title: PEM-seq_HEK293T_Nme2-C.NR_VEGFA

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the VEGFA locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: PEM-seq_HEK293T_AsCpf1_VEGFA

status: Public on Jan 01 2025

type: SRA

city: Beijing

first: Changchang

last: Xin

state: Beijing

address: No.5 Yiheyuan Road Haidian District,Beijing,P.R.China

country: China

institute: Peking University

library_source: genomic

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg38
Supplementary files format and content: tab file
Library strategy: PEM-seq

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Followed the PEM-seq protocol that described in Yin et al., 2019.
Followed the PEM-seq protocol that described in Yin et al., 2019.

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the VEGFA locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

value: WT

tag: treatment

value: plasmid transfection

tag: crispr-cas nuclease

tag: editing site

value: VEGFA


title: PEM-seq_HEK293T_ISDra2_MLH1

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the MLH1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: 5hmC_Seal SEQ23014

city: Shanghai

first: Yixiang

last: Shi

address: Room 303, Building #1, 928 Shenhong Road

institute: Accrete Covenant (AC) (Shanghai) Medical Technology Co., Ltd.

data_processing:
raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Assembly: hg19
Supplementary files format and content: 5hmC_Count_Matrix.csv
Library strategy: 5hmC-Seal

source_name: Plasma

extract_protocol:
Blood samples were prospectively collected for analysis at before the first cycle of chemotherapy. Approximately ~5 mL blood was collected for each patient. Plasma was separated within 2 hrs after blood draw, followed by extraction of circulating cfDNA using the Qiagen Circulating DNA Isolation Kit. DNA quality and quantity was examined with standard molecular protocols. High-quality cfDNA samples were frozen at -80C before library construction for the 5hmC-Seal pull-down.
Tagmentation reactions were performed in a 50ml solution with 1X tagmentation buffer from Nextera DNA Sample Preparation Kit (FC-121-1031). The input DNA ranged from 5 ng to 50 ng. Reactions were performed and purified according to the manufacturer’s instruction. In brief, the fragmentation reaction was performed in 50 ml solutions containing 25 ml 23 tagmentation buffer, gDNA, and 0.5-5 X l Tagmentase, at 55℃ for 5 min. The fragmented DNA was eluted into 17.5 ml ddH2O. The glucosylation reactions were performed in a 20 ml solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, purified DNA, 100 mM N3-UDP-Glc, and 1 mM bGT, at 37℃ for 1 hr. After the reaction, 2 ml DBCO-PEG4-DBCO (Click Chemistry Tools, 20 mM stock in DMSO) was added to the reaction mixture, and the mixture was incubated at 37℃ for 2 hr. Next, the modified DNA was purified by a Micro Bio-Spin 30 Column (Bio-Rad). The purified DNA was incubated with 5 ml C1 Streptavidin beads (Life Technologies) in 23 buffer (13 buffer: 5 mM Tris [pH 7.5], 0.5 mM EDTA, and 1 M NaCl) for 15 min according to the manufacture’s instruction. The beads were subsequently undergone six 5 min washes with 1X buffer. All binding and washing were done at room temperature with gentle rotation. The captured DNA fragments were amplified with 12–17 cycles of PCR amplification using the enzyme mix supplied in the Nextera kit. The PCR products were purified using AMPure XP beads according to the manufacture’s instruction. Separate input libraries were made by direct PCR from fragmented DNA without labeling and capture according to the manufacture’s instruction in the Nextera kit.
Briefly, each cfDNA sample was first prepared and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase (β-GT) was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then installed onto the azide group using Huisgen cycloaddition (“Click”) chemistry, followed by capturing of 5hmC-containing DNA fragments using avidin beads. The 5hmC-Seal library for DNA sample was then constructed through PCR amplification, followed by paired-end sequencing (PE38) on the Illumina Next-Seq 500 platform at Shanghai Epican Genetech, Ltd. (Shanghai, China).

tag: population

value: Chinese

tag: patient id

tag: tissue

value: Plasma


title: Hep_rep2_H3K36me3

city: Tokyo

first: Takeshi

last: Katsuda

address: 7-chōme-3-1 Hongō

department: Department of Chemical System Engineering

country: Japan

institute: University of Tokyo

data_processing:
Reads were trimmed using Cutadapt with parameters “-j 4 --nextseq-trim 20 -m 15” before alignment to the mouse genome (mm10) using Bowtie2 with parameters “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 4.” The resulting sequence alignment files were sorted, and duplicates were removed using Picard (https://broadinstitute.github.io/picard/). The BAM files were then converted to BED files using BEDTools (https://bedtools.readthedocs.io/en/latest/)  with the bamtobed function with option “-bedpe.” Data was filtered to keep read pairs on the same chromosome and with a fragment length <1000 bp. For peak calling, the BEDTools genomecov tool was used to generate BedGraph files. For visualization using IGV and deepTools, the BAM files were converted to BigWig files using the bamCoverage function with options “--binSize 5 --effectiveGenomeSize 2652783500 --normalizeUsing RPGC --extendReads" and then replicates were merged using the bigWigMerge function followed by the bedGraphToBigWig function (UCSC tools).
Peak calling was conducted on the individual BedGraph files using SEACR with options “0.01 norm stringent.”  Downstream analysis was conducted DiffBind. Replicates were processed with default counting and normalization parameters with the option “minMembers=2” and the mm10 blacklist was used.
Assembly: mm10
Supplementary files format and content: BED files (for peaks), BigWig files (for genome tracks)
Library strategy: CUT&Tag

organism: Mus musculus

source_name: Liver

growth_protocol: For characterization of the reprogramming stage, 4-5 week-old mice were retro-orbitally injected with AAV:ITR-U6-sgRNA(backbone)-TBG-Cre-WPRE-hGHpA-ITR with 5 × 1011 genome copies/mouse/gene.

extract_protocol:
CUT&Tag was performed following EpiCypher® CUTANA™ CUT&RUN Protocol v1.7 with minor modifications. Cells at different stages of biliary reprogramming were harvested from the Cas9-EGFP mice challenged with 0.1% DDC for 8-9 weeks by FACS (n = 2-3).
The universal i5 primer, barcode i7 primer, and 25CUTANA High Fidelity 2X PCR Master Mix for CUT&Tag (EpiCypher) were used, and PCR was performed (1 cycle of 20 °C for 5 min; 1 cycle of 72 °C for 5 min; 1 cycle of 98 °C for 45 s, 14–21 cycles of 98 °C for 15 s and 60 °C for 10 s; 72 °C for 1 min). The DNA was cleaned up with 1.3× AMPure XP beads.  Sequencing was performed using a NextSeq2000 with 55 bp paired-end reads.

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo). Eight weeks after the DDC challenge, reprogrammed cells and biliary cells were harvested.

value: Liver

tag: group

value: Hep


title: EV_Early_Reprogrammed_Rep7

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome (GRCm39) using STAR aligner with default parameters
Gene-count matrices were produced by featureCounts.
Assembly: GRCm39
Supplementary files format and content: BAM files (sequencing reads and alignment), Counts table

molecule: polyA RNA

extract_protocol:
RNA was isolated with Nucleospin RNA kit (Takara)
Libraries were prepared and sequenced by Novogene (Sacramento, CA)

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo).

tag: batch

tag: phenotype

value: Early Reprogrammed


title: EV_Late_Reprogrammed_Rep7

value: Late Reprogrammed


title: Hep_rep2_H3K27me3


title: Nsd1KO_Late_Reprogrammed_Rep1


title: 5hmC_Seal SEQ23070


title: PEM-seq_HEK293T_CasMINI_VEGFA

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the VEGFA locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: CasMINI


title: WT 75 days

city: Paris

first: Lorenzo

last: Giordani

address: 105 bld de l'hôpital

department: Centre de Recherche en Myologie - UMRS974 Sorbonne Université

country: France

institute: INSERM

description:
Frozen Spatial Transcriptome sequencing
ID2237_A1_WT_75_1

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
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 tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots

source_name: skeletal-muscle- Tibialis Anterior and Extensor Digitorum Longus

extract_protocol:
TA and EDL muscles were isolated, embedded in OCT (VWR), and flash frozen in liquid nitrogen
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

tag: age

value: 75 days


title: 5hmC_Seal SEQ23106


title: Hep_rep2_H3K36me1


title: PEM-seq_HEK293T_ISDra2_VEGFA

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the VEGFA locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: PEM-seq_HEK293T_control_VEGFA

treatment_protocol: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.

