title: IL4c (1, 2, and 3)

first: MATTHEW

middle: Dae-Young

last: PARK

address: 50 East 98th Street, 6A-1

institute: Icahn School of Medicine at Mount Sinai

description: 10X Genomics

data_processing:
Gene expression reads were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output.
Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted.
From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
Assembly: mm10
Supplementary files format and content: Barcode.tsv.gz.gz, features.tsv.gz.gz, and matrix.mtx.gz.gz files are made available for each sample.

source_name: Bone marrow

extract_protocol:
T cells and myeloid cells were separately sorted and barcoded with 10x Cellplex oligos before being encapsulated using the 10X Chromium 3’ v3 chemistry kit according to manufacturer’s instructions. Cells sorted from the same genotype were barcoded and pooled into individual lanes. A total of 12,000 cells were loaded per lane from each condition. For scRNA-seq of BM of naïve, tumor- bearing and IL-4c treated mice, bone marrow myeloid cells and were sorted for sequencing. Due to their abundance in bone marrow, neutrophils were separately sorted and then recombined back with the above cells at a 1:10 ratio.
All sequencing libraries were prepared per manufacturer instructions.
After stringent cDNA and sequencing library quality control with the CybrGreen qPCR library quantification assay, samples were sequenced at a depth of 100 million reads per library with a 75-cycle kit on an Illumina Nextseq 550.

value: Bone marrow

value: Immune

tag: treatment


title: Naïve (1, 2, and 3)

status: Public on Dec 20 2023

type: SRA

city: New York

state: NY

country: USA

description: 10X Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

value: WT


title: KP (1, 2, and 3)

description: 10X Genomics

value: tumor cell-inoculated


title: Tumor_KO (1, 2, and 3)

description: 10X Genomics

source_name: Lung

value: Lung

value: Ms4a3-CRE x Il4ra-FLOX


title: Tumor_WT (1, 2, and 3)

description: 10X Genomics


title: subjectB_pooled_replicate8

type: genomic

city: Jupiter

first: Anderson

last: Butler

state: Florida

institute: VoLo Voundation

hyb_protocol: Deamination was carried out using EZ-96 DNA Methylation Kit (Zymo Research) according to Illumina’s recommended deamination protocol. Hybridization was carried out according to Illumina standard protocol.

data_processing: Beta values were generated using SeSAMe with package authors recommended settings

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, Cat No. 69504) with RNase treatment option, using RNAse cocktail from Ther-mofisher (AM2286).

treatment_protocol: Whole blood was collected into K2EDTA tubes, then aliquoted into 1.5mL tubes and frozen on dry ice until extraction.

tag: Sex

value: male

tag: age

tag: ethnicity

value: hispanic


title: WT B cells (IgM+, IgD-) Biological Replicate 4

city: Munich

first: Thomas

last: Korn

email: thomas.korn@tum.de, c.sie@tum.de

address: Ismaninger Str. 22

department: Experimental Neuroimmunology

country: Germany

institute: Technical University of Munich

description: TGACTGAA

library_source: transcriptomic

data_processing:
BCL files were demultiplexed using bcl2fastq v2.20.0.422
Fastq files were mapped to the GRCm38 genome using STAR (version 2.7.5b). Transcript and gene definitions were used according to GENCODE version M25.
Final raw count matrix was obtained using the published Drop-seq pipeline (v1.12) to generate sample- and gene-wise UMI tables (Macosko et al, 2015, Cell).
Raw counts of two separate sequencing runs of the same library were merged and non-overlapping genes were dropped. Genes with low expression (defined as < 1 counts per million in at least 4 samples) were removed and differential gene expression analysis was performed using the edgeR package (v3.42.4) in R (v3.1).
PCA analysis was performed using the PCA function of the FactoMineR package (v2.6) on log2 transformed cpm (counts per million)-normalized counts derived from 5 biological replicates of thymic WT_IgM and CD40KO B cells.
Gene set enrichment analysis (GSEA) was performed using unfiltered DESeq2-normalized counts, calculated using the DESeq2 package v1.40.2 (Love et al, 2014, Genome Biol.) using the GSEA 4.3.2 software (Subramanian et al., 2005, PNAS; Mootha et al. 2003, Nature Genetics) in conjunction with MSigDB v2023.1. The interrogated gene sets were derived from the M8 collection of cell type signature gene sets (MSigDB). Analysis was run with Permutation type phenotype and thus applied a false discovery rate (FDR) of 0.25.
Assembly: GRCm38
Supplementary files format and content: Sample annotations in CSV format
Supplementary files format and content: Gene Expression Matrix files for Run1 and Run2 in CSV format

source_name: thymus

extract_protocol:
Single-cell suspensions of thymi from 5 mice per genotype were incubated with LIVE/DEAD fixable dye (Invitrogen, 1:500) and mouse Fc Block (1:100) in PBS for 15 min on ice. Cells were washed with fluorescence-activated cell sorting (FACS) buffer (2% FCS in PBS) and incubated with fluorochrome-conjugated antibodies (1:300) for 25 min on ice in the dark. For each sample, 2000 cells were sorted into 10 µl TCL Buffer (Qiagen). For WT samples, the sort-gate was set to viable CD3-CD4-CD8a-NK1.1-CD11b-F4/80-CD19+B220+IgM+IgD- cells, representing the thymic B cell population known from other experiments to have the highest Aqp4 expression. For CD40KO samples, the thymic B cell population diversity was strongly diminished, containing virtually no IgM+IgD- cells, requiring us to sort the entire thymic B cell population for comparison, i.e. with the sort gate set to viable CD3-CD4-CD8a-NK1.1-CD11b-F4/80-CD19+B220+ cells.
RNA was isolated from TCL lysate via AmpureXP beads (Beckman Coulter). Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016, Sci Rep). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher, #EP0742) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. 5‘-ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing a TruSeq adapter was ligated and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to previous descriptions (Parekh et al., 2016, Sci Rep), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 65 cycles for the cDNA in read1 and 19 cycles for the barcodes and UMIs in read2.

value: thymus

value: 6-8 weeks

value: B cells

value: female


title: WT B cells (IgM+, IgD-) Biological Replicate 3

description: TTATTATG


title: WT B cells (IgM+, IgD-) Biological Replicate 1

description: TGCGTACA


title: Mock treated Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

city: Milano

first: Sara

last: Valsoni

state: MI

address: via Olgettina 60

department: TIGET

country: Italy

institute: SR-TIGET

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument and raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Reads quality was controlled with Fastqc v0.11.9, while low quality reads and the adapters were removed using Trim Galore v0.6.6 according to following parameters: --quality 20, --length 25, --paired
Remaining reads were aligned to the murine reference genome GRCm38 using STAR v2.7.6a with default parameters
Gene counts were quantified using the featureCounts function from Subread package v 2.0.1 and Gencode v M25 as gene model
Raw counts were corrected for biases due to different library preparations using the ComBat_seq function from the R/Bioconductor package sva v3.38.0
The differential expression analysis was performed using the R/Bioconductor package DESeq2 v1.30.0
Assembly: GRCm38
Supplementary files format and content: text file with raw counts

source_name: Liver

extract_protocol:
RNA exrtraction by RNeasy® Mini Kit (QIAGEN), following provider indications
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations

value: Liver

tag: cell line

value: Hepa 1-6

value: Hepatocyte

value: Mock


title: WT B cells (IgM+, IgD-) Biological Replicate 2

description: GTCGCTGT


title: subjectA_pooled_replicate8


title: BM from CML mouse 2 [5-4]

city: Glasgow

first: Vignir

last: Helgason

address: Wolfson Wohl Cancer Research Centre, Garscube Estate, Glasgow, Bearsden

country: United Kingdom

institute: The University of Glasgow

data_processing:
The sequences were checked for quality using FastQC v0.11.833 and cells with mean quality under 30 in most sequences were eliminated. The sequences were trimmed with Trim_galore v0.5.034, using the default threshold for quality and aligned to the reference genome (GRCm38) using Hisat2 v2.1.035. Cells with an alignment score lower than 50% were discarded. A count matrix was produced with FeatureCounts v1.6.2
Assembly: GRCm38
Supplementary files format and content: CSV matrix file containing read counts for fully processed samples

source_name: Bone Marrow

extract_protocol:
BM cell suspensions were treated 529 with Diisopropylfluorophosphate (1mM) prior to cell sorting. Cell suspensions were stained with monoclonal antibodies to mouse CD45.1, CD45.2, CD11b, F4/80 and single cell macrophages (CD45.1+ CD11b+ F4/80+) were sorted into 96 well-plates containing 0.2% Triton X-100 and 0.1ul of RNAase plus inhibitor (Promega N2615)/each well using BD FACS ARIA Z6001 (BD Biosciences).
In brief, oligo-dT30 primers and dNTP mix were mixed with isolated RNA and incubated with samples at 72°C for 3 min. Reverse transcription and pre-amplification steps were performed. cDNA was then purified, and library quality assessed using Tapestation D5000. Samples were subsequently tagmented and amplified according to the Nextera XT DNA Library Preparation protocol. Indexed samples were then pooled and cleaned. Libraries were then sequenced at 2x75bp paired end reads, with a total of 100M reads.

treatment_protocol: Inducible chimeric SCLtTA+/BCR-ABL+ BM was generated by mixing 7.5x105 BM cells from SCLtTA+/BCR-ABL+ (CD45.2) CML, or SCLtTA+/BCR-ABL- (CD45.2) control, with 7.5x105 BM cells from C57/Bl6 mice (CD45.1) WT. C57/Bl6 recipient mice aged between 8 to 12 weeks received two doses of 4.25 Gy, 3 hours apart and received 1.5x106 chimeric BM cells via tail vein injection. To allow for irradiation recovery, mice were maintained on tetracycline (0.5g/L) for 14 days prior to removal of tetracycline for transgene induction. Disease levels were monitored for Gr-1 (Ly6G/Ly6C) and CD11b in blood by flow cytometry. Mice were sacrificed at day 15 following BCR-ABL induction.

value: Bone Marrow

value: Macropage

tag: strain

value: 8 to 12 weeks

value: 7.5x105 BM from CD45.2 SCLtTA+/BCR-ABL+ mice

tag: disease state

value: CML


title: subjectD_pooled_replicate6


title: Mock treated Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2


title: Mock treated Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: BM from CML mouse 1 [5-3]


title: TS543 PDX mouse biol rep 2

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: Microwell-based scRNA-seq, 8-base index read, 26-base read 1, 58-base read 2

data_processing:
Read 1 and read 2 fastq files were generated on basespace. Hashtag barcodes and cell barcode and umi for gene expressions were preprocessed and extracted using DropSeqPipeline8 (https://github.com/simslab/DropSeqPipeline8).
HTO raw counts were normalized by centered log ratio (CLR) transformation and performed k-means clustering and statistical identification of singlets by fitting a negative binomial model for demultiplexing
Gene expressions matrix were recovered by EmptyDrops algorithm
Assembly: HTO libraries: TotalSeqA hashtag sequence
Assembly: TS543 Transcriptome libraries: GRCh38
Assembly: TS543 PDX mouse: GRCh38 GRCm38
Supplementary files format and content: HTO libraries: Tab-delimited text files that contain the cell barcode and cell hashtag
Supplementary files format and content: Transcriptome libraries: Tab-delimited text files that contain the gene expression level of each individual cell.

