title: e17.5A: green dominant_newly generated-α cell_4


title: TL-20-20BC96

status: Public on Sep 15 2023

type: SRA

city: St Louis

first: Bhuvic

last: Patel

state: MO

address: 660 S. Euclid Ave

department: Neurosurgery

country: USA

institute: Washington University in St. Louis School of Medicine

library_source: transcriptomic

data_processing:
Libraries were sequenced to obtain at least 50 million reads on an Illumina HiSeq 4000 System.
RNA-seq reads were aligned to the GRCh38 assembly with STAR version 2.7.2b (Parameters:--genomeDir Ensembl_GRCh38.fa --genomeLoad NoSharedMemory --outSAMmapqUnique 60 --outSAMunmapped Within KeepPairs --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif --runThreadN 8 --outStd BAM_Unsorted --outSAMtype BAM Unsorted --alignTranscriptsPerReadNmax 100000 --outFilterMismatchNoverLmax 0.1 --sjdbGTFfile Ensembl_GRCh38_genes.gtf > genome_accepted_hits.bam).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Picard version 2.6.0.
All gene counts were imported into the R (3.2.3). Bioconductor (3.2) package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: GRCh38
Supplementary files format and content: A single tab-delimited text file including non-normalized transcript counts for all samples. Column names correspond to sample names and rows correspond to genes.

molecule: total RNA

organism: Homo sapiens

source_name: sporadic vestibular schwannoma

extract_protocol:
RNA extraction was performed by Tempus, Inc. as per their protocol detailed here: https://doi.org/10.18632%2Foncotarget.25381. Briefly, FFPE tissue was digested with proteinase K and total nucleic extracted using a Chemagic360 instrument. RNA was isolated using DNAse digestion followed by magnetic bead purification.
RNA library creation was performed by Tempus, Inc. as per their protocol detailed here: https://doi.org/10.18632%2Foncotarget.25381. Briefly, RNA was fragmented with heat and cDNA amplified using random primers. Next, A-tailing, adapter ligation, bead-based cleanup, and library amplification was performed. Samples were then hybridized with the IDT xGEN Exome Research Panel and recovered using Streptavidin-coated beads, followed by amplification using the KAPA HiFi Library Amplification Kit.

tag: tissue

value: sporadic vestibular schwannoma


title: 2023013_CGATAC131_HCC4006_Rep1

city: Boston

first: Cigall

last: Kadoch

state: MA

address: 44 Binney St

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation. For ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively. For Cut & Run libraries, the CutRunTools pipeline was used to perform read trimming, quality filtering, alignment, and peak calling using default parameters.
For Cut&Run and ATACseq data, tracks were generated using deepTools bamCoverage (--normalizeUsing CPM -bs 50 --smoothLength 600 --ignoreDuplicates --samFlagInclude 64). For RNAseq data, tracks were generated using deepTools bamCoverage (--normalizeUsingRPKM).
Assembly: hg19
Supplementary files format and content: Cut&Run and ATACseq bigWig files give the normalized coverage of DNA fragments across the genome in RPM, and gene count tables give raw RNA read counts mapped to exons of given genes. RNAseq bigWig files give the give the normalized coverage of DNA fragments across the genome in RPKM.

molecule: genomic DNA

source_name: cancer cell line

growth_protocol: PC-9, PC-9_OR, HCC4006, HCC4006_OR, HCC827, and HCC827GR6 were maintained in RMPI-1640 (Gibco) supplemented with 10% fetal bovine serum (GeminiBio) and 1% penicillin-streptomycin (Gibco). PC-9_OR and HCC4006_OR cell lines were generated by continuously culturing the respective parental cell lines in 100 nM osimertinib for at least 2 months before being characterized. Unless stated otherwise, OR lines were maintained in 100 nM osimertinib and the drug was removed for 1 week before use in Cmp14 experiments.

extract_protocol:
ATAC-Seq: The Omni-ATAC protocol (Corces et al., 2017) was used with slight modifications as follows. 100,000 cells per condition were used and washed with PBS before lysis. Cell pellets were lysed in 50μl of cold ATAC-seq resuspension buffer containing 10mM Tris–HCl pH 7.4, 10mM NaCl and 3mM MgCl2, supplemented with fresh NP-40 (final 0.1% v/v), Tween-20 (final 0.1% v/v) and digitonin (final 0.01% v/v) for 3–5min on ice. Next cells were washed with 1ml of resuspension buffer supplemented with Tween-20 (final 0.1% v/v) and pelleted at 500g for 10min at 4 °C. Cell pellets were resuspended in 50μl of transposition reaction mix containing 25μl of 2× TD buffer, 2.5μl of transposase, 16.5μl of 1× PBS, 0.5μl of 1% digitonin (final 0.01% v/v), 0.5μl of 10% Tween-20 (final 0.1% v/v) and 5μl of nuclease-free water. The transposition reaction was incubated at 37 °C for 30min with constant shaking on a thermomixer. The Qiagen MinElute Reaction Cleanup Kit was used for DNA purification. A standard ATAC-seq amplification protocol with 5-7 cycles of amplification was used to amplify the tagmented library (Buenrostro et al., 2015).
RNA-Seq: One million cells were harvested from from PC9*, HCC4006 and HCC827* parental and osi- or gefitinib- resistant cell line pairs and washed with cold PBS to remove trypsin and stored in RLT buffer (Qiagen) until further processing. RNA was purified using the Qiagen RNeasy kit, and further processed using the Illumina NEBNext Ultra II Directional RNA Library Prep Kit.
CUT&RUN: 500,000 cells per sample were harvested from PC9*, HCC4006 and HCC827* parental and osi- or gefitinib- resistant cell line pairs. CUT&RUN was performed following EpiCypher’s protocol within their CUTANA ChIC/CUT&RUN kit with slight modifications to day 1. Prior to wash steps, cells were lysed using a nuclear extraction buffer 20mM HEPES–KOH, pH 7.9, 10mM KCl, 0.1% Triton X-100 and 20% glycerol, supplemented with fresh 0.5mM spermidine, and cOmplete Mini, EDTA-free protease inhibitor. Next, cells were pelleted at 500g for 3 mins. Cell pellets were then washed using protocol’s permeabilization buffer and subsequently incubated with activated Concanavalin A beads at room temperature for 15 mins. Next, beads were mixed in Antibody Buffer and incubated with appropriate primary antibodies overnight (antibodies in key resource table).
CUT&RUN libraries were prepared with Epicypher's CUTANA ChIC/CUT&RUN Library Prep Kit and sequenced on Illumina Next-seq 500 using 37 bp paired-end sequencing parameters.     ATAC-seq samples were sequenced on Illumina NovaSeq 6000 Next Gen Sequencing using 37 bp paired-end sequencing parameters.    RNA-seq libraries were prepared using NEBnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters.

treatment_protocol: PC9* and PC9-OR* cells were treated with DMSO, 1uM Compound 14 (Cmp14), 100nM Osimertinib (Osi) and 100nM Osimertinib + 30nM Trametinib (OT) for 24hrs before harvesting for ATAC-seq and RNA-seq. The PC9-OR* cells were washed to remove continuous Osimertinib growth media for 7 days prior to experimental setup and then re-challenged with Osi or OT as appropriate.

tag: cell line

tag: genotype

tag: antibody


title: mESCs_scGROseq_Exp260b_c16

city: Cambridge

first: Dig

middle: B

last: Mahat

email: mahat@mit.edu, dbm222@cornell.edu

address: Koch Institute, MIT, 500 Main St, Building 76, #417

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

description: Nascent RNA

data_processing:
Adaptor sequences were removed from paired-end fastq files using Cutadapt. Specifically, the Read 1 sequence CCCCTGTCTCTTATACACAT and the Read 2 sequence AGATCGGAAGAGCGTCGTGT were trimmed with a maximum error rate of 0.15, requiring a minimum overlap of 12 nucleotides between the read and adapter.
The resulting adapter-trimmed reads were subjected to demultiplexing using Flexbar. Cell barcodes and Unique Molecular Identifiers (UMIs) were extracted from the 5’ end of Read 1, applying a barcode error rate of 0.15 and retaining reads of at least 14 nucleotides in length.
The adapter-clipped and demultiplexed reads were first mapped to the mouse ribosomal genome using bowtie2 in --very-sensitive mode. The reads unmapped to the ribosomal genome were mapped to the mouse genome (mm10 build) also in --very-sensitive mode.
After mapping, duplicate reads were identified and removed utilizing UMI and mapping coordinates with UMI-tools.
Assembly: mm10
Supplementary files format and content: Quality filtered mapped reads in GRange format as R data object (for files with *_consolidated.rds)
Supplementary files format and content: Features X cells matrix as R data object (for files with *_mapq3qc_filtered_counts.rds)
Library strategy: scGRO-seq, inAGTuC, AGTuC

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: mESCs were cultured in Dulbecco’s Modified Eagle Medium plus 10% fetal bovine serum supplemented with 1x penicillin/streptomycin, 1x non-essential amino acids, 1x L-Glutamine, 1x β-mercaptoethanol, and 1000 U/ml leukemia inhibitory factor on tissue culture-treated 10 cm plates pre-coated with 0.2% gelatin prepared in phosphate-buffered saline. Cells were grown at 37°C and 5% CO2 and passed with Hepes buffered saline solution and 0.25% Trypsin-EDTA when 70% confluency was reached (every two days).

extract_protocol:
For nuclei isolation, the pellet was resuspended in ice-cold douncing buffer (10 mM Tris-Cl pH 7.4, 300 mM Sucrose, 3 mM CaCl2, 2 mM MgCl2, 0.1 % Triton X-100, 0.5 mM DTT, 0.1x Halt Protease inhibitor, and 0.02 U/ul RNase inhibitor) and transferred to a 7 ml dounce homogenizer. After incubation on ice for 5 minutes, the cells were dounced 25 times with a tight pestle, transferred back to the 15 ml conical tube, and centrifuged to pellet the nuclei. The pellet was washed twice in douncing buffer. For cell permeabilization, the pellet was resuspended in ice-cold permeabilization buffer (10 mM Tris-Cl pH 7.4, 300 mM Sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05 % Tween-20, 0.1% NP-40, 0.5 mM DTT, 0.1x Halt Protease inhibitor, and 0.02 U/ul RNase inhibitor). After incubation on ice for 5 minutes, the cells were centrifuged to pellet the nuclei. The pellet was washed twice in the permeabilization buffer.
A 96-well plate containing 5’-AzScBc DNA with a unique cell barcode in each well previously synthesized and aliquoted is thawed from -80°C. Sodium Ascorbate, PEG 8000, CuSO4, and accelerating ligand BTTAA was prepared and dispensed into each well of the 96-well plate containing 5’-AzScBc DNA. The CuAAC reaction mix was dispensed into individual wells containing single cells in Urea using a multi-channel pipette or a 96-well pipettor. The 96-well plates are sealed, vortexed for 10 seconds in an orbital vortexer, and centrifuged for 1 min at 500 g prior to incubation for 2 hours at 50°C. After completion of incubation, the CuAAC reaction was quenched with 5 mM EDTA and pooled from 96-wells into a single 1.5 ml eppendorf tube. PEG 8000 was removed with Trizol. Remaining CuAAC reagents (Sodium Ascorbate, CuSO4, and mM BTTAA) were removed with a centrifugal filter with 3 kDa cellulose membrane (Amicon, 2020-04). The purified RNA was fragmented with 10 mM ZnCl2 for 5 min at 65°C. Reverse transcription of the clicked RNA-DNA conjugate was performed Reverse Transcriptase lacking RNase H activity but capable of RNA-dependent and DNA-dependent polymerase activity, non-templated addition and template switching. RT reaction was incubated with RNA-DNA conjugate for 2 hours at 50°C. The cDNA was size-selected in 10% denaturing polyacrylamide gel electrophoresis (PAGE) away from the unclicked 5’-AzScBc DNA and empty cDNA formed between the 5’-AzScBc DNA and TSO. library was PCR amplified with Q5 High-Fidelity 2X Master Mix (NEB, M0492S) and 0.5 uM PCR primers with unique dual index using the two-step PCR cycles.

