title: Du145-DtxR, siRNA-BRPF1, Replica #2

description:
brpf1-II
counts2.xlsx


title: D2, WT Rep2

status: Public on Nov 17 2023

type: SRA

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
Processed using nf-core/atacseq v2.0
Specified parameters --narrow-peak and –read-length = 100
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Control or Runx1KO C2C12 cells were grown in triplicate in growth (20% FBS) media

extract_protocol:
Cells were lysed and nuclei isolated in lysis buffer (10mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) and tagmented using Tn5 transposase from Vanzyme
Libraries were made using Illumina's TruePrep DNA Library Prep Kit V2

tag: cell line

tag: genotype

value: WT

tag: time

value: 2 day

tag: treatment

value: differentiation media


title: Du145-DtxR, siRNA-BRPF1, Replica #1

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

description:
brpf1-I
counts2.xlsx

library_source: transcriptomic

data_processing:
STAR was used to align Fastq files to the latest human reference transcriptome
Salmon was used for quantification
Tximport and DEseq2 used for normalisation of counts
Assembly: GRCh38
Supplementary files format and content: XLSX files of all sample counts

molecule: total RNA

organism: Homo sapiens

source_name: Docetaxel Resistant Du145 cell line

growth_protocol:
Du145-Docetaxel Resistant cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin-streptomycin, and incubated at 37°C with 5% CO2 in a humidified environment.
Du145-Parental and Resistant cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin-streptomycin, and incubated at 37°C with 5% CO2 in a humidified environment.

extract_protocol: Total RNA was extracted with NucleoSpin™ RNA Plus Isolation Kit (Macherey Nagel, 740984.50)

treatment_protocol:
The Docetaxel-resistant Du145 cells were plated on 6-well plates with a density of 170,000 cells (60% confluency). After 24 h, the cells underwent treatment with siControl and siBRPF1. Subsequently, after an additional 24 h, the media containing the siRNA was aspirated, and fresh medium was added. Total RNA isolation was carried out 48 h later. The efficiency of knockdown was tested, revealing a knockdown efficiency greater than 80%.
Du145 (ATCC no. HTB-81) cells were maintained in RPMI-1640 medium (Gibco, 11875093) supplemented with 10% fetal bovine serum (Biowest, S1810) and 1% penicillin/streptomycin (Biowest, L0022). Cells were grown at 37°C in a humidified atmosphere with 5% CO2. Resistant clones were selected by culturing cells with docetaxel (Sigma-Aldrich, 01885) and/or cabazitaxel (Sigma-Aldrich, SML2487) for 72 h. A dose-escalation strategy was implemented, beginning at 1 nM, and doubled to reach 125 nM. After waiting for approximately 1-2 weeks for the remaining survived cells to recover, they underwent a passage before proceeding with the new dose. Cell viability experiments were set up to assess the establishment of resistance at two dose increments. Parental cells were passaged alongside as an age-matched appropriate control.

value: Docetaxel Resistant Du145 cell line

value: BRPF1 Knockdown

value: siRNA BRPF1


title: Du145-DtxR, siRNA-Control, Replica #3

description:
ctrl-III
counts2.xlsx

value: siRNA Control


title: D2, WT, Rep1


title: 7 - Disease

city: Fuzhou

first: Kaiyang

last: Lin

state: Please Select

address: No. 134, East Street, Gulou District

country: China

institute: Fujian province hospital

data_processing:
The image processing and base calling are performed using Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
Assembly: GRCh37

source_name: Plasma

extract_protocol:
After enrichment using oligo dT (rRNA depletion), the total RNA sample is processed.1-2 μg of total RNA is used for constructing RNA sequencing libraries.
RNA libraries for RNA-Seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit（Illumina） following manufacturer‘s protocol.

tag: tissue

value: Plasma

tag: disease state

value: postoperative contrast-induced acute kidney injury (CI-AKI)

tag: age

tag: Sex

value: male

value: percutaneous coronary intervention (PCI)

tag: clinical data

value: The 79-year-old male was diagnosed with contrast-induced acute kidney injury (CA-AKI) after an elective PCI procedure. His baseline estimated glomerular filtration rate (eGFR) was 86.537 ml/min. He has diabetes but does not have heart failure, hypertension, or atrial fibrillation.


title: DNA_AURKA_zygote_emb3

city: GuangZhou

first: Teng

last: Wang

address: jingxiStreet

institute: Southern Medical University

description: scCOOL-seq

data_processing:
TrimGalore (version 0.6.5) and BS-Seeker2 (version 2.1.1)
For RNA-part data, reads in R2 were grouped according to specific cell barcode35 (8 bp), then UMI information was used to extract the corresponding R1 reads. Raw sequencing reads were trimmed to remove the template switch oligo (TSO) sequence, polyA tail and low-quality bases. Next, the clean R1 reads were aligned to human reference genome (hg38, UCSC) using STAR (version 2.7.9) with the default parameters, HTSeq (version 0.12.4) was used to quantify gene expression level. The number of distinct UMIs (unique molecular identifiers) for each gene was counted as the transcript copy number and normalized to TPM (transcripts per million) value. Gene expression level was shown as log2(TPM+1).
For DNA-part data, reads were trimmed with TrimGalore71 (version 0.6.5) to remove adaptor sequences, low-quality bases and 6 bp random primers. Only reads with length more than 50 bp were retained. Reads passed quality control were then aligned to the reference genome (hg38, UCSC)68 using BS-Seeker272 (version 2.1.1) under both end-to-end and local alignment mode. Duplicated reads generated from PCR amplification were removed by Samtools73 (version 1.10). Only the unique alignments were used for the following analysis. The cells that passed four strict quality control criteria (mapping ratio of DNA-part data higher than 30%; bisulfite conversion rate higher than 98%; more than 1,000,000 WCG sites and 8,000,000 GCH sites covered; the ratio of genome coverage higher than 5%) were retained.
Assembly: hg38
Supplementary files format and content: text file
Supplementary files format and content: WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts". TPM.txt files include the expression matrix normalized to TPM (transcripts per million) value.

source_name: embryo

extract_protocol:
Here we performed single-cell multi-omics libraries referring to the methods of STRT-seq and scCOOL-seq. A mouth pipette was used to pick blastomeres and transferred into the 2.5 μl cell lysis buffer containing 4 U RNase inhibitor (Takara, Cat. 2313B), 0.25% IGEPAL CA-630 (Sigma, Cat. I3021), and in vitro methylation mix (1× GC reaction buffer, 160 μM S-adenosylmethionine and 2 U M.CviPI (NEB, Cat. M0227L). After gently vortexed for about 15 seconds, the lysate was incubated at 37°C for 20 mins and then at 65°C for 25 mins. To isolate DNA and RNA of the single cells, a 3 μl nuclear separation mixture containing 0.2 µl of Dynabeads Myone Carboxylic Acid (Invitrogen, Cat. 65011), 0.2% Tween-20 (Sigma, Cat. P1379), 1% Triton X-100 (Sigma, Cat. T8787), 4 U RNase inhibitor, 50 mM DTT and 2 µl of 5× Superscript II first-strand buffer (Invitrogen, Cat. 18064071), was added to above 2.5 μl cell lysis. The tube was placed on the magnet after mixing by vortexing and brief centrifugation. The nuclei (DNA) wrapped with magnetic beads and the cytoplasm in the supernatant were separated for subsequent use.
For the RNA-part, the supernatant containing cytoplasm was used to construct the single-cell/embryo library following STRT-seq method. Briefly, the separated supernatant was added into the 4.5 µl reverse transcription mix containing 100 U SuperScript II reverse transcriptase (Invitrogen, 18064071), 4 U RNase inhibitor, 3 µM 8bp-barcoded primer, 1 mM dNTP (Takara, 4019), 1 M Betaine (Sigma-Aldrich, B0300), 6 mM MgCl2, 10 µM TSO primer. The mixture was incubated at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min and then 70 °C for 10 min. The cDNA was subsequently amplified using KAPA HiFi HotStart ReadyMix PCR Kit (Roche, KK2631) and purified twice using 0.8× AMPure XP beads (Beckman, A63882). Biotin PCR was performed subsequently and the products were enriched using Dynabeads Myone Streptavidin C1 (Invitrogen, 65001). The cDNA library was finally prepared in accordance with the guidelines of KAPA Hyper Prep Kits for PCR Library Amplification/Illumina series (KAPA, KK8504).For the DNA-part, the magnetic beads containing cell nuclei were added with digestion buffer containing 2.5 µl M-digestion buffer (Zymo Research, D5021), 10 µg protease K (Qiagen, 19155), 2 µl H2O and were incubated for another 60 min at 50 °C to release the genomic DNA. Then the genomic DNA was treated with EZ-96 DNA Methylation-Direct MagPrep kit (Zymo Research, D5044) to perform the bisulfite conversion and purification. The purified DNA was amplified by Klenow exo- (TIANGEN, NG202-02) and scBS-seq-P5-N6-oligo1 (CTACACGACGCTCTTCCGATCTNNNNNN) in four rounds. After purified by 0.8× AMPure XP beads, the products were used to construct the second strand synthesization using Klenow exo- and scBS-seq-P7-N6-oligo2 (AGACGTGTGCTCTTCCGATCTNNNNN). Then, the DNA library was constructed with KAPA HiFi HotStart ReadyMix PCR Kit and index primers. Lastly, the samples were purified twice with 0.8× AMPure XP beads. For the preparation of the single-cell/embryo RNA-seq library, the whole cell or embryo was picked to perform library preparation using STRT-seq method as described above. All high-quality libraries were sequenced with 150 bp pair-end reads on Illumina NovaSeq 6000 platform (Haplox).

