title: THP1-T27-RPMI,Unsorted-replC

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

description: Library name: MPH_7406

data_processing:
Reads from each sample were mapped to the TKOv3 or mTKO reference library using Bowtie (v0.12.8) allowing up to two mismatches and one exact alignment (specific parameters: -v2, -m1, -p4 -sam-nohead). Successfully aligned reads were counted and combined into a matrix with guide annotations.
Read counts were normalized to 10 million reads per sample and log fold-changes (LFC) of each gRNA between each timepoint and T0 were determined. Guides with fewer than 30 or greater than 10,000 absolute read counts at T0 were removed.
The sorting arm of the screens was analyzed using a version of the quantitative genetic interaction (qGI) algorithm, as previously described (Chan et al., 2023, PMID: 36597481). LFCs in sorted samples relative to the starting time point were quantified. LFCs were M-A transformed by calculating M, the per-sgRNA difference (bottom 15% - top 15%), and A, the per-sgRNA average. Then, a LOESS curve of degree 2 and 40% span along A was fitted, followed by calculation of residuals or effect sizes by subtracting M from its LOESS-predicted value. Gene-level P-values were calculated from effect sizes by moderated t-testing, and P-values were adjusted to control the false discovery rate (FDR) using the Benjamini-Hochberg method. Significant hits were called at an FDR < 0.05.
Assembly: mTKO CRISPR Library; TKOv3 CRISPR Library
Supplementary files format and content: Tab-delimited read count matrix
Library strategy: CRISPR Screen

growth_protocol: RAW264.7 and J774A.1 cells were maintained in culture in DMEM (Wisent, #319-005-CL) supplemented with 10% fetal bovine serum (Gibco, #12483-020). BV-2, THP-1, and U-937 cells were maintained in culture in RPMI-1640 (Wisent, 350-000-CL) supplemented with 10% fetal bovine serum. RAW264.7, J774A.1, and BV-2 cells are adherent cells and were routinely detached from plates with trypsin-EDTA (Gibco, #25200056). THP-1 and U-937 grow in suspension. All cell lines were maintained in humidified incubators at 37 °C and 5% CO2 and were routinely tested for mycoplasma contamination.

extract_protocol:
Genomic DNA from cell pellets was extracted using the Wizard Genomic DNA Purification Kit (Promega, #A1120) following a previously described protocol (Ngo et al., 2022, PMID: 35953550). Briefly, unsorted cell pellets were thawed at room temperature for 5 minutes and resuspended in 1.4 mL of PBS (Wisent, #311-425-CL), lysed in 5 mL of Nuclei Lysis Solution (part of Wizard Genomic DNA Purification Kit) and mixed by pipetting. 32 µL of RNase A (Invitrogen, #12091021) to a final concentration of 100 µg/mL was added to the lysate and incubated at 37°C for 15 minutes. 1.67 mL of Protein Precipitation Solution (part of Wizard Genomic DNA Purification Kit) was added to the lysate, vortexed vigorously for 20 seconds, and centrifuged at 4500 g for 10 minutes at room temperature. The supernatant was transferred to a tube containing 5 mL of isopropanol (Caledon Laboratories, #8600-1-40) and gently mixed by inversion until DNA was observed as thread-like white strands. DNA was collected by centrifugation at 4500 g for 5 minutes and gently washed with 5 mL of 70% ethanol (Commercial Alcohols, #P006-EAAN). DNA was collected by centrifugation at 4500 g for 5 minutes, air-dried to remove residual ethanol, resuspended in 400 µL of TE buffer, and incubated at 65°C for 2-3 hours, with gently flicking every 15 minutes, until the DNA appeared completely dissolved. Sorted (fixed) cells were incubated at 55°C overnight with 120 µL of 0.5 M EDTA (BioShop, #EDT111.5000), 500 µl of Nuclei Lysis Solution, and 20 µL of proteinase K (NEB, #P8107S). The next day, the protocol described above was applied with 1/8 of the described volumes. DNA was quantified using Qubit double-stranded DNA Broad Range Assay reagents (Invitrogen, #Q33266). DNA was stored at -20°C prior to sequencing library preparation.
Sequencing libraries were prepared as previously described (Chan et al., 2019, PMID: 31545321). Briefly, libraries were prepared from 105 µg of genomic DNA from non-sorted samples or 10-20 µg of genomic DNA from sorted samples by a two-step PCR reaction. PCR1 consisted of 25 µL of NEBNext Ultra II Q5 Master Mix (NEB, #M0544X), 2.5 µL of 10 µM PCR1 forward and reverse primers, 3.5 µg of purified genomic DNA, and UltraPure™ DNase/RNase-Free distilled water to reach a 50 µL reaction volume. PCR1 products from the same genomic DNA sample were pooled and used for a single PCR2 reaction. Each PCR2 reaction consisted of 25 µL of NEBNext Ultra II Q5 Master Mix, 2.5 µL of 10 µM i5 forward and i7 reverse primers, 5 µL of pooled PCR1 product, and 15 µL of UltraPure™ DNase/RNase-Free distilled water. PCR2 products were separated by gel electrophoresis, and ~200 bp bands corresponding to PCR2 amplicons were excised from the gel and purified using the PureLink™ Quick Gel Extraction Kit following manufacturer’s instructions. Samples were stored at -20°C prior to sequencing. Samples corresponding to the starting time point were sequenced at 500-fold library coverage. All other samples were sequenced at read depths equivalent to 200-fold coverage.

treatment_protocol: The human Toronto knockout (TKOv3) genome-scale CRISPR library (Addgene #90294) or the mouse Toronto knockout (mTKO) genome-scale CRISPR library (Addgene #159392) was used to perform pooled CRISPR knockout screens to identify modulators of SIRPA/Sirpa expression. For each screen, cells were transduced with TKOv3 or mTKO lentivirus at an MOI of ~0.3 and 200-fold library coverage. U-937 cells were infected in the presence of 8 µg/mL polybrene, RAW264.7 and THP-1 cells were infected in the presence of 4 µg/mL polybrene. RAW264.7, J774A.1, BV-2, and U-937 cells were infected for 24 hours before selection with puromycin, THP-1 cells were infected for 72 hours, instead. RAW264.7 and BV-2 cells were selected with 6 µg/mL of puromycin for 72 hours; J774A.1 and THP-1 cells were selected with 2 µg/mL of puromycin for 48 hours; and U-937 cells were selected with 1 µg/mL of puromycin for 48 hours. Cells were cultured as described, and prepared for FACS sorting as follows. Adherent cells were first detached with trypsin-EDTA (Gibco, #25200056), quenched with regular growth media, and counted. 30 to 40 million cells were collected per replicate in 10E6 cell aliquots. Each aliquot was processed separately as follows. For Fc receptor blocking, cells were washed once with PBS (Wisent, #311-425-CL) and treated with 2.5 µg of TruStain FcX™ PLUS (BioLegend, #156604) in the case of mouse cells, or 150 µL of Fc receptor blocker (Innovex Biosciences, #NB309-30) in the case of human cells, following manufacturers’ instructions. For Sirpa/SIRPA staining, mouse cells were treated with 2 µg of FITC-conjugated rat anti-mouse Sirpa antibody (BioLegend, #144006) in 200 µL of FACS buffer (1% BSA (BioShop, #ALB003.100) and 0.1% NaN3 (Sigma-Aldrich, #8032)) for 45 minutes on ice in the dark, whereas human cells were treated with 2 µg of recombinant human CD47-Fc chimera (R&D Systems, #4670-CD-050) in 100 µL of FACS buffer for 45 minutes on ice, followed by washing with FACS buffer and staining with 1.5 µg of Alexa Fluor 488-conjugated anti-Fc antibody (Jackson ImmunoResearch, #109-545-008) in 100 µL of FACS buffer on ice in the dark. Recombinant human CD47-Fc chimera was used as a surrogate of an anti-SIRPA antibody. For fixation, cells were washed twice with 1 mL of FACS buffer, resuspended in 400 µL of 1.6% ice-cold PFA (Electron Microscopy Sciences, #157-4-100) and incubated for 10 minutes at 4°C in the dark. Cells were washed twice with 1 mL of PBS, resuspended in 2 mL of FACS buffer and filtered through a 35 µm nylon mesh. Cells were sorted by FACS into HIGH (top 15%) and LOW (bottom 15%) SIRPA/Sirpa fluorescence, and sorted cells and unsorted controls were collected for genomic DNA extraction.

value: monocyte

value: Transduced with TKOv3 CRISPR library

tag: sample group


title: THP1-T17-RPMI,Unsorted-replB

status: Public on Jun 03 2025

type: SRA

description: Library name: MPH_7396

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: THP1-T27-RPMI,Unsorted-replA

description: Library name: MPH_7404


title: THP1-T17-RPMI,Top 15-replC

description: Library name: MPH_7412

value: THP1-T17-RPMI,Top 15


title: THP1-T17-RPMI,Bottom 15-replB

description: Library name: MPH_7408

value: THP1-T17-RPMI,Bottom 15


title: THP1-T17-RPMI,Top 15-replA

description: Library name: MPH_7410


title: THP1-T17-RPMI,Top 15-replB

description: Library name: MPH_7411


title: THP1-T17-RPMI,Bottom 15-replC

description: Library name: MPH_7409


title: THP1-T17-RPMI,Unsorted-replA

description: Library name: MPH_7395


title: THP1-T27-RPMI,Unsorted-replB

description: Library name: MPH_7405


title: THP1-T17-RPMI,Unsorted-replC

description: Library name: MPH_7397


title: THP1-T17-RPMI,Bottom 15-replA

description: Library name: MPH_7407


title: fc2_pub4_16h_rep3

city: Tucson

first: Jesse

middle: Daniel

last: Woodson

state: AZ

address: 1140 E. South Campus Drive, 303 Forbes Hall

department: School of Plant Sciences

country: USA

institute: University of Arizona

library_source: transcriptomic

data_processing:
Each sample is represented by two raw files. Concatenation of RAW fastq files was done as: cat file1.fastq file2.fastq > mergedfile.fastq
Data was processed and reads were aligned to the Arabidopsis TAIR10 genome using the CyVerse's Discovery Environment: RMTA (Read Mapping, Transcript Assembly) v.2.6.3 (HISAT2, Stringtie) pipeline with default parameters. Reference: Peri et al., 2020; doi: 10.3389/fgene.2019.01361. PMID: 32038716. HISAT2 (v2.1.0) was used to align sequencing reads. Reads were assembled into transcripts using StringTie (v1.3.4).
The “feature_counts.txt” file obtained from RMTA was used as input for differential gene expression statistical analyses using DESeq2 in R studio (available through CyVerse) with default parameters.
The DESeq2 was performed between samples (i.e., wt vs. mutants in 24h or cycling (16h) light conditions)
Assembly: TAIR10 reference sequence
Supplementary files format and content: feature_counts.txt: tab-delimited text file that includes feature counts of all 18 samples
Supplementary files format and content: deseq2.xlsx: Excel file that includes Gene ID, base mean, Log2Fold Change, fold change, lfcSE, p value, and padj. Each tab is a pairwise comparison between wt and a mutant (fc2 or fc2 pub4) in 24h or 16h (cycling) light conditions.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: total leaf tissue

growth_protocol: Seeds were sterilized and spread on plates containing Linsmaier and Skoog medium pH 5.7 with 0.6% micropropagation type-1 agar powder. Following 3-5 day stratification at 4°C in the dark, seeds were germinated in 24h constant light (permissive) conditions. Seven-day-old plants were then transfered to soil and grown under 120 μmol photons m-2 sec-1 light, at 21°C and 60% humidity.