value: embryonic stem cells

tag: cell type


title: TL-20-029220


title: mESCs_scGROseq_Exp236_c08

description: Nascent RNA


title: e17.5A: green dominant_newly generated-α cell_2

city: Tokyo

first: MIWA

last: HIMURO

address: Hongo 2-1-1, Bunkyo-ku

department: Department of Metabolism and Endocrinology

country: Japan

institute: Juntendo University Graduate School of Medicine

data_processing:
gene_expression e17.5 GcgTimer.xlsx:
Genedata Profiler Genome v10.1.14b
Sequence reads were aligned and mapped to GRCm38/mm10 using STAR v2.5.2b and Genedata Profiler Genome.
Read count extraction and normalization were performed using Genedata Profiler Genome.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel files include TPM values and raw gene counts for each sample.
*********************
gene_expression e17.5 GcgTimer_IRES-EGFP-mRFP added.xlsx:
DRAGEN Bio-IT Platform (3.7.5).
Sequence reads were aligned and mapped to genome GRCm39 and sequence of EGFP, mRFP1 and IRES by using DRAGEN Bio-IT Platform.
Read count extraction and normalization were performed using DRAGEN Bio-IT Platform.
Assembly: GRCm39/mm39
Supplementary files format and content: Excel files include TPM values and raw gene counts for each sample.

source_name: pancreas

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: pancreas

value: Gcg-Timer

tag: time


title: 2023013_CGATAC130_PC9_OR_Rep2

value: EGFR E746-A750del


title: e17.5A: green dominant_newly generated-α cell_3


title: mESCs_scGROseq_Exp236_c07

description: Nascent RNA


title: mESCs_scGROseq_Exp236_c06

description: Nascent RNA


title: e17.5A: green dominant_newly generated-α cell_1


title: 2023013_CGATAC128_PC9_Rep2


title: TL-19-EF93E8


title: e17.5N: non-α cell_4


title: TL-20-9067F1


title: TL-19-B38331


title: OCI-AML3 cells, 50 nM omipalisib, 24h

city: Taipei

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

data_processing:
Sequencing was sequenced on Illumina NovaSeq 6000 platform.
Paired-end sequencing alignment toward hg19 and reads mapping to known genes (feature counts)were performed by Rsubread.
Differentially expressed genes (DEGs) identification between groups were conducted with EBSeq, with a threshold of fold change ≥ 2 or ≤ 0.5 and p-value of < 0.05.
Assembly: hg19 (GRCh37)
Supplementary files format and content: *csv: comma-separated values of row and normalized counts for each known gene (EntrezID, and HGNC symbol) in columns and sample in rows.

source_name: bone marrow

growth_protocol: Cancer cells were cultured in MEM α medium suppled with 20% FBS

extract_protocol:
Total RNAs were isolated with NucleoSpin® RNA kit (Macherey-Nagel); The final library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.
Strand-specific RNA library were built by TruSeq stranded protocols from Illumina

treatment_protocol: Cells were exposure for 24 h to 50 nM omipalisib (GSK2126458) or to the vehicle control (DMSO).

value: bone marrow

value: acute myeloid leukemia

value: WT

tag: treatment

value: 50 nM omipalisib


title: mESCs_scGROseq_Exp211_c17

description: Nascent RNA


title: mESCs_scGROseq_Exp211_c18

description: Nascent RNA


title: TL-19-A588A8


title: e17.5N: non-α cell_2


title: iKAP_DOX / KRAS WT, replicate 1

city: Houston

first: Wen-Hao

last: Hsu

address: 1901 East Rd

institute: MD Anderson

description:
10x Genomics
SC180_1

library_source: transcriptomic single cell

data_processing:
raw count matrices were converted to Seurat objects for further analysis. The quality of scRNA-seq data was measured by the percentage of mitochondrial genes (percent.mt) per cell and the number of unique molecular identifiers (UMI count). Low-quality cells with a UMI count less than 800, a percent.mt greater than 25%, and doublets expressing both cell type markers were removed. The batch effect was counteracted using the reciprocal PCA-based integration method in Seurat. Then we performed unsupervised dimension reduction and clustering for cell identification. The annotation of cell identities in each cluster was based on both the canonical marker genes and the cluster differential genes.
Assembly: mm10
Supplementary files format and content: comma-separated values files and matrix files

source_name: CRC, Distal colon

extract_protocol:
Three independent samples each from iKAP, iAP, and iKAP-DOXoff (KRAS*-off) CRC tumors were collected for tumor dissociation and single cell sequencing analyses. All tumors were collected in size of 1 cm3 at 2 months after TAM/DOX tumor induction following the procedure described above. For the iKAP-DOXoff (KRAS*-off) CRC tumors, Doxycycline was retrieved for 7 days after 7 weeks of TAM/DOX tumor induction.
Single-cell capture, barcoding and library preparation were performed by following the 10X Genomics Single-Cell Chromium 3′ (PN-120237) protocol using V3 chemistry reagents (10X Genomics). The final libraries containing barcoded single-cell transcriptomes were sequenced at 100 cycles on an S2 flowcell on the Novoseq 6000 system (Illumina). Data were processed using the CASAVA 1.8.1 pipeline (Illumina), and sequence reads were converted to FASTQ files and UMI read counts using the CellRanger software (10X Genomics).

value: CRC, Distal colon

tag: strain

tag: age

value: 6-8 weeks old


title: 2023013_CGATAC129_PC9_OR_Rep1


title: mESCs_scGROseq_Exp211_c12

description: Nascent RNA


title: 2023013_CGATAC132_HCC4006_Rep2


title: OCI-AML3 cells, DMSO, 24h

value: DMSO


title: e17.5N: non-α cell_1


title: TL-19-55694E


title: TL-19-5559ED


title: LSEC_siPLVAP_3

city: Berlin

first: Paul

last: Horn

address: Augustenburger Platz 1

department: Department of Hepatology and Gastroenterology

country: Germany

institute: Charité - Universitätsmedizin Berlin

data_processing:
Adapter trimming was performed by Source BioScience using bbduk (bbmap Version 38.89).
Transcript expression was quantified using the selective-alignment mapping algorithm implemented in Salmon (v1.5.2) (61) using a decoy-aware transcriptome index built from the reference genome GRCh38.p13 and the Gencode version 38 transcriptome. Salmon quantification was run with --validateMappings, --gcBias and --seqBias options and otherwise default settings
Assembly: Gencode38, GRCh38.p13
Supplementary files format and content: salmon quant output

molecule: polyA RNA

source_name: Liver

growth_protocol: Primary human liver sinusoidal endothelial cells from three different donors were maintained in Endothelial SFM (Thermo) supplemented with 10% human serum (TCS Bioscience) + 10 ng/ml VEGF (Peprotech) and 10 ng/ml HGF (Peprotech).

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen). 600 ng of total RNA was used for the construction of sequencing libraries.
Illumina Stranded mRNA Prep (Source Bioscience)

treatment_protocol: LSEC were treated with 3.125 nM PLVAP siRNA or siRNA Negative Control for 4 hours and antibiotic- and growth factor-free culture medium and incubated for 48 hours

value: Liver

value: Liver sinusoidal endothelial cell

value: PLVAP knockdown

tag: transfection

value: siPLVAP transfection


title: mESCs_scGROseq_Exp236_c05

description: Nascent RNA


title: mESCs_scGROseq_Exp211_c08

description: Nascent RNA


title: TL-19-512ADD


title: mESCs_scGROseq_Exp211_c10

description: Nascent RNA


title: LSEC_siControl_3

value: siControl transfection


title: Utx_WT_1

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
10x Genomics
SLX18582_SIGAF7

data_processing:
Barcode processing, mapping and gene counting were performed using the Cell Ranger pipeline v6.0.1
Assembly: mm10
Supplementary files format and content: h5 file

extract_protocol:
Mouse bone marrow cells were collected from the femurs, tibiae and iliac crest and depleted of red blood cells by an ammonium chloride lysis step (STEMCELL Technologies). The cells were stained with the fluorophore-conjugated monoclonal antibodies and lineage− c-Kit+ (LK) cells were then isolated using an LSRII Fortessa (BD).
Single-cell sequencing libraries were generated using 10x Chromium (10x Genomics, Pleasanton, CA) reagent kit v2 according to the manufacturer’s protocol.

value: LK

tag: Sex

value: F

value: 16 weeks

value: pIpC


title: 2023013_CGATAC127_PC9_Rep1

value: EGFR E746-A750del


title: Utx_KO_2

description:
10x Genomics
SLX18582_SIGAA8

value: bone marrow

value: UTX KO


title: e17.5N: non-α cell_3

value: pancreas

value: Gcg-Timer


title: mESCs_scGROseq_Exp208_c01

description: Nascent RNA

value: embryonic stem cells


title: Utx_KO_1

description:
10x Genomics
SLX18582_SIGAG7


title: mESCs_scGROseq_Exp183_c03

description: Nascent RNA


title: Idh1_WT_3

description:
10x Genomics
SLX18785_SIGAD8

value: 24 weeks

value: WT


title: mESCs_scGROseq_Exp179_c02

description: Nascent RNA


title: LSEC_siControl_1

value: Liver


title: Utx_WT_2

description:
10x Genomics
SLX18582_SIGAH7


title: B2

city: Taiyuan

first: Senjie

last: Li

address: Jiefang South Road

country: China

institute: first hospital of shanxi medical university

data_processing:
llumina Casava software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or ow-quality sequence
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated usind a protocol
Assembly: http://ftp.ensembl.org/pub/release-90/gtf/rattus_norvegicus/
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: myocardial cells

extract_protocol:
RNA was harvested using Trizol reagent kit. Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using Qubit RNA test kit

treatment_protocol: The control model cells were treated with normal DMEM supplemented with 10% fetal bovine serum. The H/R model cells were exposed to glucose-free DMEM to simulate anoxic conditions. An anoxic environment was created using a three-gas incubator (anoxic conditions: 94% N2 + 5% CO2 + 1% O2). After 6 h, FBS and glucose were supplemented and placed in a sugar culture medium and normoxic incubator for reoxygenation for 16 h (normoxic conditions: 95% air + 5% CO2).

value: myocardial cells

value: hypoxia/reoxygenation (H/R)


title: B3


title: TL-19-550BBF

value: sporadic vestibular schwannoma


title: B1


title: mESCs_scGROseq_Exp168_c13

description: Nascent RNA


title: Idh1_WT_2

description:
10x Genomics
SLX18785_SIGAB8


title: Idh1_WT_1

description:
10x Genomics
SLX17006_SIGAD6

value: M

value: 19 weeks


title: LSEC_siPLVAP_2

value: Liver sinusoidal endothelial cell

value: PLVAP knockdown

value: siPLVAP transfection


title: mESCs_scGROseq_Exp208_c11

description: Nascent RNA


title: A3

value: control


title: Idh1_Mut_3

description:
10x Genomics
SLX18785_SIGAE8

value: bone marrow

value: LK

value: F

value: Idh1 R132H Het

value: pIpC


title: 633, invitro

city: Cleveland

first: Peter

last: Scacheri

state: OH

address: Biomedical Research, 2109 Adelbert Rd Building, 6th FL, Room 647

department: Genetics and Genome Sciences

institute: Case Western Reserve University School of Medicine

description: 10x genomics

library_source: genomic single cell

data_processing:
Single cell ATAC-seq data were aligned and processed using Cell Ranger ATAC v1.2 with the hg19 reference genome
The peak cell matrix and fragment file were further processed using Seurat v4.0.1 to create a Seurat object of the class ChromatinAssay (Hao et al., 2021).
Using Seurat v4.0.1, latent semantic indexing (LSI) was used to perform normalization, feature selection, and linear dimensional reduction.
Assembly: hg19
Supplementary files format and content: Tab-separated values files, matrix files, and comma-separated value files for cell meta data

growth_protocol: cells were grown in vitro in DMEM + 10%FBS + 1% pen-strep.

