title: EJ28 cells, GRHL3 clone 3

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

data_processing:
FASTQ files were generated using bcl2fastq (Illumina). Sequencing data were then processed using the nf-core/RNA-seq pipeline 3.4 with the minimal command. In brief, reads were trimmed by Trim Galore 0.6.7 and aligned to the Genecode human genome (GRCh38) v28 using STAR 2.7.9a. Gene-level assignment was done using featureCounts 1.6.457 . Transcript-level quantification was performed by Salmon v1.5.2.
Assembly: GRCh38
Supplementary files format and content: tsv file for estimated counts on gene level of all samples

source_name: urothelial bladder cancer

growth_protocol: EJ28 cells: RPMI 1640 medium, SCaBER cells: DMEM high glucose medium, both supplemented with 10% fetal bovine serum, LGPS (200mM L-glutamine, penicillin, streptomycin) and geniticine (G418) in its cell line specific concentration. Cells were cultivated at 37°C and 5% CO2

extract_protocol:
RNA isolation was performed using Nucleospin RNA Plus Kit (Macherey-Nagel), 1 µg of total RNA was used for mRNA Sequencing
The quantity of RNA was analyzed with the NanoDrop 1000 (Thermo Scientific Nano Drop Technologies). RNA quality control was done with the Eukaryote Total RNA Nano Series assay using the Agilent 2100 Bioanalyzer system (Agilent Technologies, Inc., Santa Clara, USA). An RNA Integrity Number (RIN) of at least 8 verified the quality of the RNA. Illumina libraries were generated from 1 μg of total RNA using the NEBNext Ultra II Directional mRNA Library Prep Kit for Illumina as described by the manufacturer (New England Biolabs). The libraries were run on an Illumina NextSeq500 platform using the High Output v2.5 kit with 150 cycles (Illumina).

value: urothelial bladder cancer

value: GRHL3 overexpression


title: ACC.etr13.24h.R4.R1

status: Public on Jun 20 2024

type: SRA

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

country: USA

institute: Virginia Commonwealth University

library_source: transcriptomic

data_processing:
FastQC v0.11.8 and MultiQC v1.7 were used for assessing read quality.
Adaptors were trimmed from reads using CutAdapt v1.18, and reads trimmed to less than 25bp were removed.
Trimmed reads were then processed with the BBMap tool BBDuk to identify and remove rRNA contamination.
Read quantification was performed directly on the processed fastq files with the Salmon v0.12.0 “quant” algorithm in mapping mode using the “--validateMapping” flag, setting the library type to “IU”.
Counts were imported into R v3.6.0 using the tximport R package v1.12.3 and summarized to the gene level.
Genome_build: TAIR10 reference transcriptome
Supplementary_files_format_and_content: Contains raw read counts from Salmon summarized to the gene level in a tab-delimited format.  No normalization or other transformations were done to the processed data for this submission.  Raw fastq files are original and unprocessed.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: whole root tissue from seedlings (age 5 days + length of treatment)

growth_protocol: Plants were grown on 1x Murashige and Skoog medium, pH 5.6, Murashige and Skoog vitamins, and 0.8% agar, buffered with 0.05% MES and supplemented with 1% Suc, on top of a nylon filter (03-100/32; Sefar Filtration) pressed against the plate. Approximately 100 sterilized seeds were placed on each filter; 2 plates were combined for each biological replicate. After stratification for 72 h at 4C, plants were grown under 100umol m-2s-1 continuous cool-white light.

extract_protocol:
Frozen samples were ground in liquid nitrogen, and RNA isolation was performed according to the Qiagen plant RNeasy kit protocol, with the addition of the Qiagen RNase-free DNase treatment. After RNA isolation, samples were quantified by A260 using a Nanodrop spectrophotometer. Each sample yielded at least 3ug, and on average 15ug, of RNA. One Col-0 ethylene 4 hour treatment had an RNA integrity number (RIN) less than 6 and was not sequenced.
Library prep was performed by GENEWIZ, LLC as part of sequencing services.

treatment_protocol: Plants were treated on day 5 after germination. For time 0 treatments, the nylon filter containing 5-day-old plants was transferred to new control medium and root tissue was immediately harvested. For ACC treatment, the plants on nylon were transferred to growth medium with 1uM ACC for the given treatment time and then root tissue was harvested. For ethylene treatment, the nylon was transferred to new control medium, and plants were placed in clear treatment tanks with constant flow-through of 0.3 ppm ethylene gas for the given treatment time and then root tissue was harvested. At ttime of harvesting, roots were cut from seedlings and flash frozen in liquid nitrogen.

tag: genotype

tag: treatment

value: ACC, 1uM

tag: time point

tag: biological replicate


title: ACC.etr13.0h.R4.R1


title: blood  leukocyte, 0.1THz to CIA model 3, 30min, 14days

city: xi'an

first: Qi

last: Zhang

address: No. 28 Xianning West Road

country: China

institute: Xi’an Jiaotong University

data_processing:
Illumina bcl2fastq 2.0 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
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean in DESeq2 package
Differential gene expression by DEseq2 was performed on normalized gene counts
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for samples
Supplementary files format and content: Supplementary_files_format_and_content:  excel file includes gene abundance for samples

molecule: total RNA

organism: Mus musculus

source_name: blood leukocyte

extract_protocol:
Total blood RNA samples were extracted using the TruSeq RNA Sample Preparation Kit V2 (Illumina, USA) in strict accordance with the manufacturer's instructions.
A library was constructed on the Illumina HiSeq 2500 (Illumina Inc., San Diego, CA) platform and RNA-sequencing procedures were performed in a 2×150 bp paired-end sequencing mode and obtained FastQ data

tag: tissue

value: blood leukocyte

tag: strain

tag: Sex

value: male

tag: age

value: 0.1THz to CIA model, 30min, 14days


title: EJ28 cells, GRHL3 clone 2

country: Germany

organism: Homo sapiens

tag: cell line


title: rep3 SVTKO1 42oC

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
*library strategy: multiplex small RNA sequencing (MSR-seq)
Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to curated Streptomyces Venezuelae tRNA and 5s rRNA reference genome.
The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/,Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads.
Assembly: Streptomyces venezuelae ATCC 10712
Supplementary files format and content: tsv files with gene name and abundance per sample
Supplementary files format and content: .sam.tsv files with mutation, deletion, coverage for each gene position per sample

organism: Streptomyces venezuelae

growth_protocol: Streptomyces venezuelae strains (WT and mutant derivaties; ATCC 10712) were cultured in both ISP2 media and Glucose-Isoleucine media under standard and stress conditions (6% EtOH or 42oC)

extract_protocol:
Total RNA was extracted from samples using a Trizol extraction along with bead beating.
MSR-seq (PMID 35513407)

treatment_protocol: Total RNA was extracted from each sample and used as input material for the sequencing libraries

tag: cell type


title: blood  leukocyte, 0.1THz to CIA model 2, 30min, 14days


title: ACC.etr13.0h.R3.R1


title: EJ28 cells, mock clone 82

value: control


title: rep2 SVTKO1 42oC


title: ACC.etr13.0h.R2.R1


title: blood  leukocyte, 0.1THz to CIA model 1, 30min, 14days


title: rep1 SVTKO1 42oC


title: EJ28 cells, mock clone 70


title: C2H4.Col0.1h.R3.R1

value: wild type (Col-0)

value: Ethelyene Gas (C2H4), 3ppm


title: EJ28 cells, mock clone 43


title: blood  leukocyte, C3, Non-irradiation3

value: Non-irradiation


title: rep3 SVTKO1 EtOH

value: EtOH


title: rep2 SVWT1 Ctrl

value: WT

value: Ctrl


title: blood  leukocyte, C2,  Non-irradiation2


title: SCaBER cells, GRHL3 clone 28

source_name: squamous-like bladder cancer

value: squamous-like bladder cancer

value: SCaBER


title: blood  leukocyte, C1,  Non-irradiation1


title: rep1 SVTKO1 EtOH


title: rep2 SVTKO1 EtOH


title: colon, orthotopic MC38 tumor, rep3

city: Leuven

first: Gianluca

last: Matteoli

address: Herestraat 49

country: Belgium

institute: KU Leuven

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing and data analysis was performed using 10x's Cellranger suite using the standard parameters.
The count matrices obtained after pre-processing with Cellranger were concatenated to obtain a combined raw count matrix which was then analyzed using the Seurat R package (v3.1.3).
immune cells were selected based on canonical markers and used for downstream analysis
Assembly: mm10
Supplementary files format and content: Raw files are files obtained as output from cellranger in .bam format. Processed files are counts file of the cells included in the analysis aafter QC in tab separated format

source_name: colonic tumor

extract_protocol:
Cell suspensions of orthotopic murine tumors were processed with a 10x Chromium Next GEM Single Cell 5’ kit and loaded on a 10x chromium controller to create Single Cell Gel beads in Emulsion (GEM).
A cDNA library was created using a 10x 5’ library kit acording to manufacturer's instructions

value: colonic tumor

value: immune cells from tumors

tag: time

value: 21days after tumor injection

value: intra-colonic MC38 injection


title: ACC.Col0.4h.R2.R1

value: ACC, 1uM


title: SCaBER cells, GRHL3 clone 18

value: GRHL3 overexpression


title: SCaBER cells, GRHL3 clone 10


title: ACC.Col0.24h.R3.R1


title: rep3 SVTKO1 Ctrl


title: SCaBER cells, mock clone 44


title: colon, orthotopic MC38 tumor, rep2

value: male


title: ACC.Col0.24h.R2.R1


title: rep2 SVTKO1 Ctrl


title: SCaBER cells, mock clone 28


title: ACC.Col0.1h.R4.R1


title: rep1 SVTKO1 Ctrl


title: SCaBER cells, mock clone 17


title: wp128

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: FPKM.txt: Tab-delimited text files include FPKM values for each sample.

source_name: E17.5 nasomaxillary complex

extract_protocol:
Total RNA was extracted using TRIzol reagent.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Nasomaxillary complex

tag: developmental stage

value: Wnt1-Cre:Pth1r f/f (Mutant)


title: rep3 SVAKO2 42oC


title: ACC.Col0.4h.R3.R1

value: wild type (Col-0)


title: ACC.Col0.4h.R4.R1


title: wp127


title: ACC.Col0.1h.R3.R1


title: ACC.Col0.24h.R4.R1


title: rep2 SVAKO2 42oC


title: wp126


title: ACC.Col0.1h.R2.R1


title: MDA-MB-468 cells, Input_rep2

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

data_processing:
Paired-end reads were aligned using STAR version 2.7.3a to build version hg38 of the human genome.
Reads aligning on ribosomal RNA were discarded using RSeQC.
Strand specific normalized coverage files (bigwig) were generated from the aligned reads using deepTools.
Assembly: hg38
Supplementary files format and content: Strand specific (fwd and rev) CPM normalized coverage files in bigwig format
Library strategy: ChIRPseq

source_name: MDA-MB-468 (ATCC HTB-132)

growth_protocol: MDA-MB-468 cells were maintained in DMEM high glucose containing 10% FBS, L-Glutamine and penicillin/streptomycin.

