPT-330_treatment_biological_rep1

source_name: KPT-330 treatment, biological rep1


title: GSK-J4_treatment_biological_rep2

source_name: GSK-J4 treatment, biological rep2


title: KPT-330_treatment_biological_rep2

source_name: KPT-330 treatment, biological rep2


title: GSK-J4_treatment_biological_rep3

source_name: GSK-J4 treatment, biological rep3


title: 10 nM 1,25(OH)2D3, 04 h, rep2

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
1α,25-dihydroxyvitamin D3
125D_04h_R2

data_processing:
Read alignment and quantification via nf-core/rnaseq STAR-Salmon pipeline 3.0 (http://doi.org/10.5281/zenodo.4323183)
Filtering for protein coding genes, read counts normalization via EdgeR 3.32.1 (TMM-normalized CPM)
Genome_build: hg38, Aligned to Ensembl annotation version 103, final annotation (via Biomart) to Ensembl version 104
Supplementary_files_format_and_content: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline)

source_name: PBMC

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: treatment for 4 h, 8 h, 24 h or 48 h with either 10 nM 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% EtOH)

value: PBMC

tag: agent

value: 4 h


title: IME_0h2

value: Immature embryos are derived from barley seeds 14 days post-pollination


title: 1: control - cell tranfected with empty vector


title: KPT-330_treatment_biological_rep3

source_name: KPT-330 treatment, biological rep3


title: GSK-J4_treatment_biological_rep1

source_name: GSK-J4 treatment, biological rep1


title: DMSO_treatment_biological_rep3 (GSK-J4/KTP-330 control)

source_name: DMSO treatment, biological rep3


title: Young 2

city: Tzur Hadassa

first: Michael

last: Klutstein

state: Other

address: Yasmin 273 Tzur Hadassa

department: Institute of Dental Sciences

country: Israel

institute: Hebrew University

description:
small RNAs
Processed data file: Processed data Peera.xlsx

data_processing:
The first 3 bases of R1 reads were discarded (positions for template switching), the reads were quality-trimmed at both ends, poly-G sequences (NextSeq’s no signal), adapter sequences, and poly-A sequences were removed from the 3' end, and finally low quality reads were filtered out. Paired-end libraries were similarly processed for R2 and re-paired by read name after trimming and filtering was done. Trimming adapters and other technical bases was done with cutadapt, v2.10, and parameters -O 1, --match-read-wildcards and -m 15. Quality filtering was performed using the fastq_quality_filter program of the FASTX package, v0.0.14, with parameters -q 20 and -p 90.
Processed reads were aligned with TopHat, v2.1.1, using parameters -G genes_extended.gtf, --read-gap-length 5, --read-realign-edit-dist 1, --no-coverage-search, -g 1000, --library-type fr-secondstrand, for both single-end and paired-end libraries, and -N 2, --read-edit-dist 7, --segment-length 18, for paired-end libraries, or -N 5, --read-edit-dist 10, --segment-length 23, for single-end libraries. All libraries were aligned to the mouse genome GRCm38, supplemented with the 45S pre-rRNA (NR_046233.2), and annotations from Ensembl release 99 with additional annotations for rRNA, tRNAs (from tRNAscan) and repeat sequences (from UCSC genome browser rmsk table).
Raw counts were obtained with htseq-count, v0.12.4, with -s 'yes' and -a 0, counting all primary alignments. The annotations file was based on the Ensembl release 99 annotations, but was modified: all 5S rRNA genomic locations were treated as one gene, tRNAs (from tRNAscan predictions) were counted according to the tRNA type, and repeats (from the rmsk table) were counted by their name.
Normalization and differential expression analysis were done with the DESeq2 package, v1.22.2, using default parameters (except setting independentFiltering to FALSE), after removing genes with a sum of counts less than 10 over all samples. The model included both a batch factor, for single-end or paired-end sequencing, and the age factor.
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized counts and statistical analysis

source_name: oocytes

growth_protocol: Ovaries were collected and dissected in M2 medium (M7167). GV oocytes were collected under a binocular using a Stripper and washed in hyaluronidase (H4272-30MG) to remove granulosa cells and acidic Tyrode's Solution (T1788) to remove the Zona Pellucida.

extract_protocol:
RNA extraction was done according to the TRIzol reagent user guide, into  10 ul of nuclease-free water.
Amplification was performed using the SMARTer® smRNA-Seq Kit for Illumina®-12 Rxns, TAKARA 635029.

value: oocyte

value: 8 weeks


title: Old 2

value: 9 months


title: Old 3


title: Young 1


title: Old 1


title: 10: cells transfected with BPV-E4


title: Untreated, Time 48h, Rep 3

city: Frederick

first: Shivendra

middle: G

last: Tewari

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute

description: Gene expression data

hyb_protocol: The eight time course samples were hybridized (along with the manufacturer’s RNA spike-in controls) according to standard protocol to the 8 sectors of an Agilent 8x15K platform microarray (AMADID 037237) with separate microarray slides used for each biological replicate.

scan_protocol: Arrays were scanned with the Agilent G2600D SureScan microarray scanner using scan protocol AgilentHD_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data.

data_processing: Txt files from Agilent’s Feature Extraction Software were transferred to Partek Genomics Suite software (v7.0). Within Partek, the gProcessedSignal was imported and the intensity values were normalized using Quantile Normalization and Log Tranformation Base 2.0 after import.

organism: Plasmodium falciparum

source_name: Untreated Dd2, Time 48, Rep 3

label_protocol: From 100 ng of total RNA, Cyanine-3 labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit One-Color (Agilent).

extract_protocol: For each data point, RNA was extracted from 50 µL of packed RBC culture with Trizol Reagent and the PureLink Mini Kit (Invitrogen/Thermo Fisher Scientific). 1ml Trizol was added to each sample, followed by high-speed disruption in tubes containing Lysing Matrix D (MP Biomedical) in a FastPrep 120 Instrument at speed 6 for 20 seconds. Homogenates were subsequently processed according to the PureLink Mini Kit manufacturer’s (Invitrogen/Thermo Fisher Scientific) protocol, including on-column DNase treatment.

treatment_protocol: Sublethal dose of PA21A092 (12 nM) was added to control RPMI medium at 0 h of the experiment, which was determined using blood smears of the parasite cultures (described in the paper).

value: Blood-stage Dd2 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit

tag: replicate

value: Rep 3


title: Untreated, Time 40h, Rep 3

description: Gene expression data

source_name: Untreated Dd2, Time 40, Rep 3


title: Young 3

tag: age


title: Untreated, Time 8h, Rep 4

description: Gene expression data

source_name: Untreated Dd2, Time 8, Rep 4

value: Rep 4


title: Untreated, Time 40h, Rep 4

description: Gene expression data

source_name: Untreated Dd2, Time 40, Rep 4


title: Untreated, Time 48h, Rep 4

description: Gene expression data

source_name: Untreated Dd2, Time 48, Rep 4


title: Untreated, Time 32h, Rep 3

description: Gene expression data

source_name: Untreated Dd2, Time 32, Rep 3


title: Untreated, Time 16h, Rep 4

description: Gene expression data

source_name: Untreated Dd2, Time 16, Rep 4


title: H1

description:
H1
Hyp_Veh

value: Hypothalamus

value: Male

value: wild type

tag: body weight

value: diet-induced obesity

value: vehicle

tag: mouse id


title: Untreated, Time 24h, Rep 4

description: Gene expression data

source_name: Untreated Dd2, Time 24, Rep 4

tag: time


title: Untreated, Time 24h, Rep 3

description: Gene expression data

source_name: Untreated Dd2, Time 24, Rep 3


title: Untreated, Time 16h, Rep 3

description: Gene expression data

source_name: Untreated Dd2, Time 16, Rep 3


title: Untreated, Time 8h, Rep 3

description: Gene expression data

source_name: Untreated Dd2, Time 8, Rep 3


title: Untreated, Time 0h, Rep 4

description: Gene expression data

source_name: Untreated Dd2, Time 0, Rep 4


title: Untreated, Time 0h, Rep 3

description: Gene expression data

source_name: Untreated Dd2, Time 0, Rep 3


title: PBMCs_Control_1

city: Ningbo

first: Mengyun

last: Liu

address: Baizhang East Road

institute: the affiliated People's hospital of Ningbo University

description:
N_1
CircRNA expression in  healthy control_1

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: PBMC,healthy control1

label_protocol: cDNA labeled with a fluorescent dye (Cy3_dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop_1000 spectrophotometer.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from patients and healthy individuals by using anticoagulation tubes. Ficoll_Paque PLUS (GE Healthcare, US) was added into blood sample with an equal amount of PBS. The mixture was centrifuged at 1500 rpm for 40 min, and then PBMCs in the middle were washed with PBS. Finally, PBMCs were kept at _80℃in Trizol (Sigma_Aldrich, US) for subsequent use.