value: embryo

value: female

tag: condition

value: Human arrested zygote (3PN) from AURKA inhibited group

value: AURKA inhibition


title: DNA_AURKA_zygote_emb2

description: scCOOL-seq


title: DNA_3PN_zygote_emb8

description: scCOOL-seq

value: Human arrested zygote (3PN) from control group

value: control


title: DNA_3PN_zygote_emb7

description: scCOOL-seq


title: Du145-DtxR, siRNA-Control, Replica #2

description:
ctrl-II
counts2.xlsx

value: WT


title: Du145-DtxR, siRNA-Control, Replica #1

description:
ctrl-I
counts2.xlsx


title: DNA_AURKA_zygote_emb4

description: scCOOL-seq


title: Du145-CbzR, Replica #2

description:
Sample-29
counts.xlsx

source_name: Cabazitaxel Resistant Du145 cell line

value: Cabazitaxel Resistant Du145 cell line

value: Cabazitaxel resistance has been established


title: Du145-CbzR, Replica #1

description:
Sample-18
counts.xlsx


title: Du145-DtxR, Replica #2

description:
Sample-21
counts.xlsx

value: Docetaxel Resistant Du145 cell line

value: Docetaxel resistance has been established


title: DNA_AURKA_zygote_emb1

description: scCOOL-seq


title: Du145-DtxR, Replica #1

description:
Sample-13
counts.xlsx


title: Du145-P, Replica #2

description:
Sample-25
counts.xlsx

source_name: Du145 prostate cancer cell line

value: Du145 prostate cancer cell line

value: No treatmet


title: DNA_si_YY1_1_emb2

description: scCOOL-seq

value: Human 3PN 8-cell embryos from YY1 knockdown group

value: YY1 knockdown


title: DNA_si_YY1_2_emb2

description: scCOOL-seq


title: DNA_3PN_zygote_emb2

description: scCOOL-seq


title: DNA_3PN_zygote_emb5

description: scCOOL-seq


title: DNA_3PN_zygote_emb4

description: scCOOL-seq


title: DNA_si_YY1_1_emb3

description: scCOOL-seq


title: DNA_3PN_zygote_emb1

description: scCOOL-seq


title: DNA_si_YY1_2_emb1

description: scCOOL-seq


title: DNA_3PN_zygote_emb3

description: scCOOL-seq


title: DNA_3PN_zygote_emb6

description: scCOOL-seq


title: Du145-P, Replica #1

description:
Sample-23
counts.xlsx


title: DaGSTDP-mCherryRNAi-Rep2

city: Philadelphia

first: Alexandra

last: Perlegos

state: PA

address: 231 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

description: Total Brain RNA-seq

data_processing:
Paired-end FASTQs were trimmed using TrimGalore
Trimmed FASTQs were mapped using STAR-2.7.3a
Mapped BAM files were filtered for primary mapped reads in properly matching pairs using samtools
Count tables were produced for RNA-seq using an in-house R script utilizing the GenomicRanges summarizeOverlaps function
Differential expression tables were produced by DESeq2 from RNA-seq count tables
Assembly: dm6

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: DaGS-Atx2RNAi (BL44012), DaGS-mCherryRNAi (BL35785), DaGSTDP(52s)-Atx2RNAi (BL44012), or DaGSTDP(52s)-mCherryRNAi (BL35785)  Drosophila crosses set up in 25 degree incubator. Male progeny collected 1-2 days post eclosion for treatment and RNA extraction.

extract_protocol:
Total RNA was extracted from brains using trizol/chloroform and Zymo RNA clean and concentrator kit-5 (R1015). The RNA-seq libraries from brains were prepared using the Tru-seq stranded mRNA library prep. Library preparation and sequencing was done by Admera Health, and sequenced using illumina HiSeq with 40M paired end reads (2x150bp). Three biological replicates were done for each experimental timepoint, condition, and genotype.
The RNA-seq libraries from brains were prepared using the Tru-seq stranded mRNA library prep. Both m6A-IP and RNa-seq were sequenced with 40M paired end reads (2x150bp).

treatment_protocol: male progeny were collected and anesthetized. Brain Tissue was collected in Control or TDP-43 expressing flies after 6 d on RU486

value: Brain

tag: disease condition

value: DaGSTDP(52s)-mCherryRNAi (BL35785)


title: DaGSTDP-Atx2RNAi-Rep3

description: Total Brain RNA-seq

value: DaGSTDP(52s)-Atx2RNAi (BL44012)


title: DaGSTDP-Atx2RNAi-Rep2

description: Total Brain RNA-seq


title: DaGSTDP-mCherryRNAi-Rep3

description: Total Brain RNA-seq


title: D2, KO Rep2

value: 2 day

value: differentiation media


title: D2, KO, Rep1


title: D2, KO, Rep3


title: DNA_si_NC_emb3

description: scCOOL-seq

value: embryo

value: female

value: Human 3PN 8-cell embryos from negtive control group


title: DNA_si_YY1_1_emb1

description: scCOOL-seq


title: DaGSTDP-mCherryRNAi-Rep1

description: Total Brain RNA-seq


title: EHTs, day6_Pace (Sample 6)

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

description: RNAseq raw counts.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Raw read counts were counted by using FeatureCounts
Assembly: hg38
Supplementary files format and content: RNAseq raw counts.txt

source_name: Engineered heart tissue (EHT)

growth_protocol: iPSCs were maintained in E8 medium and routinely checked for mycoplasma contamination. Differentiation of iPSC to cardiomyocytes was carried out using the Wnt modulation protocol.

extract_protocol:
Using Qiagen RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tachypacing

value: EHTs were cultured till day 60-70 (D0 is the start of differentiation)

tag: cell type

value: iPSC derived cardiomyocytes

value: EHTs paced at 3 Hz for 6 days


title: DNA_8cell_em6_c5

description: scCOOL-seq

value: Human arrested 8-cell embryos


title: DNA_si_NC_emb1

description: scCOOL-seq

value: WT


title: EHTs, day6_Recovery (Sample 8)

description: RNAseq raw counts.txt

value: EHTs paced at 3 Hz for days and recovered for 3 days


title: DaGS-mCherryRNAi-Rep2

description: Total Brain RNA-seq

value: Control

value: DaGS-mCherryRNAi (BL35785)


title: DNA_8cell_em6_c4

description: scCOOL-seq


title: DaGS-Atx2RNAi-Rep3

description: Total Brain RNA-seq

value: DaGS-Atx2RNAi (BL44012)


title: DNA_8cell_em5_c1

description: scCOOL-seq


title: DNA_8cell_em6_c3

description: scCOOL-seq


title: EHTs, day3_Pace (Sample 4)

description: RNAseq raw counts.txt

value: EHTs paced at 3 Hz for 3 days


title: DaGSTDP-Atx2RNAi-Rep1

description: Total Brain RNA-seq

value: Brain


title: DNA_si_NC_emb2

description: scCOOL-seq


title: DNA_8cell_em4_c1

description: scCOOL-seq


title: DNA_8cell_em6_c2

description: scCOOL-seq


title: DaGS-mCherryRNAi-Rep3

description: Total Brain RNA-seq


title: DNA_8cell_em3_c7

description: scCOOL-seq


title: DNA_8cell_em3_c8

description: scCOOL-seq


title: DNA_8cell_em6_c1

description: scCOOL-seq


title: EHTs, day6_Recovery (Sample 7)

description: RNAseq raw counts.txt


title: EHTs, day3_Pace (Sample 3)

description: RNAseq raw counts.txt


title: EHTs, day3_Control (Sample 1)

description: RNAseq raw counts.txt

value: control EHTs


title: DNA_8cell_em3_c5

description: scCOOL-seq


title: DNA_8cell_em5_c2

description: scCOOL-seq


title: DNA_8cell_em3_c1

description: scCOOL-seq


title: DaGS-mCherryRNAi-Rep1

description: Total Brain RNA-seq


title: DNA_8cell_em2_c6

description: scCOOL-seq


title: EHTs, day6_Pace (Sample 5)

description: RNAseq raw counts.txt


title: DNA_8cell_em4_c3

description: scCOOL-seq


title: Control Biological replicate 1 [Ctrl_1]

city: Grand Forks

first: Alexei

last: Tulin

state: North Dakota

address: 501 N Columbia Rd Stop 9061

department: Epigenetics Department

institute: University of North Dakota

description:
Control.bedgraph
PARG-YFP.bigwig

data_processing:
Raw reads were trimmed with fastp and aligned to dm6 genome with bowtie2.
Unmapped and low-quality reads were discarded (<=20 mapQuality) using BamTools , and duplicate reads were identified and removed from mapped reads using Picard MarkDuplicates.
Peaks were called using MASC2.
Assembly: dm6
Supplementary files format and content: bedgraph were generated for control and PARG-YFP, bigwig were generated using Deeptools bigWigCompare by computing the substraction of the signals (PARG-YFP signal - Control signal) using a 50bp bin size.

source_name: 75 larvae at L3 larva puffstage 7-9

growth_protocol: Larvae were grow at 20C.

extract_protocol:
Samples were crushed in lysis buffer and then fixed with 1.8% formaldehyde for 15 minutes. After quenching chromatin was sonicated with Bioruptor sonicator (UCD-200).
Library was prepared using NEBnext multiplex oligos for Illumina kit (Index primer set 4).
Sequencing was performed on the NovaSeq 6000 system (Illumina, USA).

value: 75 larvae at L3 larva puffstage 7-9

tag: fraction

value: Whole organism

tag: chip antibody

value: TP401 (OriGene)


title: DNA_8cell_em4_c2

description: scCOOL-seq

value: embryo

value: female


title: DaGS-Atx2RNAi-Rep2

description: Total Brain RNA-seq


title: DNA_8cell_em3_c10

description: scCOOL-seq


title: DNA_8cell_em3_c6

description: scCOOL-seq


title: Spironolactone5_snATACseq

first: Katalin

last: Susztak

address: 3400 Civic Center Blvd, SCTR

description: processed data files include peak count matrix, metadata and umap files

data_processing:
Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
“cellranger count” aligned the Read2 to the rat reference genome (rn6).
Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (rn6)
The output files for 22 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell duplets). Cells were also discarded if their mitochondrial gene percentages were over 15%.
Assembly: rn6
Supplementary files format and content: EXPORT_snRNAseq_counts.rds: combined count matrix of all 22 samples; EXPORT_snRNAseq_metadata.txt: combined metadata; EXPORT_snRNAseq_umap.txt: UMAP embedding values for identified cell types.
Cell Ranger ATAC v. 1.1.0 (http://10xgenomics.com) was used to process Chromium single cell ATAC-seq output.
The output files for 9 samples were aggregated into one matrix using Signac v. 1.3.0.
The poor quality cells were removed from the matrix using the following criteria: peak_region_fragments < 3000 & peak_region_fragments > 20000 & pct_reads_in_peaks < 15 & nucleosome_signal > 4 & TSS.enrichment > 2
Assembly: rn6
Supplementary files format and content: EXPORT_snATACAseq_peaks.rds: combined peaks matrix of all 9 samples; EXPORT_snATACseq_metadata.txt: combined metadata; EXPORT_snATACseq_umap.txt: UMAP embedding values for identified cell types.

organism: Rattus norvegicus

source_name: whole kidney tissue

extract_protocol:
10X Genomics Chromium Prep (10X Genomics, PN-1000120). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
The cDNA libraries were constructed using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer’s original protocol.
Chromium Next GEM Single Cell Multiome ATAC Library + Gene Expression Kit (10X Genomics, PN-1000283). Transposing and barcoding were performed according to the manufacturer's instructions.
The libraries were constructed using the library construction kit (10X Genomics, PN-1000190) according to the manufacturer’s original protocol.