extract_protocol:
After the washing steps, the whole recovered material was used for RNA purification with TRIzol and cleaned-up using RNA Clean & Concentrator TM-5 columns (Zymo Research, Cat. N°R1015). RNA was eluted in 20 µl of H2O and 4µl were used for reverse transcription using SuperScript™ IV VILO™ Master Mix (Invitrogen) to check enrichment for MALAT1 vs. LacZ and Input samples. RNAseq was performed on DNase-treated RNA recovered from ChIRP experiments, and from Input samples as well, on the Illumina platform (NextSeq instrument). The RNA of the ChIRP experiments was controlled on a Bioanalyzer with the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA) to verify the suitable size distribution and to simultaneously quantify the low RNA amounts.
The RNA libraries for the RNA sequencing were prepared using the SMARTer Stranded Total RNA Sample Prep Kit - Low Input Mammalian (Takara Bio. USA, Inc). Each ChIRP-RNA-Seq was conducted combining two independent biological replicates. For the input we used 60ng total RNA and performed ribosomal depletion with RiboGone (Takara Bio. USA, Inc) prior to cDNA and library preparation. For the RNA deriving from the ChIRP experiments we used 1200pg for cDNA and library preparation following the manufacturer’s instructions. The quality of the resulting libraries was controlled on a Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA). The quantification of the libraries was performed by qPCR. Sequencing was carried out on a NextSeq 500 instrument (Illumina Inc., San Diego, CA, USA), sequencing in paired-end mode 76bp.
OTHER: ChIRP followed by RNAseq

treatment_protocol: To perform ChIRP experiments 70% confluent MDA-MB-468 cells were fixed with 1% glutaraldehyde for 10min at RT and quenched with 125 mM Glycine solution for 5min at RT. ChIRP was performed as described [Chu C et al. Chromatin isolation by RNA purification (ChIRP). J Vis Exp. 2012 Mar 25;(61):3912. doi: 10.3791/3912]. 20 million cells were used for each condition. 1/100 of lysate volume was used for Input sample preparation. The biotinylated oligonucleotides directed to MALAT1 and to control LacZ are:  16 ologonucleotides Bio_MALAT1_ 1 GCTTCTGCGTTGCTAAAATG/3BioTEG/ to Bio_MALAT1_ 16 CTTCAAGATTCCTTCGGAT/3BioTEG/; Bio_LacZ_1, GTCATATGCATAAAGCGTTG/3’BioTEG; Bio_LacZ_2, TTAACGCCGCAGTGGTAGAA/3’BioTEG. Biotinylated oligonucleotides were recovered after hybridization step using Dynabeads® MyOne™ Streptavidin C1 (Invitrogen).

value: MDA-MB-468 (ATCC HTB-132)

value: Triple-negative breast cancer cell line

value: fixing with 1% glutaraldehyde

tag: chirp target

value: Input


title: MDA-MB-468 cells, Input_rep1


title: ACC.Col0.0h.R4.R1


title: MDA-MB-468 cells, Malat1_rep2


title: rep3 SVAKO2 EtOH

value: EtOH


title: rep1 SVAKO2 42oC


title: MDA-MB-468 cells, Malat1_rep1


title: ACC.Col0.0h.R3.R1


title: colon, orthotopic MC38 tumor, rep1

value: WT


title: ACC.Col0.0h.R2.R1


title: rep2 SVAKO2 EtOH


title: wp123

value: Pth1r f/f (Flox control)


title: MS9_NAWM, snRNASeq

city: Odense

first: Anne

last: Hartebrodt

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

description: 10x Genomics

data_processing:
cellranger software version 6.1.2 with the reference refdata-gex-GRCh38-2020-A, using the –include-introns option recommended for single nucleus RNA sequencing data.
Empty droplets were removed using the R package DropletUtils, multiplets predicted using the hybrid method. We included only barcodes with at least 200 and fewer than 4000 genes and a mitochondrial read fraction of less than 1%
Scuttle’s pseudobulk aggregation was used to compute the meta cells for all cell types per sample. EdgeR’s likelihood ratio test accounting for the sex as an additional covariate was used to test for DE for WM vs lesion for each major cell type
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A)
Supplementary files format and content: {sample_name}_raw_feature_bc_matrix.h5, unfiltered cellranger output

source_name: white matter

extract_protocol:
FANS-sorted nuclei from postmortem human brain tissue
Guidelines from 10x Genomics (CG000183 Rev A)
Indexed adapters pooling single nucleus 3ʹ mRNA-sequencing with 1% PhIX

treatment_protocol: Fresh frozen tissue blocks

value: white matter

tag: lesion

value: NAWM

tag: postmortem delay


title: P0 mouse, snATAC-seq, rep M2

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

description:
mouse_snATAC-seq_P0_M2
10X Chromium Single Cell ATAC v1.1

library_source: genomic

data_processing:
Sequencing reads were aligned to the mouse genome (atac-mm10-1.2.0) with the Cell Ranger atac software (version 1.2.0) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger-atac aggr. The files used in the analysis are provided (fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv, filtered_peak_bc_matrix.h5) compressed into tar.gz files.
Assembly: atac-mm10-1.2.0
Supplementary files format and content: fragments.tsv.gz
Supplementary files format and content: fragments.tsv.gz.tbi
Supplementary files format and content: singlecell.csv
Supplementary files format and content: filtered_peak_bc_matrix.h5

molecule: genomic DNA

source_name: Kidney tissue

extract_protocol:
From the harvested P0 mouse kidneys, nuclei were isolated as previously described in(Wilson et al., 2019). Briefly, flash frozen kidney pieces were thawed on ice and dissected into smaller pieces (<1mm) with a razor blade and then dounced in cold Nuclei EZ Lysis Buffer (Sigma, N3408) supplemented with protease inhibitor (Roche; 05892791001) and RNAse inhibitors (Promega, N2615; Thermo Fisher Scientific, AM2696). The tissue was dounce grinded 30 times with a loose pestle (Sigma, P0485), and then filtered through a 200um strainer (pluriSelect, 43-50200). The tissue was dounce grinded 10 times with a tight pestle, and then incubated for 5 mins on ice. Cells were filtered through 40uM filter (pluriSelect ,43-50040) and pelleted at 500g for 5min at 4°C in a swinging bucket centrifuge. Supernatant was removed and nuclei pellet resuspended in Nuclei EZ lysis buffer with RNAse inhibitors, incubated an additional 5 mins on ice and pelleted again. The final pellet was resuspended in 4°C Nuclei Buffer (10X Genomics, #2000207).
Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v1.1_UserGuide (CG000209)

value: Kidney tissue

value: Kidney cells

value: at day of birth (postnatal day 0)


title: MC38_JAK1ko_TIC and LCMV_S, ADT- and HTO-derived cDNA

city: San Diego

first: John

middle: R

last: Teijaro

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

description:
10X Genomics
CITE-seq
MC38_JAK1ko_TIC_and_LCMV_S_barcodes.tsv.gz
MC38_JAK1ko_TIC_and_LCMV_S_features.tsv.gz
MC38_JAK1ko_TIC_and_LCMV_S_matrix.mtx.gz

library_source: other

data_processing:
Raw data generated by Illumina sequencers were converted to FASTQ using cellranger mkfastq (10X Genomics) then subjected to quality control using fastqc and fastqcr.
Cell identification, cDNA counting and antibody-dependent tag counting were performed using cellranger v7.0.0 (10X Genomics) with the --include-intron=true option. The processed data uploaded are given as generated by cellranger count in the directory filtered_bc_feature_matrix.
For raw RNA-seq analysis, demultiplexed FASTQ files were aligned to the mouse genome (mm10) using STAR v2.7.6a with Ensembls v101 transcriptome annotations. The processed data provided are raw read counts generated by STAR.
Assembly: mm10
Supplementary files format and content: CITE-seq: count matrices generated by cellranger count
Supplementary files format and content: bulk RNA-seq: raw counts generated by STAR

molecule: protein

source_name: tumor, spleen

extract_protocol:
Single-cell suspensions were stained with CD45 antibody and viability dye, then live CD45+ cells sorted by flow cytometry. Individual sorted cell samples were stained using the TotalSeq-B hashtag antibodies (Biolegend) according to the manufacturer's specifications and the combined cells were stained using Biolegend's TotalSeq-B protein-targeted antibodies according to the manufacturer's protocol. Stained cells were subjected to library preparation using the 3' single-cell dual index transcriptome kit (10X Genomics) targeting 30,000 total cells. For bulk RNA-seq experiments, cells sorted by flow cytometry were subjected to RNA isolation using the Arcturus PicoPure kit (Thermo Scientific) followed by library preparation targeting polyA+ RNA.
The Chromium Single Cell 3' Reagent Kit v3.1 (Dual Index) (10X Genomics) was used according to the manufacturer's specifications. Bulk RNA-seq libraries were constructed using the SMARTer v4 kit (Takara Bio).
mRNA-derived libraries were constructed independently; a combined library containing hashtag and antibody dependent tag oligos was also constructed (ADT_library). For bulk RNA-seq experiments, polyA+ RNA was converted to cDNA, subjected to amplification and library preparation using SMARTer v4 (Takara) for Illumina single-end sequencing.
CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: tumor, spleen

value: tumor-infiltrating CD45+ cells, CD45+ splenocytes

tag: antibodies/tags


title: rep3 SVAKO2 Ctrl

value: Ctrl


title: rep1 SVAKO2 EtOH


title: MC38_JAK1ko_TIC and LCMV_S, mRNA-derived cDNA


title: AGS-DMSO3

city: Guangzhou，China

first: jide

last: Wang

state: Guangdong ，China

address: 1838 Guangzhou Avenue North

department: Department of Digestive Medicine

institute: Nanfang Hospital, Southern Medical University

description: replicate 3

data_processing:
After quality control, the reads were 3’5’-adaptor trimmed and filtered 15 bp reads with cutadapt software.
The trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch.
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) ).
To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.
Genome_build: human miRBase v21
Supplementary_files_format_and_content: Matrix table with raw tag counts or normalized tag counts for every gene and every sample.

source_name: AGS-DMSO

growth_protocol: The cells were grown using RPMI 1640 culture media (Sigma, St. Louis, MO, USA) with 10% fetal bovine serum (FBS, Sigma, St. Louis, MO, USA). Cultures were maintained at 37 °C in 5% CO2.

extract_protocol:
Total RNA was isolated by TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA concentration was quantitated using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).

treatment_protocol: The human gastric cancer cells were treated with SAHA (5 µM) or vehicle (DMSO) for 24 hours.

value: AGS

value: gastric cancer cells

value: vehicle (DMSO) for 24 hrs


title: P0 mouse, snATAC-seq, rep F2

description:
mouse_snATAC-seq_P0_F2
10X Chromium Single Cell ATAC v1.1


title: rep2 SVAKO2 Ctrl


title: AGS-DMSO1

description: replicate 1


title: CORT-Ket (#9971)

first: Andiara

last: Espindola de Freitas

address: Gilman Drive

department: Biological Sciences

institute: UC San Diego (UCSD)

data_processing:
The sequencing data were processed using the Cell ranger software to demultiplex the samples, generate FASTQ files, align the reads to mm9 genome and generate feature-barcode matrices. The filtered featured matrices were individually analyzed using Seurat R package (v3.1.1) and submitted to quality control (gene count per cell, percent of mitochondrial transcripts).
Genome_build: mm9
Supplementary_files_format_and_content: filtered_feature_bc_matrix folder (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)
Supplementary_files_format_and_content: raw_feature_bc_matrix

source_name: Brain (PFC)

extract_protocol:
Brains were harvested, and the prefrontal cortices were rapidly dissected and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1ml B27 and 0.15 ml Glutamax). The tissues were enzymatically dissociated into single cell suspension, and the cells were captured with the 10X Chromium platform (10X Genomics, Pleasanton, CA).
Reverse transcription, cDNA amplification and library construction were performed according to the manufacturer’s instructions and used for sequencing.