extract_protocol:
RNA was harvested from total leaf tissue was collected from 19-day-old plants one hour after subjective dawn. Samples were collected in biological triplicates, each replicate consisting of leaves pooled from three plants. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) and residual DNA was removed with the RNase-Free DNase Kit (Qiagen).
A Qubit 2.0 Fluorometer was used to calculate RNA concentration and 4 mg of total RNA was used to prepare libraries with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, US).

treatment_protocol: Plants were grown under constant (24h) light conditions for 17 days and then shifted to cycling (16h) light conditions (16h light / 8h dark) for 2 days. As a control. A second set of plants reminaed in 24 constant light conditions for the full 19 days.

tag: tissue

value: total leaf tissue

tag: genotype

value: 17 days constant light, 2 days 16hlight/8hdark cycling light

tag: time point

value: harvested 1 hour post subjective dawn on day 19


title: HCC1806_sgC1_rep1

city: West Lafayette

first: Kyle

middle: A

last: Cottrell

state: IN

address: 201 S University Street

department: Medicine

institute: Purdue University

description:
Library name: 1-HCC1806-sgC1
rRNA depleted

data_processing:
Sequence reads were processed using Trimmomatic v.0.36 to remove adapter sequences and poor quality nucleotides. Trimmed reads were aligned to GRCh38 reference genome using STAR aligner v2.5.2b (RRID:SCR_004463). Gene counts were determined using featureCounts from Subread v.1.5.2 (RRID:SCR_009803), only unique exonic reads were counted.
Assembly: GRCh38
Supplementary files format and content: Gene counts from featureCounts, in txt file

source_name: cell line

extract_protocol:
Total RNA was purified using the Nucleospin RNA kit (Macherey-Nagel).
RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Germantown, MD, USA ), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: cell line

value: TNBC cell line


title: THP1-T0-RPMI

description: Library name: MPH_7382


title: J774_wt_ctrl_LPS_rep3

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

description: Library name: 23L006277

data_processing:
NGS data quality was assessed with FastQC (RRID: SCR 014583, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Gene-level quantification was performed with Salmon version 1.9.0 (RRID: SCR_017036 ). Settings were: -libType A, -gcBias, -biasSpeedSamp 5 using the mm39 (M28, GRCm38, mm39) reference transcriptome provided by Gencode.
Gene count normalization and differential expression analysis were performed with DESeq2 version 1.44.0 (RRID: SCR_015687 ) after import of gene-level estimates with “tximport” version 1.32.0 (RRID: SCR_016752 ) in R (RRID: SCR_001905, R version 4.4.1 ).
For gene annotation, Ensembl gene IDs were mapped to MGI symbols using the Bioconductor package “AnnotationHub” version 3.12.0 (RRID: SCR_024227), and genome information was provided by Ensembl (GRCm39 release 105).
Assembly: mm39
Supplementary files format and content: TXT files with length-scaled TPMs and Differential Expression Analysis (DESeq2) results (Log2FoldChange, p-values) for BMDMs.
Supplementary files format and content: CSV file with counts and Differential Expression Analysis (DESeq2) results (Log2FoldChange, p-values) for J774.1 cells comparing LPS-stimulated Ctbp1,2dKO cells to wild type cells.

molecule: polyA RNA

organism: Mus musculus

growth_protocol: For bone marrow-derived macrophages (BMDMs): Humerus, femur and tibia were isolated from 6-12 weeks old C57BL6/N mice (RRID:MGI:7466658), disinfected with ethanol and transferred to the cell culture hood. Using scissors, tweezers and a syringe with G27 needle, bones were opened and bone marrow was flushed into a 50 ml conical tube filled with cold RPMI 1640. Cells were collected by centrifugation (300 xg, 5 min), supernatant was aspirated and cells were suspended in AKC lysis buffer (1M NH4Cl, 1M KHCO3, 0.5M EDTA) to lyse red blood cells. Subsequently, cells were suspended in PBS, carefully layered over Ficoll Paque (GE Healthcare 17144002) and subjected to density centrifugation (500xg, 45 min, slow acceleration and deceleration). The top layer was aspirated and middle fraction was collected in a fresh conical tube filled with Differentiation medium (30% L929 supernatant, 20% FBS, 1% Penicillin/ Streptomycin, 49% DMEM high glucose). Cells were pelleted by centrifugation, supernatant was aspirated and cells were suspended and plated in Differentiation medium on 15 cm bacterial plates. After 3 days of incubation at 5% CO2 and 37 °C in a humidified incubator, half of the medium was exchanged by fresh Differentiation medium and differentiation was continued until day 6. Cells were detached by incubation in Versene (Thermo Fisher Scientific, 11518876 ) and subjected to counting using a Neubauer chamber. Finally, differentiated cells in macrophage serum free medium (Thermo Fisher Scientific, 12065074) were seeded at 905000 cells/cm2 in tissue culture treated dishes and incubated at 5% CO2 and 37 °C in a humidified incubator.; For J774.1: J774.1 (RRID: CVCL_4770) cells were cultured in DMEM high glucose (Sigma, #D6429) supplemented with 10% FBS (Sigma, #S0615) and 1% Penicillin/Streptomycin (Sigma, #P4333) at 5% CO2 and 37 °C in a humidified incubator on tissue-culture treated dishes. At approximately 70-80 % confluence cells were passaged by scraping and suspending in fresh medium pre-warmed to 37 °C. J774.1 wt and CTBP1,2dKO cells were generated by transfection of fluorescently-labeled RNP complexes with guid RNAs against CTBP1 and CTBP2, followed by FACS sorting and single cell outgrowth. Single cell clones were genotyped and knockouts were confirmed by western blot. A non-mutated single cell clone from these single cell outgrowth was used as wild type (wt) and a mutated single cell clone was used as Ctbp1/2 dKO.

extract_protocol:
RNA was isolated using the ReliPrep RNA miniprep system (Promega) following the manufacturers instructions. In brief, cells were lysed in BL+TG buffer and lysates stored at -70 °C. For isolation of RNA, lysates were mixed with 2-propanol, bound to a silica membrane washed and DNA was digested by DNAseI. After additional washes RNA was eluted in nuclease-free water. RNA concentration was measured using a Nanophotometer (Implen) and 100-1000 ng of RNA were reverse transcribed using the  Reverse Transcription System with random hexamers (Promega) following the manufacturers instructions. Thereby a control without reverse transcription was included to assess potential DNA contaminations during qPCR.
The RNA quality was determined on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano kit, following the manufacturer’s instructions. Library preparation and rRNA depletion were conducted using the TruSeq unstranded mRNA Library Prep kit (Illumina) starting with 500 ng of RNA for each biological triplicate. The samples were sequenced on the Illumina NovaSeq 6000 or NovaSeq X PLUS.

treatment_protocol: Cells were seeded and incubated over night at normal growth condition. Then vehicle (PBS) or LPS (#LPS25 Sigma, 100ng/mL) were added and cells were incubated for 4 h for RNAseq experiments

tag: Sex

value: female

value: wildtype

value: 4 h 100 ng/ml LPS

tag: replicate

tag: strain

value: BALB/c


title: Multiome, Veh Sample 1, GEX

city: Chicago

first: Serdar

middle: E.

last: Bulun

state: IL

address: 303 E Superior Street

department: Obstetrics & Gynecology

institute: Northwestern Feinberg School of Medicine

description: Library name: 1590_veh_GEX

library_source: transcriptomic single cell

data_processing:
Multiome files were demultiplexed using Cellranger mkfastq
Demultiplexed data were processed and aligned to the mm10 genome using the CellrangerArc 2.0.2 pipeline
Raw RNA counts were first decontaminated, and then low-quality cells were filtered using both RNA and ATAC QC factors. After filtering, RNA data was log-normalized, and ATAC accessibility values were normalized.
Assembly: mm10
Supplementary files format and content: The processed data from all samples used in this study is stored in a single Seurat object (.rds format).

molecule: nuclear RNA

source_name: Lower abdominal muscle

extract_protocol:
Nuclei isolated from entire LAM utilizing the Chromium Nuclei Isolation Kit with RNase Inhibitor (10X Genomics, #PN-1000494).
Libraries were constructed according to the default manual from 10X Genomics, with further details listed in You et. al. Role of progesterone receptor in inguinal hernia formation via skeletal muscle fibrosis.

treatment_protocol: WT mice 8-10 weeks of age were treated with with placebo/vehicle, E2+P4, or E2+P4+RU486 for 10 weeks before harvesting the LAM.

value: Lower abdominal muscle

value: FVB/N

value: wild-type

value: Vehicle


title: fc2_pub4_16h_rep2


title: HREC, activin, 24h, rep3

first: Andrius

last: Kazlauskas

address: 1855 W Taylor Street

department: Ophthalmology & Visual Sciences

institute: University of Illinois Chicago

description:
Library name: activin3
Column name in hrec_activin_counts.txt: activin3

data_processing:
Data processing consisted of general quality-control using FastQC before reads were aligned to the v.hg38 human reference genome in a splice-aware manner using STAR.
The abundance of genomic features (e.g., genes) were quantified as raw counts based on read alignments using featureCounts.
Gene isoforms were quantified using Kallisto, using k-mer based pseudo-alignment and expectation maximization to probabilistically assign reads to isoforms.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Human Retinal Endothelial Cells

growth_protocol: HRECs were seeded onto tissue culture dishes that were coated with a 0.04% gelatin in PBS, and cultured in Lonza EBM basal media supplemented with EGM SingleQuots, 5% penicillin–streptomycin solution and D-glucose to a final concentration of 30 mM. Cells were cultured in this medium for at least 10 days prior to use. Cells cultured in high glucose were used to model DM, and thereby are a more appropriate match to endothelial cells from patients with DM.  The culture medium was refreshed every 24 h; the cells were passaged within 24-48 h of reaching confluence.