value: Peripheral blood mononuclear cells

tag: gender

value: female

tag: subject status/id

value: healthy control1


title: PBMCs_Control_4

description:
N_4
CircRNA expression in healthy control_4

source_name: PBMC,healthy control4

value: male

value: healthy control4


title: PBMCs_DR_4

description:
DR_4
CircRNA expression in diabetic retinopathy patient_4

source_name: PBMC,diabetic retinopathy4

value: diabetic retinopathy4


title: Untreated, Time 48h, Rep 2

description: Gene expression data

source_name: Untreated Dd2, Time 48, Rep 2

value: Rep 2


title: Untreated, Time 40h, Rep 2

description: Gene expression data

source_name: Untreated Dd2, Time 40, Rep 2


title: PBMCs_DR_1

description:
DR_1
CircRNA expression in diabetic retinopathy patient_1

source_name: PBMC,diabetic retinopathy1

value: diabetic retinopathy1


title: PBMCs_DM_2

description:
DM_2
CircRNA expression in diabetes mellitus patient_2

source_name: PBMC,diabetes mellitus2

value: diabetes mellitus2


title: PBMCs_DR_2

description:
DR_2
CircRNA expression in diabetic retinopathy patient_2

source_name: PBMC,diabetic retinopathy2

value: diabetic retinopathy2


title: PBMCs_Control_3

description:
N_3
CircRNA expression in healthy control_3

source_name: PBMC,healthy control3

value: healthy control3


title: Untreated, Time 16h, Rep 2

description: Gene expression data

source_name: Untreated Dd2, Time 16, Rep 2

value: Blood-stage Dd2 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit


title: Untreated, Time 8h, Rep 2

description: Gene expression data

source_name: Untreated Dd2, Time 8, Rep 2


title: Untreated, Time 24h, Rep 2

description: Gene expression data

source_name: Untreated Dd2, Time 24, Rep 2


title: Untreated, Time 32h, Rep 1

description: Gene expression data

source_name: Untreated Dd2, Time 32, Rep 1

value: Rep 1


title: PBMCs_DM_4

description:
DM_4
CircRNA expression in diabetes mellitus patient_4

source_name: PBMC,diabetes mellitus4

value: diabetes mellitus4


title: PBMCs_DR_3

description:
DR_3
CircRNA expression in diabetic retinopathy patient_3

source_name: PBMC,diabetic retinopathy3

value: diabetic retinopathy3


title: PBMCs_Control_2

description:
N_2
CircRNA expression in healthy control_2

source_name: PBMC,healthy control2

value: healthy control2


title: PBMCs_DM_1

description:
DM_1
CircRNA expression in  diabetes mellitus patient_1

source_name: PBMC,diabetes mellitus1

value: diabetes mellitus1


title: PBMCs_DM_3

description:
DM_3
CircRNA expression in diabetes mellitus patient_3

source_name: PBMC,diabetes mellitus3

value: Peripheral blood mononuclear cells

value: diabetes mellitus3


title: Untreated, Time 32h, Rep 2

description: Gene expression data

source_name: Untreated Dd2, Time 32, Rep 2


title: Untreated, Time 16h, Rep 1

description: Gene expression data

source_name: Untreated Dd2, Time 16, Rep 1


title: Untreated, Time 40h, Rep 1

description: Gene expression data

source_name: Untreated Dd2, Time 40, Rep 1


title: Untreated, Time 24h, Rep 1

description: Gene expression data

source_name: Untreated Dd2, Time 24, Rep 1


title: Untreated, Time 8h, Rep 1

description: Gene expression data

source_name: Untreated Dd2, Time 8, Rep 1


title: Untreated, Time 48h, Rep 1

description: Gene expression data

source_name: Untreated Dd2, Time 48, Rep 1


title: Treated, Time 48h, Rep 4

description: Gene expression data

source_name: PYZ-treated Dd2, Time 48, Rep 4

value: Blood-stage Dd2 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and 12 nM PA21A092

value: Rep 4


title: Untreated, Time 0h, Rep 2

description: Gene expression data

source_name: Untreated Dd2, Time 0, Rep 2


title: Treated, Time 40h, Rep 4

description: Gene expression data

source_name: PYZ-treated Dd2, Time 40, Rep 4


title: Treated, Time 24h, Rep 4

description: Gene expression data

source_name: PYZ-treated Dd2, Time 24, Rep 4


title: Untreated, Time 0h, Rep 1

description: Gene expression data

source_name: Untreated Dd2, Time 0, Rep 1


title: Treated, Time 16h, Rep 4

description: Gene expression data

source_name: PYZ-treated Dd2, Time 16, Rep 4


title: Treated, Time 8h, Rep 4

description: Gene expression data

source_name: PYZ-treated Dd2, Time 8, Rep 4


title: Treated, Time 32h, Rep 4

description: Gene expression data

source_name: PYZ-treated Dd2, Time 32, Rep 4


title: Treated, Time 0h, Rep 4

description: Gene expression data

source_name: PYZ-treated Dd2, Time 0, Rep 4


title: Treated, Time 40h, Rep 3

description: Gene expression data

source_name: PYZ-treated Dd2, Time 40, Rep 3

value: Rep 3


title: Treated, Time 48h, Rep 3

description: Gene expression data

source_name: PYZ-treated Dd2, Time 48, Rep 3


title: Treated, Time 24h, Rep 3

description: Gene expression data

source_name: PYZ-treated Dd2, Time 24, Rep 3


title: Treated, Time 16h, Rep 3

description: Gene expression data

source_name: PYZ-treated Dd2, Time 16, Rep 3


title: Treated, Time 32h, Rep 3

description: Gene expression data

source_name: PYZ-treated Dd2, Time 32, Rep 3


title: Treated, Time 8h, Rep 3

description: Gene expression data

source_name: PYZ-treated Dd2, Time 8, Rep 3


title: Treated, Time 48h, Rep 2 repeat

description: Gene expression data

source_name: PYZ-treated Dd2, Time 48, Rep 2


title: Treated, Time 0h, Rep 3

description: Gene expression data

source_name: PYZ-treated Dd2, Time 0, Rep 2


title: Treated, Time 48h, Rep 2

description: Gene expression data


title: Treated, Time 16h, Rep 2

description: Gene expression data

source_name: PYZ-treated Dd2, Time 16, Rep 2


title: Treated, Time 40h, Rep 2

description: Gene expression data

source_name: PYZ-treated Dd2, Time 40, Rep 2


title: Cd11b+F4/80+CD169+CX3CR1neg sorted cells - rep 3

city: Adelaide

first: Andrew

last: Zannettino

state: SA

address: SAHMRI, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

data_processing:
Raw Illumina single-end FASTQ reads were assessed for quality using FastQC
FASTQ reads were trimmed for adapters using AdapterRemoval
Trimmed reads were aligned to GRCh38/mm10 using the transcriptome algorithm STAR
Aligned reads were summarised to gene intervals using featureCounts in Rsubread
Optical duplicates were assessed using MarkDuplicates
Gene counts were analysed using edgeR
Supplementary_files_format_and_content: Tab-delimited text files include tpm values for each sample.

extract_protocol:
Bone marrow was isolated from the hind limbs (tibiae and femur) by lightly crushing with a mortar and pestle, followed by sorting for population of interest. Cells were sorted into Trizol and RNA isolated using manufacturer's protocol with isopropanol precipitation.
cDNA libraries were prepared using NEXTflex mRNA-sequencing kit (BIOO Scientific) and sequenced using a NextSeq500 sequencer (Illumina)

value: bone marrow

value: Cd11b+F4/80+CD169+CX3CR1neg macrophages


title: Cd11b+F4/80+CD169+CX3CR1neg sorted cells - rep 2


title: E10.5ant_H3K27me3_CnT_rep3

city: Austin

first: Steven

middle: A.

last: Vokes

state: Texas

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

institute: University of Texas at Austin

library_source: genomic

data_processing:
Library strategy: Cut&Tag
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using MACS2 or SEACR.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: mouse limb buds

extract_protocol:
limbs were dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes.
Libraries were prepared with the following number of amplification cycles, for each given experiment: CUT&Tag/Run- 14 cycles, ChIP- 15 cycles, ATAC- 11 cycles. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.
ChIP & CUT&RUN library- NEBNext Ultra II DNA Library Prep Kit; ATAC & CUT&Tag- NEBNext HF 2x PCR Master Mix; RNA-seq- NEBNext Ultra II RNA Library Prep Kit

tag: strain/background

value: Swiss Webster

value: 2 pairs ant FLs (100k cells)

