title: YPW2690_rep4 [120007]

description:
120007_TCTCGCGC-TAATCTTA_S27_L005
processed data file: Strain_2690.txt

source_name: haploid yeast culture_YPW2690


title: Patient 3 Colon

status: Public on May 25 2021

type: SRA

city: Aurora

first: Kristine

middle: A

last: Kuhn

state: Colorado

address: 1775 Aurora Ct. Mail Stop B115

department: Medicine

country: USA

institute: University of Colorado School of Medicine

description: All.combined.metadata.csv

library_source: transcriptomic

data_processing:
10X Genomics library sequence fastq files aligned and cell gene expression matrices generated with Cellranger v2.0.0 cellranger count with default settings
Created Seurat object for each sample with Seurat Read10X
Subset each seurat object to keep nFeature_RNA >200 and <4000, percent.mt<10 & nCount_RNA<20000
Removed batch effects with FindIntegrationAnchors, dims=1:20 and IntegrateData, dims=1:20
Clusters defined with FindNeighbors, reduction=“pca”, dims=1:20 and FindClusters, resolution=0.25

molecule: total RNA

organism: Homo sapiens

source_name: Retrosigmoid Colon

extract_protocol:
For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ
For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ.

tag: disease state

value: Spondyloarhtritis


title: Ctrl-BAC050117-048

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
We trimmed the adapter sequences of raw sequencing reads using the Trim Galore software (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). We used RSEM to calculate RNA expression levels using scRNA-seq data. We created an RSEM index with the combination of the human hg38 transcriptome (GENCODE version 28) and 3 spike-in molecules. We calculated RNA expression using RSEM 1.3.0 with the default parameters and Bowtie2 as the aligner. We normalized the expression levels of endogenous genes to that of the highest expressed spike-in molecule. Given N single cells, to control the dynamic regulation of endogenous gene expression in single cell k, the TPM value of gene j is normalized to that of spike-in 1 (s), which is the highest spike-in molecule. As the RNA capturing complexity of the scRNA-seq library is ~10% of bulk RNA-seq20, we divided the above-normalized TPM values by 10, and the expression level of gene j in cell k was quantified as the E-value Ejk.
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression E-values

molecule: polyA RNA

growth_protocol: A2780 ovarian endometroid adenocarcinoma cells were a gift from Dr. Chia-Peng Huang Yang at the Albert Einstein College of Medicine obtained from Dr. Elizabeth de Vries at the University Medical Center Groningen. The cells were cultured in RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, Waltham, MA) on 35-mm six-well glass bottom plates (Cellvis, Mountain View, CA) until 60 to 85% confluent. All cells were given at least 24 hours to readhere before drug treatment.

extract_protocol:
Cells were treated with 75 μM celecoxib for 2 and 16 hours, 5 nM paclitaxel for 16 and 48 hours, or a combination of 75 μM celecoxib and 5 nM paclitaxel for 16 hours prior to trypsinization and resuspension in growth medium. Cell suspensions were sorted with a C1 single-cell capture system (Fluidigm, South San Francisco, CA) by the University of Illinois at Chicago Genomics Core.
scRNA-seq libraries were prepared according to the Smart-seq2 protocol and sequenced using the NextSeq 500 Sequencing System (Illumina, San Diego, CA) by the University of Illinois at Chicago Sequencing Core. A predesigned set of three polyA-tailed spike-in RNAswas added to each well during the library preparation.
C1 Fluidigm based SMART-seq2

treatment_protocol: Cells were treated with 75 μM celecoxib, 5 nM paclitaxel, or a combination of 75 μM celecoxib and 5 nM paclitaxel for 48 hours.

tag: cell line

tag: treatment

value: Ctrl


title: Ctrl-BAC050117-042


title: YPW3296_rep4 [120009]

city: Ann Arbor

first: Patricia

middle: J

last: Wittkopp

state: MI

address: 1105 N University Ave

department: Department of Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description:
120009_ATTACTCG-CAGGACGT_S29_L005
processed data file: Strain_3296.txt

data_processing:
Raw reads were run through the fastqc (version 0.11.5) read quality software, which indicated high quality reads for all samples sequenced. Reads were then trimmed using cutadapt (version 1.10)
Reads were pseudo-mapped to the a transcriptome index generated using salmon (version 0.9.1) on S. cerevisiae cDNA (Ensemble, release 38)
Read counts from salmon were imported into R using TxDb (version 3.2.2). Read counts for the entire dataset were supplied to DESeq2 to model gene expression levels. The DESeq2 ‘contrast’ wrapper was then used to estimate log2 fold changes for each strain relative to its appropriate reference and identify differentially expressed genes.
Genome_build: S. cerevisiae s288c cDNA (Ensemble, release 38, retrieved from ftp://ftp.ensemblgenomes.org/pub/release-38/fungi/fasta/saccharomyces_cerevisiae/cdna/).
Supplementary_files_format_and_content: three types of processed data files are provided: output of differential expression measures for each strain relative to the appropriate wild type reference as calculated by DESeq2 as tab delimited text files, read count abundance measures as output from salmon for both the endogenous and transgenes present as .sf files, and a raw read count matrix for all samples also as a tab delimited text file.

organism: Saccharomyces cerevisiae

source_name: haploid yeast culture_YPW3296

growth_protocol: For a total of four replicates, each replicate set of strains, including mutants and controls, were randomly arrayed across the inner wells of a 96 well plate surrounded by an outer row of wells filled with non-inoculated media. Each of the four plate arrays was grown to saturation in YPD, and then glycerol stocked in 80% glycerol and stored at -80C. The glycerol stocks were thawed by transfer using a pin tool onto solid YPG agar plates and strains were grown up for ~3 days at 30C. Strains were then transferred by pin tool again into 500uL liquid YPD in 1mL 96-well plates with glass beads and grown at 30C while shaking at 250rpms for 2 days, until all strains were once again at saturation. 100uL of the saturated culture was then transferred to a Costar 96 well plate and OD measured using a Tecan Sunrise. The OD was then used to calculate cell density. A separate 1mL 96 well plate was then filled with  500uL of YPD in each well, and each well inoculated with a volume of the saturated culture calculated to grow to a cell density of 5x10^6 cell per mL (an OD of about 0.4) after 12.5hr, based on empirical determination of each strain’s growth rate. These cultures were then grown spinning on a wheel at 30C for 12.5hrs, after which 100uL was removed and used to measure OD to ensure all cultures were between an OD of 0.26 to 0.48. Plates were then spun down for 5min at 3000g, and liquid media pipetted off. Remaining cell pellets were frozen by plunging the entire plate containing cell pellets into liquid nitrogen. Plates were sealed with foil and stored at -80C until RNA extractions were performed.

extract_protocol:
Frozen cell pellets were resuspended in 700uL of a lysis buffer containing beta-mercaptoethanol and transferred to a plate containing ~250uL of acid-washed 425-600um beads. Beaded plates were beaten 10x for 1min each with 1min on ice in between. Plates were spun down at 3000rpm at 4C for 4min, and 400uL of lysis supernatant were removed and transferred into a new 96 well plate containing oligodT magnetic beads (Dynabeads mRNA DIRECT Kit, Ambion, cat# 61011). Beads and lysate were incubated at room temperature with agitation for 5 minutes, and then placed on a magnetic stand. Beads were then washed according to the Dynabeads mRNA direct kit user guide. After extraction, several representative samples were run on Agilent Bioanalyzer to check RNA quality and concentration before moving on to library preparation. In addition, selected wells were tested for the presence of NAT or KAN resistance markers present in distinct strains and controls by RT-PCR and visualized on a gel to ensure well-cross contamination had not taken place at any step previous to library prep.
RNA sequencing libraries were prepared using a modified, ⅓ volume reaction TruSeq RNA Sample Preparation v2 Guide, and using multiplexable adapters from the TruSeq RNA CD Index Plate (cat# 20019792).

tag: cell type

value: alpha

tag: genotype/variation

value: TDH2 deletion


title: Patient 5 Colon

description: All.combined.metadata.csv

value: Healthy Control


title: Ctrl-BAC050117-041


title: YPW1188_rep4 [120008]

description:
120008_AGCGATAG-TAATCTTA_S28_L005
processed data file: Strain_1188.txt

source_name: haploid yeast culture_YPW1188

value: A

value: cis-regulatory mutant to TDH3


title: Ctrl-BAC050117-047


title: YPW2919_rep4 [120006]

description:
120006_TCCGCGAA-TAATCTTA_S26_L005
processed data file: Strain_2919.txt

source_name: haploid yeast culture_YPW2919

value: trans-regulatory mutant to TDH3


title: Patient 3 Blood

description: All.combined.metadata.csv

source_name: Periperhal Blood


title: Ctrl-BAC050117-049


title: Ctrl-BAC050117-046


title: Patient 7 Colon

description: All.combined.metadata.csv

value: Crohn's Disease


title: YPW3088_rep4 [120005]

description:
120005_CGGCTATG-TAATCTTA_S25_L005
processed data file: Strain_3088.txt

source_name: haploid yeast culture_YPW3088


title: Ctrl-BAC050117-043


title: Patient 5 Blood

description: All.combined.metadata.csv


title: Ctrl-BAC050117-039


title: Ctrl-BAC050117-044


title: Ctrl-BAC050117-038


title: Patient 2 Blood

description: All.combined.metadata.csv

value: Co-morbid Crohn's and Spondyloarthritis


title: Patient 2 Colon

description: All.combined.metadata.csv


title: Ctrl-BAC050117-037


title: Ctrl-BAC050117-040


title: Ctrl-BAC050117-036


title: MCF7 shSRSF1 rep2

city: Shanghai

first: Junxian

last: Du

state: Shanghai

address: Fudan university,Shanghai,China

country: China

institute: Fudan 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 GRCH38 whole genome using Hisat2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCH38
Supplementary_files_format_and_content: excel files include RPKM values for each Sample
Supplementary_files_format_and_content: excel files with raw gene counts for every gene and every sample

source_name: MCF7 breast cancer cell line

growth_protocol: DMEM (Gibco) containing 10% FBS (Gibco) was used to culture MCF7 cell lines in a humidified incubator at 37℃ with 5% CO2

extract_protocol:
Cells were extracted, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF7 cells were transfected with NC/shSRNSF1 lentiviruses and filtered with puromycin

tag: knockdown


title: YPW3256_rep4 [120003]

description:
120003_CTGAAGCT-TAATCTTA_S23_L005
processed data file: Strain_3256.txt

source_name: haploid yeast culture_YPW3256


title: Ctrl-BAC050117-033


title: Ctrl-BAC050117-034


title: Ctrl-BAC050117-035


title: YPW3285_rep4 [120002]

description:
120002_GAATTCGT-TAATCTTA_S22_L005
processed data file: Strain_3285.txt

source_name: haploid yeast culture_YPW3285


title: YPW3291_rep4 [120001]

description:
120001_ATTCAGAA-TAATCTTA_S21_L005
processed data file: Strain_3291.txt

source_name: haploid yeast culture_YPW3291

value: TDH1 deletion


title: MCF7 NC rep2

value: control


title: Ctrl-BAC050117-031


title: Ctrl-BAC050117-030


title: YPW3203_rep4 [120004]

description:
120004_TAATGCGC-TAATCTTA_S24_L005
processed data file: Strain_3203.txt

source_name: haploid yeast culture_YPW3203


title: MCF7 NC rep1


title: YPW1177_rep4 [120000]

description:
120000_GAGATTCC-TAATCTTA_S20_L005
processed data file: Strain_1177.txt

source_name: haploid yeast culture_YPW1177

value: TDH3 deletion


title: Dermal fibroblasts 124_TD_21_c

city: Saint Louis

first: Ya-Lin

last: Lu

state: MO

address: 660 S. Euclide Avenue

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were aligned to human reference genome (GRCh38) by STAR (Dobin and Gingeras, 2015).
Counts were normalized by trimmed mean of M-values (TMM) using edgeR (Robinson et al., 2010).
EdgeR (Robinson et al., 2010) was used to identify differentially expressed genes.
Bigwig files were generated using bamCoverage (Ramírez et al., 2016).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of replicates for RNA-seq experiments

source_name: Dermal fibroblasts

growth_protocol: Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).