molecule: polyA RNA

source_name: Brain tumor tissue resection

growth_protocol:
For PW073 to PW079: TS543 cells were plated at density 1 × 104 viable cells/cm2 and cultured with NeuroCult™ NS-A basal medium supplemented with NeuroCult™ NS-A proliferation supplement, 20 ng/ml EGF, 10 ng/ml bFGF, and 2 µg/ml heparin (Stem Cell Technologies) in a humidified incubator with 5% CO2 at 37°C.
For PLZ019: Mice were bred in house and housed under standard conditions. TS543 cells (100,000 cells in 2 μL, passage 8) were injected in 8-week old female nude mice (CrTac:NCr-Foxn1nu,Taconic)

extract_protocol:
For PW073 to PW079: At the end of culture, neurospheres were collected and dissociated to single cells by pipetting and stained with with TotalSeq™-A hashtag antibodies (BioLegend), then pooled for scRNA-seq.
For PLZ019: Mice were sacrificed for collecting brain tumor tissues 21 post-injection. Freshly resected tumor tissues were kept in ice-cold PBS for transportation prior to dissociation. Mouse brain tumor resections were collected for dissociation using Papain Dissociation System (Worthington) as previously described(Mizrak et al., 2020; Mizrak et al., 2019) with following modifications. Briefly, minced tissue was digested with papain (Worthington, 10 units per sample) in PIPES solution (120 mM NaCl, 5 mM KCl, 20 mM PIPES (Sigma), 0.45% glucose, DNase I (Worthington, 100 units per sample), 1xAntibiotic/Antimycotic (GIBCO), pH adjusted to 7.6) for 30 min at 37°C on gentleMACS™ Octo Dissociator with Heaters (Miltenyi Biotec, program 37C_ABDK). After digestion, the cell suspension was applied to a MACS SmartStrainer (70 μm, Miltenyi Biotec) and centrifuged at 300xg for 10 minutes at 4°C. The cell pellets were then subjected to red blood cell removal (Red Blood Cell Lysis Solution (10x), Miltenyi Biotec) and debris removal (Debris Removal Solution, Miltenyi Biotec) according to the manufacturer’s instructions.
For PW073 to PW079: mRNA and hashtag molecues were captured using bead-bound oligo dT(30). Captured mRNA and hashtag molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. Cell Hashtag (HTO)-containing fraction and the large cDNA library were separated by SPRI (Beckman Ampure XP beads). Purified large cDNA PCR products were used as the input for Nextera XT reactions to generate sequencing library. Purified Cell Hashtag (HTO)-containing fraction were used as input for PCR amplification using TruSeq DNA D703 primer and P5-SMARTpcr primer to generate the Cell Hashtag library.
For PLZ019: mRNA molecues were captured using bead-bound oligo dT(30). Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.
For PW073 to PW079: scRNA-seq with TotalseqA hashtag
For PLZ019: scRNA-seq

treatment_protocol: For PW073 to PW079: When the diameters of neurospheres reached to approximately 50 to 100 μm after about 5 days’ culture, the culture medium of neurospheres were replaced with pre-warmed medium containing RSL3 or corresponding volume of vehicle (DMSO).

value: Brain tumor tissue resection

value: Neurosephere

value: sp/sp

tag: tumor stage

value: 21 days post-injection

tag: background strain


title: subjectD_pooled_replicate5

value: male

value: hispanic


title: subjectD_pooled_replicate4


title: Bone marrow stromal cells WT rep1

city: changsha

first: Jian xi

last: Zhu

state: -- Select state --

address: XiangYa hospital

department: Department of Orthopaedics

country: China

institute: Xiangya Hospital, Central South University

data_processing:
Solexa pipeline 1.8 (Off-Line Base Caller software, version 1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 software.
Using StringTie software to estimate transcript abundance with reference to official database annotation information
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Ballgown.
Assembly: mm10
Supplementary files format and content: Matrix table with FPKM for every gene/ transcript and every sample

source_name: primary cells

extract_protocol:
BMSCs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary cells

value: Bone marrow stromal cells

value: WT


title: BM from control mouse 1 [5-1]

value: 7.5x105 BM from CD45.2 SCLtTA+/BCR-ABL- mice


title: Cas9 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

value: Liver

value: Hepa 1-6

value: Hepatocyte

value: Cas9 against Pcsk9


title: subjectC_pooled_replicate7


title: Cas9 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2


title: subjectC_pooled_replicate6


title: subjectD_pooled_replicate3


title: dCas9-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

value: dCas9-ETRs against Pcsk9


title: dCas9-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2


title: Cas9 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: subjectC_pooled_replicate5


title: BM from control mouse 2 [5-2]

value: Bone Marrow

value: Macropage

value: 8 to 12 weeks


title: subjectB_pooled_replicate7


title: untargetd ZFP-ETRs treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

value: untargeted ZFP-ETRs


title: dCas9-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: subjectA_pooled_replicate7


title: subjectC_pooled_replicate4


title: untargetd ZFP-ETRs treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2


title: untargetd ZFP-ETRs treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: subjectC_pooled_replicate3


title: Placenta-Middle-A

type: RNA

city: Katsushika

first: Masakazu

last: Umezawa

state: Tokyo

address: 6-3-1 Niijuku

department: Department of Medical and Robotic Engineering Design, Faculty of Advanced Engineering

country: Japan

institute: Tokyo University of Science

description: Gene expression in placenta of mice treated with CB-NP (15)

hyb_protocol: Cy3-labelled RNA was hybridized to a SurePrint G3 Mouse GE 8x60K microarray according to the protocol of Takara Bio, Inc. (Shiga, Japan).

scan_protocol: The microarray was washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and scanned by a DNA microarray Scanner G2565CA (Agilent Technologies).

data_processing: Scanner output images were normalized and digitalized by Agilent Feature Extraction software according to the Minimum Information About a Microarray Experiment (MIAME) guidelines (Brazma et al., 2001) and a pre-processing method for Agilent data (Zahurak et al., 2007).

source_name: Placenta, CB-NP 15 μg/kg, replication 1

label_protocol: After purification of RNA by ethanol precipitation and RNeasy Micro Kit (Qiagen, Hilden, Germany), the integrity of extracted RNA was evaluated with capillary electrophoresis using a Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). Total RNAs were pooled for each group. Each of the pooled RNA samples was labeled by Cy3.

growth_protocol: ICR mice were purchased from SLC Inc. (Hamamatsu, Shizuoka, Japan) and were housed under controlled temperature (23 ± 1 °C) and humidity (55% ± 5%), with a 12-hr dark/light cycle and ad libitum access to food and water. All animals were treated and handled in accordance with national guidelines for the care and use of laboratory animals and with the approval of institutional animal care and use committee.

extract_protocol: Isolated and dissected tissues were homogenized in Isogen (Nippon Gene Co., Ltd., Tokyo, Japan). Total RNA was isolated according to the manufacturer's protocol and suspended in RNase-free water.

treatment_protocol: Pregnant ICR mice were treated twice, on gestational days (GD) 5 and 9, with CB-NP (2.9-95 microg/kg/time) via intranasal instillation. Control animals were treated with distilled water (1 mL/kg body weight) weight each time. For ascorbic acid pretreatment group, it was administed via intraperitoneal injection at 1 h before the CB-NP instillation.

value: placenta

tag: gender

value: female

value: GD 13

value: ICR

value: CB-NP 15 μg/kg


title: Placenta-High-A

description: Gene expression in placenta of mice treated with CB-NP (73)

source_name: Placenta, CB-NP 73 μg/kg, replication 1

value: CB-NP 73 μg/kg


title: Placenta-Control-B

description: Gene expression in placenta of control mice

source_name: Placenta, CB-NP 0 μg/kg, replication 2

value: CB-NP 0 μg/kg


title: 6-Brain-High-B

description: Gene expression in cerebral cortex of mice prenatally treated with CB-NP (73)

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 73 μg/kg, replication 2

value: cerebral cortex

value: male

value: 6 weeks


title: ZFP-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

value: Liver

value: Hepa 1-6

value: Hepatocyte

value: ZFP-ETRs against Pcsk9


title: 6-Brain-Control-B

description: Gene expression in cerebral cortex of control mice

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 0 μg/kg, replication 2


title: subjectB_pooled_replicate6

value: hispanic


title: 6-Brain-Middle-B

description: Gene expression in cerebral cortex of mice prenatally treated with CB-NP (15)

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 15 μg/kg, replication 2


title: 12-B

source_name: 12-wk-old offspring, cerebral cortex, control in the CB-NP and ascorbic acid study, replication 2

value: 12  weeks


title: Placenta-Middle-B

source_name: Placenta, CB-NP 15 μg/kg, replication 2


title: 6-Brain-Middle-A

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 15 μg/kg, replication 1


title: Placenta-Low-B

description: Gene expression in placenta of mice treated with CB-NP (2.9)

source_name: Placenta, CB-NP 2.9 μg/kg, replication 2

value: CB-NP 2.9 μg/kg


title: Placenta-Low-A

source_name: Placenta, CB-NP 2.9 μg/kg, replication 1

value: placenta


title: subjectB_pooled_replicate5


title: Placenta-High-B

source_name: Placenta, CB-NP 73 μg/kg, replication 2

value: female


title: 12-A

source_name: 12-wk-old offspring, cerebral cortex, control in the CB-NP and ascorbic acid study, replication 1


title: Placenta-Control-A

source_name: Placenta, CB-NP 0 μg/kg, replication 1

value: GD 13


title: 6-Brain-High-A

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 73 μg/kg, replication 1

value: ICR


title: 6-Brain-Control-A

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 0 μg/kg, replication 1


title: ZFP-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1

source_name: Liver


title: 12-VtC-B

description: Gene expression in cerebral cortex of mice prenatally treated with CB-NP (2.9)

source_name: 12-wk-old offspring, cerebral cortex, ascorbic acid alone, replication 2

value: ascorbic acid alone


title: 6-Brain-Low-B

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 2.9 μg/kg, replication 2


title: 6-Brain-Low-A

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 2.9 μg/kg, replication 1


title: 12-VtC-A

source_name: 12-wk-old offspring, cerebral cortex, ascorbic acid alone, replication 1


title: AS153

city: Nanjing

first: Qiuhua

last: Cao

address: No. 639 Longmian Avenue, Jiangning District, Nanjing, Jiangsu Province, China

institute: China Pharmaceutical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads.
Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome.
The gene alignment and FPKM were calculated using featureCounts v1.6.2 / StringTie v1.3.4d.
DESeq2 v1.22.1 / edgeR v3.24.3 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression.
Assembly: GRCm39.104
Supplementary files format and content: FPKM, counts

source_name: colon tissue

extract_protocol:
Colon tissue were removed, flash frozen on dry ice, and total RNA was extracted using tissue total RNA isolation kit (Vazyme, China) and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: C57BL/6J mice were intraperitoneally injected with 10 mg/kg AOM on the first day and drunk 2% DSS three times intermittently to induce colorectal cancer. Half of the mice were confined to a ventilated 50 mL centrifuge tube and stressed for 3-4 hours per day.