value: control


title: PEM-seq_HEK293T_ISYmu1_VEGFA

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the VEGFA locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.


title: EV_Late_Reprogrammed_Rep6


title: 5hmC_Seal SEQ23115


title: PEM-seq_HEK293T_control_TIGIT

value: TIGIT


title: 5hmC_Seal SEQ23108


title: 5hmC_Seal SEQ23034


title: 5hmC_Seal SEQ23103


title: Hep_rep2_H3K27ac


title: Nsd1KO_Early_Reprogrammed_Rep1


title: PEM-seq_HEK293T_ISAam1_VEGFA

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the VEGFA locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: EV_Early_Reprogrammed_Rep6


title: 5hmC_Seal SEQ23012


title: EV_Early_Reprogrammed_Rep5


title: Hep_rep1_H4K20me3


title: Hep_rep1_H4K20me2


title: Hep_rep1_H4K20me1


title: EV_Late_Reprogrammed_Rep5


title: PEM-seq_HEK293T_SpCas9_TIGIT

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting TIGIT locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: Hep_rep1_H3K4me2_CUTAC


title: Hep_rep1_H3K4me1


title: PEM-seq_HEK293T_AsCpf1_TIGIT

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the TIGIT locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.


title: 5hmC_Seal SEQ23105


title: Hep_rep1_H3K4me3


title: PEM-seq_HEK293T_Nme2-C.NR_TIGIT

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the TIGIT locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: EV_Early_Reprogrammed_Rep4


title: Hep_rep1_H3K36me3


title: PEM-seq_HEK293T_ISYmu1_TIGIT

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the TIGIT locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.


title: 5hmC_Seal SEQ23100


title: PEM-seq_HEK293T_ISAam1_TIGIT

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the TIGIT locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: Kdm2aKO_Early_Reprogrammed_Rep4


title: 5hmC_Seal SEQ23087


title: PEM-seq_HEK293T_CasMINI_TIGIT

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the TIGIT locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: 5hmC_Seal SEQ23064


title: Kdm2aKO_Late_Reprogrammed_Rep3


title: PEM-seq_HEK293T_ISDra2_TIGIT

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the TIGIT locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: 5hmC_Seal SEQ23068


title: Hep_rep0_H3K36me3


title: PEM-seq_HEK293T_AsCpf1_TET3

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the TET3 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.


title: EV_Late_Reprogrammed_Rep3


title: 5hmC_Seal SEQ23073


title: 5hmC_Seal SEQ23030


title: Hep_rep1_H3K36me1


title: EV_Late_Reprogrammed_Rep4


title: Kdm2aKO_Early_Reprogrammed_Rep3


title: Hep_rep1_H3K27me3


title: 5hmC_Seal SEQ23039


title: Kdm2aKO_Early_Reprogrammed_Rep2


title: PEM-seq_HEK293T_CasMINI_TET3

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the TET3 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: BEC_rep3_H3K36me1

value: BEC


title: 5hmC_Seal SEQ23059


title: Hep_rep1_H3K27ac


title: PEM-seq_HEK293T_SpCas9_TET3

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting TET3 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: PEM-seq_HEK293T_ISDge10_TET3

treatment_protocol: The cells were transfected with the gRNA-ISDge10 plasmid targeting the TET3 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDge10 plasmid) on Day 3.


title: 5hmC_Seal SEQ23032


title: BEC_rep2_H4K20me3

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo). Eight weeks after the DDC challenge, reprogrammed cells and biliary cells were harvested.


title: PEM-seq_HEK293T_Nme2-C.NR_TET3

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the TET3 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: Kdm2aKO_Late_Reprogrammed_Rep2

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo).


title: EV_Early_Reprogrammed_Rep1


title: BEC_rep3_H3K36me3


title: PEM-seq_HEK293T_ISDra2_TET3

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the TET3 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: 5hmC_Seal SEQ23110


title: EV_Early_Reprogrammed_Rep3


title: 5hmC_Seal SEQ23097


title: 5hmC_Seal SEQ23029


title: 5hmC_Seal SEQ23082


title: EV_Late_Reprogrammed_Rep2


title: BEC_rep2_H4K20me2


title: BEC_rep2_H3K4me1


title: BEC_rep2_H4K20me1


title: PEM-seq_HEK293T_ISYmu1_TET3

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the TET3 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.


title: PEM-seq_HEK293T_ISAam1_TET3

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the TET3 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: EV_Early_Reprogrammed_Rep2


title: EV_Late_Reprogrammed_Rep1


title: PEM-seq_HEK293T_control_TET3

treatment_protocol: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.


title: BEC_rep2_H3K4me3


title: 5hmC_Seal SEQ23036


title: Kdm2aKO_Late_Reprogrammed_Rep1


title: 5hmC_Seal SEQ23028


title: PEM-seq_HEK293T_AsCpf1_KCNMA1

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the KCNMA1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.


title: BEC_rep2_H3K36me1


title: 5hmC_Seal SEQ22341


title: BEC_rep2_H3K36me3


title: PEM-seq_HEK293T_SpCas9_KCNMA1

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting KCNMA1 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: BEC_rep2_H3K27me3


title: 5hmC_Seal SEQ23088


title: Three pooled e15.5 eye cups from Rx>cre Myrf fl/fl strain

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

country: USA

institute: University of Michigan

library_source: transcriptomic single cell

data_processing:
Sequencing outputs were demultiplexed using 10x Genomics Cell Ranger 7.1.0 software and FASTQ files were aligned to the Genome Reference Consortium Mouse Build 38, mm10 genome (Church et al., 2009; Mouse Genome Sequencing et al., 2002; Zheng et al., 2017, https://genomes.ucsc.edu).
Seurat/4.1.1 (Butler et al., 2018; Stuart et al., 2019) scRNAseq software was utilized to normalize data using the NormalizeData and FindVariableFeatures commands with nfeatures set to 2000. Poor quality cells were removed using cutoffs of nFeature_RNA < 200 and % mitochondrial RNA >15%. Doublet cells were considered those with nCounts > 2000 and removed from the study.
Data from all time points and genotypes was anchored and integrated prior to scaling, principal component analysis and Uniform Manifold Approximation and Projection (UMAP) clustering.
Assembly: Genome Reference Consortium Mouse Build 38, mm10 genome
Supplementary files format and content: zipped versions of the matrix tables, with list of barcodes (column names for matrix) and features (i.e. genes, row names for matrix)

source_name: eye cup

extract_protocol:
Eyes were collected from e13.5, e15.5, and P0 litters, the cornea, lens, and optic nerve were removed, and the eyecups were place on ice in 1 X HBSS (Invitrogen, 14175095) while samples were genotyped using a rapid genotyping protocol (Truett et al., 2000). Three Myrffl/fl and three Rx>cre Myrffl/fl samples were pooled for each time point.  Eyecups were dissociated into single cells in a Papain solution containing 5mM L Cysteine (Sigma, C7352), 1mM EDTA (Sigma, E4884), 0.6 mM 2-mercaptoethanol (Sigma, M6250), and 1mg/ml Papain (Roche, 10108014001) for 10 minutes at 37°C with trituration every 2 minutes.  The dissociation was stopped using Neurobasal Media (Invitrogen, 12348017) with 10% Fetal Bovine Serum (FBS) (Corning, MT35010CV), single cells were collected by centrifugation for 5 minutes at 300 RCF at 4°C.  The supernatant was aspirated, and the single cells were resuspended in cold Neurobasal Media with 3% FBS.
Single cell libraries were prepared by the University of Michigan Advanced Genomics Core and sequencing was performed using the 10X Genomics Chromium platform using manufacturer’s protocol for 10x Single Cell Expression 3’ and sequenced on the NovaSeq (S4) 300 cycle (Illumina, San Diego, CA).

value: eye cup

value: Total eye cup cells

value: Rx>cre Myrf fl/fl


title: PEM-seq_HEK293T_CasMINI_KCNMA1

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the KCNMA1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: Human embryonic kidney

value: WT


title: BEC_rep2_H3K4me2_CUTAC


title: Three pooled P0 eye cups from Myrf fl/fl strain

value: Myrf fl/fl


title: PEM-seq_HEK293T_ISDge10_KCNMA1

treatment_protocol: The cells were transfected with the gRNA-ISDge10 plasmid targeting the KCNMA1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDge10 plasmid) on Day 3.