extract_protocol:
Total RNA was extracted using a combination of Trizol (Invitrogen, USA) and RNeasy plus micro kit (QIAGEN, USA).
SMARTer Ultra Low Input RNA Kit (Clontech, USA)

treatment_protocol: Cell treated with either TuD-miR-NS or TuD-miR-124 for 21 days

value: Coriell GM02171

value: Dermal fibroblasts


title: Ctrl-BAC050117-029


title: YPW2682_rep4 [119999]

source_name: haploid yeast culture_YPW2682

value: duplication control


title: Ctrl-BAC050117-027


title: Ctrl-BAC050117-028


title: Dermal fibroblasts 124_TD_21_b


title: Ctrl-BAC050117-023


title: Ctrl-BAC050117-024


title: Ctrl-BAC050117-026


title: Ctrl-BAC050117-025


title: Ctrl-BAC050117-032


title: Dermal fibroblasts 124_TD_21_a


title: Ctrl-BAC050117-022


title: MCF7 shSRSF1 rep1


title: YPW3068_rep4 [119997]

description:
119997_ATTACTCG-TAATCTTA_S17_L005
processed data file: Strain_3068.txt

source_name: haploid yeast culture_YPW3068


title: Dermal fibroblasts CTL_TD_21_c

value: TuD-miR-NS


title: YPW2911_rep4 [119998]

description:
119998_TCCGGAGA-TAATCTTA_S18_L005
processed data file: Strain_2911.txt

source_name: haploid yeast culture_YPW2911


title: Ctrl-BAC050117-019


title: YPW3202_rep4 [119996]

description:
119996_AGCGATAG-AGGCGAAG_S16_L005
processed data file: Strain_3202.txt

source_name: haploid yeast culture_YPW3202


title: Ctrl-BAC050117-020


title: Ctrl-BAC050117-021


title: Dermal fibroblasts CTL_TD_21_a


title: Dermal fibroblasts CTL_TD_21_b


title: Ctrl-BAC050117-015


title: Human neurons 124TD_shELAVL3_b

source_name: Human neurons

growth_protocol: Primary neurons were cultured with Neuronal Media from ScienCell

extract_protocol:
Total RNA was extracted using a combination of Trizol (Invitrogen, USA) and RNeasy plus micro kit (QIAGEN, USA).
TruSeq Stranded total RNA

treatment_protocol: Primary human neurons treated with either TuD-miR-NS with shCTL or TuD-miR-124 with shELAVL3 for 8 days

value: ScienCell, 1520

value: Human neurons


title: YPW3254_rep4 [119995]

description:
119995_TCTCGCGC-AGGCGAAG_S15_L005
processed data file: Strain_3254.txt

source_name: haploid yeast culture_YPW3254

value: alpha


title: Ctrl-BAC050117-014

value: Ctrl


title: Ctrl-BAC050117-016


title: Ctrl-BAC050117-017


title: Ctrl-BAC050117-013


title: Human neurons 124TD_shELAVL3_a


title: YPW3290_rep4 [119993]

description:
119993_CGGCTATG-AGGCGAAG_S13_L005
processed data file: Strain_3290.txt

source_name: haploid yeast culture_YPW3290


title: Human neurons CTLTD_shCTL_b

value: shCTL


title: Human neurons CTLTD_shCTL_a


title: Ctrl-BAC050117-010


title: YPW2525_rep4 [119991]

description:
119991_CTGAAGCT-AGGCGAAG_S11_L005
processed data file: Strain_2525.txt

source_name: haploid yeast culture_YPW2525


title: siKRT18_3rd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
KRT18 knockdown in AGS cells
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC; end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. When several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: expressed_gene_reads.txt: Tab-delimited text file includes read counts for each Sample.
Supplementary_files_format_and_content: expressed_gene_FPKM.txt: Tab-delimited text file includes gene FPKM values for each Sample.

source_name: AGS cells

growth_protocol: AGS cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion) and was further purified with two phenol-chloroform treatments. The purified RNA was then treated with RQ1 DNase (RNase free) (Promega, Madison, WI, USA) and its quality and quantity were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Novaseq 6000 system was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

value: AGS

tag: sirna


title: Ctrl-BAC050117-009


title: Ctrl-BAC050117-011


title: Ctrl-BAC050117-018


title: Ctrl-BAC050117-012


title: YPW1156_rep4 [119992]

description:
119992_TAATGCGC-AGGCGAAG_S12_L005
processed data file: Strain_1156.txt

source_name: haploid yeast culture_YPW1156

value: A

value: cis-regulatory mutant to TDH3


title: Ctrl-BAC050117-008


title: YPW3284_rep4 [119994]

description:
119994_TCCGCGAA-AGGCGAAG_S14_L005
processed data file: Strain_3284.txt

source_name: haploid yeast culture_YPW3284

value: trans-regulatory mutant to TDH3


title: Ctrl-BAC050117-007


title: YPW3059_rep4 [119989]

description:
119989_ATTCAGAA-AGGCGAAG_S9_L005
processed data file: Strain_3059.txt

source_name: haploid yeast culture_YPW3059

value: overexpression of TDH3


title: YPW2800r2_rep4 [119990]

description:
119990_GAATTCGT-AGGCGAAG_S10_L005
processed data file: Strain_2800.txt

source_name: haploid yeast culture_YPW2800r2


title: siKRT18_1st


title: Ctrl-BAC050117-006


title: Ctrl-BAC050117-004


title: Ctrl-BAC050117-005


title: siKRT18_2nd


title: Ctrl-BAC050117-003


title: YPW3247_rep4 [119987]

description:
119987_CGCTCATT-AGGCGAAG_S7_L005
processed data file: Strain_3247.txt

source_name: haploid yeast culture_YPW3247


title: Ctrl-BAC050117-002


title: Ctrl-BAC050117-001


title: siCtrl_2nd

description:
Control AGS cells
expressed_gene_FPKM.txt
expressed_gene_reads.txt

value: siCtrl


title: siCtrl_3rd


title: YPW3283_rep4 [119986]

description:
119986_TCCGGAGA-AGGCGAAG_S6_L005
processed data file: Strain_3283.txt

source_name: haploid yeast culture_YPW3283


title: siCtrl_1st


title: YPW3298r1_rep4 [119985]

description:
119985_ATTACTCG-AGGCGAAG_S5_L005
processed data file: Strain_3298.txt

source_name: haploid yeast culture_YPW3298r1

value: TDH2/3 double deletion


title: PBS-3

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

institute: USC

data_processing:
raw sequencing reads were first checked for overall quality and adapter contamination using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) prior to downstream analysis
Reads were quantifying transcript abundances with Salmon using the GENCODE version 31 reference including only protein coding genes.
abundances were summarized to gene level counts using functions in the Bioconductor package tximport
Significantly differentially expressed genes were identified using the Bioconductor package DESeq2 with a significance threshold of FDR < 0.1 and fold change of at least 1.5 when compared to paired control (PBS) samples.
Genome_build: Gencode v31
Supplementary_files_format_and_content: comma-separated counts values (TPM)

source_name: M2-like macrophages treated with PBS, donor 3

growth_protocol: CD14+ monocytes were plated at 1x10e6 /well in 6-well plate in RPMI 1640 with 50ng/mL of M-CSF plus 5% FBS for 5 days at 37˚C/ 5% CO2.

extract_protocol:
Cells were then harvested in Buffer RLT (Qiagen) + 1% 2-Mercaptoethanol (Sigma-Aldrich) and RNA was extracted using Rneasy Mini kit (Qiagen) following manufacture's instructions.
Illumina Truseq Stranded was use for mRNA library preparation kit according to the manufacturer’s protocol (Illumina). Prepared libraries were sequenced on the Illumina Nextseq 500 at 3 million reads per sample at 2x75 cycles.

treatment_protocol: After differentiation, M2-like macrophages were stimulated for 24h with RPMI + 5%FBS media plus PBS (unstimulated control), or 50ug/mL of native low-density lipoprotein (Kalen Biomedical LLC), medium oxidized LDL (Kalen Biomedical LLC), or high oxidized LDL (Kalen Biomedical LLC).

tag: individual

value: donor 3

value: M2-like macrophage

value: untreated


title: Healthy_MSC_3

city: London

first: Quentin

last: Heydt

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute

data_processing:
RNA-Seq reads were aligned to the human genome (hg38) using Hisat2.
Count files were generated by mapping reads to the human genome (hg38) p5 using HTSeq
Differential expression analysis was performed using Limma
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each sample

source_name: Primary MSCs

growth_protocol: BM-MNC’s were seeded at densities of 10x106 cells per 175 cm2 in MesenCult™ MSC Basal Medium (05401, STEMCELL Technologies) supplemented with MesenCult™ MSC Stimulatory Supplement (05402, STEMCELL Technologies), 100 units/ml penicillin and 100 µg/ml streptomycin (15140122, Thermo Fisher Scientific), 2 mM L-Glutamine and 1 ng/ml recombinant human FGF (233-FB, R&D Systems) and incubated at 37ºC, 5% CO2 under humidified conditions for 21 days. The culture medium was changed on day 2 and every week thereafter to remove non-adherent cells. At day 21, adherent cells, corresponding to BM-MSC populations at P1. We performed RNAseq studies on MSC’s from three healthy and three low “performer” ALL-BMs (ALL12-14) at P4 expansion stage.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (74104, Qiagen)
Libraries were prepared according to Illumina's instructions by the company Novogene

tag: tissue

value: Blood

tag: disease

value: Healthy

value: MSC


title: nLDL-5

source_name: M2-like macrophages treated with native LDL, donor 5

value: donor 5

value: native LDL


title: PBS-4

source_name: M2-like macrophages treated with PBS, donor 4

value: donor 4


title: YPW1189r1_rep4 [119984]

source_name: haploid yeast culture_YPW1189r1

value: a type wild type control


title: PBS-1

source_name: M2-like macrophages treated with PBS, donor 1

value: donor 1


title: nLDL-4

source_name: M2-like macrophages treated with native LDL, donor 4


title: YPW1189r2_rep4 [119983]