treatment_protocol: The rats were divided into 5 groups: (i) sham operated rats as control, (ii) uninephrectomized rats treated with weekly subcutaneous injections of deoxycorticosterone acetate (DOCA, 50 mg/kg) and daily gavage with vehicle (10% ethanol, 40% solutol, 50% water), (iii) uninephrectomized rats treated with weekly subcutaneous injections of DOCA (50 mg/kg) and finerenone (10mg/kg/d), (iv) uninephrectomized rats treated with weekly subcutaneous injections of DOCA (50 mg/kg) and spironolactone (50mg/kg/d), and (v) uninephrectomized rats treated with weekly subcutaneous injections of DOCA (50 mg/kg) and amiloride (20mg/kg/d)

tag: strain

value: Sprague-Dawley

value: adult kidney

value: 6 Weeks

value: DOCA + Spironolactone


title: DNA_8cell_em3_c9

description: scCOOL-seq

value: Human arrested 8-cell embryos


title: DNA_8cell_em2_c3

description: scCOOL-seq


title: EHTs, day3_Control (Sample 2)

description: RNAseq raw counts.txt

value: EHTs were cultured till day 60-70 (D0 is the start of differentiation)

value: iPSC derived cardiomyocytes


title: DaGS-Atx2RNAi-Rep1

description: Total Brain RNA-seq

value: Control


title: Parg -YFP Biological replicate 2 [PARG_2]

description:
PARG-YFP.bedgraph
PARG-YFP.bigwig


title: DNA_8cell_em3_c2

description: scCOOL-seq


title: Parg -YFP Biological replicate 1 [PARG_1]

description:
PARG-YFP.bedgraph
PARG-YFP.bigwig


title: DNA_8cell_em3_c4

description: scCOOL-seq


title: DNA_8cell_em1_c1

description: scCOOL-seq


title: DOCA5_snATACseq

value: DOCA


title: DNA_8cell_em2_c5

description: scCOOL-seq


title: DNA_4cell_em7_c2

description: scCOOL-seq

value: Human arrested 4-cell embryos


title: Control Biological replicate 2 [Ctrl_2]

description:
Control.bedgraph
PARG-YFP.bigwig


title: DNA_8cell_em2_c4

description: scCOOL-seq


title: DNA_8cell_em3_c3

description: scCOOL-seq


title: DNA_4cell_em7_c1

description: scCOOL-seq


title: DNA_4cell_em6_c4

description: scCOOL-seq


title: Amiloride2_snATACseq

value: DOCA + Amiloride


title: DNA_8cell_em2_c2

description: scCOOL-seq


title: DNA_8cell_em2_c1

description: scCOOL-seq


title: Control4_snATACseq

description: processed data files include count matrix, metadata and umap files


title: Finerenone5_snATACseq

value: DOCA + Finerenone


title: DNA_8cell_em1_c2

description: scCOOL-seq


title: Spironolactone5_snRNAseq


title: DNA_4cell_em6_c1

description: scCOOL-seq


title: DOCA5_snRNAseq


title: DNA_4cell_em6_c3

description: scCOOL-seq


title: Finerenone5_snRNAseq


title: DNA_4cell_em5_c4

description: scCOOL-seq


title: DNA_4cell_em5_c3

description: scCOOL-seq


title: Finerenone3_snRNAseq


title: DNA_4cell_em4_c3

description: scCOOL-seq


title: DNA_4cell_em4_c4

description: scCOOL-seq


title: DNA_4cell_em5_c2

description: scCOOL-seq


title: DNA_4cell_em3_c3

description: scCOOL-seq


title: Control4_snRNAseq


title: DNA_4cell_em4_c2

description: scCOOL-seq


title: Finerenone4_3Weeks_snRNAseq

value: 3 Weeks


title: DNA_4cell_em5_c1

description: scCOOL-seq


title: DNA_4cell_em3_c2

description: scCOOL-seq


title: Spironolactone4_3Weeks_snRNAseq


title: DNA_4cell_em6_c2

description: scCOOL-seq


title: DNA_4cell_em2_c4

description: scCOOL-seq


title: DNA_4cell_em3_c1

description: scCOOL-seq


title: Control5_snRNAseq

description: processed data files include raw count matrix and TPM matrix


title: DNA_4cell_em4_c1

description: scCOOL-seq


title: T47D cells treated with PBS 24 hrs Biol rep 2

city: Maywood

first: Clodia

last: Osipo

state: Illinois

address: 2160 S. First Ave

institute: Loyola University Chicago

data_processing:
cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina)
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) softwar
Assembly: NCBI/UCSC/Ensembl
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes RPKM for each sample

source_name: Breast Cancer

growth_protocol: Cells were maintained in RPMI supplemented with 10% fetal bovine serum in at 30oC, 95% O2, and 5% CO2 incubator

extract_protocol:
RNA was extracted from cells using the RNAeasy mini Kit from Qiagen according to the manufacturer's instructions. 1ug RNA  was sent to Novogene for Library preparation and RNA sequenicng
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: Cells were treated with PBS (P) or 5mg/mL EPS (E) for 24 hours

value: Breast Cancer


title: DNA_4cell_em1_c3

description: scCOOL-seq


title: T47D cells treated with PBS 24 hrs Biol rep3


title: DNA_4cell_em2_c1

description: scCOOL-seq


title: DNA_4cell_em2_c2

description: scCOOL-seq


title: DOCA4_3Weeks_snRNAseq


title: DNA_4cell_em2_c3

description: scCOOL-seq


title: Amiloride1_snRNAseq


title: DNA_4cell_em1_c1

description: scCOOL-seq


title: DNA_4cell_em1_c2

description: scCOOL-seq


title: T47D cells treated with EPS 24 hrs Biol rep3


title: M108

city: hangzhou

first: zhengtao

last: liu

address: 8 shuren street

institute: zhejiang shuren university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: Liver

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lewis

tag: genotype/variation

value: Male

tag: group

value: longterm survivor


title: M107


title: DNA_2cell_em12_c1

description: scCOOL-seq

value: embryo

value: female

value: Human arrested 2-cell embryos


title: DNA_2cell_em13_c1

description: scCOOL-seq


title: T47D cells treated with EPS 24 hrs Biol rep 2


title: DNA_2cell_em11_c2

description: scCOOL-seq


title: DNA_2cell_em11_c1

description: scCOOL-seq


title: T47D cells treated with PBS 24 hrs Biol rep 1


title: day5_3

city: wenzhou

first: Jiansen

last: Miao

state: zhejiang province

address: No. 1111, East Section of Wenzhou Avenue, Longwan District

department: Orthopaedics

institute: The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow monocytes

growth_protocol: Bone marrow monocytes(BMMs) were maintained in α-MEM supplemented with 10% fetal bovine serum(FBS) and antibiotics and M-CSF(50ng/ml) in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: BMMs were treated with or without RANKL(50ng/ml) for 5 days.

value: bone marrow monocytes

value: RANKL

value: DAY 5


title: T47D cells treated with EPS 24 hrs Biol rep 1


title: M106


title: M105


title: M104


title: DNA_2cell_em9_c1

description: scCOOL-seq


title: MCF-7 cells treated with PBS 24 hrs Biol rep3


title: day5_2


title: DNA_2cell_em10_c1

description: scCOOL-seq


title: MCF-7 cells treated with PBS 24 hrs Biol rep 2


title: day5_1


title: M102


title: MCF-7 cells treated with PBS 24 hrs Biol rep 1


title: day0_3

value: DAY 0


title: DNA_2cell_em7_c1

description: scCOOL-seq


title: DNA_2cell_em8_c1

description: scCOOL-seq


title: M101


title: day0_2


title: M26

value: post-transplant


title: MCF-7 cells treated with EPS 24 hrs Biol rep3


title: MCF-7 cells treated with EPS 24 hrs Biol rep 2


title: day0_1


title: M25


title: DNA_2cell_em5_c1

description: scCOOL-seq


title: DNA_2cell_em6_c1

description: scCOOL-seq


title: M24


title: DNA_2cell_em4_c1

description: scCOOL-seq


title: DNA_2cell_em4_c2

description: scCOOL-seq


title: MCF-7 cells treated with EPS 24 hrs Biol rep 1


title: DDA/TDB/3M-05_M+CTH522

city: Copenhagen

first: Julie

last: Zimmermann

address: Artillerivej 5

country: Denmark

institute: Statens Serum Institut

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger sorftware v.6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
Lymph nodes where taken from mice on day 44, and cells where filtered through a 70 μm nylon mesh, and washed. Three mice from each vaccine group where pooled.
Cells where run on the 10x Chromium (10x Genomics) following a library preparation with Chromium Next GEM Single cell 3’ Reagent Kit v.3.1 (10x Genomics). Libraries were sequenced on the NovaSeq 6000 with the NovaSeq 6000 SP reagent kit v1.5 (Illumina).

value: Lymph node


title: M23

value: pre-transplant


title: DDA/TDB+CTH522

description: 10x Genomics


title: DNA_2cell_em3_c1

description: scCOOL-seq


title: M22


title: MDA-MB-468 cells treated with PBS 24 hrs Biol rep 2


title: M103


title: TRIS

description: 10x Genomics


title: DNA_2cell_em2_c1

description: scCOOL-seq


title: Replicate 4 Dataset 2, dDAVP alone

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 106). Transcript per million (TPM) and expected counts were generated by RSEM. All samples are of high percentage of uniquely mapped reads (> 80%) and are included for downstream analysis. Unless otherwise specified, the computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
Assembly: Ensemble release 106
Supplementary files format and content: excel file include counts and TPM values for each sample

source_name: Kidney

extract_protocol:
RNA was extracted using Direct-zol RNA MicroPrep kit
Trizol-extracted RNA was proceeded to cDNA generation using the SMARTer V4 Ultra Low RNA Kit (Takara Bio).cDNA was generated with 8 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform.