value: plasmid transfection


title: 5hmC_Seal SEQ23026

value: Chinese

value: Plasma


title: 5hmC_Seal SEQ23079


title: BEC_rep2_H3K27ac

value: Liver


title: PEM-seq_HEK293T_ISDra2_KCNMA1

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the KCNMA1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: BEC_rep1_H4K20me3


title: 5hmC_Seal SEQ22972


title: Three pooled e13.5 eye cups from Rx>cre Myrf fl/fl strain


title: BEC_rep1_H4K20me2


title: Three pooled P0 eye cups from Rx>cre Myrf fl/fl strain


title: PEM-seq_HEK293T_ISYmu1_KCNMA1

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the KCNMA1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.


title: PEM-seq_HEK293T_ISAam1_KCNMA1

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the KCNMA1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: BEC_rep1_H4K20me1


title: PEM-seq_HEK293T_Nme2-C.NR_KCNMA1

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the KCNMA1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: 5hmC_Seal SEQ23015


title: BEC_rep1_H3K4me3


title: 5hmC_Seal SEQ23085


title: PEM-seq_HEK293T_control_KCNMA1


title: Heart, HFD, Renin, rep5

city: Philadelphia

first: Daniel

last: Kelly

state: PA

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
We used Salmon v1.10.2 to count reads in GRCm38 (mm10) reference transcripts
The counts were summarized at gene level and differentially expressed genes were identified with DESeq2 1.40.2
Assembly: GRCm38
Supplementary files format and content: *raw_counts.tsv: Salmon transcript-level count for the sample, tab-separated values
Supplementary files format and content: data_matrix.tsv: FPKM values and statistical test results from DESeq2, tab-separated values

molecule: total RNA

source_name: Heart

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) and the RNase-Free DNase Set (QIAGEN) according to the manufacturer’s instructions. cDNA was synthesized using the Affinity Script cDNA Synthesis Kit (Agilent Technologies) with 0.25 μg total RNA.
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ), per their standard operating procedure

value: Heart

tag: diet

value: HFD

value: Renin


title: PEM-seq_HEK293T_SpCas9_TET2

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting TET2 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: Heart, HFD, Renin, rep4


title: Three pooled e15.5 eye cups from Myrf fl/fl strain


title: Heart, HFD, Renin, rep3


title: 5hmC_Seal SEQ23071


title: PEM-seq_HEK293T_AsCpf1_TET2

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the TET2 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.


title: 5hmC_Seal SEQ23007


title: BEC_rep1_H3K4me1

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo). Eight weeks after the DDC challenge, reprogrammed cells and biliary cells were harvested.


title: 5hmC_Seal SEQ23094


title: PEM-seq_HEK293T_Nme2-C.NR_TET2

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the TET2 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: Heart, HFD, Renin, rep2


title: 5hmC_Seal SEQ23016


title: Three pooled e13.5 eye cups from Myrf fl/fl strain


title: Heart, HFD, Renin, rep1


title: PEM-seq_HEK293T_CasMINI_TET2

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the TET2 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: CasMINI


title: 5hmC_Seal SEQ23162


title: BEC_rep1_H3K36me1


title: BEC_rep1_H3K36me3


title: Heart, HFD, novirus, rep6

value: novirus


title: PBMC of patient #28 after TTF treatment

city: SOUTH PASADENA

first: SON

middle: B

last: LE

state: CA

address: 1645 Amberwood Drive, Unit 11

institute: University of Southern California

data_processing:
Conversion of the raw sequencing data from the bcl to fastq format and the subsequent alignment to the reference genome GRCh38 (GENCODE v.24) and gene count were performed using the cellranger software (10x Genomics, version 4.0.0) with the command cellranger mkfastq, the STAR aligner, and the command cellranger count, respectively.
Results from all libraries and batches were pooled together using the command cellranger aggr without normalization for dead cells as it will be handled downstream.
UMAP coordinates calculations were performed by using Seurat package (3.2.2), using top 75 PCA principle components as input features.
Cell clustering was  done using graph-based clustering approach implemented in the Seurat package(3.2.2) with command FindClusters
Genome_build: hg38
Supplementary_files_format_and_content: barcodes.tsv cell barcodes for all samples
Supplementary_files_format_and_content: features.tsv features for all samples
Supplementary_files_format_and_content: matrix.mtx Filtered feature-barcode matrices  in  sparse matrix MEX format for all samples
Supplementary_files_format_and_content: cell_metadata.txt metadata for each single cell, including information about cell barcode , nCount_RNA, nFeature_RNA  , percent.mt,  percent.tubulinA ,  library_id, patient , timepoint , batch, seurat_clusters, UMAP_1, UMAP_2 in tab -delimited text format
Supplementary_files_format_and_content: seurat_object.RDS seurat object file in RDS R object serialized format

source_name: Peripheral blood mononuclear cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from blood by density gradient centrifugation (Ficoll-Hypaque) and cryopreserved at liquid nitrogen until processed.

extract_protocol:
Frozen PBMC samples were quickly taken from liquid nitrogen and counted 1.2e4 cells putting on a 10x Chromium instrument (10x Genomics) to export labeled RNA fragments using Chromium Single Cell 3′ v3 Reagent Kit (PN-1000075).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v3 library construction Kit (PN-1000075)
End repair, A-tailing, adaptor ligation

treatment_protocol: Blood was draw before and one month after TTField plus TMZ treatment started

tag: sample id

tag: sample collection time

value: post  TTFields +TMZ

tag: disease

value: Glioblastoma


title: PEM-seq_HEK293T_ISDra2_TET2

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the TET2 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.

tag: cell line


title: PBMC of patient #28 before TTF treatment

value: pre TTFields +TMZ


title: Heart, HFD, novirus, rep4


title: BEC_rep1_H3K27ac

value: BEC


title: PEM-seq_HEK293T_ISYmu1_TET2

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the TET2 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.

tag: cell type


title: BEC_rep1_H3K4me2_CUTAC

tag: genotype


title: NRVMs, KLF2 overexpression

city: ShenZhen

first: Juan

last: Huang

address: Langshan Road

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences

description: Library name: Klf2-OE

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore.
Trimmed sequence reads were mapped to mratbn7.2 using STAR.
Read count extraction was performed using featureCounts
Assembly: mratbn7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

organism: Rattus norvegicus

source_name: NRVMs

growth_protocol: NRVMs were maintained in DMEM medium containing 1% Insulin-Transferrin-Selenium (ITSS-10201, OriCell, China) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using Quick-RNA Microprep Kit (R1050, ZYMO RESEARCH, USA). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations.

treatment_protocol: The cardiac hypertrophy model was established by treating with 100 µM PE (HY-B0769, MedChemExpress, USA) for 36 hours in NRVMs.To investigate whether KLF2  deficiency aggravates cardiac hypertrophy, NRVMs were infected with siNeg or siKlf2 for 12 hours and subsequently treated with or without PE for 36 hours; To explore whetherKLF2 overexpression attenuates cardiac hypertrophy, NRVMs were treated with or without PE for 12 hours and subsequently infected with Ad-GFP or Ad-Klf2 for another 24 hours.

value: NRVMs

value: neonatal rat ventricular myocytes


title: Heart, HFD, novirus, rep3

tag: treatment


title: PBMC of patient #25 after TTF treatment


title: PEM-seq_HEK293T_ISAam1_TET2

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the TET2 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.

value: Human embryonic kidney

value: WT

tag: crispr-cas nuclease


title: PBMC of patient #25 before TTF treatment


title: Heart, HFD, novirus, rep2


title: FPE RNA -R-case 129, RNA

type: RNA

city: Donostia-San Sebastián

first: María

last: Armesto

state: NorthEurope

address: Paseo Dr. Begiristain s/n

department: Molecular Oncology

country: Spain

institute: IIS Biogipuzkoa

description: gene expression data from RNA from FFPE RNA from ccRCC cases

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA processed in affymetrix TAC (v.4.0.3)

label: biotin

source_name: FFPE

label_protocol: standard Affymetrix protocol

growth_protocol: ccRCC were classified as responders and non responders to sunitinib treatment, RNA was extracted from FFPE biopsy material from ccRCC cases

extract_protocol: RNA was extracted from ccRCC cases using the RecoverAll kit according to manufacturers

tag: case

value: case 129

value: sunitinib responder

value: ccRCC


title: PEM-seq_HEK293T_control_TET2

treatment_protocol: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.

