title: DKO_0.35uM_1i_Epi

first: Helene

last: Kretzmer

address: Ihnestraße 63

institute: Max Planck Institute for Molecular Genetics

description: WGBS

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads).
Genome build: mm9
processed data files format and content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

source_name: E6.5 Epiblast

growth_protocol: Embryos were cultured in standard embryo media. In brief, 25uL of KSOM media drops were added to the petridish and covered with mineral oil. The culture dish with KSOm was pre-gassed prior to transfer of embryos.

extract_protocol:
Genomic DNA was isolated from cells through phenol-chloroform extraction
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

treatment_protocol: Zygotes electroporated with Cas9-RNP with guides targeting Dnmt3a and Dnmt3b; 2C stage embryos were treated with 0.35uM Dnmt1i (GSK3484862) until blastocyst stage

value: E6.5 Epiblast

value: Dnmt3a + Dnmt3b KO + Dnmt1 inhibitor


title: CRISPRa_RBN_R2

status: Public on Jun 18 2021

type: SRA

city: Cambridge

first: Mario

last: Niepel

state: MA

address: 35 Cambridgepark Dr Suite 300

country: USA

institute: Ribon Therapeutics, Inc.

library_source: genomic

data_processing:
Library strategy: CRISPR screen
Analysis of NGS data sets e.g. sgRNA abundance was achieved using Horizon’s data processing scripts, based on published analysis tool MAGeCK (PMID:25476604)
Dual screen analysis was achieved by normalizing average log-fold changes in guide abundance by the difference in population doubling for each screen track: Phenotype score = LFC (DMSO vs RBN)/ΔPD (DMSO vs RBN).
Genome_build: hg38
Supplementary_files_format_and_content: "CRISPRa_Raw_counts.txt" and "CRISPRi_Raw_counts.txt" contain the abundance of each sgRNA in each sample, "CRISPRa_REF_Library.txt" and "CRISPRi_REF_Library.txt" contain the sgRNA sequences and target genes for each sgRNA.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: For transduction by spinfection, cells were seeded in multiple 12-well plates (2x106 cells/well) in the presence of 8 μg/ml polybrene.  Horizon high complexity off-the-shelf library lentivirus was added to each well and cells centrifuged.  Appropriate section marker (e.g. Puromycin for CRISPRi, combination of Blasticidin/Puromycin or Zeocin for CRISPRa) was applied 48 hrs post transduction.

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Blood Maxi kit (Qiagen #51194). Samples were prepared and purified for amplicon sequencing using an Illumina NextSeq next generation sequencing platform.
Genomic DNA was extracted using the QIAamp DNA Blood Maxi kit (Qiagen #51194). Samples were prepared and purified for amplicon sequencing using an Illumina NextSeq next generation sequencing platform.

treatment_protocol: The screen cultures were maintained at >300-fold library coverage, or a minimum of 32 x 106 cells per replicate and were treated with RBN-2397 at each split. After the DMSO control treated populations had reached 12 doublings, all screen end pellets were collected.

tag: cell line

tag: crispr library

value: CRISPRa

tag: treatment

value: Compound (RBN012397, 2.5nM) treated sample


title: U2OS 7h Input (2)

city: Malmö

first: Maria

middle: Alvarado

last: Kristensson

address: 59 Jan Waldenströms street

country: Sweden

institute: Lund University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie 2, version 2.1.0. The option “-k 1” was chosen so that only uniquely mapped reads are allowed. The mapping results in SAM are converted to BAM and sorted by coordinates using samtools, version 1.7-13-g8dee2a2.
Peaks were identified using MACS2 (parameters: callpeak -B -g hs --nomodel --extsize 200 -q 0.05). BAM files of replicate samples were merged into one file before peak calling was performed. FDR cut-off of 0.05 was used to determining significant peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were generated; Scores represent signal values

source_name: osteosarcoma

growth_protocol: U2OS osteosarcoma epitelial cells were grown in McCoy'5A medium supplemented with 5% fetal calf serum and 1% PEST.

extract_protocol:
Nuclei were lysed and  chromatin was micrococcal treated. The fragmented chromatin was pre-cleared  with Dynabeads. Gamma-tubulin-, PCNA-, Mcm5-, and FoxM1-DNA-complexes were isolated with the correspondant antibody and isolated with Dynabeads.
ChIP DNA using the Smarter ThruPLEX DNA-seq Kit (cat# R400676, Takara) with HT dual indexes (cat# R400660, Takara)

treatment_protocol: Cells were subjected to dubble thymidine syncronization and released for 3h, 7h, 9h prior to harvest. Alternatively, non-synchronous cells were harvested.

tag: tissue

value: bone

tag: time point

tag: antibody


title: IVF.BDC.4

city: Logan

first: Abby

middle: D

last: Benninghoff

state: UT

address: 4815 Old Main Hill

department: Animal, Dairy and Veterinary Sciences

institute: Utah State University

library_source: transcriptomic

data_processing:
For the large RNAseq data, high quality sequencing data were confirmed with FastQC and visualized across samples with MultiQC.  A STAR index was generated for read alignment using B. taurus UMD3.1 using the parameter --sjdbOverhang 74. Reads were aligned with default parameters including --quantMode GeneCounts to generate feature count tables.
Count tables were imported to R where the DESeq2 R package was used to identify differentially expressed genes with a Benjamini–Hochberg false discovery rate (FDR) adjusted p-value < 0.05.
Genome_build: UMD3.1
Supplementary_files_format_and_content: txt file for normalized reads for annotated mRNA transcripts organized by sample ID across columns and Ensembl transcript ID in the first column

molecule: total RNA

organism: Bos taurus

source_name: IVF Blastocyst-derived cells

growth_protocol: Following 22 to 24 hr of maturation, MII oocytes were fertilized using the laboratory’s standard in vitro fertilization protocol [46]. Briefly, one straw of cryopreserved bovine semen obtained from a Holstein bull (Hoffman AI, Logan, Utah) was removed from the liquid nitrogen tank and placed into a 35C water bath to thaw. Live sperm were isolated by centrifugation through a 45%/90% percoll gradient (MP Biomedical, Irvine, California), suspended (final concentration 1x106/ml) in Tyrode’s albumin lactate pyruvate containing 10 microgram/ml procine heparin and used to fertilize the oocytes. Twenty to 22 hr post-IVF, cumulus cells were removed by vortexing, and fertilized zygotes were washed in phosphate buffered saline with 0.32 mM sodium pyruvate, 5.55 mM glucose, and 3 mg/ml bovine serum albumin (PB1+). After washing, zygotes were cultured on a monolayer of bovine cumulus cells in 50 microliters of synthetic oviductal fluid (SOFaa) [47] with 3% FBS (Hyclone, lot number AC10240545) overlaid with mineral oil. The embryos were cultured at 38.5 deg C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture.

extract_protocol:
RNA was isolated based on size using the RNA Clean & ConcentratorTM 5 kit (Zymo) from three pools each of oocytes, 2-cell stage embryos, 8-cell stage embryos, morula stage embryos, or blastocyst stage embryos according to the manufacturer’s protocol for purification of small RNA (<200 nt) and large RNA (>200 nt) as separate fractions.  The large RNA fraction was used to generate sequencing libraries using the Ovation SoLo RNA-Seq System (NuGen Technologies, San Carlos, California) as directed by the manufacturer’s protocol for total RNA input.
Briefly, first strand cDNA synthesis, cDNA processing, second strand synthesis, and end repair were conducted according to manufacturer’s protocols, and samples were then stored at -20°C overnight.  Then, adaptor ligation and purification were performed, followed by PCR amplification of the sequence libraries (optimized to 16 cycles per instructions) and bead purification (twice) of the resulting samples.  Library DNA concentrations were quantified using the Qubit dsDNA HS Assay (Thermo Fisher Scientific, Waltham, Massachusetts).  Because DNA concentrations were low, the PCR amplification step was repeated once more with an additional 19 cycles to improve yield.  Next, InDA-C treatment was conducted (Ovation SoLo RNA-Seq System kit), a third round of PCR was performed, and the resulting libraries were bead-purified according to the manufacturer’s protocol.

tag: developmental stage

value: Blastocyst-derived cells

tag: production method

value: In vitro fertilization

tag: molecule subtype

value: total RNA > 200 nt in length


title: DKO_0.35uM_1i_E35

city: Berlin

department: Genome Regulation

country: Germany

description: WGBS

organism: Mus musculus

source_name: E3.5 Blastocyst

tag: cell type

value: E3.5 Blastocyst

tag: strain

tag: genotype


title: NT.2c.1

source_name: scNT 2-cell stage embryos

growth_protocol: Frozen/thawed cells were grown to 80-100% confluence then passaged, with cells from passages 4-5 used as nuclear donors. Three days prior to a cloning session, donor fibroblast cells were thawed and propagated, and incubated in DMEM medium (Hyclone) supplemented with 15% (v/v) FBS at 39 deg C with 5% CO2. Bovine fibroblasts at 80-90% confluence were serum-starved by replacing culture medium with DMEM containing 0.5% (v/v) FBS 24 hr prior to scNT.Oocytes were matured for 18-20 hr, then denuded using 100 microliters of 1% (v/v) hyaluronidase (MP Biomedical), incubated for 5 min at 38.5 deg C with 5% CO2, followed by gentle pipetting. The removed cumulus cells were centrifuged at 500xg for 5 min at room temperature, and the supernatant was removed. Cumulus cells were then cultured in SOFaa under oil for use in embryo culture. The denuded oocytes were then rinsed using PB1+, and oocytes with polar bodies were selected and separated. ScNT was performed according to established protocols [49-51]. Briefly, oocytes with polar bodies were incubated in 0.6 microgram/ml demecolcine for 30-40 min and a metaphase plate and a polar body were removed using a beveled pipette. Fibroblast cells were covered in 0.25% trypsin (Gibco, Carlsbad, CA) for 1 min, and then the trypsin was removed and fibroblasts were incubated for anther 6 min at 39 deg C with 5% CO2. Once fibroblast cells were detached, they were rinsed in warm medium and centrifuged at 150xg for 6 min. The supernatant was removed, and the cellular pellet was resuspended in 100 microliters Hepes SOF medium [47]. One fibroblast cell was injected into the perivitelline space of the recipient oocyte, and fused using one direct pulse of 1.2 kV/cm for 22 μs by an Electro Cell Manipulator 2001 (BTX, San Diego, CA) in 0.28 M sorbitol, 0.05% (w/v) BSA, 0.1 mM CaCl2, 0.5 mM MgCl2, and 0.5 mM Hepes. Following fusion, embryos were washed through Hepes SOF, and incubated in embryo culture medium for 1 hr. Activation was then performed, with successfully fused embryos cultured in 5 μM ionomycin for 5 min, followed by 4 hr of incubation in activation medium composed of SOFaa medium with 10 μg/ml cyclohexamide and 1 mM 6-dimethylamino¬pyridine at 38.5 deg C with 5% CO2. Following activation, embryos were cultured on a monolayer of bovine cumulus cells in 50 µl drops of SOFaa with 3% (v/v) FBS overlaid with mineral oil. The embryos were cultured at 38.5 deg C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture.

