title: HEK293T cell, VEGFA, A3C, loop2-34-31-7, PE2, rep3

description:
5309
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: SMA R6-Mo CS83 replicate 3

status: Public on Nov 17 2025

type: SRA

city: Rozzano

first: Simona

last: Lodato

address: via Manzoni 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description:
Library name: SMA_SCRAMBLE_CS83_3
BULK-SAM-156

library_source: transcriptomic

data_processing:
Sequence reads were aligned to GRCh38 and counted using STAR (v 2.7.10a, --chimSegmentMin 2, --alignIntronMax 1000000, --alignSJDBoverhangMin 6, --outSAMmapqUnique 254, --outFilterMismatchNmax 3).
Assembly: GRCh38
Supplementary files format and content: .txt table of raw counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: Spinal Cord Organoids were generated by harvesting iPSCs using Accutase and approximately 9,000 iPSCs were plated in each well of an ultra-low attachment 96-well plate in pluripotent stem cell media containing low recombinant human FGF-basic (4 ng/ml) and Y-27632 (50 μM ROCK inhibitor). On day 2, half of the medium was changed to fresh medium containing a final concentration of 4 ng/ml bFGF, 50 μM Y-27632, 3 μM CHIR 99021 (GSK3 inhibitor), 2 μM SB-431542 (Activin/BMP/TGF-β pathway inhibitor), and 0.2 μM LDN-193189 (inhibitor of the bone morphogenetic protein [BMP] pathway). On day 4, the medium was replaced, adding the same small molecules (excluding bFGF and Y-27632). On day 6, the EBs were transferred into ultra-low attachment 24-well plates and cultured in NIM plus 100 nM retinoic acid. On day 12 EBs embedded in Cultrex and cultured with SCO differentiation media (SCODM, composed of 1:1 DMEM/F12 and Neurobasal with 0.5% N2 supplement, 1% B27, 2-mercaptoethanol, 0.025% insulin, 1% Glutamax, and 0.5% MEM-NEAA). 1 μM Smoothened Agonist was added to the media. On day 14, SCOs were transferred to spinning bioreactors and cultured with SCODM supplemented with RA and SAG. On day 28, concentrations of RA and SAG were reduced to 50% and neurotrophic factors BDNF, GDNF, and IGF-1 were added at 10 ng/ml each.

extract_protocol:
Total RNA was extracted using the ReliaPrep RNA Cell Miniprep System (Promega, Z6010).
Libraries were prepared starting from 50 ng of total RNA derived from 9 control, 6 SMA, and 16 morpholino-treated SMA (8 r6-MO, 8 r6-MO-scrambled) organoids, using the SMARTer Stranded RNA-Seq Kit, TaKaRa) and following the manufacturer’s instructions. Samples underwent a high coverage paired-end 150-bp strand-specific sequencing using a NextSeq 2000 platform (Illumina).

treatment_protocol: Anti-sense oligonucleotide morpholino (MO)10-34 sequence conjugated with r6 peptide (r6-MO). Details of specific MO used: (i) r6-MO targeting the SMN2 ISS-N1 region downstream of exon 7; (ii) negative control r6-MO with scrambled sequence. SMA SCOs were treated with growing concentrations of MO or r6-MO. The solution containing 2.4 nmoles MO or r6-MO was added directly to each well and incubated for 48h. Afterward, the culture medium was changed and fresh aliquots of 2.4 nmoles MO or r6-MO were added for an additional 48 h. The medium was then replaced with fresh medium for 72 h. Lastly, the organoids were treated again with 4.8 nmoles of MO or r6-MO for 48 h.

tag: cell line

tag: genotype

value: SMA

tag: treatment


title: Rat retina – Nanoceria + Light damage (biol rep 4)

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

institute: University of Messina

description:
Library name: mRNA-RAT-nano-LD-4_S47
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

data_processing:
Raw reads were trimmed for adapter sequences and low-quality bases using Trimmomatic (v0.39).
High-quality reads were aligned to the Rattus norvegicus reference genome (rn6, Ensembl release XX) using STAR (v2.7.9a) with default parameters.
Aligned reads were assigned to genes using featureCounts (Subread v2.0.1).
Count matrices were normalized and analyzed for differential expression using DESeq2 (v1.30.1) in R (v4.0).
Pathway and gene ontology enrichment analyses were performed using clusterProfiler (v3.18).
Assembly: Rattus norvegicus (rn6)
Supplementary files format and content: count_matrix.csv: rows = genes, columns = samples; raw and normalized counts.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Retina

growth_protocol: Adult rats were housed under standard conditions (12 h light/dark cycle, temperature 22±1°C, food and water ad libitum) until treatment.

extract_protocol:
Retinas were rapidly dissected under RNase-free conditions. Total RNA was extracted using the Qiagen RNeasy Mini Kit, following manufacturer’s instructions, including on-column DNase I treatment. RNA quality was assessed by Agilent Bioanalyzer; samples with RIN ≥ 7 were used.
RNA-seq libraries were prepared using the Watchmaker RNA Library Prep Kit (Twist Bioscience). Poly(A)-enriched mRNA was fragmented, reverse-transcribed, end-repaired, ligated to adapters, and PCR amplified according to manufacturer’s protocol. Libraries were indexed and pooled for sequencing.

treatment_protocol: Light-induced retinal degeneration was induced by high-intensity light exposure (15,000 lux, 24 h). Rats were treated with intravitreal injection of cerium oxide nanoparticles (nanoceria, 1 mM) or vehicle. Control animals received no treatment.

tag: tissue

value: Retina

value: Nanoceria + Light damage


title: HEK293T cell, VEGFA, A3C, loop2-34-31-7, PE2, rep1

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

description:
5307
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1

library_source: genomic

molecule: genomic DNA

growth_protocol: The culture conditions for HEK293T cells typically involve maintaining the cells in a high-glucose Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin antibiotic solution. The medium is further enriched with 2 mM L-glutamine for optimal cell growth and health. Cells should be cultured at 37°C in a humidified atmosphere with 5% CO2. Regular media replacement is essential, usually every 2-3 days, to prevent the accumulation of metabolic waste and to supply fresh nutrients. When the cell confluence reaches about 80-90%, subculturing is recommended to avoid overgrowth, commonly achieved by detaching the cells using trypsin and splitting them into fresh culture flasks at a suitable dilution ratio, typically around 1:10.

extract_protocol:
Genomic DNA was extracted by the addition of 20 µl of freshly prepared lysis buffer (10 mM Tris-HCl, pH 7.5; 0.05% SDS (ThermoFisher Scientific); 25 µg/ml proteinase K (Tiangen)) directly into each tube which 30,000 cells were sorted from each sample. The genomic DNA mixture was incubated at 37 °C for 1.5 h, followed by an 80 °C enzyme inactivation step for 30 min.
Use site-specific primers with second-generation sequencing adapters to amplify target sites via PCR for library construction.

treatment_protocol: HEK293T cells were seeded on 12-well poly-d-lysine coated plates (Corning). Between 16 and 24 h after seeding, cells were transfected at approximately 70% confluency with lipofectamine 3000 (ThermoFisher Scientific) according to the manufacturer’s protocols and 3249 ng All in one(PE2) plasmid, and 1083 ng sgRNA plasmid (for PE2 and PE3). Unless otherwise stated, cells were cultured for 2 days following transfection, after which the medium was removed, the cells were washed with 1 ml 1×PBS (ThermoFisher Scientific), then digested with 0.25% Trypsin-EDTA (1X) (Gibco) for 1 min, 1 ml DMEM complete medium was added to terminate the reaction. Centrifugation at 300 g for 5 min, discard supernatant and resuspended with 150 ul 1×PBS (ThermoFisher Scientific). After resuspended, all positive cells (single or double fluorescence positive) were sorted and collected into a 1.5 ml low adsorption centrifuge tube (ThermoFisher Scientific) by MULTI-APPLICATION CELL SORTER MA900 (Sony). Centrifugation at 11,200 g for 1 min, discard supernatant and store at -20°C for a long time.

value: base editing by prime editing


title: Rat retina – Nanoceria + Light damage (biol rep 3)

description:
Library name: mRNA-RAT-nano-LD-3_S41
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: SMA scramble CS83 replicate 3

description:
Library name: SMA_R6-MO_CS83_3
BULK-SAM-152

value: Scramble


title: HEK293T cell, VEGFA, A3C, loop2-34-20-7, PE2, rep3

description:
5300
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Liver_ctrl_ce_4

city: Ithaca

first: Philip

last: Ruppert

state: NY

address: 244 Garden Avenue

department: Division of Nutritional Sciences

country: USA

institute: Cornell University

description:
Library name: B081_Liver_ctrl_ce
Mouse ID: JWK-1317

data_processing:
Sequencing reads were aligned to the mouse reference genome (Gencode vM25) (12) using STAR aligner (v2.7.9a) (13) with the following parameters: --outSAMunmapped Within, --outFilterType BySJout, --outSAMattributes NH HI AS NM MD, --outFilterMultimapNmax 10, --outFilterMismatchNoverReadLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --alignSJoverhangMin 8, and --alignSJDBoverhangMin 1. Gene-level quantification was performed using featureCounts (v2.0.3) (14). In parallel, transcript-level quantification was performed using Salmon (v1.9.0) (15) and Gencode vM25, with parameters --seqBias, --useVBOpt, and --numBootstraps 30. Transcript abundance estimates were imported and summarized to the gene level using the tximport package (16). Quality control was summarized with MultiQC v1.19. All RNA-seq samples passed the QC.
Differential gene expression analysis was performed using DESeq2 (v1.46.0) (17) with shrinkage of fold-changes using apeglm (18). Genes with fewer than 10 total counts across all samples were excluded prior to normalization. The following interaction model was applied: ~ diet + temperature + diet:temperature, allowing detection of diet effects, temperature effects, and their statistical interaction. Specifically, the model tested: (i) the main effect of diet (MetR vs. Ctrl), (ii) the main effect of temperature (CE vs. RT), and (iii) the diet × temperature interaction (whether the effect of MetR differs between RT and CE). Genes with an adjusted p-value < 0.05 and an absolute log2FC ≥ 0.585 were considered significantly differentially expressed. Gene set enrichment analysis (GSEA) was performed using the gseKEGG() function from the clusterProfiler package (v4.14.6) (19) with parameters: organism = "mmu", pvalueCutoff = 1, pAdjustMethod = "BH", minGSSize = 0, seed = TRUE, and eps = 0. Quality control metrics and preprocessing approaches were done as previously described (20).
Assembly: mm10
Supplementary files format and content: Liver_Matrix_Raw_counts.txt, iBAT_iWAT_Matrix_Raw_counts.txt and gWAT_Matrix_Raw_counts.txt

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNAs from tissues were isolated using the TRI reagent (Sigma) followed by clean-up with RPE buffer (Qiagen, Germany). The quality of RNA was validated by the Agilent RNA 6000 Nano-Kit in Agilent 2100 Bioanalyzer according to the manufacturer's protocol (Agilent Technologies, Waldbronn, Germany). mRNA sequencing was performed in-house.
After quality control 500 ng RNA in a final volume of 25 μL DEPC-treated water was prepared and sample preparation was performed as described in the NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II RNA Library Prep Kit (cat no: #E7770, New England Biolabs, Ipswich, MA, USA). The amplified libraries were validated by Agilent 2100 Bioanalyzer using a DNA 1000 kit (Agilent Technologies, Inc., Santa Clara, CA, USA) and quantified by qPCR using the KaPa Library Kits (KaPa Biosystems, Wilmington, MA, USA). Hereafter, 2x50bp paired-end sequencing was performed on Illumina Novaseq 6000.