value: Kidney

tag: cell line

value: mpkCCD


title: MDA-MB-468 cells treated with PBS 24 hrs Biol rep 1


title: M21


title: MDA-MB-468 cells treated with EPS 24 hrs Biol rep3


title: M20


title: Replicate 2 Dataset 2, dDAVP alone


title: MDA-MB-468 cells treated with EPS 24 hrs Biol rep 2


title: MDA-MB-468 cells treated with PBS 24 hrs Biol rep3


title: DNA_zygote_em15

description: scCOOL-seq

value: Human arrested zygote


title: M19


title: MDA-MB-468 cells treated with EPS 24 hrs Biol rep 1

value: Breast Cancer


title: DNA_zygote_em14

description: scCOOL-seq


title: Replicate 4 Dataset 2, Tolvaptan plus dDAVP


title: M18

value: Lewis


title: MDA-MB-231 cells treated with PBS 24 hrs Biol rep3


title: DNA_zygote_em13

description: scCOOL-seq


title: M17

value: Male


title: Replicate 1 Dataset 2, dDAVP alone


title: DNA_zygote_em12

description: scCOOL-seq


title: DNA_zygote_em11

description: scCOOL-seq


title: MDA-MB-231 cells treated with PBS 24 hrs Biol rep 1


title: MDA-MB-231 cells treated with PBS 24 hrs Biol rep 2


title: M15


title: Replicate 3 Dataset 2, Tolvaptan plus dDAVP


title: Replicate 2 Dataset 2, Tolvaptan plus dDAVP


title: DNA_2cell_em1_c1

description: scCOOL-seq


title: MDA-MB-231 cells treated with EPS 24 hrs Biol rep3


title: Replicate 3 Dataset 2, dDAVP alone


title: M13


title: Replicate 1 Dataset 2, Tolvaptan plus dDAVP


title: MDA-MB-231 cells treated with EPS 24 hrs Biol rep 2


title: GFP- Splenocytes,  Replicate 2

city: San Antonio

first: Venkatesh

last: Kumaresan

state: TX

address: 3.230, BSE Building, One UTSA circle

department: Molecular Microbiology and Immunology

institute: The University of Texas at San Antonio

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using CellRanger v7.1.0
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Splenocytes, GFP-

extract_protocol:
Spleens were removed from euthanized mice, homogenized using 70µm cell-strainer and single cell suspension was then filtered through 40µm cell-strainer. Splenocytes were pelleted by centrifugation at 500 × g for 5 min. To lyse the red blood cells, the cell pellet was suspended in 5 mL of 0.14M ammonium chloride solution for 5 min at room temperature. RBC lysis was stopped by adding 10 mL of R10 media (RPMI media supplemented with 10% FBS) and centrifuged at 500 × g for 5 min and resuspended in R10 media at 1x106/mL concentration. Further, the cells were plated in tissue-culture treated 6-well plate and allowed to adhere for 2 hrs. Non-adherent cells were removed and the adherent cells were infected with GFP-Bb at a multiplicity of infection (MOI) of 1:1.
10x Genomics single cell libraries were generated by the University of Texas at San Antonio (UTSA) Genomics Core. Cell suspensions were loaded into 10x Genomics microfluidics chips and onto the 10x Chromium to capture single cells in Gel Beads-in-emulsion (GEMs) reactions. 10,000 cells/sample were targeted for capture in GEMs preceding library prep following manufacture’s recommendations for the 3’ Gene Expression v3 kit.

value: 6-8 weeks

value: Female

tag: infection

value: Borrelia burgdorferi infection for 45 minutes

value: Splenocytes, GFP-


title: M12


title: DNA_zygote_em9

description: scCOOL-seq

value: embryo

value: female


title: GFP+ Splenocytes,  Replicate 2

description: 10x Genomics

source_name: Splenocytes, GFP+

value: Splenocytes, GFP+


title: M16


title: MDA-MB-231 cells treated with EPS 24 hrs Biol rep 1


title: Amiloride2_snRNAseq

value: Sprague-Dawley

value: adult kidney

value: 6 Weeks

value: DOCA + Amiloride


title: DNA_zygote_em8

description: scCOOL-seq


title: M11

value: post-transplant


title: DNA_zygote_em7

description: scCOOL-seq


title: GFP- Splenocytes,  Replicate 1

description: 10x Genomics


title: GFP+ Splenocytes,  Replicate 1

description: 10x Genomics


title: DNA_zygote_em10

description: scCOOL-seq


title: DNA_zygote_em5

description: scCOOL-seq


title: DNA_zygote_em6

description: scCOOL-seq


title: M9

value: pre-transplant


title: Old MuSCs, 4

city: Los Angeles

first: Jengmin

last: Kang

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

data_processing:
Raw reads were pre-processed with Trim Galore (v0.4.2) to remove adapters and improve the quality of the reads.
Trimmed reads were then aligned to the mouse GRCm39 genome using STAR aligner
Subread package (v1.5.1) with featurecounts module was used to generate raw count reads mapped on exonic regions.
Raw counts analysis was done using RStudio software (v4.0.4).
DESeq2 package was used for differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: Excel files include normalized count values for each Sample

source_name: limb muscle

growth_protocol: MuSCs were isolated from mouse hindlimbs as previously described (Liu et al., 2015).

extract_protocol:
RNA was extracted from 200,000 MuSCs using a miRNeasy kit (Qiagen; # 217084) according to the manufacturer’s protocol.
Illumina Nextra-XT kit (# FC-131-1024) was used to generate libraries from 150 pg of amplified cDNA.

value: limb muscle

value: old (20-month-old)

value: Muscle stem cells

tag: genotype

value: WT

value: Freshly-isolated


title: DNA_zygote_em4

description: scCOOL-seq

value: Human arrested zygote


title: M8

value: Lewis

value: Male


title: M7


title: Old MuSCs, 3

tag: treatment


title: DNA_zygote_em3

description: scCOOL-seq

tag: tissue

value: embryo


title: Spinner flask day 6 control, replicate 2

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description:
PCR-amplified sgRNA sequences from genomic DNA
Combined_controls

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from different sequencing lanes for the same sample were summed and counts for all control samples were summed.
Assembly: For Nalm-6 screens: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core RefSeq gene-targeting sgRNA set of of the library.
Supplementary files format and content: Tab-separated sgRNA read counts per sample
Library strategy: CRISPR screening

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C.

extract_protocol:
Samples were PBS-washed and cell pellets frozen. Genomic DNA was extracted using the QIAamp DNA blood maxi kit (Qiagen).
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices.
CRISPR/Cas9 knockout screen based on sgRNA locus sequencing

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 8 days (see Bertomeu et al., 2017 for details). During induction, cell were split into two spinner flasks to have enough cells at the start of the screen. The cells from each spinner flask were then split into different T-75 flasks, compounds added, and propagated for 8 days. Fresh media and compound was added at each cell passage.

value: pre-B lymphoid cell line

value: untreated for 6 days after Cas9 induction


title: Spinner flask day 8 control, replicate 2

value: untreated for 8 days after Cas9 induction


title: Old MuSCs, 2


title: M6


title: Spinner flask day 4 control, replicate 2

value: untreated for 4 days after Cas9 induction


title: DNA_zygote_em2

description: scCOOL-seq

value: female


title: M5


title: Young MuSCs, 4

value: young (3-month-old)


title: DNA_zygote_em1

description: scCOOL-seq


title: Spinner flask day 6 control, replicate 1


title: Spinner flask day 8 control, replicate 1


title: Spinner flask day 4 control, replicate 1


title: M3


title: LF1, AD12, 3

city: Providence

first: John

last: Sedivy

address: 70 Ship St

institute: Brown University

data_processing:
Reads were preprocessing with fastp (v0.23.4), including quality control, adapter trimming and quality filtering.
Reads were mapped with STAR (2.7.3a).
Reads were assigned to genes with featureCounts (in Subread version 2.0.3).
Counts were normalized and differential expression analysis was performed in DESeq2.
Pathway analysis was performed using GSEA.
Assembly: Hg38
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

source_name: lung

growth_protocol: LF1 cells were grown in Ham’s F-10 nutrient mixture media supplemented with 15% FBS, 2 mM glutamine, and penicillin and streptomycin. Cells were maintained in senescence for 3 months prior to the start of treatment.

extract_protocol:
Trizol/chloroform extraction followed by RNeasy MinElute Cleanup Kit.
Total RNA was sent to Azenta for library construction using the ultra-low input protocol.

treatment_protocol: Cells were treated with vehicle (0.1% DMSO), 10μM 3TC, or 50μM AD12 for 4 weeks, with changes of media containing vehicle or inhibitor every 3 to 4 days.

value: lung

value: ES-derived lung fibroblast cells

value: L1 endonuclease inhibitor AD18


title: Old MuSCs, 1

value: limb muscle

value: old (20-month-old)


title: M2

value: pre-transplant


title: Spinner flask day 2 control, replicate 1

value: untreated for 2 days after Cas9 induction


title: Young MuSCs, 2

value: Muscle stem cells

value: WT

value: Freshly-isolated


title: Young MuSCs, 1


title: ALI, Ca2+ stripping, time course

city: Boston

first: Kalki

last: Kukreja

state: MA

address: 200 Longwood Avenue

institute: Harvard University

description: Time course experiment for Ca2+ depletion of air-liquid interface hBEC cultures

data_processing:
Raw FASTQ were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. We have performed two sequencing runs for all samples using Nextseq and hence have 8 FASTQ files (1 lane x 4 inDrops reads x 2 runs). The read files from an inDrops run have the following content: *_R1_001.fastq.gz : contains the 3' UTR cDNA read *_R2_001.fastq.gz : contains the first half of the cell barcode *_R3_001.fastq.gz : contains the library index for demultiplexing libraries *_R4_001.fastq.gz : contains the second half of the barcode and the UMI.  All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis (github.com/indrops), using the parameter values specified in the ali_time_coure.yaml file provided in the supplementary files. The yaml files also provide library indices that can be used for demultiplexing.
To obtain the final counts matrix used for data analysis, total count and a mitochondrial count filters were applied as described in McCauley,Kukreja et. al. 2022, biorXiv
Assembly: GRCh38/91
Supplementary files format and content: Raw counts (tsv.gz): library identity, barcode, gene names, and raw counts for all cells
Supplementary files format and content: Library barcodes and metadata (metadata.csv.gz): library identity, barcode, and associated metadata for all cells across in the sample

source_name: Airway epithelium

growth_protocol: Primary human bronchial epithelial cells (HBECs) from normal donors were obtained from Lonza (Cat. # CC-2540) and were expanded for two passages with Growth Medium (BEGM supplemented with one SingleQuots kit, Lonza Cat. # CC-3171) in uncoated T75 flasks (Corning Cat. # 430641U). After expansion, cells were seeded on uncoated 12-well TransWell (Corning Cat. # 3460) plates at a density of 1e6 cells per plate and expanded for 7 days in Differentiation Medium (50:50 BEGM (Lonza Cat. # CC-3171)/high-glucose DMEM (ThermoFisher Cat. # 11965175) supplemented with one SingleQuots kit with no T3 and final retinoic acid concentration of 50 nM, Lonza # CC-4175). After 7 days at air-liquid interface, media was removed from the apical surface and cells were differentiated at air-liquid interface for an additional 7-21 days with media replaced every 48-72 hours.

extract_protocol:
HBECs were collected 14 days post-injury by treating with 0.05% Trypsin-EDTA (prepared by dilution of 0.25% Trypsin- EDTA (ThermoFisher Cat. # 25200056) with calcium/magnesium-free PBS), for 20 minutes at 37 °C. Trypsin dissociation was halted with Trypsin Neutralizer Solution (ThermoFisher Cat. # R002100) at 1:1 dilution and cells were filtered through a 40 μm strainer and pelleted by centrifugation at 300x g for 5 minutes. Cells were resuspended in phosphate buffered saline (ThermoFisher Cat. # 10010072) with 0.1% bovine serum albumin (ThermoFisher Cat. # B14) and counted on a Countess Cell Counter (ThermoFisher) to determine cell number and viability. For cell counting, 10 μL of cell suspension was mixed with 10 μL of Trypan Blue Solution (ThermoFisher Cat. # 15250061) and 10 μL of that 1:1 mix was loaded into Countess chip and read with default program. Viable cell numbers were used to determine cell concentration. Optiprep Density Gradient Medium (Sigma Cat. # D1556) was added to achieve a final concentration of 15% Optiprep and 120-150,000 cells/ml. Cells were captured by inDrops as detailed in Zilionis, R. et al. Single-cell barcoding and sequencing using droplet microfluidics. Nat. Protoc. 12, 44–73 (2017).
Library construction as detailed in Zilionis, R. et al. Single-cell barcoding and sequencing using droplet microfluidics. Nat. Protoc. 12, 44–73 (2017).
inDrops v3 scRNA-seq

treatment_protocol: After differentiation at air-liquid interface, cells were washed 3X with warm 1XS PBS and treated with MEM (ThermoFisher Cat. # 10370088, 500 μL apical, 1 mL basal) for 1 hour at 37°C to remove differentiated luminal cells. Following incubation, luminal cells were removed by pipetting gently up and down 3-5X before removing apical media and washing with 500 μL MEM in apical chamber. Cells were harvested at timepoints from 1hr to 14 days post-stripping for single cell analysis.