value: PFC

value: 13 weeks old

value: wild type

value: CORT-Ket


title: AGS-DMSO2

description: replicate 2


title: rep1 SVAKO2 Ctrl


title: P0 mouse, snATAC-seq, rep M1

description:
mouse_snATAC-seq_P0_M1
10X Chromium Single Cell ATAC v1.1


title: wp124

value: Nasomaxillary complex


title: Mouse_heart_opti-KAS-seq, rep1

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
To align Opti-KAS-seq and KAS-seq data to the reference genome of interest, we utilized the trim_galore package to trim off low-quality sequence, adaptor sequence and primer sequence from single-end or paired-end raw fastq files
Subsequently, we employed bowtie2 to perform the read alignment of Opti-KAS-seq and KAS-seq data. Mapped reads in sam files from the aligners are sorted and converted to bam files using ‘samtools sort’, which are subsequently deduplicated using ‘picard MarkDuplicates’ (pair-end data) or ‘samtools rmdup’ (single-end data).
For single-end Opti-KAS-seq or KAS-seq data, mapped reads were extended to 150bp as default, irrespective of the initial sequencing data's read length. For paired-end KAS-seq data, the KAS-Analyzer incorporates a Python script, facilitating the merging of "properly paired" mapped reads into a singular interval
Peak calling for broad KAS-seq was executed using epic2, which identified broad peaks maintaining a false discovery rate (FDR) of 0.05 and a 1.5-fold change relative to the Input. Comprehensive quality control measures, such as library complexity metrics, inter-replicate correlation analyses, fingerprint plots, saturation analyses, genomic distribution of KAS-seq peaks, enrichment within gene-coding regions, and the Fraction of Reads in Peaks (FRiP) metric, were executed with the KAS-Analyzer package.
Deduplicated mapped KAS-seq reads were converted to bedGraph and bigWig using deeptools bamCoverage and UCSC tools.
Assembly: mm10
Supplementary files format and content: bed, peaks list.
Supplementary files format and content: bigWig, read density.
Library strategy: Opti-KAS-seq

source_name: Heart

growth_protocol: Murine embryonic stem (ES) cells were purchased from ATCC (CRL-1821) and were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1 mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1% (v/v) nonessential amino acid stock (100x, Gibco), 1% penicillin/streptomycin stock (100x, Gibco), and 1,000 U/mL LIF (Millipore)

extract_protocol:
Then, 1 µg genomic DNA was suspended in 95 µL DNA elution buffer supplemented with 5 µL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma, 760749), 25 mM K3BO3, and incubated at 37 °C for 1.5 h while being gently shaken. Next, 5 µL RNase A (Thermo, 12091039) was added into the reaction mixture followed by incubation at 37 °C for 5 min. Biotinylated gDNA was then recovered by DNA Clean & Concentrator-5 kit (Zymo, D4013).
gDNA was suspended into 100 µL water and was fragmented to 150–350 bp size by using Bioruptor Pico at 30s-on/30s-off setting for 30 cycles; 5% of the fragmented DNA was saved as input, and the remaining 95% was used to enrich biotin-tagged DNA by incubation with 10 µL pre-washed Dynabeads MyOne Streptavidin C1 (Thermo, 65001) at room temperature for 15 min. The beads were washed, and DNA was eluted by heating the beads in 15 µL H2O at 95 °C for 10 min. Eluted DNA and its corresponding input were used for library construction by using Accel-NGS Methyl-seq DNA library kit (Swift, 30024).

treatment_protocol: Cells harvested from the culture dish or Fluorescence-activated cell sorting (FACS) cells were washed with DPBS and subsequently resuspended in 50 µL of ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. After gentle pipetting, the suspension was incubated on ice for 3 minutes. The cells were then treated with 1 mL of cold ATAC-RSB containing 0.1% Tween-20 and centrifuged at 500 RCF for 5 minutes at 4ºC. Following a wash with 1 mL DPBS, the cells underwent N3-kethoxal labeling at 37 ºC with continuous agitation. The labeling process involved a 15-minute incubation in 5mM N3-kethoxal in PBS.

value: Heart

value: Mouse heart

value: WT

value: No treatment


title: wp138

value: Pth1r f/f (Flox control)


title: CORT-Ket (#9968)


title: rep3 SVAKO1 42oC


title: AGS-SAHA2

description: replicate 2

source_name: AGS-SAHA

value: SAHA (5 µM) for 24hrs


title: CORT-Ket (#9967)


title: EhracJ gene silenced strain replicate 3

city: Bunkyo-ku

first: Misato

last: Shimoyama

state: Tokyo

address: Hongo 7-3-1

department: School of Molecular and Cellular Biology, Graduate School of Medicine

institute: The University of Tokyo

data_processing:
CASAVA(bcl2fastq): bcl2fastq v2.19 was used for base calling.
Sequence reads were trimmed for adapter contamination, uncertain nucleotides, which constitute more than 10 percent of either read (N > 10%), and low-quality reads (Base Quality less than 5), which constitute more than 50 percent of the read, using fastp software (default parameters).
Trimmed sequence reads were aligned to the reference genome using Hisat2 v2.0.5 (default parameters).
Mapped reads were assembled using Stringtie software ver. 1. 3. 3b  default parameters).
Read count extraction and normalization were performed using featureCounts v1.5.0-p3 (default parameters).
Assembly: JCVI-ESG2-1.0
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include differentially expressed genes in mock vector-transfected and EhracM gene silenced strains.
Supplementary files format and content: tab-delimited text files include differentially expressed genes in mock vector-transfected and EhracJ gene silenced strains.

organism: Entamoeba histolytica

source_name: trophozoite

growth_protocol: Standard protocl for E. histolytica axenic cuture with BIS medium.

extract_protocol:
Logarithmic growth phase of E. histolytica trophozoites were harvested then total RNA was extracted using Trizol reagent.
RNA-seq libraries were generated using a directional library preparation protocol. The process included polyA-plus RNA purification, RNA fragmentation, random hexamer primed cDNA synthesis with dUTP, end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, PCR amplification, and purification. The libraries were then subjected to quality control checks with Qubit, real-time PCR, and bioanalyzer before sequencing on Illumina platforms. Finally, the libraries were pooled and sequenced on Illumina Novaseq 6000.

value: trophozoite

tag: transfected plasmid

value: psAP2-EhracJ (vector for silencing EhracJ)

tag: expression of_ehracm

value: normal

tag: expression of_ehracj

value: silenced


title: AGS-SAHA3

description: replicate 3

value: AGS

value: gastric cancer cells

tag: treatment


title: rep2 SVAKO1 42oC


title: AGS-SAHA1

description: replicate 1


title: CORT-Sal (#9970)

value: PFC

tag: genotype

value: CORT-Sal


title: EhracJ gene silenced strain replicate 2


title: EhracJ gene silenced strain replicate 1


title: rep1 SVAKO1 42oC


title: CORT-Sal (#9969)

tag: tissue

value: 13 weeks old

value: wild type


title: HGC-27-DMSO3

description: replicate 3

value: vehicle (DMSO) for 24 hrs


title: rep3 SVAKO1 EtOH

value: EtOH


title: EhracM gene silencing strain replicate 3

data_processing:
CASAVA(bcl2fastq): bcl2fastq v2.19 was used for base calling.
Sequence reads were trimmed for adapter contamination, uncertain nucleotides, which constitute more than 10 percent of either read (N > 10%), and low-quality reads (Base Quality less than 5), which constitute more than 50 percent of the read, using fastp software (default parameters).
Trimmed sequence reads were aligned to the reference genome using Hisat2 v2.0.5 (default parameters).
Mapped reads were assembled using Stringtie software ver. 1. 3. 3b  default parameters).
Read count extraction and normalization were performed using featureCounts v1.5.0-p3 (default parameters).
Assembly: JCVI-ESG2-1.0
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include differentially expressed genes in mock vector transfected and EhracM gene silencing strain. tab-delimited text files include differentially expressed genes in mock vector-transfected and EhracJ gene silenced strains.

tag: strain

value: psAP2-EhracM (vector for silencing EhracM)

tag: expression of ehracm

tag: expression of ehracj


title: P0 mouse, snATAC-seq, rep F1

description:
mouse_snATAC-seq_P0_F1
10X Chromium Single Cell ATAC v1.1

value: Kidney tissue

value: Kidney cells

tag: age

value: at day of birth (postnatal day 0)


title: BCD-Ket (#9986)

value: BCD-Ket


title: rep2 SVAKO1 EtOH

tag: cell line

tag: cell type


title: HGC-27-DMSO2

description: replicate 2


title: BCD-Ket (#9949)


title: EhracM gene silencing strain replicate 1

value: trophozoite


title: rep1 SVAKO1 EtOH


title: BCD-Ket (#9946)


title: EhracM gene silencing strain replicate 2


title: HGC-27-DMSO1

description: replicate 1


title: HGC-27-SAHA3

description: replicate 3

value: SAHA (5 µM) for 24hrs


title: rep3 SVAKO1 Ctrl

value: Ctrl


title: psAP2 vector control replicate 2

value: psAP2 (empty vector)

value: normal


title: BCD-Sal (#9947)

value: BCD-Sal


title: psAP2 vector control replicate 3


title: HGC-27-SAHA2

description: replicate 2

value: gastric cancer cells


title: rep1 SVAKO1 Ctrl


title: rep2 SVAKO1 Ctrl


title: HGC-27-SAHA1

description: replicate 1


title: psAP2 vector control replicate 1


title: IC_215

status: Public on Jun 19 2024

city: Houston

first: Ethan

last: Roy

state: TX

address: 7000 Fannin St

institute: UT Health Science Center Houston

data_processing:
Novogene
Assembly: mm10
Supplementary files format and content: Excel spreadsheet contains FPKM values for all samples
Supplementary files format and content: Excel spreadsheet contains FPKM values for all samples

source_name: brain (cortex)

extract_protocol:
Total RNA from bulk cortical tissues was extracted with Direct-zol RNA Microprep Kits.
Libraries for sequencing were constructed with the NEB Next Ultra RNA Library Prep Kit (NEB) for Illumina.