value: 2-cell stage

value: somatic cell nuclear transfer


title: DKO_DMSO_E35

description: WGBS

treatment_protocol: Zygotes electroporated with Cas9-RNP with guides targeting Dnmt3a and Dnmt3b; 2C stage embryos were treated with DMSO

value: Dnmt3a + Dnmt3b KO + DMSO


title: U2OS 3h IP Mcm5 (2)


title: CRISPRa_RBN_R1


title: CRISPRa_LIB_R2

value: Library sample


title: U2OS 3h IP Mcm5 (1)


title: NT.2c.3


title: Dnmt1_KO_E3.5

description: WGBS

treatment_protocol: Zygotes electroporated with Cas9-RNP with guides targeting Dnmt1

value: Dnmt1 KO


title: IVF.BDC.2


title: U2OS 3h IP FoxM1 (2)


title: CRISPRa_LIB_R1


title: CRISPRa_DMSO_R2

value: DMSO treated sample


title: U2OS 3h IP FoxM1 (1)


title: IVF.BDC.1


title: IVF.Bl.4

source_name: IVF blastocyst stage embryos

value: Blastocyst stage


title: Dnmt3ab_DKO_E3.5_rep2

description: WGBS

treatment_protocol: Zygotes electroporated with Cas9-RNP with guides targeting Dnmt3a and Dnmt3b

value: Dnmt3a + Dnmt3b KO


title: Dnmt3ab_DKO_E3.5_rep1

description: WGBS


title: CRISPRa_DMSO_R1


title: U2OS 7h Input (1)


title: WT_E3.5_rep2

description: WGBS

treatment_protocol: Zygotes electroporated with Cas9-RNP with guides targeting GFP (mock)

value: WT


title: IVF.Bl.3


title: U2OS 3h IP PCNA (1)

value: PCNA


title: IVF.BDC.3


title: U2OS 3h IP TUBG (2)

value: gamma tubulin


title: WT_E3.5_rep1

description: WGBS


title: HCT116_mAID_TOP2A_TOP2Bko_Factory_async_ctrl_rep1

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

institute: University Medical Center Goettingen

description:
nascsent RNA
TOP2A_ctrl_x_TOP2AB_aux_factory_gene_irnaseq_GRCh38_qval0.05.csv
RNA_factory_TOP2AB_irnaseq_gene_quant_GEO.txt
imb_roukos_2020_04_1_top2atop2b_aux_1_S7_sorted.bam

data_processing:
alignment with STAR aligner
count quantification with iRNAseq tool
normalization with RUV-seq
differential gene expression analysis with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Raw read gene level quantification table for all the samples

source_name: human colorectal carcinoma cell line

growth_protocol: mAID-POLR2A(RPB1)-mClover DLD-1 and TO2B-/-TOP2A- mAID HCT116 cells were passaged in RPMI-1640 medium supplemented with 10% FBS under 5% CO2.

extract_protocol:
Nascent RNA from ~10 million mAID-RPB1-mCLover DLD-1 or TO2B-/-  -TOP2A-mAID HCT116 cells was isolated according to “factory-seq” protocol. Briefly, cells were gently scraped and lysed in isotonic “physiological buffer” supplemented with 0.5% NP40 buffer. After assessing lysis and nuclei integrity on a hemocytometer microscopy, nuclei were treated with DNase I for 30 min at 33°C, washed, and nuclei were lysed in “native lysis buffer” and treated with caspase group III enzyme mix, pelleted by centrifugation, before the supernatant holding nascent RNA was collected in TRIzol and purified using the Direct-Zol RNA purification kit.
TruSeq RNA library kit (Illumina)

treatment_protocol: Inducible depletion of RPB1 or TOP2A initiated via treatment with doxycycline for 24 h to induce TIR1 expression, before addition of 500 µM indole-3-acetic acid solution (“auxin”) for  14 h (asynchronised) to induce RPB1 degradation. Asynchronous cells treated with auxin were harvested, where applicable resuspended in 1 µg/ml propidium iodide to counterstain DNA, and sorted to isolate G1 cells using a FACS Canto II flow cytometer.

value: 14h treatment with Auxin

tag: agent


title: TKO_Dnmt1_inactive

description: WGBS

source_name: KH2 mESC

growth_protocol: mES cells were cultured in Knock Out DMEM media (Gibco) containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF. For ES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CD1 mouse embryonic fibroblasts (MEFs) were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells per well of a six-well plate and were split every 3–4 days.

extract_protocol:
Purelink Genomic DNA mini kit (Invitrogen)
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

treatment_protocol: Ectopic catalytically inactive Dnmt1 integrated using piggybac vector system

value: mESC

value: Dnmt3a + Dnmt3b + Dnmt1 KO + ectopically catalytically inactive Dnmt1


title: HCT116_mAID_TOP2A_TOP2Bko_Factory_async_ctrl_rep2

description:
nascsent RNA
TOP2A_ctrl_x_TOP2AB_aux_factory_gene_irnaseq_GRCh38_qval0.05.csv
RNA_factory_TOP2AB_irnaseq_gene_quant_GEO.txt
imb_roukos_2020_04_1_top2atop2b_aux_2_S8_sorted.bam


title: U2OS 3h IP TUBG (1)

value: bone


title: TKO_Dnmt1_rescue

description: WGBS

treatment_protocol: Ectopic Dnmt1 integrated using piggybac vector system

value: Dnmt3a + Dnmt3b + Dnmt1 KO + ectopically Dnmt1


title: HCT116_mAID_TOP2A_Factory_async_ctrl_rep2

description:
nascsent RNA
TOP2A_ctrl_x_TOP2AB_aux_factory_gene_irnaseq_GRCh38_qval0.05.csv
RNA_factory_TOP2AB_irnaseq_gene_quant_GEO.txt
imb_roukos_2020_04_1_top2a_ctrl_2_S2_sorted.bam

value: untreated


title: IVF.Mo.4

source_name: IVF morula stage embryos

value: Morula stage

value: In vitro fertilization

value: total RNA > 200 nt in length


title: IVF.Bl.1


title: HCT116_mAID_TOP2A_Factory_async_ctrl_rep1

description:
nascsent RNA
TOP2A_ctrl_x_TOP2AB_aux_factory_gene_irnaseq_GRCh38_qval0.05.csv
RNA_factory_TOP2AB_irnaseq_gene_quant_GEO.txt
imb_roukos_2020_04_1_top2a_ctrl_1_S1_sorted.bam


title: IVF.Mo.3


title: TKO

description: WGBS

value: Dnmt3a + Dnmt3b + Dnmt1 KO


title: IVF.Mo.2


title: U2OS 3h IP PCNA (2)


title: DKO0_P15

description: WGBS

source_name: J1 mESC

treatment_protocol: Passaged fifteen times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid


title: DKO0_P5

description: WGBS

treatment_protocol: Passaged five times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid


title: Rad21_ctrl

data_processing:
Library strategy: Cut&Tag-seq
Trimming of adapters (Cutadapt)
Mapping to human and E. Coli genome (Bowtie2)
Calibration of human mapped reads with E. Coli derived scaling factors (in R and with bedtools)
Peak calling with SEACR
Genome_build: hg38 and ASM584v2
Supplementary_files_format_and_content: E. Coli reads scaled Cut&Tag bigwig

source_name: colorectal adenocarcinoma cell lines

growth_protocol: POLR2A-mAID-mClover DLD-1 (previously described; Nagashima et al, 2019) were passaged in RPMI-1640 medium supplemented with 10% FBS under 5% CO2.

extract_protocol:
Cut&Tag experiment was carried out with CUT&Tag-IT™ Assay Kit (Active Motif) according to manufacturers instructions.
Cut&Tag libraries were constructed as a part of CUT&Tag-IT™ Assay Kit (Active Motif) according to manufacturers instructions.

treatment_protocol: Inducible depletion of RPB1 initiated via treatment with doxycycline for 24 h to induce TIR1 expression, before addition of 500 µM indole-3-acetic acid solution (“auxin”). For cell synchronization, G2/M arrest was achieved by addition of 10 µM RO-3306 inhibitor for 21 h. Following this incubation time, cells were washed with PBS, and auxin-supplemented medium was added for up to 6 h to allow cells to quantitatively enter G1. At this point, cells were harvested, where applicable resuspended in 1 µg/ml propidium iodide to counterstain DNA, and sorted using a FACS Canto II flow cytometer.

tag: cell cycle

value: synchronous G1 reenter sorted

tag: chip antibody

value: anti-Rad21:ab992, Abcam


title: Rad21_aux


title: U2OS 3h Input (2)


title: HIC_Reenter_TOP2A2B_bothcontrol_rep2

description:
G2 phase arrest by 21h treatment with a RO-3306 inhibitor, washout, cells continue in the cell cycle for 6 h and Re-enter G1 phase
TOP2A2B_bothcontrol_30.hic

data_processing:
Pair-end reads were separately aligned to reference hg38 using BWA through the Juicer(1.11.09) software to generate .hic files
We considered only high MAPQ (-q 30) in all our data, _30.hic
Genome_build: hg38
Supplementary_files_format_and_content: hic file

extract_protocol: Arima HIC KIT

value: colorectal adenocarcinoma


title: U2OS 3h Input (1)


title: IVF.Bl.2

value: Blastocyst stage


title: IVF.Mo.1


title: IVF.8c.4

source_name: IVF 8-cell stage embryos

value: 8-cell stage


title: IGG_aux

value: IGG:12-371, Milipore


title: HIC_Reenter_TOP2A2B_degron_rep2

description: G2 phase arrest by 21h treatment with a RO-3306 inhibitor, 8h treatment with Auxin, washout, cells continue in the cell cycle for 6 h with Auxin and Re-enter G1 phase

treatment_protocol: Inducible depletion of RPB1 initiated via treatment with doxycycline for 24 h to induce TIR1 expression, before addition of 500 µM indole-3-acetic acid solution (“auxin”, Sigma-Aldrich). For cell synchronization, G2/M arrest was achieved by addition of 10 µM RO-3306 inhibitor for 21 h. Following this incubation time, cells were washed with PBS, and auxin-supplemented medium was added for up to 6 h to allow cells to quantitatively enter G1. At this point, cells were harvested, where applicable resuspended in 1 µg/ml propidium iodide to counterstain DNA, and sorted using a FACS Canto II flow cytometer (Becton Dickinson).

value: 8h treatment with Auxin


title: DKO0_P1

description: WGBS

treatment_protocol: Passaged once after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid

value: Dnmt3a + Dnmt3b KO


title: IVF.8c.2


title: TKOL

description: WGBS

value: mESC

value: Dnmt3a + Dnmt3b KO + Dnmt1 shRNA


title: HIC_Reenter_TOP2A2B_control_rep2

description: G2 phase arrest by 21h treatment with a RO-3306 inhibitor, washout, cells continue in the cell cycle for 6 h and Re-enter G1 phase


title: IGG_ctrl


title: IVF.8c.3


title: HIC_Reenter_TOP2A2B_control_rep1


title: CTCF_ctrl

value: anti-CTCF:61311, Active Motif


title: HIC_Reenter_TOP2A2B_degron_rep1


title: SMC1A_aux

value: 14h treatment with Auxin

value: anti-SMC1a:ab9262, Abcam


title: IVF.8c.1


title: HIC_Reenter_sync_RNAPll_degron_rep1


title: IVF.2c.4

source_name: IVF 2-cell stage embryos

value: 2-cell stage


title: empty3D1

city: Guangzhou

first: Yuxin

last: Chen

address: Nanfang Dadao Street, Baiyun district

country: China

institute: Nanfang Hospital of Southern Medical University

data_processing:
RNA quality was verified on an Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Quality control on raw sequence data was performed using the FastQC tool. To obtain high-quality, clean data for analysis, adaptor sequence trimming and removal of low-quality reads were performed. RNA expression levels were determined by reads per kilobase per million (RPKM) mapped reads using quartile normalization and per-condition dispersion. Genes with RPKM > 1 were used for further analysis. Hierarchical clustering of representative mRNAs expressions was performed to reveal reproducibility in biological replicates. The DESeq package was used to detect differently expressed mRNAs (DEMs) between the System, Model, DPCs-P0, and Control groups, with thresholds of a two-fold change and an FDR less than 0.05.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq X Ten platform and single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 15 nt or longer than 35 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Genome_build: hg18
Supplementary_files_format_and_content: tab-deimited text files include FPKM values for each Sample.