value: Airway epithelium

tag: donor id


title: M10

value: Lewis

value: Male


title: Spinner flask day 0 control, replicate 2

value: pre-B lymphoid cell line

value: Cas9 induced with Doxycycline for 8 days


title: Young MuSCs, 3

tag: age


title: LF1, AD12, 1


title: Spironolactone4_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK6.2_BulkRNAseq

data_processing:
Fastq files were trimmed for adapters and low-quality reads using Trim-Galore v. 0.4.5.
The trimmed fastq files were aligned to the rat genome (rn6/Rnor_6.0) using STAR (v2.7.3a)
The expression of different genes was measured using RSEM by calculating uniquely mapped reads as transcripts per million (TPM).
Supplementary_files_format_and_content: EXPORT_BulkRNAseq_Raw_Count.txt: Raw count matrix of all 16 samples; EXPORT_BulkRNAseq_TPM_Count.txt: TPM count matrix of all 16 samples; EXPORT_BulkRNAseq_metadata.txt: metadata of 16 samples.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit (catalog #74106) according to manufacturer's protocol.
The cDNA libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina according to manufacturer’s original protocol.

value: Sprague-Dawley

value: adult kidney

value: 6 Weeks

value: DOCA + Spironolactone


title: Spironolactone3_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK6.1_BulkRNAseq


title: LF1, 3TC, 3

value: lung

value: ES-derived lung fibroblast cells

value: L1 reverse transcriptase inhibitor 3TC


title: KO rep 4

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.6.0/RTA v3.4.4) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for adaptor sequence and trimming for low-quality regions using TrimGalore, then mapped to mm10 whole genome using STAR
FeatureCounts were used to generate the raw counts and FPKM and TPM values were generated with StringTie
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including FPKM and TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Ovary

extract_protocol:
Ovaries were snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent with the RNeasy Mini Kit (Qiagen). Illumina TruSeq Stranded mRNA Library Prep Kit with poly-A tail selection was used for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were fed a HFD (60% fat) or a matched control diet (CD) for 13 weeks. Starting from 10 weeks of HFD, the mice were injected intraperitoneal (i.p.) with estrogenic ligands every other day for a total of 9 injections with 5 mg/kg BW of 2,3-bis(4-Hydroxyphenyl)-propionitrile (DPN, Tocris, N = 9) or vehicle.

value: KO

value: ovary

value: Untreated


title: KO rep 3


title: Untreated for 8 days, replicate 2

value: untreated for 8 days after Cas9 induction


title: M4

value: pre-transplant


title: Spinner flask day 2 control, replicate 2

value: untreated for 2 days after Cas9 induction


title: Spironolactone2_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK4.2_BulkRNAseq


title: Spironolactone1_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK4.1_BulkRNAseq


title: KO rep 2


title: Untreated for 8 days, replicate 1


title: KO rep 1


title: LF1, 3TC, 1


title: LF1, AD12, 2

value: L1 endonuclease inhibitor AD18


title: Treated with 0.1% ethanol for 8 days, replicate 2

value: 0.1percent ethanol control for 8 days after Cas9 induction


title: WT rep 5

value: WT


title: LF1, SEN, 3

value: vehicle


title: LF1, SEN, 2


title: LF1, SEN, 1


title: WT rep 4


title: Treated with 0.1% ethanol for 8 days, replicate 1

value: pre-B lymphoid cell line


title: Finerenone2_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK3.1_BulkRNAseq

value: Sprague-Dawley

value: adult kidney

value: DOCA+Finerenone


title: Finerenone4_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK3.2_BulkRNAseq

value: 6 Weeks


title: Treated with 0.1% DMSO for 8 days, replicate 2

value: 0.1percent DMSO control for 8 days after Cas9 induction


title: Finerenone3_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK2.2_BulkRNAseq


title: WT rep 3


title: Treated with 0.35uM samuraciclib for 8 days

description:
PCR-amplified sgRNA sequences from genomic DNA
ICEC0942_0_35uM

value: Samuraciclib 0.35uM for 8 days after Cas9 induction


title: Treated with 0.1% DMSO for 8 days, replicate 1


title: WT rep 2


title: Spinner flask day 0 control, replicate 1

value: Cas9 induced with Doxycycline for 8 days


title: Cut&Tag KO BACH1

city: Shanghai

first: Jieyu

last: Guo

state: Shanghai

address: 138 Yixueyuan Rd,

institute: fudan university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
Bigwig files
Assembly: hg19
Supplementary files format and content: BW

source_name: human embryonic stem cells derived vascular smooth muscle cells

growth_protocol: hESCs were plated on dishes coated with Matrigel at a density of 10,000 cells per square centimeter. Then the hESCs were treated with CHIR99021 and h-BMP4 in N2B27 medium from day 0 to day 3. Next, cells were treated with h-PDGF-BB and ActivinA in N2B27 medium for VSMCs generation from day 4 to day 6.

extract_protocol:
80,000 cells were harvested and immobilized them in 10 μL ConA beads for 10 min at room temperature
Sequencing libraries were prepared by using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina
cut&tag seq

treatment_protocol: BACH1-KO hESCs were generated with CRISPR-Cas9 genome editing technology

tag: antiboday


title: Cut&Tag WT BACH1


title: WT rep 1

value: ovary


title: t-hESC VXN 10uM #2

city: Ottawa

first: Yannick

middle: D.

last: Benoit

address: 451 Smyth road

institute: University of Ottawa

description:
benoit_human_counts220314.txt
t_hESC_VXN_vs_t_hESC_DMSO220314.txt

data_processing:
The analysis performed is based on the recommended process (Jin and Hammell 2018) using the TEtranscripts tools (Jin et al. 2015). Reads are trimmed for quality and adapters using fastp 0.20.1
The trimmed FASTQ files were analyzed using FASTQC 0.11.9 (Andrews and others 2017) to determine quality parameters.
The fastp trimmed reads were mapped to GENCODE GRCh38 human v37 STAR indexes using version 2.6.1a (Dobin et al. 2013) generating BAM files of per sample aligned read with parameters as recommended by the documented protocol (Jin and Hammell 2018).
Tetranscripts 2.2.1 was then run to estimate gene/TE abundance.
Fold change estimation between conditions was performed using DESeq2 1.34.0 (Love, Huber, and Anders 2014) with fold change shrinkage using apeglm (Zhu, Ibrahim, and Love 2019) package to moderate fold change estimates when their uncertainty is high.
Assembly: Human GENCODE v37, hg38
Supplementary files format and content: fastq.gz files contain raw fastq reads corresponding to each sample are come from GSE154057 amd are reprocesed as described above
Supplementary files format and content: log2FoldChange, counts

source_name: cell line

extract_protocol:
RNA was extracted using the total RNA purification kit by Norgen Biotech Corp, following the manufacturer's guidelines. Quantification of total RNA samples was performed with a Qubit HS RNA assay (ThermoFisher Scientific), and fragment size was evaluated with a Fragment Analyzer HS NGS assay (AATI). RNA quality numbers (RQNs) of 8.0 (or higher) were considered satisfactory for library construction.
Library construction was performed with a Truseq RNA v2 (Illumina). Libraries were prepared with unique barcodes compatible with the Illumina NextSeq 500 platform. Quantification of the libraries was performed with a Qubit HS DNA assay, and library fragment size was evaluated with a Fragment Analyzer HS NGS assay. Libraries were normalized to the same concentration, and then samples were pooled in equal amounts.

value: cell line

value: t-hESC

value: Transformed pluripotent stem cells

value: 48 hours DMSO


title: LF1, 3TC, 2

value: lung

value: ES-derived lung fibroblast cells

value: L1 reverse transcriptase inhibitor 3TC


title: DOCA4_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK8.1_BulkRNAseq

value: DOCA


title: Finerenone1_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK2.1_BulkRNAseq


title: DOCA3_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK8.2_BulkRNAseq


title: DOCA2_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK7.2_BulkRNAseq


title: HT29 VXN 10uM #2

description:
benoit_human_counts220314.txt
HT29_VXN_vs_HT29_DMSO220314.txt

value: Colorectal cancer cell line


title: t-hESC VXN 10uM #1


title: Peripheral LN CD4

type: RNA

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

hyb_protocol: Followed NanoString nCounter XT gene expression assay protocol. Briefly, hybridization buffer was mixed with the nCounter  Mouse Cancer Immunology reporter codeset to prepare a master mix. Master mix, sample and Rnase-fee water was combined with nCounter Mouse Cancer Immunology Panel Capture codeset. Samples were then incubated for 18 h at 65 deg C.

scan_protocol: Raw counts of mRNA hybridized to oligos were counted using the NanoString nCounter instrument at CCR Genomics Core (NCI, NIH).

data_processing: Expression data was analyzed in the nSolver Analysis Software 4.0.70 platform, using the nCounter Advanced Analysis (version 2.0.134) tool from nanoString technologies. With PBS as the reference, custom analyses were performed by omitting low count data. Stable housekeeping probes automatically selected using the geNorm algorithm (Vandesompele, 2002) was used to normalize the raw expression data. Differential expression analysis was performed with a P-value threshold of 0.05 and P-value adjustment with Benjamini-Yekutieli method. A fold change of 2 was considered significant for further analyses.

label: biotin

source_name: Peripheral LN

label_protocol: Capture probe-3'biotin, Reporter probe-5' barcode signal

growth_protocol: WT or Rag2-/- IRBP-/- R161H mice on the B10.RIII background were bred in-house and maintained under specific pathogen free (SPF) conditions and fed standard facility chow ad libitum. The animal study protocols (NEI-581 and NEI-688) were approved by the Institutional Animal Care and Use Committee.

extract_protocol: Cells were spun down and RNA was isolated using the RNeasy kit (Qiagen).

treatment_protocol: Mice were immunized with 10 ug IRBP161-180 peptide emulsified in complete Freud’s adjuvant (CFA).WT B10.RIII mice were given a mixture of broad-spectrum antibiotics (ampicillin (1 g/L), metronidazole (1 g/L), neomycin (1 g/L), vancomycin (0.5 g/L) 1, and gentamicin (0.4 g/L)) in Medidrop Sucralose gel (clearH2O) (to minimize settling of the antibiotic suspension) for 1 week (short-term) or at least 4 weeks (long-term) prior to immunization for EAU.