source_name: haploid yeast culture_YPW1189r2

value: A


title: Healthy_MSC_2


title: YPW3198_rep4 [119988]

description:
119988_GAGATTCC-AGGCGAAG_S8_L005
processed data file: Strain_3198.txt

source_name: haploid yeast culture_YPW3198

value: alpha


title: YPW1189r3_rep4 [119982]

source_name: haploid yeast culture_YPW1189r3


title: nLDL-1

source_name: M2-like macrophages treated with native LDL, donor 1


title: nLDL-3

source_name: M2-like macrophages treated with native LDL, donor 3


title: nLDL-2

source_name: M2-like macrophages treated with native LDL, donor 2

value: donor 2


title: Mox-5

source_name: M2-like macrophages treated with MoxLDL, donor 5

value: MoxLDL


title: YPW3016r5_rep4 [119981]

source_name: haploid yeast culture_YPW3016r5

value: trans-regulatory mutant to TDH3


title: PBS-2

source_name: M2-like macrophages treated with PBS, donor 2


title: ALL_MSC_13

value: Acute Lymphoblastic Leukaemia


title: ALL_MSC_22


title: Mox-4

source_name: M2-like macrophages treated with MoxLDL, donor 4


title: YPW3016r4_rep3 [115120]

source_name: haploid yeast culture_YPW3016r4

value: alpha wild type control


title: YPW2919_rep3 [115116]

description:
115119_TCCGCGAA-GGCTCTGA_S42_L007
processed data file: Strain_2919.txt

source_name: haploid yeast culture_YPW2919


title: Mox-3

source_name: M2-like macrophages treated with MoxLDL, donor 3

value: donor 3

value: M2-like macrophage


title: Mox-1

source_name: M2-like macrophages treated with MoxLDL, donor 1


title: PBS-5

source_name: M2-like macrophages treated with PBS, donor 5

value: untreated


title: YPW3288_rep3 [115114]

description:
115118_CGGCTATG-GGCTCTGA_S41_L007
processed data file: Strain_3288.txt

source_name: haploid yeast culture_YPW3288


title: Hox-5

source_name: M2-like macrophages treated with HoxLDL, donor 5

value: HoxLDL


title: Hox-4

source_name: M2-like macrophages treated with HoxLDL, donor 4


title: ALL_MSC_12

source_name: Primary MSCs

value: Blood

value: MSC


title: Pac16h-BAC050117-210


title: Pre_adipocyte_1

data_processing:
RNA-Seq reads were aligned to the human genome (hg38) using Hisat2.
Count files were generated by mapping reads to the human genome (hg38) p5 using HTSeq
Differential expression analysis was performed using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each sample

source_name: Nalm-6 co-cultured with 3T3-L1 Pre-adipocytes

growth_protocol: Nalm-6 cells co-cultured with 3T3-L1 pre-adipocytes or 3T3-L1 adipocytes for 24 hours

value: Acute Lymphoblastic Leukaemia (ALL) cell line

tag: culture condition

value: co-cultured with 3T3-L1 Pre-adipocytes


title: Hox-3

source_name: M2-like macrophages treated with HoxLDL, donor 3


title: HUVEC Static2

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

data_processing:
Mapping: The raw reads were mapped to the merged genome of mm10 (mouse) and hg38 (human) using cellranger (10X Genomics).
Counting: Reads containing the same UMI were collapsed and then assigned to individual cells by their cell barcodes.
QC doublets removal: The digital gene expression matrixes outputted from cellranger were analyzed in R. First, mouse-human multiplets containing both mouse and human reads were excluded. Total multiplet rate (including cross-species multiplets and intra-species multiplets) were inferred to be 0.34% based on MEF cell percentage and observed cross-species multiplets in each sample.
QC: Low-quality cells failed to match the following criteria were filtered out: number of genes detected >= 200, 1% < % of mitochondria encoded genes < 10 % for HUVEC flow and MEF cells or 0.5% < % of mitochondria encoded genes < 6 % for HUVEC static cells. Genes undetected in all HUVEC cells were also excluded, resulting 20722 detected genes for the dataset. A total of 5251 high quality HUVEC cells passed all filters, with median UMI counts per sample and median number of genes detected per sample between 8072 and 13370, and between 2404 and 3129, respectively.
Genome_build: GRCh38 and mm10
Supplementary_files_format_and_content: csv file containing raw UMI counts for each gene in each HUVEC cell (post QC) from all four samples.

source_name: HUVEC

growth_protocol: HUVEC (Lonza, #C2519A, passages 2-4) were cultured in EBM-2 Endothelial Cell Growth Basal Medium-2 (Lonza, #CC-3156) supplemented with EGM-2 SingleQuots Supplements (Lonza, #CC-4176) at 37°C and 5% CO2.

extract_protocol:
HUVECs under flow or static conditions were digested with 0.05% trypsin-EDTA (Gibco, 25300-054) at 37°C for 3 min, neutralized with 50% newborn calf serum (Gibco, 16010-159) in PBS, collected with 1 ml syringe, pelleted by centrifugation at 100 xg and 4°C for 5 min, washed once with 0.04% bovine serum albumin (BSA) in PBS, filtered with flowmi 40µm cell strainer (Sigma, BAH136800040), counted using Countess (Life Technology, AMQAX1000), diluted to 1000 cells/µl with 0.04% BSA in PBS, mixed with 10% MEF also in 0.04% BSA in PBS, and loaded onto 10X Genomics Chromium Controller for droplet generation. HUVECs from three ibidi channel slides connected to one same flow unit were combined for each static or flow sample. Viability of HUVECs were above 95% in all samples according to trypan blue staining at the cell counting step on Countess. A total of 4000 cells (3600 HUVEC and 400 MEF) per sample were loaded.
Reverse transcription and library preparation were performed with the Single Cell 3′ Library & Gel Bead Kit v2 according to 10X Genomics’ standard protocol except that 13 cycles were used for cDNA amplification.
Libraries of two flow experiments (Flow1 and Flow2) and two static experiments (Static1 and Static2) were combined and sequenced in one NextSeq500 run using the high output kit at the UNC Translational Genomics Lab (TGL) core. About 1-1.5 x 108 150bp paired-end reads were obtained for each sample.

treatment_protocol: HUVEC (passage 4) were were plated at 100% confluency in a µ-Slide I Luer 0.4 (Ibidi, #80176) coated with fibronectin (Millipore Sigma, F2006, 5ug/mL) and culured for 2 hr in their normal growth media. Then the slides were washed 3 times in flow medium (EBM-2 with 10% FBS (Gibco, #26140-079) and 1X Antibiotic-Antimycotic (Gibco, #15240-062)), and incubated in flow medium for 2 hr prior to flow onset. Uniform laminar shear stress was generated by attaching slide chambers to a pump system (Ibidi, #10902) with both the slide and the pump apparatus kept at 37C and 5% CO2. To reduce cell shearing off the slide, flow was applied for 30 min at 5 d/cm2, then 30 min at 10 dynes/cm2, followed by 72 hr at 15 d/cm2.

value: human umbilical vein endothelial cells (HUVEC)

value: Static


title: YPW3291_rep3 [115102]

description:
115115_GAATTCGT-GGCTCTGA_S38_L007
processed data file: Strain_3291.txt

source_name: haploid yeast culture_YPW3291

value: TDH1 deletion


title: Hox-2

source_name: M2-like macrophages treated with HoxLDL, donor 2


title: Healthy_MSC_1

value: Healthy


title: Pre_adipocyte_2


title: YPW3068_rep3 [115119]

description:
115111_ATTACTCG-GGCTCTGA_S34_L007
processed data file: Strain_3068.txt

source_name: haploid yeast culture_YPW3068

value: alpha


title: Mox-2

source_name: M2-like macrophages treated with MoxLDL, donor 2

value: donor 2

value: MoxLDL


title: YPW3092_rep3 [115085]

description:
115112_TCCGGAGA-GGCTCTGA_S35_L007
processed data file: Strain_3092.txt

source_name: haploid yeast culture_YPW3092

value: trans-regulatory mutant to TDH3


title: Pre_adipocyte_3


title: Hox-1

source_name: M2-like macrophages treated with HoxLDL, donor 1

value: donor 1


title: YPW3287r2_rep3 [115108]

description:
115116_CTGAAGCT-GGCTCTGA_S39_L007
processed data file: Strain_3287.txt

source_name: haploid yeast culture_YPW3287r2


title: HUVEC Flow1

value: Flow


title: YPW3283_rep3 [115118]

description:
115110_AGCGATAG-CCTATCCT_S33_L007
processed data file: Strain_3283.txt

source_name: haploid yeast culture_YPW3283


title: HUVEC Static1


title: HUVEC Flow2


title: nfrkb1/2/3_SD_repeat3

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 version 2.2.0 with the default parameters.
The differentially expressed genes and transposable elements were identified with |log2FC| >1 and P value<0.01 using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long-day (LD) photoperiod (23℃, 16 h light/ 22℃, 8 h darkness) or short-day (SD) photoperiod (23℃, 8h light/ 22℃, 16 h darkness).

extract_protocol:
Total RNA was isolated from 11-day-old seedlings in LD or 14-day-old seedlings in SD using Trizol reagent.
Sequencing libraries were built for RNA-seq (the single-ended 50-bp strategy).

tag: genotype

value: Seedlings

tag: growth conditions

value: short day (8 h light, 16 h dark)


title: YPW2800_rep3 [115099]

description:
115114_GAGATTCC-GGCTCTGA_S37_L007
processed data file: Strain_2800.txt

source_name: haploid yeast culture_YPW2800


title: nfrkb1/2/3_SD_repeat4


title: YPW2798_rep3 [115112]

description:
115117_TAATGCGC-GGCTCTGA_S40_L007
processed data file: Strain_2798.txt

source_name: haploid yeast culture_YPW2798


title: Adipocyte_1

source_name: Nalm-6 co-cultured with 3T3-L1 adipocytes

value: cocultured with 3T3-L1 Adipocytes


title: Adipocyte_2


title: YPW2911_rep3 [115115]

description:
115108_TCCGCGAA-CCTATCCT_S31_L007
processed data file: Strain_2911.txt

source_name: haploid yeast culture_YPW2911


title: Adipocyte_3


title: YPW3296_rep3 [115113]

description:
115107_CGGCTATG-CCTATCCT_S30_L007
processed data file: Strain_3296.txt

source_name: haploid yeast culture_YPW3296

value: TDH2 deletion


title: uch1/2_SD_repeat3


title: ino80_SD_repeat3


title: uch1/2_SD_repeat4


title: ino80_SD_repeat4


title: YPW2506_rep3 [115117]

description:
115109_TCTCGCGC-CCTATCCT_S32_L007
processed data file: Strain_2506.txt

source_name: haploid yeast culture_YPW2506


title: YPW3088_rep3 [115111]

description:
115106_TAATGCGC-CCTATCCT_S29_L007
processed data file: Strain_3088.txt

source_name: haploid yeast culture_YPW3088


title: YPW3256_rep3 [115110]

description:
115105_CTGAAGCT-CCTATCCT_S28_L007
processed data file: Strain_3256.txt

source_name: haploid yeast culture_YPW3256


title: INO80-FL_SD_repeat4


title: Col-0_SD_repeat4

value: wild type


title: YPW3161_rep3 [115109]

description:
115104_GAATTCGT-CCTATCCT_S27_L007
processed data file: Strain_3161.txt

source_name: haploid yeast culture_YPW3161


title: atx4/5;jmj24_SD_repeat4


title: YPW3282_rep3 [115088]

description:
115113_CGCTCATT-GGCTCTGA_S36_L007
processed data file: Strain_3282.txt

source_name: haploid yeast culture_YPW3282


title: atx4/5;jmj24_SD_repeat3


title: Col-0_SD_repeat3


title: YPW3254_rep3 [115107]

description:
115103_GAGATTCC-CCTATCCT_S26_L007
processed data file: Strain_3254.txt

source_name: haploid yeast culture_YPW3254


title: YPW3275_rep3 [115105]

description:
115101_TCCGGAGA-CCTATCCT_S24_L007
processed data file: Strain_3275.txt

source_name: haploid yeast culture_YPW3275


title: Stromal cells from RLN7

type: RNA

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

description:
Stromal cells from reactive LN 7
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed by using the RMA algorithm using GC content from the Partek Genomics Suite software (Partek, St Louis, MO).  Dataset was then filtering by eliminating PS with no expression in all dataset and/or no gene symbol annotations.