value: brain (cortex)

value: 24 mo


title: IC_232


title: IC_230


title: IC_211


title: IC_218


title: IC_191


title: IC_231


title: IC_212


title: IC_214


title: IC_206


title: IC_193


title: MKO51

value: 3 mo


title: MKO49


title: MKO48


title: MKO41


title: MKO42


title: MKO58


title: MKO40


title: BCD-Sal (#9901)

value: PFC

value: 13 weeks old

value: wild type


title: NIA 17


title: NIA 18


title: NIA 16


title: NIA 15


title: NIA 14


title: NIA 13


title: NIA 11


title: NIA 10


title: NIA 8


title: NIA 6


title: NIA 2


title: NIA 4


title: 4-1BB_rep3

city: Milano

first: Chiara

last: Laura

address: Via Olgettina 58

institute: San Raffaele Scientific Institute

data_processing:
Reads were trimmed using the JAVA tool trimmomatic (V 0.32)
Raw reads were alignmed using STAR aligner V 2.5.3a
Read counts per gene calculated using the featureCounts function from the Rsubread package (V 1.32.4), based on GENCODE gene annotation M16
TPM values where calculated using an in-house script
Assembly: GRCm38 (GENCODE)
Supplementary files format and content: Tab-separated values

source_name: Liver

extract_protocol:
RNA was purified using RaliaPrep RNA Cell Miniprep System (Promega) following manual instruction. 4 ng total RNA was used for the construction of sequencing library
RNA libraries for RNA seq were prepared using Smart-seq 2 protocol (Picelli et al., Nature Protocol, 2014)

value: Liver

value: CD8 T cells


title: 4-1BB_rep2


title: NIA 1


title: NIA 5


title: MKO56


title: OX40_rep1


title: NIA 12


title: OX40_rep2


title: OX40_rep3


title: 4-1BB_rep1


title: BC10_rep1


title: HCprimed_rep2


title: 72h after injure, rostral 0.5mm from epicenter

city: Guangzhou

first: Guangdun

last: Peng

address: Kaiyuan Ave 190

department: Guangzhou Institute of Biomedicine and Health

institute: Chinese Academy of Sciences

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
The raw Visium spatial RNA-seq data and histological H&E images were processed using the Space Ranger pipeline (v.1.0.0, 10x Genomics) to align and summarize unique molecular identifier (UMI) counts according to the reference genome “Mouse Genome mm10”.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count of each tissue spot in Hierarchical Data Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spot
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tiisue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: spinal cord

growth_protocol: Adult female mice of 8-9 weeks old were used in the SCI.

extract_protocol:
Four consecutive spinal cord cryosections were cut at 20-μm thickness each and attached to one of the four capture areas of the Visium Spatial Gene Expression slides (10x Genomics, 1000184).
The spatial transcriptomics library was constructed according to the Visium Spatial Gene Expression Reagent Kits User Guide (10x Genomics, CG000239 Rev D).

treatment_protocol: a complete transection of the spinal cord of C57BL/6J mice at the tenth thoracic vertebra was performed.

value: spinal cord

value: transection


title: 24h after injure, caudal 1mm from epicenter


title: HCprimed_rep1


title: HCprimed_rep3


title: 72h after injure, caudal 1mm from epicenter


title: BC10_rep2


title: NIA 7


title: 72h after injure, rostral 1mm from epicenter


title: NIA 9


title: BC10_rep3


title: 24h after injure, caudal 0.5mm from epicenter


title: 24h after injure, rostral 0.5mm from epicenter


title: 3h after injure, caudal 1mm from epicenter


title: ASN4 Tumor

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

data_processing:
bcl to fastq was performed using Illumina bcl2fastq conversion software version 2.20.0.422
paired-end FASTQ files were used as input for salmon version 0.9.1 (https://combine-lab.github.io/salmon/getting_started/)
the salmon transcriptome index was prepared using the following command: "salmon index -t v0.14 Mm_latest_rna.fna -i v0.14 Mm_latest_rna.fna_transcripts_index -k 31"; the v0.14 Mm_latest_rna.fna was obtained from NCBI via ftp.ncbi.nlm.nih.gov
the following parameters were used with salmon processing:
libType: A
numBootstraps: 100
index: v0.14_Mm_latest_rna.fna_transcripts_index
Assembly: v0.14_Mm
Supplementary files format and content: tab-delimited text files including transcript per million (TPM) values; each sample has a separate file labeled "Sample_name.quant.sf"

source_name: MPNST tumor

growth_protocol: 67C-4 and #5NPCIS cell lines were maintained in Dulbecco's Modified Eagle Medium(DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), penicillin (100 U/ml), and streptomycin (10 mg/ml). The murine MPNST cell line SN4-4 was cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS), sodium pyruvate (1 mM), penicillin (100 U/ml), and streptomycin (10 mg/ml). Prior to use, all cell lines were tested and confirmed to be negative for mycoplasma contamination by IDEXX Bioanalytics (Columbia, MO).

extract_protocol:
High Pure isolation kit (Roche Life Science)
Paired-end 2 x 150 bp reads (300 cycles)
Illuminia NEBNext Ultra II Directional RNA library kit

treatment_protocol: Non-treated

value: MPNST tumor


title: uninjure, rostral 1mm from epicenter

value: sham


title: M3-9M B Muscle

source_name: Adjacent muscle

value: Adjacent muscle


title: 3h after injure, caudal 0.5mm from epicenter


title: M3-9M A Tumor


title: 3h after injure, rostral 1mm from epicenter


title: M3-9M B Tumor


title: uninjure, caudal 0.5mm from epicenter


title: 76-9 Muscle


title: 24h after injure, rostral 1mm from epicenter


title: K7m2 Tumor


title: F420 Tumor


title: uninjure, rostral 0.5mm from epicenter


title: 5NPCIS Tumor


title: CD8 T cells, KC_primed, d28

data_processing:
Raw sequencing data were demultiplexed with the mkfastq application (Cell Ranger v.6.0.2). UMI-Tools (v.1.0.0) whitelist and extract commands were used to identify and select the number of cell barcodes to use in downstream analysis. Reads were mapped to the reference genome using STAR v.2.5.3a and assigned to genes with featureCounts v.1.6.4. GRCm38 was used as the reference genome. Bam files were sorted with samtools (v1.9). Finally, Umi-Tools count was used to processing the UMIs aligned to each gene in each cell to find the number of distinct, error-corrected UMIs mapping to each gene. The UMI count tables of each cellular barcode were used for further analysis.
Single cell data analysis was performed using Seurat (v4.0.2) (Stuart et al., 2019).
Cells were obtained after applying a filter of at least 200 genes expressed per cell and only genes expressed in at least 3 cells were retained. Moreover, cells with more than 10% of reads mapped to mitochondrial genes were also excluded from the analysis.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values

extract_protocol:
Single-cell suspensions from spleens and livers were stained with Viobility 405/520 fixable dye (Miltenyi), with PB-conjugated anti-CD8α (clone 53-6.7) and PE-conjugated anti-CD45.1 (clone A20) antibodies. Live CD8+ CD45.1+ cells were sorted on a MoFlo Legacy (Beckman Coulter) cell sorter in a buffer containing PBS with 2% FBS
Single cells were processed on the Chromium platform (10x) using the Chromium Next GEM Single Cell 3’ v3.1 (Dual Index). After quality controls and quantification on TapeStation instrument (Agilent), libraries were sequenced on NovaSeq6000 platform (Illumina) generating around 25'000 reads/cell.

value: KC-primed

tag: timepoint

value: day 28


title: CD8 T cells, HC_primed, d28

value: HC-primed


title: CD8 T cells, HC_primed, d7, rep2

value: day 7


title: oshho3-KO_root_3

type: RNA

first: Yasuhito

last: Sakuraba

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

description:
Gene expression in root tissues
SAMPLE 12

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryza sativa

source_name: Rice seedlings

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Maxwell RSC RNA kit (Promega) following the manufacturer's recommendations.

treatment_protocol: Shoot and root tissues from 27 day-old wild-type and oshho3-KO seedlings grown under nitrogen-sufficient conditions

value: root tissues

value: oshho3 KO


title: CD8 T cells, HC_primed, d7, rep1


title: CD8 T cells, HC_primed, d5, rep2

value: day 5


title: 3h after injure, rostral 0.5mm from epicenter


title: uninjure, caudal 1mm from epicenter


title: oshho3-KO_root_2

description:
Gene expression in root tissues
SAMPLE 11


title: 76-9 Tumor


title: oshho3-KO_shoot_2

description:
Gene expression in shoot tissues
SAMPLE 8

value: shoot tissues


title: CD8 T cells, HC_primed, d3, rep2

value: day 3


title: oshho3-KO_root_1

description:
Gene expression in root tissues
SAMPLE 10


title: eGFPhi _ LT_HSCs, rep3

city: Chongqing

first: Mengjia

last: Hu

address: Gaotanyan Street 30

institute: Third Military Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

value: Bone marrow

value: long-term hematopoietic stem cells

value: eGFPhi _ LT_HSCs

value: Isolation of eGFPhi _LT_HSCs from Trim47+/eGFP mice


title: oshho3-KO_shoot_3

description:
Gene expression in shoot tissues
SAMPLE 9


title: M3-9M A Muscle


title: CD8 T cells, HC_primed, d3, rep1

value: Liver

value: CD8 T cells


title: CD8 T cells, Naive

value: Naive


title: 67C-4 Tumor

value: MPNST tumor


title: WT_root_3

description:
Gene expression in root tissues
SAMPLE 6

value: WT


title: oshho3-KO_shoot_1

description:
Gene expression in shoot tissues
SAMPLE 7


title: eGFPhi _ LT_HSCs, rep2


title: eGFPhi _ LT_HSCs, rep1

value: Isolation of eGFPhi_LT_HSCs from Trim47+/eGFP mice


title: WT_shoot_1

description:
Gene expression in shoot tissues
SAMPLE 1


title: WT_root_1

description:
Gene expression in root tissues
SAMPLE 4


title: Trim47-/--5-FU -3 LT-HSCs, rep3

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the GRCm38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

value: Trim47 mutant

value: Isolation of LT-HSCs from Trim47-/- mice treated with 5-FU for 10 days


title: eGFPlo _ LT_HSCs, rep3

value: eGFPlo _ LT_HSCs

value: Isolation of eGFPlo _LT_HSCs from Trim47+/eGFP mice


title: CD8 T cells, HC_primed, d14

value: HC-primed

value: day 14


title: WT_shoot_2

description:
Gene expression in shoot tissues
SAMPLE 2

value: shoot tissues


title: WT_shoot_3

description:
Gene expression in shoot tissues
SAMPLE 3


title: eGFPlo _ LT_HSCs, rep1

value: Bone marrow


title: CD8 T cells, HC_primed, d5, rep1

value: day 5


title: eGFPlo _ LT_HSCs, rep2

value: long-term hematopoietic stem cells


title: WT-5-FU-3 LT-HSCs, rep3

value: Wild type

value: Isolation of LT-HSCs from WT mice treated with 5-FU for 10 days


title: MNase-seq, HBV dslDNA assembled into chromatin using Nap1, 1-4X rep3

city: New York

first: Andres

last: Mansisidor

state: NY

address: 1230 York Ave Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: Rockefeller University

description: MNase-seq

data_processing:
UMI demultiplexing (custom script)
adapter trimming (custom script)
alignment to HBV genome (Bowtie2 v2.3.4.3)
nucleosome coverage mapping (nucleoATAC)
Bedgraphs from both RNA- and MNase-seq were plotted using Sushi package v1.30.0 in R v4.1.0
Assembly: NC_003977.2 (offset by 500 bp)
Supplementary files format and content: bedgraph files that include coverage of fragment centers (50 bp windows)