value: colon tissue

value: colorectal cancer cell

value: WT

value: AOM/DSS,chronic restraint stress


title: ZFP-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2


title: subjectD_pooled_replicate2

value: male


title: 12-CB-B

source_name: 12-wk-old offspring, cerebral cortex, CB-NP 95 μg/kg, replication 2

value: cerebral cortex

value: CB-NP 95 μg/kg


title: 12-CB-A

source_name: 12-wk-old offspring, cerebral cortex, CB-NP 95 μg/kg, replication 1


title: AS78


title: 12-CB-VtC-B

source_name: 12-wk-old offspring, cerebral cortex, CB-NP 95 μg/kg with ascorbic acid, replication 2

value: CB-NP 95 μg/kg with ascorbic acid


title: subjectC_pooled_replicate2


title: 12-CB-VtC-A

source_name: 12-wk-old offspring, cerebral cortex, CB-NP 95 μg/kg with ascorbic acid, replication 1


title: subjectB_pooled_replicate3


title: subjectB_pooled_replicate4


title: AS58


title: A49

value: AOM/DSS


title: 6-A

source_name: 6-wk-old offspring, cerebral cortex, control in the CB-NP and ascorbic acid study, replication 1

value: 6 weeks


title: 6-B

source_name: 6-wk-old offspring, cerebral cortex, control in the CB-NP and ascorbic acid study, replication 2


title: subjectA_pooled_replicate6

value: hispanic


title: subjectB_pooled_replicate2


title: A40


title: Hep3B cells, sgRFX6_rep3

city: Guangzhou

first: Zhiyu

last: Qiu

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
CLC genomics workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: tumor cells

extract_protocol:
Total RNAs were isolated from HCC cells by Trizol reagent (Life Technologies, Carlsbad, California, USA) according to the manufacturer’s instructions.
The cDNA libraries were sequenced on the Illumina sequencing platform.

value: tumor cells

value: Human hepatocellular carcinoma

value: RFX6 knockout


title: Hep3B cells, sgRFX6_rep1


title: subjectA_pooled_replicate5


title: A28


title: Hep3B cells, sgControl_rep3


title: Hep3B cells, sgRFX6_rep2


title: 6-VtC-B

description: Gene expression in cerebral cortex of mice prenatally treated with ascorbic acid

source_name: 6-wk-old offspring, cerebral cortex, ascorbic acid alone, replication 2


title: 6-CB-B

description: Gene expression in cerebral cortex of mice prenatally treated with CB-NP (95)

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 95 μg/kg, replication 2


title: RA rep3

city: Detroit

first: Daniel

last: Rappolee

address: 275 E Hancock St

department: OBGYN

institute: Wayne State University

description: RAtoNS.xlsx

data_processing:
Data were demultiplexed using Illumina’s CASAVA 1.8.2 software.
Alignment to the mouse genome (mm9) using STAR
Tabulation using htseq-count
Differential expression analysis in edgeR
Genome_build: mm9
Supplementary_files_format_and_content: Excel files comparing triplicate stimulus data to triplicate Normal Stemness (NS) data.

source_name: Embryonic Stem Cell

growth_protocol: ESC passaged and grown with LIF+ media for ~18hr until ~24% confluence. They were then stimulated with their corresponding toxicant with LIF. A few were treated without LIF.

extract_protocol:
Cells were then washed and lysed using Trizol.
Lexogen 3' Quant-seq protocol

treatment_protocol: Cells were grown under stimulation for 72hr.

value: FUCCI

value: RA 1uM

tag: lif presence

value: negative

tag: treatment time


title: Hep3B cells, sgControl_rep2


title: subjectA_pooled_replicate4


title: RA rep2

description: RAtoNS.xlsx


title: 6-CB-VtC-B

description: Gene expression in cerebral cortex of mice prenatally treated with CB-NP (95) and ascorbic acid

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 95 μg/kg with ascorbic acid, replication 2

value: ICR


title: 6-CB-VtC-A

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 95 μg/kg with ascorbic acid, replication 1


title: Hep3B cells, sgControl_rep1


title: C+V 72hpi 48, cells infected with C. parvum and bovine coronavirus [C+V48A]

city: Ås

first: Alejandro

last: Jimenez Melendez

address: Elizabeth Stephansens vei 15

department: PARAFAG

country: Norway

institute: NMBU

data_processing:
low quality read trimming - Trimmomatic V 0.36
rRNA removal - sortmerna V 1.7
sequence alignment - TopHat V 2.1.1
transcriptome assembly - Cufflinks V 2.1.1
expression normalization - Cufflinks V 2.1.1
differential expression - Cufflinks V 2.1.1
Assembly: GRCh37

growth_protocol: HCT-8 cells were grown in RPMI 1640 plus 10% FBS and split twice a week

extract_protocol:
QIAGEN RNAeasy plus
Strand specific TruSeq mRNA-seq library prep

treatment_protocol: Infection with bovine coronavirus, cryptosporidium parvum or both. Uninfected controls

value: Infected with C. parvum and bovine coronavirus

tag: sample/time point

value: C+V 72hpi


title: subjectA_pooled_replicate3


title: subjectA_pooled_replicate2


title: RA rep1

description: RAtoNS.xlsx


title: 6-VtC-A

source_name: 6-wk-old offspring, cerebral cortex, ascorbic acid alone, replication 1

value: ascorbic acid alone


title: C+V 72hpi 46, cells infected with C. parvum and bovine coronavirus [C+V46A]


title: PFOA 100uM rep3

description:
IC75
PFOA100toNS.xlsx

value: PFOA 100uM

value: positive


title: 6-CB-A

source_name: 6-wk-old offspring, cerebral cortex, CB-NP 95 μg/kg, replication 1

value: cerebral cortex

value: male

value: CB-NP 95 μg/kg


title: subjectC_pooled_replicate1


title: C+V 72hpi 44, cells infected with C. parvum and bovine coronavirus [C+V44A]


title: PFOA 100uM rep2

description:
IC75
PFOA100toNS.xlsx


title: C+V 24hpi 42, cells infected with C. parvum and bovine coronavirus [C+V42A]

value: C+V 24hpi


title: C+V 72hpi 45, cells infected with C. parvum and bovine coronavirus [C+V45A]


title: subjectD_pooled_replicate1

value: hispanic


title: C+V 24hpi 41, cells infected with C. parvum and bovine coronavirus [C+V41A]


title: C+V 24hpi 38, cells infected with C. parvum and bovine coronavirus [C+V38A]


title: C+V 24hpi 40, cells infected with C. parvum and bovine coronavirus [C+V40A]


title: subjectA_pooled_replicate1


title: PFOA 100uM rep1

description:
IC75
PFOA100toNS.xlsx


title: C+V 24hpi 39, cells infected with C. parvum and bovine coronavirus [C+V39A]


title: subjectB_pooled_replicate1


title: Crypto 72hpi 36, cells infected with C. parvum [Cp36A]

value: Infected with C.parvum

value: Crypto 72hpi


title: C+V 72hpi 47, cells infected with C. parvum and bovine coronavirus [C+V47A]


title: PFOA 60uM rep2

description:
LOAEL
PFOA60toNS.xlsx

value: PFOA 60uM


title: C+V 24hpi 37, cells infected with C. parvum and bovine coronavirus [C+V37A]


title: PFOA 60uM rep3

description:
LOAEL
PFOA60toNS.xlsx

value: FUCCI


title: PFOA 60uM rep1

description:
LOAEL
PFOA60toNS.xlsx


title: Crypto 72hpi 35, cells infected with C. parvum [Cp35A]


title: Crypto 72hpi 34, cells infected with C. parvum [Cp34A]


title: NS rep3

value: Normal Stemness


title: Crypto 72hpi 33, cells infected with C. parvum [Cp33A]


title: Crypto 72hpi 32, cells infected with C. parvum [Cp32A]


title: cardiac organoids, IL1bOrgs.1

city: Charleston

first: Dimitrios

last: Arhontoulis

state: South Carolina

address: 68 President St

department: Bioengineering

institute: MUSC

data_processing:
Paired-end reads (fastq) were aligned to the hg38 human reference genome (Genecode GRCh38.p13) using RNA STAR [doi: 10.1093/bioinformatics/bts635] (v2.7.8a) utilizing the Galaxy Project online platform (v21.01, https://galaxyproject.org/).
gene counts were generated using htseq-count (v13.5) utilizing the Galaxy Project online platform (v21.01, https://galaxyproject.org/).
Secondary analysis were performed using R studio.  In particular, the package, bioconductor was used to perform principal component analysis and differential gene expression (DESeq2)
Assembly: HG38
Supplementary files format and content: il1b_rawcounts_041621.xlsx
Supplementary files format and content: IL1B_MedianofRatios_Normalization.xlsx

source_name: cardiac organoids

growth_protocol: organoids were fabricated and devoped for 4 days and then treated with IL1B for 4 days.

extract_protocol:
30-35 organoids were collected immediately out of culture and put in lysis buffer on D10 (2 days after last media change) Total RNA was extracted with an Omega bio-tek E.Z.N.A Total RNA kit
125 ng of total RNA was used for the construction of the library using the New England Biolabs NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# 7490L) and Ultra II Directional RNA Library Prep Kit for Illumina (Cat# 7760L) according to the manufacturer’s instructions.  Indexed libraries were pooled and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000(Illumina, Inc.; San Diego, CA, USA), producing paired-end 150 bp reads at a sequencing depth of 25 millions reads/sample.

treatment_protocol: IL1B treatment went for 4 days

value: cardiac organoids

value: hiPSC-CM donor 01434

value: CM, Fb, EC, PC

value: IL-1 cytokine


title: cardiac organoids, IL1bOrgs.3


title: cardiac organoids, IL1bOrgs.2


title: C+V 72hpi 43, cells infected with C. parvum and bovine coronavirus [C+V43A]

value: Infected with C. parvum and bovine coronavirus

value: C+V 72hpi


title: cardiac organoids, Vehicle.3

value: control


title: cardiac organoids, Vehicle.2


title: NS rep1

value: positive


title: NS rep2


title: Crypto 24hpi 27, cells infected with C. parvum [Cp27A]

value: Crypto 24hpi


title: Crypto 24hpi 30, cells infected with C. parvum [Cp30A]


title: Crypto 24hpi 28, cells infected with C. parvum [Cp28A]


title: Crypto 24hpi 29, cells infected with C. parvum [Cp29A]


title: Crypto 72hpi 31, cells infected with C. parvum [Cp31A]


title: cardiac organoids, Vehicle.1


title: Crypto 24hpi 26, cells infected with C. parvum [Cp26A]


title: Virus 72hpi 23, cells infected with bovine coronavirus [V23A]

value: Infected with Bovine coronavirus

value: Virus 72hpi


title: Crypto 24hpi 25, cells infected with C. parvum [Cp25A]


title: ND rep3

description: NDtoNS.xlsx

value: Normal Differentiation

value: negative


title: Virus 72hpi 24, cells infected with bovine coronavirus [V24A]


title: Virus 72hpi 21, cells infected with bovine coronavirus [V21A]


title: ND rep1

description: NDtoNS.xlsx


title: DEP 10uM rep3

description:
IC75
DEP10toNS.xlsx

value: DEP 10uM


title: HGC27, wt, H3K27ac HiChIP, rep1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

library_source: genomic

data_processing:
*library strategy: HiChIP
Basecalls were performed using bcl2fastq.
H3K27ac HiChIP reads were processed using HiC-Pro v2.11.4.
HiChIP matrix file (hic file) was generated using the Juicer-tools v1.9.862.
Assembly: hg19
Supplementary files format and content: hic

growth_protocol: MEM, 10% fetal bovine serum, 1x penicillin/streptmycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes.
Cross-linked cells were lysed and digested with a restriction enzyme, MboI. Digested chromatin was labeled with biotin–14-dATP and blunt-end ligated. Ligated chromatin samples were fragmented using Covaris S220 and immunoprecipitated using anti-H3K27ac antibody, followed by reversal of the crosslinking and DNA purification. Biotinylated DNA fragments were pulled down with streptavidin beads and performed tagmentation with Tn5 transposase (Illumina, Cat. No. 20034198). Bead-conjugated DNA was amplified by PCR and libraries were sequenced using Illumina Hiseq1500 or Novaseq6000.