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen).
Libraries were prepared and sequenced by the University of Chicago Genomics Facility.

treatment_protocol: Triplicate dishes of HRECs were plated onto 60 mm gelatin-coated plates and grown to confluency and then exposed to vehicle or activin (50 ng/ml) for 24h.

value: Human Retinal Endothelial Cells

value: Activin (50ng/mL)

tag: time

value: 24 hours


title: U937-T12-RPMI,Unsorted-replC

description: Library name: MPH_7070

value: monocyte

value: Transduced with TKOv3 CRISPR library


title: ChIP_SKMEL5_OE2_HMGB2

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: Library name: ChIP_SKMEL5_OE2_HMGB2

data_processing:
ChIP sequencing reads were trimmed and filtered for quality and library adapters using version 0.4.5 of TrimGalore with a quality setting of 15, and running cutadapt96 (v1.15) and FastQC (v0.11.5). Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie297 and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools. To ascertain enriched regions, MACS298 was used with a p-value setting of 0.001 and run against a matched control for each condition. A peak atlas was created by combining the superset of all peaks using the ‘merge’ function in the BEDTools suite v2.29.2. Read density profiles were created using deepTools 'bamCoverage’ v3.3.0, normalized to 10 million uniquely mapped reads and with read pileups extended to 200 bp. Version 1.6.1 of featureCounts was used to build a raw counts matrix and DESeq2 was used to calculate differential enrichment for all pairwise contrasts for experiments with replicates. For single sample data, MACS2 was run by swapping bams of different conditions to find differential regions. Peak-gene associations were created by assigning all intragenic peaks to that gene, while intergenic peaks were assigned using linear genomic distance to transcription start site. Gene set enrichment analysis91 was performed with the pre-ranked option and default parameters, where each gene was assigned the single peak with the largest (in magnitude) log2 fold change associated with it. Composite and tornado plots were created using deepTools100 (v3.3.0) by running computeMatrix and plotHeatmap on normalized bigwigs with average signal sampled in 25 bp windows and flanking region defined by the surrounding 2 kb. Motif signatures were obtained using HOMER101 (v4.5).
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Tumor

extract_protocol:
For profiling of HMGB2 binding in A375 and SKMEL5 cells, freshly harvested cells (~20 million cells/replicate/condition) were cross-linked first with 1.5 mM EGS (Thermo Fisher 21565) for 20 min at room temperature, and subsequently with 1% formaldehyde (Thermo Fisher 28906) for 40 min at 4°C. The reaction was quenched by the addition of glycine to the final concentration of 0.125 M. Fixed cells were washed twice with PBS and resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail, Roche). The resulting nuclei were spun down, resuspended in the immunoprecipitation buffer (100 mM NaCl, 100 mM TrisHCl pH 8.0, 5 mM EDTA, 5% Triton X-100) at 1 mL per 0.5 million cells mixed in 2:1 ratio, with the addition of 1x protease inhibitor cocktail (Millipore Sigma 11836170001). Nuclei were processed on a Covaris E220 Focused-ultrasonicator to achieve an average fragment length of 200-300 bp with the following parameters: PIP=140, Duty Factor=5, CBP/Burst per sec=200, Time = 20 min (for A375 cells) or 45 min (for SKMEL5 cells). Chromatin concentrations were estimated using the Pierce™ BCA Protein Assay Kit (Thermo Fisher 23227) according to the manufacturer’s instructions. The immunoprecipitation reactions were set up in 500 µL of the immunoprecipitation buffer in Protein LoBind tubes (Eppendorf 22431081) and pre-cleared with 50 µL of Protein G Dynabeads (Thermo Fisher 10004D) for two hours at 4°C. After pre-clearing, the samples were transferred into new Protein LoBind tubes and incubated overnight at 4°C with 5 µg of HMGB2 (abcam ab67282), V5 (abcam ab9116, used for SKMEL5 ChIP only) and H3K4me3 (Epicypher 13-0041) antibodies. For normalization purposes, 5 µL of Drosophila spike-in chromatin (Active Motif 53083) and 2 µL of spike-in antibody (Active Motif 61686) were added to each reaction.
The next day, 50 µL of BSA-blocked Protein G Dynabeads were added to each reaction and incubated for 2 hours at 4°C. The beads were then washed two times with low-salt washing buffer (150mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), two times with high-salt washing buffer (500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), two times with LiCL wash buffer (250 mM LiCl, 10 mM TrisHCl pH8.0, 1 mM EDTA, 1% Na-deoxycholate, 1% IGEPAL CA-630) and one time with TE buffer (10 mM TrisHCl pH 8.0, 1 mM EDTA). The samples were then reverse-crosslinked overnight in the elution buffer (1% SDS, 0.1 M NaHCO3) and purified using the ChIP DNA Clean & Concentrator kit (Zymo Research D5205) following the manufacturer’s instructions. After quantification of the recovered DNA fragments, libraries were prepared using the ThruPLEX®DNA-Seq kit (Takara R400676) following the manufacturer’s instructions, purified with SPRIselect magnetic beads (Beckman Coulter B23318), and quantified using a Qubit Flex fluorometer (Thermo Fisher) and profiled by TapeStation (Agilent). The libraries were sent to MSKCC Integrated Genomics Operation core facility for sequencing on an Illumina NovaSeq 6000 (~30-40 million 100 bp paired-end reads per library).

value: Tumor

value: Melanoma


title: J774_wt_ctrl_LPS_rep2

description: Library name: 23L006268


title: fc2_pub4_16h_rep1

value: total leaf tissue

value: 17 days constant light, 2 days 16hlight/8hdark cycling light

value: harvested 1 hour post subjective dawn on day 19


title: U937-T12-RPMI,Unsorted-replB

description: Library name: MPH_7069


title: Multiome, Veh Sample 1, ATAC

description: Library name: 1590_veh_ATAC

library_source: genomic single cell


title: fc2_24h_rep3

value: 19 days constant light


title: U937-T12-RPMI,Unsorted-replA

description: Library name: MPH_7068


title: HREC, activin, 24h, rep1

description:
Library name: activin1
Column name in hrec_activin_counts.txt: activin1


title: J774_Ctbp1,2dKO_ctrl_LPS_rep1

description: Library name: 23L006286

value: female

value: Ctbp1/2 double-knockout

value: 4 h 100 ng/ml LPS


title: J774_Ctbp1,2dKO_ctrl_LPS_rep2

description: Library name: 23L006295

value: BALB/c


title: HREC, vehicle, 24h, rep2

description:
Library name: veh2
Column name in hrec_activin_counts.txt: veh2

value: vehicle


title: fc2_24h_rep2


title: fc2_16h_rep3


title: J774_Ctbp1,2dKO_ctrl_LPS_rep3

description: Library name: 23L006304


title: HREC, vehicle, 24h, rep1

description:
Library name: veh1
Column name in hrec_activin_counts.txt: veh1


title: U937-T6-RPMI,Top 15-replC

description: Library name: MPH_7073

value: U937-T6-RPMI,Top 15


title: BMDMs_aCtbp2_LPS3

description: Library name: 197845

data_processing:
NGS data quality was assessed with FastQC (RRID: SCR 014583, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
ChIP-seq paired-end reads were mapped to the murine reference genome mm39 (Ensembl GRCm39) with BWA-MEM version 0.7.17 (RRID: SCR 010910 ) and PCR duplicates were removed using Picard Tools version 3.2.0 (RRID: SCR -006525, http://picard.sourceforge.net/).
For visualization, bam files were filtered for properly paired and mapped reads, and multimappers were removed with Samtools version 1.9 (RRID: SCR 002105 ). Alignments were converted to bigwig files, merging 10 bp per bin using ‘bamCoverage’ from the Deeptools package version 3.5.1 (RRID: SCR -016366). Coverage files are normalized to scale factors derived from background reads, which were counted from 100 kB consecutive windows across the mm39 genome using bedtools (RRID:SCR_006646).
Peaks were called with MACS version 3.0.0a5 in BAMPE mode and an FDR cutoff of 0.05. ChIP-seq peaks were called over matched input controls. Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed .gz) were lifted to mm39 and removed from analyses. Peaks were annotated to the closest gene expressed in macrophages in any of our conditions with the ‘ChIPpeakAnno’ package version 3.40.0 (RRID: SCR 012828) in R version 4.4.1 (RRID: SCR 014601).
Differential binding of LPS -treated versus vehicle treated CTBP2 cistromes was performed using DiffBind version 3.16 (RRID: SCR_012918 ).
Assembly: mm39
Supplementary files format and content: TXT files contain peak information on the CTBP2 universe across treatment including position, read counts and results of the differential binding analysis.
Supplementary files format and content: BW files contain coverage tracks normalized to the background signal in each sample.

source_name: bone marrow-derived macrophages

growth_protocol: Humerus, femur and tibia were isolated from 6-12 weeks old C57BL6/N mice (RRID:MGI:7466658), disinfected with ethanol and transferred to the cell culture hood. Using scissors, tweezers and a syringe with G27 needle, bones were opened and bone marrow was flushed into a 50 ml conical tube filled with cold RPMI 1640. Cells were collected by centrifugation (300 xg, 5 min), supernatant was aspirated and cells were suspended in AKC lysis buffer (1M NH4Cl, 1M KHCO3, 0.5M EDTA) to lyse red blood cells. Subsequently, cells were suspended in PBS, carefully layered over Ficoll Paque (GE Healthcare 17144002) and subjected to density centrifugation (500xg, 45 min, slow acceleration and deceleration). The top layer was aspirated and middle fraction was collected in a fresh conical tube filled with Differentiation medium (30% L929 supernatant, 20% FBS, 1% Penicillin/ Streptomycin, 49% DMEM high glucose). Cells were pelleted by centrifugation, supernatant was aspirated and cells were suspended and plated in Differentiation medium on 15 cm bacterial plates. After 3 days of incubation at 5% CO2 and 37 °C in a humidified incubator, half of the medium was exchanged by fresh Differentiation medium and differentiation was continued until day 6. Cells were detached by incubation in Versene (Thermo Fisher Scientific, 11518876 ) and subjected to counting using a Neubauer chamber. Finally, differentiated cells in macrophage serum free medium (Thermo Fisher Scientific, 12065074) were seeded at 905000 cells/cm2 in tissue culture treated dishes and incubated at 5% CO2 and 37 °C in a humidified incubator.

extract_protocol:
4*10^6 cells were fixed with 2 mM DSG for 30 min at room temperature followed by 10 min with 1% formaldehyde. Crosslinking was quenched by addition of 85 mM glycine and 5 min incubation. Cross-linked cells were washed twice with ice-cold PBS, scraped into microcentrifugation tubes and pelleted at 1000 xg for 5 min at 4 °C. The supernatant was aspirated and cell pellets were frozen at -70°C. Cells were thawed by addition of 1 mL Fast IP buffer (167.5 mM NaCl, 5 mM EDTA, 50 mM Tris pH 7.5, 1% Triton X-100, 0.5% Nonidet P-40, proteinase inhibitor) and suspended by pipetting. The cell suspension was incubated on ice for 10 min to destabilize cell membranes and pulled through an insulin syringe during that time to lyse cell membranes. Cells were pelleted, and the previous step was repeated once. Then the pellet containing nuclei was suspended in 1 ml shearing buffer (10 mM EDTA, 50 mM Tris (pH 8.0), 1% SDS) to lyse nuclei and free cross-linked chromatin. The solution was divided into 2x 500 µl aliquots and transferred into Diagenode tubes. Samples were then subjected to 18 cycles sonication (30s on/ 30s off) at 4°C using the Biorupter Plus (Diagenode) at “high” to generate DNA fragments of 500-1000 bp. Chromatin was cleared from precipitates by centrifugation (10 min, 14,000 xg, 4°C) and diluted 1:10 in dilution buffer (168 mM NaCl, 1.2 mM EDTA, 16.7 mM Tris pH 8.0 , 0.01 % SDS, 1.1 % Triton X-100). Then 16 mL chromatin dilution was incubated with 10 µl CTBP2-specific antibody (Active Motif, #61261) at 4 °C overnight. Next day, lysates were cleared from precipitates by centrifugation (14,000 xg, 10 min, 4 °C) and top 90% were carefully transferred to a fresh 1.5 mL low-DNA binding microcentrifugation tube pre-filled with 10 µl Dynabeads (Thermo Fisher Scientific, #11204D) in dilution buffer. Tubes were rotated at 4 °C for 5 h to immobilize protein-DNA-antibody complexes at the bead surface. Subsequently, beads were placed on a magnet and supernatant was removed by aspiration. Beads were washed 6-times with ice-cold dilution buffer and one time with TE buffer before elution targeted protein-DNA complexes in bead elution buffer (100 mM NaHCO3, 1% SDS). Crosslinking was reversed by incubation with 195 mM NaCl at 65 °C overnight. RNA was removed by addition of RNAse A (50 ng/µl) and incubation for 30 min at 37 °C and proteins were digested by addition of proteinase K (45 ng/µl) and incubation at 56 °C for 1 h before DNA was cleaned using the ChIP and DNA concentrator kit (Zymogen) following the manufacturer’s instructions. ChIP DNA was eluted in nuclease-free water and frozen at -20 °C.
The DNA was quantified via Qubit, and the enrichment was validated by qPCR. Libraries were performed with the Kappa Hyperprep kit (Roche #07962363001) according to the manufacturer’s instructions and sequenced on an Illumina NovaSeq6000 machine at 100-bp paired-end.