value: plasmid transfection

value: control

tag: editing site


title: FPE RNA -NR-case 110, RNA

value: case 110

value: sunitinib non-responder


title: Heart, HFD, novirus, rep1

value: Heart

value: HFD


title: PBMC of patient #24 after TTF treatment

value: post  TTFields +TMZ


title: PEM-seq_HEK293T_SpCas9_CBLB

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting CBLB locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.

value: CBLB


title: PBMC of patient #24 before TTF treatment

value: pre TTFields +TMZ

value: Glioblastoma


title: BEC_rep1_H3K27me3

value: Liver

value: BEC


title: Heart, HFD, novirus, rep5

value: novirus


title: FPE RNA -NR-case 102, RNA

value: case 102


title: PEM-seq_HEK293T_AsCpf1_CBLB

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the CBLB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.

value: Human embryonic kidney

value: WT


title: PEM-seq_HEK293T_ISDge10_TET2

treatment_protocol: The cells were transfected with the gRNA-ISDge10 plasmid targeting the TET2 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDge10 plasmid) on Day 3.


title: Heart, chow, Renin, rep6

value: chow

value: Renin


title: PBMC of patient #23 after TTF treatment


title: Heart, chow, Renin, rep5


title: PEM-seq_HEK293T_Nme2-C.NR_CBLB

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the CBLB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: plasmid transfection


title: PBMC of patient #23 before TTF treatment


title: FPE RNA -NR-case 99, RNA

value: case 99

value: ccRCC


title: PEM-seq_HEK293T_CasMINI_CBLB

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the CBLB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: CasMINI


title: FPE RNA -NR-case 72, RNA

value: case 72

value: sunitinib non-responder


title: Heart, chow, Renin, rep4

value: Heart


title: PBMC of patient #22 after TTF treatment

value: post  TTFields +TMZ


title: Heart, chow, Renin, rep3


title: PBMC of patient #22 before TTF treatment

value: pre TTFields +TMZ

value: Glioblastoma


title: PEM-seq_HEK293T_ISDge10_CBLB

treatment_protocol: The cells were transfected with the gRNA-ISDge10 plasmid targeting the CBLB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDge10 plasmid) on Day 3.

value: CBLB


title: FPE RNA -NR-case 44, RNA

value: case 44


title: Heart, chow, Renin, rep2


title: PEM-seq_HEK293T_ISDra2_CBLB

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the CBLB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: FPE RNA -R-case 43, RNA

value: case 43

value: sunitinib responder


title: Heart, chow, Renin, rep1


title: PBMC of patient #19 after TTF treatment


title: FPE RNA -R-case 103, RNA

value: case 103


title: Heart, chow, novirus, rep4

value: chow

value: novirus


title: FPE RNA -NR-case 33, RNA

value: case 33


title: PBMC of patient #19 before TTF treatment


title: PEM-seq_HEK293T_ISYmu1_CBLB

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the CBLB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.

value: Human embryonic kidney

value: WT

value: plasmid transfection


title: PEM-seq_HEK293T_ISAam1_CBLB

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the CBLB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: FPE RNA -NR-case 10, RNA

value: case 10

value: ccRCC


title: PEM-seq_HEK293T_control_CBLB

value: control


title: Heart, chow, novirus, rep3

value: Heart


title: PBMC of patient #18 after TTF treatment

value: post  TTFields +TMZ


title: PBMC of patient #18 before TTF treatment

value: pre TTFields +TMZ

value: Glioblastoma


title: Heart, chow, novirus, rep2


title: Kdm2aKO_Early_Reprogrammed_Rep1

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo).

value: Liver

value: Early Reprogrammed


title: FPE RNA -R-case 8, RNA

value: case 8

value: sunitinib responder


title: FPE RNA -NR-case 6 , RNA

value: case 6

value: sunitinib non-responder


title: Heart, chow, novirus, rep1

value: chow

value: novirus


title: PEM-seq_HEK293T_AsCpf1_APOB

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the APOB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.

value: Human embryonic kidney

value: WT

value: APOB


title: PBMC of patient #12 before TTF treatment

treatment_protocol: Blood was draw before and one month after TTField plus TMZ treatment started


title: shCux1 Ezh2i ENU Rep3

city: Chicago

first: Matthew

last: Jotte

address: 900 E 57th Street

institute: University of Chicago

description: Sample 39

data_processing:
Sequenced reads were aligned to the mm10 reference genome with STAR aligner. Differential gene expression analysis was conducted with DESeq2 (Love et al. 2014). Adjusted p-values were calculated with the Benjamini-Hochberg method. Genes with adjusted p-values less than 0.05 or 0.01 were used in downstream analyses.
Gene rank lists were calculated by multiplying the fold-change, -log10(pvalue), and sign of change. Rank lists were used to assess gene set enrichment (Subramanian et al. 2005).
Assembly: mm10
Supplementary files format and content: Jotte_featurecounts.txt is a raw count matrix of Samples 1-24. Jotte_ENU_featurecounts.txt is a raw count matrix of Samples 25-39.

source_name: Bone marrow

growth_protocol: Cells were grown on fibronectin-coated plates with either SFEM base media supplemented with 1% antibiotic/antimycotic and 50 ng/mL murine SCF, TPO, and FLT-3 ligand, or Ham's F12 nutrient mix supplemented with 10 mM HEPES, 1x Insulin-Transferrin-Selenium-Ethanolamine, 1 mg/mL polyvinyl alcohol, 1x penicillin-streptomycin-glutamine, 100 ng/mL murine TPO, and 10 ng/mL murine SCF. In both cases media was supplemented with 1.5 µg/mL doxycycline to insuce shRNA.

extract_protocol:
LSKs were sorted directly into TRIzol, and total RNA was extracted with Qiagen Rneasy micro columns.
Barcoded libraries were created by the University of Chicago Genomics Facility

treatment_protocol: Cells were cultured with 1.5 µg/mL doxycycline to induce shRNA and 1 µM tazemetostat to inhibit EZH2. After four days, tazemetostat was replenished and 0.025 mg/mL ENU was added for 72 hours.

value: Bone marrow

value: LSK

value: Tazemetostat, ENU


title: shCux1 Ezh2i ENU Rep2

description: Sample 38


title: PBMC of patient #16 after TTF treatment

value: post  TTFields +TMZ


title: PEM-seq_HEK293T_CasMINI_APOB

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the APOB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: plasmid transfection

value: CasMINI


title: PBMC of patient #16 before TTF treatment

value: pre TTFields +TMZ

value: Glioblastoma


title: PEM-seq_HEK293T_Nme2-C.NR_APOB

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the APOB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: PEM-seq_HEK293T_ISDge10_APOB

treatment_protocol: The cells were transfected with the gRNA-ISDge10 plasmid targeting the APOB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDge10 plasmid) on Day 3.


title: shCux1 Ezh2i ENU Rep1

description: Sample 37


title: Homo sapiens, Human non-small cell lung cancer cells, knock out CHD6, biol rep2

first: Yingji

last: Chen

address: 2005 Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

description:
Library name: KO2
Column name Counts.csv: KO2

data_processing:
The raw sequencing data was filtered using the Fastp software to discard sequences containing adapters and low-quality bases. The resulting clean data was then aligned to the human hg19 genome using HISAT2. Transcriptome assembly and gene expression quantification were performed using StringTie.
Assembly: hg19
Supplementary files format and content: Comma separated table count values of genes for each sample

source_name: lung cancer cells

growth_protocol: NCI-H1437 (Accession number:CVCL_1472; ATCC) were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS; Invitrogen, Carlsbad, CA, USA), penicillin (100U/mL; Invitrogen) and streptomycin (100 U/mL; Invitrogen). Cells were maintained at 37°C with 5% CO2. CBP60111

extract_protocol:
Total RNA was isolated from each sample using the TRIzol Total RNA Extraction Reagent Kit (Takara, Cat.No.DP424), with each sample yielding >2μg of total RNA.
Libraries were constructed by APExBIO according to the manufacturer's instructions for Illumina library preparation. Briefly, polyA-tailed mRNA was captured using oligo(dT) magnetic beads, the captured mRNA was fragmented, and then reverse transcribed and converted to double-stranded cDNA. The cDNA products were purified using the AMPure XP system (Beckman Coulter, Beverly, USA).