value: Peripheral Lymph Node


title: Peripheral LN CD8


title: DOCA1_BulkRNAseq

institute: University of Pennsylvania

description:
processed data files include raw count matrix and TPM matrix
RK7.1_BulkRNAseq

value: Sprague-Dawley

value: adult kidney


title: PRMT5i_1

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

description: drug inhibition

data_processing:
FPKM data
Assembly: hg38

source_name: pancreatic

growth_protocol: BxPC-3 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: pancreatic

value: BxPC-3 cells

value: pancreatic cancer cells

value: the treat group of inhibition of PRMT5 by PRMT5 inhibitor (GSK3326595)


title: PRMT5i_2

description: drug inhibition


title: HT29 VXN 10uM #1


title: Control3_BulkRNAseq

city: Philadelphia

description:
processed data files include raw count matrix and TPM matrix
RK12.3_BulkRNAseq

value: 6 Weeks

value: Control


title: DMSO_3

description: drug inhibition

value: the control group of inhibition of PRMT5 by PRMT5 inhibitor (GSK3326595)


title: HT29 DMSO #2

value: cell line


title: Control2_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK12.2_BulkRNAseq


title: t-hESC BIX 1uM #2

description:
benoit_human_counts220314.txt
t_hESC_BIX_vs_t_hESC_DMSO220314.txt

value: t-hESC

value: Transformed pluripotent stem cells

value: 48 hours DMSO


title: DMSO_1

description: drug inhibition


title: DMSO_2

description: drug inhibition


title: Mesenteric LN CD4

source_name: Mesenteric LN

value: Mesenteric Lymph Node


title: Control1_BulkRNAseq

description:
processed data files include raw count matrix and TPM matrix
RK11.3_BulkRNAseq

source_name: whole kidney tissue


title: Tumor infiltrating immune cells

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: 10X 5' chemistry

data_processing:
Sequnce data were processed with CellRanger (v4.0.0) to generate count matrices.
Assembly: hg38
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: pancreatic cancer tissue

extract_protocol:
Freshly collected surgical samples from pancreatic cancer patients were dissected and digested with Tumor Dissociation Kit and gentle MACS Octo Dissociator from Miltenyi Biotec. CD45positive cells were collected with MACS sorting kit
Library was constructed according to the manufacturer's instructions (10X 5' v1.1)

value: pancreatic cancer tissue


title: PRMT5i_3

description: drug inhibition


title: Control4_BulkRNAseq

first: Katalin

last: Susztak

address: 3400 Civic Center Blvd, SCTR

description:
processed data files include raw count matrix and TPM matrix
RK10.3_BulkRNAseq


title: t-hESC BIX 1uM #1


title: Mesenteric LN CD8


title: Small Intestine Lamina Propria CD8

source_name: Small Intestine Lamina Propria

value: Small Intestine


title: Small Intestine Lamina Propria CD4


title: SS2021309

description: 10X visium

data_processing:
Raw sequencing data were processed with 10X Genomics Space Ranger (v1.3.1) pipleline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings
Gene expression level of coding genes were quantifiied using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresssion count data in Matrix Market Exchange Format
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count data in HDF5 format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
FFPE block were sectioned for 10X Genomics Visium Spatial Gene Expresssion Slides according to manufacturer's instruction
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit


title: Spironolactone_snATACseq

description: processed data files include peak count matrix, metadata and umap files

data_processing:
Cell Ranger ATAC v. 1.1.0 (http://10xgenomics.com) was used to process Chromium single cell ATAC-seq output.
The output files for 4 samples were aggregated into one matrix using Signac v. 1.3.0.
The poor quality cells were removed from the matrix using the following criteria: peak_region_fragments < 1000 & peak_region_fragments > 20000 & pct_reads_in_peaks < 15 & nucleosome_signal > 4 & TSS.enrichment > 2
Genome_build: rn6
Supplementary_files_format_and_content: EXPORT_snATACAseq_peaks.rds: combined peaks matrix of all 4 samples; EXPORT_snATACseq_metadata.txt: combined metadata; EXPORT_snATACseq_umap.txt: UMAP embedding values for identified cell types.

extract_protocol:
Chromium Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000110). Transposing and barcoding were performed according to the manufacturer's instructions.
The libraries were constructed using the Chromium Single Cell ATAC Library & Gel Bead Kit and Chromium i7 Multiplex Kit N (10X Genomics, PN-1000084) according to the manufacturer’s original protocol.

treatment_protocol: The rats were divided into 4 groups: (i) sham operated rats as control, (ii) uninephrectomized rats treated with weekly subcutaneous injections of deoxycorticosterone acetate (DOCA, 50 mg/kg) and daily gavage with vehicle (10% ethanol, 40% solutol, 50% water), (iii) uninephrectomized rats treated with weekly subcutaneous injections of DOCA (50 mg/kg) and finerenone (10mg/kg/d), and (iv) uninephrectomized rats treated with weekly subcutaneous injections of DOCA (50 mg/kg) and spironolactone (50mg/kg/d)

value: DOCA + Spironolactone


title: Finerenone_snATACseq

value: Sprague-Dawley

value: DOCA+Finerenone


title: t-hESC DMSO #2

description:
benoit_human_counts220314.txt
t_hESC_BIX_vs_t_hESC_DMSO220314.txt
t_hESC_VXN_vs_t_hESC_DMSO220314.txt


title: Intraepithelial Lymphocytes CD4CD8

source_name: Intraepithelial Lymphocytes

value: Intraepithelial


title: t-hESC DMSO #1


title: Intraepithelial Lymphocytes CD8


title: HT29 DMSO #1

value: Colorectal cancer cell line


title: DOCA_snATACseq

value: adult kidney

value: DOCA


title: SS2002154

description: 10X visium


title: RNA-seq of C. elegans: adult day 5 miR-239b(ap432) hermaphrodites (rep3)

city: Cambridge

first: Laura

last: Chipman

address: 1 Portland St

institute: Pfizer

data_processing: Reads were aligned to the C. elegans genome WBcel282 assembly using STAR and the average percent of uniquely mapped reads was 94% (Dobin et al. 2013). Aligned reads were sorted using Samtools (Danecek et al. 2021) and reads were then quantified using featureCounts using WBcel282 gene annotations (Liao, Smyth, and Shi 2014). Differential expression was calculated using DESeq2 (Love, Huber, and Anders 2014). Genes with +/- 1 Log2FC, a basemean of at least 10, and adjusted p-value of < 0.05 were considered significantly mis-regulated.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Adult C. elegans were separated from eggs and progeny daily by washing plates with M9 into conical tubes and allowing the adults to settle by gravity for a few minutes on a bench top. The supernatant containing larvae and eggs was then removed, and this process was repeated 3-15 times until eggs and larvae were no longer visible.

extract_protocol: RNA was isolated from wildtype (N2), miR-238(n4112), miR-239a(ap439), and miR-239b(ap432) day 5 adults. Adult C. elegans were separated from eggs and progeny on a daily basis by washing plates with M9 into conical tubes and allowing the adults to settle by gravity for a few minutes on a bench top. The supernatant containing larvae and eggs was then removed, and this process was repeated 3-10 times until eggs and larvae were no longer visible.Three independent poly(A) selected RNA-seq libraries were prepared from each strain for sequencing with the Illumina TruSeq mRNA Library Prep Kit. cDNA libraries were sequenced on an Illumina NovaSeq 6000.

value: whole organism

tag: developmental stage

value: adult day 5

value: polyA RNA


title: shCTRL VNN r3

description:
592182
te_benoit_human_counts230210.txt
te_shCTRL_V_vs_shCTRL_D230210.txt

data_processing:
The analysis performed is based on the recommended process (Jin and Hammell 2018) using the TEtranscripts tools (Jin et al. 2015). Reads are trimmed for quality and adapters using fastp 0.20.1
The trimmed FASTQ files were analyzed using FASTQC 0.11.9 (Andrews and others 2017) to determine quality parameters.
The fastp trimmed reads were mapped to GENCODE GRCh38 human v37 STAR indexes using version 2.6.1a (Dobin et al. 2013) generating BAM files of per sample aligned read with parameters as recommended by the documented protocol (Jin and Hammell 2018).
Tetranscripts 2.2.1 was then run to estimate gene/TE abundance.
Fold change estimation between conditions was performed using DESeq2 1.34.0 (Love, Huber, and Anders 2014) with fold change shrinkage using apeglm (Zhu, Ibrahim, and Love 2019) package to moderate fold change estimates when their uncertainty is high.
Assembly: Human GENCODE v37, hg38
Supplementary files format and content: counts

tag: disease

value: Colorectal cancer

value: WT

value: shCTRL VXN


title: Control_snATACseq

value: 6 Weeks

value: Control


title: SS1960050

description: 10X visium

value: pancreatic cancer tissue


title: Intraepithelial Lymphocytes CD4


title: shCTRL VXN r2

description:
592181
te_benoit_human_counts230210.txt
te_shCTRL_V_vs_shCTRL_D230210.txt


title: SS1945070

description: 10X visium


title: shCTRL VXN r1

description:
592180
te_benoit_human_counts230210.txt
te_shCTRL_V_vs_shCTRL_D230210.txt


title: shSLC6A3 DMSO r3

description:
590326
te_benoit_human_counts230210.txt
te_shDAT_D_vs_shCTRL_D230210.txt

value: shSLC6A3 DMSO


title: Spironolactone3_snRNAseq

description: processed data files include count matrix, metadata and umap files

data_processing:
Cell Ranger v. 3.0.2 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
“cellranger count” aligned the Read2 to the rat reference genome (rn6).
Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (rn6)
The output files for 11 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >2,500 unique expressed genes (as they are potentially cell duplets). Cells were also discarded if their mitochondrial gene percentages were over 25%.
Genome_build: rn6
Supplementary_files_format_and_content: EXPORT_snRNAseq_counts.rds: combined count matrix of all 11 samples; EXPORT_snRNAseq_metadata.txt: combined metadata; EXPORT_snRNAseq_umap.txt: UMAP embedding values for identified cell types.

extract_protocol:
10X Genomics Chromium Prep (10X Genomics, PN-1000120). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
The cDNA libraries were constructed using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer’s original protocol.