treatment_protocol: Cells were seeded and incubated over night at normal growth condition. Then vehicle (PBS) or LPS (#LPS25 Sigma, 100ng/mL) were added and cells were incubated for 3 h for ChIP experiments

value: bone marrow-derived macrophages

tag: antibody

value: male

value: wildtype

value: 3h 100ng/ml LPS


title: fc2_24h_rep1


title: U937-T6-RPMI,Top 15-replA

description: Library name: MPH_7071

value: monocyte

value: Transduced with TKOv3 CRISPR library


title: HREC, activin, 24h, rep2

description:
Library name: activin2
Column name in hrec_activin_counts.txt: activin2

value: Human Retinal Endothelial Cells

value: Activin (50ng/mL)

value: 24 hours


title: fc2_16h_rep2

value: total leaf tissue

value: 17 days constant light, 2 days 16hlight/8hdark cycling light

value: harvested 1 hour post subjective dawn on day 19


title: U937-T6-RPMI,Bottom 15-replC

description: Library name: MPH_7076

value: U937-T6-RPMI,Bottom 15


title: BMDMs_aCtbp2_LPS2

description: Library name: 197844


title: U937-T6-RPMI,Bottom 15-replB

description: Library name: MPH_7075


title: J774_wt_ctrl_LPS_rep1

description: Library name: 23L006259

value: female

value: 4 h 100 ng/ml LPS


title: EW8 cells, Panobinostat 10 nM, biol rep 3

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

data_processing:
FastQC was used to assess the quality of the sequencing reads. Reads were then mapped against the human reference genome (version hg38) using the STAR aligner.
The raw counts were normalized and transformed using the rlog function and principal components analysis (PCA) was performed to visualize sample clusters. No outlier samples were identified or removed from the analysis.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for each gene and sample

growth_protocol: The cell line was cultured in DMEM with 10% FBS.

extract_protocol:
RNA was isolated from cell lines using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA protocols.

treatment_protocol: EW8 cells were treated with DMSO, panobinostat 5 nM, panobinostat 10 nM, romidepsin 2.5 nM, and romidepsin 5 nM for 24 hours.

value: cell line

value: Ewing  sarcoma

value: WT

value: Panobinostat 10 nM


title: EW8 cells, Panobinostat 10 nM, biol rep 2


title: fc2_16h_rep1


title: wt_24h_rep3

value: wild type (Col-0)

value: 19 days constant light


title: BMDMs_aCtbp2_LPS1

description: Library name: 197843

value: bone marrow-derived macrophages

value: male

value: wildtype

value: 3h 100ng/ml LPS


title: EW8 cells, Panobinostat 10 nM, biol rep 1


title: HREC, vehicle, 24h, rep3

description:
Library name: veh3
Column name in hrec_activin_counts.txt: veh3

value: Human Retinal Endothelial Cells

value: vehicle

value: 24 hours


title: U937-T6-RPMI,Top 15-replB

description: Library name: MPH_7072

value: monocyte

value: Transduced with TKOv3 CRISPR library

value: U937-T6-RPMI,Top 15


title: BMDMs_aCtbp2_veh3

description: Library name: 197842

value: vehicle (PBS)


title: EW8 cells, Panobinostat 5 nM, biol rep 3

value: cell line

value: Panobinostat 5 nM


title: BMDMs_aCtbp2_veh2

description: Library name: 197841


title: U937-T6-RPMI,Unsorted-replB

description: Library name: MPH_7060


title: wt_16h_rep3

value: total leaf tissue

value: 17 days constant light, 2 days 16hlight/8hdark cycling light

value: harvested 1 hour post subjective dawn on day 19


title: EW8 cells, Panobinostat 5 nM, biol rep 2

value: Ewing  sarcoma

value: WT


title: wt_24h_rep1

value: wild type (Col-0)

value: 19 days constant light


title: BMDMs_aCtbp2_veh1

description: Library name: 197840

value: bone marrow-derived macrophages

value: male

value: wildtype


title: U937-T6-RPMI,Unsorted-replA

description: Library name: MPH_7059


title: U937-T6-RPMI,Unsorted-replC

description: Library name: MPH_7061


title: HSC_scRNAseq

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: The University of Tokyo

description:
Library name: Sample1
10x Genomics

data_processing:
Sequencing data were mapped to the reference genome using CellRanger. Subsequent analysis was conducted using the Seurat and Signac R packages.
Assembly: mm10
Supplementary files format and content: CellRanger outputs files

source_name: Hematopoietic cells

growth_protocol: Ex vivo expanded HSCs were collected after 7 days of culture in a Soluplus-based expansion medium.

extract_protocol:
Ex vivo expanded HSCs were sorted via fluorescence-activated cell sorting (FACS) using an Aria III cell sorter (BD) equipped with a 100 µm nozzle and appropriate filters and settings. Subsequently, nuclei were isolated according to the protocol of the Chromium Nuclei Isolation Kit.
Libraries were prepared using the Single Cell 3’ Reagent Kit v.3.1 (10x Genomics) and sequenced on an Illumina NovaSeq X platform.

treatment_protocol: Murine HSCs were cultured in Ham’s F12 medium (Wako), enriched with 10 mM HEPES (Thermo Fisher Scientific), recombinant cytokines murine TPO (100 ng/mL, Peprotech), and SCF (10 ng/mL, Peprotech), Soluplus (BASF), as well as insulin-transferrin-selenium (ITS, Thermo Fisher Scientific, 1:100 dilution) and 1% Penicillin-Streptomycin-L-Glutamine (PSG, Wako).

value: Hematopoietic cells

value: HSC

value: Ex vivo expanded HSC

value: Ex vivo expansion


title: wt_24h_rep2


title: wt_16h_rep2


title: EW8 cells, Panobinostat 5 nM, biol rep 1


title: EW8 cells, Romidepsin 5 nM, biol rep 2

value: Romidepsin 5 nM


title: pbmc,RA7

city: Nanjing

first: Jingjing

last: Zhang

state: Jiangsu

address: 321 Zhongshan Road

country: China

institute: Nanjing University

description:
Library name: C9
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:C9

data_processing:
Raw data of FASTQ format were filtered to obtain clean data with high quality. Clean reads for each sample were mapped to hg38 with the software HISAT2 and Bowtie.
Assembly: hg38
Supplementary files format and content: matrix files for each sample

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from PBMCs using Trizol reagent (Vazyme). RNA quality control was performed using NanoPhotometer and Agilent 2100 RNA Nano 6000 Assay Kit (AgilentTechnologies, CA, USA). Each sample was prepared using a total of 5 μg RNA.
Libraries were generated by TruSeq® RNA Sample Prep Kit (Illumina, USA) following manufacturer’s recommendations.

value: Peripheral blood

value: pbmc

value: RA


title: wt_16h_rep1

value: total leaf tissue

value: 17 days constant light, 2 days 16hlight/8hdark cycling light


title: U937-T0-RPMI

description: Library name: MPH_7052

value: monocyte

value: Transduced with TKOv3 CRISPR library


title: old-1, 21M

first: Shi

last: Runqing

address: Department of Gerontology 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
Low-quality reads were filter out by Trimmomatic (version 0.36) and clean reads were mapped to the GRCm39 (mm10) genome by Bwa (version 0.7.15), while potential PCR duplicates were removed by Samtools (version 1.3.1). MACS2 software (version 2.1.1.20160309) was employed to call peaks by default parameters (bandwidth, 300 bp; model fold, 5, 50; q value, 0.05).The peaks were assigned to the genes with closest TSS located to the midpoint of the peak. Motif occurrence within peaks were predicted by HOMER (version3) with default settings for a maximum motif length of 12 base pairs.
Assembly: mm10
Supplementary files format and content: bed, Peak  (except for Input sample)

source_name: Gastrocnemius muscle

extract_protocol:
Gastrocnemius muscle tissues were washed twice in cold PBS buffer and cross-linked with 1% formaldehyde for 10 minutes at room temperature before quenched by addition of glycine  (125 mmol/L). Afterwards, samples were resuspended in lysis buffer  (50mM Tris-HCl  (pH 8.0), 10mM EDTA, 1%SDS, 1×protease inhibitor cocktail) and sonicated to obtain soluble sheared chromatin  (average DNA length of 200–500 bp). 100μL chromatin was immunoprecipitated by 10 μg anti-TRα antibodies  (ab53729， abcam) at 4 ℃ overnight and further incubated with 30 μL of protein beads for 3h. The beads were next washed extensively and bound material was then eluted from the beads in 300μL of elution buffer  (100 mM NaHCO3, 1%SDS). Immunocomplexes were then treated with RNase A  (8μg/mL) during 6h at 65℃ and decrosslinked with proteinase K  (345μg/mL) overnight at 45℃.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-seq Library Prep Kit for Illumina® Sequencing（NOVA-5143-02， Bioo Scientific） and sequenced on Illumina Novaseq 6000 with PE 150 method.

value: Gastrocnemius muscle

tag: chip antibody

value: TRα (ab53729, abcam)


title: EW8 cells, Romidepsin 5 nM, biol rep 3

value: cell line

value: Ewing  sarcoma

value: WT


title: EW8 cells, Romidepsin 5 nM, biol rep 1


title: old-2, 21M


title: RAW264.7-Cas9-T10-DMEM,Unsorted-replC

description: Library name: MUS_506

value: monocyte/macrophage-like

value: Transduced with mTKO CRISPR library


title: pbmc,RA6

description:
Library name: C6
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:C6


title: U937-T6-RPMI,Bottom 15-replA

description: Library name: MPH_7074

value: U937-T6-RPMI,Bottom 15


title: mid-2, 15M


title: RAW264.7-Cas9-T10-DMEM,Unsorted-replB

description: Library name: MUS_505


title: mid-1, 15M


title: pbmc,RA5

description:
Library name: C5
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:C5


title: RAW264.7-Cas9-T7-DMEM,Top 15%-replC

description: Library name: MUS_503

value: RAW264.7-Cas9-T7-DMEM,Top 15%


title: pbmc,RA4

description:
Library name: C4
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:C4


title: youth-2, 6M


title: EW8 cells, Romidepsin 2.5 nM, biol rep 1

value: Romidepsin 2.5 nM


title: RAW264.7-Cas9-T10-DMEM,Unsorted-replA

description: Library name: MUS_504


title: EW8 cells, Romidepsin 2.5 nM, biol rep 2


title: youth-1, 6M


title: pbmc,RA2

description:
Library name: C2
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:C2

value: Peripheral blood


title: RAW264.7-Cas9-T7-DMEM,Top 15%-replB

description: Library name: MUS_502


title: EW8 cells, DMSO, biol rep 3

value: DMSO


title: pbmc,RA1

description:
Library name: C1
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:C1

value: pbmc

value: RA


title: EW8 cells, DMSO, biol rep 2


title: RAW264.7-Cas9-T7-DMEM,Top 15%-replA

description: Library name: MUS_501


title: G1E-ER4 Async RCMC, Biological Replicate 1, NovaSeqS1

city: Cambridge

first: Viraat

middle: Yogi

last: Goel

state: Massachusetts

department: Biological Engineering

institute: Massachusetts Institute of Technology (MIT)

description: Processed data file merges biological replicates 1 & 2. Raw data files from the NovaSeq 6000 contain "NovaS1" in their filename while raw data files from the NovaSeq X contain "NovaX" in their filename.