source_name: dermal papilla cell aggregates

extract_protocol:
Total mRNAs from DHT2D, DHT3D, empty2D, and empty3D were extracted and subjected to miRNA sequencing by TRIzol reagent (Invitrogen, Gaithersburg, USA) per manufacturer instructions.
Libraries for mRNA sequencing were generated using the NEBNext Multiplex RNA Library Prep Kit for Illumina (NEB,USA) according to the manufacturer’s instructions. Briefly, First of all, ligated the 3′ SR Adaptor. Mixed 3′ SR Adaptor for Illumina, RNA and Nuclease-Free Water, mixture system after incubation for 2 minutes at 70 degrees in a preheated thermal cycler. Tube was transfer to ice. Then, add 3′ Ligation Reaction Buffer (2X) and 3′ Ligation Enzyme Mix ligate the 3′ SR Adaptor. Incubated for 1 hour at 25°C in a thermal cycler. To prevent adaptor-dimer formation, the SR RT Primer hybridizes to the excess of 3′ SR Adaptor (that remains free after the 3′ ligation reaction) and transforms the single stranded DNA adaptor into a double-stranded DNA molecule. dsDNAs are not substrates for ligation mediated. The second, ligated the 5′ SR Adaptor. Then, reverse transcription synthetic first chain. Last, PCR amplification and Size Selection. PAGE gel was used to electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: dermal papilla cells


title: empty3D2


title: HIC_Reenter_sync_control

value: untreated


title: IVF.2c.3

value: In vitro fertilization

value: total RNA > 200 nt in length


title: empty3D3


title: IVF.2c.2


title: IVF.2c.1


title: HIC_14h_G1_sorted_RNAPll_degron_auxin_2hTrip

description: 1ug/ml doxycycline treatment 24h and 500uM Auxin treatment with 14h, added Triplotide in the last 2h, sorted at G1

value: asynchronous; G1 sorted

value: Totally 14h treatment with Auxin and 2h treatment with Triplotide in the last 2h


title: CTCF_aux

value: synchronous G1 reenter sorted


title: empty2D3

source_name: dermal papilla cells

value: two-dimensional (2D)-cultured


title: Pt_I

city: München

first: Thomas

last: Magg

address: Lindwurmstr. 2a

institute: Dr. von Haunersches Kinderspital der LMU München

data_processing:
The raw reads were trimmed for raw quality reads by  Trimmomatic (Bolger et al., 2014).
The reads were mapped to human transcriptome annotations and reference  genome sequence (Ensemble 88, GRCh38) using STAR (Dobin et al., 2013).
RSEM was used for estimating  gene-level expression reported as TPM (transcripts per million) with strand-specific option (Li and Dewey,  2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: Differentially expressed genes were assessed by edgeR and pathway analysis was performed by gene set enrichment analysis (GSEA).

molecule: polyA RNA

source_name: macrophages

growth_protocol: Small clusters of human iPSCs treated with CTK solution [1mM CaCl2 (Sigma-Aldrich, St. Louis, USA), 0.25% Trypsin (Thermo Fisher Scientific), 20% KnockOut Serum Replacement (Thermo Fischer Scientific) in D-PBS (FUJIFILM Wako, Osaka, Japan)] were transferred onto mitomycin-treated or irradiated C3H10T1/2 cells (RIKEN BRC, Tsukuba, Japan) and co-cultured in IMDM medium (Sigma-Aldrich, St. Louis, USA) plus 15% FBS (Nichirei Bio, Tokyo, Japan ) containing VEGF (20ng/ml, R&D systems), insulin (10g/mL), transferrin (5.5g/mL), sodium selenite (5ng/mL), L-glutamine (2mM), monothioglycerol (0.45mM), and ascorbic acid (50g/mL) under hypoxic conditions (0.5% O2 and 0.5% CO2) for 7 days. Then, iPSCs were transferred into normoxic conditions and cultured for 7 days. On day 14, HPCs in iPSC-sacs were harvested, transferred onto ultralow attachment plates (Corning Inc.) and cultured in MEMα medium (Thermo Fisher Scientific, Waltham, USA) plus 10% FBS containing GM-CSF (100ng/mL, PeproTech Inc., Hamburg, Germany), M-CSF (50ng/mL, PeproTech Inc., Hamburg, Germany), and monothioglycerol (0.1mM) for 7 days. For macrophage terminal differentiation, cells were transferred into StemSpan ACF medium (STEMCELL technologies) containing M-CSF (100 ng/mL) and cultured for 5-7 days.

extract_protocol:
Total RNA was extracted and purified by using an RNeasy kit  (Qiagen) following manufacturer’s instructions.
Poly-A tailed mRNA isolation, library preparation and quantification were performed with NEBNext kits (New England Biolabs, Ipswich, USA) following manufacture’s instructions.
Libraries were sequenced on a NextSeq 500 (Illumina, San Diego, USA).

treatment_protocol: iPSC-derived macrophages were stimulated with 1,000 IU/mL (f/c) of human recombinant IFNa(R&D Systems, Minneapolis, USA).

value: iPSC-derived macrophages


title: Pt_I-IFNa

value: stimulated with 1,000 IU/mL (f/c) of human recombinant IFNa (R&D Systems, Minneapolis, USA)


title: Pt_C-IFNa


title: HIC_14h_G1_sorted_RNAPll_degron_auxin

description: 1ug/ml doxycycline treatment 24h and 500uM Auxin treatment with 14h, sorted at G1

value: colorectal adenocarcinoma


title: SMC1A_ctrl


title: Oo.4

source_name: MII stage oocytes

growth_protocol: The oocytes were cultured in TCM199 maturation medium containing Earle’s salts, L-glutamine, and sodium bicarbonate (Hyclone, Logan, Utah) supplemented with 10% (v/v) fetal bovine serum (FBS) (Hyclone, lot number AC10240545), 0.05 mg/ml bovine follicle stimulating hormone (Sioux Biochemicals, Sioux city, IA), 5 mg/ml bovine luteinizing hormone (Sioux Biochemical, Sioux Center, Iowa), 100 U/ml penicillin, and 100 mg/ml streptomycin.

value: MII oocyte

value: oocyte culture


title: empty2D1


title: DHT3D3

source_name: DHT treated dermal papilla cell aggregates


title: Oo.3


title: HIC_14h_G1_sorted_control

description: normal cultured cells and sorted at G1


title: HIC_Reenter_sync_RNAPll_degron_rep2

value: 8h treatment with Auxin


title: DHT3D2


title: Pt_A-IFNa


title: HIC_2h_async_RNAPll_degron_rep2

description: 1ug/ml doxycycline treatment 24h and 500uM Auxin treatment with 2h

value: asynchronous

value: 2h treatment with Auxin


title: empty2D2


title: DHT3D1


title: DHT2D3

source_name: DHT treated dermal papilla cells

value: dihydrotestosterone (DHT)-treated two-dimensional (2D)-cultured


title: HIC_2h_async_RNAPll_degron_rep1


title: Ct2-IFNa


title: Pt_A


title: Oo.1


title: Fb.4

source_name: Fibroblast cells

growth_protocol: Primary bovine fibroblast cultures were established from ear biopsy tissues from a Brahma Spanish bull cross using well-established procedures (Kubota, et al. 2000. PNAS 97:990-995).

value: fibroblast

value: fibroblast culture


title: HIC_2h_async_control_rep2

value: untreated


title: DHT2D2

value: dermal papilla cells


title: DHT2D1


title: Fb.3

value: total RNA > 200 nt in length


title: Ct1-IFNa


title: Pt_C


title: Oo.2


title: Fb.2


title: Fb.1


title: Ct1


title: Human Galbladder

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

data_processing:
Basecalls performed using BCL2Fastq version 2.20
Sequenced reads were trimmed for low-quality sequence by using Sickle (V1.33).
Adapter sequence were trimmed by using CutAdapt (v1.5)
After preprocessing, the sequenced reads were mapped to hg19 human reference genome using RSEM (v.1.2.31) with STAR (v2.5.2b)
Merged expression level from paired end reads and orphan read and calculate merged transcript per million (TPM) by using in-house script.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file which contains gene & transcript ID, transcript size, effective size, count, and TPM.

source_name: Human gallbladder tissue

growth_protocol: Generation of hCdHs was done through a two-step collagenase perfusion, hepatocytes were extracted and seeded on a collagen-coated plate (STEMCELL Technologies, BC, Canada) for a day in William’s E media (Gibco, CA, USA). The next day, the media was changed to DMEM/F12 (Gibco, CA, USA) supplemented with 20 ng/ml of hepatocyte growth factor (HGF) (Peprotech), 3 μM CHIR99021 (STEMCELL Technologies), and 4 μM A83-01 (Gibco) named HAC. A week later, hCdHs were generated. Cholangiocyte differentiation of these hCdHs to hCdH-chols was also done following a previously published method. To induce differentiation of the hCdHs to cholangiocytes (hCdH-chols), we used our recently published protocol . Briefly, hCdHs were seeded in a gelatin (Sigma) coated plated with DMEM/F12 supplemented for two weeks with 7.5 ng/ml epithelial growth factor (EGF), 7.5 μM CHIR and 7.5 ng/ml HGF as well as 10 μM sodium taurocholate hydrate (Sigma) on day 12-14 named CDM media.

extract_protocol:
Total RNAs were isolated using Trizol Reagent (Gibco). 1-μg RNA samples were reverse transcribed using a Transcriptor First Strand cDNA Synthesis Kit (Roche, PA, USA).
A library was independently prepared with 1 µg of total RNA for each sample using an Illumina TruSeq Stranded mRNA Sample Prep Kit (#RS-122-2101, Illumina, Inc., San Diego, CA, USA). The initial step of library preparation involved purifying poly‐A containing mRNA molecules using poly‐T-attached magnetic beads. After this step, the purified mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved mRNA fragments were copied to the top strand of cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers, and the reverse complement strand of cDNA was synthesized using DNA polymerase I, RNase H, and dUTP. These cDNA fragments underwent the ends repair process including the addition of a single ‘A’ base and adapter ligation. After these steps, the final cDNA libraries were created, purified, and enriched with PCR

value: primary cholangiocytes


title: WT_2

city: Shanghai

first: Bo O.