value: DOCA + Spironolactone


title: RNA-seq of C. elegans: adult day 5 miR-239b(ap432) hermaphrodites (rep4)


title: SS1905133

description: 10X visium


title: SS2005094

description: 10X visium


title: SS1923404

description: 10X visium


title: Spironolactone1_snRNAseq

value: Sprague-Dawley


title: Spironolactone2_snRNAseq


title: RNA-seq of C. elegans: adult day 5 miR-239a(ap439) hermaphrodites (rep6)


title: Cut&Tag KO H3R17me2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
Bigwig files
hg19
BW

extract_protocol:
hESCs were plated on dishes coated with Matrigel at a density of 10,000 cells per square centimeter. Then the hESCs were treated with CHIR99021 and h-BMP4 in N2B27 medium from day 0 to day 3. Next, cells were treated with h-PDGF-BB and ActivinA in N2B27 medium for VSMCs generation from day 4 to day 6.
BACH1-KO hESCs were generated with CRISPR-Cas9 genome editing technology
80,000 cells were harvested and immobilized them in 10 μL ConA beads for 10 min at room temperature
Sequencing libraries were prepared by using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina

tag: antibody


title: Finerenone2_snRNAseq

value: DOCA+Finerenone


title: RNA-seq of C. elegans: adult day 5 miR-239a(ap439) hermaphrodites (rep4)


title: Finerenone1_snRNAseq


title: RNA-seq of C. elegans: adult day 5 miR-239b(ap432) hermaphrodites (rep2)


title: RNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep6)


title: shCTRL DMSO r3

description:
590323
te_benoit_human_counts230210.txt
te_shCTRL_V_vs_shCTRL_D230210.txt
te_shDAT_D_vs_shCTRL_D230210.txt

value: shCTRL DMSO


title: Cut&Tag WT H3R17me2


title: shSLC6A3 DMSO r1

description:
590324
te_benoit_human_counts230210.txt
te_shDAT_D_vs_shCTRL_D230210.txt


title: Cut&Tag KO2 CARM1


title: shCTRL DMSO r2

description:
590322
te_benoit_human_counts230210.txt
te_shCTRL_V_vs_shCTRL_D230210.txt
te_shDAT_D_vs_shCTRL_D230210.txt


title: shSLC6A3 DMSO r2

description:
590325
te_benoit_human_counts230210.txt
te_shDAT_D_vs_shCTRL_D230210.txt


title: Cut&Tag KO1 CARM1


title: DOCA2_snRNAseq


title: RNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep4)


title: shCTRL DMSO r1

description:
290321
te_benoit_human_counts230210.txt
te_shCTRL_V_vs_shCTRL_D230210.txt
te_shDAT_D_vs_shCTRL_D230210.txt


title: RNA-seq of C. elegans: adult day 5 miR-239a(ap439) hermaphrodites (rep5)


title: DOCA1_snRNAseq


title: RNA-seq of C. elegans: adult day 5 miR-238(n4112) hermaphrodites (rep3)


title: ATAC_T24_rescue_rep1

city: Houston

first: H. Courtney

last: Hodges

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: ATAC-seq in control SMARCB1 rescue T24 cells.

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis. 200 bp pseudofragments were created at the positions corresponding to the transposition sites, and peak calls were made using MACS 2.1.2 without modeling of fragment size. Reads within peaks were counted using bedtools.
The table of all counts was processed using DESeq2, using default parameters.
Bigwig files were created based on 200 bp pseudofragments, with intermediate files created using bedtools 2.28.0. All bigWig files are unscaled and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage.

source_name: T24 cells

growth_protocol: Cells were cultured in 10% FBS McCoys 5a medium using standard approaches.

extract_protocol:
Nuclei were permeabilized and transposed according to the Omni-ATAC protocol.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: T24 cells were engineered for SMARCB1 knockout ("KO") by transfection of CRISPR reagents and gRNAs targeting the SMARCB1 locus and selecting clones. Non-targeting ("control") cells were created by transfection with CRISPR reagents and non-targeting control gRNA. KO cells re-expressing SMARCB1 ("rescue") were created by transducing KO cells with constructs expressing SMARCB1 cDNA.

value: SMARCB1 rescue


title: hESCs-VSMCs KO2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hista2
Cufflinks was employed to obtain Fragments Per Kilobase Million (FPKM) for each gene.
hg38
xlsx files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent
non-ribosomal RNA was isolated from 1 μg total RNA by using a TrueLib Poly (A) mRNA Magnetic Isolation Module, and sequencing libraries were prepared by using the TrueLib mRNA Library Prep Kit for Illumina

value: Bach1 knockout


title: ATAC_T24_rescue_rep2


title: RNA-seq of C. elegans: adult day 5 miR-238(n4112) hermaphrodites (rep2)


title: Control2_snRNAseq

value: adult kidney


title: ATAC_T24_KO_rep2

description: ATAC-seq in control SMARCB1 knockout T24 cells.

value: SMARCB1 KO


title: Control1_snRNAseq


title: RNA-seq of C. elegans: adult day 5 miR-238(n4112) hermaphrodites (rep1)

value: whole organism

value: adult day 5


title: DOCA3_snRNAseq

value: DOCA


title: ATAC_T24_KO_rep1


title: hESCs-VSMCs WT2

value: WT


title: ATAC_T24_control_rep2

description: ATAC-seq in control T24 cells.


title: RNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep2)

value: polyA RNA


title: RNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep3)


title: Cut&Tag WT2 CARM1


title: hESCs-VSMCs WT1


title: Control3_snRNAseq

value: 6 Weeks


title: ATAC_T24_control_rep1

description: ATAC-seq in control T24 cells.

value: Control


title: Cut&Tag WT1 CARM1


title: Hypothalamus, acrolein (Hy9_S2)

status: Public on Nov 16 2023

city: Research Triangle Park

first: Devin

middle: Issac

last: Alewel

state: NC

address: 109 TW Alexander Drive

department: CPHEA/PHITD/CIB

institute: U.S. EPA

data_processing:
Sequenced mRNA reads were mapped to the rat genome (rn7) using ensemble release 105 (Partek Flow suite, R version 4.1.3), resulting in 24,091 identified genes. Genes with fewer than 1 read in 10  were removed, leaving 20,580 genes. An average of 15.5 million reads were mapped per sample with a standard deviation of 5.5 million. PCA was performed to identify any samples that did not cluster within tissue and should be removed prior to analysis. After removal of those tissues, remaining samples had 15.8 million reads per sample with a standard deviation of 5.3 million, with an average read per gene of 766. DEGs were assessed in DESeq2 package in R (v1.34.0) [81] and normalized reads were assessed for air vs. acrolein effects.
Assembly: rat genome (rn7)
Supplementary files format and content: Processed data is provided as normalized transcript counts as a .csv file for each tissue.

source_name: Hypothalamus

extract_protocol:
Uniform portions of frozen tissue were sectioned  and processed with RNeasy non-fibrous, fibrous, or lipid tissue mini kits (Qiagen, Valencia, CA) following manufacturer directions (kit dependent upon tissue type). RNA quantity and purity (260/230 and 260/280 ratios) were spectrophotometrically quantified using a Nanodrop 1000 (ThermoFisher Scientific Inc., Waltham, MA). RNA integrity was assessed by the RNA 6000 LabChip® kit and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using a RIN cutoff of 7. Samples processing for mRNA sequencing was performed on the Apollo324 automated system (Takara Bio Inc., Kusatsu, Japan) for library prep with PrepX mRNA 48 protocol v19, using the PrepXTM RNA-seq for Illumina Library Kit (Takara), SuperScript III reverse transcriptase (ThermoFisher), and AMPure XP Beads (Agilent). PCR amplification with 48 index primers was run for 16 cycles and resulting PCR product quality was analyzed again via Qubit (ThermoFisher) and bioanalyzer.
An RNA-seq library was prepared with Wafergen’s PrepX mRNA 48 protocol and dsDNA products were prepared from cDNA. Each library was sequenced according to Illumina NextSeq 500, with a final concentration of 2.2 pM + 2% PhiX and run for 75 cycles (Illumina Inc., San Diego, CA).

value: Hypothalamus

value: Wistar-Kyoto

value: acrolein


title: Hypothalamus, acrolein (Hy15_S1)


title: Hypothalamus, acrolein (Hy11R1_S4)


title: Hypothalamus, acrolein (Hy14_S16)


title: Hypothalamus, acrolein (Hy10_S3)


title: Hypothalamus, air (Hy8_S12)

value: air


title: Hypothalamus, air (Hy5_S2)


title: Hypothalamus, air (Hy7_S12)


title: Hypothalamus, air (Hy1_S6)


title: Hippocampus, acrolein (Hi15_S6)

source_name: Hippocampus

value: Hippocampus


title: hESCs-VSMCs KO1


title: Hippocampus, acrolein (Hi12_S11)


title: Hypothalamus, air (Hy3_S7)


title: Hippocampus, acrolein (Hi11R_S15)


title: RNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep1)


title: Hippocampus, acrolein (Hi10R2_S11)


title: Hippocampus, acrolein (Hi9_S14)


title: Hippocampus, air (Hi6_S4)


title: Hippocampus, air (Hi5_S18)


title: Hippocampus, air (Hi4R1_S8)


title: Hypothalamus, acrolein (Hy12_S16)


title: Hippocampus, air (Hi8_S5)


title: Hippocampus, air (Hi2B_S9)


title: Muscle, acrolein (M15R1_S10)

source_name: Muscle

value: Muscle


title: Muscle, acrolein (M14_S1)


title: Muscle, acrolein (M10_S16)


title: Muscle, acrolein (M12_S17)


title: Muscle, acrolein (M11_S6)


title: Hypothalamus, air (Hy6_S3)


title: Muscle, air (M7_S12)


title: Muscle, air (M6_S13)


title: Muscle, air (M2R1_S17)


title: Hippocampus, acrolein (Hi14_S8)


title: Muscle, acrolein (M9_S15)


title: Adipose, acrolein (ad15_S11)

source_name: Adipose

value: Adipose


title: Adipose, acrolein (ad14_S10)


title: Muscle, air (M4_S5)


title: Adipose, acrolein (ad12_S3)


title: Adipose, air (ad8_S8)


title: Adipose, air (Ad8_S17)


title: Adipose, air (ad5_S15)


title: Adipose, air (ad2_S15)


title: Hippocampus, air (Hi7_S11)


title: Adipose, air (ad7_S19)


title: Muscle, air (M8R_S14)


title: Adipose, air (ad1_S3)


title: Adrenal, acrolein (a10_S8)

source_name: Adrenal

value: Adrenal


title: Adrenal, acrolein (a9_S20)


title: Adrenal, acrolein (a12_S17)


title: Adrenal, acrolein (a11_S5)


title: Adrenal, air (a8_S14)


title: Adrenal, air (a7_S7)


title: Adrenal, air (a5_S21)


title: Adrenal, air (a6_S12)


title: Adrenal, air (a3_S20)


title: Liver, acrolein (l16_S1)

source_name: Liver

value: Liver


title: Adrenal, air (a2_S18)


title: Muscle, air (M5R_S13)


title: Liver, acrolein (l15_S19)


title: Adipose, acrolein (ad10_S10)


title: Liver, acrolein (l13_S13)


title: Liver, acrolein (l14_S11)


title: Liver, acrolein (l11_S12)


title: Liver, acrolein (l9_S16)