extract_protocol:
MG63.3 cells were isolated and processed according to the Nuclei Isolation for Single Cell ATAC Sequencing Demonstrated Protocol (10X Genomics, CG000169) with the following modifications: 1% BSA in PBS was used for the washes, and cells were lysed for 3 minutes on ice.
Sequencing libraries were created using the Chromium Single Cell ATAC Reagent Kits User Guide (10X Genomic, CG000168)

value: osteosarcoma cell line

value: wild-type


title: mESCs_scGROseq_Exp168_c06

description: Nascent RNA

value: embryonic stem cells


title: A2

value: myocardial cells


title: LSEC_siControl_2

value: Liver

value: WT

value: siControl transfection


title: SCH22_snRNA

description:
10x Genomics 3' v3.1
sch.all.counts.tsv.gz

data_processing:
Gene expression libraries were sequenced on Illumina NovaSeq 6000 S4 flow cells at a target depth of 50,000 read pairs per cell. Single cell RNA and single nucleus RNA sequencing reads were aligned to human reference GRCh38 v2020-A from 10x Genomics using the 10x Genomics Cellranger-4.0.0 and Cellranger-6.0.0 (include-introns flag set to true) pipelines, respectively.
Assembly: GRCh38 v2020-A from 10x Genomics
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
Samples processed as single cells were collected at the time of surgical resection and immediately processed. Tumor samples were minced and dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotech, Bergisch Gladbach, Germany) per manufacturer guidelines. The dissociated cell suspensions were then passed through a 40µm filter, pelleted through centrifugation, and resuspended in AutoMACS Rinsing Solution with 0.5% bovine serum albumin (BSA; Miltenyi Biotech). Red blood cell lysis was performed on all samples with Gibco ACK Lysing Buffer and was followed by debris removal via density gradient when necessary (Debris Removal Solution, Miltenyi Biotech). Cell viability was confirmed to be >80% using 0.4% Trypan Blue staining and manual counting with a hemocytometer.   Samples processed as single nuclei were collected at the time of surgical resection and immediately frozen in OCT compound embedding media (Tissue-Tek, Torrance, California) on a pre-chilled aluminum block resting on dry ice, and stored at -80°C. Tissue scrolls were cut at 30 µm using a Cryostat (50-100 scrolls were cut per sample, depending on the tissue size) and maintained at -80°C until the time of nuclei isolation. Lysis buffer (consisting of Tris-HCl, NaCl, MgCl2, Nonidet P40 Substitute, 0.1M DTT, RNase inhibitor, and nuclease free water) was added to the tissue scrolls, which were homogenized using a Pellet Pestle while on ice. Additional lysis buffer was then added, and the mixture was incubated on ice for 5 minutes. The suspension was passed through a 70 µm strainer and centrifuged before being washed with a solution of PBS with 1% BSA and 1U/µl Rnase inhibitor, incubated on ice for 5 minutes, centrifuged, and resuspended in PBS with 1% BSA and 1 U/µl Rnase inhibitor. The nuclei were then labeled with DRAQ5 (Thermo Scientific) and selected using FACS sorting before being carried forward for single nuclei library creation.
Single cell and single nuclei suspensions were processed using 10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 per manufacturer protocols. Briefly, cells/nuclei were added onto the 10X Next GEM Chip G to form Gel Bead-in-Emulsions (GEMs) in the Chromium instrument followed by cell lysis, barcoding, cDNA amplification, fragmentation, adaptor ligation, and sample indexed library amplification.

value: sporadic vestibular schwannoma

tag: tissue preparation

value: frozen tissue, single nucleus


title: A1


title: SCH21_snRNA


title: mESCs_scGROseq_Exp160_c16

description: Nascent RNA


title: SCH20_snRNA


title: LSEC_siPLVAP_1

value: Liver sinusoidal endothelial cell

value: PLVAP knockdown


title: Idh1_Mut_2

description:
10x Genomics
SLX18785_SIGAC8

value: 24 weeks


title: mESCs_scGROseq_Exp168_c02

description: Nascent RNA


title: Idh1_Mut_1

description:
10x Genomics
SLX17006_SIGAE6

value: bone marrow

value: M

value: 19 weeks


title: SCH18_snRNA


title: mESCs_scGROseq_Exp160_c14

description: Nascent RNA


title: SCH14_scRNA

value: fresh tissue, single cell


title: SynIII-chrI RNA-seq replicate 2

city: New York

first: Jitong

last: Cai

state: NY

address: 435 E 30th street

department: NYU Langone Health

institute: NYU Langone Health

description: strain yJL269 with wild-type chromosome I fused with SynIII as control

data_processing:
Trimmed reads were mapped to S288C reference genome (sacCer2) using TopHat.
Aligned reads with more than 2 mismatches were excluded from the downstream analysis.
RPKM were calculated using cufflinks and differentially expressed genes were analysed using cuffdiff. Genes that have been deleted in the fusion chromosomes were excluded in the analysis. The thresholds we used for differentially expressed genes areP < 10−5and |fold change|>2.
Assembly: S288C
Supplementary files format and content: tab-delimited txt file contains a list of differential expression genes and related statistics

organism: Saccharomyces cerevisiae

growth_protocol: Colonies were grown in YPD liquid medium at 30 °C with rotation to saturation. The next day, an overnight culture was diluted to A600 = 0.1 and regrown. Cells were harvested at A600 = 0.4–0.6.

extract_protocol:
Total RNA was extracted from three independent log-phase cultures using a QIAGEN RNeasy mini kit (Cat No.74106).
The library was prepared with 500 ng total RNA as input, using a TruSeq RNA sample Preparation v2 kit (set A RS-122-2001 and set B RS-122-2002) with 13 cycles of amplification. The library was sequenced as 150 bp single end reads on an Illumina NextSeq 500.

value: SynIII-chrI


title: SynIII-I RNA-seq replicate 3

description: strain yJL632 with SynIII-I

value: SynIII-I


title: Flt3_WT_1

description:
10x Genomics
SLX17003_SIGAG5

value: LK

value: 13 weeks


title: SCH13_scRNA


title: SynIII-chrI RNA-seq replicate 1


title: mESCs_scGROseq_Exp160_c13

description: Nascent RNA

value: embryonic stem cells


title: mESCs_scGROseq_Exp160_c12

description: Nascent RNA


title: Flt3_Mut_3

description:
10x Genomics
SLX17003_SIGAA6

value: 14 weeks

value: Flt3 ITD


title: Flt3_Mut_2

description:
10x Genomics
SLX17003_SIGAH5


title: Flt3_Mut_1

description:
10x Genomics
SLX17003_SIGAF5


title: SynIII-I RNA-seq replicate 2

description: strain yJL632 with SynIII-I


title: SynIII-I RNA-seq replicate 1

description: strain yJL632 with SynIII-I


title: mESCs_scGROseq_Exp160_c10

description: Nascent RNA


title: SCH8_scRNA


title: mESCs_scGROseq_Exp160_c11

description: Nascent RNA


title: mESCs_scGROseq_Exp160_c08

description: Nascent RNA


title: Ezh2_WT_2

description:
10x Genomics
SLX20061_SIGAC10

value: F

value: WT

value: pIpC


title: Ezh2_WT_1

description:
10x Genomics
SLX20061_SIGAB10


title: HCC tumor sample 35, African-American

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Quality control at each processing step was performed using the FastQC tool (quality base calls, CG content distribution, duplicate levels, complexity level). Sequencing adapters were removed using Trimmomatic. Reads were aligned to the latest assembly of the human genome (GRCh38/hg38) using the subread v.1.6.2 aligner.
Gene-level count summaries for each sample were obtained using the featureCounts v.1.6.2 software.
RNA-seq counts were quantile-normalized by library size, and genes differentially expressed between AA/black and white groups were detected using the edgeR v.3.18.1 R package.
Assembly: GRCh38/hg38
Supplementary files format and content: featureCount

extract_protocol:
Total RNA from tumor tissues was isolated with MagMax-96 for Microarrays Total RNA Isolation Kit (ThermoFisher) according to the manufacturer’s recommendations. RNA integrity (RIN) and yield were assessed on an Agilent 2100 Bioanalyzer, and samples with RIN ≥ 7 were selected. Prior to the RNA-Seq, ribosomal RNA was depleted from the samples using the RiboMinus™ Human/Mouse Transcriptome Isolation Kit (Thermo Fisher Scientific, Waltham, MA).
RNA-Seq library was prepared using Illumina TruSeq stranded mRNA sample preparation kit and all samples were sequenced on the Illumina Hi-Seq 2500 according to Illumina’s sequencing-by-synthesis protocol.

tag: disease

value: HCC

value: Liver

tag: race

value: African-American

tag: gender

value: Female

tag: hcv status

value: Yes

tag: hbv status

value: No


title: HCC tumor sample 34, African-American

tag: tissue


title: mESCs_scGROseq_Exp160_c07

description: Nascent RNA

tag: cell line


title: SCH5_scRNA

value: sporadic vestibular schwannoma

value: fresh tissue, single cell


title: Ezh2_KO_2

description:
10x Genomics
SLX20061_SIGAD10

value: bone marrow

tag: genotype

value: Ezh2 KO


title: mESCs_scGROseq_Exp160_c04

description: Nascent RNA


title: SCH4_scRNA

description:
10x Genomics 3' v3
sch.all.counts.tsv.gz


title: SCH3_scRNA


title: SCH9_scRNA


title: mESCs_scGROseq_Exp160_c03

description: Nascent RNA


title: HCC tumor sample 30, Caucasian

value: Caucasian

value: Male


title: mESCs_scGROseq_Exp160_c02

description: Nascent RNA

value: embryonic stem cells


title: HCC tumor sample 31, Caucasian


title: SCH2_scRNA


title: Calr_Mut_2

description:
10x Genomics
SLX18580_SIGAH6

value: LK

value: 41 weeks

value: Calr 52-bp del Hom


title: SCH6_scRNA


title: HCC tumor sample 29, African-American


title: SCH7_scRNA


title: SCH1_scRNA


title: SCH14_scATAC

description: 10x genomics scATAC v1.1

data_processing:
snATAC-seq libraries were sequenced in Illumina NovaSeq S1 flow cells at a target depth of 250M total read pairs per sample.
FASTQ files were aligned to GRCh38 v2020-A and processed data files were generated using the 10x Genomics Cellranger ATAC-1.2.0 count function (default parameters).
Assembly: GRCh38 v2020-A from 10x Genomics
Supplementary files format and content:  Tabix-sorted text files containing scATAC-seq fragments and the corresponding cell IDs. One fragment per line, one tabix file and accompanying index file per sample.

extract_protocol:
Tumor tissue was collected at the time of surgical resection and immediately processed. Tumor samples were minced and dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotech, Bergisch Gladbach, Germany) per manufacturer guidelines. The dissociated cell suspensions were then passed through 40µm filter, pelleted through centrifugation, and resuspended in AutoMACS Rinsing Solution with 0.5% bovine serum albumin. Red blood cell lysis was performed on all samples with Gibco ACK Lysing Buffer and was followed by debris removal via density gradient when necessary (Debris Removal Solution, Miltenyi Biotech). Cell viability was confirmed to be >80% using 0.4% Trypan Blue staining and manual counting with a hemocytometer. Nuclei isolation was then performed according to the 10X Demonstrated Protocol “Nuclei Isolation for Single Cell ATAC Sequencing” (Rev D).
scATAC-seq libraries were prepared using the 10X Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10X Genomics) according to the manufacturer’s protocols (SingleCell_ATAC_ReagentKits_v1.1_UserGuide_RevD). In brief, nuclei were incubated in a transposition mixture including a transposase to fragment open chromatin regions. Transposed nuclei were then loaded onto the 10X Next GEM Chip H to generate GEMs, followed by sample indexed library amplification.