last: Zhou

address: 320 Yueyang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

data_processing:
Aligned reads and gene-barcode matrices were then generated from FASTQ files including Read 1, Read 2 and i7 index using Cell Ranger (v.2.1.1) processing pipeline
Further analyses were performed with R package Seurat (v3.1). Genes expressed in fewer than three cells in a sample were excluded. Threshold of unique counts over 5000 or less than 500 was set to filter cell doublets. Low-quality cells that have > 10% mitochondrial counts were filtered
To correct batch effects between different samples, we used the Seurat alignment method which used canonical correlation analysis (CCA) for data integration.
The key parameters of ‘FindClusters’ were set with dims.use = 1:15 and resolution = 0.06.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts

source_name: liver

extract_protocol:
gradient centrifugation with 25% and 50% percoll
Single cell library was generated using Chromium Single Cell 3’ Library Kit v2
10X genomics

treatment_protocol: enzymatic dissociation of mouse livers

value: liver

tag: age


title: Quant-Seq Day 9 Brownjohn-iMicroglia PBS Rep 01

status: Public on Jun 17 2021

city: San Francisco

first: Martin

last: Kampmann

state: CA

address: 675 Nelson Rising Ln

institute: UCSF

data_processing:
QuantSeq: Alignment and mapping were performed using Salmon version 1.4.0 (Patro et al., 2017), with the --noLengthCorrection flag and either the human reference genome GRCh38 (Gencode, release 37), or a custom GRCh38 reference genome containing the references for each 3TF transgene integrated in iTF-iPSCs, to obtain transcript abundance counts. CROP-Seq: Alignment and gene expression quantification was performed on scRNAseq libraries and sgRNA-enriched libraries using Cell Ranger (version 5.0.1, 10X Genomics) with default parameters and reference genome GRCh38-3.0.0. Cellranger aggr was used to aggregate counts belonging to the same sample across different GEM wells. The resulting gene vs. cell barcode matrix contained 58,302 cells which had on average 41,827 reads per cell, and a median of 3,346 genes per cell.
QuantSeq: Tximport version 1.18.0 (Soneson et al., 2015) was used to obtain gene-level count estimates. Genes with zero counts across all samples were removed from the analysis. CROP-seq: sgRNA unique molecular identifier (UMI) counts for each cell barcode were obtained using a previously described mapping workflow (Hill et al., 2018). To facilitate sgRNA identity assignment, a combination of demuxEM (Gaublomme et al., 2019) and a z-score cut-off method we previously described (Tian et al., 2019) were used such that only cells with a single sgRNA as determined by both methods were carried forward in the analysis.
QuantSeq: For differential gene expression analysis of LPS-treated vs. PBS-treated iTF-Microglia samples, DESeq2 version 1.30.1 (Love et al., 2014) was used to calculate the log-fold-change and p-values and perform shrinkage of log-fold-change for downstream visualization using ggplot2 version 3.3.3. CROP-seq: The raw gene vs. barcode matrix outputted by Cell Ranger was converted into a SingleCellExperiment (SCE) object using the read10xCounts function from the DropletUtils package version 1.10.3 (Lun et al., 2019) in R (v 4.0.3). sgRNA assignments were appended to the SCE metadata and filtered to only include cells with a single sgRNA, resulting in 28,905 cells. The SCE was converted into a Seurat object using Seurat::as.Seurat version 4.0.1 (Hao et al., 2020).
CROP-Seq: The data was normalized and highly variable genes were identified using Seurat::SCTransform (Hafemeister and Satija, 2019). For initial data exploration, principal-component analysis was performed using Seurat::RunPCA to determine the number of principal components to retain. UMAP dimensional reduction using Seurat::RunUMAP and clustering using Seurat::FindNeighbors and Seurat::FindClusters were performed on the retained principal components with resolution = 0.7.
CROP-Seq: To determine the differentially expressed genes between UMAP clusters, Seurat::FindAllMarkers was used.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data files for CROP-seq are hdf5 formatted matrices of UMI counts, with rows as genes and columns as cell barcodes, obtained from running cellranger count.

source_name: Day 9 Brownjohn-iMicroglia

growth_protocol: For CROP-seq, inducible CRISPRi-iTF-iPSCs were infected with the pooled sgRNA library at <0.15 MOI and then selected for lentiviral integration. For both QuantSeq and CROP-seq, iTF-iPSCs were differentiated into iTF-microglia and cultured with the addition of TMP with the following conditions: iTF-iPSCs were grown in StemFlex until reaching at least 50% confluency and were grown for at least 24h without ROCK inhibitor. They were dissociated with Accutase and centrifuged and pelleted cells were resuspended in Day 0 differentiation medium containing the following: Essential 8™ Basal Medium (Gibco; Cat. No. A15169-01) as a base, 10nM ROCK inhibitor, and 2 mg/ml Doxycycline (Clontech; Cat. No. 631311). iTF-iPSCs were counted and seeded onto double coated plates (Poly-D-Lysine-precoated Bio plates (Corning, assorted Cat. No.) + Matrigel coating) with the following seeding densities: 10,000 cells/well for 96-well plate, 0.1 Mio/well for 12-well plate, 0.15 Mio/well for 6-well plate, 2 Mio/dish for 10-cm dish, and 8 Mio/dish for 15-cm dish. On day 2, media was replaced with Day 2 differentiation media containing Advanced DMEM/F12 Medium (Gibco; Cat. No. 12634-010) as a base medium containing the following: 1X Antibiotic-Antimycotic (Anti-Anti) (Gibco; Cat. No. 15240-062), 1X GlutaMAX™ (Gibco; Cat. No. 35050-061), 2 mg/ml doxycycline, 100 ng/ml Human IL34 (Peprotech; Cat. No. 200-34) and 10 ng/ml Human GM-CSF (Peprotech; Cat. No. 300-03). On day 4 and day 6, the medium was replaced with iTF-Microglia medium, containing Advanced DMEM/F12 as a base medium and the following: 1X Anti-Anti, 1X GlutaMAX, 2 mg/ml doxycycline, 100 ng/ml Human IL-34 and 10 ng/ml Human GM-CSF, 50 ng/ml Human M-CSF (Peprotech; Cat. No. 300-25) and 50 ng/ml Human TGFB1 (Peprotech; Cat. No. 100-21C).

extract_protocol:
For QuantSeq, cell culture medium was aspirated, cells were washed once with DPBS, and RNA lysis buffer was added directly to wells containing either Day 0 iTF-iPSCs, Day 9 iTF-Microglia or Brownjohn-iMG +/- 100 ng/ml 24h LPS treatment, or Day 15 iTF-Microglia. Biological triplicates for each condition (approximately 0.15 Mio cells each) were pelleted, snap frozen, and stored at -80°C. RNA was extracted using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1055). For CROP-seq, Day 8 iTF-Microglia were washed 3X with DPBS, dissociated with TrypLE, and resuspended in nuclease-free water before loading onto four wells of the 10x Chromium Controller (10x Genomics, v3.1) according to the manufacturer’s protocol, with 35,000 cells recovered per sample as the target.
For QuantSeq, libraries were prepared from total RNA (473 ng per sample) using the QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) (Lexogen; Cat. No. 015UG009V0252) following the manufacturer’s instructions. Library amplification was performed with 14 total PCR cycles. mRNA-seq library concentrations (mean of 1.13 ± 0.66 ng/uL) were measured with the Qubit dsDNA HS Assay Kit (Invitrogen; Cat. No. Q32851) on a Qubit 2.0 Fluorometer. Library fragment-length distributions (mean of 287 ± 28 bp) were quantified with High Sensitivity D5000 Reagents (Agilent Technologies; Cat. No. 5067-5593) on the 4200 TapeStation System. The libraries were sequenced on an Illumina NextSeq 2000 instrument with single-end reads. For CROP-seq, sample preparation was performed using the Chromium Next GEM Single Cell 3′ Reagent Kits version 3.1 (10x Genomics, cat. no. PN-1000121) according to the manufacturer’s protocol, reserving 10-30 ng full-length cDNA to facilitate sgRNA assignment by amplifying sgRNA-containing transcripts using hemi-nested PCR reactions adapted from a previously published approach (Hill et al., 2018; Tian et al., 2019). cDNA fragment analysis was performed using the 4200 TapeStation System and sgRNA enrichment libraries were separately indexed and sequenced as spike-ins alongside the whole-transcriptome scRNA-seq libraries using a NovaSeq 6000 using the following configuration: Read 1: 28; i7 index: 8; i5 index: 0; Read 2: 91.

treatment_protocol: For QuantSeq, treatment with PBS (control) or 100 ng/ml 24h LPS treatment on Day 8 iTF-Microglia or Brownjohn-iMicroglia

value: Brownjohn-iMicroglia

value: Day 9 PBS


title: Quant-Seq Day 9 Brownjohn-iMicroglia PBS Rep 03


title: Quant-Seq Day 9 Brownjohn-iMicroglia PBS Rep 02


title: Quant-Seq Day 9 Brownjohn-iMicroglia LPS Rep 01

value: Day 9 LPS


title: Quant-Seq Day 15 iTF-Microglia Rep 03

source_name: Day 15 iTF-Microglia

value: iTF-Microglia

value: Day 15 LPS


title: Ct2

value: iPSC-derived macrophages


title: Quant-Seq Day 9 Brownjohn-iMicroglia LPS Rep 03


title: Quant-Seq Day 9 Brownjohn-iMicroglia LPS Rep 02


title: HIC_2h_async_control_rep1

value: colorectal adenocarcinoma


title: Quant-Seq Day 15 iTF-Microglia Rep 01


title: hCdH-Chols

source_name: Cholagiocytes derived from human chemically induced hepatic stem cells (hCdHs)

value: cholangiocytes from hCdHs


title: Quant-Seq Day 9 iTF-Microglia PBS Rep 02

source_name: Day 9 iTF-Microglia


title: Quant-Seq Day 9 iTF-Microglia PBS Rep 03


title: Quant-Seq Day 9 iTF-Microglia PBS Rep 01


title: Quant-Seq Day 9 iTF-Microglia LPS Rep 02


title: Quant-Seq Day 9 iTF-Microglia LPS Rep 03


title: Quant-Seq Day 0 iTF-Microglia Rep 02

source_name: Day 0 iTF-Microglia

value: Day 0 LPS


title: WT_1


title: SoyV-stage3-rep2

city: Blacksburg

first: Song

last: Li

state: VA

institute: Virginia Tech

description:
PA_ABEV_merged_samples.featurecount
V32

data_processing:
Raw reads were trimmed and filtered using Skewer (version 0.2.2) to remove adapter sequences and low-quality reads and bases (<Q30)
Using STAR (version 2.5.2b), the cleaned reads were aligned to ‘Williams82,’ the well-annotated soybean reference genome (Wm82.a2.v1, downloaded from Phytozome)
Transcript abundances were calculated from the mapping results using featureCounts
These results were subsequently used for differential expression analysis with DESeq2 (version 1.22.2) in R (version 3.5.1)
Genome_build: Wm82.a2.v1, downloaded from Phytozome
Supplementary_files_format_and_content: PA_ABEV_merged_samples.featurecount

organism: Glycine max

source_name: seeds

growth_protocol: Tissue from each line was sampled at three stages of seed germination in biological triplicate with ten seeds per sample. The germination stages used were mature dry seeds (stage 1), eight hour imbibed seeds (stage 2), and germinated seeds (defined as radicle emergence; stage 3). For stage 1, seeds were ground to a fine powder using a P14 mill (Pulverisette 14, Fritsch) and stored at -80°C until use. Seeds for stages 2 and 3 were sterilized for two minutes with a 10% hypochlorite + Tris solution, washed in DI water three times for five minutes, and dried overnight. The seeds were then germinated on germination plates with filter paper and DI water in the dark at 29°C.

extract_protocol:
Once the appropriate stage was reached, seed coats and radicles were removed, and the tissue was flash frozen with liquid nitrogen and stored at -80°C until use. The tissue from these stages was ground to powder with mortar, pestle, and liquid nitrogen.
Total RNA from all stages was extracted using the RNeasy Plant Kit with on-column DNase digestion and RLC buffer (QIAGEN, Hilden, Germany). RNA quality was determined by UV spectrophotometry (260 nm, NanoDrop1000, Thermo Fischer Scientific, Waltham, MA) and RNA integrity numbers (RIN) (BioAnalyzer, Agilent Technologies, Santa Clara, CA). Samples with a RIN value >8.0 and 260/280 ratios >2.0 were submitted to Novogene (Sacramento, CA) for mRNA sequencing. A total of 72 samples (8 lines x 3 germination stages x 3 biological replicates) were sequenced (Illumina, San Diego, CA) to acquire 30 million, 150 PE reads per sample.