organism: Hepatitis B virus

source_name: in vitro

extract_protocol:
In vivo MNase-seq was performed on purified nuclei at different timepoints after transfection with HBV cccDNA or on in vitro reconstituted chromatin.
For MNase-seq on in vitro reconstituted chromatin, titration of MNase was performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested chromatin arrays. Chromatinized DNA (100 ng) was digested using MNase (NEB) in 25 µL reactions with 2.5–25 units of enzymes that was incubated for 5 minutes at 37°C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37°C. The reaction was stopped by adding 20 mM EDTA and 1% SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index Barcodes or Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out using only 5 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). For MNase-seq on cell cultured samples, HEK293T cells were transfected with recombinant cccDNA 4 or 24-hours prior to harvest for MNase-seq. The nuclei of HEK293, HepG2.2.15, and HepAD38 cells were purified by incubating cells in Nuclei isolation buffer for 10 minutes (0.1% Igepal, 0.1% Triton X -100, 1 mM DTT in 1 X PBS), mechanically lysing with 10 strokes of loose (A) pestle Dounce homogenizer, and washing nuclei twice in 10 mL of Wash Buffer with Tween (10 mM Tris-HCl pH 7.5, 2.5 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Titration of MNase was similarly performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested genomic DNA. MNase (NEB) was added to 2 x 106 nuclei in 50 µL reaction volume with 125–2000 units of enzyme that was incubated for 5 minutes at 37 °C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37 °C. The reaction was stopped by adding 20 mM EDTA and 1 % SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). Libraries were then pooled and enriched for HBV-containing reads using custom-designed xGen Lockdown probes (Integrated DNA Technology) of 60 bp each tiling the entire HBV genome and oligo capture protocol was followed per manufacture’s protocol. Enriched libraries were subsequently amplified using 11 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and purified using Ampure XP beads.

value: in vitro

value: not applicable

value: reconstituted nucleosomes


title: MNase-seq, HBV dslDNA assembled into chromatin using Nap1+ACF, 1-4X rep3

description: MNase-seq


title: Trim47-/--5-FU -2 LT-HSCs, rep2


title: MNase-seq, HBV dslDNA assembled into chromatin using Nap1, 1-0X rep1

description: MNase-seq


title: WT-5-FU-1 LT-HSCs, rep1


title: Trim47-/- -2, LT-HSCs, rep2

value: Isolation of LT-HSCs from Trim47-/- mice


title: MNase-seq, HBV dslDNA assembled into chromatin using Nap1+ACF, 1-2X rep2

description: MNase-seq


title: MNase-seq, HBV dslDNA assembled into chromatin using Nap1+ACF, 1-0X rep1

description: MNase-seq


title: SC073 Single-nuclei RNAseq of osteosarcoma patient metastasis. Lung

first: Matt

last: Cannon

department: Center for Childhood Cancer

description: SC073 Human patient lung tumor - single nuclei RNAseq

data_processing:
BCL files were converted to fastq files using cellranger mkfastq
Fastq files were processed using cellranger count
Further processing and analyses performed are outlined on GitHub (https://github.com/kidcancerlab/epithelial)
Assembly: hg19
Supplementary files format and content: Tar files for each sample include the contents of the filtered_feature_bc_matrix folder output by Cellranger count (barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz)

source_name: lung tumor

extract_protocol:
Following dissociation into either nuclei or single cell suspension, single-cell 3’ RNA-Seq or 10x multiomics libraries were prepared using Chromium Single Cell system (10x Genomics) according to the manufacturer's instructions
Libraries were constructed per 10x protocols

value: lung tumor


title: SC072 Single-nuclei RNAseq of osteosarcoma patient metastasis. Lung

description: SC072 Human patient lung tumor - single nuclei RNAseq


title: Trim47-/- -3, LT-HSCs, rep3

value: Trim47 mutant


title: WT-5-FU-2 LT-HSCs, rep2


title: SC069 Single-nuclei RNAseq of osteosarcoma patient metastasis. Lung

description: SC069 Human patient lung tumor - single nuclei RNAseq


title: Wild type-3 LT-HSCs, rep3

value: Isolation of LT-HSCs from WT mice


title: Trim47-/- -1, LT-HSCs, rep1


title: Trim47-/--5-FU -1 LT-HSCs, rep1

value: Isolation of LT-HSCs from Trim47-/- mice treated with 5-FU for 10 days


title: NCHS-015 Single-cell RNAseq of osteosarcoma patient metastasis. Right Hilar I lobe

description: S0217 Human patient lung tumor - 3' single cell RNAseq


title: NCHS-015 Single-cell RNAseq of osteosarcoma patient metastasis. Right upper lobe

description: S0218 Human patient lung tumor - 3' single cell RNAseq


title: NCHS-009 Single-cell RNAseq of osteosarcoma patient metastasis. Hilar lobe

description: S0058 Human patient lung tumor - 3' single cell RNAseq


title: KP scRNA-Seq

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: 10x genomics

data_processing:
For data processing, alignment, filtering, barcode counting, and UMI counting were performed with Cellranger count module to generate feature-barcode matrix and determine clusters, Downstream analyses were performed in R using the Seurat package. Principal component analysis (PCA) and nearest neighborhood graphs were calculated in order to visualize on auniform manifold approximation and projection. Unsupervised clustering using a shared nearest neighbor modularity optimization based algorithm (resolution parameter 1.5) identified 28 distinct clusters. For classification of immune cell populations, differential expression analysis was performed between each cluster. Then we used these markers for artificial annotation and divided the cells into 15 clusters. Top differential expression results for each cluster were cross-referenced with canonical markers for a comprehensive range of immune cell populations, yielding a consensus panel of transcriptional markers for each of the 15 clusters. The dot density map was generated with gnuplot. Gnuplot-iostream (https://github.com/dstahlke/gnuplot-iostream) serves as gnuplot interface.
Assembly: mm10
Supplementary files format and content: Tab-separated barcode files
Supplementary files format and content: Tab-separated features files
Supplementary files format and content: Tab-separated matrix files

source_name: allogroft tumour

extract_protocol:
Tumours were dissected from mice on day 14 after inoculation and disassociated using the Miltenyi Mouse Tumour Dissociation Kit and gentleMACS Octo-Dissociator (Miltenyi) as per the manufacturer’s instructions. Isolation of immune cells was performed by density centrifugation with Percoll. Cells were stained using anti-CD45 APC (BioLegend, 103112, 1:200), LIVE/DEAD FITC (Invitrogen, L34969, 1:1000) antibodies followed by selection of live CD45 positive single cells with FACS.
Cell capture and cDNA synthesis was using single cell 3’libray and Gel Bead kit V3.1 (10x Genomics, 1000121) and Chromium single cell G Chip Kit (10x Genomics, 1000120) according to the manufacture’s introduction. Single cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1.

value: allogroft tumour

value: lymphocytes

value: immune cells

value: WT

value: FACS sorting


title: Wild type-1 LT-HSCs, rep1

value: Bone marrow


title: MNase-seq, HBV dslDNA assembled into chromatin using Nap1, 1-2X rep2

description: MNase-seq


title: KPT scRNA-Seq

description: 10x genomics

value: Tdg KO


title: KP_TdgKO2 stranded RNA-Seq

data_processing:
To assess the transcription level of transposable elements (TE), the clean data were mapped to mouse reference genome mm10 using Hisat2 with the parameters -k 100 --no-unal --no-mixed --no-discordant. Then the TEcount function of TEtranscripts (v2.2.1) were applied to count TE and genes with the parameter --mode multi. Differentially expressed TE and genes analysis was performed by using DESeq2 package. Only TE and genes with P value less than 0.05 and at least 2-fold-change were considered to be differentially expressed.
To quantify the transcription level of transposable elements in a strand-specific manner, piPipes was used to assign reads to sense strand or antisense strand. Mouse mm10 genome was installed with the parameters: genome_MM=1 and transposon_MM=3. The clean reads of each library were subject to single-sample mode for RNA-seq. Subsequently, the raw counts of each single base in every TE subfamily were acquired from the summary reports and were then normalized according to the library size. Finally, the average signals of duplicates were calculated for each genotype and subject to GraphPad for plotting.
Assembly: mm10
Supplementary files format and content: table for the average signals across different features

source_name: KP

growth_protocol: KP and B16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA for each sample was extracted using TRIzoI (Thermo Fisher Scientific) according to the manufacturer’s instruction.
For library preparation, the purified total RNA from KP or B16 cells was quantified by Qubit (Invitrogen) and analyzed by an Agilent Bioanalyzer to assess RNA integrity. 1 μg RNA was used to generate rRNA-depleted RNA with a rRNA Depletion Kit (NEB, E7400) according to the manufacturer’s instructions. The rRNA-depleted RNA was analyzed in an Agilent Bioanalyzer to ensure the complete removal of rRNA, and then used to generate directional RNA library with NEBNextUltra™ DirectionalRNA Library Prep Kit for Illumina (NEB, E7760) according to the manufacturer’s instructions.

value: KP

value: LUAD


title: NCHS-009 Single-cell RNAseq of osteosarcoma patient metastasis. Lower lobe

description: S0059 Human patient lung tumor - 3' single cell RNAseq


title: KP_TdgKO1 stranded RNA-Seq


title: KP_WT2 stranded RNA-Seq


title: KP_TdgKO3 stranded RNA-Seq


title: HepG2, cccDNA-transfected, 500nM CBL137, Pol2, rep2

data_processing:
adapter trimming (TrimGalore v0.4.5, cutadapt v1.15, FastQC v0.11.5)
alignment to hg38 and HBV genome (bowtie2 v2.3.4.1
deduplication (Picard Tools v2.16.0)
read density profiling (BEDTools v2.29.2)
Assembly: hg38 (human alignment), NC_003977.2 (offset by 500 bp, HBV alignment)
Supplementary files format and content: bigwig

extract_protocol:
Frozen cell pellets  were resuspended in SDS buffer (100mM NaCl, 50mM Tris-HCl pH 8.0, 5mM EDTA, 0.5 % SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spun down, resuspended in the immunoprecipitation buffer at 1mL per 0.5 million cells (SDS buffer and Triton Dilution buffer [100mM NaCl, 100mM Tris-HCl pH 8.0, 5mM EDTA, 5% Triton X-100] mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail) and processed on a Covaris E220 Focused-ultrasonicator to achieve an average fragment length of 200-300bps with the following parameters: PIP=140, Duty Factor=5, CBP/Burst per sec=200, Time = 1200s. Chromatin concentrations were estimated using the Pierce™ BCA Protein Assay Kit (ThermoFisher Scientific) according to the manufacturer’s instructions. The immunoprecipitation reactions were set up in 500uL of the immunoprecipitation buffer in Protein LoBind tubes (Eppendorf) and pre-cleared with 50 µL of Protein G Dynabeads (ThermoFisher Scientific) for two hours at 4 °C. After pre-clearing, the samples were transferred into new Protein LoBind tubes and incubated overnight at 4 °C with the indicated antibodies (Key Resources Table). The next day, 50 µL of BSA-blocked Protein G Dynabeads were added to the reactions and incubated for 2 hours at 4 °C. The beads were then washed two times with low-salt washing buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), two times with high-salt washing buffer (500 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), two times with LiCL wash buffer (250 mM LiCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1 % Na-Deoxycholate, 1 % IGEPAL CA-630) and one time with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The samples were then reverse-crosslinked overnight in elution buffer (1 % SDS, 0.1M NaHCO3) and purified using the ChIP DNA Clean & Concentrator kit (Zymo Research) following manufacturer instructions.
After quantification of the recovered DNA fragments, libraries were prepared using the ThruPLEX®DNA-Seq kit (Takara) following the manufacturer’s instructions, purified with SPRIselect magnetic beads (Beckman Coulter), and quantified using a Qubit Flex fluorometer (ThermoFisher Scientific) and profiled with a TapeStation (Agilent).