value: lung cancer cells

value: Human non-small cell lung cancer cells

value: Experiment group knock out CHD6


title: Homo sapiens, Human non-small cell lung cancer cells, knock out CHD6, biol rep3

description:
Library name: KO3
Column name Counts.csv: KO3


title: PEM-seq_HEK293T_ISDra2_APOB

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the APOB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: Homo sapiens, Human non-small cell lung cancer cells, knock out CHD6, biol rep1

description:
Library name: KO1
Column name Counts.csv: KO1


title: FPE RNA -R-case 9, RNA

value: case 9

value: sunitinib responder

value: ccRCC


title: PBMC of patient #14 before TTF treatment


title: shCux1 ENU Rep 2

description: Sample 35

value: ENU


title: PBMC of patient #9 after TTF treatment


title: Homo sapiens, Human non-small cell lung cancer cells, control blank, biol rep3

description:
Library name: WT3
Column name Counts.csv: WT3

value: Control blank


title: PBMC of patient #12 after TTF treatment


title: PEM-seq_HEK293T_SpCas9_APOB

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting APOB locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.

value: Human embryonic kidney

value: WT

value: APOB


title: shCux1 ENU Rep 1

description: Sample 34

value: Bone marrow

value: LSK


title: PEM-seq_HEK293T_ISAam1_APOB

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the APOB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.

value: plasmid transfection


title: PBMC of patient #9 before TTF treatment


title: PBMC of patient #14 after TTF treatment

value: post  TTFields +TMZ


title: shCux1 ENU Rep 3

description: Sample 36


title: PBMC of patient #7 after TTF treatment


title: shCtrl Ezh2i ENU Rep3

description: Sample 33

value: shCtrl

value: Tazemetostat, ENU


title: PEM-seq_HEK293T_control_APOB

treatment_protocol: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.

value: control


title: Homo sapiens, Human non-small cell lung cancer cells, control blank, biol rep1

description:
Library name: WT1
Column name Counts.csv: WT1

value: lung cancer cells

value: Human non-small cell lung cancer cells


title: FPE RNA -NR-case 2, RNA

value: case 2

value: sunitinib non-responder


title: PEM-seq_HEK293T_SpCas9_EMX1

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting EMX1 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: PBMC of patient #7 before TTF treatment

value: pre TTFields +TMZ

value: Glioblastoma


title: shCtrl Ezh2i ENU Rep1

description: Sample 31


title: Urine derived cell-NR

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Generally, cellranger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file.
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices.
Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each single cell

source_name: urine-derived cell

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
Sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: urine-derived cells

value: membranous nephropathy

tag: status

value: no remission(NR)


title: PEM-seq_HEK293T_ISYmu1_APOB

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the APOB locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.

value: Human embryonic kidney

value: WT

value: APOB


title: Urine derived cell-CR

value: complete remission(CR)


title: PEM-seq_HEK293T_Nme2-C.NR_EMX1

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the EMX1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: plasmid transfection


title: PEM-seq_HEK293T_CasMINI_EMX1

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the EMX1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: CasMINI


title: gh3a, dnOPDA, 3

city: Madrid

first: Salvador

last: Torres Montilla

address: Calle Darwin, 3

institute: Centro Nacional de Biotecnologia

data_processing:
PE150, Q30≥85%
Raw paired-end reads were trimmed using default parameters with fastp tool
Sequences were mapped and quantified to the reference genome MpTak1_v6.1 with salmon
Assembly: MpTak1_v6.1.genome.fa
Supplementary files format and content: tab-delimited text file include TPM values for each sample

organism: Marchantia polymorpha

source_name: whole plant

growth_protocol: Plants were grown 2 weeks in GB5 1% agar plates, 21ºC and Long Day photoperiod.

extract_protocol:
The RNA extracted with FavorPrep Plant Total RNA Mini Kit (Vienna, Austria), whereas genomic DNA was removed by DNase digestion. Sample quality was evaluated in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
Illumina NovaSeq X Plus

treatment_protocol: 2 hours in 25μM dn-OPDA or ethanol as mock

tag: tissue

value: whole plant

value: 25μM dn-OPDA


title: shCtrl ENU Rep 1

description: Sample 28

value: Bone marrow

value: LSK

value: shCtrl

value: ENU


title: PEM-seq_HEK293T_ISDge10_EMX1

treatment_protocol: The cells were transfected with the gRNA-ISDge10 plasmid targeting the EMX1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDge10 plasmid) on Day 3.


title: shCtrl ENU Rep 2

description: Sample 29


title: gh3a, dnOPDA, 2


title: PEM-seq_HEK293T_ISDra2_EMX1

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the EMX1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: gh3a, dnOPDA, 1


title: shCtrl Veh Rep 3

description: Sample 27


title: Homo sapiens, Human non-small cell lung cancer cells, control blank, biol rep2

description:
Library name: WT2
Column name Counts.csv: WT2

value: lung cancer cells

value: Human non-small cell lung cancer cells

value: Control blank


title: PEM-seq_HEK293T_ISYmu1_EMX1

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the EMX1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.


title: shCtrl Veh Rep 2

description: Sample 26


title: KYSE-180R, biological rep2

first: Aiping

last: Luo

address: Panjiayuannanli 17, Chaoyang District

institute: National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Gene expression data from esophageal cancer radioresistant cells recovered 2 weeks after 60Gy irradiation
KYSE-180R-2

hyb_protocol: The labeled RNA were hybridized for 16 hours at 48°C on Affymetrix GeneChip miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

label: Biotin

source_name: KYSE-180R radioresistant cells

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

growth_protocol: The ESCC cell lines (KYSE series) were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The radioresistant cells were established according the following scheme. Cells (KYSE30, KYSE70 and KYSE180) were grown to 50% confluence, treated with 2 Gy of X-IR, and then incubated. Upon reaching 90% confluence, the cells were trypsinized and then incubated. When the cells reached 50% confluence, they were irradiated again (second fraction), and then this process repeated a total of 30 times to reach 60 Gy. The parental cells were subjected to identical trypsinization and culture conditions but were not irradiated.

tag: type

value: Radioresistant cells

value: esophageal squamous cell carcinoma


title: shCtrl Ezh2i ENU Rep2

description: Sample 32

treatment_protocol: Cells were cultured with 1.5 µg/mL doxycycline to induce shRNA and 1 µM tazemetostat to inhibit EZH2. After four days, tazemetostat was replenished and 0.025 mg/mL ENU was added for 72 hours.

value: Tazemetostat, ENU


title: gh3a, Mock, 3

value: Mock


title: shCtrl Veh Rep 1

description: Sample 25


title: PEM-seq_HEK293T_ISAam1_EMX1

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the EMX1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.

value: Human embryonic kidney

value: WT


title: shCtrl ENU Rep 3

description: Sample 30


title: gh3a, Mock, 2


title: KYSE-180R, biological rep1

description:
Gene expression data from esophageal cancer radioresistant cells recovered 2 weeks after 60Gy irradiation
KYSE-180R-1


title: shCux1 gKmt2c Rep 4

description: Sample 24

value: shCux1 gKmt2c


title: PEM-seq_HEK293T_control_EMX1

value: plasmid transfection

value: control


title: PEM-seq_HEK293T_AsCpf1_EMX1

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the EMX1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.


title: shCux1 gKmt2c Rep 3

description: Sample 23


title: KYSE-180, biological rep1

description:
Gene expression data from esophageal cancer parental cells
KYSE-180-1

source_name: KYSE-180 parental cells

value: Parental cells


title: Tak1, dnOPDA, 3

value: whole plant

value: 25μM dn-OPDA


title: IL15LN5

city: St. Louis

first: Kavita

last: Rwat

state: MO

address: St. Louis

department: Oncology

institute: Washington University in St. Louis

data_processing:
CLC Genomics Workbench 24
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package. GATK (v4.1.1.0) software was used to perform SNP calling. rMATS(4.1.0) software was used to analysis the AS event.
Assembly: hg38
Supplementary files format and content: tab-delimited xls file include raw counts for each sample
Supplementary files format and content: tab- delimited xls file include sample readCount, FKPM and FKPM of each gene group

source_name: PBMC

growth_protocol: sip-T was resuspended in RPMI complete

extract_protocol:
Sample RNA was isolated using TRizol  following manufacturer’s recommendation.
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
Sample RNA was isolated using TRizol (Invitrogen) following manufacturer’s recommendation. Illumina sequencing libraries were constructed by Novogene Co., Ltd.