title: D1-4_PGC_E12.5Fem

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
RNA-Seq datasets were aligned to a custom genome containing the Mus musculus genome assembly (GRCm38/mm10 Dec. 2011) and ERCC92 sequences using STAR (Dobin et al., 2013) with parameters "-outFilterMultimapNmax 300 -outMultimapperOrder Random -outSAMmultNmax 1 -alignIntronMin 20 -alignIntronMax 1000000", allowing multimappers with up to 300 matches in the genome and choosing positions for multimappers randomly
A random transcript isoform for each gene was chosen from Bioconductor annotation package TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.2.2) and exonic genomic regions for the random transcript isoforms for each gene were used in further analyses.
Expression quantification for selected exonic genomic regions was done using QuasR R package (Gaidatzis et al., 2015) selecting only uniquely mapped reads (mapqMin=255).
Assembly: mm10
Supplementary files format and content: CSV file contatining read count table for exonic regions of each gene (column ENTREZID), total length of genomic regions for each gene (column width) and each single oocyte.

source_name: E12.5 female gonad, C57BL/6J

extract_protocol:
To prepare pooled PGCs, E12.5 female embryonic gonads were harvested from inbred C57BL/6J fetuses. PGCs, positive for both SSEA1 and integrin β3, were collected using a FACSAria III (BD Bioscience). D6 PGCLCs derived from a BVSC-iPSC line were also collected at day 8 of the culture by following the same protocol as the start of the IVD culture. Four replicates of respective PGC and PGCLC pools, consisting of 30,000 to 340,000 cells, were prepared from independent experiments. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including removal of genomic DNA. The RNA quality was determined by 2200 TapeStation (Agilent Technologies). All samples had a RIN value of greater than 8.
Extracted RNA was prepared for sequencing using the TruSeq Stranded mRNA (Illumina) following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 (Illumina), with sequencing depth of 20 million reads per sample and sequencing configuration of single-end 100 bp.

value: E12.5 female gonad, C57BL/6J

value: E12.5 female PGC

value: PGCs positive for both SSEA1 and integrin β3 were collected


title: HCC tumor sample 33, African-American

value: HCC

value: Liver

value: African-American


title: HCC tumor sample 28, Caucasian

value: No


title: mESCs_scGROseq_Exp153_c11

description: Nascent RNA


title: SCH13_scATAC

description: 10x genomics scATAC v1.1

value: sporadic vestibular schwannoma


title: D1-2_PGC_E12.5Fem


title: Ezh2_KO_1

description:
10x Genomics
SLX20061_SIGAA10

value: F

value: 13 weeks

value: pIpC


title: HCC tumor sample 27, Caucasian

value: Caucasian

value: Female


title: HCC tumor sample 32, African-American

value: Male

value: Yes


title: mESCs_scGROseq_Exp153_c04

description: Nascent RNA

value: embryonic stem cells


title: HCC tumor sample 26, Caucasian


title: D1-1_PGC_E12.5Fem


title: Calr_WT_2

description:
10x Genomics
SLX18580_SIGAF6

value: bone marrow

value: LK

value: 41 weeks

value: WT


title: SCH7_scATAC

description: 10x genomics scATAC v1.1


title: mESCs_scGROseq_Exp153_c03

description: Nascent RNA


title: HCC tumor sample 25, African-American

value: HCC


title: mESCs_scGROseq_Exp153_c02

description: Nascent RNA


title: HCC tumor sample 24, African-American

value: Liver


title: SCH6_scATAC

description: 10x genomics scATAC v1.1


title: A1-4_PGCLC_d6

source_name: BVSC-iPSC

value: BVSC-iPSC

value: BVSC-iPSC-derived day 6  PGCLC

value: Day 6 PGCLCs positive for both Blimp1-Venus and Stella-ECFP were collected


title: mESCs_scGROseq_Exp156_c13

description: Nascent RNA


title: mESCs_scGROseq_Exp156_c09

description: Nascent RNA


title: D1-3_PGC_E12.5Fem

value: E12.5 female gonad, C57BL/6J

value: E12.5 female PGC

value: PGCs positive for both SSEA1 and integrin β3 were collected


title: A1-3_PGCLC_d6


title: HCC tumor sample 23, African-American

value: African-American

value: No


title: A1-2_PGCLC_d6


title: SCH5_scATAC

description: 10x genomics scATAC v1.1

value: sporadic vestibular schwannoma


title: mESCs_scGROseq_Exp153_c01

description: Nascent RNA


title: mESCs_scGROseq_Exp149_c09

description: Nascent RNA


title: SCH9_scATAC

description: 10x genomics scATAC v1.1


title: A549, evDNA, EBSS

city: Changsha

first: Yunsheng

last: Zhang

state: Hunan province

address: Tianma Road

institute: Hunan University

data_processing:
fastp (version 0.20.0, parameter: ‘-q 15 -u 40 -n 6 -l 15 ’) was used to trim adaptors and low-quality reads.
The quality of NGS short reads by searching them on the FastQC (version 0.11.8) program
The remaining reads were aligned to human genome hg38 by bwa men (version 0.7.17,parameter: ‘-t 20’), since ChIP-Seq and evDNA-Seq interrupted fragments were usually small and the percentage of unique sequences in the total number of sequences was the focus of attention.
peak calling of the aligned reads was made using macs3 (version 3.0.0a6, parameter: ‘-f BAM -g hs -p 0.1 -B’), and peaks were annotated using the R/Bioconductor package ChIPseeker.
Browser views of peaks are shown using Integrated Genomics Viewer (IGV; broadinstitute.org/igv)
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: evDNA-seq

growth_protocol: For ChIP-seq, DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2; For evDNA-seq, DMEM, no-fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library quantifications were assessed on the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina Hiseq platform and 50 bp single-end reads or 150 bp paired-end reads were generated.

value: epithelial cell

tag: chip antibody

value: Incubated with EBSS for 3 days and collected EVs


title: A549, evDNA, Control

tag: cell type


title: mESCs_scGROseq_Exp149_c07

description: Nascent RNA

value: embryonic stem cells


title: HCC tumor sample 21, Caucasian

value: Caucasian

value: Male

value: Yes


title: A1-1_PGCLC_d6


title: HCC tumor sample 22, Caucasian

value: HCC


title: KM6B, Brain, Keto, Male, 3

city: Parkville

first: David

middle: K

last: Gardner

state: VIC

address: University of Melbourne

department: School of BioSciences

country: Australia

institute: University of Melbourne

description:
KM6B
limma-voom_ketobrainM-control2brainM.tabular

data_processing:
NovaSeq Control Software (NCS) v1.7.5 and Real Time Analysis (RTA) v3.4.4 were used for basecalling
Illumina DRAGEN BCL Convert 07.021.624.3.10.8 pipeline was used to generate sequence data.
The quality of raw FASTQ data files was assessed with FastQC
Raw fastq files were concatenated using Concatenate datasets tail-to-head (cat)
The quality of concatenated FASTQ data files was assessed with FastQC
Cutadapt was used to trim the 19bp (CTGTCTCTTATACACATCT) Illumina standard adapters, and the 1 bp T-overhang from the 5' end of reads.
Trimmed reads were aligned to the mm10 reference genome with HISAT2
FeatureCounts was used to measure gene expression as counted reads
limma-voom was used to identify differentially expressed genes (DEGs) and their fold changes from count data and factordata matrix files
Assembly: mm10
Supplementary files format and content: countdata txt/tabular file contains Entrez ID, sample names, and normalised counts for each gene
Supplementary files format and content: factordata txt/tabular file contains sample name, treatment tissue sex interaction, treatment tissue interaction, tissue sex interaction, RNA extraction batch date, and RNA clean batch date. These factors were included in the limma-voom model.
Supplementary files format and content: limma-voom tabular files contain Entrez ID, Ensemble Gene IDs (ENSEMBL) gene symbol, gene name, log2(fold change), average expression, t-statistic, P value, P value adjusted with the Benjamini-Hochberg procedure which controls false discovery rate (FDR), and B-statistic, for each gene

source_name: Murine 13.5 Brain

growth_protocol: Embryos were collected from superovulated female mice and cultured in groups of 10 in 20uL drops under 5% Oxygen. D4 blastocysts were transferred to the uteri of pseudopregnant female mice and allowed to grow for 10 days. Fetuses and placentas were collect on E14.5 and tissues harvested for RNA extraction

extract_protocol:
Livers, brains and placentas were removed, flash frozen in Liquid nitrogen. Tissues were lysed and total RNA was harvested using Qiagen RNeasy Mini kit (liver, placenta) or Qiagen RNeasy Micro Kit (brain). RNA was analysed on the Illumina NovaSeq 6000 system at the Australian Genome Research Facility (AGRF)  with 1 ug of total RNA as input for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Embryos (and resultant fetal tissues) designated treatment were cultured in G series media supplemenented with 2 mM bOHB or without (control1), or with a combination of 0.8 mM AcAc + 2 mM bOHB (Keto) or without (control2) for the duration of the culture period.

value: C57BI/6 x CBA F1

tag: developmental stage

value: Murine 13.5 Brain

value: Keto


title: HCC tumor sample 20, African-American

value: Liver


title: KM5B, Brain, Keto, Male, 2

description:
KM5B
limma-voom_ketobrainM-control2brainM.tabular

tag: treatment


title: A549, Input, CST

data_processing:
fastp (version 0.20.0, parameter: ‘-q 15 -u 40 -n 6 -l 15 ’) was used to trim adaptors and low-quality reads.
The quality of NGS short reads by searching them on the FastQC (version 0.11.8) program
The remaining reads were aligned to human genome hg38 by bwa men (version 0.7.17,parameter: ‘-t 20’), since ChIP-Seq and evDNA-Seq interrupted fragments were usually small and the percentage of unique sequences in the total number of sequences was the focus of attention.
peak calling of the aligned reads was made using macs3 (version 3.0.0a6, parameter: ‘-f BAM -g hs -p 0.1 -B’), and peaks were annotated using the R/Bioconductor package ChIPseeker.
Browser views of peaks are shown using Integrated Genomics Viewer (IGV; broadinstitute.org/igv)
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)


title: mESCs_scGROseq_Exp149_c01

description: Nascent RNA


title: A549, LC3, CST


title: mESCs_scGROseq_Exp93b_c04

description: Nascent RNA


title: HCC tumor sample 19, African-American

value: Female


title: KM4B, Brain, Keto, Male, 1

description:
KM4B
limma-voom_ketobrainM-control2brainM.tabular

tag: strain


title: HCC tumor sample 18, Caucasian

tag: age


title: KF4B, Brain, Keto, Female, 2

description:
KF4B
limma-voom_ketobrainF-control2brainF.tabular


title: A549, FOXM1, CST


title: 143b, in vivo, day 22, atac, 5

description: omni-ATAC-seq protocol

data_processing:
Data was aligned to hg19 and mm9 with BWA-MEM
Mouse reads were removed using the XenofilteR package in R
PCR duplicates were removed using Picard Tools
Peaks were called using Genrich on default ATAC-seq mode
Bigwigs were generated using DeepTools with RPGC normalization
Assembly: hg19
Supplementary files format and content: BigWigs

growth_protocol: cells were grown in vitro in DMEM + 10%FBS + 1% pen-strep. Cells grown in vivo were injected IV into female NSG mice 8-10 weeks old.