treatment_protocol: see growth protocol

value: seed


title: Quant-Seq Day 0 iTF-Microglia Rep 03


title: SoyV-stage3-rep3

description:
PA_ABEV_merged_samples.featurecount
V33


title: Quant-Seq Day 0 iTF-Microglia Rep 01


title: SoyV-stage3-rep1

description:
PA_ABEV_merged_samples.featurecount
V31


title: SoyV-stage2-rep3

description:
PA_ABEV_merged_samples.featurecount
V23


title: SoyV-stage2-rep1

description:
PA_ABEV_merged_samples.featurecount
V21


title: Quant-Seq Day 9 iTF-Microglia LPS Rep 01


title: Quant-Seq Day 15 iTF-Microglia Rep 02


title: SoyV-stage2-rep2

description:
PA_ABEV_merged_samples.featurecount
V22


title: SoyV-stage1-rep1

description:
PA_ABEV_merged_samples.featurecount
V11


title: SoyE-stage2-rep3

description:
PA_ABEV_merged_samples.featurecount
E23


title: SoyE-stage2-rep2

description:
PA_ABEV_merged_samples.featurecount
E22


title: SoyE-stage3-rep1

description:
PA_ABEV_merged_samples.featurecount
E31


title: SoyE-stage1-rep1

description:
PA_ABEV_merged_samples.featurecount
E11


title: SoyE-stage1-rep3

description:
PA_ABEV_merged_samples.featurecount
E13


title: SoyE-stage1-rep2

description:
PA_ABEV_merged_samples.featurecount
E12


title: BAA-stage3-rep3

description:
PA_ABEV_merged_samples.featurecount
B33


title: BAA-stage3-rep1

description:
PA_ABEV_merged_samples.featurecount
B31


title: BAA-stage2-rep2

description:
PA_ABEV_merged_samples.featurecount
B22


title: BAA-stage2-rep1

description:
PA_ABEV_merged_samples.featurecount
B21


title: BAA-stage3-rep2

description:
PA_ABEV_merged_samples.featurecount
B32


title: BAA-stage1-rep2

description:
PA_ABEV_merged_samples.featurecount
B12


title: SoyV-stage1-rep2

description:
PA_ABEV_merged_samples.featurecount
V12


title: BAA-stage1-rep1

description:
PA_ABEV_merged_samples.featurecount
B11


title: ABB-stage3-rep3

description:
PA_ABEV_merged_samples.featurecount
A33


title: ABB-stage3-rep2

description:
PA_ABEV_merged_samples.featurecount
A32


title: ABB-stage2-rep3

description:
PA_ABEV_merged_samples.featurecount
A23


title: ABB-stage3-rep1

description:
PA_ABEV_merged_samples.featurecount
A31


title: SoyV-stage1-rep3

description:
PA_ABEV_merged_samples.featurecount
V13


title: SoyE-stage3-rep2

description:
PA_ABEV_merged_samples.featurecount
E32


title: SoyE-stage3-rep3

description:
PA_ABEV_merged_samples.featurecount
E33


title: C57BL/6 mouse embryonic stem cells, clone 2 #1

city: New York

first: Claudia

middle: A

last: Doege

state: New York

address: 1150 Saint Nicholas Ave

department: Pathology

institute: Columbia University

description:
944410_B6E_1
mESC B6-2_1

data_processing:
Raw sequence data (BCL files) were converted to FASTQ format via Illumina Casava 1.8.2
All samples were aligned to mouse assembly GRCm38 cDNA sequence downloaded from Ensembl with Kallisto. Fragment size set as 120 with standard deviation as 20, default seed as 42, with 100 bootstrap per sample
Genome_build: GRCm38
Supplementary_files_format_and_content: .csv file

extract_protocol:
Mouse samples: PicoPure RNA Isolation Kit (Fisher Scientific, #KIT0204) with on-column DNaseI (Qiagen), mESCs: RNeasy Plus Micro Kit (Cat # 74034; Qiagen) with on-column DNaseI treatment
KAPA mRNA-Seq Library Preparation Kit (Kapa Biosystems). Twelve-cycle PCR was performed to amplify libraries. Sequencing was performed on Illumina HiSeq®2000 (Illumina) by multiplexed single-read run with 33 cycles

treatment_protocol: Dissection of adult and embryonic mouse brains, guided by the Allen Brain Atlas

value: C57BL/6 derived mESCs, clone 2


title: C57BL/6 mouse embryonic stem cells, clone 2 #2

description:
944411_B6E_2
mESC B6-2_2


title: C57BL/6 mouse embryonic stem cells, clone 1 #1

description:
944477_B6A_1
mESC B6-1_1

value: C57BL/6 derived mESCs, clone 1


title: SoyE-stage2-rep1

description:
PA_ABEV_merged_samples.featurecount
E21


title: ABB-stage2-rep2

description:
PA_ABEV_merged_samples.featurecount
A22


title: C57BL/6 mouse embryonic stem cells, clone 1 #2

description:
944478_B6A_2
mESC B6-1_2


title: ABB-stage1-rep3

description:
PA_ABEV_merged_samples.featurecount
A13


title: BAA-stage2-rep3

description:
PA_ABEV_merged_samples.featurecount
B23


title: Ventral tegmental area #3

source_name: Ventral tegmental area

value: Ventral tegmental area


title: Ventral tegmental area #2


title: ABB-stage2-rep1

description:
PA_ABEV_merged_samples.featurecount
A21


title: BAA-stage1-rep3

description:
PA_ABEV_merged_samples.featurecount
B13


title: ABB-stage1-rep2

description:
PA_ABEV_merged_samples.featurecount
A12


title: Ventromedial hypothalamic nucleus #2

source_name: Ventromedial hypothalamic nucleus

value: Ventromedial hypothalamic nucleus


title: Ventromedial hypothalamic nucleus #1


title: Uvula (IX) #3

source_name: Uvula (IX)

value: Uvula (IX)


title: ABB-stage1-rep1

description:
PA_ABEV_merged_samples.featurecount
A11


title: 2MWT-L-stage3-rep3

description:
PA_MRP_merged_samples.featurecount
W33

data_processing:
Raw reads were trimmed and filtered using Skewer (version 0.2.2) to remove adapter sequences and low-quality reads and bases (<Q30)
Using STAR (version 2.5.2b), the cleaned reads were aligned to ‘Williams82,’ the well-annotated soybean reference genome (Wm82.a2.v1, downloaded from Phytozome)
Transcript abundances were calculated from the mapping results using featureCounts
These results were subsequently used for differential expression analysis with DESeq2 (version 1.22.2) in R (version 3.5.1)
Genome_build: Wm82.a2.v1, downloaded from Phytozome
Supplementary_files_format_and_content: PA_MRP_merged_samples.featurecount (represents read counts)

extract_protocol:
Once the appropriate stage was reached, seed coats and radicles were removed, and the tissue was flash frozen with liquid nitrogen and stored at -80°C until use. The tissue from these stages was ground to powder with mortar, pestle, and liquid nitrogen.
Total RNA from all stages was extracted using the RNeasy Plant Kit with on-column DNase digestion and RLC buffer (QIAGEN, Hilden, Germany). RNA quality was determined by UV spectrophotometry (260 nm, NanoDrop1000, Thermo Fischer Scientific, Waltham, MA) and RNA integrity numbers (RIN) (BioAnalyzer, Agilent Technologies, Santa Clara, CA). Samples with a RIN value >8.0 and 260/280 ratios >2.0 were submitted to Novogene (Sacramento, CA) for mRNA sequencing. A total of 72 samples (8 lines x 3 germination stages x 3 biological replicates) were sequenced (Illumina, San Diego, CA) to acquire 30 million, 150 PE reads per sample.
paired end