treatment_protocol: Sip-T (n=5 CRPC patient samples) was treated with IL-15 {50ng/ml} or vehicle and analyzed at day 7 post the start of treatment

value: PBMC


title: KYSE-70R, biological rep1

description:
Gene expression data from esophageal cancer radioresistant cells recovered 2 weeks after 60Gy irradiation
KYSE-70R-1

source_name: KYSE-70R radioresistant cells


title: KYSE-180, biological rep2

description:
Gene expression data from esophageal cancer parental cells
KYSE-180-2


title: shCux1 gKmt2c Rep 2

description: Sample 22

value: Bone marrow

value: LSK


title: IL15LN4


title: Tak1, dnOPDA, 2


title: shCux1 gKmt2c Rep 1

description: Sample 21


title: Tak1, Mock, 3


title: IL15LN3


title: KYSE-70, biological rep2

description:
Gene expression data from esophageal cancer parental cells
KYSE-70-2

source_name: KYSE-70 parental cells


title: KYSE-70R, biological rep2

description:
Gene expression data from esophageal cancer radioresistant cells recovered 2 weeks after 60Gy irradiation
KYSE-70R-2


title: KYSE-70, biological rep1

description:
Gene expression data from esophageal cancer parental cells
KYSE-70-1


title: Tak1, dnOPDA, 1


title: KYSE-30R, biological rep2

description:
Gene expression data from esophageal cancer radioresistant cells recovered 3 weeks after 60Gy irradiation
KYSE-30R-2

source_name: KYSE-30R radioresistant cells


title: KYSE-30, biological rep2

description:
Gene expression data from esophageal cancer parental cells
KYSE-30-2

source_name: KYSE-30 parental cells


title: gh3a, Mock, 1


title: IL15LN1


title: shCux1 gEzh2 Rep 2

description: Sample 18

value: shCux1 gEzh2


title: KYSE-30R, biological rep1

description:
Gene expression data from esophageal cancer radioresistant cells recovered 3 weeks after 60Gy irradiation
KYSE-30R-1


title: shCux1 gEzh2 Rep 4

description: Sample 20


title: Tak1, Mock, 1


title: ContLN4

value: PBS


title: IL15LN2


title: KYSE-30, biological rep1

description:
Gene expression data from esophageal cancer parental cells
KYSE-30-1


title: shCux1 gEzh2 Rep 3

description: Sample 19


title: Tak1, Mock, 2


title: shCux1 gEzh2 Rep 1

description: Sample 17


title: T98G cells,oeLGP2-input

city: 上海

first: 晋

last: 李

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cell line

growth_protocol: T98G cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Briefly, cells were cultured in 10 cm dishes and fixed with formaldehyde to a final concentration of 1%, then incubated at 37°C for 10 minutes. Glycine solution (1.1 ml, 10X) was added and incubated at room temperature for 5 minutes to quench the formaldehyde. The culture dishes were then placed on ice, and the medium was aspirated.Cells were washed twice with 5-10 ml of ice-cold PBS containing 1 mM PMSF. After washing, the cells were scraped into 1 ml of ice-cold PBS with 1 mM PMSF and collected into centrifuge tubes.
The pellets were then processed for library preparation using the VAHTSTM Universal DNA Library Prep Kit for Illumina V3 (Vazyme, China), following the manufacturer's instructions, and sent to Lianchuan Bio for sequencing.

treatment_protocol: overexpressed LGP2

value: cell line

value: Glioblastoma

value: LGP2 overexpressed


title: ContLN5


title: DPCs_OS_n12(3)

city: GuangZhou

first: Jia

last: Shilin

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Institute of Stomatological Research, Sun Yat-sen University

description: Gene expression after culturing with OS for 3 days

hyb_protocol: 1.65ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25X Fragmentation Buffer and 10X Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2* GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Genome Oligo Microarrays (one-color) for 17 hours at 65°C in Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029).After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software. After setting FE Project Properties, and checking the Extraction Set Configuration, FE Project (.fep) was saved and browse for desired location, and data was eventually exported to txt.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary cultured dental papilla cells was cultured with αMEM containing 20% FBS (Gibco, Grand Island, NY, USA), 1% Gluta-Max (Gibco, Grand Island, NY, USA), along with 2% penicillin-streptomycin (Gibco, Grand Island, NY, USA), were incubated and expanded at 37°C with 5% CO2. DPCs at 3–4 passages were utilized for treatment.

extract_protocol: RNA was prepared using the TRIzol Reagent (Invitrogen life technologies) following the manufacturer's recommendations. Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette.RNA Quantification and Quality Assurance were conducted with NanoDrop ND-1000.RNA Integrity and gDNA contamination was tested by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: Rat dental papilla cells were cultured with odontogenic differentiation induction medium (OS), which is prepared using a-MEM medium comprising 8% FBS, 1% antibiotics, 0.1 mM dexamethasone, 0.2 mM ascorbic acid and 10 mM β-glycerophosphate. For melatonin treatment, 10-8M melatonin was added into OS medium. The cultures were incubated for 3 days at 37 ºC in a humidified incubator with 5% CO2.

value: Dental papilla cells (DPCs)

tag: developmental stage

value: Postnatal day1-3


title: T98G cells,oeLGP2-1

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系


title: ContLN3


title: shCux1 gActin Rep 3

description: Sample 15

value: shCux1 gActin


title: shCux1 gActin Rep 4

description: Sample 16


title: ContLN2


title: T98G cells,vector-input

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系

value: VECTOR


title: ContLN1


title: shCux1 gActin Rep 2

description: Sample 14


title: T98G cells,vector-1

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系


title: Glial 5xFAD Plcg2 KO+/- M #46

city: Stanford

first: Andy

middle: P

last: Tsai

state: California

address: 290 Jane Stanford Way E365

institute: Stanford University

description: nCounter® Neuropathology Panels

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing: Data were processed and normalized using NanoString nSolver 4.0 analysis software

label: NanoString

source_name: mouse cortex

label_protocol: standard NanoString protocol

extract_protocol: Total RNAs were prepared with Purelink RNA Mini Kit and subjected to NanoString analysis

tag: sample type

value: Male, 5xFAD PLCG2 KO HET mice, brain

tag: gender

value: Male


title: shCux1 gActin Rep 1

description: Sample 13


title: Glial 5xFAD Plcg2 KO+/- M #10

description: nCounter® Neuropathology Panels


title: HBV-KMT2B integrated HCC RNA-seq

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

institute: Tokyo Medical and Dental University

data_processing:
The TruSeq Stranded mRNA protocol was used for the preparation of RNA-seq libraries and sequenced on a HiSeq 2500 machine (Illumina), as paired-end, 101 base paires reads.
The sequencing reads were trimmed using Cutadapt v1.1 and Trimmomatic v0.32 with the following options:  --match-read-wildcards -O 1 (Cutadapt) / -phred33 LEADING:0 TRAILING:0 SLIDINGWINDOW:20:20 MINLEN:50 (Trimmomatic).
Trimmed  reads were aligned to the GRCh38 genome assembly using TopHat v2.0.14 and bowtie v1.1.1 with the following options: --library-type fr-firststrand --microexon-search --bowtie1.
FPKMs were using Cufflinks (version2.2.1) with a transcriptome reference (Ensembl Human Transcript).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values

source_name: Hepatocellular carcinoma

extract_protocol:
Total RNA was extracted by RNeasy Mini (QIAGEN, Venlo, Netherlands).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: Hepatocellular carcinoma


title: DPCs_OS+MT_n12(3)

description: Gene expression after culturing with OS+melatonin (10-8M) for 3 days


title: T98G cells,oeLGP2-2

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系

growth_protocol: 293t cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Trizol method (1) Treatment of cells: For adherant cells, the original cell medium was sucked away with a vacuum pump, then 1 mL Trizol was added, thoroughly mixed, and then blown with a pipette repeatedly.1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: astroblastoma


title: shCtrl gKmt2c Rep 4

description: Sample 12

value: shCtrl gKmt2c


title: shCtrl gKmt2c Rep 3

description: Sample 11


title: T98G cells,vector-3

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系


title: T98G cells,vector-2

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系


title: Glial 5xFAD Plcg2 KO+/- M #11

description: nCounter® Neuropathology Panels


title: Glial 5xFAD Plcg2 KO+/- M #3

description: nCounter® Neuropathology Panels


title: Glial 5xFAD Plcg2 KO+/- M #48

description: nCounter® Neuropathology Panels


title: Scrambled siRNA and Poly(I:C)