tag: Stage

value: forelimb bud


title: Treated, Time 8h, Rep 2

description: Gene expression data

source_name: PYZ-treated Dd2, Time 8, Rep 2

tag: tissue

value: Rep 2


title: Treated, Time 48h, Rep 1

description: Gene expression data

source_name: PYZ-treated Dd2, Time 48, Rep 1


title: E10.5post_H3K27me3_CnT_rep2


title: E10.5post_H3K27me3_CnT_rep3


title: Treated, Time 0h, Rep 2

description: Gene expression data


title: Treated, Time 0h, Rep 1

description: Gene expression data

source_name: PYZ-treated Dd2, Time 0, Rep 1


title: Treated, Time 24h, Rep 1

description: Gene expression data

source_name: PYZ-treated Dd2, Time 24, Rep 1


title: Treated, Time 8h, Rep 1

description: Gene expression data

source_name: PYZ-treated Dd2, Time 8, Rep 1


title: E10.5ant_H3K27me3_CnT_rep2


title: Treated, Time 16h, Rep 1

description: Gene expression data

source_name: PYZ-treated Dd2, Time 16, Rep 1


title: Untreated, Time 32h, Rep 4

description: Gene expression data

source_name: Untreated Dd2, Time 32, Rep 4

value: Blood-stage Dd2 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit


title: Treated, Time 32h, Rep 1

description: Gene expression data

source_name: PYZ-treated Dd2, Time 32, Rep 1

value: Rep 1


title: Cd11b+F4/80+CD169+CX3CR1neg sorted cells - rep 1

tag: strain


title: Ke01

city: Seoul

first: Jong Hee

last: Lee

address: 81, Irwon-ro, Gangnam-gu

department: Department of Dermatology

country: South Korea

institute: Samsung Medical Center

description: scRNA-seq

data_processing:
Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.
The 10x sequencing data was mapped to human reference genome (GRCh38; official Cell Ranger reference) for generating raw gene expression matrix.
Genome_build: hg38

source_name: Skin

extract_protocol:
the keloid tissue was washed in phosphate-buffered saline (PBS). Excised keloids were immersed in physiological saline and immediately transferred to the lab. After sample was minced into small pieces with scalpel in a petri-dish, prepared dissociation solution (2 mg/ml Liberase TL in PBS, Sigma Aldrich) was used to digest at 37ºC for 60 min. The debris were filtered out with a 70-μm cell strainer (#352340, Corning). The remaining tissue were transferred into dissociation solution containing 0.25% Trypsin for a second round of dissociation. Subsequently, the live cells were resuspended in PBS-0.04% bovine serum albumin. Cells were pelleted by centrifuging at 500 x g for 5min.
To generate single-cell gel bead emulsions, suspensions of skin cells were immediately injected into the Chromium Controller (10x Genomics) targeting 9,000 cells, respectively. Following the manufacturer’s protocols, the Chromium Single Cell 3’ Reagent V2 Chemistry Kit(10x Genomics) was used to construct single cell libraries. Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.

value: Skin

tag: pathology

value: Keloid

tag: location

value: Ear

value: Male


title: E10.5ant_H3K27me3_CnT_rep1


title: E10.5post_H3K27me3_CnT_rep1


title: E9_H3K27me3_CnT_rep2

value: 1 litter FLs (100k cells)


title: E9_H3K27me3_CnT_rep1


title: Treated, Time 40h, Rep 1

description: Gene expression data

source_name: PYZ-treated Dd2, Time 40, Rep 1


title: E9_Gli3null_H3K27ac_ChIP_rep2

data_processing:
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using MACS2 or SEACR.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

value: ~25 Gli3 mutants pooled from 19 litters FLs


title: E9_Gli3null_H3K27ac_ChIP_input


title: E9_Gli3null_H3K27ac_ChIP_rep1

value: ~25 Gli3 mutants pooled from 16 litters FLs


title: E9_WT_H3K27ac_ChIP_rep1

value: ~25 staged WT embryos from ~5 litters FLs


title: E9_WT_H3K27ac_ChIP_rep2


title: E9_WT_H3K27ac_ChIP_input


title: E10.5_HDAC2_CnR_rep2

data_processing:
Library strategy: Cut&Run
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using MACS2 or SEACR.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

value: 1 litter FLs (400k cells)


title: E10.5_HDAC2_CnR_rep1


title: NICD_NDME_ATAC-seq_rep2

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina bcl2fastq 2.19.1 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed.
Reads were aligned to mouse genome build mm10 using BWA-MEM (0.7.15).
Properly paired good quality reads were filtered with samtools (v1.3.1) using samtools view -b -h -f 0x2 -q 2.
Peaks were called using MACS2 (2.1.1.20160309 ) using macs2 callpeak -t -f BAMPE -g mm -B --nomodel --nolambda -q 0.05 --keep-dup all --broad --broad-cutoff 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file for each ChIP sample - generated by MACS2

source_name: BM LSK (Lin- Sca1+ cKit+)

extract_protocol:
50'000 LSK cells were isolated from induced bone marrow and processed as in Current Protocol in Molecular Biology by Buenrostro et al. in 2015 ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Library was amplify using NEBNext High-Fidelity 2X PCR Master Mix and size selection was performed using Agencourt AMPure XP beads.
sequencing protocol: Prepared libraries were sequenced on the Illumina NextSeq 500 with paired-end 2x75nt reads to obtain at least 35 million reads per sample.

tag: strain background

tag: transgene

value: R26 N1IC lox/+ Mx1Cre TMe -/-

tag: cre

value: Mx1Cre induction 2ug/g b.w. poly(I:C)

tag: group

value: BM LSK (Lin- Sca1+ cKit+)

tag: batch


title: E9_H3K4me1_CnT_rep1

value: Swiss Webster


title: E9_HDAC2_CnR_rep1

value: ~3 litters FLs (400k cells)

value: forelimb bud


title: NICD_ATAC-seq_rep3

value: R26 N1IC lox/+ Mx1Cre

tag: cell type

tag: replicate


title: E10.5_GLI3_CnR_rep1


title: NICD_NDME_ATAC-seq_rep1


title: NICD_ATAC-seq_rep2


title: E9_HDAC2_CnR_rep2


title: NOTCHWT_TCFWT_ATAC-seq_rep2

value: wild type

value: Controlled injection with 2ug/g body weight poly(I:C)


title: NICD_NDME_ATAC-seq_rep3


title: E10.5_HDAC1_CnR_rep2


title: NOTCHWT_TCFWT_ATAC-seq_rep1


title: E9_HDAC1_CnR_rep1


title: NICD_ATAC-seq_rep4


title: NICD_TCFWT_ATAC-seq_rep3


title: E9_GLI3_CnR_rep2


title: E10.5_HDAC1_CnR_rep1


title: E10.5_GLI3_CnR_rep2


title: NICD_TCFWT_ATAC-seq_rep2


title: NICD_TCFWT_ATAC-seq_rep1


title: E9_GLI3_CnR_rep1


title: E10.5_HDAC1_CnR_rep3


title: NICD_TCFKO_ATAC-seq_rep3

value: R26 N1IC lox/+ Tcf7 lox/lox Mx1Cre


title: NOTCHWT_TCFWT_ATAC-seq_rep3


title: NICD_ATAC-seq_rep1


title: NICD_TCFKO_ATAC-seq_rep2


title: E10.5_HDAC2_CnR_rep3


title: NICD_TCFKO_ATAC-seq_rep1


title: E9_H3K4me1_CnT_rep2


title: NICD_NDME_ATAC-seq_rep4


title: CTCF_NICD_TCF_rep3

data_processing:
Illumina bcl2fastq 2.19.1 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed.
Reads were aligned to mouse genome build mm10 using BWA (0.7.13).
Properly paired good quality reads were filtered with samtools (v1.5) using samtools view -b -h -f 0x2 -q 2.
Peaks were called using MACS2 (2.1.1.20160309) using macs2 callpeak -t -f BAMPE -g mm -B --nomodel --nolambda -q 0.05 --keep-dup all --call-summits (CTCF) or --broad --broad-cutoff 0.1 (Other ChIP).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file for each ChIP sample- generated by MACS2

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed on chromatin from 20,000 sortedLSK cells. Sorted cells were cross-linked with 1% methanol-free formaldehyde (Pierce Life Technologies Cat# 28906), quenched with 0.125 M glycine and frozen at -80 °C and stored until further processing.
ChIP reaction was performed with Diagenode True MicroChIP Kit (Diagenode Cat# C01010130) with modifications of the manual detailed below. Lysed samples were sonicated using Diagenode Bioruptor Pico (Diagenode Cat# B01060010).
ChIP and input libraries for sequencing were prepared with MicroPlex Library Preparation Kit (Diagenode Cat# C0101134). Size selection steps were performed with Agencourt AMPure XP magnetic beads (Beckman Coulter Cat# A63880).
sequencing protocol: The libraries were sequenced by Gene Expression Core Facility of EPFL using the Illumina NextSeq 500 platform and the 75-bp paired-end configuration to obtain at least 30 million reads per sample.