title: 2MWT-L-stage3-rep1

description:
PA_MRP_merged_samples.featurecount
W31


title: Uvula (IX) #1


title: 2MWT-L-stage2-rep3

description:
PA_MRP_merged_samples.featurecount
W23


title: Embryonic Terminal (rostral) and peduncular (caudal) hypothalamus #3


title: Uvula (IX) #2


title: Embryonic Terminal (rostral) and peduncular (caudal) hypothalamus #2


title: 2MWT-L-stage2-rep2

description:
PA_MRP_merged_samples.featurecount
W22


title: 2MWT-L-stage2-rep1

description:
PA_MRP_merged_samples.featurecount
W21


title: Embryonic Terminal (rostral) and peduncular (caudal) hypothalamus #1


title: Paraventricular hypothalamic nucleus #2

source_name: Paraventricular hypothalamic nucleus

value: Paraventricular hypothalamic nucleus


title: 2MWT-L-stage1-rep1

description:
PA_MRP_merged_samples.featurecount
W11


title: 2MWT-L-stage1-rep2

description:
PA_MRP_merged_samples.featurecount
W12


title: Parabrachial nucleus #3

source_name: Parabrachial nucleus

value: Parabrachial nucleus


title: 2MWT-L-stage1-rep3

description:
PA_MRP_merged_samples.featurecount
W13


title: Ventral tegmental area #1


title: 2MWT-N-stage3-rep3

description:
PA_MRP_merged_samples.featurecount
V33


title: Parabrachial nucleus #2


title: 2MWT-N-stage3-rep2

description:
PA_MRP_merged_samples.featurecount
V32


title: Parabrachial nucleus #1


title: 2MWT-L-stage3-rep2

description:
PA_MRP_merged_samples.featurecount
W32


title: Nucleus of the solitary tract #3

source_name: Nucleus of the solitary tract

value: Nucleus of the solitary tract


title: 2MWT-N-stage2-rep3

description:
PA_MRP_merged_samples.featurecount
V23


title: 2MWT-N-stage3-rep1

description:
PA_MRP_merged_samples.featurecount
V31


title: Nucleus of the solitary tract #1


title: 2MWT-N-stage2-rep2

description:
PA_MRP_merged_samples.featurecount
V22_1


title: Nucleus of the solitary tract #2


title: Embryonic Midbrain #2

source_name: Embryonic Midbrain

value: Embryonic Midbrain


title: 2MWT-N-stage1-rep3

description:
PA_MRP_merged_samples.featurecount
V13


title: Nucleus of the solitary tract #4


title: 2MWT-N-stage1-rep2

description:
PA_MRP_merged_samples.featurecount
V12


title: Paraventricular hypothalamic nucleus #1


title: Embryonic Midbrain #1


title: 2MWT-N-stage1-rep1

description:
PA_MRP_merged_samples.featurecount
V11


title: Lateral hypothalamic area #2

source_name: Lateral hypothalamic area

value: Lateral hypothalamic area


title: 2mlpa-stage3-rep2

description:
PA_MRP_merged_samples.featurecount
D32


title: 2MWT-N-stage2-rep1

description:
PA_MRP_merged_samples.featurecount
V21


title: 2mlpa-stage3-rep1

description:
PA_MRP_merged_samples.featurecount
D31


title: Lateral hypothalamic area #1


title: 2mlpa-stage2-rep2

description:
PA_MRP_merged_samples.featurecount
D22


title: Lateral hypothalamic area #3


title: Embryonic Hindbrain #3

source_name: Embryonic Hindbrain

value: Embryonic Hindbrain


title: Embryonic Hindbrain #2


title: Embryonic Hindbrain #1


title: 2mlpa-stage2-rep1

description:
PA_MRP_merged_samples.featurecount
D21


title: 2mlpa-stage3-rep3

description:
PA_MRP_merged_samples.featurecount
D33


title: Frontal pole cortex #3

source_name: Frontal pole cortex

value: Frontal pole cortex


title: 2mlpa-stage1-rep3

description:
PA_MRP_merged_samples.featurecount
D13


title: Frontal pole cortex #2


title: 2mlpa-stage1-rep2

description:
PA_MRP_merged_samples.featurecount
D12


title: Frontal pole cortex #1


title: Flocculus #4

source_name: Flocculus

value: Flocculus


title: 2mlpa-stage2-rep3

description:
PA_MRP_merged_samples.featurecount
D23


title: 2mlpa-stage1-rep1

description:
PA_MRP_merged_samples.featurecount
D11


title: 2MWT-stage3-rep2

description:
PA_MRP_merged_samples.featurecount
C32


title: 2MWT-stage3-rep3

description:
PA_MRP_merged_samples.featurecount
C33


title: Flocculus #3


title: 2MWT-stage2-rep1

description:
PA_MRP_merged_samples.featurecount
C21


title: 2MWT-stage2-rep3

description:
PA_MRP_merged_samples.featurecount
C23


title: Flocculus #2


title: 2MWT-stage2-rep2

description:
PA_MRP_merged_samples.featurecount
C22


title: Entorhinal area #1

source_name: Entorhinal area

value: Entorhinal area


title: Dorsal-vagal complex #3

source_name: Dorsal-vagal complex

value: Dorsal-vagal complex


title: Flocculus #1


title: Dorsal-vagal complex #2


title: 2MWT-stage1-rep1

description:
PA_MRP_merged_samples.featurecount
C11


title: Entorhinal area #3


title: 2MWT-stage1-rep2

description:
PA_MRP_merged_samples.featurecount
C12


title: Dorsal-vagal complex #1


title: Dorsomedial nucleus of the hypothalamus #7

source_name: Dorsomedial nucleus of the hypothalamus

value: Dorsomedial nucleus of the hypothalamus


title: Dorsomedial nucleus of the hypothalamus #6


title: 2MWT-stage3-rep1

description:
PA_MRP_merged_samples.featurecount
C31

value: seed


title: melphalan_NG25_rep3

city: Trondheim

first: Kristine

last: Misund

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: NTNU

data_processing:
Single read sequencing was performed for 75 cycles on a NextSeq500 HO flowcell (Illumina, San Diego, CA, USA), according to the manufacturer's instructions. Base calling was done on the NextSeq500 instrument by RTA 2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v2.20.0.422 (Illumina, Inc. San Diego, CA, USA).
FASTQ files were filtered and trimmed (fastp v0.20.0) and transcript counts were generated using quasi alignment (Salmon v1.3.0) to the transcriptome reference sequence (Ensembl, GRCh38 release100). Transcript sequences were imported into the R statistical software and aggregated to gene counts using the tximport (v1.14.0) bioconductor package.
Genome_build: GRCh38
Supplementary_files_format_and_content: File with raw gene counts for every gene and every sample

source_name: INA-6 (human multiple myeloma cell line)

extract_protocol:
Total RNA was then extracted using RNeasy Mini kits including DNAse digestion with Qiacube (QIAGEN, Hilden, Germany, 74104). RNA quantity, quality/integrity and purity were evaluated using Qubit (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent, CA, USA) and NanoDrop (Thermo Fisher Scientific, MA, USA).
RNA sequencing libraries were generated for 12 RNA samples, using SENSE mRNA-Seq library prep kit V2, according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria).
Libraries were quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, CA, USA). The size range of the DNA fragments were measured to be in the range of 200-450 bp with average library size 240 bp.

treatment_protocol: INA-6 cells were treated with 2 μM NG25 or 10 μM melphalan or both for 6 hours.

value: treated with 10 μM melphalan and 2 μM NG25 for 6 hours

value: human multiple myeloma


title: melphalan_NG25_rep2


title: H66

city: Atlanta

first: James

last: Dahlman

state: ga

address: 311 Ferst dr

institute: Georgia Institute of Technology

description:
Pooled Replicates (JD69)
Humanized_counts.txt

data_processing:
Used FastProNGS for preprocessing of reads, used standard preamters
Samples were mapped to both mouse and human genomes using RNAstar, paramters used "SortedByCoordinate --twopassMode None '' --quantMode - --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM ch --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outSAMunmapped Within --outBAMsortingThreadN ${GALAXY_SLOTS:-4} --outBAMsortingBinsN 50 --limitBAMsortRAM "
htseq-cout was used to create determine counts, parameters used "--mode=union --stranded=no --minaqual=5 --type='exon' --idattr='gene_id'"
iDep9.1 was used to normalize and analyze dataset
Genome_build: MM10 and GRCh38
Supplementary_files_format_and_content: tab delimited table of raw counts

extract_protocol:
Tween20 whole cell without RNA extraction
SMART-seq2 protocol scaled up to 1000 cells

value: Liver

tag: iv injection

value: LNP

tag: pooled replicates

value: Yes

tag: repopulated


title: Dorsomedial nucleus of the hypothalamus #5


title: Embryonic Forebrain

source_name: Embryonic Forebrain

value: Embryonic Forebrain


title: melphalan_NG25_rep1

tag: treatment

tag: cell line


title: Culmen lobules IV-V #4

source_name: Culmen lobules IV-V

tag: tissue

value: Culmen lobules IV-V


title: Dorsomedial nucleus of the hypothalamus #4


title: NG25_rep1

value: treated with 2 μM NG25 for 6 hours


title: Culmen lobules IV-V #3


title: NG25_rep3


title: melphalan_rep3

value: treated with 10 μM melphalan for 6 hours


title: melphalan_rep1


title: Central lobule II #3

source_name: Central lobule II

value: Central lobule II


title: Central lobule II #2


title: negative_control_rep3

value: untreated


title: Central lobule II #4


title: Culmen lobules IV-V #1


title: melphalan_rep2


title: Central lobule II #1


title: negative_control_rep2


title: negative_control_rep1


title: Cerebellar nuclei #2

source_name: Cerebellar nuclei

value: Cerebellar nuclei


title: Cerebellar nuclei #3


title: Arcuate hypothalamic nucleus #3

source_name: Arcuate hypothalamic nucleus

value: Arcuate hypothalamic nucleus


title: HepG2_EDN1_3 [G2-EDN1-3]

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

country: South Korea

institute: Chungnam National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read raw count values for each Sample

growth_protocol: HepG2 (Mock and EDN1 O/E) cells were cultured in DMEM supplemented with 10% FBS and antibiotics (100 units/mL of penicillin, 100 μg/ml of streptomycin, and 0.25 μg/ml of Fungizone; Life Technologies Corp.) at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells with RNA-spinTM (iNtRON, Republic of Korea).
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Hepatocellular carcinoma

tag: genotype/variation

value: EDN1 O/E


title: Cerebellar nuclei #1


title: HepG2_EDN1_2 [G2-EDN1-2]


title: HepG2_EDN1_4 [G2-EDN1-4]


title: NG25_rep2


title: HepG2_EDN1_1 [G2-EDN1-1]


title: HepG2_Mock_4 [G2-M4]

value: mock


title: Culmen lobules IV-V #2


title: Nucleus accumbens #3

source_name: Nucleus accumbens

value: Nucleus accumbens


title: Arcuate hypothalamic nucleus #2


title: Arcuate hypothalamic nucleus #1


title: HepG2_Mock_2 [G2-M2]


title: HepG2_Mock_3 [G2-M3]


title: HepG2_Mock_1 [G2-M1]


title: Nucleus accumbens #2


title: Anterior cingulate area #3

source_name: Anterior cingulate area

value: Anterior cingulate area


title: Nucleus accumbens #1


title: Anterior cingulate area #1


title: U2OS_siRFX7_Nutlin_3_RNAseq

city: Jena

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Quantification and quality check of libraries were performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 Kit. Sequence information was extracted in FastQ format using Illumina's bcl2FastQ v2.19.1.403.
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports. Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1. The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.92, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled (RNA-seq) or disabled (ChIP-seq). Mappings were filtered by Samtools v1.10 for uniqueness and properly aligned mate pairs. We removed duplicated reads with Picard MarkDuplicates v2.23.4.
Read quantification was performed on exon level using featureCounts v1.6.5, parametrized according to the strand specificity inferred through RSeQC v3.0.0. Differential gene expression and its statistical significance was identified using DeSeq2 v1.20.0.
Genome_build: hg38
Supplementary_files_format_and_content: .csv DESeq2 output

extract_protocol:
Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer protocol.
Libraries were constructed from 500 ng of total RNA using Illumina's TruSeq stranded mRNA Library Preparation Kit following the manufacturer's description.

treatment_protocol: Treated for 24h with 10 µM Nutlin-3a or DMSO solvent control


title: U2OS_siRFX7_Nutlin_4_RNAseq


title: Anterior cingulate area #2


title: U2OS_siRFX7_Nutlin_1_RNAseq


title: U2OS_siRFX7_DMSO_4_RNAseq

value: DMSO


title: U2OS_siRFX7_DMSO_3_RNAseq


title: U2OS_siRFX7_DMSO_2_RNAseq


title: U2OS_siRFX7_DMSO_1_RNAseq


title: U2OS_siControl_Nutlin_4_RNAseq


title: U2OS_siControl_Nutlin_3_RNAseq


title: U2OS_siRFX7_Nutlin_2_RNAseq


title: U2OS_siControl_Nutlin_1_RNAseq


title: U2OS_siControl_DMSO_2_RNAseq


title: U2OS_siControl_DMSO_3_RNAseq


title: U2OS_siControl_DMSO_4_RNAseq


title: U2OS_siControl_DMSO_1_RNAseq


title: SUM159 cells 1%-2

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
Fastq files were subject to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig

source_name: SUM159 cells

growth_protocol: Cells were cultured with DMEM or DMEM/Ham's F12+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
libraries were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina.