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

data_processing:
Illumina's CASAVA 1.8.4 was used to convert BCL files to FASTQ files using default parameters.
RSEM-1.3.0’s EBSeq was used for differential expression analysis and for running the alignments as well as generating gene and transcript expression levels. The ‘rsem-calculate-expression’ module was used.
The data were aligned to the GRCh38 reference genome using the Spliced Transcripts Alignment to a Reference (STAR) method.
Genome_build: GRCh38 reference genome
Supplementary_files_format_and_content: The processed FPKM data file, "LG01JHU506-FPKM", contains linear FPKM values in .txt format.

source_name: Human neonatal foreskins

growth_protocol: Keratinocytes were cultured in keratinocyte growth medium (KGM-Gold) supplemented with necessary growth factors and antibiotics (Lonza, 192060).

extract_protocol:
Total RNA from human keratinocytes was purified using the RNeasy Mini Kit (Qiagen, 74106). RNA was incubated with DNase I to efficiently digest DNA prior to elution. RNA purity and quantity was calculated using a UV-Vis spectrophotometer (NanoDrop2000c (Thermo Fisher Scientific, ND-2000c). Total RNA quality was assessed by measuring 28S/18S ribosomal RNA ratios and scoring RNA Quality/Integrity Number (RQN/RIN) values via capillary electrophoresis using either 2100 Bioanalyzer (Agilent, Santa Clara, CA) or Fragment Analyzer CE (Agilent, Santa Clara, CA).
TruSeq Stranded Total RNA LT Sample Prep Kit (Human Mouse Rat)/TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

treatment_protocol: Cells were seeded at 50,000 cells/well (RNA) or 100,000 cells/well (protein) in 12-well or 6-well plates respectively. Non-targeting and gene-specific siRNAs (Dharmacon) for human and mouse were used. Briefly, 25nM of siRNA was pooled with Lipofectamine® RNAiMAX transfection reagent (Thermo Fisher Scientific, 13778150) in reduced serum OPTI-MEM media (Gibco, 31985062) and added to cultured keratinocytes for 48 hours to achieve maximum gene knockdown efficiency. Cells were also treated with poly IC (10µg/ml) added directly to culture media for 48hrs.

tag: passage

value: NHEK

value: Scrambled siRNA and Poly(I:C)


title: RNAseL siRNA and Poly(I:C)

value: RNaseL-PIC/siRNaseL-PIC


title: RNAseL siRNA

value: RNAseL siRNA


title: Glial 5xFAD Plcg2 KO+/- M #13

description: nCounter® Neuropathology Panels


title: Scrambled siRNA

value: Scrambled siRNA


title: shCtrl gKmt2c Rep 1

description: Sample 9

value: Bone marrow

value: LSK


title: Glial 5xFAD M # 1270

description: nCounter® Neuropathology Panels

value: Male, 5xFAD mice, brain


title: Glial 5xFAD M # 1269

description: nCounter® Neuropathology Panels


title: shCtrl gEzh2 Rep 4

description: Sample 8

value: shCtrl gEzh2


title: Glial 5xFAD M # 1268

description: nCounter® Neuropathology Panels


title: T98G cells,oeLGP2-3

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系

value: cell line

value: LGP2 overexpressed


title: shCtrl gEzh2 Rep 3

description: Sample 7


title: W36OE_T_3

city: Kunming

first: Lirong

last: Zhao

state: Yunnan

address: No.88 Xuefu Road

department: Xishuangbanna Tropical Botanical Garden

institute: Chinese Academy of Sciences

description: Library name: Sample18

data_processing:
Pollution assessment: 10,000 sequences were randomly selected from Clean data for blastn comparison with NCBI NT database, evalue <= 1e-10 and comparison results with similarity >90% and coverage > 80% were used to calculate their species distribution.
Our screening criteria for significant differenced genes were: The expression level (TPM value) of at least one of the two compared samples was greater than or equal to 5, and the absolute value of log2FoldChange was greater than 1, and qValue < 0.05.
Assembly: rice.uga.edu, version 7.0
Supplementary files format and content: processed data.xls

organism: Oryza sativa

source_name: Total plamina joint

growth_protocol: The Oryza sativa japonica variety Nipponbare was used as the wild type. The rice seedlings were grown in a phytotron (12 hours of light/12 hours of darkness, day/night temperatures of 28°C/25°C) with a relative humidity maintained at 70%.

extract_protocol:
Total RNA was isolated from different rice tissues using TRIzol reagent (CWBIO).
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.

treatment_protocol: Lamina joint tissues or whole plants of fresh rice seedlings were collected.

value: Total plamina joint

value: OsWRKY36 overexpression


title: Glial 5xFAD M # 1181

description: nCounter® Neuropathology Panels

value: Male


title: Glial 5xFAD M # 1182

description: nCounter® Neuropathology Panels


title: W36OE_T_1

description: Library name: Sample16


title: W36OE_T_2

description: Library name: Sample17


title: shCtrl gEzh2 Rep 2

description: Sample 6


title: shCtrl gKmt2c Rep 2

description: Sample 10


title: shCtrl gEzh2 Rep 1

description: Sample 5


title: W36OE_LJ_3

description: Library name: Sample15

source_name: lamina joint

value: lamina joint


title: HDC-/- bonemarrowCD11b+cells HFD 2

city: Shanghai

first: Xiangdong

last: Yang

state: China

address: 180 Fenglin Road, Xuhui District, Shanghai

institute: Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University

description: Gene expression in bone marrow -derived CD11b+ cells of high-fat diet-fed HDC-/- mice

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Mouse Genome Oligo Microarray (4x44K, Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Results were provided in the Raw Data Folder. Normalization was performed using Agilent GeneSpring GX 11.5.1. Further Data analysis was performed using Agilent GeneSpring GX 11.5.1 software. Results were provided in the Gene Expression Profiling Data.xls file and Data Analysis Folder.

source_name: HDC-/-, bone marrow-derived CD11b+ cells, HFD

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: RNA was prepared using the TRIzol reagent. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols.

treatment_protocol: The mice were fed a high-fat diet for 3 months to establish a murine model of atherosclerosis. After the mice were sacrificed, CD11b+ cells were isolated from the spleen and bone marrow from mice, and the number of cells per tube was more than 5 x 106. CD11b+ cells of each sample were isolated from the spleen or bone marrow of 5 mice.

value: bone marrow

value: male

value: HDC-/-

tag: diet

value: HFD


title: STAT6-/- bonemarrowCD11b+cells HFD 2

description: Gene expression in bone marrow -derived CD11b+ cells of high-fat diet-fed STAT6-/- mice

source_name: STAT6-/-, bone marrow-derived CD11b+ cells, HFD


title: HDC-/- bonemarrowCD11b+cells control 2

description: Gene expression in bone marrow -derived CD11b+ cells of  normal diet-fed HDC-/- mice

source_name: HDC-/-, bone marrow-derived CD11b+ cells, control

value: control


title: Glial 5xFAD M # 1177

description: nCounter® Neuropathology Panels


title: shCtrl gActin Rep 4

description: Sample 4

source_name: Bone marrow

value: shCtrl gActin


title: Glial 5xFAD Plcg2 KO+/- F #51

description: nCounter® Neuropathology Panels

value: Female, 5xFAD PLCG2 KO HET mice, brain

value: Female


title: STAT6-/- bonemarrowCD11b+cells control 2

description: Gene expression in bone marrow -derived CD11b+ cells of  normal diet-fed STAT6-/- mice

source_name: STAT6-/-, bone marrow-derived CD11b+ cells, control


title: w36_T_3

description: Library name: Sample12

value: OsWRKY36 mutant


title: W36OE_LJ_2

description: Library name: Sample14


title: Glial 5xFAD Plcg2 KO+/- F #18

description: nCounter® Neuropathology Panels


title: STAT4-/- bonemarrow-derivedCD11b+cells HFD 2

description: Gene expression in bone marrow -derived CD11b+ cells of high-fat diet-fed STAT4-/- mice