tag: facs sorting

value: Target population from bone marrow:CD45.2+ eGFP+ Lin- Sca1+ cKit+

tag: chip antibody

value: 1μg CTCF antibody (Diagenode Cat# C15410210, RRID:AB_2753160)


title: CTCF_CTRL_rep3

value: Target population from bone marrow:Lin- Sca1+ cKit+


title: CTCF_CTRL_rep2


title: CTCF_CTRL_rep1


title: Input_NICD_rep2


title: NICD_TCFWT_rep2_Input


title: NOTCHWT_TCFWT_rep1_Input


title: CTCF_NICD_TCF_rep1


title: NICD_TCFKO_rep3_Input


title: CTCF_NICD_rep1


title: CTCF_NICD_rep3


title: CTCF_NICD_rep2


title: NOTCHWT_TCFWT_rep3_H3K27ac

value: H3K27ac antibody (Diagenode Cat# C15410196, RRID:AB_2637079)


title: Dot6_rpt4

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

institute: Weizmann Institute

data_processing:
Library strategy: Chec-Seq
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S2988C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Genome_build: GCA_000146045.2 (R64)
Supplementary_files_format_and_content: zip of *.out file contains gneome coverage for all 12,157,105  bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

tag: genotype

value: BY4741 DOT6::Dot6-Mnase

tag: expname

tag: strainid


title: Rlm1_rpt3

value: BY4741 RLM1::Rlm1-Mnase


title: CTCF_NICD_TCF_rep2


title: NOTCHWT_TCFWT_rep1_H3K27ac


title: NICD_TCFWT_rep3_H3K27ac


title: Fkh2_lactis_rpt1

value: BY4741 FKH2::K.lactis F04631-Mnase FKH1::kanMX


title: NOTCHWT_TCFWT_rep2_H3K27ac


title: Fkh2_lactis_rpt2


title: NICD_TCFWT_rep2_H3K27ac


title: Dot6_rpt3


title: NICD_TCFWT_rep1_H3K27ac


title: Rlm1_rpt4


title: Yap7_lactis_rpt3

value: BY4741 YAP7::K.lactis D14399-Mnase YAP5::kanMX


title: NICD_TCFKO_rep3_H3K27ac

value: Mx1Cre induction 2ug/g b.w. poly(I:C)


title: Input_NICD_TCF_rep3


title: Input_CTRL_rep1


title: Yap7_dYAP5_rpt4

value: BY4741 YAP7::Yap7-Mnase YAP5::kanMX


title: Nrg2_lactis_rpt3

value: BY4741 NRG2::K.lactis F18524-Mnase(kanMX) NRG1::natNT2


title: NOTCHWT_TCFKO_3 [Tcf7-Tg-3_S10]

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed. Reads were aligned to mouse genome build mm10 using HISAT2, v2.0.3beta aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with EdgeR(3.28.0) TMM method and log2 transformed with voom (limma3.42.0).
Batch effect was removed using ComBat (sva3.34.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID.

extract_protocol:
Cells were isolated from sorted bone marrow LSK and RNA was harvested using PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific, KIT0204) according to manufacturer’s instructions
We performed cDNA library with the "Illumina TruSeq RNA Library Prep kit"
We then performed a Nextera XT library prep according to Illumina protocol 15031942 Rev. E. We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation 4200. We performed a single end 75nt sequencings on NextSeq 500.

value: Tcf7 lox/lox Mx1Cre


title: Mga2_dSPT23_rpt2

value: BY4741 MGA2::Mga2-Mnase SPT23::kanMX


title: NICD_TCFKO_rep2_H3K27ac


title: NOTCHWT_TCFKO_2 [Tcf7-Tg-2_S9]


title: Tbs1_lactis_rpt3

value: BY4741 TBS1::K.lactis F02750-Mnase HAL9::kanMX


title: NICD_TCFKO_rep1_H3K27ac


title: Yap7_lactis_rpt2


title: Yhp1_lactis_rpt4

value: BY4741 YHP1::K.lactis B01584-Mnase YOX1::kanMX


title: Dot6_lactis_rpt4

value: BY4741 DOT6::K.lactis E19933-Mnase TOD6::kanMX


title: NICD_TCFKO_2 [RNIC-Tg-2_S8]

value: R26 N1IC lox/+ Tcf7 lox/lox Mx1Cre


title: NICD_TCFWT_3 [RNIC-CTRL-3_S5]

value: R26 N1IC lox/+ Mx1Cre

value: Target population from bone marrow:CD45.2+ eGFP+ Lin- Sca1+ cKit+


title: Yap7_dYAP5_rpt3


title: NICD_TCFWT_1 [RNIC-CTRL-1_S5]


title: NICD_TCFKO_1 [RNIC-Tg-1_S7]


title: Rsf2_dTDA9_rpt3

value: BY4741 RSF2::Rsf2-Mnase TDA9::kanMX


title: Swi5_lactis_rpt3

value: BY4741 SWI5::K.lactis D16456-Mnase(kanMX) ACE2::LEU


title: NOTCHWT_TCFKO_1 [Tcf7-Tg-1_S11]

value: Target population from bone marrow:Lin- Sca1+ cKit+


title: NOTCHWT_TCFWT_2 [RAD-14187_S2]

value: wild type

value: Controlled injection with 2ug/g body weight poly(I:C)


title: Stp2_dSTP1_rpt3

value: BY4741 STP2::Stp2-Mnase STP1::kanMX


title: NOTCHWT_TCFWT_3 [RAD-14190-1_S1]


title: NICD_TCFWT_2 [RNIC-CTRL-2_S6]

value: Mx1Cre induction 2ug/g b.w. poly(I:C)


title: Dal80_dGZF3_rpt5

value: BY4741 DAL80::Dal80-Mnase GZF3::kanMX


title: Mga2_dSPT23_rpt1


title: NOTCHWT_TCFWT_1 [RAD-14186_S1]


title: DE_rep2

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to GRCh38 whole genome using HISAT2 version 2.1.1.
Raw reads were counted with FeatureCounts using gencode_v31 human gene annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: featureCount.txt

source_name: definitive endoderm cells

growth_protocol: Undifferentiated human embryonic stem cells (ESCs) HUES8 were maintained in mTeSR1 (StemCell Technologies) on Matrigel-coated cell culture plate at 37℃ with 5% CO2. For targeted differentiation of ESCs to definitive endoderm, ESCs were cultured in DMEM-F12 (Gibco, Cat# C11330500BT) medium supplemented with 0.2% BSA (Yeasen Biotechnology), 100 ng/mL Activin A (PeproTech), 2.5 mM CHIR99021 (Selleck, Cat# S2924) for 24 h, then the CHIR99021 was removed from medium for the following 2-4 days.

extract_protocol:
RNA was extracted with HiPure Total RNA Mini Kit (Magen, Cat#R4111-03).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: human embryonic stem cell line HuES8

value: definitive endoderm cells


title: DE_rep1


title: D2_rep2

source_name: endoderm cells induced from hESCs for 2 days

value: endoderm cells


title: Yap7_lactis_rpt1

value: BY4741 YAP7::K.lactis D14399-Mnase YAP5::kanMX


title: NICD_TCFKO_3 [RNIC-Tg-3_S6]


title: Upc2_lactis_rpt2

value: BY4741 UPC2::K.lactis A04169-Mnase ECM22::kanMX


title: Upc2_lactis_rpt1


title: ES_rep1

source_name: embryonic stem cells

value: embryonic stem cells


title: Dot6_lactis_rpt3

value: BY4741 DOT6::K.lactis E19933-Mnase TOD6::kanMX


title: Mig3_dMIG2_rpt2


title: ES_rep2


title: D2_rep1


title: Yhp1_lactis_rpt3

value: BY4741 YHP1::K.lactis B01584-Mnase YOX1::kanMX


title: Mig3_dMIG2_rpt1


title: Yap7_dYAP5_rpt2

value: BY4741 YAP7::Yap7-Mnase YAP5::kanMX


title: Nrg2_lactis_rpt2

value: BY4741 NRG2::K.lactis F18524-Mnase(kanMX) NRG1::natNT2


title: Stp2_dSTP1_rpt2


title: Cas_Protein_szrd1_2

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

description:
Single cell  zebrafish embryos were injected with RfxCas13d protein (3ng/embryo), with gRNAs targeting szrd1 (500-600 pg/embryo).
cas_protein_szrd1_2

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner (version STAR_2.6.1c ), using projects gene models. TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: danRer11 with RFP mRNA sequence
Supplementary_files_format_and_content: TPM gene expression in excel file

organism: Danio rerio

growth_protocol: Transgenic zebrafish were kept according to the National Research Council’s and IACUC approved protocol 2016-1059 at the Stowers Institute for Medical Research zebrafish facility.

extract_protocol:
Total RNA was extracted using Trizol
mRNAseq libraries were generated from 500 ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent).  Libraries were made according to the manufacturer’s directions for the TruSeq Stranded mRNA LP Sample Prep Kit (Illumina, Cat. No. 20020594) with TruSeq RNA Single Indexes Set A and B (Illumina, Cat. No. 20020492 and 20020493). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 75bp single reads on a high-output flowcell using the Illumina NextSeq instrument.

treatment_protocol: Zebrafish embryos were injected with the indicated mRNA and/or guideRNAs and after 6 hours post injection.