treatment_protocol: 2×2 design: Control vs. MetR for 7 days at room temperature (RT: 22 °C) +/- cold exposure (CE: 4 °C) for 24 h.

value: Liver

value: WT


title: Liver_metr_rt_6

description:
Library name: B076_Liver_metr_rt
Mouse ID: JWK-1287


title: SMA scramble CS83 replicate 2

description:
Library name: SMA_R6-MO_CS83_2
BULK-SAM-151


title: HEK293T cell, VEGFA, A3C, loop2-34-20-7, PE2, rep2

description:
5299
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Liver_metr_rt_5

description:
Library name: B075_Liver_metr_rt
Mouse ID: JWK-1286


title: Rat retina – Nanoceria + Light damage (biol rep 1)

description:
Library name: mRNA-RAT-nano-LD-1_S6
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: SMA scramble CS83 replicate 1

description:
Library name: SMA_R6-MO_CS83_1
BULK-SAM-150


title: HEK293T cell, VEGFA, A3C, loop2-34-20-7, PE2, rep1

description:
5298
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Liver_metr_rt_4

description:
Library name: B074_Liver_metr_rt
Mouse ID: JWK-1326


title: Rat retina – Nanoceria + Light damage (biol rep 5)

description:
Library name: mRNA-RAT-nano-LD-5_S53
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: SMA NT CS83 replicate 3

description:
Library name: SMA_NT_CS83_3
BULK-SAM-149

value: NT


title: Liver_metr_rt_3

description:
Library name: B073_Liver_metr_rt
Mouse ID: JWK-1302


title: Rat retina – Vehicle (biol rep 6)

description:
Library name: mRNA-RAT-veh-6_S56
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Vehicle


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-7, PE2, rep3

description:
5297
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: SMA NT CS83 replicate 2

description:
Library name: SMA_NT_CS83_2
BULK-SAM-148


title: Rat retina – Vehicle (biol rep 7)

description:
Library name: mRNA-RAT-veh-7_S62
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Rat retina – Vehicle (biol rep 5)

description:
Library name: mRNA-RAT-veh-5_S50
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-7, PE2, rep2

description:
5296
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Liver_metr_rt_2

description:
Library name: B072_Liver_metr_rt
Mouse ID: JWK-1278


title: Rat retina – Vehicle (biol rep 4)

description:
Library name: mRNA-RAT-veh-4_S44
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: SMA NT CS83 replicate 1

description:
Library name: SMA_NT_CS83_1
BULK-SAM-147


title: Liver_metr_rt_1

description:
Library name: B071_Liver_metr_rt
Mouse ID: JWK-1266


title: WT A2 replicate 3

description:
Library name: WT_A2_3
BULK-SAM-110

value: CTRL


title: Rat retina – Vehicle (biol rep 3)

description:
Library name: mRNA-RAT-veh-3_S38
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: HEK293T cell, VEGFA, A3C, tetraloop-34-22-7, PE2, rep3

description:
5291
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Liver_metr_rt_7

description:
Library name: B077_Liver_metr_rt
Mouse ID: JWK-1288


title: Liver_ctrl_rt_7

description:
Library name: B070_Liver_ctrl_rt
Mouse ID: JWK-1310


title: Rat retina – Nanoceria + Light damage (biol rep 2)

description:
Library name: mRNA-RAT-nano-LD-2_S35
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Rat retina – Vehicle (biol rep 2)

description:
Library name: mRNA-RAT-veh-2_S32
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: HEK293T cell, VEGFA, A3C, tetraloop-34-22-7, PE2, rep2

description:
5290
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-22-7, PE2, rep1

description:
5289
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Rat retina – Vehicle (biol rep 1)

description:
Library name: mRNA-RAT-veh-1_S3
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: WT A2 replicate 1

description:
Library name: WT_A2_1
BULK-SAM-108


title: WT CS5 replicate 3

description:
Library name: WT_CS5_3
BULK-SAM-107


title: Liver_ctrl_rt_5

description:
Library name: B068_Liver_ctrl_rt
Mouse ID: JWK-1277


title: Rat retina – Nanoceria (biol rep 6)

description:
Library name: mRNA-RAT-nano-6_S58
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Nanoceria


title: HEK293T cell, VEGFA, A3C, tetraloop-34-20-7-M, PE2, rep3

description:
5288
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Liver_ctrl_rt_6

description:
Library name: B069_Liver_ctrl_rt
Mouse ID: JWK-1306


title: WT CS5 replicate 2

description:
Library name: WT_CS5_2
BULK-SAM-106


title: Rat retina – Nanoceria (biol rep 5)

description:
Library name: mRNA-RAT-nano-5_S52
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: WT CS5 replicate 1

description:
Library name: WT_CS5_1
BULK-SAM-105


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-7, PE2, rep1

description:
5295
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: WT A2 replicate 2

description:
Library name: WT_A2_2
BULK-SAM-109


title: HEK293T cell, VEGFA, A3C, tetraloop-34-20-7-M, PE2, rep1

description:
5286
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Rat retina – Nanoceria (biol rep 4)

description:
Library name: mRNA-RAT-nano-4_S46
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Liver_ctrl_rt_2

description:
Library name: B065_Liver_ctrl_rt
Mouse ID: JWK-1299


title: HEK293T cell, VEGFA, A3C, tetraloop-34-20-7, PE2, rep3

description:
5285
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: WT R1 replicate 2

description:
Library name: WT_R1_2
BULK-SAM-103


title: HEK293T cell, VEGFA, A3C, tetraloop-34-20-7, PE2, rep2

description:
5284
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: WT R1 replicate 3

description:
Library name: WT_R1_3
BULK-SAM-104


title: Liver_ctrl_rt_1

description:
Library name: B064_Liver_ctrl_rt
Mouse ID: JWK-1298


title: Rat retina – Nanoceria (biol rep 1)

description:
Library name: mRNA-RAT-nano-1_S5
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: 4T1 RBdCDK Dox treated

city: Buffalo

first: Jianxin

last: Wang

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description:
Library name: 4T1-RBdCDKplusDox
10X Genomics

library_source: transcriptomic single cell

data_processing:
nf-core/rnaseq  version 3.3.
Assembly: GRCh38, GRCm38
Supplementary files format and content: Tab delimited text files, contain raw read counts at isoform level.

source_name: PDX, mamary gland

growth_protocol: AT-3 and MDA-MB 231 cells  with RBΔCDK isoform were grown in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic. 4T1 and HCC1806 cells  with RBΔCDK isoform were grown in RPMI 1640 supplemented with 10% FBS and 1% antibiotic-antimycotic.

extract_protocol:
RNA was extracted using Quiagen Rneasy plus mini Kit.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The cells were treated with 0.1% DMSO and Doxycycline (1 μg/mL) up to 48 hours

value: PDX, mamary gland

tag: cell type

value: Cancer

value: Dox


title: WT R1 replicate 1

description:
Library name: WT_R1_1
BULK-SAM-102


title: 4T1 RBdCDK Vehicle

description:
Library name: 4T1-RBdCDKminusDox
10X Genomics


title: Liver_ctrl_rt_3

description:
Library name: B066_Liver_ctrl_rt
Mouse ID: JWK-1300


title: HEK293T cell, EMX1, G5T, loop2-25-22-7, PE2, rep1

description:
5262
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Input-Nat10 KO-pool

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
Reads of the samples were trimmed for adapters and low-qality bases using Cutadapt before alignment
Trimmed sequence reads were mapped to the reference genome (mm10) and annotated transcripts using STAR
Assembly: mm10
Supplementary files format and content: bigWig

molecule: nuclear RNA

growth_protocol: 4T1 cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco), supplemented with 9% fetal bovine serum (FBS) (Gemini), 1% L-glutamine (Gibco), and 1% penicillin–streptomycin (Gemini).

extract_protocol:
After RNA-ChIP, RNA was purified using TriPure Isolation Reagent (Millipore-Sigma). To remove residual DNA, the purified RNA was treated with DNase I, followed by further purification using the RNA Clean & Concentrator-5 Kit (Zymo).
A total RNA library was then prepared using the Illumina Stranded Total RNA-seq Library Prep Kit with RiboZero Plus. Samples were pooled and sequenced on NextSeq 2000 P2 using paired-end sequencing.

value: Mouse mammary tumor cells

value: Knockout

tag: time


title: HEK293T cell, VEGFA, A3C, tetraloop-34-20-7, PE2, rep1

description:
5283
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Rat retina – Nanoceria (biol rep 2)

description:
Library name: mRNA-RAT-nano-2_S34
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Rat retina – Nanoceria (biol rep 3)

description:
Library name: mRNA-RAT-nano-3_S40
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Liver_ctrl_rt_4

description:
Library name: B067_Liver_ctrl_rt
Mouse ID: JWK-1301


title: Input-WT-pool


title: HEK293T cell, VEGFA, A3C, tetraloop-34-20-7-M, PE2, rep2

description:
5287
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Rat retina – Light damage (biol rep 6)

description:
Library name: mRNA-RAT-LD-6_S55
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Light damage


title: tgf-β+TFA, rep3

city: Nanjing

first: Qian

last: Li

state: Jiangsu

address: Xianlin Avenue 138

institute: Nanjing University of Traditional Chinese Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the human sapiens（ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Colorectal

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (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 was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were 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 were 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 librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Colorectal

value: DLD-1 cells

value: adenocarcinoma epithelial cells

value: Use tgf-β and TFA to treat cells for 26 hours


title: Day 10 Kupffer cells

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: Library name: Day10

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-2.2.0).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (GRCm38/mm10) and analyzed using "cellranger count".
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mouse livers were dissociated by perfusion and collagenase digestion and total non-parenchymal cells were isolated by differential centrifugation. Non parenchymal cells were further purified by FACS and live F4/80-high, CD11b-Intermediate cells were used for the single cell RNAseq protocol.
The 10X Genomics Single Cell 3’ Expression library preparation is performed using the 10X Genomics Chromium Controller. The cells prepared from disassociated tissue or tissue culture are validated for viability and cell concentration using the Countess Automated Cell Counter (Life Technologies) targeting ≥75% cell viability. The cell emulsification is performed on the 10X Chromium Controller using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics PN-120267) and Chromium Single Cell A Chip Kit (10X Genomics PN-1000009). Well 1 of Chip A is loaded with the reverse transcription (RT) Master Mix + cell suspension containing ~16,000 cells to target 10,000 emulsified cells at ~65% efficiency of emulsification. Well 2 of Chip A is filled with 40ul of the GEL Beads. Well 3 of Chip A is filled with 270ul Partitioning Oil. Any unused wells are filled with 50% glycerol at a volume designated for the well number. A gasket is applied to the Chip A and the loading cassette is inserted into the Chromium Controller for GEM creation using the Chromium Chip A Single Cell run program. Emulsified GEMs are recovered from each well and transferred to 200ul strip tubes. The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576). Single cell library quantification is completed using a Roche LightCycle96 using FastStart Essential Green Master (Roche 06402712001) and KAPA Library Quant (Illumina) DNA Standards (KAPA KK4903). Library concentrations are adjusted and pooled to 1.5nm for a final clustering concentration of 300pM on a NovaSeq6000. The sequencing was performed using a NovaSeq6000 100 cycle Reagent Kit (Illumina 20012865) with an asymmetrical sequencing profile ( read 1 - 26 cycle :  i7 index read - 8 cycle : i5 index read – 0 cycle : read 2 – 91 cycles ). Bcl2fastq conversion and demultiplexing is performed using the 10X Genomics Cell Ranger and Loupe Browser software suite.