extract_protocol:
In vivo extraction was done with the Miltenyi tumor dissociation kit and mouse cell depletion kit.
omni-ATAC-seq

value: osteosarcoma cell line

value: in vitro

tag: time

value: 22 days


title: KF9B, Brain, Keto, Female, 3

description:
KF9B
limma-voom_ketobrainF-control2brainF.tabular

tag: Sex


title: 3-ERG

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: selection marker: lineage negative progenitors lineage markers antibody cocktail (MACS Miltenyi Biotec), followed by Anti-Biotin MicroBeads according to manufacturer protocol

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
10x genomics according to the manufacturer protocol
single cell RNA-seq 3'

value: Bone Marrow

tag: genotype/variation

value: constitutive transgenic ERG

value: 4 weeks


title: HCC tumor sample 16, African-American

tag: disease

value: African-American

value: No


title: 4-ERG_GATA2_P_M

value: double mut Gata2 het/ERG


title: 2-GATA2_P_M

value: Gata2 heterozygote


title: HCC tumor sample 15, Caucasian

tag: race

value: Caucasian

value: Male


title: KF3B, Brain, Keto, Female, 1

description:
KF3B
limma-voom_ketobrainF-control2brainF.tabular

value: C57BI/6 x CBA F1


title: 1-WT

value: untreated, control donor


title: 143b, in vivo, day 22, atac, 4

description: omni-ATAC-seq protocol


title: 143b, in vivo, day 22, atac, 3

description: omni-ATAC-seq protocol


title: HCC tumor sample 14, Caucasian

value: HCC

tag: gender


title: 143b, in vivo, day 22, atac, 1

description: omni-ATAC-seq protocol


title: 0M11B, Brain, Con2, Male, 3

description:
0M11B
limma-voom_ketobrainM-control2brainM.tabular

value: Murine 13.5 Brain


title: 0M10B, Brain, Con2, Male, 2

description:
0M10B
limma-voom_ketobrainM-control2brainM.tabular


title: Serum-derived exosomes, DM-CAD, 2

city: Nanjing

first: Yihai

last: Liu

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

data_processing:
cutadapt, 1.14
Fastx-Toolkit, 0.0.13, -q 20 -p 80
bowtie, 1.1.1, -f -p 20
DESeq2, 1.16.1, padj<0.05, |log2FoldChange|>1
miranda, 3.3a, -sc 150 -en -30 -strict
Assembly: hg 19
Supplementary files format and content: counts

source_name: serum

extract_protocol:
The Peripheral blood was subjected to 3000g Centrifuge for 15min and the upper serum was obtained. We added an appropriate amount of Exosome Precipitation Solution (System Biosciences, USA) at a ratio of 63ul of solution per 250ul of serum. After pre-cooling at 4°C for 30min, the mixture was centrifuged at 1500g for 30min to precipitate exosomes. The total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following standard procedures.The purity and integrity of the RNA were assessed using a ND-1000 Spectrophotometer (NanoDrop).
The raw reads from small RNA sequencing are in fastq format, and the linker sequence is removed using cutadapt. Use fastx_toolkit (version 0.0.13) software to perform Q20 quality control on sequences, retaining sequences with Q20 of 80 and above. NGSQCToolkit (version 2.3.2) was then used to filter out reads containing N-bases. The result is high-quality clean reads that can be used for subsequent analysis. Statistics were performed on the length distribution of clean reads to initially assess the distribution of small RNAs in the sample. Using blastn software, clean reads are compared with Rfam (version 10.0) databases to annotate sequences such as rRNA, snRNA, snoRNA, tRNA, etc. Using the RepeatMasker software, the filtered sequences are compared to the repeat database to identify possible repeats. Small RNA sequences on unannotated devices were predicted using Mirdeep2 software for new miRNAs and secondary structures of miRNAs were predicted using RNAfold software. The miRNA expression calculation uses TPM (transcript per million) to calculate the metric, TPM = number of reads per miRNA / total sample alignment read number x106.

value: serum

tag: disease state

value: DM-CAD

tag: individual

value: patient 2


title: 143b, in vivo, day 22, atac, 2

description: omni-ATAC-seq protocol

value: osteosarcoma cell line

value: in vitro

value: 22 days


title: Serum-derived exosomes, DM-CAD, 3

tag: tissue

value: patient 3


title: Serum-derived exosomes, DM-CAD, 1

value: patient 1


title: HCC tumor sample 13, African-American

value: Liver

value: African-American

tag: hcv status

value: Yes

tag: hbv status

value: No


title: HCC tumor sample 12, African-American

value: Female


title: 0M6B, Brain, Con2, Male, 1

description:
0M6B
limma-voom_ketobrainM-control2brainM.tabular

value: C57BI/6 x CBA F1

value: Male


title: 0F9B, Brain, Con2, Female, 3

description:
0F9B
limma-voom_ketobrainF-control2brainF.tabular


title: 143b, in vivo, day 1, atac, 3

description: omni-ATAC-seq protocol

tag: cell line

value: 1 day


title: HCC tumor sample 11, Caucasian

value: HCC

value: Caucasian


title: Serum-derived exosomes, DM-CMD, 3

value: serum

value: DM-CMD


title: 143b, in vivo, day 1, atac,2

description: omni-ATAC-seq protocol

tag: cell type

value: osteosarcoma cell line


title: HCC tumor sample 9, African-American


title: 0F7B, Brain, Con2, Female, 2

description:
0F7B
limma-voom_ketobrainF-control2brainF.tabular

tag: developmental stage

value: Murine 13.5 Brain


title: Serum-derived exosomes, DM-CMD, 2

value: patient 2


title: 143b, in vivo, day 1, atac, 1

description: omni-ATAC-seq protocol

tag: treatment

value: in vitro


title: HCC tumor sample 8, African-American


title: 0F6B, Brain, Con2, Female, 1

description:
0F6B
limma-voom_ketobrainF-control2brainF.tabular

tag: strain


title: 143b, in vitro, atac,3

description: omni-ATAC-seq protocol


title: Serum-derived exosomes, DM-CMD, 1

value: patient 1


title: HCC tumor sample 7, African-American

value: Liver

tag: age


title: KM6P, Placenta, Keto, Male, 3

description:
KM6P
limma-voom_ketoplacentaM-control2placentaM.tabular

source_name: Murine 13.5 Placenta

value: Murine 13.5 Placenta

value: Keto


title: Serum-derived exosomes, DM, 3

value: DM

value: patient 3


title: KM5P, Placenta, Keto, Male, 2

description:
KM5P
limma-voom_ketoplacentaM-control2placentaM.tabular

value: C57BI/6 x CBA F1


title: HCC tumor sample 6, African-American

value: African-American

value: Male

value: Yes

value: No


title: 143b, in vitro, atac, 2

description: omni-ATAC-seq protocol

tag: time


title: Serum-derived exosomes, DM, 2

value: serum


title: 143b, in vitro, atac, 1

description: omni-ATAC-seq protocol


title: Serum-derived exosomes, DM, 1


title: HCC tumor sample 5, Caucasian

value: HCC

value: Caucasian


title: KM4P, Placenta, Keto, Male, 1

description:
KM4P
limma-voom_ketoplacentaM-control2placentaM.tabular

tag: Sex


title: HCC tumor sample 4, African-American


title: HCC tumor sample 3, Caucasian


title: 14H_NaCl_swo1_R2

city: Shanghai

first: Zhidan

last: Wang

address: Chenhua Road 3888

institute: Chinese academy of sciences

data_processing:
RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer’s instructions
Then clean reads were separately aligned to reference genome with orientation mode using TopHat
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method
RSEM was used to quantify gene abundances. R statistical package software EdgeR was utilized for differential expression analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel table with FPKM value

organism: Arabidopsis

growth_protocol: All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark)  photoperiod at 23 °C for 7 days.

extract_protocol: Total RNAs were extracted  using a RNeasy Plant Mini kit (Qiagen)

treatment_protocol: 250 mM NaCl treatment in liquid 1/2 MS medium for indicated time

tag: genotype/variation

value: swo1 mutant

value: 7-day-old seedlings

value: 257 mM NaCl for 14hrs

value: roots


title: 14H_NaCl_swo1_R1

value: 256 mM NaCl for 14hrs


title: 633, d22, 3, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invivo_d22_3_h19

data_processing:
Data was aligned to hg19 and mm9 with HISAT2
Mouse reads were removed using the XenofilteR package in R
Sleuth was used to generate TPM values
Assembly: hg19
Supplementary files format and content: tab-separated text file

extract_protocol:
In vivo extraction was done with the Miltenyi tumor dissociation kit and mouse cell depletion kit.
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

value: osteosarcoma cell line

tag: genotype

value: wild-type

value: in vivo

value: 22 days


title: 633, d22, 4, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invivo_d22_4_h19


title: KF9P, Placenta, Keto, Female, 3

description:
KF9P
limma-voom_ketoplacentaF-control2placentaF.tabular

value: C57BI/6 x CBA F1

value: Murine 13.5 Placenta

value: Female

value: Keto


title: HCC tumor sample 1, Caucasian

tag: disease

value: Liver

tag: race

value: Male

value: No


title: KF4P, Placenta, Keto, Female, 2

description:
KF4P
limma-voom_ketoplacentaF-control2placentaF.tabular


title: KF3P, Placenta, Keto, Female, 1

description:
KF3P
limma-voom_ketoplacentaF-control2placentaF.tabular


title: 633, d22, 2, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invivo_d22_2_h19


title: MAF E2 shKDM1A replicate 2 (RNA)

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

data_processing:
Reads were aligned to the hg19 genome using STAR 2.7.0e  with outFilterMismatchNoverLmax = 0.05 and all others parameters set to default values
Aligned BAM files were sorted and indexed using Sambamba v0.5.9
Per-gene counts were generated with featureCounts function from the Rsubread R package
Differential expression was performed with DESeq2 with processing batch as covariate.
Assembly: hg19
Supplementary files format and content: RPKM expression matrix

growth_protocol: MCF7 cells were maintained in hormone-deprived medium (HD) [phenol-red free DMEM (Gibco) supplemented with 5% charcoal-stripped FBS (Capricorn Scientific), glutamine 0.29 mg/mL, penicillin 100 units/mL and streptomycin 0.1 mg/mL for 72 h before E2 (10 nM,  Sigma-Aldrich) or vehicle addition.