tag: tissue

value: embryos


title: Cas_Protein_szrd1_1

description:
Single cell  zebrafish embryos were injected with RfxCas13d protein (3ng/embryo), with gRNAs targeting szrd1 (500-600 pg/embryo).
cas_protein_szrd1_1


title: Rsf2_dTDA9_rpt2

value: BY4741 RSF2::Rsf2-Mnase TDA9::kanMX


title: Swi5_lactis_rpt2

value: BY4741 SWI5::K.lactis D16456-Mnase(kanMX) ACE2::LEU


title: Sut2_dSUT1_rpt3

value: BY4741 SUT2::Sut2-Mnase SUT1::kanMX


title: Cas_protein_2

description:
Single cell  zebrafish embryos were injected with RfxCas13d protein (3ng/embryo) (control for szrd1).
cas_protein_2


title: Dal80_dGZF3_rpt4


title: Cas_protein_1

description:
Single cell  zebrafish embryos were injected with RfxCas13d protein (3ng/embryo) (control for szrd1).
cas_protein_1


title: Smp1_dRLM1_rpt3

value: BY4741 SMP1::Smp1-Mnase RLM1::kanMX


title: Tbs1_lactis_rpt2

value: BY4741 TBS1::K.lactis F02750-Mnase HAL9::kanMX


title: Cas_P_dnd_GFP_2

description:
Single cell  zebrafish embryos were injected with RfxCas13d protein (3npg/embryo), with gfp mRNA (40 pg/embryo) containing the 3’UTR of nanos and with gRNAs targeting dnd1 (500-600 pg/embryo).
cas_p_dnd_gfp_2


title: Yhp1_lactis_rpt2


title: Cas_P_dndcontrol_2

description:
Single cell  zebrafish embryos were injected with RfxCas13d protein (3ng/embryo), with gfp mRNA (40 pg/embryo) containing the 3’UTR of nanos (control for dnd1).
cas_p_dndcontrol_2


title: Nrg2_lactis_rpt1


title: Cas_P_dnd_GFP_1

description:
Single cell  zebrafish embryos were injected with RfxCas13d protein (3ng/embryo), with gfp mRNA (40 pg/embryo) containing the 3’UTR of nanos and with gRNAs targeting dnd1 (500-600 pg/embryo).
cas_p_dnd_gfp_1


title: Ecm22_Upc2_DBD_rpt2

value: BY4741 ECM22::Ecm22-Upc2DBD-Mnase


title: Cas_2

description:
Single cell zebrafish embryos were injected with RfxCas13d mRNA (200-250 pg/embryo) (control for szrd1).
cas_2


title: Yhp1_Yox1_DBD_rpt2

value: BY4741 YHP1::Yhp1-Yox1DBD-Mnase


title: Tod6_Dot6_DBD_rpt3

value: BY4741 TOD6::Tod6-Dot6DBD-Mnase


title: Cas_P_dndcontrol_1

description:
Single cell  zebrafish embryos were injected with RfxCas13d protein (3ng/embryo), with gfp mRNA (40 pg/embryo) containing the 3’UTR of nanos (control for dnd1).
cas_p_dndcontrol_1


title: 6_2

description:
Single cell zebrafish embryos were injected with RfxCas13d mRNA (200-250 pg/embryo) and with gRNAs targeting szrd1 (500-600 pg/embryo).
6_2


title: Tos8_Cup9_DBD_rpt4

value: BY4741 TOS8::Tos8-Cup9DBD-Mnase


title: Swi5_Ace2_DBD_rpt3

value: BY4741 SWI5::Swi5-Ace2DBD-Mnase


title: Rph1_Gis1_DBD_rpt4

value: BY4741 RPH1::Rph1-Gis1DBD-Mnase


title: Cas_1

description:
Single cell zebrafish embryos were injected with RfxCas13d mRNA (200-250 pg/embryo) (control for szrd1).
cas_1


title: Gis1_Rph1_DBD_rpt4

value: BY4741 GIS1::Gis1-Rph1DBD-Mnase


title: Dot6_Tod6_DBD_rpt2

value: BY4741 DOT6::Dot6-Tod6DBD-Mnase


title: Acrolein

city: Kagoshima

first: Takuro

last: Nishikawa

address: Sakuragaoka 8-35-1

department: Pediatrics

institute: Kagoshima University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: heart tissue, Acrolein

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: C57BL/6J mice were housed individually in a temperature-controlled facility (22 ± 2 ℃) under a 12 hours light/dark cycle (light from 7:00 to 19:00). All mice were free access to water and food.

extract_protocol: The total RNA was isolated from heart tissue using NucleoSpin® RNA/Protein kit (MACHEREY-NAGEL., Düren, Germany).

treatment_protocol: Six-week-old female mice were intraperitoneally injected with cyclophosphamide (CY, 400 mg/kg), acrolein (5 mg/kg), or N-acetyl cysteine (200 mg/kg) + CY once a daily for two days. Control mice received only normal saline.

tag: strain

value: heart


title: 6_1

description:
Single cell zebrafish embryos were injected with RfxCas13d mRNA (200-250 pg/embryo) and with gRNAs targeting szrd1 (500-600 pg/embryo).
6_1


title: NAC_CY

source_name: heart tissue, N-acethyl cysteine and Cyclophosphamide


title: CY

source_name: heart tissue, Cyclophosphamide


title: Fkh2_Fkh1_DBD_rpt3

value: BY4741 FKH2::Fkh2-Fkh1DBD-Mnase


title: Non_injected_6h_Rep1

description: Single cell transgenic zebrafish embryos expressing RFP (maternally provided) none injected.

extract_protocol:
Total RNA was extracted using Trizol
mRNAseq libraries were generated from 500 ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent).  Libraries were made according to the manufacturer’s directions for the TruSeq Stranded mRNA LP Sample Prep Kit (Illumina, Cat. No. 20020594) with TruSeq RNA Single Indexes Set A and B (Illumina, Cat. No. 20020492 and 20020493). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 75bp single reads on a high-output flowcell using the Illumina NextSeq instrument.
Poly(A)_enrichment

tag: developmental stage

tag: treatment

value: none injected.


title: Cas13d_RFP_6h_Rep1

description: Single cell transgenic zebrafish embryos expressing RFP (maternally provided) were injected with RfxCas13d mRNA (200-250 pg/embryo) and with gRNAs targeting rfp (500-600 pg/embryo).

value: embryos


title: Cas13d_RFP_6h_Rep2

value: injected with RfxCas13d mRNA (200-250 pg/embryo) and with gRNAs targeting rfp (500-600 pg/embryo).


title: NS

source_name: heart tissue, Normal saline


title: Fkh1_Fkh2_DBD_rpt4

value: BY4741 FKH1::Fkh1-Fkh2DBD-Mnase


title: Non_injected_6h_Rep2


title: Cas13d_nanog_6h_Rep2

description: Single cell transgenic zebrafish embryos expressing RFP (maternally provided) were injected with RfxCas13d mRNA (200-250 pg/embryo) and with gRNAs targeting nanog (500-600 pg/embryo).


title: Yox1_Yhp1_DBD_rpt3

value: BY4741 YOX1::Yox1-Yhp1DBD-Mnase


title: Cas13d_nanog_6h_Rep1

value: injected with RfxCas13d mRNA (200-250 pg/embryo) and with gRNAs targeting nanog (500-600 pg/embryo).


title: Cas13d_DND_6h_554_Rep2

description: Single cell transgenic zebrafish embryos expressing RFP (maternally provided) were injected with RfxCas13d mRNA (200-250 pg/embryo), with gfp mRNA (40 pg/embryo) containing the 3’UTR of nanos and with gRNAs targeting dnd (500-600 pg/embryo).


title: Pdr8_Yrr1_DBD_rpt3

value: BY4741 PDR8::Pdr8-Yrr1DBD-Mnase


title: Yrr1_Pdr8_DBD_rpt4

value: BY4741 YRR1::Yrr1-Pdr8DBD-Mnase


title: Cas13d_DND_6h_554_Rep1

value: injected with RfxCas13d mRNA (200-250 pg/embryo), with gfp mRNA (40 pg/embryo) containing the 3’UTR of nanos and with gRNAs targeting dnd (500-600 pg/embryo).


title: Cas13d_6h_Rep1

description: Single cell transgenic zebrafish embryos expressing RFP (maternally provided) were injected with RfxCas13d mRNA (200-250 pg/embryo).


title: Stp2_dSTP1_rpt1

value: BY4741 STP2::Stp2-Mnase STP1::kanMX


title: Vhr2_Vhr1_DBD_rpt3

value: BY4741 VHR2::Vhr2-Vhr1DBD-Mnase


title: Vhr1_Vhr2_DBD_rpt3

value: BY4741 VHR1::Vhr1-Vhr2DBD-Mnase


title: Yhp1_lactis_rpt1

value: BY4741 YHP1::K.lactis B01584-Mnase YOX1::kanMX


title: Cas13d_6h_Rep2

value: injected with RfxCas13d mRNA (200-250 pg/embryo).


title: Smp1_dRLM1_rpt2

value: BY4741 SMP1::Smp1-Mnase RLM1::kanMX


title: Cas13d_6h_554_Rep2

description: Single cell transgenic zebrafish embryos expressing RFP (maternally provided) were injected with RfxCas13d mRNA (200-250 pg/embryo) and gfp mRNA (40 pg/embryo) containing the 3’UTR of nanos.


title: C03_N-9-CALGB03-1049913-1

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description:
Sample_PRE_RNA_443
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

data_processing:
Basecalls by Casava.
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a.
Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.030 in ‘-quant’ mode, based on the STAR alignments.
Fixed upper quartile normalization.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: CALGB40603.389PreTreat.JUNCTION.salmon_gene_normalized.matrix_FOR_GEO.v2.txt: Tab-delimited, normalized, transcript abundance estimates.