value: wildtype

tag: chip antibody


title: MHCC-97H, input

data_processing:
Libraries were sequenced on an Illumina HiseqXten platform.
MACS version 2.1.0.2 software was run with the mapped reads to detect the statistically significant ChIP-enriched peaks with a significant cut-off q value threshold of 0.01
Assembly: GRCh37
Supplementary files format and content: bed, narrow peaks

extract_protocol:
1% formaldehyde (Sigma-Aldrich, Germany) solution was added to induce MHCC-97H cells crosslinking followed by glycine solution to quench the reaction
Libraries were sequenced on an Illumina HiseqXten platform.

value: tumor cells

value: Human hepatocellular carcinoma


title: ND rep2

description: NDtoNS.xlsx

value: FUCCI

tag: treatment


title: MHCC-97H, HA-RFX6, ChIP

tag: tissue


title: DEP 10uM rep2

description:
IC75
DEP10toNS.xlsx


title: Virus 72hpi 20, cells infected with bovine coronavirus [V20A]


title: Virus 24hpi 18, cells infected with bovine coronavirus [V18A]

value: Virus 24hpi


title: Virus 72hpi 19, cells infected with bovine coronavirus [V19A]


title: Virus 24hpi 17, cells infected with bovine coronavirus [V17A]


title: DEP 10uM rep1

description:
IC75
DEP10toNS.xlsx


title: Virus 24hpi 16, cells infected with bovine coronavirus [V16A]


title: DEP 5uM rep3

description:
LOAEL
DEP5toNS.xlsx

value: DEP 5uM


title: Virus 24hpi 14, cells infected with bovine coronavirus [V14A]


title: Cells 72hpi 12, uninfected cells [C-12A]

source_name: Cells 72hpi 12, uninfected cells

value: Uninfected

value: Cells 72hpi


title: Virus 24hpi 13, cells infected with bovine coronavirus [V13A]


title: NELFB-2h-Pol-II-Rep2 DFF-ChIP

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry and Molecular Biology

institute: University of Iowa

data_processing:
Adapter sequences were trimmed and reads were mapped to the UCSC hg38/sf21 combined genome for PRO-Seq and to a hg38/mm10 combined genome for DFF-Seq.
BAM files were converted to BED files. These files were converted to bedgraphs and normalized with correction factors obtained from spike-in analysis as described in Ball et la., 2019. Spike-in normalized bedgraphs were converted to bigwigs.
Assembly: UCSC hg38/JQCY02 (moth) for PRO-Seq and hg38/mm10 for DFF-Seq
Supplementary files format and content: bigwigs of each replicate

growth_protocol: HAP1 cells were grown to 90% confluence in 6 well-plates (Corning 3516) at 37°C and 5% CO2in IMDM (Gibco 12440053) supplemented with 10% FBS (Gibco 26140079). Sf21 cells were kept in Sf-900™ III SFM (1X) (Gibco 12658019) at room temperature.

extract_protocol:
PRO-Seq and DFF-Seq libraries were prepared as previously described (Santana et al., 2022 and Spector et al., 2022)
PRO-Seq and DFF-Seq libraries were prepared as previously described (Santana et al., 2022 and Spector et al., 2022)

treatment_protocol: dTAGV-1 (a gift from Nathanael S. Gray) or Flavopiridol (Flavo) (NIH AIDS Reagent Program 9925) was dissolved in DMSO. Flavo treatments were performed at a final concentration of 1 µM for 1 h. dTAGV-1treatments were performed at a final concentration of 400 nM for 2 or 48 h.  For combined treatments of Flavo was added for the last hour of dTAGV-1 treament. PAF1 cells were treated with DMSO or dTAGV-1 for 48 h. RTF1 cells were treated with DMSO or dTAGV-1 for 2 h. NELFB cells were treated with DMSO or dTAGV-1 for 2 or 48 h, Flavo or Flavo+dTAGV-1 for 2 or 48 h. Two biological replicates were used for each treatment( PRO-Seq or DFF-Seq). However, one of the duplicates for NELFB-Flavo was lost during preparation of the PRO-Seq library.

tag: cell type

value: NELFB depletion

value: Pol-II, Santa Cruz sc-55492


title: DEP 5uM rep2

description:
LOAEL
DEP5toNS.xlsx

value: positive


title: NELFB-2h-Pol-II-Rep1 DFF-ChIP

tag: genotype


title: H3K36me3-TAF1-Rep1 DFF-ChIP

value: WT

value: H3K36me3, Abcam ab9050


title: DEP 5uM rep1

description:
LOAEL
DEP5toNS.xlsx


title: Cells 72hpi 10, uninfected cells [C-10A]

source_name: Cells 72hpi 10, uninfected cells


title: Virus 72hpi 22, cells infected with bovine coronavirus [V22A]

value: Infected with Bovine coronavirus

value: Virus 72hpi


title: Cortisol 60uM rep3

description:
IC75
Cort60toNS.xlsx

value: Cortisol 60uM


title: Cells 72hpi 9, uninfected cells [C-9A]

source_name: Cells 72hpi 9, uninfected cells


title: Cells 72hpi 8, uninfected cells [C-8A]

source_name: Cells 72hpi 8, uninfected cells


title: Cells 72 hpi 7, uninfected cells [C-7A]

source_name: Cells 72 hpi 7, uninfected cells

value: Cells 72 hpi


title: H3K36me3-TAF1-Rep2 DFF-ChIP


title: Cells 24hpi 6, uninfected cells [C-6A]

source_name: Cells 24hpi 6, uninfected cells

value: Cells 24hpi


title: NELFB-Pol-II-Rep2 DFF-ChIP

value: DMSO


title: Cortisol 60uM rep1

description:
IC75
Cort60toNS.xlsx


title: Cortisol 60uM rep2

description:
IC75
Cort60toNS.xlsx


title: Cells 24hpi 5, uninfected cells [C-5A]

source_name: Cells 24hpi 5, uninfected cells


title: Cells 24hpi 4, uninfected cells [C-4A]

source_name: Cells 24hpi 4, uninfected cells


title: Cortisol 10uM rep3

description:
LOAEL
Cort10toNS.xlsx

value: Cortisol 10uM


title: Virus 24hpi 15, cells infected with bovine coronavirus [V15A]


title: Cells 24hpi 3, uninfected cells [C-3A]

source_name: Cells 24hpi 3, uninfected cells


title: H3K36me3-NELFB-Rep1 DFF-ChIP


title: Cells 24hpi 2, uninfected cells [C-2A]

source_name: Cells 24hpi 2, uninfected cells


title: Cells 72hpi 11, uninfected cells [C-11A]

source_name: Cells 72hpi 11, uninfected cells


title: H3K4me3-NELFB-48h-Rep2 DFF-ChIP

value: H3K4me3, Abcam ab8580


title: Cells 24hpi 1, uninfected cells [C-1A]

source_name: Cells 24hpi 1, uninfected cells


title: scr2

city: Cleveland

first: Han

last: Sun

state: OH

address: 9500 Euclid Ave

department: QHS

institute: Cleveland Clinic

data_processing:
RNAseq data were processed and count data were normalized with the R package limma voom.
Assembly: not provided
Supplementary files format and content: normalized_gene.txt

source_name: left atrial appendage

growth_protocol: iCell cardiomyocytes grown in maintenace media supplied by Fujifilm.

extract_protocol: Total RNA was isolated with TRIzol (ThermoFisher, Cat#15596018) extraction and purification using the RNeasy Micro Kit.

treatment_protocol: 50 nM/well of control scrambled (Scr) siRNA (ThermoFisher/Ambion silencer select, Cat#4390843) or FAM13B siRNA (Thermo-Fisher/Ambion, Cat# 439242, id S27906) were transfected into iCell cardiomyocytes using the TransIT-TKO transfection reagent (Mirus Bio, Cat#MIR2150).  The cells were incubated with the siRNA-reagent complexes for 72 hours followed by total RNA isolation.

value: left atrial appendage

value: iCell cardiomyocytes

value: control


title: scr3


title: Cortisol 10uM rep1

description:
LOAEL
Cort10toNS.xlsx

source_name: Embryonic Stem Cell

value: FUCCI


title: Cortisol 10uM rep2

description:
LOAEL
Cort10toNS.xlsx


title: H3K4me3-NELFB-48h-Rep1 DFF-ChIP

value: NELFB depletion


title: H3K4me3-NELFB-2h-Rep2 DFF-ChIP


title: NELFB-Pol-II-Rep1 DFF-ChIP

value: Pol-II, Santa Cruz sc-55492


title: H3K36me3-NELFB-Rep2 DFF-ChIP


title: FAM13B KD 3

value: Knock down


title: H3K4me3-NELFB-2h-Rep1 DFF-ChIP


title: BP 4uM rep3

description:
IC75
BP4toNS.xlsx

value: BP 4uM

value: positive


title: BP 4uM rep1

description:
IC75
BP4toNS.xlsx


title: FAM13B KD 1


title: H3K4me3-NELFB-Rep1 DFF-ChIP

value: WT


title: H3K4me3-NELFB-Rep2 DFF-ChIP


title: PBS treated pancreas, replicate 2

data_processing:
Reads quality was controlled with Fastqc v0.11.9 while low-quality reads and adapters were removed using Trim_Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --rrbs
Remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0
In detail, reads were aligned to both unconverted and converted genomes (GRCm38) using bismark with the --local and –non_directional parameters and the methylation status was obtained using bismark_methylation_extractor script using only the reads mapping to the bottom strand (OB and CTOB)
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered to retain only cytosines from CpG context in the amplified windows and normalized using the normalizeCoverage function
The information from the different samples was merged using the unite function considering the positions covered in all the 3 replicates per condition. The methylation percentage at each position was calculated using the percMethylation function.
Assembly: GRCm38
Supplementary files format and content: Bismark coverage

source_name: Pancreas

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and bisulfite conversion by EpiTect Bisulfite Kit, following provider indications. Finally, the promoter region of Pcsk9 was amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations
DNA amplicons

value: Pancreas

value: PBS


title: EvoETRs 8 against Pcsk9 treated pancreas, replicate 3

value: EvoETRs 8 against Pcsk9


title: EvoETRs 8 against Pcsk9 treated pancreas, replicate 1


title: PBS treated pancreas, replicate 3


title: PBS treated pancreas, replicate 1


title: BP 1uM rep3

description:
LOAEL
BP1toNS.xlsx

value: BP 1uM


title: EvoETRs 8 against Pcsk9 treated pancreas, replicate 2


title: RTF1-VHL-Rep2 PRO-Seq

extract_protocol: PRO-Seq and DFF-Seq libraries were prepared as previously described (Santana et al., 2022 and Spector et al., 2022)

value: RTF1 depletion


title: PBS treated lung, replicate 3

source_name: Lung

value: Lung


title: RTF1-VHL-Rep1 PRO-Seq


title: scr1


title: FAM13B KD 2


title: BP 1uM rep1

description:
LOAEL
BP1toNS.xlsx


title: NELFB-Flavo-VHL-2h-Rep2 PRO-Seq

value: NELFB depletion and flavo

value: dTAGV-1 and Flavopiridol


title: PBS treated lung, replicate 1


title: EvoETRs 8 against Pcsk9 treated lung, replicate 2


title: BP 4uM rep2

description:
IC75
BP4toNS.xlsx


title: EvoETRs 8 against Pcsk9 treated lung, replicate 3


title: 300mM Sorbitol rep3

value: 300mM Sorbitol


title: NELFB-Flavo-VHL-2h-Rep1  PRO-Seq


title: PBS treated spleen, replicate 3

source_name: Spleen

value: Spleen


title: 300mM Sorbitol rep2

value: FUCCI


title: EvoETRs 8 against Pcsk9 treated lung, replicate 1


title: PBS treated spleen, replicate 1


title: NELFB-VHL-2h-Rep2  PRO-Seq

value: NELFB depletion


title: BP 1uM rep2

description:
LOAEL
BP1toNS.xlsx


title: NELFB-VHL-2h-Rep1  PRO-Seq


title: 300mM Sorbitol rep1


title: EvoETRs 8 against Pcsk9 treated spleen, replicate 3


title: RTF1-DMSO-Rep1 PRO-Seq

value: DMSO


title: AAVS1 Day25

city: Beijing

first: Baoyang

last: Hu

state: Select State/Province

address: Beichenxilu

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology

data_processing:
DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process.
The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study.
The DNBSEQ-T7 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
Assembly: hg19 (GRCh37)
Supplementary files format and content: fpkm.txt

extract_protocol:
Total RNA was extracted from approximately 10^6 cells using the miRNeasy Mini Kit (QIAGEN, 217004).
mRNA were purified using poly-T oligo-attached magnetic beads. Then, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The first strand cDNA were produced from cleaved RNA fragments using reverse transcriptase and random primers and then second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were purified and enriched with PCR amplification. Finally, we quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library..