value: Human hepatoma cells

value: HBV cccDNA transfection 24 hours before harvest


title: HepG2, cccDNA-transfected, 500nM CBL137, H3K4me3, rep1

value: H3K4me3 (Epicypher, #13004)


title: HepG2, cccDNA-transfected, 500nM CBL137, H3, rep2


title: KP_WT1 stranded RNA-Seq


title: Wild type-2 LT-HSCs, rep2

value: long-term hematopoietic stem cells

value: Wild type


title: B16_TdgKO2 stranded RNA-Seq

value: Melanoma


title: HepG2, cccDNA-transfected, 500nM CBL137, H3, rep1


title: HepG2, cccDNA-transfected, 500nM CBL137, H3K4me3, rep2


title: NIA 3

value: brain (cortex)

value: 24 mo


title: HepG2, cccDNA-transfected, 500nM CBL137, H2B, rep2


title: B16_TdgTrp53_DKO1 stranded RNA-Seq

value: Tdg Trp53 DKO


title: HepG2, cccDNA-transfected, 500nM CBL137, H2B, rep1


title: B16_TdgKO1 stranded RNA-Seq


title: HepG2, cccDNA-transfected, 500nM CBL137, H2A, rep2


title: B16_TdgTrp53_DKO2 stranded RNA-Seq


title: HepG2, cccDNA-transfected, 500nM CBL137, Input, rep1


title: B16_Trp53KO2 stranded RNA-Seq

value: Trp53 KO


title: HepG2, cccDNA-transfected, 500nM CBL137, H2A, rep1


title: HepG2, cccDNA-transfected, 500nM CBL137, Pol2, rep1


title: KP_TdgKO Bisulfite-Seq

data_processing:
For data processing, raw data were trimmed by Trim Galore with default settings. Then, the clean data were mapped to mm10 mouse reference genome using Bismark (v0.20.1)  with the parameters -X 2000 --score_min L,0,-0.6. Duplicates were removed using Picard (v2.22.4). Bigwig files were generated using bedGraphToBigWig (v4) and visualized in Integrative Genomics Viewer (IGV). CGmapTools (v0.1.2) was used for DMR calling, for which only the CpG sites with at least 3×coverage were kept. DMRs were defined by a dynamic fragment strategy: the length (the maximal distance between two adjacent common cytosines is 100 bp, and the maximal DMR size is 1000 bp), methylation level difference (at least 25% absolute methylation level difference), P value (less than 0.05) and CpG number (at least 6 CpG sites) were considered. All the annotated information was downloaded from the UCSC Genome Browser (mm10). Promoters were defined as ± 2.5 kb from the TSS (Transcription Start Site).
Assembly: mm10
Supplementary files format and content: bedgraph files for level and sequencing depth of 5mC

source_name: cell line

extract_protocol:
Total DNA was extracted from cells using Phenol-chloroform DNA extraction protocol.
Briefly, 200-1000 ng genomic DNA was used for WGBS library construction. DNA was sonicated to ~250 bp fragments with the Diagenode Bioruptor Pico. Then DNA was subjected to end-repair, A-tailing, and ligation using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) and methylated adaptor (Roche) according to the manufacturer’s instructions. DNA was purified with VAHTS DNA Clean Beads. Subsequently, library was bisulfite modified using QIAGEN EpiTect Fast DNA Bisulfite Kit (59824) and amplified with KAPA2G Robust HotStart PCR Kits with dNTPs (Sigma-Aldrich). Library was finally subjected to 150 bp paired-end sequencing using the Illumina Novaseq6000 instrument.

value: cell line


title: HepG2, cccDNA-transfected, DMSO, H3K4me3, rep2


title: B16_Trp53KO1 stranded RNA-Seq


title: B16_WT2 stranded RNA-Seq

value: WT


title: HepG2, cccDNA-transfected, DMSO, Pol2, rep2


title: HepG2, cccDNA-transfected, DMSO, Pol2, rep1


title: HepG2, cccDNA-transfected, DMSO, H3K4me3, rep1


title: B16_TdgTrp53_DKO2 Bisulfite-Seq

value: Tdg p53 DKO


title: KP_WT Bisulfite-Seq


title: HepG2, cccDNA-transfected, DMSO, H3, rep1


title: B16_TdgTrp53_DKO1 Bisulfite-Seq


title: B16_Trp53KO Bisulfite-Seq


title: HepG2, cccDNA-transfected, DMSO, H3, rep2


title: B16_TdgKO2 Bisulfite-Seq


title: HepG2, cccDNA-transfected, DMSO, H2B, rep2


title: B16_TdgTrp53Mavs_TKO2 RNA-Seq

data_processing:
Raw data were trimmed by Trim Galore (v0.6.6) with default settings. Then, the clean data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Gene count matriceswere calculated by featureCounts (v1.6.4) with the parameters -p -M -O. Differentially expressed gene (DEG) analysis was performed by using DESeq2 package. Only genes with adjusted P value < 0.05 and fold change > 2 were considered to be differentially expressed. DEGs were submitted to DAVID (2021 Update) (https://david.ncifcrf.gov/) for gene ontology (GO) and KEGG pathway enrichment analyses. GSEA was performed using clusterProfiler package.
Assembly: mm10
Supplementary files format and content: comma-separated values file, raw counts for gene expression.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen).
1 μg total RNA was used for the following library preparation. RNAseq libraries were prepared with VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611). The poly(A) mRNA isolation was performed using Oligo(dT) beads. Using divalent cations and high temperatures, mRNA fragmentation was achieved and the priming process was carried out using random primers. Then first strand cDNA and the second-strand cDNA were synthesized. Once the double-stranded cDNA was purified, adaptors were added to both ends after end repair and dA-tailing. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Libraries were finally subjected to 150 bp paired-end sequencing using the Illumina NovaSeq 6000 platform.

value: Tdg Trp53 Mavs TKO


title: B16_WT Bisulfite-Seq


title: B16_TdgKO1 Bisulfite-Seq

value: Tdg KO


title: HepAD38, DMSO, Input, rep1

value: Human hepatoma cell line with integrated HBV genome expressed under the control of a tetracycline repressor

value: not applicable


title: HepG2, cccDNA-transfected, DMSO, H2A, rep1

value: Human hepatoma cells


title: HepG2, cccDNA-transfected, DMSO, H2A, rep2

value: HBV cccDNA transfection 24 hours before harvest


title: HepAD38, DMSO, Pol2, rep2


title: B16_TdgTrp53_DKO2 RNA-Seq


title: B16_TdgTrp53Mavs_TKO1 RNA-Seq


title: HepG2, cccDNA-transfected, DMSO, H2B, rep1


title: HepAD38, DMSO, Pol2, rep1


title: HepAD38, DMSO, H3k4me3, rep2

value: H3K4me3 (Epicypher, #13004)


title: B16_WT1 stranded RNA-Seq


title: B16_TdgTrp53_DKO1 RNA-Seq


title: B16_Trp53KO2 RNA-Seq


title: HepAD38, DMSO, H3k4me3, rep1


title: B16_TdgKO2 RNA-Seq


title: B16_TdgKO1 RNA-Seq


title: B16_WT2 RNA-Seq


title: B16_WT1 RNA-Seq


title: HepG2, cccDNA-transfected, DMSO, Input, rep1


title: KPT4 RNA-Seq

source_name: lung tumour

value: lung tumour

value: KPT tumour

value: LUAD

value: Kras G12D/+,  Trp53 KO, Tdg KO


title: KPT1 RNA-Seq


title: KP2 RNA-Seq

value: KP tumour

value: Kras G12D/+,  Trp53 KO


title: Cas9a-SLCxEnzyme_week6_glu_rep2

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Combinatorial Cas9 library

data_processing:
read trimming (Cas9 libraries only): Read1 reads were trimmed using cutadapt (Galaxy Version 4.8+galaxy1) to remove up- and downstream flanking sequences. The two gRNAs from read1 and read2 were then joined using FASTQ Joiner (Galaxy Version 2.0.1.1+galaxy0) before mapping to the reference sequences.
read mapping: MAGeCK count (Galaxy Version 0.5.9.2.4).
Assembly: Human NCBI genome build 36
Supplementary files format and content: tab-delimited raw gRNA pair count tables
Library strategy: Amplicon-Seq

molecule: other

growth_protocol: For standard culture conditions, HCT116 cells were grown in RPMI (R8758 Sigma) supplemented with 10% Fetal Bovine Serum (10270-106, Lot 42F8381K, Gibco) and Penicillin-Streptomycin (15140-122, Gibco)

extract_protocol:
For the Cas12a-Metal-SLCxSLC, Cas12a- and Cas9-SLCxEnzymes, and Cas12a- and Cas9-SLCxSLC, gDNA was purified from 2x10e7 (QIAamp DNA Mini Kit), 1.7x10e7 (QIAGEN Genomic-tip 100/G) or 2.2x10e8 cells (QIAGEN Genomic-tip 500/G), respectively. gDNA from Cas12a- and Cas9-SLCxSLC screens was digested with restriction enzymes to improve PCR amplification of sgRNA regions. Up to 1.5 mg gDNA was digested with 200 U PacI (Cas12a-SLCxSLC) or 100 U PacI and 100 U XbaI (Cas9-SLCxSLC) (all NEB) for 48 hours.
sgRNA sequences from Cas12a library gDNA samples were amplified with barcoded FW and RV primer that introduce Illumina adapter and read1 sequencing primer binding sites. Up to 1.2 mg gDNA was used as template in 12 ml volume (divided in 96 x 125 µl PCRs) in the following program: 98°C for 30 sec.; 5 cycles: 98°C for 10 sec., 61°C for 30 sec, 72°C for 30 sec; 19 cycles: 98°C for 10 sec., 72°C for 1 min.; 72°C for 2 min. For the samples of the metal transporter and SLC family-wide sub-screen 1, Q5 Polymerase (NEB) was used, SLC vs SLC sub-screen 2-4 and SLC vs metabolic enzymes samples were processed with self-purified Pfu-Sso7d polymerase  and Phusion HF buffer (NEB). Primer sequences are shown in Supplementary Table SX. PCR products we double size selected with DNA purification bads and multiplexed for Illumina sequencing. sgRNA sequences from Cas9 library gDNA samples were first amplified with staggered FW and RV primer that contain partial Illumina adapter sequences at the 5’ end using the same PCR program as above. Up to 1.2 mg gDNA was used as template (125 µg/125 µl volume PCR) and amplified with self-purified Pfu-Sso7d polymerase. An aliquot of the pooled amplified PCR products was double size selected with DNA purification bads and purified fragments were barcoded in a second PCRs (98°C for 30 sec; 6-8 cycles: 98°C for 10 sec., 61°C for 30 sec, 72°C for 30 sec; 72°C for 2 min). PCR products we double size selected with DNA purification bads and multiplexed for Illumina sequencing.

treatment_protocol: Cas9 pools were cultivated in standard media (glu) or in hypoxia (hyp) conditions (1% oxygen), if indicated. Cas12a pools were cultivated in standard media (glu), under hypoxia (hyp), in presence of 50 mM antimycin (ant) or in  low glucose media with galactose (gal) replacement (week 1-3: 20% glucose/80% galactose, week 3-4: 100% galactose, week 4-5: 10% glucose/90% galactose), if indicated. Treatments were started after one (Cas12a samples) or two (Cas9 samples) weeks after transduction. Cells from Cas12-SLCxSLC and Cas9-SLCxSLC samples were cultured in the presence of 100 U/ml Nystatin (Merck, #N3503-5MU) to prevent fungal contaminations.