source_name: Breast

extract_protocol: Fresh-frozen RNA was isolated with Qiagen RNeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002).

value: Breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: C03_N-1-CALGB03-1051010-1

description:
Sample_PRE_RNA_435
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1046160-I-25

description:
Sample_PRE_RNA_436
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1035353-I-1

description:
Sample_PRE_RNA_438
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tos8_Cup9_DBD_rpt3

value: BY4741 TOS8::Tos8-Cup9DBD-Mnase


title: Yhp1_Yox1_DBD_rpt1

value: BY4741 YHP1::Yhp1-Yox1DBD-Mnase


title: Ecm22_Upc2_DBD_rpt1

value: BY4741 ECM22::Ecm22-Upc2DBD-Mnase


title: CALGB03-1048441-M-9

description:
Sample_PRE_RNA_439
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Dot6_Tod6_DBD_rpt1

value: BY4741 DOT6::Dot6-Tod6DBD-Mnase


title: C03_N-36-CALGB03-1052399-1

description:
Sample_PRE_RNA_426
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1049305-M-31

description:
Sample_PRE_RNA_434
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tod6_Dot6_DBD_rpt2

value: BY4741 TOD6::Tod6-Dot6DBD-Mnase


title: C03_R-39-CALGB03-1070415-1

description:
Sample_PRE_RNA_433
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rph1_Gis1_DBD_rpt3

value: BY4741 RPH1::Rph1-Gis1DBD-Mnase


title: CALGB03-1049905-1-M-44

description:
Sample_PRE_RNA_425
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Upc2_Ecm22_DBD_rpt4

value: BY4741 UPC2::Upc2-Ecm22DBD-Mnase


title: Gis1_Rph1_DBD_rpt3

value: BY4741 GIS1::Gis1-Rph1DBD-Mnase


title: Swi5_Ace2_DBD_rpt2

value: BY4741 SWI5::Swi5-Ace2DBD-Mnase


title: CALGB03-1049578-M-26

description:
Sample_PRE_RNA_423
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1030928-I-33

description:
Sample_PRE_RNA_422
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh2_Fkh1_DBD_rpt2

value: BY4741 FKH2::Fkh2-Fkh1DBD-Mnase


title: Fkh1_Fkh2_DBD_rpt3

value: BY4741 FKH1::Fkh1-Fkh2DBD-Mnase


title: C03_N-13-CALGB03-1049910-1

description:
Sample_PRE_RNA_420
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Cas13d_6h_554_Rep1

value: embryos

value: injected with RfxCas13d mRNA (200-250 pg/embryo) and gfp mRNA (40 pg/embryo) containing the 3’UTR of nanos.


title: Yox1_Yhp1_DBD_rpt2

value: BY4741 YOX1::Yox1-Yhp1DBD-Mnase


title: CALGB03-1049385-M-20

description:
Sample_PRE_RNA_418
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1048440-M-2

description:
Sample_PRE_RNA_415
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1039843-I-11

description:
Sample_PRE_RNA_414
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-37-CALGB03-1070805-1

description:
Sample_PRE_RNA_413
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Vhr2_Vhr1_DBD_rpt2

value: BY4741 VHR2::Vhr2-Vhr1DBD-Mnase


title: C03_N-26-CALGB03-1057599-1

description:
Sample_PRE_RNA_408
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma


title: C03_N-30-CALGB03-1057435-1

description:
Sample_PRE_RNA_410
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: C03-Q-32-CALGB03-1041110

description:
Sample_PRE_RNA_405
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-5-CALGB03-1035943

description:
Sample_PRE_RNA_412
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-33-CALGB03-1041343

description:
Sample_PRE_RNA_411
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1048658-M-3

description:
Sample_PRE_RNA_398
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh2_Fkh1_DBD_rpt1


title: C03_N-14-CALGB03-1050100-1

description:
Sample_PRE_RNA_390
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yox1_Yhp1_DBD_rpt1


title: Rph1_Gis1_DBD_rpt2


title: Gis1_Rph1_DBD_rpt2


title: Swi5_Ace2_DBD_rpt1


title: Upc2_Ecm22_DBD_rpt2


title: C03_Q-39-CALGB03-1070207-1

description:
Sample_PRE_RNA_389
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-10-CALGB03-1042640

description:
Sample_PRE_RNA_387
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tos8_Cup9_DBD_rpt2

value: BY4741 TOS8::Tos8-Cup9DBD-Mnase


title: Vhr2_Vhr1_DBD_rpt1


title: Pdr8_Yrr1_DBD_rpt1

value: BY4741 PDR8::Pdr8-Yrr1DBD-Mnase


title: C03_Q-5-CALGB03-1058024-1

description:
Sample_PRE_RNA_386
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1046544-I-26

description:
Sample_PRE_RNA_385
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047141-L-28

description:
Sample_PRE_RNA_402
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Vhr1_Vhr2_DBD_rpt1

value: BY4741 VHR1::Vhr1-Vhr2DBD-Mnase


title: CALGB03-1031975-I-42

description:
Sample_PRE_RNA_383
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh1_Fkh2_DBD_rpt2


title: Upc2_Ecm22_DBD_rpt3


title: Rph1_Gis1_DBD_rpt1


title: Tod6_Dot6_DBD_rpt1


title: Pdr8_Yrr1_DBD_rpt2


title: Vhr1_Vhr2_DBD_rpt2


title: Gis1_Rph1_DBD_rpt1


title: Upc2_Ecm22_DBD_rpt1


title: Yrr1_Pdr8_DBD_rpt3

value: BY4741 YRR1::Yrr1-Pdr8DBD-Mnase


title: CALGB03-1047677-L-48

description:
Sample_PRE_RNA_381
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1051284-1-M-48

description:
Sample_PRE_RNA_388
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1049032-M-17

description:
Sample_PRE_RNA_382
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tos8_Cup9_DBD_rpt1


title: C03_Q-36-CALGB03-1067496-1

description:
Sample_PRE_RNA_379
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh1_Fkh2_DBD_rpt1


title: C03-R-4-CALGB03-1050432-1

description:
Sample_PRE_RNA_372
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yrr1_Pdr8_DBD_rpt2


title: C03-Q-34-CALGB03-1042129

description:
Sample_PRE_RNA_374
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-25-CALGB03-1039199

description:
Sample_PRE_RNA_376
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yrr1_Pdr8_DBD_rpt1


title: CALGB03-1047683-M-11

description:
Sample_PRE_RNA_371
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yap5_dYAP7_rpt2

value: BY4741 YAP5::Yap5-Mnase YAP7::kanMX


title: Rsf2_dTDA9_rpt1

value: BY4741 RSF2::Rsf2-Mnase TDA9::kanMX


title: CALGB03-1047340-L-33

description:
Sample_PRE_RNA_365
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tos8_dCUP9_rpt3

value: BY4741 TOS8::Tos8-Mnase CUP9::kanMX


title: Rlm1_lactis_rpt2

value: BY4741 RLM1::K.lactis E24025-Mnase SMP1::kanMX


title: Gzf3_lactis_rpt4

value: BY4741 GZF3::K.lactis F21296-Mnase DAL80::kanMX


title: C03-Q-12-CALGB03-1042860

description:
Sample_PRE_RNA_364
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-21-CALGB03-1028673

description:
Sample_PRE_RNA_356
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Swi5_lactis_rpt1

value: BY4741 SWI5::K.lactis D16456-Mnase(kanMX) ACE2::LEU


title: CALGB03-1048009-L-42

description:
Sample_PRE_RNA_355
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-24-CALGB03-1052191-1

description:
Sample_PRE_RNA_353
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yap7_dYAP5_rpt1

value: BY4741 YAP7::Yap7-Mnase YAP5::kanMX


title: CALGB03-1031547-I-39

description:
Sample_PRE_RNA_350
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yap5_dYAP7_rpt1


title: Dal80_dGZF3_rpt3

value: BY4741 DAL80::Dal80-Mnase GZF3::kanMX


title: Yap1_lactis_rpt4

value: BY4741 YAP1::K.lactis A01760-Mnase(kanMX) YAP2::natNT2


title: CALGB03-1049338-M-25

description:
Sample_PRE_RNA_343
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047964-L-47

description:
Sample_PRE_RNA_344
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-44-CALGB03-1070626-1

description:
Sample_PRE_RNA_349
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-23-CALGB03-1051770-1

description:
Sample_PRE_RNA_342
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tda9_dRSF2_rpt3

value: BY4741 TDA9::Tda9-Mnase RSF2::kanMX


title: C03-R-11-CALGB03-1065957-1

description:
Sample_PRE_RNA_370
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tos8_dCUP9_rpt2


title: Gzf3_lactis_rpt3


title: Yap1_lactis_rpt3


title: CALGB03-1031056-I-37

description:
Sample_PRE_RNA_337
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tda9_dRSF2_rpt4