treatment_protocol: 8 week old mice were fed either normal chow diet, Lieber-DeCarli alcohol diet for 3 days, or Lieber-DeCarli alcohol diet for 10 days.

value: Kupffer cells

tag: Sex

value: Male

value: 10-day EtOH


title: Day 3 Kupffer cells

description: Library name: Day3

value: Liver

value: 3-day EtOH


title: p300-RNA-ChIP-Nat10 KO biol rep3


title: tgf-β+TFA, rep2

value: Use tgf-β and TFA to treat cells for 25 hours


title: Rat retina – Light damage (biol rep 7)

description:
Library name: mRNA-RAT-LD-7_S61
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Retina


title: Rat retina – Light damage (biol rep 5)

description:
Library name: mRNA-RAT-LD-5_S49
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Day 0 Kupffer cells

description: Library name: Chow

value: Chow


title: p300-RNA-ChIP-Nat10 KO biol rep2


title: tgf-β+TFA, rep1

value: Use tgf-β and TFA to treat cells for 24 hours


title: p300-RNA-ChIP-Nat10 KO biol rep1


title: tgf-β, rep3

value: Use tgf-β to treat cells for 26 hours


city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

description: Library name: SI_39269_MNSC_10mM_Citraconate_R1_H3K27me3

data_processing:
aligned to hg38 using bwa mem
filtered alignments using samtools and picard
macs peak calling
Assembly: mm10, hg38
Supplementary files format and content: bigwigs (.bw)
Supplementary files format and content: bed peak files (.bed)

source_name: Mouse Brain

growth_protocol: EPN-1425 cells  were cultured in DMEM media (Gibco #11965092) supplemented with 10% fetal bovine serum (VWR #89510-186) and L-glutamine, 200mM (Thermo Fisher Scientific #A2916801). ZFTA-RELA mNSCs were cultured in Neurobasal media (Gibco #21103049) with 0.2 % heparin solution (StemCell Technologies Inc. #07980), 20ng/μL EGF (Shenandoah #100-26) and 20ng/μL FGF-Basic 154aa (Shenandoah #100-146).

extract_protocol:
1 million cells were used per ChIP reaction with 2ug of antibody. Briefly, cells were crosslinked for 10 minutes in a 1% formaldehyde solution, followed by quenching with 1/10th the volume of 1.25M glycine for 5 minutes at room temperature. Following this, the cells were lysed and sonicated (Bioruptor Pico, Diagenode) to a desired chromatin size of about 200bp using the Easy mode cycle.
About 1-10ng of ChIP DNA were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase [New England BioLabs (NEB)]. Klenow fragment (3′ to 5′ exo minus; NEB) was used to add a single adenine base to fragment ends, followed by ligation of Illumina adaptors (Quick ligase, NEB). PCR enriched the adaptor-ligated DNA fragments using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza), followed by gel extraction using QIAEX II reagents (Qiagen). Quantified libraries quality-checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: EPN1425 and ZFTA-RELA mNSCs were treated with DMSO/10mM Citraconate for 24h/48h or 10µM GSK343 for 96h

value: Mouse Brain

value: ZFTA-RELA mNSC

value: Neural Stem Cell

value: Citraconate 10mM

tag: antibody

value: H3K27me3 Chip Antibody:Millipore, # 07-449


title: Rat retina – Light damage (biol rep 3)

description:
Library name: mRNA-RAT-LD-3_S37
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Light damage


title: p300-RNA-ChIP-WT biol rep3

value: Mouse mammary tumor cells

value: WT


title: SI_39268_MNSC_DMSO_R2_H3K27me3

description: Library name: SI_39268_MNSC_DMSO_R2_H3K27me3

value: DMSO


title: tgf-β, rep2

value: Colorectal

value: DLD-1 cells

value: adenocarcinoma epithelial cells

value: Use tgf-β to treat cells for 25 hours


title: tgf-β, rep1

value: Use tgf-β to treat cells for 24 hours


title: Rat retina – Light damage (biol rep 2)

description:
Library name: mRNA-RAT-LD-2_S31
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Retina


title: p300-RNA-ChIP-WT biol rep2


title: Rat retina – Control (biol rep 6)

description:
Library name: mRNA-RAT-Ctrl-6_S54
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Control


title: Rat retina – Light damage (biol rep 1)

description:
Library name: mRNA-RAT-LD-1_S2
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: chimpanzee-iPS-0402F-1

city: Inuyama

first: Yusuke

last: Hamazaki

state: Aichi

country: Japan

institute: Center for the Evolutionary Origins of Human Behavior, Kyoto University

data_processing:
Using the first reads of paired-end reads in all the datasets, adaptor and quality trimming were performed by Trim Galore. The preprocessed reads were mapped to all of the human (hg38), chimpanzee (panTro6), and bonobo (panPan3) reference genomes using STAR, regardless of species origin. Only reads that were successfully mapped to all three references were used for downstream analysis. After conversion from the bam format to bed format and removal of PCR duplicates, the intersectBed command in bedtools was used to sum up reads overlapping with exons. The Pandas was used to calculate transcripts per kilobase million (TPM) for normalization. Gene expression in humans, chimpanzees, and bonobos was calculated by the annotation of hg38. For the investigation of retrotransposon expression, the first 50 bp of the first reads were mapped onto the consensus sequences of 647 retrotransposons present in the Homo and/or Pan genomes using HISAT2. The same reads were also mapped to their respective genomes of origin (hg38, PanTro6, or PanPan3) using HISAT2. Reads that overlapped annotated exonic regions in the respective genomes were excluded from the retrotransposon counts.
Assembly: hg38, PanTro6, PanPan3
Supplementary files format and content: xlsx file including TPM value of gene expressions
Supplementary files format and content: xlsx file including RPM value of retrotransposon expressions

organism: Pan troglodytes

source_name: iPSC

growth_protocol: Peripheral blood samples from two bonobos (GAIN-ID 0008; female, 0009; male) and one chimpanzee (0402; female) were collected for medical examination at Kumamoto Sanctuary Wildlife Research Center, Kyoto University and stored in liquid nitrogen for 5-10 years. PBMCs were isolated from the blood samples using BD Vacutainer CPT (362761; BD Biosciences, San Jose, CA, USA) and cultured in Advanced Roswell Park Memorial Institute (RPMI) 1640 medium (12633-012; Gibco, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS), 1× GlutaMAX Supplement (35050061; Gibco), and 100 U/ml penicillin and 100 µg/ml streptomycin (168-23191; Wako, Osaka, Japan) at 37°C with 5% CO2. SRV transduction was performed using SRV iPSC-2 Vector (S1011694A; TOKIWA-Bio, Ibaraki, Japan) or SRV iPSC-4 Vector (S1011696A; TOKIWA-Bio) with a modified protocol. Briefly, 1 × 105 PBMCs were incubated with either SRV-2 or SRV-4 at a multiplicity of infection of 3 at 37°C for 2 or 6 hours, followed by washing with 10% FBS/RPMI medium and plating onto the iMatrix 511 (892024; Matrixome, Osaka, Japan)-coated 60-mm culture dishes. On day 1, 3, 5, and 7 after transduction, 1 ml of StemFit medium (AK02N; Ajinomoto, Tokyo, Japan) was added to the cell culture. Since day 9, the medium was changed to fresh StemFit medium change every other day. The iPSC-like colonies were mechanically isolated and dissociated with TrypLE Express (12604021; Gibco). The cells were expanded on mitomycin C-treated mouse embryonic fibroblasts (RCHEFC003; REPROCELL, Kanagawa, Japan) in StemFit medium supplemented with 2.5 µM IWR-1 (037-25131; Wako).

extract_protocol:
Total RNA of bonobo and chimpanzee iPSCs was extracted using ISOGEN (317-02503; Nippon Gene, Tokyo, Japan) and Direct-zol RNA Miniprep (R2050; Zymo Research, Irvine, USA).
cDNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs) and sequenced on Illumina NovaSeq with 2 x 150 bp paired-end read configuration.

value: iPSC


title: p300-RNA-ChIP-WT biol rep1


title: LNCaP_HOXB13_IP_rep2_ChIP-seq

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

country: Canada

institute: Vancouver Prostate Centre

description:
LNCaP_HOXB13_IP_rep2_ChIP-seq
LNCaP.HOXB13.merges.hg38.genomecov.rawcount.bigWig
LNCaP.HOXB13.merges.hg38_peaks.narrowPeak

data_processing:
Paired reads are aligned to UCSC hg38 genome using bwa with default parameters. Alignments that have MAPQ < 30 filtered out.
FASTQ files of replicates are merged.
After mates are fixed using samtools fixmate, alignments are sorted according to corrdinates. Duplicates are marked and removed using samtools markdup. Only properly paired alignments included in the next step.
NarrowPeaks are called with MACS3 callpeak with ' -BAMPE -g hs -q 0.00001 -B' parameters.
BedGraph files generated using bedtools genomecov with -bg as input of BAM files. The BedGraph files are converted to BigWig files using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: narrowPeak

source_name: LNCaP

growth_protocol: LNCaP cells were cultured in RPMI 1640 with L-glutamine (Lonza, Switzerland #12-702Q) supplemented with 10% tetracycline-free fetal bovine serum (Biowest, Franse #S181T) and 1% penicillin/streptomycin (Gibco, USA #15140122). PC3 cells were cultured in RPMI 1640 with L-glutamine (Lonza, Switzerland #12-702Q) supplemented with 10% fetal bovine serum (Biowest, France #S1300) and 1% penicillin/streptomycin (Gibco, USA #15140122).

extract_protocol:
Cells were crosslinked with 1% methanol-free formalin for 10 min at room temperature with gentle shaking. After lysis and nuclear enrichment, immunoprecipitation was carried out using HOXB13 (Cat # ab227879, Abcam), SMARCD2 (Cat # ab221168, Abcam) -conjugated protein G Dynabeads (Cat # 10003D, Invitrogen) overnight at 40C. After washing, the DNA was eluted and de-crosslinked at 650C for 8 hours. The DNA was purified using a Monarch DNA purification kit (Cat # T1030, NEB) and quantified by a Qubit high-sensitivity DNA kit (Cat # Q33230, Invitrogen).
DNA (5ng) was used for sequencing library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat # E7645, NEB) according to the manufacturer's instructions. The library was amplified for 10 cycles and quantified by Bioanalyzer (Agilent) and sequenced using Illumina NovaSeq 6000.