label: biotin

source_name: RLN_In vitro expanded stroma cells

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA)

growth_protocol: Stromal cells were obtained as previously described (Guilloton F, Blood 2012).

extract_protocol: RNA extraction was  performed using RNEasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Stromal cells were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)

tag: status

value: non-malignant reactive (RLN)

value: Lymph node

value: In vitro expanded stroma cells


title: uch1/2_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 version 2.2.0 with the default parameters.
The differentially expressed genes and transposable elements were identified with |log2FC| >1 and P value<0.01 using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_expression.txt: Tab-delimited text file includes normalized reads for each sample.

tag: age

value: 14 days


title: YPW3191_rep3 [115104]

description:
115100_ATTACTCG-CCTATCCT_S23_L007
processed data file: Strain_3191.txt

source_name: haploid yeast culture_YPW3191


title: Stromal cells from RLN8

description:
Stromal cells from reactive LN 8
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: INO80-FL_SD_repeat3


title: Stromal cells from RLN5

description:
Stromal cells from reactive LN 5
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: YPW3298_rep3 [115106]

description:
115102_CGCTCATT-CCTATCCT_S25_L007
processed data file: Strain_3298.txt

source_name: haploid yeast culture_YPW3298

value: A

value: TDH2/3 double deletion


title: YPW1200_rep3 [115101]

description:
115098_TCCGCGAA-ATAGAGGC_S21_L007
processed data file: Strain_1200.txt

source_name: haploid yeast culture_YPW1200

value: cis-regulatory mutant to TDH3


title: Stromal cells from RLN3

description:
Stromal cells from reactive LN 3
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: Stromal cells from RLN1

description:
Stromal cells from reactive LN 1
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: YPW3016r2_rep3 [115103]

source_name: haploid yeast culture_YPW3016r2

value: alpha

value: alpha wild type control


title: Stromal cells from RLN6

description:
Stromal cells from reactive LN 6
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: TOVII2D_cells_8%_oxygen

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

data_processing:
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.14)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the deafult parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalised and statistically anlaysed using the DESeq2 package (version 1.18.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited file containing raw miRNA counts

source_name: Cells

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit and QIAzol Reagent for cells following the manufacturer's instructions.
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 1 ug of RNA was used as input for library construction.


title: SKOV-3_cells_8%_oxygen


title: YPW3198_rep3 [115100]

description:
115097_CGGCTATG-ATAGAGGC_S20_L007
processed data file: Strain_3198.txt

source_name: haploid yeast culture_YPW3198

value: trans-regulatory mutant to TDH3


title: Stromal cells from FL15

description:
Stromal cells from FL15
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)

source_name: FL_LN_In vitro expanded stroma cells

value: Follicular lymphoma  (FL)


title: nfrkb1/2/3_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt

source_name: Arabidopsis seedlings


title: YPW3284_rep3 [115098]

description:
115096_TAATGCGC-ATAGAGGC_S19_L007
processed data file: Strain_3284.txt

source_name: haploid yeast culture_YPW3284


title: Stromal cells from RLN4

description:
Stromal cells from reactive LN 4
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: INO80-(335-1540)_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: Stromal cells from RLN2

description:
Stromal cells from reactive LN 2
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: OVTOKO_cells_8%_oxygen

value: OVTOKO


title: OVCAR-429_cells_8%_oxygen


title: INO80-(335-1540)_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt

value: Seedlings


title: nfrkb1/2/3_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt

value: short day (8 h light, 16 h dark)


title: uch1/2_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: Stromal cells from FL13

description:
Stromal cells from FL13
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: INO80-(1-550)_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: YPW3286_rep3 [115097]

description:
115095_CTGAAGCT-ATAGAGGC_S18_L007
processed data file: Strain_3286.txt

source_name: haploid yeast culture_YPW3286


title: OVCAR-420_cells_8%_oxygen


title: Stromal cells from FL16

description:
Stromal cells from FL16
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: OVCAR-3_cells_8%_oxygen


title: YPW1188_rep3 [115096]

description:
115094_GAATTCGT-ATAGAGGC_S17_L007
processed data file: Strain_1188.txt

source_name: haploid yeast culture_YPW1188


title: Stromal cells from FL14

description:
Stromal cells from FL14
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: INO80-(1-550)_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: Stromal cells from FL11

description:
Stromal cells from FL11
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: YPW2690_rep3 [115094]

description:
115092_GAGATTCC-ATAGAGGC_S15_L007
processed data file: Strain_2690.txt

source_name: haploid yeast culture_YPW2690


title: ino80_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: Stromal cells from FL12

description:
Stromal cells from FL12
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: HEY_cells_8%_oxygen

value: HEY


title: OV90_cells_8%_oxygen


title: miR-412-3p mimic_rep3

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were build index by hisat2, and masked for low-complexity or low-quality sequence
Mapped to GRCH38 whole genome using hisat2 and  exported StringTie readable format files
Expression values for all genes in each sample (FPKM) were calculated by StringTie
Differentially expressed miRNAs between the paired groups were analyzed by using DEGseq
Genome_build: GRCH38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 786-0 cells

extract_protocol:
Total RNA was extracted from each tissue sample using Trizol method
RNA libraries were prepared for sequencing using standard illumina protocls

value: ccRcc


title: YPW3059_rep3 [115093]

description:
115091_CGCTCATT-ATAGAGGC_S14_L007
processed data file: Strain_3059.txt

source_name: haploid yeast culture_YPW3059

value: overexpression of TDH3


title: YPW3245_rep3 [115095]

description:
115093_ATTCAGAA-ATAGAGGC_S16_L007
processed data file: Strain_3245.txt

source_name: haploid yeast culture_YPW3245


title: miR-412-3p mimic_rep2


title: INO80-FL_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: Stromal cells from FL9

description:
Stromal cells from FL9
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)


title: CAOV-3_cells_8%_oxygen


title: YPW3228_rep3 [115092]

description:
115090_TCCGGAGA-ATAGAGGC_S13_L007
processed data file: Strain_3228.txt

source_name: haploid yeast culture_YPW3228


title: miR-412-3p mimic_rep1


title: YPW3241_rep3 [115091]

description:
115089_ATTACTCG-ATAGAGGC_S12_L007
processed data file: Strain_3241.txt

source_name: haploid yeast culture_YPW3241


title: miR-NC mimic_rep2

value: normal control_mimic


title: INO80-FL_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: E11.5 + 7 days

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

description:
TM78
PMC-TM-78_AHVGY7BGX7_S5

data_processing:
Illumina base calling
processing using the Sharq pipeline (https://doi.org/10.1101/250811), briefly:  merging cell bar code and UMI from read1 with read2;  trimming read2; mapping using STAR 2.6.1a;  feature assignment (using featureCounts v1.5.2 ); read tallying
Genome_build: mouse genome GRCm38.p5 with gencode vM14 intron junctions.  Sequences for EGFP_IRES_Crem, tdTom and NeoR contructs are included, as are those of the ERCC external controls
Supplementary_files_format_and_content: processed data is represented in tab-delimited form, with rows being genes and columns  cells. Gene names are ENSEMBL gene ids combined with the MGI gene symbol. Column names are coordinates of the wells in the 384-well plates (each containing one cell). The first column ('UNK') represents the reads that had uncorrectable misreads in their cell bar code. Wells [A-O]24 are left empty for control purposes

organism: Mus musculus

source_name: ex vivo cultured mouse embryonic kidney cells

growth_protocol: Explanted kidneys were grown in a 24-well tissue culture dish containing 600ul medium Dulbecco’s modified Eagle medium supplemented with 10% fetal calf serum and 1% Streptomycin/penicillin.

extract_protocol:
Mouse embryo kidneys and explants were disaggregated into single cells by collagenase treatment and sorted in to 384 well plate using a BD FACSAria II cell sorter.
Libraries were prepared using the Sort-seq method
scRNAseq (SORT-seq protocol). NOTE: the sequencing is formally paired-end, but read1 only contains cell barcode and unique molecular identifier, so analysis is single-end

tag: strain background

tag: genetic modifications

tag: developmental stage

value: E11.5 + 5d ex vivo culture

tag: control wells

tag: wells containing > 1 cell


title: miR-NC mimic_rep1

tag: cell type


title: Col-0_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt

value: wild type


title: YPW3285_rep3 [115090]

description:
115088_AGCGATAG-TATAGCCT_S11_L007
processed data file: Strain_3285.txt

source_name: haploid yeast culture_YPW3285

tag: genotype/variation


title: E12.5 + 5 days

description:
TM77
PMC-TM-77_AHVGY7BGX7_S4

value: E12.5 + 5d ex vivo culture

value: ex vivo cultured mouse embryonic kidney cells


title: miR-NC mimic_rep3


title: E11.5

description:
TM13
PMC-TM-13_AHWTVGBGX2_S6

source_name: mouse embryonic kidney cells

value: mouse embryonic kidney cells


title: Stromal cells from FL10

description:
Stromal cells from FL10
MSC were expanded from lymph node mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)

value: Lymph node

value: In vitro expanded stroma cells


title: YPW3247_rep3 [115089]

description:
115087_TCTCGCGC-TATAGCCT_S10_L007
processed data file: Strain_3247.txt

source_name: haploid yeast culture_YPW3247

value: alpha


title: ino80_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt

value: 14 days


title: arp5_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: arp5_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: YPW2728_rep3 [115087]

description:
115086_TCCGCGAA-TATAGCCT_S9_L007
processed data file: Strain_2728.txt

source_name: haploid yeast culture_YPW2728

value: trans-regulatory mutant to TDH3


title: YPW3203_rep3 [115086]

description:
115085_CGGCTATG-TATAGCCT_S8_L007
processed data file: Strain_3203.txt

source_name: haploid yeast culture_YPW3203


title: atx4/5;jmj24_SD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: YPW3289_rep3 [115084]

description:
115084_TAATGCGC-TATAGCCT_S7_L007
processed data file: Strain_3289.txt

source_name: haploid yeast culture_YPW3289


title: atx4/5;jmj24_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt

source_name: Arabidopsis seedlings


title: uch1/2_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt

value: 11 days

value: long day (16 h light, 8 h dark)


title: uch1/2_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt

value: Seedlings


title: PDGFR-Control-3

first: Xueyi

last: Teng

state: Beijing

address: No. 15 Datun road

institute: Institute of biophysics, CAS

data_processing:
The APEX-seq libraries were preprocessed with adaptor removal by Trimmomatics v0.38
Reads were then mapped to hg38 genome with HISAT v2.1.0
Read counts and FPKM were calculated by Rsubread and edgeR with GENCODE v27 annotation
Genome_build: hg38
Supplementary_files_format_and_content: Expression matrix