title: C03_Q-28-CALGB03-1067168-1

description:
Sample_PRE_RNA_369
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-R-3-CALGB03-1049379

description:
Sample_PRE_RNA_366
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-7-CALGB03-1039716

description:
Sample_PRE_RNA_336
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Swi5_rpt2

value: BY4741 SWI5::Swi5-Mnase(kanMX) , ho::Nat-GFP


title: C03_Q-22-CALGB03-1067129-1

description:
Sample_PRE_RNA_334
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma


title: Ace2_rpt2


title: C03_N-16-CALGB03-1050640-1

description:
Sample_PRE_RNA_351
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: C03-Q-1-CALGB03-1031844

description:
Sample_PRE_RNA_333
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047574-I-29

description:
Sample_PRE_RNA_332
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh2_rpt2

value: BY4741 FKH2::Fkh2-Mnase(kanMX)


title: Rlm1_lactis_rpt1


title: Ace2_dSWI5_rpt2


title: CALGB03-1048654-M-14

description:
Sample_PRE_RNA_328
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh1_rpt2

value: BY4741 FKH1::Fkh1-Mnase(kanMX)


title: Swi5_dACE2_rpt2


title: C03_Q-21-CALGB03-1064504-1

description:
Sample_PRE_RNA_325
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh2_dFKH1_rpt2


title: C03-Q-26-CALGB03-1039362

description:
Sample_PRE_RNA_341
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-19-CALGB03-1048930

description:
Sample_PRE_RNA_321
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1049306-M-40

description:
Sample_PRE_RNA_322
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Nrg1_dNRG2_rpt2


title: Mig2_dMIG3_rpt2


title: CALGB03-1049345-M-41

description:
Sample_PRE_RNA_323
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-21-CALGB03-1057515-1

description:
Sample_PRE_RNA_320
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Nrg2_dNRG1_rpt2


title: Stp1_dSTP2_rpt2

value: BY4741 STP1::Stp1-Mnase STP2::kanMX


title: C03_N-22-CALGB03-1051649-1

description:
Sample_PRE_RNA_318
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Sut2_dSUT1_rpt2

value: BY4741 SUT2::Sut2-Mnase SUT1::kanMX


title: Dal80_dGZF3_rpt2


title: CALGB03-1049343-M-19

description:
Sample_PRE_RNA_317
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Met32_dMET31_rpt2

value: BY4741 MET32::Met32-Mnase MET31::kanMX


title: CALGB03-1047508-L-37

description:
Sample_PRE_RNA_313
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Met31_dMET32_rpt3

value: BY4741 MET31::Met31-Mnase MET32::kanMX


title: CALGB03-1049117-M-23

description:
Sample_PRE_RNA_309
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1046869-L-38

description:
Sample_PRE_RNA_312
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Dal80_dGZF3_rpt1


title: CALGB03-1049463-M-28

description:
Sample_PRE_RNA_308
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-4-CALGB03-1049761-1

description:
Sample_PRE_RNA_326
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Swi5_rpt1


title: CALGB03-1048563-M-13

description:
Sample_PRE_RNA_327
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh1_dFKH2_rpt2


title: C03-Q-28-CALGB03-1042137

description:
Sample_PRE_RNA_306
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh1_rpt1


title: C03-R-2-CALGB03-1048955

description:
Sample_PRE_RNA_303
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-3-CALGB03-1037177

description:
Sample_PRE_RNA_302
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1035294-I-34

description:
Sample_PRE_RNA_301
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh2_rpt1


title: Ace2_dSWI5_rpt1


title: Swi5_dACE2_rpt1


title: Ace2_rpt1


title: C03-R-5-CALGB03-1050731-1

description:
Sample_PRE_RNA_298
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Fkh2_dFKH1_rpt1


title: Fkh1_dFKH2_rpt1


title: Nrg2_dNRG1_rpt1


title: C03_Q-35-CALGB03-1065572-1

description:
Sample_PRE_RNA_295
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1048041-M-6

description:
Sample_PRE_RNA_300
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1040149-I-15

description:
Sample_PRE_RNA_297
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1049218-I-32

description:
Sample_PRE_RNA_316
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Nrg1_dNRG2_rpt1


title: Sut1_dSUT2_rpt2

value: BY4741 SUT1::Sut1-Mnase SUT2::kanMX


title: C03_N-12-CALGB03-1051444-1

description:
Sample_PRE_RNA_291
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Mig2_dMIG3_rpt1


title: Smp1_dRLM1_rpt1

value: BY4741 SMP1::Smp1-Mnase RLM1::kanMX


title: C03_Q-33-CALGB03-1067279-1

description:
Sample_PRE_RNA_286
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1049339-M-32

description:
Sample_PRE_RNA_287
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-29-CALGB03-1052502-1

description:
Sample_PRE_RNA_288
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Stp1_dSTP2_rpt1


title: Sut1_dSUT2_rpt1


title: C03-Q-31-CALGB03-1041254

description:
Sample_PRE_RNA_282
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1042508-K-44

description:
Sample_PRE_RNA_279
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1048006-M-10

description:
Sample_PRE_RNA_283
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rph1_dGIS1_rpt5

value: BY4741 RPH1::Rph1-Mnase GIS1::kanMX


title: Tbs1_dHAL9_rpt5

value: BY4741 TBS1::Tbs1-Mnase HAL9::kanMX


title: Yap2_dYAP1_rpt3


title: Yap1_dYAP2_rpt3


title: C03_Q-17-CALGB03-1066096-1

description:
Sample_PRE_RNA_270
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1039679-I-9

description:
Sample_PRE_RNA_271
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-7-CALGB03-1050667-1

description:
Sample_PRE_RNA_277
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1036043-I-35

description:
Sample_PRE_RNA_276
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tda9_dRSF2_rpt2


title: CALGB03-1050651-1-M-45

description:
Sample_PRE_RNA_269
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Msn4_dMSN2_rpt2


title: Ixr1_lactis_rpt2

value: BY4741 IXR1::K.lactis E18481-Mnase ABF2::kanMX


title: CALGB03-1030944-I-36

description:
Sample_PRE_RNA_268
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-R-8-CALGB03-1057523-1

description:
Sample_PRE_RNA_290
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tda9_lactis_rpt2

value: BY4741 TDA9::K.lactis B04477-Mnase RSF2::kanMX


title: Sut2_dSUT1_rpt1


title: Met31_dMET32_rpt2


title: CALGB03-1048804-M-29

description:
Sample_PRE_RNA_284
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-10-CALGB03-1058284-1

description:
Sample_PRE_RNA_274
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-24-CALGB03-1066063-1

description:
Sample_PRE_RNA_266
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Met32_dMET31_rpt1


title: Tbs1_lactis_rpt1

value: BY4741 TBS1::K.lactis F02750-Mnase HAL9::kanMX


title: Vhr1_lactis_rpt2

value: BY4741 VHR1::K.lactis C08151-Mnase VHR2::kanMX


title: Ixr1_dABF2_rpt2

value: BY4741 IXR1::Ixr1-Mnase ABF2::kanMX


title: C03-Q-20-CALGB03-1047685

description:
Sample_PRE_RNA_260
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma


title: Skn7_lactis_rpt2

value: BY4741 SKN7::K.lactis A10219-Mnase HMS2::kanMX


title: C03_R-9-CALGB03-1068170-1

description:
Sample_PRE_RNA_258
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: C03_N-17-CALGB03-1050852-1

description:
Sample_PRE_RNA_259
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yap1_lactis_rpt2

value: BY4741 YAP1::K.lactis A01760-Mnase(kanMX) YAP2::natNT2


title: Tos8_dCUP9_rpt1

value: BY4741 TOS8::Tos8-Mnase CUP9::kanMX


title: CALGB03-1048661-L-45

description:
Sample_PRE_RNA_255
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1039849-I-10

description:
Sample_PRE_RNA_251
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1037609-I-3

description:
Sample_PRE_RNA_250
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Ixr1_dABF2_rpt1


title: C03_Q-4-CALGB03-1057817-1

description:
Sample_PRE_RNA_246
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047373-L-26

description:
Sample_PRE_RNA_243
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tda9_dRSF2_rpt1

value: BY4741 TDA9::Tda9-Mnase RSF2::kanMX


title: Rph1_dGIS1_rpt4


title: Yap2_dYAP1_rpt2


title: Tbs1_dHAL9_rpt4


title: Yap1_dYAP2_rpt2


title: CALGB03-1050822-1-M-46

description:
Sample_PRE_RNA_241
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Msn4_dMSN2_rpt1


title: Ixr1_lactis_rpt1


title: C03-Q-35-CALGB03-1042329

description:
Sample_PRE_RNA_240
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-43-CALGB03-1069389-1

description:
Sample_PRE_RNA_236
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tda9_lactis_rpt1


title: C03_R-8-CALGB03-1068100-1

description:
Sample_PRE_RNA_264
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1050333-1-M-22

description:
Sample_PRE_RNA_262
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rph1_lactis_rpt2

value: BY4741 RPH1::K.lactis C17710-Mnase GIS1::kanMX


title: Rph1_lactis_rpt1


title: CALGB03-1048198-L-43

description:
Sample_PRE_RNA_230
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047800-M-12