value: hESC-derived MHLCs

value: hESCs

value: Hepatocytes differentiation


title: PBS treated lung, replicate 2


title: EvoETRs 8 against Pcsk9 treated spleen, replicate 2


title: RTF1-DMSO-Rep2 PRO-Seq

value: WT


title: PBS treated kidney, replicate 3

source_name: Kidney

value: Kidney


title: ALB Day25

source_name: ALB


title: WT Day25

source_name: WT


title: PBS treated kidney, replicate 1

value: PBS


title: EvoETRs 8 against Pcsk9 treated spleen, replicate 1

value: EvoETRs 8 against Pcsk9


title: NELFB-Flavo-DMSO-2h-Rep1  PRO-Seq

value: NELFB flavo

value: Flavopiridol


title: PBS treated kidney, replicate 2


title: EvoETRs 8 against Pcsk9 treated kidney, replicate 1


title: PBS treated spleen, replicate 2


title: NELFB-DMSO-Rep2 PRO-Seq


title: Rorc.WT.8

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: 16S sequencing of colonic microbes in denoted mouse.

data_processing:
Raw sequencing data were imported to QIIME2 and demultiplexed, then DADA2 were used for sequence quality control and feature table construction.
The representative sequences were taxonomically classified by Greengenes reference database (version 13_8).
Assembly: Greengenes
Supplementary files format and content: Feature table with taxonomy annotation
Library strategy: 16s rRNA-seq

source_name: stool

extract_protocol:
DNA was isolated from stool samples using phenol/chloroform and the QIAquick PCR purification kit (Qiagen)
For 16S rDNA profiling, the V4 region of 16S rRNA gene was amplified with primers 515F and 806R (65), and ~390-bp amplicons were purified and sequenced (Illumina MiSeq, 251 nt x 2 pair-end reads)

value: stool

value: colonic microbe

value: Rorc wt Foxp3 cre


title: open_ret_12h_ck36Fl_s623

first: Debora

last: Nickla

address: 424 Beacon St

department: Dept. of Biosciences and Disease

institute: New England College of Optometry

data_processing:
raw data was processed by the standard Illumina pipeline to yeild trimmed fastq files
fastq data counted against transcripts (ensembl v105) with salmon
data summarized to gene-level with tximeta (bioconductor)
Assembly: GRCg6a (gene models – ensembl v105)
Supplementary files format and content: gzipped tab-delimited text – raw counts per ensembl gene ID per sample

organism: Gallus gallus

source_name: retina

extract_protocol:
RNA was extracted from choroid and retinal tissues using the QIAgen RNAeasy kit
Illumina TruSeq stranded kit using roughly equal amounts of RNA (between 100 and 300ng)

treatment_protocol: chick eyes were goggled (occl) or open

value: retina

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex

value: F


title: NELFB-DMSO-Rep1 PRO-Seq

tag: cell line

value: DMSO


title: NELFB-Flavo-VHL-48h-Rep2 PRO-Seq

value: NELFB depletion and flavo

value: dTAGV-1 and Flavopiridol


title: Rorc.WT.7


title: Rorc.WT.6


title: open_ret_12h_ck35Fl_s619


title: Rorc.WT.2


title: Rorc.WT.3


title: EvoETRs 8 against Pcsk9 treated kidney, replicate 3

tag: strain


title: occl_ret_12h_ck35Fr_s617

value: occl

value: right


title: EvoETRs 8 against Pcsk9 treated kidney, replicate 2

value: Kidney


title: Rorc.WT.1


title: open_ret_12h_ck34Fl_s615


title: Rorc.WT.10


title: Rorc.KO.9

value: Rorc fl/fl Foxp3 cre


title: open_ret_20h_ck24Fl_s423


title: PAF1-VHL-Rep2 PRO-Seq

value: PAF1 depletion


title: occl_ret_12h_ck34Fr_s613


title: Rorc.WT.9


title: occl_ret_12h_ck36Fr_s621


title: Rorc.KO.7


title: open_ret_12h_ck33Fl_s611


title: PAF1-VHL-Rep1  PRO-Seq


title: Rorc.KO.8


title: Rorc.KO.6


title: occl_ret_12h_ck33Fr_s609


title: Rorc.KO.5


title: Rorc.WT.5


title: Rorc.KO.4


title: PAF1-DMSO-Rep2 PRO-Seq

value: WT


title: NELFB-Flavo-VHL-48h-Rep1  PRO-Seq


title: Rorc.WT.4


title: open_ret_12h_ck32Fl_s607


title: Rorc.KO.3


title: NELFB-VHL-48h-Rep1  PRO-Seq

value: NELFB depletion


title: PAF1-DMSO-Rep1 PRO-Seq


title: Rorc.KO.12

value: stool


title: open_ret_12h_ck31Fl_s603


title: occl_ret_12h_ck32Fr_s605


title: HOS_2D3,Day7

city: Shanghai

first: Lei

last: Cui

address: No. 50 Chifeng Road, Siping Street, Yangpu District, Shanghai

institute: Tongji university

data_processing:
Use FastQC software to evaluate the quality of the raw data obtained from sequencing
Using fastp software to filter sequences, the main purpose is to exclude the following sequences:1. Remove the sequencing primer connector sequence contained in reads;2. Remove bases with a mass Q of less than 20 from the 3 'end of reads;3. Remove reads with sequence length less than 25;4. Remove ribosome RNA reads from the sequencing target species.
Using Hisat2 software, compare the obtained clean reads to the known reference genome GRCh38.108 to locate what genes each read represents and the specific segment positions on the genome
Analyze the coverage of sequencing quantity on the genome and classify the comparison results of reads in different regions of the genome. Displaying the Comparison Genome Location Using Circos Software Package
Count the fragments within each gene segment using Stringtie software, and then normalize using the TMM algorithm. Calculate the expression level of each gene using FPKM as the calculation quantity, analyze the relationship between samples, and then perform principal component analysis. Use edgeR software to perform differential analysis of sample gene expression, calculate differential expression multiples, display differential gene graphs, and finally perform enrichment analysis of differential genes. Annotate and display each gene based on Gene Ontology and KEGG databases
Assembly: GRCh38.108
Supplementary files format and content: Raw file in fastq format
Supplementary files format and content: Processing files in xlsx format includeFPKM values for each samle

source_name: MNNG/HOS Cl #5

growth_protocol: All cells were cultured in high sugar complete medium (DMEM) (Gibco, 11995065, USA) containing 4 mM L-glutamine (Invitrogen, 35050061) supplemented with 10% fetal bovine serum (FBS) (Sciencell, 0500), and 1% penicillin-streptomycin (HyClone, USA), and maintained in an incubator with 5% humidified CO2 at 37 °C.

extract_protocol:
As indicated by the manufacturer's instructions, RNA was extracted from OS cells with TRIzol reagent (Invitrogen, USA).
PloyA enrichment → mRNA fragmentation → first strand cDNA synthesis → magnetic bead purification of the first strand → second strand cDNA synthesis → strand end repair → addition of A at the 3 'end → addition of connector → purification and library amplification → completion of sequencing sample library construction

treatment_protocol: Seed  MNNG/HOS Cl #5 within in demineralized bone matrix scaffold (dBMS) and  2D for 7days, respectively.

value: MNNG/HOS Cl #5

value: Osieosarcoma cells

value: cultured in 2D


title: Rorc.KO.10

value: colonic microbe


title: Rorc.KO.1


title: occl_ret_12h_ck31Fr_s601

value: retina


title: NELFB-VHL-48h-Rep2 PRO-Seq


title: Rorc.KO.2


title: Helios.WT.6

value: Helios wt Foxp3 cre


title: HOS_2D2,Day7


title: HOS_2D1,Day7


title: Rorc.KO.11


title: HOS-dBM3,Day7

value: cultured in 3D


title: Helios.WT.4


title: Helios.WT.5


title: Helios.WT.2


title: open_ret_08h_ck29Fl_s519

value: open

value: left

value: F


title: open_ret_08h_ck30Ml_s523

value: M


title: Helios.WT.3


title: occl_ret_08h_ck30Mr_s521

value: occl

value: right


title: Helios.KO.6

value: Helios fl/fl Foxp3 cre


title: Helios.WT.1


title: HOS-dBM1,Day7

value: WT


title: HOS-dBM2,Day7


title: Helios.KO.7


title: occl_ret_08h_ck29Fr_s517


title: Helios.KO.5


title: Helios.KO.4


title: Helios.KO.2


title: D8_90kPa_Aligned

city: Los Angeles

first: Megan

last: McCain

state: CA

address: 1042 Downey Way

department: Biomedical Engineering

institute: University of Southern California

data_processing:
Partek Flow software was used for data processing
Sequenced reads were trimmed from both ends based on a Phred quality score of 20 and a minimum read length of 25 remaining bases
STAR alignment to the hg38 genome
Noise reduction filter where the maximum ≤ 1
Assembly: hg38
Supplementary files format and content: tab delimited text file with raw gene counts for every gene and every sample

source_name: HUtSMC

growth_protocol: Commercial myometrial cells were maintained in smooth muscle cell media and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Trizol reagent. RNA isolation was performed using Qiagen miRNeasy micro kit (Qiagen) and protocol, then cleaned using Zymo RNA Clean and Concentrator kit.
RNA libraries for RNA-seq were prepared with the NEBNext Ultra II RNA library kit for non-directional libraries by Illumina. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size  distribution detection. Libraries were multiplexed and sequenced on a NovaSeq 6000 S4 using 150bp paired-end sequencing.

treatment_protocol: Tissues were formed on polyacrylamide gel substrates with stiffness 13 kPa or 90 kPa, micropatterned with fibronectin as lanes or in an isotropic pattern.