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% (v/v) Fetal Bovine Serum and 1% (v/v) Penicillin/Streptomycin.

extract_protocol:
Total RNA was extracted by TRIzol reagent.To enrich biotinylated RNAs, we used Pierce streptavidin magnetic beads, using 20 μl beads per 50 μg of RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 18-24 h after plating HEK293T cells stably expressing the corresponding APEX2 fusion construct, APEX2 labeling was initiated by changing the medium to fresh medium containing 500 mM biotin-phenol. This was incubated at 37℃ under 5% CO2 for 30 min. H2O2 was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 min. The reaction was quenched by replacing the medium with an equal volume of 5 mM Trolox, 10 mM sodium ascorbate and 10mMsodium azide in cold PBS. Cells were washed with cold PBS containing 5 mM Trolox and 10 mM sodium ascorbate three times.

tag: cell line

tag: target

value: PDGFR


title: YPW3272_rep3 [115082]

description:
115082_GAATTCGT-TATAGCCT_S5_L007
processed data file: Strain_3272.txt

source_name: haploid yeast culture_YPW3272


title: PDGFR-Control-1


title: YPW1156_rep3 [115083]

description:
115083_CTGAAGCT-TATAGCCT_S6_L007
processed data file: Strain_1156.txt

source_name: haploid yeast culture_YPW1156

value: A

value: cis-regulatory mutant to TDH3


title: Col-0_SD_repeat1

description:
MGISEQ-2000
gene_expression.txt

value: short day (8 h light, 16 h dark)


title: PDGFR-Control-2


title: YPW3202_rep3 [115079]

description:
115079_TCCGGAGA-TATAGCCT_S2_L007
processed data file: Strain_3202.txt

source_name: haploid yeast culture_YPW3202


title: YPW3016r1_rep3 [115080]

source_name: haploid yeast culture_YPW3016r1

value: alpha wild type control


title: PDGFR-APEX-3


title: nfrkb1/2/3_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: YPW3287_rep3 [115078]

description:
115078_ATTACTCG-TATAGCCT_S1_L007
processed data file: Strain_3287.txt

source_name: haploid yeast culture_YPW3287


title: INO80-(335-1540)_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: INO80-(335-1540)_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: YPW2690_rep2 [114838]

description:
114838_TCCGCGAA-GTACTGAC_S46_L007
processed data file: Strain_2690.txt

source_name: haploid yeast culture_YPW2690


title: CD28-Control-3


title: PDGFR-APEX-1


title: INO80-(1-550)_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: CD28-Control-2


title: YPW2504_rep3 [115081]

description:
115081_GAGATTCC-TATAGCCT_S4_L007
processed data file: Strain_2504.txt

source_name: haploid yeast culture_YPW2504


title: YPW3282_rep2 [114833]

description:
114837_CGGCTATG-GTACTGAC_S45_L007
processed data file: Strain_3282.txt

source_name: haploid yeast culture_YPW3282


title: INO80-(1-550)_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: YPW3016r2_rep2 [114831]

source_name: haploid yeast culture_YPW3016r2


title: CD28-APEX-3


title: ino80_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: KRAS_eIF2a_AA_T3

city: Montreal

first: Antonis

last: Koromilas

state: Quebec

address: 3755 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: 1Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital

data_processing:
The Bcl to FastQ conversion was performed using ‘bcl2fastq2 v2.19’ from the CASAVA software suite.
Reads mapped to mm10 using HISAT 2.1.0
Quantified according to script from "An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. [Ramskold et al., 2009]"
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Modified KRAS G12D Cell Line

extract_protocol:
Trizol
TruSeq Stranded Total RNA (Illumina), 50 bp single-end sequencing

value: eIF2a AA

tag: replicate


title: ino80_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt

tag: tissue


title: KRAS_eIF2a_AA_T4


title: INO80-FL_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: nfrkb1/2/3_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt


title: YPW2682_rep2 [114822]

source_name: haploid yeast culture_YPW2682

value: duplication control


title: PDGFR-APEX-2


title: KRAS_eIF2a_AA_T2


title: CD28-APEX-1


title: CD28-APEX-2


title: YPW3283_rep2 [114839]

description:
114839_TCTCGCGC-GTACTGAC_S47_L007
processed data file: Strain_3283.txt

source_name: haploid yeast culture_YPW3283


title: Lck-Control-3

value: Lck


title: KRAS_eIF2a_SS_T4

value: eIF2a SS


title: INO80-FL_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: KRAS_eIF2a_AA_T1


title: YPW3254_rep2 [114816]

description:
114834_GAATTCGT-GTACTGAC_S42_L007
processed data file: Strain_3254.txt

source_name: haploid yeast culture_YPW3254


title: Col-0_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt

value: wild type


title: KRAS_eIF2a_SS_T3


title: CD28-Control-1


title: YPW3288_rep2 [114801]

description:
114832_GAGATTCC-GTACTGAC_S40_L007
processed data file: Strain_3288.txt

source_name: haploid yeast culture_YPW3288


title: Lck-Control-2


title: YPW3016r3_rep2 [114837]

source_name: haploid yeast culture_YPW3016r3


title: Col-0_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: Lck-Control-1


title: KRAS_eIF2a_SS_T2


title: YPW3272_rep2 [114836]

description:
114830_TCCGGAGA-GTACTGAC_S38_L007
processed data file: Strain_3272.txt


title: Lck-APEX-3


title: Lck-APEX-2


title: arp5_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt


title: YPW3289_rep2 [114815]

description:
114833_ATTCAGAA-GTACTGAC_S41_L007
processed data file: Strain_3289.txt

source_name: haploid yeast culture_YPW3289


title: Lck-APEX-1


title: YPW3198_rep2 [114832]

description:
114827_TCTCGCGC-CAGGACGT_S35_L007
processed data file: Strain_3198.txt

source_name: haploid yeast culture_YPW3198


title: Tumor tissue from HCD mice, dataset 2, number 3

city: shanghai

first: Fu

last: jing

address: No.225 Changhai road

department: Liver Centre of SMMU

institute: Eastern Hepatobiliary Surgery Hospital

description: Tumor tissue from HCD mice were harvested and total RNA were extracted

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat(version:2.0.9)
Gene abundance measurements were generationed and normalized  using HTSeq. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed  using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: melanoma

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Pairedend libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.

value: B16F10 cells were cultured in DMEM supplemented with 10% FBS,and then subcutaneously injected into C57BL/6J mice fed with high cholesterol diet.

tag: strain

value: Tumor tissue in C57BL/6J mice


title: Lyn11-Control-4


title: Tumor tissue from HCD mice, dataset 2, number 2

tag: culture condition


title: Lyn11-Control-3


title: YPW2728_rep2 [114829]

description:
114825_CGGCTATG-CAGGACGT_S33_L007
processed data file: Strain_2728.txt

data_processing:
Raw reads were run through the fastqc (version 0.11.5) read quality software, which indicated high quality reads for all samples sequenced. Reads were then trimmed using cutadapt (version 1.10)
Reads were pseudo-mapped to the a transcriptome index generated using salmon (version 0.9.1) on S. cerevisiae cDNA (Ensemble, release 38)
Read counts from salmon were imported into R using TxDb (version 3.2.2). Read counts for the entire dataset were supplied to DESeq2 to model gene expression levels. The DESeq2 ‘contrast’ wrapper was then used to estimate log2 fold changes for each strain relative to its appropriate reference and identify differentially expressed genes.
Genome_build: S. cerevisiae s288c cDNA (Ensemble, release 38, retrieved from ftp://ftp.ensemblgenomes.org/pub/release-38/fungi/fasta/saccharomyces_cerevisiae/cdna/).
Supplementary_files_format_and_content: three types of processed data files are provided: output of differential expression measures for each strain relative to the appropriate wild type reference as calculated by DESeq2 as tab delimited text files, read count abundance measures as output from salmon for both the endogenous and transgenes present as .sf files, and a raw read count matrix for all samples also as a tab delimited text file.

source_name: haploid yeast culture_YPW2728

value: alpha


title: YPW3088_rep2 [114830]

description:
114826_TCCGCGAA-CAGGACGT_S34_L007
processed data file: Strain_3088.txt

source_name: haploid yeast culture_YPW3088

value: trans-regulatory mutant to TDH3


title: Tumor tissue from HCD mice, dataset 2, number 4


title: Lyn11-Control-2


title: Tumor tissue from HCD mice, dataset 2, number 1


title: Tumor tissue from ND mice, dataset 2, number 4

description: Tumor tissue from ND mice were harvested and total RNA were extracted

value: B16F10 cells were cultured in DMEM supplemented with 10% FBS,and then subcutaneously injected into C57BL/6J mice fed with normal diet.


title: Lyn11-Control-1


title: arp5_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt

source_name: Arabidopsis seedlings

tag: genotype

value: 11 days

value: long day (16 h light, 8 h dark)


title: YPW2525_rep2 [114828]

description:
114824_TAATGCGC-CAGGACGT_S32_L007
processed data file: Strain_2525.txt

source_name: haploid yeast culture_YPW2525


title: KRAS_eIF2a_SS_T1


title: YPW3290_rep2 [114827]

description:
114823_CTGAAGCT-CAGGACGT_S31_L007
processed data file: Strain_3290.txt

source_name: haploid yeast culture_YPW3290


title: Tumor tissue from ND mice, dataset 2, number 3


title: YPW1156_rep2 [114835]

description:
114829_ATTACTCG-GTACTGAC_S37_L007
processed data file: Strain_1156.txt

source_name: haploid yeast culture_YPW1156


title: Lyn11-APEX-4


title: atx4/5;jmj24_LD_repeat2

description:
MGISEQ-2000
gene_expression.txt

value: Seedlings

tag: growth conditions


title: YPW3161_rep2 [114826]

description:
114822_GAATTCGT-CAGGACGT_S30_L007
processed data file: Strain_3161.txt

source_name: haploid yeast culture_YPW3161


title: CS-HUCMSC 1

city: Kepala Batas

first: Noridzzaida

last: Ridzuan

state: pulau pinang

address: BERTAM

country: Malaysia

institute: Institut perubatan dan pergigian termaju, Universiti Sains Malaysia

description: Gene expression of rat lung exposed to cigarette smoke for 12 weeks, and then treated with h-UC-MSC

hyb_protocol: The sample were added with 2x Hi-RPM hybridization buffer and sample were hybridized at 65oC for 17 hours

scan_protocol: cDNA were washed and loaded onto the slide and scanned using Agilent Surescan microarray scanner (Agilent Technology, USA).