title: Liver, air (l8_S2)


title: Liver, air (l7_S5)


title: Liver, air (l5_S4)


title: Lung, acrolein (Lu15_S13)

source_name: Lung

value: Lung


title: Liver, air (L2_S15)


title: Liver, air (L1_S4)


title: Lung, acrolein (lu9_S9)


title: Lung, acrolein (lu10_S17)


title: Lung, acrolein (Lu14_S7)


title: Lung, acrolein (lu12_S6)


title: Lung, air (lu8_S4)


title: Lung, acrolein (lu13_S6)


title: Lung, air (lu6_S7)


title: Lung, air (lu7_S9)


title: Lung, air (lu2_S1)


title: Lung, air (lu1_S18)


title: Lung, air (lu3_S14)


title: Lung, air (lu5_S13)


title: Lung, air (lu4_S16)


title: Nasal epithelium, acrolein (N15_S10)

source_name: Nasal epithelium

value: Nasal epithelium


title: Nasal epithelium, acrolein (N14_S8)


title: Nasal epithelium, acrolein (N11R1_S3)


title: Nasal epithelium, acrolein (N12_S2)


title: Nasal epithelium, acrolein (N9R1_S9)


title: Nasal epithelium, air (N8_S18)


title: Nasal epithelium, air (N6R_S10)


title: Nasal epithelium, air (N5R_S14)


title: Nasal epithelium, acrolein (N10R3_S7)


title: liver, Experimental sample 2

city: Guangzhou

first: Xinheng

last: Zhang

address: 483 Wushan Road

institute: South China Agricultural University

description:
mRNA Expression Profiling.xlsx
CASE6

data_processing:
fastqc
bwa alignment to genome and gene set
lncRNA assembly by the unaligned reads and lncRNA identificaton
circRNA identification and quantitive analysis
mRNA  quantitive analysis and DE analysis
Assembly: ASM2538873v1
Supplementary files format and content: xlsx file includes FPKM and count values for each Sample

organism: Anser cygnoides

source_name: liver

extract_protocol:
mRNA was purified from total RNA using probes to remove  rRNA.After the RNA sample is qualified, the RRNA (part of the lncRNA has the same PolyA tail structure as the mRNA from the total RNA sample, and the method of removing the rRNA can be retained to the greatest extent by removing the rRNA).
Add Fragmentation Buffer to the rich RNA to interrupt RNA into small fragments. Then use the fragmented RNA as the template, add 6bp random primer (Random Hexamers) to reverse the first chain of the synthetic cDNA, and then add the buffer, DNA POLYMERASE I and RNase H synthesis, DNA Polymerase I and RNase H synthetic cDNA second chain. After the synthetic dual -chain cDNA is purified, the end repair, the addition of A, and the connection sequencing connector, the USER enzyme is used to degrade the second chain containing U and enriches PCR. Specific library. After the construction of the library is completed, first use Qubit 2.0 for preliminary quantitative, dilute the library, and then use the Agilent 2100 to detect the size of the insertion fragment of the library. Guarantee the quality of the library.

tag: breed

value: Lion-head goose

value: liver

value: high-intake fed


title: liver, Experimental sample 3

description:
mRNA Expression Profiling.xlsx
CASE7


title: liver, Control sample 3

description:
mRNA Expression Profiling.xlsx
CONTROL5

value: normally-fed


title: liver, Control sample 2

description:
mRNA Expression Profiling.xlsx
CONTROL3


title: liver, Experimental sample 1

description:
mRNA Expression Profiling.xlsx
CASE2


title: Nasal epithelium, air (N4R1_S5)


title: Nasal epithelium, air (N2_S9)


title: MB109

type: genomic

city: Southampton

first: Matthew

last: Hewitt

state: Hampshire

address: Institute of developmental sciences, 216 Tremona Road

department: Human Development and Health

country: United Kingdom

institute: University of Southampton

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan scanner using standard recommended Illumina scanner setting

data_processing:
The processing of myoblast Infinium Human MethylationEPIC data and all statistical analysis was conducted in R (v3.4.2).
Average Beta or normalized (provide the normalization method) Average Beta

label: Cy3 and Cy5

source_name: Myoblast gDNA isolated and cultured from vastus lateralis muscle tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (gDNA) was extracted from actively proliferating myoblasts using the GenEluteTM Mammalian Genomic DNA miniprep Kit (Merck) following manufacturer’s instructions.

tag: Sex

value: Female


title: MB107


title: MB105


title: MB106


title: MB104


title: MB102


title: H3K9me2, lsd1 delta hmg, rep2

city: Winston-Salem

first: Ke

last: Zhang Reid

address: 1834 Wake Forest Rd

institute: Wake Forest University

description: C3_lsd1deltahmgftp_C1_wtbackground_log2_combined.bw

data_processing:
Reads were first trimmed of adapters using Trimmomatic v0.39 under the default settings using adaptors from TruSeq2-PE. Fa
DNA reads were then mapped to the S. pombe reference genome ASM294v2 55 using bwa mem v0.7.17
Narrow peaks for each strain were identified using MACS2 v2.2.7.1 using the default settings specifically for narrow peak detection
Differential binding was scrutinized first by using BEDTools v2.17.0 closestBed argument and the ASM294v2 annotated feature file
Log2 comparisons of each strain to the input were performed using the readCount scale factoring method in deepTools
Assembly: ASM294v2
Supplementary files format and content: bigwig

organism: Schizosaccharomyces pombe

source_name: whole cell

growth_protocol: Strains were cultured in 100 mL to the exponential growth phase, and protein-DNA crosslinking was performed with Paraformaldehyde with slow shaking for 30 minutes.

extract_protocol:
Whole cell extracts were incubated with 50 units of AcTEV protease (Invitrogen Corp. Catalog#: 12575015, Massachusetts, USA) and 50µL IgG Sepharose (GE Healthcare, Catalog#: 17096901, Illinois, USA) at 4 °C overnight. The next morning, pre-cleared whole cell extracts were collected after centrifugation at 17,530 × g for 10 min, followed by adding the antibody (Anti-myc, Abcam ab9132). Reverse cross-linking and elution were performed at 65o C overnight.
ChIP DNA was purified using DNA purification columns (Thermo Fisher, K0512), and quantified by quantitative-PCR (QuantStudio 3, Applied Biosystems) using SYBR Select Master Mix (Applied Biosystems, 4472908).

treatment_protocol: FTP-tagged ChIP was performed using 50 µL IgG Sepharose (GE Healthcare) for 4-6 hours at 4o C. myc-ChIPs that were performed in FTP (Protein A-, TEV cleavage site, and Flag- double epitope-tag) backgrounds were modified.

value: whole cell

value: lsd1 delta hmg

tag: chip antibody


title: H3K9me2, lsd1 clr4 del, rep2

description: C4_lsd1ftpclr4del_C1_wtbackground_log2_combined.bw

tag: strain

value: lsd1 clr4


title: H3K9me2, lsd1 set1 del, rep2

description: C5_lsd1ftpset1del_C1_wtbackground_log2_combined.bw

value: lsd1 set1 del


title: H3K9me2, wt input, rep2

value: WT


title: H3K9me2, lsd1 clr4 del set1 del, rep2

description: C6_lsd1ftpclr4set1del_C1_wtbackground_log2_combined.bw

value: lsd1 clr4 del set1 del


title: MB95

value: Male


title: H3K9me2, lsd1, rep2

description: C2_lsd1ftp_C1_wtbackground_log2_combined.bw


title: MB94


title: H3K9me2, lsd2 set1 del, rep2

description: A4_lsd2ftpset1del_C1_wtbackground_log2_combined.bw

value: lsd2 set1 del


title: H3K9me2, lsd2 delta c, rep2

description: A2_lsd2deltacftp_C1_wtbackground_log2_combined.bw

value: lsd2 delta c


title: MB161


title: MB112


title: H3K9me2, lsd2, rep2

description: A1_lsd2ftp_C1_wtbackground_log2_combined.bw


title: H3K9me2, lsd2 clr4 del set1 del, rep2

description: A3_lsd2ftpclr4set1del_C1_wtbackground_log2_combined.bw

value: lsd2 clr4 del set 1 del


title: liver, Control sample 1

description:
mRNA Expression Profiling.xlsx
CONTROL1


title: H3K9me2, wt input, rep1


title: H3K9me2, lsd1 clr4 del set1 del, rep1


title: MB86


title: MB90


title: H3K9me2, lsd2 clr4 del, rep2

description: A5_lsd2ftpclr4del_C1_wtbackground_log2_combined.bw

value: lsd2 clr4 del


title: MB84


title: H3K9me2, lsd1 set1 del, rep1


title: MB82


title: MB92


title: MB83


title: H3K9me2, lsd1, rep1


title: H3K9me2, lsd1 delta hmg, rep1


title: MB93


title: MB158


title: H3K9me2, lsd2 clr4 del, rep1


title: MB166


title: H3K9me2, lsd2 set1 del, rep1


title: H3K9me2, lsd1 clr4 del, rep1


title: H3K9me2, lsd2 clr4 del set1 del, rep1


title: MB165


title: 16HBE WT [257236334414_S01_GE1_107_Sep09_2_4]

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: WT non treated

hyb_protocol: Agilent-072363 Whole Human Genome Microarray 8x60 v3 were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: 16HBE WT

label_protocol: manufacturer's instructions

growth_protocol: MEM, 10% FBS and 1% Zell-Shield, 37°C, 5% CO2

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: 16HBE WT and 16HBE ex14 were starved (0% FBS) during 2 hours and next stimulated 24 hours by HGF (20 ng/ml)

tag: agent


title: 16HBE YY + HGF [257236334414_S01_GE1_107_Sep09_2_2]

description: WT treated by HGF

source_name: 16HBE YY + HGF

value: HGF


title: 16HBE WT [257236334414_S01_GE1_107_Sep09_1_1]

description: WT non treated


title: H3K9me2, lsd2 delta c, rep1


title: 16HBE YY + HGF [257236334414_S01_GE1_107_Sep09_1_3]

description: WT treated by HGF


title: 16HBE ex14 + HGF [257236334414_S01_GE1_107_Sep09_1_4]

description: ex14 treated by HGF

source_name: 16HBE ex14 + HGF


title: 16HBE ex14 + HGF [257236334414_S01_GE1_107_Sep09_2_1]

description: ex14 treated by HGF


title: MB164


title: 16HBE YY + HGF [257236334397_S01_GE1_107_Sep09_2_3]

description: WT treated by HGF


title: MB163


title: 16HBE ex14 [257236334414_S01_GE1_107_Sep09_1_2]

description: ex14 non treated

source_name: 16HBE ex14


title: 16HBE ex14 [257236334414_S01_GE1_107_Sep09_2_3]

description: ex14 non treated


title: 16HBE WT [257236334397_S01_GE1_107_Sep09_2_1]

description: WT non treated


title: MB162


title: H3K9me2, lsd2, rep1