value: LNCaP

tag: chip antibody


title: LNCaP_SMARCD2_IP_rep2_ChIP-seq

description:
LNCaP_SMARCD2_IP_rep2_ChIP-seq
LNCaP.SMARCD2.merges.hg38.genomecov.rawcount.bigWig
LNCaP.SMARCD2.merges.hg38_peaks.narrowPeak

value: SMARCD2 (Abcam, #ab221168)


description: Library name: SI_39266_MNSC_10mM_Citraconate_R2_H3K4me3

value: Mouse Brain

value: ZFTA-RELA mNSC

value: Neural Stem Cell

value: H3K4me3 Chip Antibody:CST, # 9751S


title: SI_39264_MNSC_DMSO_R2_H3K4me3

description: Library name: SI_39264_MNSC_DMSO_R2_H3K4me3


title: Rat retina – Control (biol rep 5)

description:
Library name: mRNA-RAT-Ctrl-5_S48
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


description: Library name: SI_39270_MNSC_10mM_Citraconate_R2_H3K27me3

value: Citraconate 10mM

value: H3K27me3 Chip Antibody:Millipore, # 07-449


title: SI_39263_MNSC_DMSO_R1_H3K4me3

description: Library name: SI_39263_MNSC_DMSO_R1_H3K4me3

value: DMSO


title: imb_keller_2022_15_10_HA_Act5Yob_Rep2

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
Library name: Sample 10
HA_Act5Yob_Rep2

data_processing:
Reads were trimmed with cutadapt (4.0).
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (2.4.5)
Coverage signal tracks (bigWigs) of alignments were generated using Samtools (v1.9) and DeepTools (v3.5.1)
Peaks were called with MACS version 2.1.2.
A greylist was generated from IgG samples and applied for peak filtering
DiffBind (v 3.6.1) was use to determine differential binding, with normalization to background bins (15000 bp). Only peaks with FDR<0.05 in were considered as differentially bound.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Library strategy: CUT&Tag

organism: Anopheles gambiae

source_name: Ag55 cell line

growth_protocol: Ag55 cells were cultured in Leibovitz L15 media with 10% FBS (Gibco, 10270-10,6 Lot: 2260092) and 1x penicillin-streptomycin (Gibco, 15140122) at 27°C at 80% humidity.

extract_protocol:
The cell suspension was counted and 0.4 Mio cells were used for each reaction. The experiment was performed following the native protocol dx.doi.org/10.17504/protocols.io.bcuhiwt6. Antibodies are listed with the respective samples. We used pA-Tn5 prepared by the IMB protein production core facilty.
CUT&Tag libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing.

treatment_protocol: 2 Mio. Ag55 cells were seeded in a 6-well plate. After 16 hours, 600 μl of a selected baculovirus in Sf-900 media was added to the cells. After 6 hours the media was changed to fresh L15. Cells were collected for further processing 48h from the addition of the baculovirus.

value: Ag55 cell line

value: HA.11 Mouse (Biolegend, BLD-901502)

tag: ectopic expression

value: HA-tagged Yob


title: Rat retina – Light damage (biol rep 4)

description:
Library name: mRNA-RAT-LD-4_S43
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Light damage


title: Rat retina – Control (biol rep 4)

description:
Library name: mRNA-RAT-Ctrl-4_S42
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: imb_keller_2022_15_13_H3K27me3_empty_Rep1

description:
Library name: Sample 13
H3K27me3_empty_Rep1

value: H3K27me3, Rabbit, Active Motif, 39055

value: HA-tagged empty control


title: LNCaP_HOXB13_IP_rep1_ChIP-seq

description:
LNCaP_HOXB13_IP_rep1_ChIP-seq
LNCaP.HOXB13.merges.hg38.genomecov.rawcount.bigWig
LNCaP.HOXB13.merges.hg38_peaks.narrowPeak

value: WT


title: imb_keller_2022_15_12_HA_empty_Rep2

description:
Library name: Sample 12
HA_empty_Rep2


title: SI_33929_mNSC_ZFTA_RELA_dmCitra_Rep2

description: Library name: SI_33929_mNSC_ZFTA_RELA_dmCitra_Rep2

data_processing:
aligned to mm10 using bwa mem
filtered alignments using samtools and picard
macs peak calling
Assembly: mm10
Supplementary files format and content: bigwigs (.bw)
Supplementary files format and content: bed peak files (.bed)

source_name: brain

growth_protocol: ZFTA-RELA mNSCs were cultured in Neurobasal media (Gibco #21103049) with 0.2 % heparin solution (StemCell Technologies Inc. #07980), 20ng/μL EGF (Shenandoah #100-26) and 20ng/μL FGF-Basic 154aa (Shenandoah #100-146).

extract_protocol:
In brief, 50,000 mouse neural stem cells (Empty vector/ZFTA-RELA fusion)  were washed in cold PBS and resuspended in lysis buffer (10mM Tris HCL, pH7.4, 10mM NaCl, 3mM MgCl2, Digitonin, NP-40 and Tween-20, Protease and Phosphatase inhibitor). This single-cell suspension was incubated on ice for 5 minutes with gentle mixing by pipetting every 2 min, followed by quenching in the resuspension buffer. The lysate was centrifuged at 1,300g for 5 min at 4 °C.
Nuclei were resuspended in a 50ul reaction containing 25ul of 2× TD buffer, 1ul of Tn5 enzyme for 30 min at 37 °C using the Nextera DNA Library Preparation Kit. Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; #M0541L). Optimal PCR cycles were determined via qPCR, and the amplified libraries were further purified using a Qiagen minElute column and SPRI beads (Beckman Coulter). Libraries were quantified and quality-checked using the Bioanalyzer 2100 (Agilent). Finally, the ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 platform, utilizing a 2x50-nucleotide paired-end read length with a sequence depth of 40-45M

treatment_protocol: ZFTA-RELA mNSCs treated with DMSO/10mM Citraconate for 24h/48h or 10µM GSK343 for 96h

value: brain

value: neural stem cell

value: Citraconate (10mM)


title: Rat retina – Control (biol rep 1)

description:
Library name: mRNA-RAT-Ctrl-1_S1
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Retina

value: Control


title: LNCaP_SMARCD2_IP_rep1_ChIP-seq

description:
LNCaP_SMARCD2_IP_rep1_ChIP-seq
LNCaP.SMARCD2.merges.hg38.genomecov.rawcount.bigWig
LNCaP.SMARCD2.merges.hg38_peaks.narrowPeak

value: LNCaP

value: SMARCD2 (Abcam, #ab221168)


title: SI_39267_MNSC_DMSO_R1_H3K27me3

description: Library name: SI_39267_MNSC_DMSO_R1_H3K27me3

value: Mouse Brain

value: ZFTA-RELA mNSC

value: Neural Stem Cell


description: Library name: SI_39265_MNSC_10mM_Citraconate_R1_H3K4me3

value: Citraconate 10mM

value: H3K4me3 Chip Antibody:CST, # 9751S


title: LNCaP_HOXB13_input_ChIP-seq

description:
LNCaP_HOXB13_input_ChIP-seq
none


title: SI_33927_mNSC_ZFTA_RELA_GSK_Rep2

description: Library name: SI_33927_mNSC_ZFTA_RELA_GSK_Rep2


title: PC3_HOXB13_input_ChIP-seq

description:
PC3_HOXB13_input_ChIP-seq
none


title: Rat retina – Control (biol rep 2)

description:
Library name: mRNA-RAT-Ctrl-2_S30
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: plt345-PLT5-1

city: Wuhan

first: Qi

address: Lion Rock Street

department: Hongshan District

institute: Huazhong Agricultural University

data_processing:
Clean reads were mapped to the rice genome (MSU7.0) by Bowtie2 (version 2.4.4).
The bigwig files were generated using bamCoverage with the parameters “-bam  –normalize Using RPKM” in deepTools (version 3.5.0).
MACS2 (version 2.2.7.1) was used to call histone modification peaks
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

organism: Oryza sativa Japonica Group

source_name: root tip

growth_protocol: Seedlings were grown in one-half-strength Murashige and Skoog medium under 14-h light/10-h dark cycles at 28/24 °C

extract_protocol:
Nuclei of rice root tip (Approx. 0.8cm) cells were isolated seven days after germination and performed CUT&Tag (Vazyme, TD903)
library construction by Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202)

value: root tip

value: triple mutant of PLT3, PLT4 and PLT5


title: DU145_siNC_OE_HOXB13_ATAC-seq

description:
DU145_siNC_OE_HOXB13_ATAC-seq
DU145.siNC_HOXB13.hg38.callsummit.bw
DU145.siNC_HOXB13.hg38.callsummit_peaks.narrowPeak

data_processing:
Adapters are removed using CUTADAPT with ' -A CTGTCTCTTATA -a CTGTCTCTTATA' parameters.
FASTQ files of replicates are merged for each condition.
Paired reads are aligned to UCSC hg38 genome using bwa with default parameters. Alignments that have MAPQ < 30 filtered out.
After mates are fixed using samtools fixmate, alignments are sorted according to corrdinates. Duplicates are marked and removed using samtools markdup. Additionally, mitochondrial alignments are removed. Only primary aligned properly paired alignments included in the next step.
NarrowPeaks are called with MACS3 callpeak with '-BAMPE -g hs -q 0.01 --call-summits -B' parameters.
The treatment pileup BedGraph files from MACS3 outpurt used to generate the BigWig files using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: narrowPeak

growth_protocol: DU145 cells were cultured in RPMI 1640 with L-glutamine (Lonza, Switzerland #12-702Q) supplemented with 10% fetal bovine serum (Biowest, France #S1300) and 1% penicillin/streptomycin (Gibco, USA #15140122).

extract_protocol:
50,000 live DU145 cells expressing GFP or HOXB13 were lysed in 50 ul of cold lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Digitonin, and 0.1% Tween-20) on ice for exactly 3 mins. The intact nucleus was tagmented with 2.0 ul of Tn5 Transposase (Cat # FC-121-1030, Illumina) and incubated at 370C on a thermomixer at 1000 RPM. The DNA was purified by the Minielute reaction cleanup kit (Cat # 28206, Qiagen).
The DNA was amplified with unique barcoded primers and subjected to sequencing using Illumina Novaseq with a minimum of 30M reads for each sample.

tag: treatment 2

value: siNC


title: Rat retina – Control (biol rep 3)

description:
Library name: mRNA-RAT-Ctrl-3_S36
Rat retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: SI_33924_mNSC_ZFTA_RELA_DMSO_Rep1

description: Library name: SI_33924_mNSC_ZFTA_RELA_DMSO_Rep1

value: PBS/Vehicle


title: plt345-IgG-2

value: IgG (ABclonal, AC005)


title: PC3_HOXB13_IP_rep2_ChIP-seq

description:
PC3_HOXB13_IP_rep2_ChIP-seq
PC3.HOXB13.merges.hg38.genomecov.rawcount.bigWig
PC3.HOXB13.merges.hg38_peaks.narrowPeak

value: WT


title: imb_keller_2022_15_09_HA_empty_Rep1

description:
Library name: Sample 9
HA_empty_Rep1

value: Ag55 cell line

value: HA.11 Mouse (Biolegend, BLD-901502)

value: HA-tagged empty control


title: imb_keller_2022_15_07_HA_Act5Yob_Rep1

description:
Library name: Sample 7
HA_Act5Yob_Rep1

value: HA-tagged Yob


title: PC3_HOXB13_IP_rep1_ChIP-seq

description:
PC3_HOXB13_IP_rep1_ChIP-seq
PC3.HOXB13.merges.hg38.genomecov.rawcount.bigWig
PC3.HOXB13.merges.hg38_peaks.narrowPeak


title: DU145_OE_HOXB13_rep2_ATAC-seq

description:
DU145_OE_HOXB13_rep2_ATAC-seq
DU145.plx302HOXB13.merges.hg38.callsummit.bw
DU145.plx302HOXB13.merges.hg38.callsummit_peaks.narrowPeak


title: imb_keller_2022_15_06_IgG_empty_Rep2

description:
Library name: Sample 6
IgG_empty_Rep2

value: IgG control Rabbit (Abcam ab37415)