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm39 genome using bowtie2 v2.2.5 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2 --drop-sam --drop-readid.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. Remaining reads were indexed (pairix v0.3.7) and filtered to retain only those reads where both read mates lie in a locus of interest. These filtered reads were subsequently converted to .cool format using cooler (v0.8.11) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Loops were manually annotated within each captured locus.
Assembly: mm39
Supplementary files format and content: mcool:multi-resolution contact map
Library strategy: Region Capture Micro-C

growth_protocol: The G1E-ER4 cell line and its sublines were cultured in IMDM supplemented with 2% penicillin/streptomycin, 15% fetal bovine serum, Kit ligand, erythropoietin, and monothioglycerol. Cells were maintained at a density less than 1 million cells per 1mL.

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified using a DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size-selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 5-7 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio to a total of 2-4 µg of DNA. 80-mer biotinylated probes were designed end-to-end to tile across regioins of interest with Twist Bioscience. Capture was performed using the custom target enrichment panels using Twist Bioscience's Standard Hybridization Target Enrichment Protocol (Twist Bioscience, 104178) with the inclusion of Mouse Cot-1 DNA (Invitrogen) blocker solution. The library pool was hybridized to custom probe panels for loci of interest and bound to streptavidin coated beads. Bead-bound fragments were pulled down, amplified with 4 PCR cycles on the thermocycler using Equinox Library Amp Mix (Twist), and purified using Twist Binding and Purification Beads (Twist). Following qPCR quantification, the target enriched library pool was submitted for sequencing.

value: proerythroblast


title: RAW264.7-Cas9-T7-DMEM,Bottom15%-replC

description: Library name: MUS_500


title: pbmc,SLET6

description:
Library name: B11
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:B11

value: SLET


title: G1E-ER4 Late G1 RCMC, Biological Replicate 1, NovaSeqS1


title: G1E-ER4 Mid G1 RCMC, Biological Replicate 1, NovaSeqS1


title: RAW264.7-Cas9-T7-DMEM,Bottom15%-replB

description: Library name: MUS_499


title: EW8 cells, DMSO, biol rep 1


title: HepG2, H3K27ac, 16h, input

city: Temporarily undisclosed

first: Temporarily undisclosed

last: Temporarily undisclosed

address: Temporarily undisclosed

institute: Temporarily undisclosed

data_processing:
First, merge the ChIP-seq data obtained from the same sample library, Similar to ATAC-seq analysis method, sequence alignment was performed using Bowtie2 v2.5.0. Samtools v1.16.1 and Picard were used to remove low-quality reads and PCR duplicates.
Visualization of the ChIP-seq data was achieved using bamCompare v3.5.1 with parameters (--normalizeUsing CPM --operation subtract --binSize 50 --smoothLength 60).
The multiBigwigSummary v3.5.1 software was used to quantify the H3K27ac levels of enhancer and promoter regions.
Peak calling was conducted using MACS2 v2.2.7.1 with parameters (-f BED -q 0.05 -B -g hs --keep-dup all --SPMR).
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Liver

extract_protocol:
First, the samples were crosslinked by adding the final concentration of 1% formaldehyde solution to the culture medium and incubating at room temperature for 10 minutes. Crosslinking was then terminated with the final concentration of 0.125M glycine solution. After crosslinking, cells underwent H3K27ac ChIP-seq. Briefly, DNA degradation and contamination in the ChIP samples were monitored on agarose gels. DNA purity was assessed with the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured with the Qubit® 3.0 Fluorometer (Life Technologies, CA, USA) using the Qubit® DNA Assay Kit.
Purified DNA was used for ChIP-seq library preparation, which was constructed by Novogene (Beijing, China). The samples were then subjected to paired-end sequencing on the Illumina platform (Illumina, CA, USA). Library quality was evaluated on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The cells were cultured with complete medium containing DOX at a final concentration of 0.5μg/mL. The cells were treated for various durations (0h,  8h,  16h) before samples were extracted .

value: Liver

value: Dox 16h


title: G1E-ER4 Early G1 RCMC, Biological Replicate 1, NovaSeqS1


title: RAW264.7-Cas9-T7-DMEM,Bottom15%-replA

description: Library name: MUS_498


title: pbmc,SLET5

description:
Library name: B10
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:B10


title: EW8 cells, Romidepsin 2.5 nM, biol rep 3


title: pbmc,RA3

description:
Library name: C3
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:C3


title: pbmc,SLET4

description:
Library name: B5
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:B5


title: HepG2, H3K27ac, 16h, ChIP


title: G1E-ER4 AnaTelophase RCMC, Biological Replicate 1, NovaSeqS1


title: Sample_PAX2+ PDX441

city: Dallas

first: Subhransu

middle: S

last: Sahoo

state: Texas

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
bcl files were converted to fastq using bcl2fastq
fastq files were mapped to reference genome using STAR
gene quantification was performed using subread module featurecount using igenomes gtf
differential expression analysis was performed using edgeR
Assembly: hg19
Supplementary files format and content: Normalized TPM counts as a text file

source_name: PDX

growth_protocol: The endometrial cancer patient tumor samples were subcutaneously implanted into female NOD scid gamma mice and once the tumors grown the mice were euthanized, and the tumors harvested.

extract_protocol:
Total RNA from PAX2+ PDX and PAX2- PDX were isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) following the manufacturer's instructions.

treatment_protocol: The mice were fed ad libitum on standard chow diet without any treatment.

value: PDX

value: tumor cells (mixed)


title: pbmc,SLET3

description:
Library name: B3
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:B3


title: RAW264.7-Cas9-T7-DMEM,Unsorted-replB

description: Library name: MUS_496


title: HepG2, H3K27ac, 8h, ChIP

value: Dox 8h


title: RAW264.7-Cas9-T7-DMEM,Unsorted-replC

description: Library name: MUS_497


title: G1E-ER4 Prometaphase RCMC, Biological Replicate 1, NovaSeqS1


title: pbmc,SLET2

description:
Library name: B2
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:B2


title: RAW264.7-Cas9-T7-DMEM,Unsorted-replA

description: Library name: MUS_495


title: HepG2, H3K27ac, 0h, input

value: Dox 0h


title: pbmc,SLET1

description:
Library name: B1
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:B1


title: ILC3, 1B23SCF, 6h, rep3

city: Taipei

first: Jheng-Syuan

last: Shao

address: 128 Sec. 2, Academia Rd.

country: Taiwan

institute: Academia Sinica

data_processing:
Sequencing reads were trimmed for adaptor sequence and low quality sequence using fastp (v0.20.0) (bases with quality score Phred less than 30 were trimmed from both ends)
Trimmed sequence reads were then mapped to the Mus_musculus.GRCm38.99 using HISAT2 (v2.1.0)
Read counts were performed using FeatureCounts (v2.0.1)
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: small intestine ILC3

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s recommendations

value: small intestine ILC3


title: ILC3, 1B23SCF, 6h, rep4


title: HepG2, H3K27ac, 0h, ChIP


title: pbmc,SLE6

description:
Library name: D11
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:D11

value: SLE


title: HepG2, ATAC, 16h

data_processing:
Trimming was performed using fastp v0.20.0 to obtain clean reads. Bowtie2 v2.5.0 was then used to construct an index of the reference genome (hg38), and sequences were aligned with parameter (--no-unal).Samtools v1.16.1 was employed to retain reads with MAPQ≥30, with parameters (-f 2 and -q 30), and PCR duplicates were removed using Picard.
Following the methods outlined in the ENCODE-ATAC-Seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline), BAM files were converted to tagAlign format.The multiBigwigSummary v3.5.1 software was used to quantify the chromatin accessibility levels of enhancer and promoter regions.
Peak calling was conducted using MACS2 v2.2.7.1 with parameters (-f BED -q 0.05 -B -g hs --nomodel --shift -100 --extsize 200 --keep-dup all --SPMR).
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Nuclei were extracted from the samples and resuspended in the Tn5 transposase reaction mixture. The transposition reaction was incubated at 37°C for 30 minutes. After transposition, equal amounts of Adapter1 and Adapter2 were added, followed by PCR amplification of the library.
Post-PCR, the library was purified using AMPure beads and its quality was assessed using Qubit. Indexed samples were clustered on the cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina). After cluster generation, sequencing was performed on the Illumina platform, producing 150 bp paired-end reads.


title: J774.1-T16-DMEM,Unsorted-replC

description: Library name: MUS_6597

data_processing:
Reads from each sample were mapped to the TKOv3 or mTKO reference library using Bowtie (v0.12.8) allowing up to two mismatches and one exact alignment (specific parameters: -v2, -m1, -p4 -sam-nohead). Successfully aligned reads were counted and combined into a matrix with guide annotations.
Read counts were normalized to 10 million reads per sample and log fold-changes (LFC) of each gRNA between each timepoint and T0 were determined. Guides with fewer than 30 or greater than 10,000 absolute read counts at T0 were removed.
The sorting arm of the screens was analyzed using a version of the quantitative genetic interaction (qGI) algorithm, as previously described (Chan et al., 2023, PMID: 36597481). LFCs in sorted samples relative to the starting time point were quantified. LFCs were M-A transformed by calculating M, the per-sgRNA difference (bottom 15% - top 15%), and A, the per-sgRNA average. Then, a LOESS curve of degree 2 and 40% span along A was fitted, followed by calculation of residuals or effect sizes by subtracting M from its LOESS-predicted value. Gene-level P-values were calculated from effect sizes by moderated t-testing, and P-values were adjusted to control the false discovery rate (FDR) using the Benjamini-Hochberg method. Significant hits were called at an FDR < 0.05.
Assembly: mTKO CRISPR Library; TKOv3 CRISPR Library
Supplementary files format and content: Tab-delimited read count matrix
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA from cell pellets was extracted using the Wizard Genomic DNA Purification Kit (Promega, #A1120) following a previously described protocol (Ngo et al., 2022, PMID: 35953550). Briefly, unsorted cell pellets were thawed at room temperature for 5 minutes and resuspended in 1.4 mL of PBS (Wisent, #311-425-CL), lysed in 5 mL of Nuclei Lysis Solution (part of Wizard Genomic DNA Purification Kit) and mixed by pipetting. 32 µL of RNase A (Invitrogen, #12091021) to a final concentration of 100 µg/mL was added to the lysate and incubated at 37°C for 15 minutes. 1.67 mL of Protein Precipitation Solution (part of Wizard Genomic DNA Purification Kit) was added to the lysate, vortexed vigorously for 20 seconds, and centrifuged at 4500 g for 10 minutes at room temperature. The supernatant was transferred to a tube containing 5 mL of isopropanol (Caledon Laboratories, #8600-1-40) and gently mixed by inversion until DNA was observed as thread-like white strands. DNA was collected by centrifugation at 4500 g for 5 minutes and gently washed with 5 mL of 70% ethanol (Commercial Alcohols, #P006-EAAN). DNA was collected by centrifugation at 4500 g for 5 minutes, air-dried to remove residual ethanol, resuspended in 400 µL of TE buffer, and incubated at 65°C for 2-3 hours, with gently flicking every 15 minutes, until the DNA appeared completely dissolved. Sorted (fixed) cells were incubated at 55°C overnight with 120 µL of 0.5 M EDTA (BioShop, #EDT111.5000), 500 µl of Nuclei Lysis Solution, and 20 µL of proteinase K (NEB, #P8107S). The next day, the protocol described above was applied with 1/8 of the described volumes. DNA was quantified using Qubit double-stranded DNA Broad Range Assay reagents (Invitrogen, #Q33266). DNA was stored at -20°C prior to sequencing library preparation.
Sequencing libraries were prepared as previously described (Chan et al., 2019, PMID: 31545321). Briefly, libraries were prepared from 105 µg of genomic DNA from non-sorted samples or 10-20 µg of genomic DNA from sorted samples by a two-step PCR reaction. PCR1 consisted of 25 µL of NEBNext Ultra II Q5 Master Mix (NEB, #M0544X), 2.5 µL of 10 µM PCR1 forward and reverse primers, 3.5 µg of purified genomic DNA, and UltraPure™ DNase/RNase-Free distilled water to reach a 50 µL reaction volume. PCR1 products from the same genomic DNA sample were pooled and used for a single PCR2 reaction. Each PCR2 reaction consisted of 25 µL of NEBNext Ultra II Q5 Master Mix, 2.5 µL of 10 µM i5 forward and i7 reverse primers, 5 µL of pooled PCR1 product, and 15 µL of UltraPure™ DNase/RNase-Free distilled water. PCR2 products were separated by gel electrophoresis, and ~200 bp bands corresponding to PCR2 amplicons were excised from the gel and purified using the PureLink™ Quick Gel Extraction Kit following manufacturer’s instructions. Samples were stored at -20°C prior to sequencing. Samples corresponding to the starting time point were sequenced at 500-fold library coverage. All other samples were sequenced at read depths equivalent to 200-fold coverage.