value: HUtSMC

value: human uterine smooth muscle cells

value: 90kPa Aligned


title: D7_90kPa_Aligned


title: D6_90kPa_Aligned


title: Helios.KO.3

value: stool


title: Helios.KO.1


title: D5_90kPa_Aligned


title: occl_ret_08h_ck28Mr_s513


title: occl_ret_08h_ck27Mr_s509


title: Gata3.WT.8

value: Gata3 wt Foxp3 cre


title: open_ret_08h_ck27Ml_s511


title: Gata3.WT.6

value: colonic microbe


title: Gata3.WT.5


title: Gata3.WT.7


title: D4_90kPa_Aligned


title: open_ret_08h_ck26Ml_s507

value: retina


title: Gata3.WT.4


title: D3_90kPa_Aligned


title: open_ret_08h_ck25Ml_s503


title: Gata3.WT.3


title: Gata3.WT.2


title: Gata3.WT.1


title: D2_90kPa_Aligned


title: Helios.WT.7

value: Helios wt Foxp3 cre


title: Gata3.KO.9

value: Gata3 fl/fl Foxp3 cre


title: Gata3.KO.7


title: Gata3.KO.6


title: D1_90kPa_Aligned


title: Gata3.KO.5


title: occl_ret_08h_ck25Mr_s501


title: occl_ret_20h_ck24Fr_s421


title: C7_90kPa_Isotropic

value: 90kPa Isotropic


title: Gata3.KO.3


title: C6_90kPa_Isotropic


title: Gata3.KO.2


title: open_ret_20h_ck23Ml_s419

value: open

value: left


title: Gata3.KO.1


title: Gata3.KO.4


title: Gata3.KO.8


title: occl_ret_08h_ck26Mr_s505

value: M


title: cMaf.WT.6

value: cMaf wt Foxp3 cre


title: C5_90kPa_Isotropic


title: C8_90kPa_Isotropic


title: cMaf.WT.5


title: open_ret_20h_ck22Fl_s415

value: F


title: occl_ret_20h_ck23Mr_s417

value: occl

value: right


title: cMaf.WT.4


title: cMaf.WT.3


title: C3_90kPa_Isotropic

value: HUtSMC


title: cMaf.WT.2


title: open_ret_08h_ck28Ml_s515


title: cMaf.WT.1


title: cMaf.KO.5

value: cMaf fl/fl Foxp3 cre


title: C2_90kPa_Isotropic

value: human uterine smooth muscle cells


title: C4_90kPa_Isotropic


title: open_ret_20h_ck21Ml_s411


title: occl_ret_20h_ck21Mr_s409


title: cMaf.KO.3

value: stool


title: cMaf.KO.1


title: B6_13kPa_Aligned

value: 13kPa Aligned


title: open_ret_20h_ck19Fl_s403


title: PBS treated hepatocytes, replicate 1

first: Sara

last: Valsoni

address: via Olgettina 60

institute: SR-TIGET

data_processing:
Since each amplicon was very long, reads were aligned to the 400bp sequence around the guide cutting site for Cas9 related samples and to the 300bp sequence around ZFP recognition sequence middle point for EvoETRs 8 related samples using bowtie2 in paired mode and default parameters.
After that, original fastq files were subset to only retain the reads mapping to the region of interest using the filterbyname module of the BBMap aligner contained in the BBTools suite (sourceforge.net/projects/bbmap/).
Remaining reads were analyzed with CRISPResso2 in paired-end mode setting the options for Trimmomatic software (http://www.usadellab.org/cms/?page=trimmomatic) to remove low quality positions (score < 30) and Illumina adapters (--trim_sequences --trimmomatic_command trimmomatic --trimmomatic_options_string 'ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 MINLEN:100').
Then, each couple of paired-end reads was merged using the FLASh software to produce a single contig, which was mapped to the input amplicon reference (promoter region or first exon, depending on the experiment).
The gRNA/ZFP sequence was provided to focus the analysis on the target region, and the quantification window was set to 20 bp per side around the cut site (Cas9 samples) or ZFP middle point (EvoETRs 8 samples).
Identified alleles were quantified by measuring the number of reads and their relative abundance based on total read counts considering only insertions and deletions (substitutions were not considered since they are likely to be the result of amplification/sequencing errors).
Assembly: GRCm38
Supplementary files format and content: CRISPResso allele quantification table
Library strategy: DNA amplicons

source_name: Liver

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and the promoter region of Pcsk9 was amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations

value: Liver

value: Hepatocytes

value: PBS


title: EvoETRs 8 against Pcsk9 treated hepatocytes, replicate 1

value: EvoETRs 8 against Pcsk9


title: occl_ret_20h_ck19Fr_s401

value: retina


title: C1_90kPa_Isotropic

value: 90kPa Isotropic


title: open_ret_20h_ck20Fl_s407

value: open

value: left


title: cMaf.KO.2

value: colonic microbe


title: PBS treated hepatocytes, replicate 3

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and the exon 1 of Pcsk9 was amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina following the manufacturer’s recommendations


title: occl_ret_20h_ck20Fr_s405

value: F


title: B8_13kPa_Aligned


title: EvoETRs 8 against Pcsk9 treated hepatocytes, replicate 3


title: EvoETRs 8 against Pcsk9 treated hepatocytes, replicate 2


title: open_ret_16h_ck18Ml_s323

value: M


title: cMaf.KO.4


title: PBS treated hepatocytes, replicate 2


title: occl_ret_20h_ck22Fr_s413

value: occl

value: right


title: PBS treated hepatocytes, replicate 3


title: occl_ret_16h_ck18Mr_s321


title: B3_13kPa_Aligned

value: HUtSMC


title: B5_13kPa_Aligned

value: human uterine smooth muscle cells


title: PBS treated hepatocytes, replicate 1


title: Cas9 against Pcsk9 treated hepatocytes, replicate 3

value: Cas9 against Pcsk9


title: B7_13kPa_Aligned

value: 13kPa Aligned


title: PBS treated hepatocytes, replicate 2

value: Liver


title: open_ret_16h_ck17Ml_s319


title: B4_13kPa_Aligned


title: Cas9 against Pcsk9 treated hepatocytes, replicate 2

value: Hepatocytes


title: B2_13kPa_Aligned


title: Cas9 against Pcsk9 treated hepatocytes, replicate 1


title: occl_ret_16h_ck17Mr_s317


title: PBS treated hepatocytes, replicate 3

data_processing:
Reads quality was controlled with Fastqc v0.11.9 while low-quality reads and adapters were removed using Trim_Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --rrbs
Remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0
In detail, reads were aligned to both unconverted and converted genomes (GRCm38) using bismark with the --local and –non_directional parameters and the methylation status was obtained using bismark_methylation_extractor script using only the reads mapping to the bottom strand (OB and CTOB)
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered to retain only cytosines from CpG context in the amplified windows and normalized using the normalizeCoverage function
The information from the different samples was merged using the unite function considering the positions covered in at least 1 replicate per condition. The methylation percentage at each position was calculated using the percMethylation function.
Assembly: GRCm38
Supplementary files format and content: Bismark coverage

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and biisufite conversion by EpiTect Bisulfite Kit, following provider indications. Finally, the promoter region of Arid1b and Shroom1 was amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations

value: PBS


title: B1_13kPa_Aligned


title: PBS treated hepatocytes, replicate 2


title: A8_13kPa_Isotropic

value: 13kPa Isotropic


title: occl_ret_16h_ck16Fr_s313

value: retina


title: open_ret_16h_ck16Fl_s315


title: PBS treated hepatocytes, replicate 1


title: ZFP-ETRs against Pcsk9 treated hepatocytes, replicate 2

value: ZFP-ETRs against Pcsk9


title: A7_13kPa_Isotropic


title: PBS treated hepatocytes, replicate 3

data_processing:
Reads quality was controlled with Fastqc v0.11.9 while low-quality reads and adapters were removed using Trim_Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --rrbs
Remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0
In detail, reads were aligned to both unconverted and converted genomes (GRCm38) using bismark with the --local and –non_directional parameters and the methylation status was obtained using bismark_methylation_extractor script using only the reads mapping to the top strand (OT and CTOT)
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered to retain only cytosines from CpG context in the amplified windows and normalized using the normalizeCoverage function
The information from the different samples was merged using the unite function considering the positions covered in at least one replicate per condition. The methylation percentage at each position was calculated using the percMethylation function.
Assembly: GRCm38
Supplementary files format and content: Bismark coverage

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and bisulfite conversion by EpiTect Bisulfite Kit, following provider indications. Finally, the regions containing the DMRs were amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations


title: A6_13kPa_Isotropic


title: occl_ret_16h_ck15Mr_s309


title: A5_13kPa_Isotropic


title: PBS treated hepatocytes, replicate 1


title: PBS treated hepatocytes, replicate 2


title: open_ret_16h_ck15Ml_s311

value: open


value: EvoETRs 8 against Pcsk9


title: ZFP-ETRs against Pcsk9 treated hepatocytes, replicate 1


title: A4_13kPa_Isotropic


title: occl_ret_16h_ck14Mr_s305


title: ZFP-ETRs against Pcsk9 treated hepatocytes, replicate 3


title: PBS treated hepatocytes, replicate 3

data_processing:
Reads quality was controlled with Fastqc v0.11.9 while low-quality reads and adapters were removed using Trim_Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --rrbs
Remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0
In detail, reads were aligned to both unconverted and converted genomes (GRCm38) using bismark with the --local and –non_directional parameters and the methylation status was obtained using bismark_methylation_extractor script using only the reads mapping to the top strand (OT and CTOT)
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered to retain only cytosines from CpG context in the amplified windows and normalized using the normalizeCoverage function
The information from the different samples was merged using the unite function considering the positions covered in all the 3 replicates per condition. The methylation percentage at each position was calculated using the percMethylation function.
Assembly: GRCm38
Supplementary files format and content: Bismark coverage


title: A3_13kPa_Isotropic


title: A2_13kPa_Isotropic


title: PBS treated hepatocytes, replicate 2


title: PBS treated hepatocytes, replicate 3

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and bisulfite conversion by EpiTect Bisulfite Kit, following provider indications. Finally, the promoter region of Pcsk9 was amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations


title: GSC23, ShG12, 542

city: La Jolla

first: Olga

middle: M

last: Chaim

address: 9500 Gilman Drive

department: Department of Pharmacology

institute: University of California, San Diego

data_processing:
QC of raw fastq files with MultiQC
Raw reads were trimmed, aligned to reference genome hg19 using STAR.
Differentially expressed genes were calculated using adjusted P-value of <0.05 with a 2-fold change DEseq2 workflow (BasePair software; https://app.basepairtech.com/).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include count distribution, fpkm and tpm values for each Sample sorted by gene
Supplementary files format and content: tab-delimited text files include count distribution, fpkm and tpm values for each Sample sorted by transcript

source_name: brain tumor

extract_protocol:
Total RNA isolation from tumors was achieved by Trizol reagent and Monarch Total RNA Miniprep Kit (Invitrogen and NEB) according to the manufacturer’s protocol. RNA quantity and 260/280 ratio quality were assessed by Nanodrop. RNA tumor samples from mice injected with Ga12 KD and control GSC23 cells (4 mice tumors for biological replicates in each group) were submitted to UCSD IGM Genomics Center for RNA integrity analysis (Agilent Bioanalyzer, Tapestation results eRIN >8.5)
UCSD IGM Genomics Center performed ribodepleted library preparation and sequencing using Illumina NovaSeq 6000 (run set PE100 and 25M reads).