title: imb_keller_2022_15_04_IgG_Act5Yob_Rep2

description:
Library name: Sample 4
IgG_Act5Yob_Rep2


title: SI_33926_mNSC_ZFTA_RELA_GSK_Rep1

description: Library name: SI_33926_mNSC_ZFTA_RELA_GSK_Rep1

value: brain

value: neural stem cell


title: DU145_OE_eGFP_rep2_ATAC-seq

description:
DU145_OE_eGFP_rep2_ATAC-seq
DU145.plx302eGFP.merges.hg38.callsummit.bw
DU145.plx302eGFP.merges.hg38.callsummit_peaks.narrowPeak


title: WT-IgG-2

value: wild-type


title: DU145_siSMARCD2_OE_HOXB13_ATAC-seq

description:
DU145_siSMARCD2_OE_HOXB13_ATAC-seq
DU145.siSMARCD2_HOXB13.hg38.callsummit.bw
DU145.siSMARCD2_HOXB13.hg38.callsummit_peaks.narrowPeak


title: imb_keller_2022_15_03_IgG_empty_Rep1

description:
Library name: Sample 3
IgG_empty_Rep1


title: SI_33921_mNSC_EmptyVector_Rep2

description: Library name: SI_33921_mNSC_EmptyVector_Rep2

value: Empty Vector mNSC


title: CTRL, rep3

description: Library name: Lib_SLO_17

data_processing:
Samples were sequenced on an Illumina NextSeq 500 platform, generating raw base call (BCL) files. Raw sequencing reads were processed using Cell Ranger v6.1.0 (10x Genomics, 2021). The demultiplexing of the BCL files was performed using the cellranger mkfastq pipeline, which converts BCL files into FASTQ files while preserving sample index information. The resulting FASTQ files were subsequently processed with the cellranger count pipeline to perform alignment, filtering, barcode counting, and UMI counting.
Reads were mapped to the human reference genome GRCh38 using the refdata-gex-GRCh38-2020-A reference package provided by 10x Genomics*. The mapping and quantification steps were conducted with default parameters, with the additional options --r1-length=26 and --r2-length=55 specified to adjust read lengths accordingly. These parameters were chosen to optimize compatibility with the sequencing chemistry and ensure high-quality read alignment*.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Organoids were dissociated using an optimized protocol based on the Worthington Papain Dissociation System Kit (Worthington Biochemical). Single cell suspensions were collected on ice-cold PBS (without calcium and magnesium) with 0.04% BSA at 1×10^6 /ml as counted by an automatic cell counter.
Library was performend accordingly to manufacter's instructions (10X Genomics). Briefly, approximately 8000 cells from each sample prepared as described above were loaded into one channel of the Single Cell Chip B using the Single Cell 3’ v3 reagent kit (10X Genomics) for gel bead emulsion generation in the Chromium system. Following capture and lysis, cDNA was synthesized and amplified for 14 cycles following the manufacturer’s protocol (10X Genomics). The amplified cDNA (50 ng) was then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq550 Illumina sequencing platform following the 10x Genomics instructions for read generation. A sequencing depth of ~45,000 reads/cell was obtained for each sample.

value: CTRL


title: plt345-PLT5-2


title: imb_keller_2022_15_01_IgG_Act5Yob_Rep1

description:
Library name: Sample 1
IgG_Act5Yob_Rep1


title: SI_33923_mNSC_ZFTA_RELA_Rep2

description: Library name: SI_33923_mNSC_ZFTA_RELA_Rep2

value: ZFTA-RELA mNSC


title: plt345-IgG-1

value: root tip


title: SI_33922_mNSC_ZFTA_RELA_Rep1

description: Library name: SI_33922_mNSC_ZFTA_RELA_Rep1


title: CTRL, rep4

description: Library name: Lib_SLO_18


title: WT-IgG-1


title: DU145_OE_HOXB13_rep1_ATAC-seq

description:
DU145_OE_HOXB13_rep1_ATAC-seq
DU145.plx302HOXB13.merges.hg38.callsummit.bw
DU145.plx302HOXB13.merges.hg38.callsummit_peaks.narrowPeak


title: SI_33928_mNSC_ZFTA_RELA_dmCitra_Rep1

description: Library name: SI_33928_mNSC_ZFTA_RELA_dmCitra_Rep1

value: Citraconate (10mM)


title: ZH11-PLT5-1

data_processing:
TrimGalore (version 0.6.6) was used to trim the adaptors and remove low quality reads from the raw reads.
Clean reads were mapped to the rice genome (MSU7.0) by Bowtie2 (version 2.4.4).
The bigwig files were generated using bamCoverage with the parameters “-bam -binSize 10 –normalize Using RPKM” in deepTools (version 3.5.0).
MACS2 (version 2.2.7.1) was used to call histone modification peaks
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: bigWig, broadPeak
Library strategy: CUT&Tag


title: SMA, rep4

description: Library name: Lib_SLO_16

value: SMA


title: plt345-EMF2b-2

value: triple mutant of PLT3, PLT4 and PLT5


title: 4T1, Dox treated, bio rep 4

description: Library name: 4T1, Dox treated, bio rep 4

source_name: TNBC cell lines

value: TNBC cell lines

value: Cancer


title: DU145_OE_eGFP_rep1_ATAC-seq

description:
DU145_OE_eGFP_rep1_ATAC-seq
DU145.plx302eGFP.merges.hg38.callsummit.bw
DU145.plx302eGFP.merges.hg38.callsummit_peaks.narrowPeak


title: ZH11-PLT5-2


title: 4T1, Dox treated, bio rep 2

description: Library name: 4T1, Dox treated, bio rep 2


title: SI_39606_MNSC_Citraconate_50K_Rep1

description: Library name: SI_39606_MNSC_Citraconate_50K_Rep1


title: ZH11-EMF2b-1


title: SI_33925_mNSC_ZFTA_RELA_DMSO_Rep2

description: Library name: SI_33925_mNSC_ZFTA_RELA_DMSO_Rep2

value: PBS/Vehicle


title: CTRL, rep1

description: Library name: Lib_SLO_13


title: SMA, rep2

description: Library name: Lib_SLO_12


title: SMA, rep3

description: Library name: Lib_SLO_15


title: SI_39607_MNSC_Citraconate_50K_Rep2

description: Library name: SI_39607_MNSC_Citraconate_50K_Rep2


title: 4T1, Dox treated, bio rep 3

description: Library name: 4T1, Dox treated, bio rep 3


title: plt345-EMF2b-1


title: CTRL, rep2

description: Library name: Lib_SLO_14


title: ZH11-EMF2b-2


title: SI_39604_MNSC_DMSO_50K_Rep2

description: Library name: SI_39604_MNSC_DMSO_50K_Rep2

value: DMSO/Vehicle


title: SI_33920_mNSC_EmptyVector_Rep1

description: Library name: SI_33920_mNSC_EmptyVector_Rep1


title: 4T1, Control, bio rep 4

description: Library name: 4T1, Control, bio rep 4


title: SMA, rep1

description: Library name: Lib_SLO_11


title: plt345-H3K4me3-2

value: H3K4me3 (Abcam, ab8580)


title: SI_39603_MNSC_DMSO_50K_Rep1

description: Library name: SI_39603_MNSC_DMSO_50K_Rep1


title: RV d7 CD4, HTO, biol rep 2

city: Toronto

first: Kei

last: Haniuda

state: Ontario

address: 1 King’s College Circle, MSB7310

department: Department of Immunology

institute: University of Toronto

description: Library name: D7_2_HTO

library_source: other

data_processing:
The demultiplexing, barcoded processing, HTO counts, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). MLN_VP4: TotalSeq C Hashtag 1, ACCCACCAGTAAGAC MLN_VP6: TotalSeq C Hashtag 2, GGTCGAGAGCATTCA PP_VP4: TotalSeq C Hashtag 3, CTTGCCGCATGTCAT PP_VP6: TotalSeq C Hashtag 4, AAAGCATTCTTCACG Total: TotalSeq C Hashtag 5, CTTTGTCTTTGTGAG
Assembly: mm10
Supplementary files format and content: CellRanger output files: D7_1_barcodes.tsv.gz, D7_1_features.tsv.gz, D7_1_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: D7_2_barcodes.tsv.gz, D7_2_features.tsv.gz, D7_2_matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Mouse CD4 T cells

extract_protocol:
Single cell suspension of pooled Peyer’s patches (PPs) and mesenteric lymph nodes (MLNs) from rotavirus (RV) infected mice were stained with VP4:p:I-Ab or VP6:p:I-Ab tetramers and tetramer-binding cells were enriched by magnetic beads and the beads-unbound fractions were also collected. The bead-bound and unbound cells were stained for cell surface markers for flow cytometric sorting as well as hashtag oligonucleotides (HTOs) Abs. Each sample was stained with unique HTO-labeled antibodies to CD45 and MHCI (Biolegend, TotalSeq C anti-mouse Hashtag Abs): HTO1 (for MLN_VP4, M1/42; 30-F11, 155861), HTO2 (for MLN_VP6, M1/42; 30-F11, 155863), HTO3 (for PP_VP4, M1/42; 30-F11, 155865), HTO4 (for PP_VP6, M1/42; 30-F11, 155867) and HTO5 (for Total, M1/42; 30-F11, 155869). Then, by flow cytometric sorting, Dump (B220, CD11b, CD11c, F4/80 and viability dye)-negative CD3+CD4+CD8–p:I-Ab+ cells from the bead-bound fractions (referred as VP4:I-Ab+ and VP6:I-Ab+) and an equal number of Dump-negative CD3+CD4+CD8–p:I-Ab– cells from the bead-unbound fraction (referred as Total CD4+) were sorted into the same collection tube.
The sorted cells were counted for viability and immediately subjected to library preparation using 10X Chromium Next GEM Single Cell 5’ Reagent Kits V2 and Chromium Single Cell Mouse TCR Amplification Kit according to the manufacturer’s instructions.

treatment_protocol: Rotavirus infection

value: Mouse CD4 T cells

value: C57BL/6 WT

value: RV infected

tag: library type

value: HTO


title: Atopic dermatitis patient #10, After treatment, Non-Lesion

type: RNA

city: Seoul

first: Seo Hyeong

last: Kim

address: 97, Uisadang-daero, Yeongdeungpo-gu

country: South Korea

institute: Cutis Biomedical Research Center Co. Ltd.

description: GeneChip™ Human Gene 2.0 ST Array; Minimally invasive skin sampling using microneedle patches

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: Atopic dermatitis patient, After treatment, Non-Lesion

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

extract_protocol: Total RNA extraction was performed according to the manufacturer's instructions from QIAGEN.