value: murine macrophage

value: Transduced with mTKO CRISPR library


title: J774.1-T16-DMEM,Unsorted-replB

description: Library name: MUS_6596


title: HepG2, ATAC, 8h


title: pbmc,SLE4

description:
Library name: D5
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:D5


title: ILC3, 1B23, 6h, rep4


title: HepG2, H3K27ac, 8h, input


title: J774.1-T16-DMEM,Unsorted-replA

description: Library name: MUS_6595


title: pbmc,SLE3

description:
Library name: D3
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:D3


title: HepG2_16h_Dox_rep3

data_processing:
The HISAT2 v2.1.0 software was used to build the index of the reference genome (hg38) and perform sequence alignment of the RNA-seq data with default parameters.
FeatureCounts (v2.0.3) software was used to quantify the RNA-seq read counts of genes, with parameters (-p --countReadPairs -O).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes row counts for each sample

extract_protocol:
The RNA integrity was assessed using the Fragment Analyzer 5400 (Agilent Technologies, CA, USA). Total RNA was used as the input material for RNA sample preparation
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s instructions, and sequencing was performed on the Illumina NovaSeq 6000 platform, producing 150 bp paired-end reads.


title: J774.1-T9-DMEM,Top 15-replC

description: Library name: MUS_6591


title: ILC3, 1B23, 6h, rep2


title: HepG2, ATAC, 0h


title: J774.1-T9-DMEM,Top 15-replB

description: Library name: MUS_6590


title: pbmc,SLE5

description:
Library name: D10
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:D10


title: pbmc,SLE1

description:
Library name: D1
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:D1


title: ILC3, 1B23, 6h, rep3


title: Sample_AN3CA_Sh_EV_2

description:
S2.TPM
AN3CA.igenomes.genes_normalized.counts.TPM.tab

source_name: Uterus

growth_protocol: AN3CA cells with or without PAX2 were cultured in MEM medium supplemented with 10% FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 370C containing 5% CO₂.

extract_protocol:
Total RNA from AN3CA cells with or without PAX2 was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) following the manufacturer's instructions.

treatment_protocol: AN3CA cells with or without PAX2 were treated with puromycin to select positively transduced cells.

value: Uterus

value: epithelial cells

value: WT


title: RAW264.7-Cas9-T0-DMEM

description: Library name: MUS_494

value: monocyte/macrophage-like


title: pbmc,HC6

description:
Library name: A9
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:A9

value: Peripheral blood

value: pbmc

value: HC


title: ILC3, 1B23SCF, 6h, rep2


title: pbmc,HC7

description:
Library name: A10
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:A10


title: HepG2_16h_Dox_rep1

value: Liver


title: ILC3, 1B23, 6h, rep1


title: J774.1-T9-DMEM,Bottom 15-replC

description: Library name: MUS_6588

value: J774.1-T9-DMEM,Bottom 15


title: J774.1-T9-DMEM,Bottom 15-replB

description: Library name: MUS_6587


title: CIF9

city: Irvine

first: Cholsoon

last: Jang

state: CA

address: 839 Health Sciences Rd

department: Biological Chemistry

institute: University of California Irvine

data_processing:
The quality of raw sequencing data was assessed using the FastQC. All samples passed the quality control analysis.
Raw sequencing reads were aligned to the mice reference genome mm10 (GRCm38) using STAR and used featureCounts to get raw counts. These raw counts were further analyzed using DESeq2 for the differential gene expression analysis.
Assembly: GrCm39 (mm10)
Supplementary files format and content: Raw gene counts extracted from featureCounts using mm10.ncbiRefSeq.gtf

growth_protocol: 8–week-old male C57BL/6 mice were group-housed on a normal light–dark cycle (7:00–19:00) with free access to chow and water. Mice were fed either control (Research diets, D21050401) or 10% (gm%) inulin diet (Research diets, D21050402) for 30 weeks.

extract_protocol:
For RNA-sequencing, RNA samples were prepared using TRIzol® Reagent (Invitrogen) according to the manufacturer's instructions.
Ribosomal RNA depletion and sample library preparation were done using the Illumina TruSeq Stranded Total RNA

treatment_protocol: Liver tissues were quickly dissected and snap-frozen in liquid nitrogen with a pre-cooled Wollenberger clamp.

value: switched from control diet to inulin diet with continual provision of HFCS water (CIF)

value: male


title: HepG2_8h_Dox_rep3

value: Dox 8h


title: HepG2_8h_Dox_rep2


title: ILC3, 1B23SCF, 6h, rep1


title: pbmc,SLE2

description:
Library name: D2
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:D2


title: CIF7


title: pbmc,HC5

description:
Library name: A7
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:A7


title: J774.1-T9-DMEM,Bottom 15-replA

description: Library name: MUS_6586


title: HepG2_16h_Dox_rep2

value: Dox 16h


title: CIF2


title: HepG2_8h_Dox_rep1


title: J774.1-T9-DMEM,Top 15-replA

description: Library name: MUS_6589


title: pbmc,HC4

description:
Library name: A5
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:A5


title: CIF1


title: HepG2_0h_Dox_rep3

value: Dox 0h


title: IF5

value: inulin diet with HFCS water (IF)


title: J774.1-T9-DMEM,Unsorted-replB

description: Library name: MUS_6584

value: murine macrophage


title: pbmc,HC3

description:
Library name: A4
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:A4


title: HepG2_0h_Dox_rep2


title: pbmc,HC2

description:
Library name: A2
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:A2


title: IF4


title: pbmc,HC1

description:
Library name: A1
Column name in anno_genes.FPKM.xls/circ_TPM.xls/lnc_transcripts.readcount.xsl:A1


title: IF3


title: HepG2_0h_Dox_rep1


title: J774.1-T0-DMEM

description: Library name: MUS_6576

value: Transduced with mTKO CRISPR library


title: Human_ESC, Control3

first: Leijie

last: Li

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

description:
Hcontrol_3
Hcontrol_count.txt

data_processing:
Hisat2 v 2.1.0 and Stringtie v 2.1.7 pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore v 0.6.10
Trimmed sequence reads were mapped to GRCh38/GRCm39 genomics by using Hisat2 v 2.1.0
Read count extraction using StringTie v 2.1.7
Assembly: GRCh38 for human;  Pan_tro 3.0 for chimpanzee; Susie_PAB v2 for orangutan
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: All parental (contributor) and composite PSC lines were cultured in mTeSR Plus on Matrigel in a humidified atmosphere with 5% CO2 at 37*C.

extract_protocol:
RNA was harvested using the RNeasy Mini Plus Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's protocols.

treatment_protocol: Contributor and composite PSC lines were collected at ~70% confluency for lysis and RNA extraction.

value: pluripotent stem cells


title: BV-2-Cas9-T22-RPMI,Unsorted-replB

first: Jason

last: Moffat

institute: Hospital for Sick Children

description: Library name: MUS_519

value: murine microglia


title: IF1


title: J774.1-T9-DMEM,Unsorted-replA

description: Library name: MUS_6583


title: Human_ESC, Control2

description:
Hcontrol_2
Hcontrol_count.txt

value: WT


title: PC-3, pSpCas9_Zhang_pUC19_sgRNA_up2_down3_clone3_S2

city: Trento

first: Francesca

last: Demichelis

state: TN

address: Via Sommarive, 9

department: Department for Cellular, Computational and Integrative Biology - CIBIO

country: Italy

institute: University of Trento

description:
Library name: PC-3_pSpCas9_Zhang_pUC19_sgRNA_up2_down3_clone3_S2
Macrodeletion: deletion of 731bp with transient transfection of pSpCas9 and two pUC19_sgRNAs

data_processing:
fastQ files were aligned to the hg38 reference human genome using STAR (Dobin et al., 2012)
Assembly: hg38
Supplementary files format and content: read counts matrix

source_name: Prostate

extract_protocol:
RNeasy kit (Qiagen, Hilden, DE)
TruSeq Stranded mRNA Kit (Illumina)

value: Prostate

value: single clone

value: no treatment

tag: batch


title: BV-2-Cas9-T22-RPMI,Unsorted-replA

address: 686 Bay Street

description: Library name: MUS_518


title: PC-3, pSpCas9_Zhang_pUC19_sgRNA_up2_down3_clone15_S4

description:
Library name: PC-3_pSpCas9_Zhang_pUC19_sgRNA_up2_down3_clone15_S4
Macrodeletion: deletion of 731bp with transient transfection of pSpCas9 and two pUC19_sgRNAs


title: PC-3, pSpCas9_Zhang_pUC19_sgRNA_up2_down3_clone12_S3

description:
Library name: PC-3_pSpCas9_Zhang_pUC19_sgRNA_up2_down3_clone12_S3
Macrodeletion: deletion of 731bp with transient transfection of pSpCas9 and two pUC19_sgRNAs

value: deletion chr7:33692454-33693185  (lift over to hg38)


title: CF5

value: Liver

value: control diet with HFCS water (CF)


title: IF2


title: J774.1-T9-DMEM,Unsorted-replC

description: Library name: MUS_6585


title: BV-2-Cas9-T13-RPMI,Top 15%-replB

description: Library name: MUS_516

value: BV-2-Cas9-T13-RPMI,Top 15%


title: Human_ESC, Control1

description:
Hcontrol_1
Hcontrol_count.txt


title: CAL27_CCL20_2

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
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. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: FileincludeCount and FPKM valuesforeachsample

growth_protocol: The human OSCC cell line CAL27 was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The OSCC cell line were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The CAL27 cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, OSCC cells were transfected with letivirus (Genechem) to establish CCL20-overexpression cell line. After validation of the overexpression efficiency of CCL20, cells were harvested for RNA sequencing.