treatment_protocol: Cells were exposed to 20% or 1% O2 for 24 hrs


title: SUM159 cells 1%-1


title: Pool 2 Stimulated 6h rep2

type: RNA

city: CUSANO MILANINO

first: Raffaella

last: Rossetti

state: Italy

address: VIA ZUCCHI 18

country: Italy

institute: IRCCS ISTITUTO AUXOLOGICO ITALIANO

description:
5635005036_J.idat
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation by the function normaliseIllumina in the Bioconductor package beadarray

label: biotin

source_name: granulosa cells

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion) for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed by spectrophotometric determination of OD 260/280

value: granulosa cells

value: ovary

tag: beadchip

tag: pool

value: Stimulated

tag: time


title: U2OS_siControl_Nutlin_2_RNAseq


title: Pool 2 Stimulated 6h rep1

description:
5635005036_H.idat
Replicate 1

tag: cell type


title: Pool 2 Stimulated 2h rep3

description:
5635005036_F.idat
Replicate 3


title: Pool 2 Non-stimulated 2h rep3

description:
5635005035_L.idat
Replicate 3

value: Non-stimulated


title: Pool 2 Stimulated 0h rep3

description:
5635005036_K.idat
Replicate 3


title: Pool 2 Stimulated 2h rep1

description:
5635005036_B.idat
Replicate 1


title: SUM159 cells 20%-1


title: Pool 2 Non-stimulated 6h rep2

description:
5635005036_C.idat
Replicate 2


title: Pool 2 Stimulated 6h rep3

description:
5635005036_L.idat
Replicate 3


title: Pool 2 Non-stimulated 6h rep3

description:
5635005036_E.idat
Replicate 3


title: Pool 2 Stimulated 2h rep2

description:
5635005036_D.idat
Replicate 2


title: SUM159 cells 20%-2


title: Pool 2 Stimulated 0h rep1

description:
5635005036_G.idat
Replicate 1


title: Entorhinal area #2

tag: strain

value: Entorhinal area


title: Pool 2 Stimulated 0h rep2

description:
5635005036_I.idat
Replicate 2

tag: genotype


title: MDA-MB-231 cells 1%-2

source_name: MDA-MB-231 cells


title: Pool 2 Non-stimulated 6h rep1

description:
5635005036_A.idat
Replicate 1


title: MDA-MB-231 cells 1%-1


title: Pool 2 Non-stimulated 0h rep3

description:
5635005035_F.idat
Replicate 3


title: MDA-MB-231 cells 20%-2


title: 20OE2

data_processing:
Basecalls performed using bcl2fastq (v2.17)
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
ChIP-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc), fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and mapped to human genome (hg19) using bowtie2 (version 2.2.3), filtering out alignments with mapping quality less than 10. Duplicate alignments were removed using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). The ChIP-seq peaks were called using MACS2 (version 2.0.10), with a q-value threshold of 0.05 and using the input ChIP samples as controls.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig
Supplementary_files_format_and_content: Read counts

growth_protocol: Cells were cultured with DMEM+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen). Chromatin was isolated, sonicated to 200-300 bp in length, and subjected to immunoprecipitation overnight with respective antibodies. The ChIP DNA was eluted, decrosslinked, and purified.
mRNA-seq libraries were prepared with a KAPA mRNA Hyper Prep kit. ChIP-seq libraries were prepared with a ThruPlex DNA-seq kit.

tag: overexpression


title: MDA-MB-231 cells 20%-1


title: 20OE1


title: 20EV2

value: empty vector


title: 20EV1


title: Pool 2 Non-stimulated 2h rep2

description:
5635005035_J.idat
Replicate 2


title: Pool 2 Non-stimulated 0h rep2

description:
5635005035_D.idat
Replicate 2


title: Pool 2 Non-stimulated 0h rep1

description:
5635005035_B.idat
Replicate 1


title: 1OE2


title: 1OE1


title: Pool 2 Non-stimulated 2h rep1

description:
5635005035_H.idat
Replicate 1


title: Pool 1 Stimulated 6h rep3

description:
5635005035_K.idat
Replicate 3


title: Pool 1 Stimulated 2h rep3

description:
5635005035_E.idat
Replicate 3


title: Pool 1 Stimulated 6h rep2

description:
5635005035_I.idat
Replicate 2


title: HIF-2A_CHIPSEQ

value: HIF-2alpha (HOMEMADE)


title: 1EV1


title: Pool 1 Stimulated 0h rep3

description:
5635005034_L.idat
Replicate 3


title: Pool 1 Stimulated 2h rep1

description:
5635005035_A.idat
Replicate 1


title: Pool 1 Stimulated 2h rep2

description:
5635005035_C.idat
Replicate 2


title: dORFH1

city: Haifa

first: Marina

last: Katsman

address: Technion City

department: Biotechnology and Food Engineering

country: Israel

institute: Technion

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adaepter trimming: trim galore (uses cutadapt version 1.10)
Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: Htseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.18.1
Supplementary_files_format_and_content: raw counts

source_name: NIH3T3 with deleted dNVEGF under hypoxia

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Library preparation kit v2 was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To study the effect N-VEGF removal on cellular transcriptome profile, RNA was extracted from cells expressing either dN-VEGF or NIH3T3 wt and subjected in triplicates to RNA-Seq using next-generation sequencing (NGS).

value: mouse embryonic fibroblasts

value: dNVEGF deletion

value: hypoxia


title: Pool 1 Stimulated 0h rep2

description:
5635005034_J.idat
Replicate 2


title: dORFH3


title: Pool 1 Stimulated 6h rep1

description:
5635005035_G.idat
Replicate 1


title: 1EV2


title: dORFH2


title: dORFN2

source_name: NIH3T3 with deleted dNVEGF under normoxia

value: normoxia


title: Pool 1 Stimulated 0h rep1

description:
5635005034_H.idat
Replicate 1


title: Donor 3 control IgG1

city: Erlangen

first: Andrej

last: Stoll

address: Schwabachanlage 12

department: Department of Medicine 5 - Hematology and Oncology

institute: Friedrich-Alexander University Erlangen Nuremberg

data_processing:
Reads in FASTQ format were analysed withfastqc (v0.11.9) and remaining adapter sequences were trimmed by cutadapt (v2.8) with the following parameters: -j 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -m 40
Reads were mapped against the human genome (GENCODE GRCh38.p13 v33) using STAR v2.7.3a with the following parameters:  --runThreadN 4  --genomeLoad LoadAndKeep   --outSAMtype BAM SortedByCoordinate  --outSAMunmapped Within --outSAMattributes Standard
All non-multimapping and non-multi-overlapping reads mapping to exons were counted using featureCounts (v2.0.0) using the following parameters: featureCounts -T 4 -s 2 -t exon -g gene_id -a gencode.v33.annotation.gtf

source_name: Monocyte

growth_protocol: PBMC were isolated by density gradient centrifugation of peripheral blood of healthy donors. Monocytes were purified by MACS and subsequently cultured in antibody-coated 48-well platesfor 4d. Cells were detached using EDTA.

extract_protocol:
RNA was isolated from the cells using an innuPREP DNA/RNA Mini Kit (analytic Jena, 845-KS-2080250) according to the manufacturer’s recommended protocol. Approx. 300 ng RNA of each total RNA sample was used as template.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wells of TC plate used for culture were pre-coated with either mouse IgG1 control mAb or CD137 agonistic mAb 4B4-1

value: Monocyte

value: control IgG1

tag: donor

value: healthy donor


title: H44

value: Liver

value: PBS

value: Yes


title: dORFN1


title: Donor 2 control IgG1


title: dORFN3


title: 3T3H3

source_name: NIH3T3 wt cells under hypoxia

value: wild type


title: Pool 1 Non-stimulated 6h rep1

description:
5635005034_B.idat
Replicate 1

value: granulosa cells

value: ovary


title: Pool 1 Non-stimulated 6h rep2

description:
5635005034_D.idat
Replicate 2

value: Non-stimulated


title: Pool 1 Non-stimulated 2h rep3

description:
5635005034_K.idat
Replicate 3


title: Pool 1 Non-stimulated 0h rep2

description:
5635005034_C.idat
Replicate 2


title: Pool 1 Non-stimulated 2h rep2

description:
5635005034_I.idat
Replicate 2


title: Pool 1 Non-stimulated 6h rep3

description:
5635005034_F.idat
Replicate 3


title: Donor 1 control IgG1


title: Pool 1 Non-stimulated 0h rep1

description:
5635005034_A.idat
Replicate 1


title: 3T3H2


title: Pool 1 Non-stimulated 0h rep3

description:
5635005034_E.idat
Replicate 3


title: Pool 1 Non-stimulated 2h rep1

description:
5635005034_G.idat
Replicate 1


title: 3T3H1


title: Donor 3 CD137  triggering

value: CD137 triggering


title: Donor 2 CD137  triggering


title: 3T3N3

source_name: NIH3T3 wt cells under normoxia


title: Donor 1 CD137 triggering


title: 3T3N1


title: 2MWT-stage1-rep3

description:
PA_MRP_merged_samples.featurecount
C13

source_name: seeds

value: seed


title: 3T3N2


title: U2OS_RFX7_Nutlin_1

data_processing:
Quantification and quality check of libraries were performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 Kit. Sequence information was extracted in FastQ format using Illumina's bcl2FastQ v2.20.0.422.
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports. Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1. The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.92, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled (RNA-seq) or disabled (ChIP-seq). Mappings were filtered by Samtools v1.10 for uniqueness and properly aligned mate pairs. We removed duplicated reads with Picard MarkDuplicates v2.23.4.
biological replicates of each input and IP were pooled prior to peak calling with MACS2 v2.2.7.1 with q-value cutoff 0.05. MACS2 was executed in both available modes utilizing either the learned or a customized shifting model parameterized according to the assumed mean fragment length of 150bp as extension size. The resulting peak sets were merged by overlap with BEDTools v2.29.2. Per interval, the strongest enrichment signal under the associated peak summits as well as the lowest p-value and q-value was kept. ENCODE blacklist regions were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: .narrowPeak file contains the RFX7 ChIP peaks that have been called by MACS2

extract_protocol:
ChIP was performed with the SimpleChIP Kit (Cell Signaling Technology) following the manufacturer instructions. 3 µg of RFX7 (#A303-062A Bethyl Laboratories) antibody was used per IP
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, Frankfurt am Main, Germany) following the manufacturer's description.


title: ORF_dox2_290419

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adaepter trimming: trim galore (uses cutadapt version 1.10)
Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: Htseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.18.1
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: raw count text file

source_name: MEFs_expressing N-VEGF following dox treatment

treatment_protocol: To study the effect of nuclear NLS-N-VEGF on cellular transcriptome profile, RNA was extracted from cells expressing either N-VEGF or NLS-N-VEGF prior or following exposure to dox and subjected in triplicates to RNA-Seq using next-generation sequencing (NGS).

tag: genotype/treatment


title: U2OS_RFX7_DMSO_2

value: DMSO


title: U2OS_RFX7_Nutlin_2


title: U2OS_RFX7_DMSO_1


title: ORF_dox1_120519

value: mouse embryonic fibroblasts

value: expressing N-VEGF following dox treatment


title: U2OS_Input_Nutlin_2


title: ORF_dox2_120519


title: ORF2_290419

source_name: MEFs_expressing N-VEGF

value: expressing N-VEGF


title: U2OS_Input_Nutlin_1


title: ORF2_120519


title: H2O2-treated HDFs_rep2

first: Ji-Hwan

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

hyb_protocol: The amplified cRNA was hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 microarray chips containing 62,976 probes for 23,627 annotated genes.

scan_protocol: The hybridized chips were scanned with an Agilent Microarray Scanner D (Agilent, Santa Clara, CA).

data_processing: Quantile-normalization was performed on the log2-intensities from gMedianSignal

source_name: Human diploid fibroblasts (HDFs), H2O2-treated, passage=12

label_protocol: The RNA was amplified and labeled with Cy3-dCTP, according to the standard Agilent One-Color microarray protocol (Agilent, V6.5, 2010).

growth_protocol: Normal neonatal HDFs (PCS-201-010, American Type Culture Collection) were cultured in Dulbecco’s Modified Eagle’s Medium (1×) with 10% fetal bovine serum (Hyclone) containing 100 U/ml penicillin and 100μg/ml streptomycin (Hyclone). Cells were grown at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated from young HDFs and young HDFs treated with LMB, WGA, RCC shRNA, H2O2, doxorubicin, and RasV12, as well as HDFs at passage = 53. RNA purity and integrity were evaluated by ND-1000 spectrophotometer (NanoDrop) and Bioanalyzer 2100 (Agilent), respectively. The RNA integrity number of the samples was 9.4 on average.

treatment_protocol: For WGA or LMB treatment, cells were treated with either 6 μg/ml WGA (Sigma) or 0.1 μg/ml LMB (Sigma). Cells were serially passaged, and young proliferating and senescent cells were collected at doubling time (DT) ≤ 1 day and ≥ 14 days, respectively. For RasV12 overexpression, young HDFs (5x105) were infected with RasV12-expressing lentivirus at a MOI of 2. For H2O2, young HDFs were treated with 250 μM of H2O2 for 1 day and further grown in media without drug for 7 days. For doxorubicin treatement, young HDFs were treated with 0.5 μM of doxorubicin for 1 day and further grown in media without drug for 7 days.

value: HDFs

tag: passage number

tag: batch

tag: replicate


title: Doxorubicin-treated HDFs_rep2

source_name: Human diploid fibroblasts (HDFs), Doxorubicin-treated, passage=12

value: Doxorubicin


title: H2O2-treated HDFs_rep3


title: HDFs overexpressing RasV12_rep2

source_name: Human diploid fibroblasts (HDFs), Overexpression of RasV12, passage=12


title: Young HDFs_batch 3_rep1

description: Controls to compare with H2O2 Doxorubicin-treated HDFs

source_name: Human diploid fibroblasts (HDFs), No treatment, passage=12

value: No treatment


title: U2OS_Input_DMSO_2


title: TGF

city: Suita

first: Sho

last: Tabata

state: Osaka

address: 3-2 Yamadaoka

department: Institute for Protein Research,ces

country: Japan

institute: Osaka University

description:
AR1833_08_TGF
Gene expression in A549 cells treated with TGF-beta for 72h.