value: Skin


title: 4T1, Dox treated, bio rep 1

description: Library name: 4T1, Dox treated, bio rep 1


title: plt345-H3K27me3-2


title: 4T1, Control, bio rep 3

description: Library name: 4T1, Control, bio rep 3


title: RV d7 CD4, HTO, biol rep 1

description: Library name: D7_1_HTO


title: plt345-H3K4me3-1


title: Atopic dermatitis patient #10, After treatment, Lesion

source_name: Atopic dermatitis patient, After treatment, Lesion


title: RV d7 CD4, GEX, biol rep 2

description: Library name: D7_2_GEX

data_processing:
The demultiplexing, barcoded processing, HTO counts, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). MLN_VP4: TotalSeq C Hashtag 1, ACCCACCAGTAAGAC MLN_VP6: TotalSeq C Hashtag 2, GGTCGAGAGCATTCA PP_VP4: TotalSeq C Hashtag 3, CTTGCCGCATGTCAT PP_VP6: TotalSeq C Hashtag 4, AAAGCATTCTTCACG Total: TotalSeq C Hashtag 5, CTTTGTCTTTGTGAG
Assembly: mm10
Supplementary files format and content: CellRanger output files: D7_1_barcodes.tsv.gz, D7_1_features.tsv.gz, D7_1_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: D7_2_barcodes.tsv.gz, D7_2_features.tsv.gz, D7_2_matrix.mtx.gz

value: mRNA


title: plt345-H3K27me3-1


title: 4T1, Control, bio rep 1

description: Library name: 4T1, Control, bio rep 1


title: AT3, Dox treated, bio rep 3

description: Library name: AT3, Dox treated, bio rep 3


title: RV d7 CD4, GEX, biol rep 1

description: Library name: D7_1_GEX


title: ZH11-H3K4me3-1

value: wild-type


title: Atopic dermatitis patient #9, After treatment, Lesion


title: ZH11-H3K4me3-2


title: Atopic dermatitis patient #9, After treatment, Non-Lesion


title: AT3, Dox treated, bio rep 2

description: Library name: AT3, Dox treated, bio rep 2


title: KPsh,off-dox+sgPcyt2+Pcyt2-cDNA,rep2

city: New York

first: Lydia

last: Finley

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequencing files were trimmed with trimmoatic
Reads were mapped to the reference mouse genome sequence (mm10) with STAR (2.6.1c)
Gene expressions were calculated by Homer with Gencode gene annotation GTF file
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: pancreas

growth_protocol: KPsh cells were cultured in complete DMEM supplemented with 10% fetal bovine serum (FBS; Gemini) and 1 μg/ml doxycycline (Sigma) on collagen-coated plates (PurCol, Advanced Biomatrix, 0.1 mg/ml). Medium was refreshed every other day. KPsh cells cultured on or off doxycycline for ten days. Pcyt2-knockout KPsh cells or Pcyt2-knockout KPsh cells complemented with guide-resistant Pcyt2 cDNA cultured on or off doxycycline for six days. KPnull cells (p53-ON system cells) were cultured in complete DMEM supplemented with 10% FBS on collagen-coated plates and 1 μg/ml doxycycline was administered 48 hours prior to harvest.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: On and off doxycycline, as described in growth conditions above.

value: pancreas

value: KPsh

value: PDAC cell line


title: ZH11-H3K27me3-2

value: root tip


title: KPsh,off-dox+sgPcyt2+Pcyt2-cDNA,rep1


title: KPsh,on-dox+sgPcyt2+Pcyt2-cDNA,rep1


title: Atopic dermatitis patient #9, Before treatment, Non-Lesion

source_name: Atopic dermatitis patient, Before treatment, Non-Lesion


title: 4T1, Control, bio rep 2

description: Library name: 4T1, Control, bio rep 2

data_processing:
nf-core/rnaseq  version 3.3.
Assembly: GRCh38, GRCm38
Supplementary files format and content: Tab delimited text files, contain raw read counts at isoform level.


title: Atopic dermatitis patient #10, Before treatment, Non-Lesion


title: KPsh,on-dox+sgPcyt2+Pcyt2-cDNA,rep2


title: AT3, Control, bio rep 2

description: Library name: AT3, Control, bio rep 2


title: ZH11-H3K27me3-1


title: Atopic dermatitis patient #7, After treatment, Non-Lesion


title: AT3, Control, bio rep 3

description: Library name: AT3, Control, bio rep 3


title: Atopic dermatitis patient #9, Before treatment, Lesion

source_name: Atopic dermatitis patient, Before treatment, Lesion


title: KPsh,off-dox+sgPcyt2,rep2


title: Atopic dermatitis patient #7, After treatment, Lesion


title: Atopic dermatitis patient #10, Before treatment, Lesion


title: Mock-innoculated rice leaf sheath, 36 hpi, rep2

city: Lincoln

first: Richard

middle: A.

last: Wilson

state: NE

institute: University of Nebraska-Lincoln

description:
Library name: Sample 5
Raw sequencing data, adaptor sequence removed.

data_processing:
Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification.
Assembly: MG8: version 8 of the Magnaporthe oryzae (also known as Pyricularia oryzae) genome assembly.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism: Oryza sativa

source_name: Uninfected rice leaf epidermis cells.

extract_protocol:
Trizol extraction of total RNA from fungi/Mock-innoculated rice leaf sheath.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

value: Uninfected rice leaf epidermis cells.

value: Uninfected rice cells

value: Mock; WT rice

value: Mock-innoculated rice leaf sheath at 36 hpi

tag: batch


title: HUVEC, siRNA-NC (control), 96h, rep4

city: Kuopio

first: Nihay

last: Laham Karam

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: Library name: HUVEC-siNC-96-4

data_processing:
RNA-seq
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM counts

source_name: HUVEC

growth_protocol: HUVECs were maintained in endothelial cell growth medium (ECGM; PromoCell) with the provided SupplementMix (PromoCell) as well as 30 µg/ml gentamicin and 15 ng/ml amphotericin B antibiotic (Lonza). The plates used for culturing HUVECs were coated with a solution of 10 µg/ml fibronectin (Corning) and 0.05 % gelatin (Sigma Aldrich) in PBS at 37 °C for at least 5 min, before removing the solution and plating the cells. Cells were cultured at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Kit according to the manufacturer's instructions. 5000 ng of RNA was DNase-treated using the TURBO DNA-free kit (Invitrogen) in a total reaction volume of 25 µl.
Library preparation was performed at Azenta Life Sciences using poly-A selection

treatment_protocol: HUVECs were transfected with siRNA using dicer-substrate oligonucleotides hs.Ri.ADAMTS18.13.1, hs.Ri.ADAMTS18.13.2, hs.Ri.ADAMTS18.13.3 (respectively, #510826292, #510826295 and #510826298) and DsiRNA control (TriEFCTA Kit DsiRNA Duples; IDTDNA) at a concentration of 10nM using Oligofectamine (Thermo Fisher Scientific, #12252011). HUVECs were collected 24 or 96 hours after transfection for RNA isolation.

value: HUVEC

value: endothelial cell

value: WT

value: siRNA-control transfection


title: Atopic dermatitis patient #7, Before treatment, Non-Lesion


title: KPsh,off-dox+sgPcyt2,rep1


title: Mock-innoculated rice leaf sheath, 36 hpi, rep3

description:
Library name: Sample 6
Raw sequencing data, adaptor sequence removed.


title: Magnaporthe oryze-infected rice leaf sheath, 36 hpi, rep3

description:
Library name: Sample 3
Raw sequencing data, adaptor sequence removed.

source_name: Fungi growing in rice leaf epidermi cells.

value: Guy11; CO39

value: Invasive hyphae in rice cells

value: WT M. oryzae; WT rice

value: Fungi-infected rice leaf sheath at 36 hpi


title: Mock-innoculated rice leaf sheath, 36 hpi, rep1

description:
Library name: Sample 4
Raw sequencing data, adaptor sequence removed.


title: AT3, Dox treated, bio rep 1

description: Library name: AT3, Dox treated, bio rep 1

extract_protocol:
RNA was extracted using Quiagen Rneasy plus mini Kit.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: TNBC cell lines

value: Cancer


title: KPsh,on-dox+sgPcyt2,rep2

value: pancreas

value: KPsh


title: KPsh,on-dox+sgPcyt2,rep1

value: PDAC cell line


title: HUVEC, siRNA-NC (control), 96h, rep3

description: Library name: HUVEC-siNC-96-3


title: HUVEC, siRNA-NC (control), 96h, rep2

description: Library name: HUVEC-siNC-96-2


title: KPsh,on-dox,rep3

value: on-dox


title: Atopic dermatitis patient #7, Before treatment, Lesion

value: Skin


title: Atopic dermatitis patient #5, After treatment, Non-Lesion


title: Magnaporthe oryze-infected rice leaf sheath, 36 hpi, rep2

description:
Library name: Sample 2
Raw sequencing data, adaptor sequence removed.

value: Fungi growing in rice leaf epidermi cells.


title: AT3, Control, bio rep 1

description: Library name: AT3, Control, bio rep 1


title: KPsh,on-dox,rep2


title: HUVEC, siRNA-NC (control), 96h, rep1

description: Library name: HUVEC-siNC-96-1


title: HUVEC, siRNA-NC (control), 24h, rep4

description: Library name: HUVEC-siNC-24-4


title: Atopic dermatitis patient #5, After treatment, Lesion


title: Atopic dermatitis patient #5, Before treatment, Non-Lesion


title: KPsh,on-dox,rep1


title: imb_keller_2021_03_23_pCK574_Rep4

description:
Library name: Sample 23
emptyR4

data_processing:
Reads were trimmed with cudadapt (1.18) to remove adapter sequences
Reads were mapped to the ribosomal RNA sequences extracted from ensembl AgamP4 genome using the Ensembl AgamP4 annotation (release 48) with STAR (v. 2.7.3a) with the following parameters: outFilterMultimapNmax 1000000 outFilterMismatchNoverLmax 0.04 outFilterMismatchNmax 999. Unmapped reads are used in downstream processing.
Reads were mapped to the ensembl AgamP4 genome together with AcMNVP (L22858.1) genome, EGFP, and Blasticidin resistance gene sequences using the Ensembl AgamP4 annotation (release 48) together with lncRNA annotation from 10.1186/s12864-015-1507-3 with STAR  (v. 2.7.3a) using the following parameters: outFilterMismatchNoverLmax 0.04 outFilterMismatchNmax 999. Only uniquely mapped reads were used for downstream analysis
Coverage signal tracks (bigWigs) of primary alignments generated using Samtools (v1.9) and DeepTools (v3.1.0)
Primary alignments were assigned to features using subread featureCounts 1.6.5 with the AgamP4 annotation (release 48) combined with lncRNA annotation 10.1186/s12864-015-1507-3 as a reference.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Supplementary files format and content: featureCounts count matrix as tab-delimited .txt file

extract_protocol:
RNA was extracted using Trizol  (Fisher Scientific, Cat. No.15-596-026) and the Direct-zol RNA MicroPrep Kit (Zymo Research, Cat. No. R2062).
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (June 2020) (Document # 1000000124518 v00).

treatment_protocol: 0.75 Mio. cells were seeded per each well of a 24-well plate. After 16 hours, 200 μl of baculovirus in Sf-900 media was added. After 6 hours the media was changed to fresh L15. Cells were collected for extraction after 48h from the addition of the baculovirus.

value: Ag55 cell line

value: empty control (HA-tagged)


title: KPsh,off-dox,rep3

value: off-dox


title: Atopic dermatitis patient #5, Before treatment, Lesion


title: imb_keller_2021_03_20_pCK551_Rep4

description:
Library name: Sample 20
YobR4

value: Yob, HA-tagged


title: HUVEC, siRNA-NC (control), 24h, rep3

description: Library name: HUVEC-siNC-24-3

value: HUVEC

value: endothelial cell

value: WT

value: siRNA-control transfection


title: Atopic dermatitis patient #2, After treatment, Non-Lesion


title: HUVEC, siRNA-NC (control), 24h, rep2

description: Library name: HUVEC-siNC-24-2


title: HUVEC, siRNA-NC (control), 24h, rep1

description: Library name: HUVEC-siNC-24-1


title: imb_keller_2021_03_19_uninfected_Rep4

description:
Library name: Sample 19
uninfectedR4


title: KPsh,off-dox,rep1


title: imb_keller_2021_03_17_pCK574_Rep3

description:
Library name: Sample 17
emptyR3


title: Atopic dermatitis patient #2, After treatment, Lesion


title: HUVEC, siRNA-ADMATS18-3, 96h, rep4

description: Library name: HUVEC-siAD18-3-96-4

value: siRNA-ADAMTS18 transfection


title: imb_keller_2021_03_14_pCK551_Rep3

description:
Library name: Sample 14
YobR3


title: KPnull,TAD12m,rep2

value: KPnull


title: Atopic dermatitis patient #2, Before treatment, Non-Lesion


title: Magnaporthe oryze-infected rice leaf sheath, 36 hpi, rep1

description:
Library name: Sample 1
Raw sequencing data, adaptor sequence removed.