value: brain tumor

value: glioblastoma patient- derived xenograft cell line

value: shRNA G{alpha}12 knockdown

value: not treated


title: open_ret_04h_ck12Fl_s223

value: left

value: F


title: occl_ret_16h_ck13Fr_s301

value: occl

value: right


title: open_ret_16h_ck13Fl_s303


title: A1_13kPa_Isotropic

value: HUtSMC

value: human uterine smooth muscle cells


title: GSC23, ShG12, 541


city: Milano

value: Liver

value: Hepatocytes


title: open_ret_04h_ck11Fl_s219


title: open_ret_16h_ck14Ml_s307

value: M


title: PBS treated hepatocytes, replicate 1

value: PBS


value: ZFP-ETRs against Pcsk9


title: PBS treated hepatocytes, replicate 2


title: GSC23, ShG12, 534


title: occl_ret_04h_ck12Fr_s221

value: retina


title: GSC23, ShG12, 533


value: EvoETRs 8 against Pcsk9


title: occl_ret_04h_ck11Fr_s217


title: PBS treated hepatocytes, replicate 1


title: open_ret_04h_ck10Fl_s215

value: open


title: Day3-1_S7_L001_001

city: Fujisawa

first: Masato

last: Yugami

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: Research

institute: Takeda Pharmaceutical Company

data_processing:
processed with OmicSoft ArrayStudio (v11, QIAGEN)
Sequence reads were mapped to mm10 and counted by RNA-seq pipeline workflow in OmicSoft ArrayStudio
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: primary oligodendrocyte precursor cells

growth_protocol: Mouse primary oligodendrocyte precursor cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 80 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit for NeoPrep followingthe manufacturer's protocol.

treatment_protocol: Oligodencryotes differentiation was induced by chaning differentiation medium including T3.

value: primary oligodendrocyte precursor cells

value: WT

tag: time


title: GSC23, ShCTL, 513

value: brain tumor

value: glioblastoma patient- derived xenograft cell line

value: shRNA control

value: not treated


title: GSC23, ShCTL, 514


title: Day3-2_S8_L001_001


title: occl_ret_04h_ck10Fr_s213

value: occl

value: right

value: F


title: Day2-2_S6_L001_001


title: open_ret_04h_ck9Ml_s211

value: left


title: Day2-1_S5_L001_001


title: occl_ret_04h_ck9Mr_s209


title: Day1-1_S3_L001_001


title: Day1-2_S4_L001_001


title: Day0-1_S1_L001_001


title: open_ret_04h_ck8Ml_s207


title: Day0-2_S2_L001_001


title: GSC23, ShCTL, 511


title: GSC23, ShCTL, 512


title: UM004 trametinib S3

city: Philadelphia

first: Andrew

middle: E

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

data_processing:
De-multiplexing and data aggregation was performed using the Braod Picard Pipeline
RNA sequencing fastq files were aligned to the GRCh38 human reference genome using Star aligner (v 2.6.1a), GENCODE v31
RSEM was used to quantify gene and transcript level expression
transcripts per million data were calculated using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for log normalized counts per million for each sample

source_name: metastatic uveal melanoma cells

growth_protocol: PDX4 cells were cultured in RPMI 1640 medium (15% FBS, 50 IU penicillin and 50 µg/ml streptomycin),UM004 cells were cultured in MEM medium (10% heat-inactivated FBS,50 IU penicillin and 50 µg/ml streptomycin, 1% L-glut)

extract_protocol:
Qiagen RNeasy mini kit
Illumina TruSeq™ Stranded mRNA Sample Preparation Kit

treatment_protocol: Cells were treated with DMSO, trametinib (50nM), binimetinib (5uM), BVD523 (2uM) or SCH772984 (500nM) for 24 hours

value: trametinib

tag: treatment type

value: MEKi

tag: sample number


title: Untreated hepatocytes after partial hepatectomy, replicate 4

data_processing:
Reads quality was controlled with Fastqc v0.11.9 while low-quality reads and adapters were removed using Trim_Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --rrbs
Remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0
In detail, reads were aligned to both unconverted and converted genomes (GRCm38) using bismark with the --local and –non_directional parameters and the methylation status was obtained using bismark_methylation_extractor script using only the reads mapping to the bottom strand (OB and CTOB)
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered using the filterByCoverage function (low count filter equal to 10^5 to remove cytosine from non-CpG context probably covered by reads which accumulate errors due to the extremely high coverage) and normalized using the normalizeCoverage function
The information from the different samples was merged using the unite function considering the positions covered in all the 3 replicates per condition. The methylation percentage at each position was calculated using the percMethylation function.
Assembly: GRCm38
Supplementary files format and content: Bismark coverage

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and biisufite conversion by EpiTect Bisulfite Kit, following provider indications. Finally, the promoter region of Pcsk9 was amplified by PCR.
Libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina following the manufacturer’s recommendations

value: Liver

tag: partial hepatectomy

value: YES

value: Hepatocytes

value: Untreated


title: Untreated hepatocytes before partial hepatectomy, replicate 3

value: NO


title: UM004 trametinib S2


title: Untreated hepatocytes before partial hepatectomy, replicate 4


title: open_ret_04h_ck7Ml_s203

value: retina

value: open

value: M


title: occl_ret_04h_ck8Mr_s205


title: occl_ret_04h_ck7Mr_s201


title: UM004 trametinib S1


title: Untreated hepatocytes after partial hepatectomy, replicate 3


title: Untreated hepatocytes after partial hepatectomy, replicate 2


title: Untreated hepatocytes before partial hepatectomy, replicate 2


title: UM004 SCH772984 S3

value: ERKi


title: Untreated hepatocytes before partial hepatectomy, replicate 1


title: Untreated hepatocytes after partial hepatectomy, replicate 1


title: UM004 SCH772984 S2


title: ZFP-ETRs against Pcsk9 treated hepatocytes before partial hepatectomy, replicate 4

value: ZFP-ETRs against Pcsk9


title: occl_ret_00h_ck6Mr_s121


title: open_ret_00h_ck5Fl_s119


title: ZFP-ETRs against Pcsk9 treated hepatocytes after partial hepatectomy, replicate 3


title: ZFP-ETRs against Pcsk9 treated hepatocytes before partial hepatectomy, replicate 2


title: UM004 DMSO S3

value: DMSO


title: open_ret_00h_ck4Ml_s115


title: occl_ret_00h_ck5Fr_s117

value: occl


title: ZFP-ETRs against Pcsk9 treated hepatocytes after partial hepatectomy, replicate 2


title: UM004 DMSO S1


title: ZFP-ETRs against Pcsk9 treated hepatocytes after partial hepatectomy, replicate 1


title: occl_ret_00h_ck4Mr_s113

value: right


title: Hashtags of late TS543 culture passage

city: New York

first: Peter

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: HTO library from microwell-based scRNA-seq. Read1 file contains cell barcode and UMI; Read2 file contains hashtag-derived reads. Pooled hashtages include TotalSeq-A0251 anti-human Hashtag 1  (DMSO-treated sample), TotalSeq-A0252 anti-human Hashtag 2, TotalSeq™-A0253 anti-human Hashtag 3, TotalSeq-A0254 anti-human Hashtag 4.

data_processing:
Read 1 and read 2 fastq files were generated on basespace. Hashtag barcodes and cell barcode and umi for gene expressions were preprocessed and extracted using DropSeqPipeline8 (https://github.com/simslab/DropSeqPipeline8).
HTO raw counts were normalized by centered log ratio (CLR) transformation and performed k-means clustering and statistical identification of singlets by fitting a negative binomial model for demultiplexing
Gene expressions matrix were recovered by EmptyDrops algorithm
Assembly: HTO libraries: TotalSeqA hashtag sequence
Assembly: TS543 Transcriptome libraries: GRCh38
Assembly: TS543 PDX mouse: GRCh38 GRCm38
Supplementary files format and content: HTO libraries: Tab-delimited text files that contain the cell barcode and cell hashtag
Supplementary files format and content: Transcriptome libraries: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: Neurosphere culture

extract_protocol:
For PW073 to PW079: At the end of culture, neurospheres were collected and dissociated to single cells by pipetting and stained with with TotalSeq™-A hashtag antibodies (BioLegend), then pooled for scRNA-seq.
For PLZ019: Mice were sacrificed for collecting brain tumor tissues 21 post-injection. Freshly resected tumor tissues were kept in ice-cold PBS for transportation prior to dissociation. Mouse brain tumor resections were collected for dissociation using Papain Dissociation System (Worthington) as previously described(Mizrak et al., 2020; Mizrak et al., 2019) with following modifications. Briefly, minced tissue was digested with papain (Worthington, 10 units per sample) in PIPES solution (120 mM NaCl, 5 mM KCl, 20 mM PIPES (Sigma), 0.45% glucose, DNase I (Worthington, 100 units per sample), 1xAntibiotic/Antimycotic (GIBCO), pH adjusted to 7.6) for 30 min at 37°C on gentleMACS™ Octo Dissociator with Heaters (Miltenyi Biotec, program 37C_ABDK). After digestion, the cell suspension was applied to a MACS SmartStrainer (70 μm, Miltenyi Biotec) and centrifuged at 300xg for 10 minutes at 4°C. The cell pellets were then subjected to red blood cell removal (Red Blood Cell Lysis Solution (10x), Miltenyi Biotec) and debris removal (Debris Removal Solution, Miltenyi Biotec) according to the manufacturer’s instructions.
For PW073 to PW079: mRNA and hashtag molecues were captured using bead-bound oligo dT(30). Captured mRNA and hashtag molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. Cell Hashtag (HTO)-containing fraction and the large cDNA library were separated by SPRI (Beckman Ampure XP beads). Purified large cDNA PCR products were used as the input for Nextera XT reactions to generate sequencing library. Purified Cell Hashtag (HTO)-containing fraction were used as input for PCR amplification using TruSeq DNA D703 primer and P5-SMARTpcr primer to generate the Cell Hashtag library.
For PLZ019: mRNA molecues were captured using bead-bound oligo dT(30). Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.
For PW073 to PW079: scRNA-seq with TotalseqA hashtag
For PLZ019: scRNA-seq

value: Neurosphere culture

value: Neurosephere

tag: time point

value: 7 days


title: UM004 BVD523 S3


title: Transcriptome of late TS543 culture passage

description: transcriptome library from microwell-based scRNA-seq.  8-base index read, 26-base read 1, 58-base read 2.


title: Transcriptome of TS543 treated with RSL3 or DMSO for 3 day

value: drug vehicle (DMSO) or RSL3


title: occl_ret_00h_ck3Mr_s109


title: open_ret_00h_ck3Ml_s111

value: left


title: open_ret_00h_ck6Ml_s123


title: UM004 BVD523 S2


title: Transcriptome of TS543 treated with RSL3 or DMSO for 1 day


title: Hashtags of TS543 treated with RSL3 or DMSO for 3 day

description: HTO library from microwell-based scRNA-seq. Read1 file contains cell barcode and UMI; Read2 file contains hashtag-derived reads. Pooled hashtages include TotalSeq-A0251 anti-human Hashtag 1  (DMSO-treated sample), TotalSeq-A0252 anti-human Hashtag 2, TotalSeq™-A0253 anti-human Hashtag 3 (RSL3-treated sample), TotalSeq-A0254 anti-human Hashtag 4.


title: Hashtags of TS543 treated with RSL3 or DMSO for 1 day

description: HTO library from microwell-based scRNA-seq. Read1 file contains cell barcode and UMI; Read2 file contains hashtag-derived reads. Pooled hashtages include TotalSeq-A0251 anti-human Hashtag 1  (DMSO-treated sample), TotalSeq-A0252 anti-human Hashtag 2 (RSL3-treated sample), TotalSeq™-A0253 anti-human Hashtag 3, TotalSeq-A0254 anti-human Hashtag 4.