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (11.5.1.1) (10.10.1.1) (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor.

source_name: cell line: A549 cells treated with TGF-beta

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: A549 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer's protocol, including on-column DNase I incubation for 15 min at room temperature to reduce genomic DNA contamination. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: A549 cells were treated with 5ng/ml TGF-beta for 72 h.

value: TGF-beta

tag: duration

tag: gender

value: male

tag: age


title: CONT

description:
AR1833_07_CONT
Gene expression in A549 cells treated with vehicle for 72h.

source_name: cell line: A549 cells (control)

tag: cell line

tag: treatment

value: Vehicle


title: ORF1_120519


title: H2O2-treated HDFs_rep1


title: Doxorubicin-treated HDFs_rep3


title: Doxorubicin-treated HDFs_rep1


title: NLS_DOX2_290419

source_name: MEFs_expressing NLS-N-VEGF following dox treatment


title: RCC1 shRNA-treated HDFs_rep1

source_name: Human diploid fibroblasts (HDFs), RCC1 shRNA-treated, passage=12

value: RCC1 shRNA


title: Young HDFs_batch 3_rep2


title: HDFs overexpressing RasV12_rep3


title: HDFs overexpressing control ORF_rep3

description: Controls to compare with HDFs overexpressing RasV12

source_name: Human diploid fibroblasts (HDFs), Overexpression of control ORF, passage=12

value: control ORF


title: Control shRNA-treated HDFs_rep1

description: Controls to compare with RCC1 shRNA-treated HDFs

source_name: Human diploid fibroblasts (HDFs), Control shRNA-treated, passage=12

value: Control shRNA


title: RCC1 shRNA-treated HDFs_rep2


title: HDFs overexpressing control ORF_rep1


title: RCC1 shRNA-treated HDFs_rep3


title: NLS_DOX2_120519

value: expressing NLS-N-VEGF following dox treatment


title: Control shRNA-treated HDFs_rep3


title: NLS_DOX1_120519


title: HDFs overexpressing control ORF_rep2


title: Control shRNA-treated HDFs_rep2


title: HDFs overexpressing RasV12_rep1


title: RS HDFs_rep1

source_name: Human diploid fibroblasts (HDFs), No treatment, passage=53


title: RS HDFs_rep2


title: RS HDFs_rep3


title: LMB-treated HDFs_rep2

source_name: Human diploid fibroblasts (HDFs), LMB-treated, passage=12

value: LMB


title: NLS2_290419

source_name: MEFs_expressing NLS-N-VEGF

value: expressing NLS-N-VEGF


title: DOT1L KD HEL Ser2p ChIP-seq

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, PRO-seq and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, PRO-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.

source_name: DOT1L KD HEL Ser2p ChIP-seq

growth_protocol: Human cells HEL cells were cultured in RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin + 2 mM L-Glutamine + 55 μM β-mercaptoethanol. Human cells K562 were cultured in 90% DMEM + 10% FBS+ 2% Penicillin/Streptomycin + 2 mM L-Glutamine.

extract_protocol:
For immunoprecipitation, on day 1 antibodies were diluted in RIPA-0.3 and bound to Dynabeads protein A (Thermo, cat. no. 10002D) by incubating at 4 °C for 3 hours. Afterwards, the bead-antibody complexes were washed twice with RIPA-0.3 and then incubated with sonicated chromatin at 4 °C overnight. On day 2, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.25% NP-40, and 0.25% NaDOC, pH 7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, 0.2 M NaCl, and 1% SDS, pH 7.4) supplemented with 10 µg/ml RNase A for both elution and RNA digestion, and incubated at 55 °C for 1 hour. Then Proteinase K was added to a final concentration of 200 µg/ml, and after 30 min incubation the temperature was increased to 65 °C for crosslink reversal. After incubation for 4 to 6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205).
ChIP-seq libraries: The libraries were constructed with 2–10 ng immunoprecipitated DNA. After end-repair, A-tailing, and barcode ligation, barcoded DNA was amplified by 16-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

treatment_protocol: For double fixation with EGS (Thermo, cat. no. 21565) and formaldehyde, cells were fixed initially with 1.5 mM EGS at room temperature for 30 min, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For double fixation with DMA (Thermo, cat. no. 20660) and formaldehyde, cells were fixed initially with 25 mM DMA at room temperature for 1 hour, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For sonication, fixed cells were washed twice with PBS and resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH 7.4) supplemented with Protease Inhibitor Cocktail (Millipore, cat. no. 535140) at a concentration of 40 million cells/ml; genomic DNA was disrupted to a size range of 100 to 500 bp.

value: HEL

tag: genotype/variation

value: DOT1L knockdown

tag: fixation

value: EGS + FA

tag: chip antibody

value: Pol II (ser-2p)


title: DOT1L KD HEL Pol II ChIP-seq

source_name: DOT1L KD HEL Pol II ChIP-seq

value: DMA + FA

value: Pol II


title: WGA-treated HDFs_rep2

source_name: Human diploid fibroblasts (HDFs), WGA-treated, passage=12

tag: cell type

value: HDFs

value: WGA


title: control HEL Pol II ChIP-seq

source_name: control HEL Pol II ChIP-seq

value: control


title: LMB-treated HDFs_rep1


title: control HEL Ser2p ChIP-seq

source_name: control HEL Ser2p ChIP-seq


title: NLS2_120519

value: mouse embryonic fibroblasts


title: WGA-treated HDFs_rep3


title: Young HDFs_batch 1_rep3

description: Controls to compare with RS and WGA- and LMB-treated HDFs

value: No treatment


title: LMB-treated HDFs_rep3


title: U4_EDL

city: Tokyo

first: Ruslan

last: Deviatiiarov

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

department: Intractable Disease Research Center

institute: Juntendo University

description: nAnTi-CAGE

data_processing:
Reads were trimmed using fastx_trimmer and removeN scripts from Moirai pipeline (http://fantom.gsc.riken.jp/software/). Adapters were removed by using Trimmomatic-0.38
Trimmed reads mapped on Rnor_6.0 Ensembl genome assembly for Rattus norvegicus using BWA, unmapped reads remapped by Hisat2 and merged into processed BAM files
BAM files used to generate CTSS (CAGE transcription start site) tables in OSC format (https://zenbu-wiki.gsc.riken.jp/zenbu/wiki/index.php/OSCtable) using PromoterPipeline script level1.py (https://github.com/Population-Transcriptomics/C1-CAGE-preview/blob/master/tutorial.md)
OSC files merged into Level2_table.osc by using level2.py from PromoterPipeline.
Genome_build: Rnor_6.0 (GCA_000001895.4)
Supplementary_files_format_and_content: OSC files contain information about position and strand of mapped CAGE reads, column for raw and TPM (tags per million) normalized counts included. Level2_table.osc table contains clustered CAGE signal representing putative promoter regions with expression level within all experiments in raw and TPM normalized counts for these clusters.

organism: Rattus norvegicus

source_name: hindlimb

extract_protocol:
Total RNA was extracted from EDL and Soleus muscles using RNeasy Fibrous Tissue Mini Kit QIAGEN
5 µg of total RNA RIN≥7 processed into cDNA by reverse transcriptase. CAGE libraries prepared according to Murata et al., 2014 (doi: 10.1007/978-1-4939-0805-9_7).

tag: tissue

value: EDL muscle

tag: protocol

value: unloading 7 days; recovery 3 days


title: U19_EDL

description: nAnTi-CAGE

value: unloading 7 days; recovery 7 days


title: U19_Sol

description: nAnTi-CAGE

value: soleus muscle


title: shSC_20%_2

data_processing:
Basecalls performed using bcl2fastq (v2.17)
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Genome_build: hg19
Supplementary_files_format_and_content: TXT

source_name: MDA-MB-231 cells

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
mRNA-seq libraries were prepared with a  KAPA mRNA  Hyper Library Preparation kit.

value: MDA-MB-231 cells

tag: knockdown

value: scrambled control


title: shSC_20%_1


title: U10_EDL

description: nAnTi-CAGE

value: unloading 3 days


title: control HEL PRO-seq

data_processing:
library strategy: PRO-seq
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, PRO-seq and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, PRO-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.

source_name: control HEL PRO-seq

extract_protocol:
Nuclear run-on and RNA isolation, RNA fragementation and Biotin RNA enrichment.
3' RNA adaptor ligation and second biotin RNA enrichment, enzymatic modification of the RNA 5' ends, 5‘ RNA adaptor ligation and biotin RNA enrichment, Reverse transcription, PCR amplification and library size selection, and then sequencing.

value: HEL


title: Young HDFs_batch 1_rep2

source_name: Human diploid fibroblasts (HDFs), No treatment, passage=12


title: Young HDFs_batch 1_rep1


title: WGA-treated HDFs_rep1


title: shCHD4_20%_2


title: DOT1L KD HEL RNA-seq rep2

description:
RLib28_GTGAAA_L003
processed data file: HEL.RNA-seq.read_count.txt

source_name: DOT1L KD HEL RNA-seq

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

value: DOT1L knockdown


title: DOT1L KD HEL RNA-seq rep1

description:
RLib27_CCGTCC_L003
processed data file: HEL.RNA-seq.read_count.txt


title: shCHD4_20%_1


title: U16_EDL

description: nAnTi-CAGE


title: U5_EDL

description: nAnTi-CAGE


title: U13_Sol

description: nAnTi-CAGE


title: U16_Sol

description: nAnTi-CAGE


title: DOT1L KD HEL PRO-seq

source_name: DOT1L KD HEL PRO-seq


title: U24_EDL

description: nAnTi-CAGE

value: unloading 24 hours


title: shSC_1%_2


title: control HEL RNA-seq rep1

description:
RLib25_CAGATC_L003
processed data file: HEL.RNA-seq.read_count.txt

source_name: control HEL RNA-seq


title: U13_EDL

description: nAnTi-CAGE


title: U12_EDL

description: nAnTi-CAGE


title: U5_Sol

description: nAnTi-CAGE


title: U4_Sol

description: nAnTi-CAGE


title: shSC_1%_1