value: Guy11; CO39

value: Invasive hyphae in rice cells

value: WT M. oryzae; WT rice

value: Fungi-infected rice leaf sheath at 36 hpi


title: HUVEC, siRNA-ADMATS18-3, 96h, rep3

description: Library name: HUVEC-siAD18-3-96-3


title: Atopic dermatitis patient #2, Before treatment, Lesion


title: KPnull,TAD12m,rep1

value: pancreas

value: PDAC cell line


title: imb_keller_2021_03_13_exp1_uninfected_Rep3

description:
Library name: Sample 13
uninfectedR3


title: imb_keller_2021_03_11_pCK574_Rep2

description:
Library name: Sample 11
emptyR2


title: Atopic dermatitis patient #1, After treatment, Non-Lesion

value: Skin


title: KPnull,TAD2m,rep2


title: HUVEC, siRNA-ADMATS18-3, 96h, rep2

description: Library name: HUVEC-siAD18-3-96-2


title: HUVEC, siRNA-ADMATS18-2, 96h, rep4

description: Library name: HUVEC-siAD18-2-96-4


title: imb_keller_2021_03_08_pCK551_Rep2

description:
Library name: Sample 8
YobR2

value: Ag55 cell line


title: Atopic dermatitis patient #1, Before treatment, Non-Lesion


title: HUVEC, siRNA-ADMATS18-3, 96h, rep1

description: Library name: HUVEC-siAD18-3-96-1


title: KPnull,TAD2m,rep1


title: HUVEC, siRNA-ADMATS18-2, 96h, rep3

description: Library name: HUVEC-siAD18-2-96-3


title: Atopic dermatitis patient #1, After treatment, Lesion


title: imb_keller_2021_03_07_uninfected_Rep2

description:
Library name: Sample 7
uninfectedR2


title: KPnull,TAD1m,rep2


title: KPsh,off-dox,rep2

value: KPsh


title: HUVEC, siRNA-ADMATS18-2, 96h, rep2

description: Library name: HUVEC-siAD18-2-96-2


title: LX-2 cells, PRP-SLC27A2, TGFb1, EVT0185, biol rep 3

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

department: Medicine

institute: McMaster University

description: Library name: A2 EVT0185 3

data_processing:
Raw sequencing files imported into Galaxy (usegalaxy.org) for quality control and processing steps
FastQC tool used to check read quality
Cutadapt tool used to trim adaptor sequences and low quality reads
Remaining reads were mapped reference genome with HISAT2 tool. Cell data was mapped to the hg38 reference human genome.
Counts were quantified with the featureCounts tool and imported into R for DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes featureCounts (from Galaxy) for each sample used for DESeq2 analysis

source_name: HSC immortalized cells

extract_protocol:
Cells treated with vehicle of TGFβ1 plus DMSO or 30 µM EVT0185 for 24 hours, were lysed in TRIzol reagent and cell fractions were separated using chloroform. After centrifuging, the supernatant (aqueous phase) was applied to the RNeasy kit (Qiagen, 74106) for subsequent total RNA extraction and purification according to the manufacturer’s protocol.
For both cells and liver tissue, RNA-Sequencing RNA sample quality was first assessed using Agilent 2100 Bioanalyzer G2938C with the Aligent RNA6000 Nano Kit (Agilent; Santa Clara, CA, USA). Next, the NEBNext Poly(A) mRNA Isolation Module (NEB, Ipswich, MA, USA) was used for mRNA enrichment, followed by NEBNext® Ultra™ II Directional RNA library kit (NEB, Ipswich, MA, USA) library preparation. Cell libraries were sequenced on an Illumina NextSeq 2000 machine (P2, 2x50 bp).

value: HSC immortalized cells

value: hepatic stellate cells

tag: plasmid condition

value: 400 ng PRP-SLC27A2

tag: tgfb1 dose

value: 2.5 ng/mL

tag: treatment dose

tag: treatment time

value: 24 hours


title: imb_keller_2021_03_05_pCK574_Rep1

description:
Library name: Sample 5
emptyR1

tag: cell line

value: empty control (HA-tagged)


title: KPnull,TAD1m,rep1


title: Atopic dermatitis patient #1, Before treatment, Lesion


title: imb_keller_2021_03_01_uninfected_Rep1

description:
Library name: Sample 1
uninfectedR1


title: KPnull,WT,rep2


title: imb_keller_2021_03_02_pCK551_Rep1

description:
Library name: Sample 2
YobR1

value: Yob, HA-tagged


title: LX-2 cells, PRP-SLC27A2, TGFb1, EVT0185, biol rep 2

description: Library name: A2 EVT0185 2


title: KPnull,WT,rep1

value: KPnull


title: HUVEC, siRNA-ADMATS18-2, 96h, rep1

description: Library name: HUVEC-siAD18-2-96-1

value: HUVEC

value: endothelial cell

tag: genotype

value: WT

value: siRNA-ADAMTS18 transfection


title: HUVEC, siRNA-ADMATS18-1, 96h, rep4

description: Library name: HUVEC-siAD18-1-96-4

tag: treatment


title: LX-2 cells, PRP-SLC27A2, TGFb1, DMSO, biol rep 3

description: Library name: A2 DMSO 3

tag: tissue

value: DMSO


title: Kpnull,WT-p53,p53,ChIP

data_processing:
Reads were aligned to mouse assembly mm10 using bowtie2  with default parameters.
Duplicate reads were removed using samtools
Peaks in the ChIP-seq data were identified using MACS2
Reads over these peaks were quantified using Bedtools
Bigwig files of ChIP-Seq data were generated using Deeptools
Assembly: mm10
Supplementary files format and content: BigWig

growth_protocol: KPnull cells (p53-ON system cells) were cultured in complete DMEM supplemented with 10% FBS on collagen-coated plates and 1 μg/ml doxycycline was administered 48 hours prior to harvest.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. After quenching and cell lysis, samples were processed for sonication by sequential resuspension with the following buffers: cold Lysis Buffer 1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× protease inhibitors) for 10 min at 4°C, cold Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitors) for 10 min at room temperature, and finally, Sonication Buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.5% SDS).
ChIP-Seq libraries and sequencing was performed by the Memorial Sloan Kettering Cancer Center Integrated Genomics Operation.

value: pancreas

tag: cell type

value: PDAC cell line

value: p53 (1C12) antibody (Cell Signaling Technology)


title: Kpnull,vector,p53,ChIP

value: vector


title: LX-2 cells, PRP-SLC27A2, TGFb1, DMSO, biol rep 1

description: Library name: A2 DMSO 1

value: HSC immortalized cells


title: WT Hnrnph2 ASO 3 weeks replicate 3 (3362925_AKR91_3)

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Library name: 3362925_AKR91_3

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Paired-end reads were mapped by STAR(v2.7.1a)
Read duplication was marked with MarkDuplicates from GATK (v4.0.4.0)
RSEM was used to quantify read counts per gene
Assembly: mm10
Supplementary files format and content: gene-based TPM txt file for all 35 samples

organism: Mus

extract_protocol:
Cortex was dissected, flash frozen and stored at - 80 degrees. Frozen samples were treated with RNAlater-ICE (Thermo Fisher Scientific, AM7030), and total RNA was extracted with Qiagen’s RNeasy Universal plus mini kit (73404, Qiagen).
A sequencing library was prepared with a TruSeq Stranded Total RNA Kit (Illumina).

value: brain

tag: treament

value: Hnrnph2 ASO

tag: strain

value: Male

tag: age

value: 3 weeks


title: KPnull,vector,rep2


title: R206W Hnrnph2 ASO 3 weeks replicate 2 (3362927_AKR89_3)

description: Library name: 3362927_AKR89_3

tag: Sex


title: LX-2 cells, PRP-SLC27A2, TGFb1, EVT0185, biol rep 1

description: Library name: A2 EVT0185 1

value: hepatic stellate cells

value: 400 ng PRP-SLC27A2

value: 2.5 ng/mL

value: 24 hours


title: R206W Hnrnph2 ASO 3 weeks replicate 3 (3362928_AKR91_6)

description: Library name: 3362928_AKR91_6


title: HUVEC, siRNA-ADMATS18-3, 24h, rep4

description: Library name: HUVEC-siAD18-3-24-4

value: HUVEC

value: endothelial cell

tag: time


title: LX-2 cells, PRP-SLC27A2, TGFb1, DMSO, biol rep 2

description: Library name: A2 DMSO 2


title: KPnull,vector,rep1

value: KPnull


title: HUVEC, siRNA-ADMATS18-1, 96h, rep2

description: Library name: HUVEC-siAD18-1-96-2

value: WT

value: siRNA-ADAMTS18 transfection


title: HUVEC, siRNA-ADMATS18-1, 96h, rep3

description: Library name: HUVEC-siAD18-1-96-3


title: Ntn1fl/fl and ap2-cre mice WAT-2

city: guangzhou

first: shi

last: hang

address: 58 Zhongshan Second Road, Yuexiu District, Guangzhou City, Guangdong Province

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool
The clean reads obtained were then aligned to the mm10 mouse genome using HISAT2
Assembly: mm10
Supplementary files format and content: processed data.xlsx reprots FPKMs for all samples

source_name: white adipose tissue

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry. High-quality RNA  with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing.
Illumina library construction was performed according to the manufacturer's instructions (Illumina,USA). Oligo-dT primers are used to transverse mRNA to obtain cDNA(APExBIO, Cat. No. K1071). Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA). After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads.