data_processing: Data processing were performed using Agilent GeneSpring GX software versuib 14.9.1 (Agilent Technology, USA),

organism: Rattus norvegicus

source_name: Rat lung

label_protocol: Cyanine-3 (Cy3) labeled cDNA were prepared from 200ng of RNA

growth_protocol: Animal were exposed to CS for 12 weeks in smoking chamber

extract_protocol: Total RNA was extracted from 30mg lung tissue using Rneasy mini kit (Qiagen, USA) according to manufacturer's instruction.

treatment_protocol: Approximately 2.5x10^6 hUCM-MSC and hUC-MSC-EV isolated from 2.5x10^6 hUCM-MSC were given as treatments via intratracheal delivery at week 13

tag: gender

value: male

value: lung tissue

tag: treatment

value: exposed to cigarette smoke for 12 weeks, treated with hUC-MSC


title: Tumor tissue from ND mice, dataset 2, number 2


title: YPW3059_rep2 [114825]

description:
114821_ATTCAGAA-CAGGACGT_S29_L007
processed data file: Strain_3059.txt

source_name: haploid yeast culture_YPW3059

extract_protocol:
Frozen cell pellets were resuspended in 700uL of a lysis buffer containing beta-mercaptoethanol and transferred to a plate containing ~250uL of acid-washed 425-600um beads. Beaded plates were beaten 10x for 1min each with 1min on ice in between. Plates were spun down at 3000rpm at 4C for 4min, and 400uL of lysis supernatant were removed and transferred into a new 96 well plate containing oligodT magnetic beads (Dynabeads mRNA DIRECT Kit, Ambion, cat# 61011). Beads and lysate were incubated at room temperature with agitation for 5 minutes, and then placed on a magnetic stand. Beads were then washed according to the Dynabeads mRNA direct kit user guide. After extraction, several representative samples were run on Agilent Bioanalyzer to check RNA quality and concentration before moving on to library preparation. In addition, selected wells were tested for the presence of NAT or KAN resistance markers present in distinct strains and controls by RT-PCR and visualized on a gel to ensure well-cross contamination had not taken place at any step previous to library prep.
RNA sequencing libraries were prepared using a modified, ⅓ volume reaction TruSeq RNA Sample Preparation v2 Guide, and using multiplexable adapters from the TruSeq RNA CD Index Plate (cat# 20019792).

value: A

value: overexpression of TDH3


title: Tumor tissue from ND mice, dataset 2, number 1


title: Lyn11-APEX-3


title: CS-HUCMSC-EV 2

description: Gene expression of rat lung exposed to cigarette smoke for 12 weeks, and then treated with h-UC-MSC-EV

value: exposed to cigarette smoke for 12 weeks, treated with hUC-MSC-EV


title: Lyn11-APEX-2


title: in3

city: Erzurum

first: Selçuk

last: Özdemir

address: Atatürk University Faculty of Veterinary Medicine

country: Turkey

institute: Atatürk University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl  and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et  al., 2009) without mismatch to analyze their expression and distribution on the  reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0  was used as reference, modified software mirdeep2(Friedlander et al., 2011) and  srna-tools-cli were used to obtain the potential miRNA and draw the secondary  structures.
To remove tags originating from protein-coding genes, repeat sequences, rRNA,  tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker,  Rfam database or those types of datas from the specified species itself. Exploring the occurrence of miRNA families identified from the samples in other  species. In our analysis pipeline, known miRNA used miFam.dat  (http://www.mirbase.org/ftp.shtml) to look for families; novel miRNA precursor  was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam  families. Predicting the target gene of miRNA was performed by psRobot_tar in psRobot  (Wu et al, 2012) for plants or miRanda (Enright et al, 2003) for animals.
miRNA expression levels were estimated by TPM (transcript per million) through  the following criteria (Zhou et al., 2010):  Normalization formula: Normalized expression = mapped readcount/Total  reads*1000000
Genome_build: UMD3.1
Supplementary_files_format_and_content: GTF and Fastq formats were used for each sample.

organism: Bos taurus

source_name: mammary gland

extract_protocol:
Mammary gland tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The RNA sample was preparated by using total of 2 µg RNA. Firstly, Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA) was used to remove ribosomal RNA, and ethanol precipitation was perfomed to clean the rRNA free residue. Subsequently, the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) was used to generate sequencing cDNA libraries following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mammary gland tissue

tag: disease state

value: Mycoplasma bovis infected


title: YPW1177_rep2 [114824]

first: Patricia

last: Wittkopp

address: 1105 N University Ave

institute: University of Michigan

description:
114820_GAGATTCC-CAGGACGT_S28_L007
processed data file: Strain_1177.txt

source_name: haploid yeast culture_YPW1177

value: TDH3 deletion


title: Lyn11-APEX-1


title: in2


title: YPW3256_rep2 [114823]

description:
114819_CGCTCATT-CAGGACGT_S27_L007
processed data file: Strain_3256.txt

source_name: haploid yeast culture_YPW3256


title: YPW2506_rep2 [114821]

description:
114818_TCCGGAGA-CAGGACGT_S26_L007
processed data file: Strain_2506.txt

source_name: haploid yeast culture_YPW2506


title: YPW3296_rep2 [114834]

description:
114828_AGCGATAG-CAGGACGT_S36_L007
processed data file: Strain_3296.txt

source_name: haploid yeast culture_YPW3296

value: TDH2 deletion


title: in1


title: Dermal fibroblasts PID21_9124

data_processing:
Raw reads were aligned to human reference genome (GRCh38) by STAR (Dobin and Gingeras, 2015).
Counts were normalized by trimmed mean of M-values (TMM) using edgeR (Robinson et al., 2010).
Bigwig files were generated using bamCoverage (Ramírez et al., 2016).
Differential peaks using MACS (Feng et al., 2012; Zhang et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of replicates for RNA-seq experiments

source_name: Dermal fibroblasts

extract_protocol:
Day 14 and day 21 cells were harvested for HITS-CLIP following the published protocol (Moore et al., 2014) with modifications. Briefly, cross-linked cells were lysed and treated with RQ1 DNase (Promega, M6101) and RNaseA (Thermo). Complex containing AGO-miRNA-mRNA were immunoprecipitated overnight at 4C with pan-AGO antibody. The immunoprecipitated complex was radio-labelled and extracted after running on NuPAGE gel (Thermo). RNA from the 130kDa band was extracted for sequencing using TruSeq Small RNA Library Preparation Kits (San Diego, CA).
TruSeq Small RNA Library Preparation Kits (San Diego, CA).

value: ScienCell, 2310

value: Dermal fibroblasts


title: YPW3228_rep2 [114820]

description:
114817_ATTACTCG-CAGGACGT_S25_L007
processed data file: Strain_3228.txt

source_name: haploid yeast culture_YPW3228

value: alpha

value: trans-regulatory mutant to TDH3


title: Dermal fibroblasts PID14_9124


title: WT-CMs

first: Bin

last: Li

address: Dong'an Road

department: Department of Physiology and Pathophysiology

institute: Fudan University

data_processing:
Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website; Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence; Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

source_name: HiPSC-derived cardiomyocytes

extract_protocol:
Total mRNAs were isolated from wild type and DMD mutant hiPSC-derived cardiomyocytes using TRIZOL (Invitrogen) according to the directions. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit.
CDNA libraries were prepared for sequencing using standard Illumina protocols.

value: Wild type

value: cardiomyocytes


title: Dermal fibroblasts PID21_NS

first: Ya-Lin

last: Lu

address: 660 S. Euclide Avenue

institute: Washington University School of Medicine

value: miR-NS


title: DMD-CMs

value: DMD disease


title: Dermal fibroblasts PID14_NS


title: Cont

value: control


title: SS_genomic

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

description: Potassium permanganate footprinting naked DNA control

library_source: genomic

data_processing:
DNA sequences were first processed with cutadapt (Martin, 2011) to remove readthrough adapter sequences
Reads were mapped to the WS230 C. elegans genome sequence edition using Bowtie (Langmead et al., 2009), retaining only uniquely mapped reads.
Normalized bigwig files were generated using deepTools2 with bamCoverage command with - offset 1 option.
To generate finla SS-seq signal file genomic control was subtracted using deepTools2 bigwigCompare command.
Genome_build: WS230
Supplementary_files_format_and_content: BigWig files contain reads normalized to the whole genome in 1 bp resolution

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: mixed-stage embryos

growth_protocol: Wild-type C. elegans nematodes (N2 Bristol) were grown to adulthood on NG agar plates with the E. coli strain HB101. Gravid adults were bleached to obtain embryos, and the embryos were hatched in M9 medium without food to obtain developmentally arrest, synchronized L1 larvae (L1s). To obtain mixed-stage embryos for analysis, approximately 1x105 starved, synchronized L1s were cultured on NG agar plates with HB101 for 96 hours, and the resulting gravid adults were bleached to obtain mixed-stage embryos.

extract_protocol:
Approximately 2 x106 intact embryos or ground L1s were resuspended in low salt buffer (15 mM Tris ph7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM EGTA, 300 mM Sucrose). A freshly prepared solution of 100 mM KMnO4 was added to each sample to a final concentration of 40 mM and incubated for 80 seconds at room temperature. To stop the reaction, an equal volume of stop solution (700 mM β-mercaptoethanol, 50 mM ETA, 1% SDS) was added. Samples were digested with Proteinase K (10 μg/ml final) at 55°C for 1 hour. DNA was extracted once with phenol-chloroform, precipitated once with ethanol, resuspended in 500 μl of H2O, treated with Rnase A (10 μg/ml final) at 37°C for 1 hour, extracted with phenol-chloroform, and precipitated with ethanol. To block free 3’ DNA ends from being cleaved before nuclease treatment by enzymes such as topoisomerase, samples were treated with Cordycepin 5′-triphosphate sodium salt. Approximately 25 μg of extracted DNA was incubated with 100 μM Cordycepin 5′-triphosphate sodium salt and 40 U of Terminal transferase TdT in a final reaction of 150 μl at 37°C for 1 hour. DNA was extracted once with phenol-chloroform and precipitated once with ethanol. About 5 μg of precipitated DNA was digested with 100 U of S1 nuclease in a 50 μl reaction at 37°C for 20 minutes. DNA was extracted with phenol-chloroform and ethanol precipitated.
DNA ends were repaired with the DNA End Repair kit from Epicenter (34 μl of DNA, 5 μl 10XEnd-Repair buffer, 5 μl of 2.5 mM dNTP mix, 5 μl of 10 mM ATP, 1 μl End-Repair enzyme mix, and incubated for 45 minutes at room temperature). To add 3'-end A overhangs, 34 μl of DNA was mixed with 5 μl NEB buffer 2, 10 μl of 10 mM dATP, 1 U of Klenow fragment (3'-5'- exo), and incubated at 37ºC for 30 minutes. DNA was cleaned using a Qiagen PCR purification column after each step. Hairpin biotinylated adapters were ligated using 2 ul of Quick Ligase (NEB) in a 30 μl reaction at room temperature with 0.08 μM adapter for 15 minutes. DNA was purified with a Qiagen PCR purification column and eluted in 20 μl of EB. To remove unligated adapters, 20 μl of sample was mixed with 10 μl of AMPure beads. DNA was eluted with 130 μl of EB and sonicated to an average size of 300 bp using a Covaris sonicator. Before DNA was incubated with 50 μl of magnetic Dynabeads MyOne Stretavidin T1 (Invitrogen), the beads were washed with wash buffer WB, resuspended in 130 μl of high salt WB.  Next, 50 μl of Dynabeads were added to 130 μl of DNA (1 M final salt) and incubated for 1 hour while rotating. Beads were washed 3 times with WB, once with EB, resuspended in 34 μl of EB, and subjected to end repair and 3'-end overhang addition reactions as described above. After the final wash, beads were resuspended in 22 μl of EB. Second hairpin biotinylated adapters were ligated in 50 μl reactions with 0.08 μM adapter concentration and 3 μl of Quick DNA Ligase. After ligation, beads were washed and resuspended in 45 μl of EB. Hairpins were digested to remove DNA from the beads using 1 U of USER enzyme (NEB) in a 50 μl reaction at 37°C for 1 hour. DNA was purified on a Qiagen column and PCR amplified with barcoded Truseq primers (37 μl of DNA, 10 μl 5x Phusion HF Buffer, 0.4 μl 25 mM dNTP, 1μl of Truseq Universal primer at 6.5 μM, 1μl of Truseq Barcoded primer at 6.5 μM, 1 μl Phusion DNA Polymerase) using the following program (2 min at 98°C, [30 sec at 98°C, 30 sec at 65°C, 60 seq at 72°C] for 16 cycles, 5 min 72°C).
End-seq