value: OSCC cell line


title: CF4

value: male


title: BV-2-Cas9-T13-RPMI,Top 15%-replA

description: Library name: MUS_515


title: CF3


title: PC-3, pSpCas9_Zhang_pUC19_sgRNA_A_sgRNA_E_S17

description:
Library name: PC-3_pSpCas9_Zhang_pUC19_sgRNA_A_sgRNA_E_S17
Microdeletion: deletion of  50bp with transient transfection of pSpCas9 and two sgRNAs

value: pool

value: deletion chr7:33692698-33692745 (lift over to hg38)


title: CAL27_NC_2

value: negative control


title: BV-2-Cas9-T13-RPMI,Bottom 15%-replB

description: Library name: MUS_513

value: BV-2-Cas9-T13-RPMI,Bottom 15%


title: CF2


title: PC-3, LvCas9_px330_sgRNA_scramb_CTRL3_S11

description:
Library name: PC-3_LvCas9_px330_sgRNA_scramb_CTRL3_S11
Editing of 7p14.3 locus  with Lv_Cas9 and px330_(Puro resistant)_sgRNAs

value: wt


title: BV-2-Cas9-T13-RPMI,Bottom 15%-replA

description: Library name: MUS_512

value: Transduced with mTKO CRISPR library


title: CAL27_NC_1


title: PC-3, LvCas9_px330_sgRNA_A_clone_PA4_6_S14

description:
Library name: PC-3_LvCas9_px330_sgRNA_A_clone_PA4_6_S14
Editing of 7p14.3 locus  with Lv_Cas9 and px330_(Puro resistant)_sgRNAs

value: deletion chr7:33692751-33692780  (lift over to hg38)


title: CF1


title: BV-2-Cas9-T13-RPMI,Unsorted-replB

description: Library name: MUS_510

value: murine microglia


title: PC-3, LvCas9_px330_sgRNA_A_clone_PA3_S12

description:
Library name: PC-3_LvCas9_px330_sgRNA_A_clone_PA3_S12
Editing of 7p14.3 locus  with Lv_Cas9 and px330_(Puro resistant)_sgRNAs

value: Prostate

value: deletion chr7:33692751-33692780 (lift over to hg38)


title: IW7

value: inulin diet with normal water (I)


title: PC-3, LvCas9_px330_sgRNA_A_clone_PA3_5_S13

description:
Library name: PC-3_LvCas9_px330_sgRNA_A_clone_PA3_5_S13
Editing of 7p14.3 locus  with Lv_Cas9 and px330_(Puro resistant)_sgRNAs

value: single clone

value: no treatment


title: IW6

value: Liver


title: BV-2-Cas9-T13-RPMI,Unsorted-replA

description: Library name: MUS_509


title: DIFF MOCK

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: 10x genomics

data_processing:
Sequenced reads were aligned to the human genome using CellRanger from 10x version 5.0.1
Remain reads were aligned to the brazil zika genome (KX811222.1) and integrated into count/matrix files using scViralQuant
Analysis was performed with Seurat v4
Assembly: Hg19

source_name: neuronal tissue

growth_protocol: NPCs were derived from iPSCs utilizing the established CV cell line (Young et al., 2015) and maintained in culture in growth medium containing: a base of DMEM:F12 (1:1 mixture), supplemented with B-27, N2, L-glutamine, antibiotic/antimycotic, basic FGF (20 ng/mL), with weekly passaging onto tissue-culture plastic coated with poly-l-ornithine and laminin. For differentiation, cells were plated into a 6-well dish and switched into differentiation medium containing: a base of DMEM:F12 (1:1 mixture), supplemented with B-27 without vitamin A, N2, L-glutamine, antibiotic/antimycotic, BDNF (20ng/mL) and LIF (20 ng/mL).

extract_protocol:
Freshly collected cells were resuspended in ice-cold Hibernate E medium supplemented with 0.25% BSA at a cell concentration of 1,100 cells/µl for single-cell RNAseq
Indexed libraries were prepared from 10 µl of cDNA using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics). Library and cDNA quality were evaluated using the Agilent 2100 Bioanalyzer Instrument and quantified using the ViiA 7 Real-Time PCR system.
Constructed libraries were sequenced on an Illumina NovaSeq 6000 using paired-end reads to achieve a final sequencing depth of approximately 80,000 reads per cell.

treatment_protocol: 96 hours prior to harvest, all cells were switched into treatment medium containing: a base of DMEM:F12 (1:1 mixture), supplemented with B-27, N2, L-glutamine, antibiotic/antimycotic, basic FGF (20ng/mL), BDNF (20ng/mL), and LIF (20 ng/mL). 48 hours prior to harvest, cells were infected with a Brazilian isolate of Zika virus (BRZ; Genbank KX811222, passaged once in NPCs in growth medium) at a target MOI of 15 based on Vero-derived PFU titers. Adsorption was performed for 6 hours. As a control for Zika infection, mock treatment was performed with NPC-conditioned medium (to mimic viral growth medium). Six hours prior to harvest, an additional set of cells were treated with IFNb (100 IU/mL), and a final set of cells were left untreated (IFN CTL). Conditions were replicated in two adjacent wells of a 6-well plate and cells from paired wells were combined for single cell RNA sequencing. On the day of sequencing, cells were released from the dish using Accutase and gently triturated to produce a single-cell suspension in ice-cold Hibernate E containing 0.25% BSA. Cells were loaded with eFluor 780 viability dye and sorted using FACS to isolate live cells only. These were prepared and loaded onto a 10x Chromium single cell controller per the manufacturer's specifications.

value: neuronal tissue

value: CV line - male

value: differentiated neural cells

value: retroviral reprogrammed fibroblast from apparently healthy male

value: Mock (conditioned medium)


title: DIFF ZIKV

description: 10x genomics

value: ZIKV Brazil


title: CAL27_CCL20_1

value: OSCC cell line


title: BV-2-Cas9-T0-RPMI

city: Toronto

description: Library name: MUS_507


title: PC-3, LvCas9_pSp_sgRNA_scramb_CTRL1_S5

description:
Library name: PC-3_LvCas9_pSp_sgRNA_scramb_CTRL1_S5
Editing of 7p14.3 locus with Lv_Cas9 and pSp(Neo Resistant)_sgRNAs

value: wt


title: IW5

value: male


title: NPCs ZIKV

description: 10x genomics

value: NPCs


title: IW3


title: LP-1_SCR

city: Shanghai

first: Wei

last: Yusheng

state: New York

address: 227,South Road of Chongqian,Shanghai,China

institute: Shanghai Jiao Tong University of Medicine

description: Human MM cell lines

data_processing:
CLC Genomics Workbench V11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: BM

growth_protocol: MM cell lines were maintained in 1640 supplemented with 10% FBS and antbotics in humidifed atmosphere with 5% CO2 at 37°

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen), 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libranries for RNA-seq were prepared using SMARTER Mrna-seq Library Prep Kit following manufacture's protocols.

treatment_protocol: Knockdown the expression of LILRB4 in APR1, OPM2 and LP-1 cells

value: BM

value: multiple myeloma

value: Scramble


title: PC-3, LvCas9_pSp_sgRNA_C_cloneC3_S9

description:
Library name: PC-3_LvCas9_pSp_sgRNA_C_cloneC3_S9
Editing of 7p14.3 locus with Lv_Cas9 and pSp(Neo Resistant)_sgRNAs

value: Prostate

value: deletion chr7:33692737-33692762  (lift over to hg38)


title: PC-3, LvCas9_pSp_sgRNA_C_cloneC14_S10

description:
Library name: PC-3_LvCas9_pSp_sgRNA_C_cloneC14_S10
Editing of 7p14.3 locus with Lv_Cas9 and pSp(Neo Resistant)_sgRNAs

value: single clone

value: deletion chr7:33692747-33692757 (lift over to hg38)

value: no treatment


title: NPCs MOCK

description: 10x genomics

value: neuronal tissue

value: CV line - male


title: DIFF IFN CTL

description: 10x genomics

value: differentiated neural cells

value: retroviral reprogrammed fibroblast from apparently healthy male

value: IFNb 100 IU/mL


title: DIFF IFN treated

description: 10x genomics

value: Control


title: PC-3, LvCas9_pSp_sgRNA_B_cloneB5_S7

description:
Library name: PC-3_LvCas9_pSp_sgRNA_B_cloneB5_S7
Editing of 7p14.3 locus with Lv_Cas9 and pSp(Neo Resistant)_sgRNAs

value: deletion chr7:33692746-33692755  (lift over to hg38)


title: LP1_B4

description: Human MM cell lines

value: Knockdown the expression of LILRB4


title: CW7

value: Liver

value: control diet with normal water (C)

value: male


title: OPM2_SCR

description: Human MM cell lines

value: BM

value: multiple myeloma

value: Scramble


title: OPM2_B4

description: Human MM cell lines


title: NPCs IFN CTL

description: 10x genomics

value: NPCs


title: PC-3, LvCas9_pSp_sgRNA_B_cloneB4_S6

description:
Library name: PC-3_LvCas9_pSp_sgRNA_B_cloneB4_S6
Editing of 7p14.3 locus with Lv_Cas9 and pSp(Neo Resistant)_sgRNAs

value: Prostate

value: single clone

value: deletion chr7:33692738-33692762  (lift over to hg38)


title: PC-3, pSpCas9_Zhang_pUC19_sgRNA_scramb_S1

description:
Library name: PC-3_pSpCas9_Zhang_pUC19_sgRNA_scramb_S1
Macrodeletion: deletion of 731bp with transient transfection of pSpCas9 and two pUC19_sgRNAs

value: pool

value: wt

value: no treatment


title: CW5


title: CW3


title: ARP1_B4

description: Human MM cell lines


title: PC-3, LvCas9_pSp_sgRNA_B_cloneB15_S8

description:
Library name: PC-3_LvCas9_pSp_sgRNA_B_cloneB15_S8
Editing of 7p14.3 locus with Lv_Cas9 and pSp(Neo Resistant)_sgRNAs

value: deletion chr7:33692749-33692759  (lift over to hg38)


title: Fetal brain IFNB

description:
10x genomics
G004_ZIKV_09_SC_FetalBrain_IFNb_48hr

data_processing:
Sequenced reads were aligned to the human genome using CellRanger from 10x version 5.0.1
Remaining reads were aligned to the brazil zika genome (KX811222.1) or FSS zika genome (MH158236.1) and integrated into count/matrix files using scViralQuant
Analysis was performed with Seurat v4
Assembly: Hg19

source_name: Fetal brain tissue, 117 day post-conception male

growth_protocol: Human primary fetal brain explant tissue was digested into a single cell suspension and plated onto poly-L-ornithine and laminin-coated tissue culture plastic. Cells were grown in neural differentiation medium consisting of a base of DMEM:F12 (1:1 mixture), supplemented with B-27 without vitamin A, N2, L-glutamine, antibiotic/antimycotic, BDNF (20ng/mL) and LIF (20 ng/mL).  After 2 weeks of growth in culture, cells were treated with either Zika infection or IFNb treatment as below.

extract_protocol:
Freshly collected cells were resuspended in ice-cold Hibernate E medium supplemented with 0.25% BSA at a cell concentration of 1,100 cells/µl for single-cell RNAseq
Indexed libraries were prepared from 10 µl of cDNA using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics). Library and cDNA quality were evaluated using the Agilent 2100 Bioanalyzer Instrument and quantified using the ViiA 7 Real-Time PCR system.
Constructed libraries were sequenced on an Illumina NovaSeq 6000 using paired-end reads; an initial sequencing run achieved an estimated 30,000 reads per cell, so a second run was performed which achieved an additional 80,000 reads per cell. Raw reads from the two sequencing runs were combined in the following steps.