title: UM004 SCH772984 S1


title: ZFP-ETRs against Pcsk9 treated hepatocytes before partial hepatectomy, replicate 3

value: Liver


title: ZFP-ETRs against Pcsk9 treated hepatocytes after partial hepatectomy, replicate 4

value: YES

value: Hepatocytes


title: UM004 BVD523 S1


title: HGC27, RUNX3KO, Input, ChIP, rep2

data_processing:
Basecalls were performed using bcl2fastq.
ChIP-seq experiment were aligned to UCSC human genome (hg19) using bowtie 1.0.1.
Duplicated reads were removed with Picard tools 2.3.0.
bigWig files were generated using HOMER 4.11.1.
Peaks were called using HOMER 4.11.1  findPeaks.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Picoruptor (Diagenode).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. 10 ng of DNA was used as starting material for Input and ChIP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Tapestation.

value: RUNX3 knock-out

tag: chip antibody

value: Input


title: HGC27, RUNX3KO, Input, ChIP, rep1


title: open_ret_00h_ck2Ml_s107

value: retina

value: open


title: UM004 DMSO S2

tag: treatment


title: ZFP-ETRs against Pcsk9 treated hepatocytes before partial hepatectomy, replicate 1

tag: tissue

value: NO


title: UM004 binimetinib S3

value: binimetinib

value: MEKi


title: occl_ret_00h_ck2Mr_s105

value: occl

value: M


title: HGC27, wt, Input, ChIP, rep2

tag: cell type

value: wildtype


title: HGC27, wt, RUNX3, ChIP, rep1


title: UM004 binimetinib S2


title: UM004 binimetinib S1


title: HGC27, wt, H3K4me3, ChIP, rep1


title: occl_ret_00h_ck1Fr_s101

value: right

value: F


title: HGC27, wt, H3K27ac, ChIP, rep1


title: PDX4 trametinib S3

value: trametinib


title: open_chor_16h_ck16Fl_s316

source_name: choroid

value: choroid

value: left


title: HCC1806-sgROSA26-D5-rep2

city: Cold Spring Harbor

first: Diogo

last: Maia e Silva

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: raw counts

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.

growth_protocol: Human cancer cell lines were cultured according to vendor recommendations in RPMI or DMEM 10% FBS supplemented with pen-strep.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation.
RNA-seq and ChIP-seq ibraries were constructed using  Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.

value: human triple negative breast cancer cell line

tag: genotype


title: HGC27, RUNX3KO, H3K27ac, ChIP, rep1


title: HCC1806-sgROSA26-D5-rep1

description: raw counts


title: PDX4 trametinib S2


title: open_chor_20h_ck24Fl_s424

tag: eye treatment


title: HCC1806-sgROSA26-D3-rep2

description: raw counts


title: PDX4 trametinib S1


title: HCC1806-sgROSA26-D3-rep1

description: raw counts


title: HCC1806-sgTP63-187e4-D3-rep2

description: raw counts


title: open_chor_12h_ck36Fl_s624

tag: timept


title: HCC1806-sgTP63-187e4-D3-rep1

description: raw counts


title: PDX4 SCH772984 S3

value: ERKi


title: HCC1806-sgTP63-51e1-D3-rep2

description: raw counts


title: open_ret_00h_ck1Fl_s103

tag: chickid


title: HGC27, wt, Input, ChIP, rep1


title: HCC1806-sgTP63-51e1-D3-rep1

description: raw counts


title: PDX4 SCH772984 S2


title: open_chor_12h_ck35Fl_s620

tag: eye


title: HGC27, RUNX3KO, H3K4me3, ChIP, rep1

value: RUNX3 knock-out


title: occl_chor_12h_ck36Fr_s622

tag: Sex


title: HCC1806-sgMED12-3-D5-rep1

description: raw counts

tag: cell line


title: occl_chor_12h_ck35Fr_s618


title: HCC1806-sgMED12-3-D5-rep2

description: raw counts


title: PDX4 SCH772984 S1


title: HCC1806-sgMED12-2-D5-rep2

description: raw counts


title: Cal33-sgROSA26-D5-rep2

description: raw counts

value: human head and neck squamous cell carcinoma cell line


title: PDX4 DMSO S2

value: DMSO


title: Cal33-sgROSA26-D5-rep1

description: raw counts


title: Cal33-sgROSA26-D3-rep2

description: raw counts


title: open_chor_12h_ck33Fl_s612

value: open


title: occl_chor_12h_ck33Fr_s610


title: PDX4 DMSO S1


title: Cal33-sgROSA26-D3-rep1

description: raw counts


title: Cal33-sgTP63-187e4-D3-rep2

description: raw counts


title: open_chor_12h_ck32Fl_s608


title: Cal33-sgTP63-187e4-D3-rep1

description: raw counts


title: PDX4 BVD523 S3


title: PDX4 BVD523 S2


title: Cal33-sgTP63-51e1-D3-rep1

description: raw counts


title: Cal33-sgMED12-3-D5-rep2

description: raw counts


title: Cal33-sgMED12-2-D5-rep2

description: raw counts


title: PDX4 DMSO S3


title: occl_chor_12h_ck32Fr_s606


title: PDX4 BVD523 S1


title: HCC1806-sgMED12-2-D5-rep1

description: raw counts


title: Cal33-sgMED12-3-D5-rep1

description: raw counts


title: open_chor_12h_ck34Fl_s616


title: Trn_S-LPS_S27

city: Bilthoven

first: Jelena

last: Cvetkovic

address: Antonie van Leewenhoeklaan 9

department: Centre for Infectious Disease Control

country: Netherlands

institute: RIVM

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq2 Conversion Software v2.20
RNAseq reads were aligned to the Homo sapiens reference genome (GRCh38) and transcript abundance was quantified using kallisto (version 0.46.1).
Assembly: GRCh38
Supplementary files format and content: Raw_counts_all_samples.txt

source_name: human monocyte

growth_protocol: Human monocytes were purified from buffy coats from healthy donors. Briefly, peripheral blood mononuclear cells (PBMC) were isolated using a Lymphoprep (Nycomed, Zurich, Switzerland) gradient.  Monocytes were isolated by negative magnetic sorting from PBMC using a MojoSort™ Human CD14+Monocytes kit (BioLegend, San Diego, CA) according to the manufacturer’s instructions. Purity of isolated monocytes was determined using anti-CD14-PE (BD Biosciences) FACS-staining. Data was acquired using the FACS Canto II (BD Biosciences) and analyzed using FlowJo software (Tree Star). CD14+ cell purity of 90% or more was obtained for each donor.

extract_protocol:
The total RNA was purified from the lysates using miRNeasy Mini Kit (Qiagen, Germany) following the manufacturer’s instructions. The RNA quality with RNA integrity number (RIN) was checked by Lab-on-Chip analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using Agilent RNA 6000 Nano Kit. The RIN of all RNA samples were >8 indicating high RNA integrity. Also, the concentration of RNA was measured by the Quantus™ Fluorometer (Promega Corporation, USA) using Qubit™ RNA HS Assay Kit (Thermo Fisher Scientific, MA, USA).
500 ng of total RNA from each samples was used to construct the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s instructions. In short, the mRNA molecules were purified from total RNA using poly-T oligo attached magnetic beads, fragmented and converted into first strand cDNA using reverse transcriptase and random hexamers in the presence of Actinomycin D. Next, to create strand specificity, dTTP was replaced with dUTP in the second-strand cDNA synthesis and then dsDNA was subjected to adenylation 3’ ends. Indexing unique dual adapters were ligated to both ends of the double-stranded cDNA and PCR was performed to enrich DNA fragments with sequencing adapters. After library amplification, the quality of DNA libraries was checked on QIAxcel Advanced System (Qiagen, Germany) and library concentration was determined by qPCR using KAPA Library Quantification Kit (Roche, Basel, Switzerland). The libraries were normalized to 4 nM, pooled at equimolar concentrations and sequenced on a NextSeq500 (Illumina, NY, USA). More than 15 million reads were obtained and analyzed for each samples. FASTQ files coming from Ilumina platform were merged and quality controls were performed with FASTQC tools.

treatment_protocol: To evaluate the effects of inactivated (i)SARS-CoV-2 training on monocyte gene expression, human monocytes were cultured in 6-well plate (1×106 cells/well) exposed to iSARS-CoV-2 at multiplicity of infection (MOI:1) or left in medium only as untrained control. After 24 hours incubation, cells were washed and allowed to rest for 5 days with a medium refreshing step on day 3. On day 6, before or 3h after LPS (10 ng/ml) stimulation, the cells were lyzed in QIAzol (Qiagen) and stored at -80°C for subsequent RNA isolation.

value: human monocyte

value: iSARS-CoV-2-trained monocytes stimulated with LPS on day 6


title: PDX4 binimetinib S1

value: binimetinib

value: MEKi


title: Unt-LPS_S25

value: untrained monocytes stimulated with LPS on day 6


title: Unt-LPS_S24


title: O24.Input

first: Dean

last: Li

address: Haike Road 100

institute: Chinese Academy of Science

data_processing:
All sequencing reads were processed with Trim Galore (v0.6.6) with the parameters “--nextseq 30 --paired” to remove the adapter sequences (AGATCGGAAGAGC) from NovaSeq-platforms, and reads longer than 20 bp were kept. Reads that passed the quality control procedure were kept and mapped to the Homo sapiens genome (GRCh38) and Drosophila melanogaster genome (dmel-all-chromosome-r6.36) using STAR (v2.7.6a) with default parameters, respectively. Uniquely mapped read pairs were counted against annotations from Homo sapiens (Ensembl: GRCh38.94) and Drosophila melanogaster (Flybase: dmel-all-r6.36) using featureCounts (v2.0.1) with parameters “-p -B -C” and summarized as gene-level counts, respectively.
Assembly: GRCh38 and dmel-all-chromosome-r6.36
Supplementary files format and content: Counts from featurecounts output were merged into csv table with each gene in rows and each sample in columns.

source_name: Peripheral mononuclear blood cell

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108). NAD-RNAs were captured following method detailed in ONE-seq manuscript (https://doi.org/10.1093/nar/gkac1136). Briefly, total RNAs were subjected to one-step chemo-enzymatic biotinylation, followed by streptavidin capture and the NudC-catalyzed elution, to specifically recover NAD-capped RNAs for epitranscriptomic profiling.
RNA libraries were prepared according to instructions of Abclonal mRNA-seq Library Prep Kit for Illumina (RK20302)
RNA-Seq; 150bp paired-end

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

value: Validation

tag: assay

value: Input

tag: age

value: 55 years

tag: gender

value: Male


title: Unt-Med_S22

value: untrained monocytes in medium only


title: Cal33-sgTP63-51e1-D3-rep2

description: raw counts

tag: time


title: Unt-LPS_S23


title: PDX4 binimetinib S3

tag: treatment type

tag: sample number


title: Unt-Med_S21

tag: treatment


title: O24.Enrich

tag: cell type

value: Enrich


title: open_chor_12h_ck31Fl_s604

extract_protocol:
RNA was extracted from choroid and retinal tissues using the QIAgen RNAeasy kit
Illumina TruSeq stranded kit using roughly equal amounts of RNA (between 100 and 300ng)

tag: tissue

value: choroid

value: left

value: F


title: Unt-Med_S20

tag: genotype


title: occl_chor_08h_ck29Fr_s518

tag: eye treatment

value: occl

tag: timept

value: right


title: PDX4 binimetinib S2


title: Trn_S-LPS_S17

value: human monocyte

value: iSARS-CoV-2-trained monocytes stimulated with LPS on day 6