extract_protocol:
RNA was extracted using PureLink RNA mini kit (Invitrogen) following the manufacturers’ instructions. RNA samples were quantified using Qubit Fluorometric Quantification (Thermo Fisher Scientific). 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 7-8 cycles of amplification

treatment_protocol: Control or MAF-overexpressing MCF7 cells (with and without KDM1A knockdown) were treated with 10 nM E2 or vehicle for 6 h prior to cell harvesting

value: breast cancer

tag: batch

tag: condition

value: MAF E2


title: 0M11P, Placenta, Con2, Male, 3

description:
0M11P
limma-voom_ketoplacentaM-control2placentaM.tabular

tag: tissue


title: 14H_NaCl_col-0_R1

value: col-0; WT

value: 7-day-old seedlings

value: 254 mM NaCl for 14hrs


title: MAF E2 shKDM1A replicate 1 (RNA)


title: 633, d1, 3, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invivo_d1_3_h19

value: 1 day


title: 633, d22, 1, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invivo_d22_1_h19

value: osteosarcoma cell line


title: 0M10P, Placenta, Con2, Male, 2

description:
0M10P
limma-voom_ketoplacentaM-control2placentaM.tabular


title: MAF HD shKDM1A replicate 2 (RNA)

value: MAF HD


title: 2H_NaCl_swo1_R1

value: swo1 mutant

value: 252 mM NaCl for 2hrs

value: roots


title: 0M6P, Placenta, Con2, Male, 1

description:
0M6P
limma-voom_ketoplacentaM-control2placentaM.tabular

value: C57BI/6 x CBA F1

value: Murine 13.5 Placenta


title: 2H_NaCl_swo1_R2

value: 253 mM NaCl for 2hrs


title: 633, d1, 2, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invivo_d1_2_h19

value: wild-type

value: in vivo


title: MAF HD shKDM1A replicate 1 (RNA)


title: 633, d22, 5, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invivo_d22_5_h19

value: 22 days


title: 0F9P, Placenta, Con2, Female, 3

description:
0F9P
limma-voom_ketoplacentaF-control2placentaF.tabular

value: Female


title: 0F7P, Placenta, Con2, Female, 2

description:
0F7P
limma-voom_ketoplacentaF-control2placentaF.tabular


title: MAF E2 replicate 3 (RNA)

value: breast cancer

value: MAF E2

value: shSc


title: 633, d1, 1, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invivo_d1_1_h19


title: 2H_NaCl_col-0_R1

value: col-0; WT

value: 7-day-old seedlings

value: 250 mM NaCl for 2hrs


title: 633, in vitro, 3, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invitro_3_h19

value: osteosarcoma cell line

value: in vitro


title: 2H_NaCl_col-0_R2

value: 251 mM NaCl for 2hrs


title: MAF E2 replicate 2 (RNA)


title: KM6L, Liver, Keto, Male, 3

description:
KM6L
limma-voom_ketoliverM-control2liverM.tabular

source_name: Murine 13.5 Liver

value: Murine 13.5 Liver

value: Male

value: Keto


title: 2H_CK_swo1_R2

value: swo1 mutant

value: roots


title: MAF E2 replicate 1 (RNA)


title: 633, in vitro, 2, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invitro_2_h19

value: wild-type


title: 0F6P, Placenta, Con2, Female, 1

description:
0F6P
limma-voom_ketoplacentaF-control2placentaF.tabular

value: C57BI/6 x CBA F1

value: Murine 13.5 Placenta


title: 2H_CK_swo1_R1


title: 14H_NaCl_col-0_R2

value: 255 mM NaCl for 14hrs


title: KM5L, Liver, Keto, Male, 2

description:
KM5L
limma-voom_ketoliverM-control2liverM.tabular


title: 633, in vitro, 1, rna

description:
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
invitro_1_h19

value: In vitro


title: p27, HD, biol rep 3

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

data_processing:
Fastq data quality was checked by fastqc and no trimming was performed because the data quality looks great. Sequencing depth ~ 20-30 million paired end reads/sample.
Fastq reads were mapped to hg38 genome by STAR with mismatch =1. Mapping rate is over 80%.
Aligned reads were counted by Htseq-count with union mode. Over 80% mapped reads are from mRNA.
Assembly: hg38
Supplementary files format and content: a csv file containing Htseq counts for all genes in all samples

source_name: HUVEC

growth_protocol: HUVEC were cultured in EBM-2 (Lonza) supplemented with Endothelial Growth Medium bullet kit (Lonza) and 1x antibiotic-antimycotic (Gibco) at 5% CO2 and 37°C

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) KAPA mRNA HyperPrep Kit (Roche)
KAPA mRNA HyperPrep Kit (Roche)

treatment_protocol: HUVEC were treated with indicated siRNA at ~80% confluency using Lipofectamine 2000 or 3000 (ThermoFisher) for 24 h. Cells were cultured onto µ-Slides (Ibidi) then exposed to either static conditions for 48h or 15dyn/cm2 shear stress for 72 h on an Ibidi flow pump. All static and flow samples were cultured in 2% FBS with no added bullet kit. For normal serum HUVEC were cultured for 24 hours in 2% FBS with no supplemented bullet kit. For serum starve conditions, HUVEC were treated with 0.2% FBS with no supplemented bullet kit for 24 hours. For low density samples, HUVEC were seeded at 50% confluency for 24 hours in normal growth protocol media. For high density, HUVEC were seeded at 1.5x 100% density for 24 hours in normal growth protocol media.

value: HUVEC

value: Endothelial cell

value: p27 siRNA

value: high density


title: KM4L, Liver, Keto, Male, 1

description:
KM4L
limma-voom_ketoliverM-control2liverM.tabular


title: 2H_CK_col-0_R1

value: col-0; WT

value: 7-day-old seedlings


title: MAF HD replicate 2 (RNA)

value: breast cancer

value: MAF HD

value: shSc


title: MAF HD replicate 1 (RNA)


title: p27, HD, biol rep 2


title: KF9L, Liver, Keto, Female, 3

description:
KF9L
limma-voom_ketoliverF-control2liverF.tabular

value: Murine 13.5 Liver

value: Female

value: Keto


title: s0485

description: 8. MAF E2 PROTAC R2

data_processing:
Cleaning of adapters was completed using Trimmomatic v0.38
Cleaned reads were aligned to hg19 using Bowtie2 v2.2.2 with “very sensitive” option and the remainder parameters set to default values
Genrich v0.5 was employed to call peaks, separately for samples in Mock, samples in Mock E2, samples in MAFHD and samples in MAF E2 (options  -j -y -r -e chrM)
Duplicate sequences were filtered out, sorted and indexed using sambamba, v-0.6.7
The union of called peaks by Genrich (consensus peaks) were annotated with Homer and used for downstream analysis
Assembly: hg19
Supplementary files format and content: Counts per consensus peaks (featureCounts R function)

growth_protocol: MCF7 cells were maintained in hormone-deprived medium (HD) [phenol-red free DMEM (Gibco) supplemented with 5% charcoal-stripped FBS (Capricorn Scientific), glutamine 0.29 mg/mL, penicillin 100 units/mL and streptomycin 0.1 mg/mL for 72 h before protac (50nM https://doi.org/10.1016/j.ejmech.2022.1147700.1) or vehicle addition. After 24h E2 (10 nM,  Sigma-Aldrich) or vehicle was added.

extract_protocol:
All samples were PCR amplified using NEBNextHigh-Fidelity 2x PCR Master Mix (New England BioLabs) with primers containing a barcode to generate libraries and a C1000 Touch Thermal Cycler (Bio-Rad). Then, DNA was purified again using a PureLink quick gel extraction and PCR purification combo kit (Invitrogen).
ATAC libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control or MAF-overexpressing MCF7 cells were treated with 1 um of ER-protac or vehicle for 24h hours before E2 (10nM) or vehicle addition for 1 h prior to cell harvesting and treatment with transposase Tn5 (Nextera DNA library preparation kit, Illumina)

tag: replicate


title: p27, HD, biol rep 1


title: KF4L, Liver, Keto, Female, 2

description:
KF4L
limma-voom_ketoliverF-control2liverF.tabular


title: Mock E2 replicate 3 (RNA)

value: Mock E2


title: s0484

description: 7. MOCK E2 PROTAC R2


title: p27, LD, biol rep 3

value: low density


title: s0483

description: 6. MAF ETOH PROTAC R2


title: Mock E2 replicate 1 (RNA)


title: KF3L, Liver, Keto, Female, 1

description:
KF3L
limma-voom_ketoliverF-control2liverF.tabular

value: C57BI/6 x CBA F1


title: Mock E2 replicate 2 (RNA)


title: p27, LD, biol rep 2


title: 0M10L, Liver, Con2, Male, 2

description:
0M10L
limma-voom_ketoliverM-control2liverM.tabular

value: Male


title: 0M11L, Liver, Con2, Male, 3

description:
0M11L
limma-voom_ketoliverM-control2liverM.tabular


title: Mock HD replicate 3 (RNA)

value: Mock HD


title: s0482

description: 5. MOCK ETOH PROTAC R2


title: s0481

description: 4. MAF E2 DMSO R2


title: MAF HD replicate 3 (RNA)


title: 2H_CK_col-0_R2

value: roots


title: NT, HD, biol rep 3

value: HUVEC

value: Endothelial cell

value: Non-targeting siRNA


title: Mock HD replicate 2 (RNA)


title: s0480

description: 3. MOCK E2 DMSO R2


title: 0F9L, Liver, Con2, Female, 3

description:
0F9L
limma-voom_ketoliverF-control2liverF.tabular


title: NT, HD, biol rep 2

value: high density


title: NT, HD, biol rep 1


title: 0F7L, Liver, Con2, Female, 2

description:
0F7L
limma-voom_ketoliverF-control2liverF.tabular


title: 0M6L, Liver, Con2, Male, 1

description:
0M6L
limma-voom_ketoliverM-control2liverM.tabular


title: Mock HD replicate 1 (RNA)


title: s0478

description: 1. MOCK EtOH DMSO R2


title: InputMAFE2_MAF

data_processing:
ChIP-seq alignment: Sequence of the reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each ChIP-seq experiment. Height of the profiles is normalized by the total number of reads mapped over the fly spike-in genome
ChIP-seq analysis: Peak detection of every sample against its corresponding Input was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format.
Assembly: hg19
Supplementary files format and content: BedGraph format for ChIP-seq genome-wide profiles
Supplementary files format and content: BED files format for ChIP vs Input peak calling

growth_protocol: Four 15 cm plates of control and MAF-overexpressing MCF7 cells per condition were prepared at 70-80% confluency. Cells were cultured in hormone-deprived medium [phenol-red free DMEM (Gibco) supplemented with 5% charcoal-stripped FBS (Capricorn Scientific), glutamine 0.29 mg/mL, penicillin 100 units/mL and streptomycin 0.1 mg/mL for 72 h before E2 (10 nM, Sigma-Aldrich) or ethanol (vehicle) addition.

extract_protocol:
Cells were crosslinked in 1% formaldehyde in DMEM for 10 min at RT. Next, glycine was added to a final concentration of 0.125 M and cells were incubated for 5 min at RT to stop the fixation. After two washes with ice-cold PBS, cells were harvested by gently scrapping on ice and centrifuged at 3,000 x g for 5 min. Cell pellets were stored at 80ºC until use.
Chromatin preparation and ChIP experiments were performed with the ChIP-IT High Sensitivity Kit (Active Motif) according to manufacturer’s protocol.

treatment_protocol: E2 (10 nM, Sigma-Aldrich) or ethanol (vehicle) was added 1h prior to fixation

tag: type

value: Input

tag: antibody


title: NT, LD, biol rep 3

tag: cell line

tag: cell type


title: MAFE2_MAF

value: breast cancer

value: IP

value: c-MAF (E-7) antibodies (sc-518062. Santa Cruz Biotechnology)


title: NT, LD, biol rep 2

tag: treatment


title: s0477

description: 8. MAF E2 PROTAC R1


title: InputMAFHD_MAF

value: MAFHD


title: 0F6L, Liver, Con2, Female, 1

description:
0F6L
limma-voom_ketoliverF-control2liverF.tabular

tag: strain

tag: developmental stage

value: Murine 13.5 Liver

value: Female


title: p27, LD, biol rep 1

value: p27 siRNA


title: CM8P, Placenta, Con1, Male, 3

description:
CM8P
limma-voom_bOHBplacentaM-control1placentaM.tabular

value: Murine 13.5 Placenta


title: NT, LD, biol rep 1

value: low density


title: CM5P, Placenta, Con1, Male, 2

description:
CM5P
limma-voom_bOHBplacentaM-control1placentaM.tabular

value: C57BI/6 x CBA F1

value: Male


title: p27, SS, biol rep 3

value: serum starve


title: MAFHD_MAF


title: s0474

description: 5. MOCK ETOH PROTAC R1


title: s0475

description: 6. MAF ETOH PROTAC R1


title: CM2, Placenta, Con1, Male, 1

description:
CM2P
limma-voom_bOHBplacentaM-control1placentaM.tabular


title: s0476

description: 7. MOCK E2 PROTAC R1


title: InputMockE2_MAF


title: MockE2_MAF


title: s0479

description: 2. MAF EtOH DMSO R2


title: CF10P, Placenta, Con1, Female, 3

description:
CF10P
limma-voom_bOHBplacentaF-control1placentaF.tabular


title: InputMAFE2_ER

data_processing:
ChIP-seq alignment: Sequence of the reads of the samples were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIP-seq analysis: Peak detection of every sample against its corresponding Input was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each ChIP-seq experiment. Height of the profiles is normalized by the total number of reads mapped over the human genome
Assembly: hg19
Supplementary files format and content: BedGraph format for ChIP-seq genome-wide profiles
Supplementary files format and content: BED files format for ChIP-seq vs Input peak calling