treatment_protocol: To obtain L1s with inhibited transcription, 4 ml of packed, starved L1s were placed into 10 ml of S-medium containing HB101 bacteria at an OD600 of 2 and α-amanitin at a final concentration of 20 μg/ml.

tag: srain

value: mixed-stage embryos

value: untreated


title: SS_emb_L1_rep2

description: Potassium permanganate footprinting

source_name: first stage larvae

tag: developmental stage

value: first stage larvae


title: SS_emb_L1_aman_96

description: Potassium permanganate footprinting

value: a-amanitin 96 hours


title: Strain

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm9 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: Cell ranger output

source_name: Bone Marrow Myeloid Cells

growth_protocol: Myeloid cells were obtained from murine bone marrow and cultured. Cells were then cultured in a 3D collagen scaffold system for 48 hours to either mechanically strain the cells or not mechanicall strain them (no strain control).

extract_protocol:
This cellular suspension was then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: 48 hours of 10% strain

tag: passages

value: first passage, primary

value: bone marrow

value: myeloid


title: CS-HUCMSC 2

value: male

value: lung tissue

value: exposed to cigarette smoke for 12 weeks, treated with hUC-MSC


title: CS-HUCMSC-EV 1

value: exposed to cigarette smoke for 12 weeks, treated with hUC-MSC-EV


title: NAÏVE 1

description: Gene expression of rat lung exposed to normal air

value: breathing normal air


title: CS 2

description: Gene expression of rat lung exposed to cigarette smoke for 12 weeks

value: exposed to cigarette smoke for 12 weeks


title: ACOT1 silenced_5

city: Toronto

first: Marc

last: Angeli

state: Ontario

address: 101 College street

department: Multi Organ Transplant

institute: University Health Network

description: Gene Expression Data from Mouse liver with ACOT1 shRNA

hyb_protocol: core facility protocol

scan_protocol: core facility protocol

data_processing: Expression values extracted from CEL files using Biobase R library, probes with expression smaller than 4 on all samples were removed. Differential expression was performed with limma as unpaired samples.

source_name: liver

label_protocol: microarray experiment performed at: The Centre for Applied Genomics (TCAG), Toronto, Ontario, Canada (http://www.tcag.ca)

growth_protocol: 6-8-week-old male C57BL/6 mice were housed in sterilized, individually-ventilated cages. After 1 week of acclimation, animals received free access to High Fat, High Carbohydrate Diet (HFD) for 16 weeks. HFHC diets consisted of 58%kcal fat diet (D12330 High-fat Diet from Research diets) supplemented with enriched water 42g/L carbohydrates at a ratio of 45% sucrose and 55% fructose on a 12:12-h light-dark cycle. injections of either an Adenoviral vector (with Adenoviral type 5 backbone) containing Ad-GFP-U6-scramble-shRNA or Ad-GFP-U6-m-ACOT1-shRNA at 1x109 PFU were performed weekly for 4 weeks (Vector Biolabs).

extract_protocol: livers tissue was extrated and RNA was extracted using RNeasy Tissue extraction kit (Qiagen)

treatment_protocol: tail vein injections of either an Adenoviral vector (with Adenoviral type 5 backbone) containing Ad-GFP-m-ACOT1 or Ad-GFP at 1x109 PFU were performed weekly for 4 weeks after 16 weeks of HF diet

value: liver

tag: Sex

value: treated mice with ACOT1-shRNA injection


title: SS_emb_wt_rep2

description: Potassium permanganate footprinting


title: SS_emb_y93_rep2

description: Potassium permanganate footprinting

value: RNAi


title: SS_emb_L1_rep1

description: Potassium permanganate footprinting


title: Control (scramble)_6

description: Gene Expression Data from Mouse liver with Scrambled Control shRNA

value: control mice with a scramble shRNA injection


title: No Strain (Controls)

tag: cell type


title: Control (scramble)_9


title: Control (scramble)_8


title: atx4/5;jmj24_LD_repeat1

description:
MGISEQ-2000
gene_expression.txt

source_name: Arabidopsis seedlings

value: Seedlings

tag: age

value: 11 days

value: long day (16 h light, 8 h dark)


title: NAÏVE 2


title: YPW3202_rep2 [114817]

city: Ann Arbor

description:
114814_TCCGCGAA-TAATCTTA_S22_L007
processed data file: Strain_3202.txt

source_name: haploid yeast culture_YPW3202

growth_protocol: For a total of four replicates, each replicate set of strains, including mutants and controls, were randomly arrayed across the inner wells of a 96 well plate surrounded by an outer row of wells filled with non-inoculated media. Each of the four plate arrays was grown to saturation in YPD, and then glycerol stocked in 80% glycerol and stored at -80C. The glycerol stocks were thawed by transfer using a pin tool onto solid YPG agar plates and strains were grown up for ~3 days at 30C. Strains were then transferred by pin tool again into 500uL liquid YPD in 1mL 96-well plates with glass beads and grown at 30C while shaking at 250rpms for 2 days, until all strains were once again at saturation. 100uL of the saturated culture was then transferred to a Costar 96 well plate and OD measured using a Tecan Sunrise. The OD was then used to calculate cell density. A separate 1mL 96 well plate was then filled with  500uL of YPD in each well, and each well inoculated with a volume of the saturated culture calculated to grow to a cell density of 5x10^6 cell per mL (an OD of about 0.4) after 12.5hr, based on empirical determination of each strain’s growth rate. These cultures were then grown spinning on a wheel at 30C for 12.5hrs, after which 100uL was removed and used to measure OD to ensure all cultures were between an OD of 0.26 to 0.48. Plates were then spun down for 5min at 3000g, and liquid media pipetted off. Remaining cell pellets were frozen by plunging the entire plate containing cell pellets into liquid nitrogen. Plates were sealed with foil and stored at -80C until RNA extractions were performed.

value: alpha

tag: genotype/variation

value: trans-regulatory mutant to TDH3


title: YPW3191_rep2 [114818]

description:
114815_TCTCGCGC-TAATCTTA_S23_L007
processed data file: Strain_3191.txt

source_name: haploid yeast culture_YPW3191


title: YPW3284_rep2 [114813]

description:
114812_TAATGCGC-TAATCTTA_S20_L007
processed data file: Strain_3284.txt

source_name: haploid yeast culture_YPW3284


title: SS_emb_wt_rep1

description: Potassium permanganate footprinting

value: mixed-stage embryos

value: untreated


title: YPW3247_rep2 [114814]

description:
114813_CGGCTATG-TAATCTTA_S21_L007
processed data file: Strain_3247.txt

source_name: haploid yeast culture_YPW3247


title: YPW2911_rep2 [114819]

description:
114816_AGCGATAG-TAATCTTA_S24_L007
processed data file: Strain_2911.txt

source_name: haploid yeast culture_YPW2911


title: CS 1

source_name: Rat lung

value: male


title: YPW3241_rep2 [114811]

description:
114810_GAATTCGT-TAATCTTA_S18_L007
processed data file: Strain_3241.txt

source_name: haploid yeast culture_YPW3241


title: YPW3203_rep2 [114812]

description:
114811_CTGAAGCT-TAATCTTA_S19_L007
processed data file: Strain_3203.txt

source_name: haploid yeast culture_YPW3203


title: ACOT1 silenced_2


title: BP_genomic_bound

description: Psoralen enriched naked DNA control

data_processing:
DNA sequences were first processed with cutadapt (Martin, 2011) to remove readthrough adapter sequences
Reads were mapped to the WS230 C. elegans genome sequence edition using Bowtie (Langmead et al., 2009), retaining only uniquely mapped reads.
Normalized bigwig files were generated using deepTools2 with bamCoverage command.
To generate final BP signal file first log2 of bound singnal over unbound was generated using deepTools2 bigwigCompare command. Then genomic control in the form of log2 genomic bound over genomic unbound was subtracted using deepTools2 bigwigCompare comand.
Genome_build: WS230
Supplementary_files_format_and_content: BigWig files contain reads normalized to the whole genome in 1 bp resolution