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06MZ-1)

value: Human colorectal carcinoma cell line

value: Contains lentiviral Cas9 expression contruct lentiCas9-Blast (Addgene #52962)


title: KP1 RNA-Seq


title: Cas9a-SLCxEnzyme_week4_hyp_rep1

description: Combinatorial Cas9 library

value: cell line

value: hyp:Incubated with 1% oxygen (2 weeks)


title: Cas9a-SLCxEnzyme_week6_glu_rep3

description: Combinatorial Cas9 library


title: Cas9a-SLCxEnzyme_week4_hyp_rep3

description: Combinatorial Cas9 library


title: Cas9a-SLCxEnzyme_week6_hyp_rep1

description: Combinatorial Cas9 library

value: hyp:Incubated with 1% oxygen (4 weeks)


title: Cas9a-SLCxEnzyme_week6_glu_rep1

description: Combinatorial Cas9 library


title: Cas9a-SLCxEnzyme_week6_hyp_rep2

description: Combinatorial Cas9 library


title: Cas9a-SLCxEnzyme_week4_glu_rep3

description: Combinatorial Cas9 library


title: Cas9a-SLCxEnzyme_week6_hyp_rep3

description: Combinatorial Cas9 library


title: Cas9a-SLCxEnzyme_week4_glu_rep2

description: Combinatorial Cas9 library


title: B16_Trp53KO1 RNA-Seq

value: Melanoma

value: Trp53 KO


title: KP_TdgKO3 RNA-Seq

value: KP

value: Tdg KO


title: Cas9a-SLCxEnzyme_week4_glu_rep1

description: Combinatorial Cas9 library


title: KP_TdgKO2 RNA-Seq


title: Cas9a-SLCxEnzyme_week3_hyp_rep2

description: Combinatorial Cas9 library

value: hyp:Incubated with 1% oxygen (1 week)


title: Cas9a-SLCxEnzyme_week3_hyp_rep3

description: Combinatorial Cas9 library


title: KP_TdgKO1 RNA-Seq


title: KP_WT3 RNA-Seq

value: WT


title: Cas9a-SLCxEnzyme_week3_hyp_rep1

description: Combinatorial Cas9 library


title: KP_WT2 RNA-Seq


title: Cas9a-SLCxEnzyme_week3_glu_rep3

description: Combinatorial Cas9 library


title: Cas9a-SLCxEnzyme_week3_glu_rep2

description: Combinatorial Cas9 library


title: KP_WT1 RNA-Seq


title: KPT3 RNA-Seq

value: lung tumour

value: KPT tumour


title: Cas9a-SLCxEnzyme_week4_hyp_rep2

description: Combinatorial Cas9 library


title: KPT2 RNA-Seq

value: LUAD

value: Kras G12D/+,  Trp53 KO, Tdg KO


title: Cas9a-SLCxEnzyme_week3_glu_rep1

description: Combinatorial Cas9 library


title: Cas9-SLCxEnzyme_week2_rep3

description: Combinatorial Cas9 library


title: Cas9-SLCxEnzyme_week2_rep2

description: Combinatorial Cas9 library


title: B16_WT_p300 CUT&Tag

data_processing:
Raw data were trimmed by Trim Galore with default settings. Then, the clean data were mapped to mouse reference genome mm10 using bowtie2 (v2.2.5) with the parameters --no-unal --no-mixed --no-discordant -X 2000. Duplicates were removed using Picard (v2.22.4). Metaplot and heatmap for H3K9me3 signal were generated using deepTools.
Assembly: mm10
Supplementary files format and content: bigwig files for H3K9me3 enrichment
Supplementary files format and content: tab-seperated files indicating H3K4me3 and P300 peaks
Library strategy: CUT&Tag

growth_protocol: B16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
The CUT&Tag assay was conducted using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903).
Briefly, 5 × 104 B16 cells were collected and washed once with 500 μl wash buffer before they were bound to activated ConA beads for 10 min at room temperature. After that, cells were incubated with 1 μg anti- H3K9me3 (CST#13969), H3K4me3 (ab8580) or p300 (active motif 61401) antibody at 4°C overnight, respectively. Anti-rabbit IgG was added and incubated for 1 h at 25°C the next day. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G-Tnp for 1 h at 25°C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37°C for 1 h. Tagmentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55°C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water. Libraries were constructed using TD202 TruePrep Index Kit V2 for Illumina from Vazyme Biotech. For library amplification, 15 μl of purifed DNA was mixed with 25 μl of 2 × CAM, along with 5 μl of uniquely barcoded i5 and i7 primers from the TruePrep Index Kit V2 for Illumina (Vazyme Biotech, TD202). A total volume of 50 μl of sample was placed in the Mastercycler nexus (Eppendorf, 6331000076) using the following program: 72°C for 3 min; 98°C for 3 min; 18 cycles of 98°C for 10 s, 60°C for 5 s, and 72°C for 1 min; and holding at 12°C. To purify the PCR products, 2 × volumes of VAHTS DNA Clean Beads (Vazyme Biotech, N411) were added and incubated at room temperature for 5 min. The beads were washed twice with 200 μl fresh 80% ethanol and eluted in 22 μl ddH2O. All CUT&Tag libraries were sequenced using the Illumina NovaSeq 6000 platform in PE150 mode.

tag: chip antibody

value: P300 (active motif, 61401)


title: B16_TdgTrp53DKO_H3K9me3 CUT&Tag


title: Cas9-SLCxSLC_week4_rep1

description: Combinatorial Cas9 library

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06MZ-1)


title: Cas9-SLCxEnzyme_week1_rep1

description: Combinatorial Cas9 library

value: Human colorectal carcinoma cell line


title: Cas9-SLCxSLC_week3_rep2

description: Combinatorial Cas9 library

value: Contains lentiviral Cas9 expression contruct lentiCas9-Blast (Addgene #52962)


title: Cas9-SLCxEnzyme_week1_rep2

description: Combinatorial Cas9 library

value: cell line


title: B16_Trp53KO_H3K9me3 CUT&Tag


title: Cas9-SLCxSLC_week3_rep1

description: Combinatorial Cas9 library


title: B16_WT_H3K4me3 CUT&Tag

value: H3K4me3 (abcam, ab8580)


title: B16_TdgKO_H3K9me3 CUT&Tag


title: Cas9-SLCxSLC_week2_rep2

description: Combinatorial Cas9 library


title: B16_WT_H3K9me3 CUT&Tag


title: B16_TdgTrp53_DKO2 ATAC-seq

data_processing:
For data analysis, raw data were trimmed by Trim Galore with default settings. Then, the clean data were mapped to mouse reference genome mm10 using bowtie2 with the parameters --no-unal --no-mixed --no-discordant -X 2000. Duplicates were removed using Picard. Bedgraph files were generated following MACS2 callpeak with the parameters --nomodel --shift -100 --extsize 200 --p 0.00001 -B -g mm. Metaplot and heatmap were generated using deepTools.
Assembly: mm10
Supplementary files format and content: bigwig files for ATAC-seq signals

extract_protocol:
A total of 5 × 104 B16 cells were collected and washed with ice-cold PBS, followed by suspending in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) to isolate nucleis.
Isolated nuclei were then tagmented with Tn5 transposase and libraries were constructed using TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme TD501). Amplified libraries were purified using MinElute columns and quantified with a Bioanalyzer using high-sensitivity DNA chips (Agilent 2100). ATAC-seq libraries were pooled and sequenced using an Illumina NovaSeq 6000 platform with paired-end reads of 150 bases.

value: Tdg Trp53 DKO


title: Cas9-SLCxSLC_week1_rep2

description: Combinatorial Cas9 library


title: B16_TdgTrp53_DKO1 ATAC-seq

value: Melanoma


title: Cas9-SLCxSLC_week1_rep1

description: Combinatorial Cas9 library


title: B16_Trp53KO ATAC-seq

value: Trp53 KO


title: B16_TdgKO ATAC-seq


title: B16_WT ATAC-seq


title: Cas12a-SLCxEnzyme_week5_hyp_rep3

description: Combinatorial Cas12a library

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06WS-Q)

value: Contains lentiviral enCas12 expression contruct pRDA_174 (Addgene #136476)

value: hyp:Incubated with 1% oxygen (4 weeks)


title: Cas12a-SLCxEnzyme_week5_hyp_rep2

description: Combinatorial Cas12a library


title: Cas12a-SLCxEnzyme_week5_hyp_rep1

description: Combinatorial Cas12a library


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t24, 2000U, 50C

description: MNase-seq

value: Human embryonic kidney cells

value: WT

value: HBV cccDNA transfected

value: 24 hr, 2000 Units MNase, 50C OligoCapture


title: Cas12a-SLCxEnzyme_week5_ant_rep3

description: Combinatorial Cas12a library

value: ant:50 mM antimycin A (4 weeks)


title: Cas9-SLCxEnzyme_week2_rep1

description: Combinatorial Cas9 library


title: Cas9-SLCxEnzyme_week1_rep3

description: Combinatorial Cas9 library


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t24, 1000U, 50C

description: MNase-seq

value: 24 hr, 1000 Units MNase, 50C OligoCapture


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t24, 0500U, 50C

description: MNase-seq

value: 24 hr, 500 Units MNase, 50C OligoCapture


title: Cas12a-SLCxEnzyme_week5_gal_rep2

description: Combinatorial Cas12a library

value: Human colorectal carcinoma cell line

value: gal:Glucose in medium replaced by galactose (4 weeks)