description:
Sample_PRE_RNA_229
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Skn7_lactis_rpt1


title: C03-Q-24-CALGB03-1035623

description:
Sample_PRE_RNA_228
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1040774-I-16

description:
Sample_PRE_RNA_227
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1041010-I-17

description:
Sample_PRE_RNA_226
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Dot6_lactis_rpt2

value: BY4741 DOT6::K.lactis E19933-Mnase TOD6::kanMX


title: Yap1_dYAP2_rpt1


title: C03_N-19-CALGB03-1052688-1

description:
Sample_PRE_RNA_224
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-48-CALGB03-1070898-1

description:
Sample_PRE_RNA_218
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-26-CALGB03-1066327-1

description:
Sample_PRE_RNA_221
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047087-L-36

description:
Sample_PRE_RNA_222
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Pdr3_dPDR1_rpt4

value: BY4741 PDR3::Pdr3-Mnase PDR1::kanMX


title: Tbs1_dHAL9_rpt3


title: C03_R-41-CALGB03-1071204-1

description:
Sample_PRE_RNA_242
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Cup9_dTOS8_rpt2

value: BY4741 CUP9::Cup9-Mnase TOS8::kanMX


title: Rlm1_dSMP1_rpt2

value: BY4741 RLM1::Rlm1-Mnase SMP1::kanMX


title: C03-Q-36-CALGB03-1041146

description:
Sample_PRE_RNA_216
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yap4_dYAP6_rpt2

value: BY4741 YAP4::Yap4-Mnase YAP6::kanMX


title: CALGB03-1046727-I-28

description:
Sample_PRE_RNA_217
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yap6_dYAP4_rpt2

value: BY4741 YAP6::Yap6-Mnase YAP4::kanMX


title: C03_Q-41-CALGB03-1068000-1

description:
Sample_PRE_RNA_215
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yox1_dYHP1_rpt2

value: BY4741 YOX1::Yox1-Mnase YHP1::kanMX


title: CALGB03-1049185-M-37

description:
Sample_PRE_RNA_235
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-16-CALGB03-1065965-1

description:
Sample_PRE_RNA_213
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yhp1_dYOX1_rpt2

value: BY4741 YHP1::Yhp1-Mnase YOX1::kanMX


title: CALGB03-1047684-M-15

description:
Sample_PRE_RNA_212
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Pdr8_dYRR1_rpt2

value: BY4741 PDR8::Pdr8-Mnase YRR1::kanMX


title: C03-Q-29-CALGB03-1040791

description:
Sample_PRE_RNA_210
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rph1_dGIS1_rpt3

value: BY4741 RPH1::Rph1-Mnase GIS1::kanMX


title: Vhr1_lactis_rpt1

value: BY4741 VHR1::K.lactis C08151-Mnase VHR2::kanMX


title: C03-Q-14-CALGB03-1046736

description:
Sample_PRE_RNA_208
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma


title: Oaf1_dPIP2_rpt3

value: BY4741 OAF1::Oaf1-Mnase PIP2::kanMX


title: Yap1_lactis_rpt1

value: BY4741 YAP1::K.lactis A01760-Mnase(kanMX) YAP2::natNT2


title: CALGB03-1048807-M-16

description:
Sample_PRE_RNA_207
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: Yap2_dYAP1_rpt1


title: Pdr3_dPDR1_rpt3


title: CALGB03-1046260-I-23

description:
Sample_PRE_RNA_205
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1039557-I-8

description:
Sample_PRE_RNA_198
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-27-CALGB03-1042221

description:
Sample_PRE_RNA_202
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tbs1_dHAL9_rpt2

value: BY4741 TBS1::Tbs1-Mnase HAL9::kanMX


title: C03-Q-13-CALGB03-1046242

description:
Sample_PRE_RNA_203
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rlm1_dSMP1_rpt1


title: Cup9_dTOS8_rpt1


title: Phd1_dSOK2_rpt2

value: BY4741 PHD1::Phd1-Mnase SOK2::kanMX


title: C03_N-34-CALGB03-1051655-1

description:
Sample_PRE_RNA_195
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047435-L-34

description:
Sample_PRE_RNA_196
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047503-L-41

description:
Sample_PRE_RNA_194
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yap4_dYAP6_rpt1


title: Yap6_dYAP4_rpt1


title: Yox1_dYHP1_rpt1


title: C03-Q-23-CALGB03-1039180

description:
Sample_PRE_RNA_190
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yhp1_dYOX1_rpt1


title: C03_N-11-CALGB03-1050429-1

description:
Sample_PRE_RNA_189
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rph1_dGIS1_rpt2


title: C03_N-2-CALGB03-1051016-1

description:
Sample_PRE_RNA_192
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Oaf1_dPIP2_rpt2


title: CALGB03-1048351-L-44

description:
Sample_PRE_RNA_188
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-12-CALGB03-1058343-1

description:
Sample_PRE_RNA_187
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1042371-I-20

description:
Sample_PRE_RNA_186
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1050993-1-M-47

description:
Sample_PRE_RNA_185
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yrr1_dPDR8_rpt2

value: BY4741 YRR1::Yrr1-Mnase PDR8::kanMX


title: CALGB03-1040022-I-12

description:
Sample_PRE_RNA_206
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-42-CALGB03-1070396-1

description:
Sample_PRE_RNA_184
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Gzf3_lactis_rpt2

value: BY4741 GZF3::K.lactis F21296-Mnase DAL80::kanMX


title: Dot6_lactis_rpt1

value: BY4741 DOT6::K.lactis E19933-Mnase TOD6::kanMX


title: CALGB03-1046337-L-35

description:
Sample_PRE_RNA_180
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Met32_lactis_rpt2

value: BY4741 MET32::K.lactis D11902-Mnase MET31::kanMX


title: CALGB03-1042369-I-21

description:
Sample_PRE_RNA_176
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1048932-M-30

description:
Sample_PRE_RNA_172
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1049625-M-43

description:
Sample_PRE_RNA_174
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Stp3_dSTP4_rpt2

value: BY4741 STP3::Stp3-Mnase STP4::kanMX


title: Oaf1_lactis_rpt2

value: BY4741 OAF1::K.lactis A03443-Mnase PIP2::kanMX


title: C03_S-1-CALGB03-1071122-1

description:
Sample_PRE_RNA_170
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Stp4_dSTP3_rpt2

value: BY4741 STP4::Stp4-Mnase STP3::kanMX


title: C03_R-5-CALGB03-1069782-1

description:
Sample_PRE_RNA_169
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Upc2_dECM22_rpt2

value: BY4741 UPC2::Upc2-Mnase ECM22::kanMX


title: C03_R-43-CALGB03-1070630-1

description:
Sample_PRE_RNA_164
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Vhr2_dVHR1_rpt2

value: BY4741 VHR2::Vhr2-Mnase VHR1::kanMX


title: Ecm22_dUPC2_rpt2

value: BY4741 ECM22::Ecm22-Mnase UPC2::kanMX


title: C03-R-10-CALGB03-1067371-1

description:
Sample_PRE_RNA_166
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Vhr1_dVHR2_rpt2

value: BY4741 VHR1::Vhr1-Mnase VHR2::kanMX


title: Tod6_dDOT6_rpt2

value: BY4741 TOD6::Tod6-Mnase DOT6::kanMX


title: C03_N-31-CALGB03-1051693-1

description:
Sample_PRE_RNA_165
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma


title: Skn7_dHMS2_rpt2

value: BY4741 SKN7::Skn7-Mnase HMS2::kanMX


title: Dot6_dTOD6_rpt3

value: BY4741 DOT6::Dot6-Mnase TOD6::kanMX


title: Pdr8_dYRR1_rpt1

value: BY4741 PDR8::Pdr8-Mnase YRR1::kanMX


title: C03_Q-20-CALGB03-1067276-1

description:
Sample_PRE_RNA_163
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: CALGB03-1048898-M-21

description:
Sample_PRE_RNA_159
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1031724-I-40

description:
Sample_PRE_RNA_161
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Phd1_dSOK2_rpt1

value: BY4741 PHD1::Phd1-Mnase SOK2::kanMX


title: Sok2_dPHD1_rpt2

value: BY4741 SOK2::Sok2-Mnase PHD1::kanMX


title: C03_Q-32-CALGB03-1066854-1

description:
Sample_PRE_RNA_151
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-6-CALGB03-1070168-1

description:
Sample_PRE_RNA_154
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tod6_dDOT6_rpt1


title: CALGB03-1031471-I-38

description:
Sample_PRE_RNA_144
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1042185-I-19

description:
Sample_PRE_RNA_148
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Skn7_dHMS2_rpt1


title: Sok2_dPHD1_rpt1


title: C03_Q-19-CALGB03-1067065-1

description:
Sample_PRE_RNA_143
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Gzf3_lactis_rpt1

value: BY4741 GZF3::K.lactis F21296-Mnase DAL80::kanMX


title: Met32_lactis_rpt1

value: BY4741 MET32::K.lactis D11902-Mnase MET31::kanMX