treatment_protocol: 48 hours prior to harvest, cells were infected with a Brazilian isolate of Zika virus (BRZ; Genbank KX811222) or a Cambodian isolate (FSS; Genbank MH368551) at a target MOI of 10 based on Vero-derived PFU titers. Adsorption was performed for 6 hours. As a control for Zika infection, mock treatment was performed with 5% FBS in DMEM (to mimic viral growth medium). Six hours prior to harvest, an additional set of cells were treated with IFNb (100 IU/mL).Conditions were replicated in two adjacent wells of a 6-well plate and cells from paired wells were combined for single cell RNA sequencing. On the day of sequencing, cells were released from the dish using Accutase and gently triturated to produce a single-cell suspension in ice-cold Hibernate E containing 0.25% BSA. Cells were loaded with eFluor 780 viability dye and sorted using FACS to isolate live cells only. These were prepared and loaded onto a 10x Chromium single cell controller per the manufacturer's specifications.

value: neural cells

tag: gender

value: IFNb


title: ARP1_SCR

description: Human MM cell lines


title: CUT_Tag_12E_rep2

city: Beijing

first: Xinyu

last: Wang

address: 15 Datun Road

institute: Institute of Biophysics

data_processing:
For RNA-seq, use Fastp software to filter low-quality sequences, undetected sequences and linker sequences. Use Hisat2 algorithm for genome alignment. Using HTSeq, select the FPKM standardization method to count the gene expression.The DESeq2 algorithm is used for differential screening to obtain differential genes that meet the Fold Change and FDR thresholds. Based on the differential screening results and the FPKM or RPKM of the sample, Volcano Plot analysis and cluster map analysis (Heatmap) are performed.
For CUT&Tag, filtered reads were subject to software MACS to identify potential peaks.
Assembly: Hg38
Supplementary files format and content: For RNA-seq, a text file includes filtered reads count values for each sample.The first row indicates the name of each sample.For CUT&Tag,  a txt file includes peak location.

source_name: Huvec

extract_protocol:
For RNA-seq, total RNA was extracted using TRIZOL.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols. For CUT&Tag, a commercial kit (Cat. No. 53160) from Active Motif was used.
RNA-seq: After depleting rRNA,  RNA samples were further fragmented into 150-200 bp using divalent cations at 94 °C for 8 min. The cleaved RNA fragments were reverse-transcribed into double-strand cDNA. The resulting cDNA fragments were end-repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads. The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent 2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina HiSeq Xten by NovelBio Corp. Laboratory, Shanghai.
CUT&Tag: In brief, the cells were captured by ConA beads and incubated with proteinA-tn5 and corresponding primary antibodies. The genomic DNA was extracted with phenol chloroform extraction. The purified DNA was further amplified by barcoded primers to construct the library.

value: Huvec

value: epithelial

value: FUS-CREB3L2 12E mutant stable expression


title: LnCap, LvCas9_pUC19_sgRNA_up2_down3_S16

description:
Library name: LnCap_LvCas9_pUC19_sgRNA_up2_down3_S16
Macrodeletion: deletion of 731bp with Lv_Cas9 and two pUC19_sgRNAs

value: LnCap

value: deletion chr7:33692454-33693185 (lift over to hg38)


title: CW2

value: Liver

value: control diet with normal water (C)

value: male


title: Fetal brain FSS ZIKV

description:
10x genomics
G003_ZIKV_09_SC_FetalBrain_FSS_48hr

value: Fetal brain tissue, 117 day post-conception male

value: ZIKV FSS


title: Fetal brain Brazil ZIKV

description:
10x genomics
G002_ZIKV_09_SC_FetalBrain_BRZ_48hr

value: ZIKV BRZ


title: LnCap, LvCas9_pUC19_sgRNA_scramb_S15

description:
Library name: LnCap_LvCas9_pUC19_sgRNA_scramb_S15
Macrodeletion: deletion of 731bp with Lv_Cas9 and two pUC19_sgRNAs

value: Prostate

value: pool


title: LnCap, LvCas9_pUC19_sgRNA_E_px330_sgRNA_A_S18

description:
Library name: LnCap_LvCas9_pUC19_sgRNA_E_px330_sgRNA_A_S18
Microdeletion: deletion of 50bp with Lv_Cas9 and two sgRNAs (Neo and Puro resistance)

value: deletion chr7:33692698-33692745 (lift over to hg38)

value: no treatment


title: IW2

value: inulin diet with normal water (I)


title: CW1


title: CUT_Tag_FUS-CREB3L2_rep2

value: FUS-CREB3L2 stable expression


title: CUT_Tag_12E_rep1

value: Huvec


title: PC-3, clone 1, GG_AR_EtOH

description:
Library name: GG_AR_EtOH
Single-base editing (Cas9), AR overexpression, EtOH

value: single clone

value: AR overexpression, EtOH


title: CUT_Tag_CREB3L2_rep2

value: epithelial

value: CREB3L2 stable expression


title: Naïve_ctrl IgG rep3

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

data_processing:
The base calling was done using bcl2fastq
Read alignment was done using  Rsubread (v. 2.0.0)
Genewise read counts were calculated using Rsubread (v. 2.0.0)
Assembly: human genome hg38
Supplementary files format and content: Processed data file is tab delimited text file containing the genewise read counts for each sample.

source_name: Naïve human induced pluripotent stem cells (hiPSC)

growth_protocol: Primed hiPSCs were cultured on Matrigel coated culture dishes in E8 medium. Naïve ctrl hiPSCs were cultured on inactivated mouse embryonic fibroblast (iMEF) monolayer in Naïve Cult expansion medium. The naïve anti-β1 hiPSCs were cultured as ctrl hiPSCs, but the culture medium was supplemented with integrin β1 function blocking antibody (MAb13; anti-β1).

extract_protocol:
RNA was isolated using NucleoSpin RNA -kit (#740955.250, Macherey-Nagel).
Illumina TruSeq® Stranded mRNA sample protocol

treatment_protocol: Primed hiPSCs were treated with IgG ctrl or anti-β1 (MAb13) antibodies for 12 hours, and naïve hiPSCs were treated with IgG ctrl or anti-β1 (MAb13) antibodies for 48 hours.

value: Naive hiPSC reverted from HEL 24.3

value: treated with IgG for 48h


title: Naïve_ctrl IgG rep2


title: PC-3, clone 9, GG, rep2

description:
Library name: GG_2
Single-base editing (Cas9)


title: NPCs IFN treated

description: 10x genomics

value: neuronal tissue

value: CV line - male

value: NPCs

value: retroviral reprogrammed fibroblast from apparently healthy male

value: Control


title: Naïve_ctrl IgG rep1


title: PC-3, clone 1, GG, rep1

description:
Library name: GG_1
Single-base editing (Cas9)

value: Prostate


title: CUT_Tag_Control_rep2

value: Wildtype


title: CUT_Tag_Control_rep1


title: Naïve_anti-β1 anti-β1 rep3

value: Naive hiPSC reverted with MAb13 from HEL 24.3

value: treated continuously with MAb13


title: Naïve_anti-β1 anti-β1 rep2


title: Fetal brain Mock

description:
10x genomics
G001_ZIKV_09_SC_FetalBrain_mock_48hr

value: Fetal brain tissue, 117 day post-conception male

value: neural cells

value: male

value: Mock


title: PC-3, clone 1, AG, rep1

description:
Library name: AG_1
Single-base editing (Cas9)

value: single clone

value: no treatment


title: CUT_Tag_FUS-CREB3L2_rep1

value: Huvec

value: epithelial

value: FUS-CREB3L2 stable expression


title: PC-3, clone 5, AA_AR_EtOH

description:
Library name: AA_AR_EtOH
Single-base editing (Cas9), AR overexpression, EtOH

value: AR overexpression, EtOH


title: RNA_seq_del-bZIP_rep2

value: FUS-CREB3L2 del-bZIP mutant stable expression


title: Naïve_anti-β1 anti-β1 rep1


title: PC-3, clone 9, AA, rep2

description:
Library name: AA_2
Single-base editing (Cas9)


title: RNA_seq_12E_rep2

value: FUS-CREB3L2 12E mutant stable expression


title: Naïve_anti-β1 IgG rep3

value: treated with IgG for 48h


title: Naïve_anti-β1 IgG rep1


title: PC-3, clone 5, AA_AR_DHT

description:
Library name: AA_AR_DHT
Single-base editing (Cas9), AR overexpression, DHT

value: Prostate

value: AR overexpression, DHT


title: PC-3, clone 9, AA, rep3

description:
Library name: AA_3
Single-base editing (Cas9)


title: Naïve_anti-β1 IgG rep2

value: Naive hiPSC reverted with MAb13 from HEL 24.3


title: CUT_Tag_CREB3L2_rep1

value: CREB3L2 stable expression


title: RNA_seq_12E_rep1


title: Naïve_ctrl anti-β1 rep3

value: Naive hiPSC reverted from HEL 24.3

value: treated with MAb13 for 48h


title: Naïve_ctrl anti-β1 rep2


title: Sample 8_KLE

data_processing:
Bcl files were demultiplexed with bcl2fastq (v2.20)
The paired-end reads were trimmed with Trim Galore (v.0.6.10)
Bismark (v.0.24.0) aligned the trimmed reads to human GRCh38 reference genome with Bowtie 2 (2.5.1)
The duplicates were removed from the alignment results with Bismark (v.0.24.0)
Bismark (v.0.24.0) identified the methylation on cytosines
Assembly: GRCh38
Supplementary files format and content: bedGraph files generated by bismark_methylation_extractor, containing the methylation percentages of the CpG cytosines

growth_protocol: Endometrial cancer cell lines were cultured in ATCC recommended culture medium supplemented with 10% FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 370C containing 5% CO₂.

extract_protocol:
The DNA was isolated from the cell lines using the QIAamp DNA Mini Kit (Qiagen) per the manufacturer’s instructions.
The DNA samples underwent Agilent SureSelectXT Methyl-seq (Agilent Technologies) analysis to investigate their DNA methylation status across the entire PAX2, MLH1 and PAX8 loci using a custom designed capture panel for methyl-seq, per manufacturer’s instructions.
Targeted Methyl-seq

treatment_protocol: No treatment

value: Uterus

value: KLE

value: epithelial cells


title: RNA_seq_TDP43-CREB3L2_rep2

value: TDP43-CREB3L2 stable expression


title: PC-3, clone 5, AA, rep1

description:
Library name: AA_1
Single-base editing (Cas9)

value: single clone

value: no treatment


title: RNA_seq_TDP43-CREB3L2_rep1

value: Huvec

value: epithelial


title: RNA_seq_FUS-CREB3L2_rep2

value: FUS-CREB3L2 stable expression


title: PC-3, clone 1, AG, rep2

description:
Library name: AG_2
Single-base editing (Cas9)


title: PC-3, clone 1, GG_AR_DHT

description:
Library name: GG_AR_DHT
Single-base editing (Cas9), AR overexpression, DHT


title: Naïve_ctrl anti-β1 rep1


title: Sample 7_RL95-2


title: RNA_seq_del-bZIP_rep1

value: FUS-CREB3L2 del-bZIP mutant stable expression


title: RNA_seq_FUS-CREB3L2_rep1


title: RNA_seq_CREB3L2_rep2


title: Sample 6_EJ

value: EJ


title: Sample 5_EI

value: EI


title: Primed anti-β1 rep2

source_name: Primed human induced pluripotent stem cells (hiPSC)

value: HEL 24.3 derived from fibroblasts

value: treated with MAb13 for 12h


title: Primed anti-β1 rep1


title: RNA_seq_Control_rep2

value: Wildtype


title: RNA_seq_Control_rep1