title: p27, SS, biol rep 1

value: HUVEC


title: s0473

description: 4. MAF E2 DMSO R1


title: s0472

description: 3. MOCK E2 DMSO R1


title: CF7P, Placenta, Con1, Female, 2

description:
CF7P
limma-voom_bOHBplacentaF-control1placentaF.tabular


title: CF4P, Placenta, Con1, Female, 1

description:
CF4P
limma-voom_bOHBplacentaF-control1placentaF.tabular


title: MAFE2_ER

value: ERα (HC-20) antibodies (sc-543. Santa Cruz Biotechnology)


title: NT, SS, biol rep 2

value: Endothelial cell

value: Non-targeting siRNA


title: p27, SS, biol rep 2


title: InputMAFHD_ER

value: Input


title: BM5P, Placenta, βOHB, Male, 3

description:
BM5P
limma-voom_bOHBplacentaM-control1placentaM.tabular

value: βOHB


title: s0470

description: 1. MOCK EtOH DMSO R1


title: BM2P, Placenta, βOHB, Male, 2

description:
BM2P
limma-voom_bOHBplacentaM-control1placentaM.tabular


title: MAFHD_ER

value: breast cancer

value: IP


title: InputMockE2_ER


title: p27, NS, biol rep 2

value: normal serum


title: p27, NS, biol rep 3


title: BF5P, Placenta, βOHB, Female, 3

description:
BF5P
limma-voom_bOHBplacentaF-control1placentaF.tabular


title: MockE2_ER


title: BM1P, Placenta, βOHB, Male, 1

description:
BM1P
limma-voom_bOHBplacentaM-control1placentaM.tabular


title: 23.MCF7 MOCK E2 PROTAC R3

description:
s0437
MOCKE2.PROTAC Replicate 3

data_processing:
Reads were aligned to the hg19 genome using STAR 2.7.0b  with outFilterMismatchNoverLmax = 0.05 and all others parameters set to default values
Per-gene counts were generated with featureCounts function from the Rsubread R package
Differential expression was performed with DESeq2 with replicate as covariate.
RPKM expression matrix
Assembly: hg19
Supplementary files format and content: xlsx file include counts values for all samples

source_name: MCF7 cells

growth_protocol: MCF7 cells were maintained in hormone-deprived medium (HD) [phenol-red free DMEM (Gibco) supplemented with 5% charcoal-stripped FBS (Capricorn Scientific), glutamine 0.29 mg/mL, penicillin 100 units/mL and streptomycin 0.1 mg/mL for 72 h. 1um of ER-Protac (https://doi.org/10.1016/j.ejmech.2022.1147700.1) was added for 24 h before E2 (10 nM,  Sigma-Aldrich) or vehicle addition.

extract_protocol:
RNA was extracted using PureLink RNA mini kit (Invitrogen) following the manufacturers’ instructions. RNA samples were quantified using Qubit Fluorometric Quantification (Thermo Fisher Scientific). 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using the kits Illumina Stranded mRNA Prep, Ligation (20040534) and IDT for Illumina RNA UD Indexes Set A (20040553), following manufacturer's instructions and 10 cycles of amplification

value: MCF7 cells


title: 24.MCF7 MAF E2 PROTAC R3

description:
s0438
MAFE2.PROTAC Replicate 3

treatment_protocol: 1um of ER-Protac (https://doi.org/10.1016/j.ejmech.2022.1147700.1) was added for 24 h before E2 (10 nM,  Sigma-Aldrich) or vehicle addition.


title: InputMockHD_ER

value: MockHD


title: BF3P, Placenta, βOHB, Female, 2

description:
BF3P
limma-voom_bOHBplacentaF-control1placentaF.tabular

value: Female


title: NT, NS, biol rep 3


title: 21.MCF7 MOCK ETOH PROTAC R3

description:
s0435
MOCKETOH.PROTAC Replicate 3


title: s0471

description: 2. MAF EtOH DMSO R1


title: 22.MCF7 MAF ETOH PROTAC R3

description:
s0436
MAFETOH.PROTAC Replicate 3


title: 20.MCF7 MAF E2 DMSO R3

description:
s0434
MAFE2.DMSO Replicate 3


title: NT, NS, biol rep 2


title: MockHD_ER


title: BF1P, Placenta, βOHB, Female, 1

description:
BF1P
limma-voom_bOHBplacentaF-control1placentaF.tabular

value: Murine 13.5 Placenta


title: 19.MCF7 MOCK E2 DMSO R3

description:
s0433
MOCKE2.DMSO Replicate 3


title: MAFE2 replicate 4 (ATAC)

data_processing:
Cleaning of adapters was completed using Trimmomatic v0.38
Cleaned reads were aligned to hg19 using Bowtie2 v2.2.2 with “very sensitive” option and the remainder parameters set to default values
Genrich v0.5 was employed to call peaks, separately for samples in Mock, samples in Mock E2, samples in MAFHD and samples in MAF E2 (options  -j -y -r -e chrM)
Duplicate sequences were filtered out, sorted and indexed using sambamba, v-0.6.7
The union of called peaks by Genrich (consensus peaks) were annotated with Homer and used for downstream analysis
Assembly: hg19
Supplementary files format and content: Normalized expression matrix (DESeq2 rlog function)

extract_protocol:
DNA was purified using a PureLink quick gel extraction and PCR purification combo kit (Invitrogen)
All samples were PCR amplified using NEBNextHigh-Fidelity 2x PCR Master Mix (New England BioLabs) with primers containing a barcode to generate libraries and a C1000 Touch Thermal Cycler (Bio-Rad). Then, DNA was purified again using a PureLink quick gel extraction and PCR purification combo kit.
ATAC libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control or MAF-overexpressing MCF7 cells were treated with 10 nM E2 or vehicle for 1 h prior to cell harvesting and treatment with transposase Tn5 (Nextera DNA library preparation kit, Illumina)


title: NT, SS, biol rep 3


title: NT, SS, biol rep 1


title: NT, NS, biol rep 1


title: MAFE2 replicate 3 (ATAC)


title: 18.MCF7 MAF ETOH DMSO R3

description:
s0432
MAFETOH.DMSO Replicate 3


title: CM5L, Liver, Con1, Male, 2

description:
CM5L
limma-voom_bOHBliverM-control1liverM.tabular

value: Murine 13.5 Liver


title: p27, FLOW, biol rep 3

value: p27 siRNA

value: 72h shear stress at 15 dyn/cm2


title: MAFE2 replicate 2 (ATAC)


title: CM2L, Liver, Con1, Male, 1

description:
CM2L
limma-voom_bOHBliverM-control1liverM.tabular

value: C57BI/6 x CBA F1

value: Male


title: 17.MCF7 MOCK ETOH DMSO R3

description:
s0431
MOCKETOH.DMSO Replicate 3


title: p27, NS, biol rep 1

value: HUVEC


title: MAFE2 replicate 1 (ATAC)


title: p27, FLOW, biol rep 1

value: Endothelial cell


title: MAF HD replicate 4 (ATAC)

value: MAFHD


title: 16.MCF7 MAF E2 PROTAC R2

description:
s0430
MAFE2.PROTAC Replicate 2


title: 15.MCF7 MOCK E2 PROTAC R2

description:
s0429
MOCKE2.PROTAC Replicate 2


title: CF4L, Liver, Con1, Female, 1

description:
CF4L
limma-voom_bOHBliverF-control1liverF.tabular


title: MAF HD replicate 3 (ATAC)


title: MAF HD replicate 2 (ATAC)


title: CM8L, Liver, Con1, Male, 3

description:
CM8L
limma-voom_bOHBliverM-control1liverM.tabular


title: BM5L, Liver, βOHB, Male, 3

description:
BM5L
limma-voom_bOHBliverM-control1liverM.tabular


title: p27, STATIC, biol rep 1

value: static condition


title: 13.MCF7 MOCK ETOH PROTAC R2

description:
s0427
MOCKETOH.PROTAC Replicate 2


title: BM1L, Liver, βOHB, Male, 1

description:
BM1L
limma-voom_bOHBliverM-control1liverM.tabular

value: βOHB


title: Mock E2 replicate 4 (ATAC)

value: breast cancer


title: BM2L, Liver, βOHB, Male, 2

description:
BM2L
limma-voom_bOHBliverM-control1liverM.tabular


title: 12.MCF7 MAF E2 DMSO R2

description:
s0426
MAFE2.DMSO Replicate 2


title: NT, FLOW, biol rep 3

value: Non-targeting siRNA


title: NT, FLOW, biol rep 2


title: Mock E2 replicate 3 (ATAC)


title: CF10L, Liver, Con1, Female, 3

description:
CF10L
limma-voom_bOHBliverF-control1liverF.tabular


title: BF5L, Liver, βOHB, Female, 3

description:
BF5L
limma-voom_bOHBliverF-control1liverF.tabular


title: NT, FLOW, biol rep 1


title: 10.MCF7 MAF ETOH DMSO R2

description:
s0424
MAFETOH.DMSO Replicate 2


title: CF7L, Liver, Con1, Female, 2

description:
CF7L
limma-voom_bOHBliverF-control1liverF.tabular


title: p27, FLOW, biol rep 2


title: Mock E2 replicate 2 (ATAC)


title: 9.MCF7 MOCK ETOH DMSO R2

description:
s0423
MOCKETOH.DMSO Replicate 2


title: p27, STATIC, biol rep 3


title: NT, STATIC, biol rep 3


title: 14.MCF7 MAF ETOH PROTAC R2

description:
s0428
MAFETOH.PROTAC Replicate 2


title: p27, STATIC, biol rep 2


title: BF1L, Liver, βOHB, Female, 1

description:
BF1L
limma-voom_bOHBliverF-control1liverF.tabular


title: NT, STATIC, biol rep 2


title: Mock HD replicate 4 (ATAC)


title: MAF HD replicate 1 (ATAC)


title: 8.MCF7 MAF E2 PROTAC R1

description:
s0422
MAFE2.PROTAC Replicate 1


title: Mock E2 replicate 1 (ATAC)


title: 7.MCF7 MOCK E2 PROTAC R1

description:
s0421
MOCKE2.PROTAC Replicate 1


title: NT, STATIC, biol rep 1


title: 11.MCF7 MOCK E2 DMSO R2

description:
s0425
MOCKE2.DMSO Replicate 2


title: 6.MCF7 MAF ETOH PROTAC R1

description:
s0420
MAFETOH.PROTAC Replicate 1


title: Mock HD replicate 3 (ATAC)


title: StressPbs_5

city: Beijing

first: yuchen

last: lu

address: Yard 27, Taiping Road

institute: Beijing Institute of Basic Medical Sciences

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 research species 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. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
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.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: Tab-delimited text files include FPKM and count values for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol 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.