value: white adipose tissue

value: Ntn1 ako

value: high fat feeding


title: HUVEC, siRNA-ADMATS18-1, 96h, rep1

description: Library name: HUVEC-siAD18-1-96-1


title: HUVEC, siRNA-ADMATS18-3, 24h, rep3

description: Library name: HUVEC-siAD18-3-24-3


title: HUVEC, siRNA-ADMATS18-3, 24h, rep2

description: Library name: HUVEC-siAD18-3-24-2


title: R206W Control ASO 3 weeks replicate 3 (3362922_AKR94_1)

description: Library name: 3362922_AKR94_1

value: Control ASO


title: LX-2 cells, PRP-empty, TGFb1, EVT0185, biol rep 1

description: Library name: Empty EVT0185 1

value: HSC immortalized cells

value: 400 ng PRP-empty


title: Wild type mice WAT-2, high fat feeding


title: LX-2 cells, PRP-empty, TGFb1, EVT0185, biol rep 3

description: Library name: Empty EVT0185 3


title: WT Hnrnph2 ASO 3 weeks replicate 2 (3362924_AKR89_5)

description: Library name: 3362924_AKR89_5

value: brain

value: Hnrnph2 ASO

value: Male


title: Wild type mice WAT-1, high fat feeding


title: R206W Control ASO 3 weeks replicate 2 (3362921_AKR90_3)

description: Library name: 3362921_AKR90_3

value: 3 weeks


title: LX-2 cells, PRP-empty, TGFb1, EVT0185, biol rep 2

description: Library name: Empty EVT0185 2

value: hepatic stellate cells

value: 2.5 ng/mL


title: HUVEC, siRNA-ADMATS18-3, 24h, rep1

description: Library name: HUVEC-siAD18-3-24-1

value: HUVEC


title: LX-2 cells, PRP-empty, TGFb1, DMSO, biol rep 3

description: Library name: Empty DMSO 3

value: DMSO

value: 24 hours


title: WT Hnrnph2 ASO 3 weeks replicate 1 (3362923_AKR89_2)

description: Library name: 3362923_AKR89_2

value: WT


title: HUVEC, siRNA-ADMATS18-2, 24h, rep4

description: Library name: HUVEC-siAD18-2-24-4

value: endothelial cell

value: siRNA-ADAMTS18 transfection


title: R206W Hnrnph2 ASO 3 weeks replicate 1 (3362926_AKR89_1)

description: Library name: 3362926_AKR89_1


title: R206W Control ASO 3 weeks replicate 1 (3362920_AKR90_1)

description: Library name: 3362920_AKR90_1


title: Input

data_processing:
Reads of the samples were trimmed for adapters using Cutadapt before alignment
Trimmed sequence reads were mapped to the reference genome (mm10) using Bowtie2
Peaks were called using Sicer and MACS2
ChIP-seq heatmap and plot profiles were generated using deeptool2 software
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Chromatin was prepared using ChIP-IT Express Enzymatic kit (Active Motif). Cells were fixed with 1% formaldehyde for appropriate time (5 minutes for H3K27ac, H3K27me3, H4K20ac and p300; 10 minutes for Nat10, Brd4-pan, Brd4-SF-V5 tag, Rrp1b endogenous, Rrp1b-HA tag and Sipa1). After lysis, chromatin was sheared using enzymatic digestion cocktail for 10 minutes.
Library was generated using SWIFT Accel-NGS 2s Plus DNA library prep kit according to manufacturer's instruction

value: Mouse mammary tumor cells

tag: chip antibody


title: LX-2 cells, PRP-empty, TGFb1, DMSO, biol rep 2

description: Library name: Empty DMSO 2


title: Sipa1

value: Sipa1 (Abcam, #ab189929)


title: Rrp1b-HA tagged


title: HUVEC, siRNA-ADMATS18-2, 24h, rep3

description: Library name: HUVEC-siAD18-2-24-3


title: WT Control ASO 3 weeks replicate 3 (3362919_AKR90_6)

description: Library name: 3362919_AKR90_6

value: Control ASO


title: LX-2 cells, PRP-empty, TGFb1, DMSO, biol rep 1

description: Library name: Empty DMSO 1

value: HSC immortalized cells


title: WT Control ASO 3 weeks replicate 2 (3362918_AKR90_4)

description: Library name: 3362918_AKR90_4


title: HUVEC, siRNA-ADMATS18-2, 24h, rep1

description: Library name: HUVEC-siAD18-2-24-1


title: BEAS-2B, Input for H3K4me1 and H3K27Ac

city: Stony Brook

first: Fei

last: Chen

address: 101 Nicolls Road, MART 8M-0501

institute: Stony Brook University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

growth_protocol: The human bronchial epithelial cell line BEAS-2B, obtained from the American Type Culture Collection (ATCC, Manassas, VA), was cultured at 37℃ in a humidified atmosphere with 5% CO2. The cells were grown in DMEM (Gibco, cat#11965092) supplemented with 5% fetal bovine serum (R&D Systems, cat#S11150), 1% penicillin-streptomycin (Gibco, cat#15140122), and 1% L-glutamine (Gibco, cat#25030081). The medium was refreshed every other day, and cells were passaged weekly.

extract_protocol:
Cells were fixed for 15 min at 25 °C with 4% formaldehyde, and the reaction was halted by adding 125 mM glycine for 5 min at room temperature. Fixed cells were washed with PBS, scraped from the culture surface, and chromatin was isolated using lysis buffer and disrupted with a Dounce homogenizer. The lysates were sonicated to shear DNA to an average length of 300–500 bp. Genomic DNA (Input) was prepared by treating chromatin with RNase and proteinase K, followed by heating for de-crosslinking and ethanol precipitation. The DNA was quantified using a NanoDrop spectrophotometer (Thermo Scientific) and the total chromatin yield was extrapolated. A 30 μg aliquot of chromatin was precleared with protein A agarose beads (Invitrogen).
ChIP was performed using 4 μg of antibodies against H3K4me1 (Thermofisher, cat#710795), H3K4me3 (Thermofisher, cat# 711958), H3K9me3 (CST, cat#4658), H3K27ac (CST, cat#8173), and KLF4 (R&D Systems, cat#AF3640). Complexes were washed, eluted with SDS buffer, treated with RNase and proteinase K, and crosslinks were reversed by overnight incubation at 65°C. ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared through end-polishing, dA-addition, and adapter ligation, followed by PCR amplification. Sequencing was performed using Illumina NextSeq 500, and 75-nt reads were aligned to the GRCh38/hg38 genome using the Burrows-Wheeler Aligner (BWA) with default settings.

treatment_protocol: BEAS-2B cells, with or without Nrf2 knockout, were treated with or without 1 μM As³⁺ for 6 hours, followed by ChIP-seq analysis.

value: normal human bronchial epithelial cells

value: Normal

value: Control


title: Rrp1b endogenous

city: Bethesda

first: Maxwell

institute: National Cancer Institute, NIH

value: Rrp1b (Millipore-Sigma, #HPA020324)


title: BEAS-2B, Input for KLF4


title: WT Control ASO 3 weeks replicate 1 (3362917_AKR90_2)

description: Library name: 3362917_AKR90_2

value: brain

value: Male

value: 3 weeks


title: Ntn1fl/fl and ap2-cre mice WAT-1

value: white adipose tissue

value: Ntn1 ako

value: high fat feeding


title: Brd4-pan


title: Brd4 short isoform-V5 tagged


title: HUVEC, siRNA-ADMATS18-1, 24h, rep3

description: Library name: HUVEC-siAD18-1-24-3

value: HUVEC

value: WT


title: P209L Hnrnph2 ASO 3 weeks replicate 2 (3341197_AK086_3)

description: Library name: 3341197_AK086_3

value: Hnrnph2 ASO


title: HUVEC, siRNA-ADMATS18-1, 24h, rep4

description: Library name: HUVEC-siAD18-1-24-4

value: endothelial cell

value: siRNA-ADAMTS18 transfection


title: BEAS-2B, 1 μM As³⁺ for 6 hours, H3K27Ac, ChIP

value: 1 μM As³⁺ for 6 hours


title: BEAS-2B, control, H3K27Ac, ChIP


title: P209L Hnrnph2 ASO 3 weeks replicate 1 (3341195_AK063_6)

description: Library name: 3341195_AK063_6


title: WT Hnrnph2 ASO 3 weeks replicate 3 (3341194_AK063_5)

description: Library name: 3341194_AK063_5


title: HUVEC, siRNA-ADMATS18-1, 24h, rep2

description: Library name: HUVEC-siAD18-1-24-2


title: HUVEC, siRNA-ADMATS18-1, 24h, rep1

description: Library name: HUVEC-siAD18-1-24-1


title: Nat10

value: Mouse mammary tumor cells


title: WT Hnrnph2 ASO 3 weeks replicate 2 (3341193_AK060_5)

description: Library name: 3341193_AK060_5


title: Input_KO biol rep2


title: WT Hnrnph2 ASO 3 weeks replicate 1 (3341192_AK053_5)

description: Library name: 3341192_AK053_5


title: Input_KO biol rep1


title: HUVEC, siRNA-ADMATS18-2, 24h, rep2

description: Library name: HUVEC-siAD18-2-24-2


title: BEAS-2B, control, KLF4, ChIP

value: normal human bronchial epithelial cells


title: HUVEC, LV-GFP, 4

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Assembly: human GRCh38/hg38
Supplementary files format and content: tab delimited text files contain raw counts for each sample

growth_protocol: HUVECs at early passage were maintained in Endothelial Cell Growth Medium (PromoCell) supplemented with Endothelial Cell Growth Medium SupplementMix (PromoCell) with gentamicin (250 ng/mL)and amphotericin (10 ug/mL)   in cell culture flasks coated with 10 µg/ml fibronectin (Corning) and 0.05% gelatine (Sigma).

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Kit according to the manufacturer's instructions.
Library preparation was performed at Azenta Life Sciences using poly-A selection

treatment_protocol: HUVEC were either transfected with siRNA and cultured for 2 days or transduced with LV and cultured for 3 days.

value: endothelial cells

value: LV-GFP transduction

value: 3 days


title: P209L Control ASO 3 weeks replicate 3 (3341191_AK084_6)

description: Library name: 3341191_AK084_6

value: brain

value: Control ASO


title: HUVEC, LV-GFP, 3


title: Input_WT biol rep2


title: BEAS-2B, 1 μM As³⁺ for 6 hours, KLF4, ChIP

value: Normal


title: HUVEC, LV-GFP, 2


title: P209L Control ASO 3 weeks replicate 2 (3341190_AK083_1)

description: Library name: 3341190_AK083_1

value: Male

value: 3 weeks


title: BEAS-2B with Nrf2 knockout, 1 μM As³⁺ for 6 hours, H3K27Ac, ChIP

value: Nrf2 Knockout


title: BEAS-2B with Nrf2 knockout, control, KLF4, ChIP

value: Control


title: HUVEC, LV-GFP, 1

value: HUVEC


title: P209L Control ASO 3 weeks replicate 1 (3341189_AK058_10)

description: Library name: 3341189_AK058_10


title: HUVEC, LV-ADAMTS18, 4

value: LV-ADAMTS18 transduction


title: BEAS-2B with Nrf2 knockout, 1 μM As³⁺ for 6 hours, KLF4, ChIP


title: WT Control ASO 3 weeks replicate 3 (3341188_AK083_6)

description: Library name: 3341188_AK083_6

value: WT


title: H3K27me3_KO biol rep1


title: BEAS-2B with Nrf2 knockout, control, H3K27Ac, ChIP


title: WT Control ASO 3 weeks replicate 2 (3341187_AK073_10)

description: Library name: 3341187_AK073_10


title: H3K27me3_WT biol rep2


title: BEAS-2B, 1 μM As³⁺ for 6 hours, H3K4me1, ChIP


title: HUVEC, LV-ADAMTS18, 2


title: WT Control ASO 3 weeks replicate 1 (3341186_AK059_1)

description: Library name: 3341186_AK059_1


title: H3K27me3_WT biol rep1


title: HUVEC, LV-ADAMTS18, 3


title: BEAS-2B, control, H3K4me1, ChIP


title: HUVEC, LV-ADAMTS18, 1


title: H4K20ac_KO biol rep2

value: H4K20ac (Millipore-Sigma, #SAB5600021)


title: P209L Hnrnph2 ASO 8 weeks replicate 3 (3341185_TCF3171)

description: Library name: 3341185_TCF3171

value: Hnrnph2 ASO

value: 8 weeks


title: Input_WT biol rep1

value: Mouse mammary tumor cells


title: BEAS-2B with Nrf2 knockout, 1 μM As³⁺ for 6 hours, H3K4me1, ChIP

value: normal human bronchial epithelial cells

value: 1 μM As³⁺ for 6 hours


title: H4K20ac_KO biol rep1


title: P209L Hnrnph2 ASO 8 weeks replicate 2 (3341184_TCF3177)

description: Library name: 3341184_TCF3177


title: H4K20ac_WT biol rep2


title: HUVEC, siCTRL, 3

value: endothelial cells

value: siRNA-CTRL

value: 2 days