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t04, 2000U, 50C

description: MNase-seq

value: 04 hr, 2000 Units MNase, 50C OligoCapture


title: Cas12a-SLCxEnzyme_week5_gal_rep1

description: Combinatorial Cas12a library

value: cell line


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t24, 0250U, 50C

description: MNase-seq

value: 24 hr, 250 Units MNase, 50C OligoCapture


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t04, 0500U, 50C

description: MNase-seq

value: 04 hr, 500 Units MNase, 50C OligoCapture


title: Cas12a-SLCxEnzyme_week5_glu_rep2

description: Combinatorial Cas12a library


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t04, 0250U, 50C

description: MNase-seq

value: 04 hr, 250 Units MNase, 50C OligoCapture


title: WT_root_2

description:
Gene expression in root tissues
SAMPLE 5

value: root tissues


title: Cas12a-SLCxEnzyme_week5_glu_rep3

description: Combinatorial Cas12a library

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06WS-Q)

value: Contains lentiviral enCas12 expression contruct pRDA_174 (Addgene #136476)


title: Cas12a-SLCxEnzyme_week5_glu_rep1

description: Combinatorial Cas12a library


title: Cas9-SLCxSLC_week2_rep1

description: Combinatorial Cas9 library

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06MZ-1)

value: Contains lentiviral Cas9 expression contruct lentiCas9-Blast (Addgene #52962)


title: MNase-seq,HEK293T cells, mock transfection, t0, 2000U, 50C

description: MNase-seq

value: Human embryonic kidney cells

value: WT

value: mock transfection

value: 00 hr, 2000 Units MNase, 50C OligoCapture


title: MNase-seq,HEK293T cells, mock transfection, t0, 1000U,50 C

description: MNase-seq

value: 00 hr, 1000 Units MNase, 50C OligoCapture


title: Cas12a-SLCxEnzyme_week3_hyp_rep3

description: Combinatorial Cas12a library

value: Human colorectal carcinoma cell line

value: hyp:Incubated with 1% oxygen (2 weeks)


title: MNase-seq,HEK293T cells, mock transfection, t0, 0500U, 50C

description: MNase-seq

value: 00 hr, 500 Units Mnase, 50C OligoCapture


title: Cas12a-SLCxEnzyme_week3_hyp_rep2

description: Combinatorial Cas12a library

value: cell line


title: Cas12a-SLCxEnzyme_week3_hyp_rep1

description: Combinatorial Cas12a library


title: MNase-seq,HEK293T cells, mock transfection, t0, 0250U, 50C

description: MNase-seq

value: 00 hr, 250 Units Mnase, 50C OligoCapture


title: Cas12a-SLCxEnzyme_week3_ant_rep3

description: Combinatorial Cas12a library

value: ant:50 mM antimycin A (2 weeks)


title: MNase-seq, HepAD38,500 nM CBL137 1000 U, rep 3

description: MNase-seq

value: Human hepatoma cell line with integrated HBV genome expressed under the control of a tetracycline repressor

value: not applicable

value: 1000 Units MNase


title: Cas12a-SLCxEnzyme_week5_gal_rep3

description: Combinatorial Cas12a library

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06WS-Q)

value: Contains lentiviral enCas12 expression contruct pRDA_174 (Addgene #136476)

value: gal:Glucose in medium replaced by galactose (4 weeks)


title: MNase-seq, HepAD38,500 nM CBL137 1000 U, rep 2

description: MNase-seq


title: Cas12a-SLCxEnzyme_week5_ant_rep2

description: Combinatorial Cas12a library

value: ant:50 mM antimycin A (4 weeks)


title: MNase-seq, HepAD38,500 nM CBL137 1000 U, rep 1

description: MNase-seq

value: WT


title: Cas12a-SLCxEnzyme_week5_ant_rep1

description: Combinatorial Cas12a library


title: MNase-seq, HEK293T cells, HBV cccDNA transfection, t04, 1000U, 50C

description: MNase-seq

value: Human embryonic kidney cells

value: HBV cccDNA transfected

value: 04 hr, 1000 Units MNase, 50C OligoCapture


title: Cas12a-SLCxEnzyme_week3_gal_rep3

description: Combinatorial Cas12a library

value: Human colorectal carcinoma cell line

value: gal:Glucose in medium replaced by galactose (2 weeks)


title: MNase-seq, HepAD38, 500 nM CBL137, 125 U, rep 3

description: MNase-seq

value: 125 Units MNase


title: MNase-seq, HepAD38, 500 nM CBL137, 125 U, rep 1

description: MNase-seq


title: Cas12a-SLCxEnzyme_week3_gal_rep1

description: Combinatorial Cas12a library

value: cell line


title: Cas12a-SLCxEnzyme_week3_gal_rep2

description: Combinatorial Cas12a library


title: Cas12a-SLCxEnzyme_week3_ant_rep1

description: Combinatorial Cas12a library


title: Cas12a-SLCxEnzyme_week3_glu_rep3

description: Combinatorial Cas12a library


title: MNase-seq, HepAD38, 500 nM CBL137, 125 U, rep 2

description: MNase-seq


title: Cas12a-SLCxEnzyme_week1_rep3

description: Combinatorial Cas12a library


title: MNase-seq, HepAD38, DMSO, 1000 U, rep 1

description: MNase-seq


title: MNase-seq, HepAD38, DMSO, 125 U, rep 3

description: MNase-seq


title: MNase-seq, HepAD38, DMSO, 1000 U, rep 2

description: MNase-seq


title: MNase-seq, HepAD38, DMSO, 1000 U, rep 3

description: MNase-seq


title: Cas12a-SLCxEnzyme_week3_glu_rep2

description: Combinatorial Cas12a library


title: Cas12a-SLCxEnzyme_week3_glu_rep1

description: Combinatorial Cas12a library


title: MNase-seq, HepAD38, DMSO, 125 U, rep 2

description: MNase-seq


title: Cas12a-SLCxEnzyme_week1_rep2

description: Combinatorial Cas12a library


title: Cas12a-SLCxEnzyme_week1_rep1

description: Combinatorial Cas12a library


title: Cas12a-SLCxEnzyme_week3_ant_rep2

description: Combinatorial Cas12a library


title: MNase-seq, HepAD38, DMSO, 125 U, rep 1

description: MNase-seq


title: Cas12a-SLCxSLC_sublib3_4_week5_rep3

description: Combinatorial Cas12a library


title: MNase-seq, HepG2.2.15 cells, 100U

description: MNase-seq

value: Human hepatoma cell line with integrated HBV genome constitutively expressed

value: 100 Units MNase


title: Maternal side placenta tissue of participant A034

type: genomic

city: Philadelphia

first: Jagadeesh

last: Puvvula

state: Pennsylvania

address: 423 Guardian Drive

department: Department of Biostatistics, Epidemiology, and Informatics

institute: University of Pennsylvania

hyb_protocol: Bisulfite conversion of the DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA), and DNA methylation levels were measured using Infinium HumanMethylation450K BeadChip (Illumina, San Diego, CA) using standard protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and following the standard recommended Illumina scanner setting.

data_processing: Raw methylation data was processing using the minfi bioconductor package. Quality control steps includes, removing samples with >5% high detection p-values (p-value >1e-7) and probes failed in one or more samples with the same cut-off. Background correction with dye-bias normalization was performed using normal-exponential out-of-band method. Bias from type-2 prob values was normalized using beta-mixture quantile normalization methods. Additionally, batch effects were corrected using an empirical Bayes framework. We also removed the CpGs located on sex chromosomes, enriched at single-nucleotide polymorphisims, and those prone to cross-reativity.

label: Cy3 and Cy5

source_name: Pregnant individual at delivery visit

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using a DNeasy Blood and Tissue kit with RNase A, following the manufacturer's protocols. DNA was then prepared for the array following the Illumina Infinium HD Assay Methylation Protocol Guide

value: Maternal side placenta tissue


title: Fetal side placenta tissue of participant A034

value: Fetal side placenta tissue


title: Cord blood mono nuclear cells of participant A034

value: Cord blood mono nuclear cells


title: Cas12a-SLCxSLC_sublib3_4_week3_rep3

description: Combinatorial Cas12a library

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06WS-Q)


title: Cas12a-SLCxSLC_sublib3_4_week5_rep1

description: Combinatorial Cas12a library

value: Contains lentiviral enCas12 expression contruct pRDA_174 (Addgene #136476)


title: Cas12a-SLCxSLC_sublib3_4_week5_rep2

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A023


title: Cas12a-SLCxSLC_sublib3_4_week3_rep1

description: Combinatorial Cas12a library


title: MNase-seq, HepG2.2.15 cells, 250U

description: MNase-seq

value: not applicable

value: 250 Units MNase


title: Cord blood mono nuclear cells of participant A023


title: Cas12a-SLCxSLC_sublib4_week2_rep1

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib4_week2_rep2

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib3_4_week3_rep2

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A017


title: Cas12a-SLCxSLC_sublib3_week2_rep3

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib3_week2_rep2

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A022


title: Fetal side placenta tissue of participant A023


title: Cas12a-SLCxSLC_sublib4_week2_rep3

description: Combinatorial Cas12a library


title: Cord blood mono nuclear cells of participant A017


title: Cas12a-SLCxSLC_sublib3_4_week1_rep3

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib3_week2_rep1

description: Combinatorial Cas12a library


title: Cord blood mono nuclear cells of participant A022


title: Fetal side placenta tissue of participant A022


title: Maternal side placenta tissue of participant A013


title: Cas12a-SLCxSLC_sublib3_4_week1_rep2

description: Combinatorial Cas12a library


title: Fetal side placenta tissue of participant A013


title: Cas12a-SLCxSLC_sublib3_4_week1_rep1

description: Combinatorial Cas12a library


title: Cord blood mono nuclear cells of participant A013


title: Cas12a-SLCxSLC_sublib2_week5_rep3

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib2_week5_rep2

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A012


title: Cas12a-SLCxSLC_sublib2_week3_rep3

description: Combinatorial Cas12a library


title: Fetal side placenta tissue of participant A012


title: Cas12a-SLCxSLC_sublib2_week5_rep1

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A011


title: Cas12a-SLCxSLC_sublib2_week3_rep1

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib2_week2_rep3

description: Combinatorial Cas12a library


title: Fetal side placenta tissue of participant A010


title: Cas12a-SLCxSLC_sublib2_week2_rep1

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A010


title: Cord blood mono nuclear cells of participant A011


title: Fetal side placenta tissue of participant A011


title: Fetal side placenta tissue of participant A017


title: Cas12a-SLCxSLC_sublib2_week1_rep3

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib2_week2_rep2

description: Combinatorial Cas12a library


title: Fetal side placenta tissue of participant A008


title: Cas12a-SLCxSLC_sublib2_week1_rep1

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A008


title: Cord blood mono nuclear cells of participant A010


title: Cas12a-SLCxSLC_sublib1_week5_rep3

description: Combinatorial Cas12a library


title: Cord blood mono nuclear cells of participant A008


title: Cas12a-SLCxSLC_sublib2_week1_rep2

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A007


title: Cas12a-SLCxSLC_sublib1_week5_rep2

description: Combinatorial Cas12a library


title: Fetal side placenta tissue of participant A007


title: Cas12a-SLCxSLC_sublib1_week3_v0_rep3

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib1_week5_rep1

description: Combinatorial Cas12a library


title: Cord blood mono nuclear cells of participant A012


title: Cord blood mono nuclear cells of participant A007


title: Cas12a-SLCxSLC_sublib2_week3_rep2

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib1_week3_v0_rep2

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A006


title: Fetal side placenta tissue of participant A006


title: Cas12a-SLCxSLC_sublib1_week3_v0_rep1

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib1_week2_rep3

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib1_week2_rep2

description: Combinatorial Cas12a library