tag: age

value: wild type


title: HeLa wild-type IFNb rep2

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave., room E251

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Raw sequences were quality and adapter trimmed using BBDuk v38.05 with arguments "-Xmx4g ktrim=r k=31 mink=11 hdist=1 tpe tbo qtrim=r trimq=10  ref=/opt/bbmap/38.05/resources/adapters.fa".
Sequences were mapped to the human genome (GRCh38, main chromosomes only)  using a 2pass mapping strategy in STAR (v2.7.3a). The latest available comprehensive gencode release (release 40; GRCh38.p13) was used as reference for the mapping process.
Aligned files were then analyzed for gene expression using FeatureCounts. The same gene annotation file used for read mapping was used as reference files.
Pairwise gene differential expression analysis was performed independently for each genotype using DESeq2 (v1.32.0). We assessed the difference in treatment effect on gene expression between wild-type and IFNAR-S KO cells setting "untreated" and "wild-type" samples as  reference levels in the experimental design: dds <- DESeqDataSetFromMatrix( countData = val, colData = coldata, design = ~ genotype + treat + genotype:treat ).
Assembly: GRCh38
Supplementary files format and content: CPM normalized signal tracks in UCSC bigwig format

source_name: HeLa cells

growth_protocol: Human cervical cancer HeLa cells (ATCC CCL-2) were routinely grown at 37C in 5% CO2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in DMEM (cat #10566016, ThermoFisher) supplemented with 10%FBS and 1% PenStrep

extract_protocol:
RNA was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057). All lysates were frozen at -80°C prior to extraction, and all extracted RNA were stored at -80°C as single-use aliquots.
Libraries were generated with 500ng RNA using KAPA mRNA HyperPrep Kit (KAPA #KK8581) according to the manufacturer's instructions. Briefly, single-indexed adapters (KAPA #KK8700) were added to each sample at a final concentration of 10 nM. Excess adapter was removed using sequential 0.63X and 0.70X KAPA Pure Bead (KAPA #KK8002) cleanups. Purified, adapter-ligated samples were amplified for 11 cycles according to the manufacturer's instructions and purified using a 1.0X KAPA Pure Bead cleanup.

treatment_protocol: Cells were seeded in 6 well plates (400,000 cells per well). After 24hrs culturing media was replaced with fresh media containing either 10U/mL of animal-free recombinant human IFNβ (Proteintech #HZ-1298) or equal volume of DPBS. Cells were treated for 4hrs.

tag: Sex

value: HeLa (ATCC CCL-2)

value: wildtype

value: IFNb

tag: time point

value: 4 hours


title: StressPbs_6

tag: genotype


title: StressPbs_4


title: Mock HD replicate 2 (ATAC)

value: MockHD


title: BF3L, Liver, βOHB Female, 2

description:
BF3L
limma-voom_bOHBliverF-control1liverF.tabular

value: Murine 13.5 Liver

value: Female


title: Mock HD replicate 1 (ATAC)


title: 5.MCF7 MOCK ETOH PROTAC R1

description:
s0419
MOCKETOH.PROTAC Replicate 1

value: MCF7 cells


title: 4.MCF7 MAF E2 DMSO R1

description:
s0418
MAFE2.DMSO Replicate 1


title: HeLa wild-type UT rep2

value: untreated


title: StressPbs_2


title: StressPbs_3


title: HeLa wild-type IFNb rep1


title: 3.MCF7 MOCK E2 DMSO R1

description:
s0417
MOCKE2.DMSO Replicate 1


title: hrp1-1 cytoplasmic

city: Göttingen

first: Heike

last: Krebber

address: Grisebachstraße 8

department: Molecular Genetics

institute: Georg-August Universität Göttingen

data_processing:
Fastq files were mapped to the S. cerevisiae genome sacCer3 with Hisat2
Hisat2 was run twice to generate strand specific bam files for downstream applications, once skipping the reverse strand and once the forward strand.
Fragment coverage of genomic regions was calculated with deeptools2 and a bin size of 1.
Transcript ends defined by Tudek et al. 2018 (GEO: GSE108550, Sample GSM2904878) were used as the center of region +/- 200 nt. The resulting table maintained the same ordering as the input file.
Assembly: sacCER3 GCA_000146045.2
Supplementary files format and content: tab delimated text file representing fragment coverage of transcript ends (+/- 200b) in Wild type and hrp1-1 cytoplasmic fraction.

source_name: yeast cells

growth_protocol: over night at 25°C

extract_protocol:
Cells were harvested at 1*10^7 cells/ml after 3h 37 °C, total RNA was extracted with Macherey-Nagel nucleospin RNA extraction Kit
A modified TruSeq Stranded Total RNA Library Prep (Cat. N°20020596) was used starting with 200 ng of total RNA.

treatment_protocol: 3h 37°C

value: yeast cells

value: 3h 37°C

tag: fraction

value: cytoplasmic


title: HeLa wild-type UT rep1


title: StressPbs_1


title: 2.MCF7 MAF ETOH DMSO R1

description:
s0416
MAFETOH.DMSO Replicate 1


title: HeLa IFNAR2-E7 KO IFNb rep2

value: IFNAR2-E7 KO


title: 1.MCF7 MOCK ETOH DMSO R1

description:
s0415
MOCKETOH.DMSO Replicate 1


title: Wild type total

value: Wild type

value: total


title: HeLa IFNAR2-E7 KO IFNb rep1


title: StressFlx_6


title: HeLa IFNAR2-E7 KO UT rep2


title: mg633, d22, 5, atac

description: omni-ATAC-seq protocol

value: osteosarcoma cell line

value: in vitro

tag: time

value: 22 days


title: mg633, d22, 4, atac

description: omni-ATAC-seq protocol


title: Vehicle treated ICH mice, Day 5_2

city: Chengdu

first: Xiao-Yi

last: Xiong

address: 37 Shierqiao Road, 610075, Chengdu, China

institute: Chengdu University of Traditional Chinese Medicine

data_processing:
Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp.
full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads.
Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1).
Assembly: GRCm38
Supplementary files format and content: gene expression of all sample

source_name: perihematomal brain tissue

extract_protocol:
perihematomal brain tissues were removed, flash frozen on dry ice, and total RNA was extracted using TRIzol reagent (Takara, Kyoto, Japan) according to the manufacturer’s instructions
cDNA libraries were constructed from 1 μg of total RNA by using a cDNA-PCR Sequencing Kit (SQK-PCS109) according to the protocol.

treatment_protocol: Mice were treated with TEPP-46 or vehicle for 5 consective days after ICH.

value: perihematomal brain tissue

value: WT

value: Vehicle

value: Day 5


title: Vehicle treated ICH mice, Day 5_3


title: HeLa IFNAR2-E7 KO UT rep1

value: HeLa (ATCC CCL-2)

value: 4 hours


title: StressFlx_3

value: wild type


title: mg633, d22, 2, atac

description: omni-ATAC-seq protocol


title: StressFlx_2


title: HeLa IFNAR2-S KO IFNb rep1

value: Female

value: IFNAR2-S KO

value: IFNb


title: HeLa IFNAR2-S KO IFNb rep2


title: StressFlx_1


title: mg633, d22, 3, atac

description: omni-ATAC-seq protocol


title: mg633, d22, 1, atac

description: omni-ATAC-seq protocol


title: hrp1-1 total

value: yeast cells

value: 3h 37°C


title: HeLa IFNAR2-S KO UT rep1

value: untreated


title: mg633, d1, 3, atac

description: omni-ATAC-seq protocol

value: 1 day


title: Wild type cytoplasmic

value: Wild type

value: cytoplasmic


title: Ctrl_6


title: TEPP-46 treated ICH mice, Day 5_2


title: TEPP-46 treated ICH mice, Day 5_1


title: Ctrl_5


title: HeLa IFNAR2-L KO IFNb rep2

value: IFNAR2-L KO


title: mg633, d1, 2, atac

description: omni-ATAC-seq protocol

value: osteosarcoma cell line

value: in vitro


title: StressFlx_4


title: IP_SWO1_GFP_R2

data_processing:
We cleaned the paired-end reads by Trimimomatic. After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters.
Enriched peaks were identified by MACS (version 1.4) with default parameters.
We defined the region of a target gene as the range from 1kb upstream of transcription start site (TSS) to transcription end site (TES). The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional up- and down-stream of the TSS and TES was performed by deepTools (version 2.4.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files with RPM value

organism: Arabidopsis thaliana

source_name: plant tissues SWO1-GFP

growth_protocol: All the plant seeds were sown and grown under a long- (16 h light/8 h dark)  photoperiod at 23 °C.

extract_protocol: Lysates were clarified from sonicated nuclei and SWO1-DNA complexes were isolated with antibody.

tag: genotype/variation

value: 14-day-old seedlings

tag: chip antibody

value: GFP anitbody


title: StressFlx_5


title: Ctrl_4


title: HeLa IFNAR2-L KO IFNb rep1

value: HeLa (ATCC CCL-2)


title: Vehicle treated ICH mice, Day 5_1

tag: tissue

value: perihematomal brain tissue

value: WT

value: Vehicle

value: Day 5


title: Ctrl_3

value: wild type


title: mg633, in vitro, 50k, atac

description: omni-ATAC-seq protocol

data_processing:
Data was aligned to hg19 and mm9 with BWA-MEM
Mouse reads were removed using the XenofilteR package in R
PCR duplicates were removed using Picard Tools
Peaks were called using Genrich on default ATAC-seq mode
Bigwigs were generated using DeepTools with RPGC normalization
Assembly: hg19
Supplementary files format and content: BigWigs


title: HeLa IFNAR2-L KO UT rep2

value: Female

value: 4 hours


title: HeLa IFNAR2-S KO UT rep2

value: IFNAR2-S KO

value: untreated


title: TEPP-46 treated ICH mice, Day 5_3


title: Input_Col-0_R2

source_name: plant tissues Col-0


title: HeLa IFNAR2-L KO UT rep1


title: mg633, In vitro, 25k, atac

description: omni-ATAC-seq protocol


title: Ctrl_1


title: Input_Col-0_R1

description: R19046125-YM20191023-ATCS-326-J_combined


title: WT, DMS, rep 1

status: Public on Sep 14 2023

city: University Park

first: Elizabeth

last: Jolley

state: PA

address: 239 Chemistry Bldg, Pennsylvania State University

institute: Pennsylvania State University

data_processing:
Read trimming using fastq_trimmer.py in StructureFold2 with Cutadapt 3.5
Read mapping using fastq_mapper.py in StructureFold2 with Bowtie 2.4.4
Read filtering using sam_filter.py in StructureFold2 with Samtools 1.16
Stop counting using sam_to_rtsc.py
Depth was calculated with Samtools 1.16
Assembly: NCBI: U00096.2, NCBI: GSE52059
Supplementary files format and content: rtsc files: contains rt stop count per nucleotide
Supplementary files format and content: depth T files: contains read depth as described in citation
Library strategy: Structure-seq2

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Escherichia coli MG1655 cells were grown to mid-exponential phase in a shaking water bath at 37 °C. Growth was stopped by using frozen slurry killing buffer (containing 10 mM Tris-HCl, 5 mM MgCl2, 25 mM NaN3, 1.5 mM chloramphenicol, and 12.5% ethanol) and immediately plunging on ice.

extract_protocol:
Total RNA was extracted using the RNeasy MINI kit (Qiagen) and then ribosomal RNA was depleted using RiboMinus (Thermo Fisher)
Structure-seq2 libraries were prepared by reverse transcription with a random hexamer primer, ligation of a hairpin adapter, and then amplification incorporating Illumina-specific primers.

treatment_protocol: Samples were treated with DMS at a final concentration of 40 mM or EDC at a final concentration of 35 mM by adding chemical to the growth media for 5 min, then reaction was quenched with DTT. Control samples had an equivalent amount of DTT added.

value: DMS


title: WT, control, rep 2

value: control


title: WT, control, rep 1


title: WT, DMS, rep 3


title: mg633, in vitro, 100k, atac

description: omni-ATAC-seq protocol

extract_protocol:
In vivo extraction was done with the Miltenyi tumor dissociation kit and mouse cell depletion kit.
omni-ATAC-seq


title: WT, DMS, rep 2


title: WT, EDC, rep 2

value: EDC


title: WT, EDC, rep 3


title: IP_SWO1_GFP_R1


title: WT, control, rep 3


title: WT, EDC, rep 1