extract_protocol:
Nuclei were isolated from frozen embryos or L1s. L1s were first ground in liquid nitrogen to disrupt them. Approximately 3-4 x106 embryos or ground L1s were resuspended in 1 ml of buffer A (15mM Tris ph 7.5, 2mM MgCl2, 340 mM sucrose, 0.2 mM spermine, 0.2 mM spermidine, 0.1% Triton, 0.25% NP-40, 0.5 mM PMSF and a Protease Inhibitor Cocktail Set III from Calbiochem 1:1000 dilution), dounced on ice in a 2 ml glass homogenizer with pestle A and pestle B for 15 times each, and spun at 4°C for 15 min at 100 x g. The nuclei-containing supernatant was saved on ice, the pellet was resuspended in 1 ml of buffer A, and the homogenization procedure above was repeated twice. Nuclei from the three supernatants were pooled together, concentrated to 200 μl by spinning at 1000 x g for 10 minutes at 4°C.
EZ-Link™ Psoralen-PEG3-Biotin (BP) (Thermo Fisher Scientific) was added to the nuclei to a final concentration of 1.38 10-2 mg/ml, nuclei were crosslinked for 30 minutes using a UVL-56 Black-Ray lamp (long wave UV 366 nm), and nuclei were pelleted for 10 min at 4°C at 1000 x g. The supernatant was removed, and the nuclei were resuspended in 200 μl of buffer A and digested with proteinase K (10 μg/ml final) at 55°C for 30 minutes. DNA was extracted once with phenol-chloroform and precipitated once with ethanol. DNA was resuspended in 130 μl of H20, treated with Rnase A (10 μg/ml final) at 37°C for 1 hour, extracted with phenol-chloroform, and precipitated with ethanol. DNA was resuspended in 130 μl of H20 and sonicated to an average size of 150 bp using a Covaris sonicator.
The BP-containing DNA was then trapped on magnetic Dynabeads MyOne Stretavidin T1 (Invitrogen) for further manipulation.  Prior to incubation with BP-containing DNA, 50 μl of Dynabeads were washed with wash buffer WB (10 mM Tris ph 7.5, 1M NaCl, 1mM EDTA), and resuspended in 130 μl of high salt WB (10 mM Tris ph 7.5, 2M NaCl, 1mM EDTA).  The washed Dynabeads were added to 130 μl of DNA (1 M final salt), and incubated for 1 hour while rotating. The DNA-containing beads were collected with a magnet, and the supernatant was saved for BP-depleted DNA samples. DNA-containing beads were washed 3 times with 200 μl of WB and resuspended in 34 μl of EB (10 mM Tris ph 7.5).
Libraries for BP-enriched samples were prepared on the beads.  Libraries for BP-depleted samples were made using approximately 1 μg of the unbound, BP-depleted DNA in the supernatant.  After each step in library preparation, the DNA-containing beads were washed three times with WB followed by one wash with EB.  The BP-depleted DNA samples were cleaned using a Qiagen PCR purification column.
To make libraries, the DNA ends were repaired using the End-it DNA End Repair kit from Epicenter (34 μl of BP-depleted DNA or DNA-containing beads, 5 μl 10XEnd-Repair buffer, 5μl of 2.5 mM dNTP mix, 5 μl of 10 mM ATP, 1 μl End-Repair enzyme mix, and incubated for 45 minutes at room temperature). To add 3'-end A overhangs, 34 μl of BP-depleted DNA or DNA-containing beads were mixed with 5 μl NEB buffer 2, 10 μl of 10 mM dATP, 1 U of Klenow fragment (3-5- exo-), and incubated at 37°C for 30 minutes. Barcoded adapters were ligated using Quick Ligase from NEB (12 μl of Input DNA or beads, 15 μl 2x DNA ligase buffer, 1 μl of 0.125 μM NextFlex adapters, 2 μl DNA ligase, and incubated for 15 minutes at room temperature). Following adapter ligation, DNA-containing beads were cleaned with WB 3 times, once with EB, and resuspended in 37 μl of EB. BP-depleted DNA was cleaned using a Qiagen PCR column and eluted in 20 μl of EB. Unligated adapters were removed from BP-depleted samples using 10 μl of AMPure beads and eluted in 50 μl of EB. Libraries were PCR amplified (37 μl of BP-depleted DNA or DNA-containing beads, 10 μl 5x Phusion HF Buffer, 0.4 μl 25 mM dNTP, 2μl of Netflex primer mix at 12 μM, 1 μl Phusion DNA Polymerase) using the following program (2 min 98°C, [30 sec at 98°C, 30 sec at 65°C, 60 seq at 72°C] for 16 – 30 cycles, 5 min 72°C). Libraries were cleaned using Qiagen PCR purification column. Some samples required an additional AMPure bead clean up to remove unused primers and adapters. Libraries were sequenced using the Illumina HiSeq-4000 platform with 50 bp single end reads.
Control genomic DNA samples were prepared using the same steps outlined above.  However, previously purified genomic DNA was used in place of DNA purified from nuclei.
BP-seq


title: MEFs_4E_Rbm8a_rep3

city: San Francisco

first: Duygu

last: Kuzuoglu Ozturk

state: California

address: 1450 3rd Street, Helen Diller Cancer Building

institute: UCSF

data_processing:
RNA-seq reads were aligned to mouse GRCm38 genome by using HISAT v2.0.5 (Kim et al., 2015)with default settings.
Gene read counts and expression values (measured by Transcripts Per Kilobase Million, TPM) were further calculated by RSEM v1.3.0 (Li and Dewey, 2011) with default settings.
Differential expression analyses were conducted with DESeq2 (Love et al., 2014) R package, where only genes with an average TPM over 0.5 were involved.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 fold change for each gene

source_name: Mouse embryonic fibroblasts (MEFs)

extract_protocol:
eIF4E+/+ and eIF4E+/- MEFs expressing scramble, Magoh, eIF4A3 and Rbm8a sgRNAs were induced with Dox for 48 hours in triplicates, total RNA was isolated by Trizol and ribosomal RNA was removed by Ribo-Zero (Illumina).
RNA seq libraries were prepared by ScriptSeq v2 RNA-seq library preparation kit (Epicenter) following the manufacturer’s protocol and sequenced as paired-end 100 bp on HiSeq 4000

treatment_protocol: All cells were treated with 0.4ug/ml doxycycline to induce dCas9-Krab expression

tag: cell line

value: Immortalized, Myc and Ras expressed eIF4E-/+ MEFs

tag: induction

value: 48h DOX induction


title: MEFs_4E_Rbm8a_rep2


title: YPW2504_rep2 [114810]

description:
114809_ATTCAGAA-TAATCTTA_S17_L007
processed data file: Strain_2504.txt

source_name: haploid yeast culture_YPW2504


title: MEFs_4E_Rbm8a_rep1


title: BP_L1_aman_24_unbound

description: Psoralen depleted

value: first stage larvae

value: a-amanitin 24h


title: MEFs_4E_Magoh_rep3


title: YPW1200_rep2 [114809]

description:
114808_GAGATTCC-TAATCTTA_S16_L007
processed data file: Strain_1200.txt

source_name: haploid yeast culture_YPW1200

value: A

value: cis-regulatory mutant to TDH3


title: BP_L1_aman_96_unbound_rep2

description: Psoralen depleted

value: a-amanitin 96h


title: BP_L1_aman_24_bound

description: Psoralen enriched


title: BP_genomic_unbound

description: Psoralen depleted naked DNA control


title: YPW3068_rep2 [114806]

description:
114805_ATTACTCG-TAATCTTA_S13_L007
processed data file: Strain_3068.txt

source_name: haploid yeast culture_YPW3068


title: YPW3286_rep2 [114808]

description:
114807_CGCTCATT-TAATCTTA_S15_L007
processed data file: Strain_3286.txt

source_name: haploid yeast culture_YPW3286


title: BP_L1_aman_96_bound_rep2

description: Psoralen enriched

source_name: first stage larvae


title: YPW3245_rep2 [114807]

description:
114806_TCCGGAGA-TAATCTTA_S14_L007
processed data file: Strain_3245.txt

source_name: haploid yeast culture_YPW3245


title: MEFs_4E_4A3_rep3


title: MEFs_4E_Magoh_rep2


title: MEFs_4E_Magoh_rep1


title: YPW3291_rep2 [114805]

description:
114804_AGCGATAG-AGGCGAAG_S12_L007
processed data file: Strain_3291.txt

source_name: haploid yeast culture_YPW3291

value: TDH1 deletion


title: MEFs_4E_4A3_rep2


title: YPW3285_rep2 [114804]

description:
114803_TCTCGCGC-AGGCGAAG_S11_L007
processed data file: Strain_3285.txt

source_name: haploid yeast culture_YPW3285


title: BP_L1_aman_96_unbound_rep1

description: Psoralen depleted


title: BP_L1_aman_96_bound_rep1

description: Psoralen enriched


title: YPW3298_rep2 [114803]

description:
114802_TCCGCGAA-AGGCGAAG_S10_L007
processed data file: Strain_3298.txt

source_name: haploid yeast culture_YPW3298

value: TDH2/3 double deletion


title: MEFs_4E_4A3_rep1


title: BP_L1_unbound_rep2

description: Psoralen depleted


title: MEFs_4E_Scr_rep3


title: BP_L1_bound_rep2

description: Psoralen enriched


title: BP_L1_unbound_rep1

description: Psoralen depleted


title: YPW3275_rep2 [114802]

description:
114801_CGGCTATG-AGGCGAAG_S9_L007
processed data file: Strain_3275.txt

source_name: haploid yeast culture_YPW3275


title: MEFs_4E_Scr_rep2


title: MEFs_4E_Scr_rep1


title: BP_L1_bound_rep1

description: Psoralen enriched


title: MEFs_Con_Rbm8a_rep2

value: Immortalized, Myc and Ras expressed WT MEFs


title: BP_Emb_y93_bound_rep2

description: Psoralen enriched

source_name: mixed-stage embryos

value: RNAi


title: circALTO1 rep 3

city: Dallas

first: Richard

last: Wang

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. The human reference genome sequence and gene annotation data, hg38, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). The qualities of RNA-sequencing libraries were estimated by mapping the reads onto mouse transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.4.3)[63]. STAR (v2.7.2b)[64] was employed to align the reads onto the mouse genome, SAMtools (v1.9) [65] was employed to sort the alignments, and HTSeq Python package [66] was employed to count reads per gene. DESeq2 R Bioconductor package [67, 68] was used to normalize read counts and identify differentially expressed (DE) genes.
Genome_build: hg38

growth_protocol: 10% FBS DMEM; 5% CO2

extract_protocol:
Qiagen RNA-Easy miniprep
NEBNext Ultra II with Poly-A Selection

tag: time

value: 48hr after transfection

tag: expression


title: MEFs_Con_Rbm8a_rep1


title: circALTO1 rep 2


title: MEFs_Con_Magoh_rep3


title: ACOT1 silenced_1

description: Gene Expression Data from Mouse liver with ACOT1 shRNA

source_name: liver

tag: tissue

value: liver

tag: strain

value: treated mice with ACOT1-shRNA injection


title: circALTO1 rep 1


title: YPW3016r1_rep2 [114797]

source_name: haploid yeast culture_YPW3016r1

value: alpha

value: alpha wild type control


title: YPW2794_rep2 [114800]

description:
114800_TAATGCGC-AGGCGAAG_S8_L007
processed data file: Strain_2794.txt

source_name: haploid yeast culture_YPW2794

value: trans-regulatory mutant to TDH3


title: YPW3287_rep2 [114798]

description:
114798_GAATTCGT-AGGCGAAG_S6_L007
processed data file: Strain_3287.txt

source_name: haploid yeast culture_YPW3287


title: YPW3092_rep2 [114795]

description:
114795_CGCTCATT-AGGCGAAG_S3_L007
processed data file: Strain_3092.txt

source_name: haploid yeast culture_YPW3092


title: YPW1188_rep2 [114799]

description:
114799_CTGAAGCT-AGGCGAAG_S7_L007
processed data file: Strain_1188.txt

source_name: haploid yeast culture_YPW1188


title: YPW2800_rep2 [114796]

description:
114796_GAGATTCC-AGGCGAAG_S4_L007
processed data file: Strain_2800.txt

source_name: haploid yeast culture_YPW2800


title: BP_Emb_wt_unbound_rep2

description: Psoralen depleted

value: mixed-stage embryos

value: untreated


title: MEFs_Con_Rbm8a_rep3

source_name: Mouse embryonic fibroblasts (MEFs)

value: 48h DOX induction


title: BP_Emb_y93_unbound_rep2

description: Psoralen depleted