source_name: STAT4-/-, bone marrow-derived CD11b+ cells, HFD


title: W36OE_LJ_1

description: Library name: Sample13


title: STAT4-/- bonemarrow-derivedCD11b+cells control 2

description: Gene expression in bone marrow -derived CD11b+ cells of  normal diet-fed STAT4-/- mice

source_name: STAT4-/-, bone marrow-derived CD11b+ cells, control


title: Glial 5xFAD Plcg2 KO+/- F #14

description: nCounter® Neuropathology Panels


title: shCtrl gActin Rep 1

description: Sample 1

value: Bone marrow

value: LSK


title: shCtrl gActin Rep 2

description: Sample 2


title: Glial 5xFAD Plcg2 KO+/- F #19

description: nCounter® Neuropathology Panels


title: w36_T_2

description: Library name: Sample11


title: LR25_MC38

city: Tianjin

first: Guorong

last: Zhang

address: qixiangtai street 22

institute: Tianjin Medical University

data_processing:
Single cell RNA sequencing data was processed by Seeksoul Tools Online (Beijing SeekGene BioSciences Co., Ltd.), an easy-to-use scSeq data analysis and visualization web server powered by R language for scientific researchers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
At day 14 after B16F10 cells inoculation, or day 26 after MC38 cells inoculation, the tumors from 3 WT and 3 Lrrc25-/- mice were harvested, and 100 mm3 of each tumor was collected. Tumor tissues from 3 mice of the same group were randomly pooled into one mixed sample, and dissociated. Cell counts and viability were determined after removal of erythrocytes , and then debris and dead cells were removed using commercial kit. Fresh cells were washed twice in RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS containing 0.04% bovine serum albumin (BSA). Finally, CD45+ immune cells were isolated using magnetic beads and mixed with the original cell suspension at a ratio of 5:1.
Single-cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (SeekGene Catalog No.K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip. After emulsion droplet generation reverse transcription were performed at 42℃for 90 minutes and inactivated at 80℃ for 15 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824)

value: tumor

value: tumor cells


title: w36_T_1

description: Library name: Sample10

value: Total plamina joint


title: WT bonemarrow-derivedCD11b+cells HFD 2

description: Gene expression in bone marrow -derived CD11b+ cells of high-fat diet-fed WT mice

source_name: WT, bone marrow-derived CD11b+ cells, HFD

value: WT


title: HDC-/- spleen-derivedCD11b+cells HFD 1

description: Gene expression in spleen-derived CD11b+ cells of high-fat diet-fed HDC-/- mice

source_name: HDC-/-, spleen-derived CD11b+ cells, HFD

value: spleen


title: WT_MC38


title: Glial 5xFAD Plcg2 KO+/- F #8

description: nCounter® Neuropathology Panels


title: w36_LJ-3

description: Library name: Sample9

value: lamina joint


title: shCtrl gActin Rep 3

description: Sample 3


title: Lr25_B16F10


title: w36_LJ-2

description: Library name: Sample8


title: Glial 5xFAD F # 1253

description: nCounter® Neuropathology Panels

value: Female, 5xFAD mice, brain


title: Glial 5xFAD F # 1249

description: nCounter® Neuropathology Panels


title: STAT6-/- spleen-derivedCD11b+cells HFD 1

description: Gene expression in spleen-derived CD11b+ cells of high-fat diet-fed STAT6-/- mice

source_name: STAT6-/-, spleen-derived CD11b+ cells, HFD

value: male


title: HDC-/- spleen-derivedCD11b+cells control 1

description: Gene expression in spleen-derived CD11b+ cells of  normal diet-fed HDC-/- mice

source_name: HDC-/-, spleen-derived CD11b+ cells, control

value: HDC-/-


title: w36_LJ-1

description: Library name: Sample7


title: STAT6-/- spleen-derivedCD11b+cells control 1

description: Gene expression in spleen-derived CD11b+ cells of  normal diet-fed STAT6-/- mice

source_name: STAT6-/-, spleen-derived CD11b+ cells, control


title: WT bonemarrow-derivedCD11b+cells control 2

description: Gene expression in bone marrow -derived CD11b+ cells of  normal diet-fed WT mice

source_name: WT, bone marrow-derived CD11b+ cells, control

value: bone marrow


title: DKD, Disease, rep2

city: Seoul

first: Yong jun

last: Kim

address: 329, Daehak-ro 103, Jongno-gu, Seoul, Republic of korea

department: biomedical science

country: South Korea

institute: Seoul National University

description: 10x Genomics

data_processing:
The generation of count tables were performed using CellRanger v7.1.0 (10x Genomics) from the fastq files.
Assembly: mm10
Supplementary files format and content: raw counts for each cells

source_name: Kidney

extract_protocol:
RNA was harvested with 10X genomics Single-cell protocols.
A single-cell suspension of mouse kidney cells was prepared following the 10x Genomics Single-Cell Protocols. Mouse kidney cells, with a concentration of approximately 800-1200/μL, were kept on ice for single-cell analysis. The single-cell suspension was mixed with the master mix and loaded, along with Single-Cell 5’ Gel Beads and Partitioning Oil, into the Chromium Next GEM Chip K. The Gel Beads were coated with unique molecular identifiers (UMI), unique primers containing 10x cell barcodes, and oligo poly(dT) sequences. The single-Cell Gel Bead-In-Emulsions (GEM) were generated and barcoded after the GEM generation step using a Chromium Controller (10x Genomics). The barcoded full-length cDNA was constructed via reverse transcription of single cells, followed by incubation using PCR. After encapsulation, cDNAs were selectively purified using Dynabeads Cleanup Mix and then amplified to construct the 5’ Gene Expression Dual Index Library.

value: Kidney

tag: disease state

value: infection


title: Nip_T_3

description: Library name: Sample6

source_name: Total plamina joint

value: Wild type


title: Nip_T_2

description: Library name: Sample5


title: DKD, Disease, rep1

description: 10x Genomics


title: Glial 5xFAD Plcg2 KO+/- F #12

description: nCounter® Neuropathology Panels

source_name: mouse cortex

value: Female, 5xFAD PLCG2 KO HET mice, brain

value: Female


title: Glial 5xFAD F # 1248

description: nCounter® Neuropathology Panels


title: Glial 5xFAD F # 1190

description: nCounter® Neuropathology Panels


title: Glial 5xFAD F # 1189

description: nCounter® Neuropathology Panels


title: DKD, Control, rep2

description: 10x Genomics

value: non-infection


title: Nip_T_1

description: Library name: Sample4


title: STAT4-/- spleen-derivedCD11b+cells HFD 1

description: Gene expression in spleen-derived CD11b+ cells of high-fat diet-fed STAT4-/- mice

source_name: STAT4-/-, spleen-derived CD11b+ cells, HFD

value: HFD


title: STAT4-/- spleen-derivedCD11b+cells control 1

description: Gene expression in spleen-derived CD11b+ cells of  normal diet-fed STAT4-/- mice

source_name: STAT4-/-, spleen-derived CD11b+ cells, control

value: control


title: WT spleen-derivedCD11b+cells HFD 1

description: Gene expression in spleen-derived CD11b+ cells of high-fat diet-fed WT mice

source_name: WT, spleen-derived CD11b+ cells, HFD


title: Glial 5xFAD F # 1180

description: nCounter® Neuropathology Panels


title: Nip_LJ_3

description: Library name: Sample3

source_name: lamina joint


title: HC3

city: Xiamen

first: Jichen

state: None Selected

address: Fujian province xiamen city

institute: Xiamen University

data_processing:
The sequenced data (raw data) was filtered by SOAPnuke (v1.4.0) (Yuxin Chen et al., 2018) and clean data was obtained. Then the clean data was assembled via Trinity (v2.0.6) and quality assessed via BUSCO (Grabherr et al., 2011). After that, the clean data was mapped to the assembled unique gene by Bowtie 2 (v2.2.5) (Langmead & Salzberg, 2012) and its expression level was calculated with RSEM (v1.2.8) (Parrish et al., 2014). The coding sequences of unigenes were identified and aligned to SwissProt by the software Transdecoder (v3.0.1) (Kim et al., 2015) and Basic Local Alignment Search Tool (Blast), respectively. Hmmscan were took out for the identified of homologous and coding sequences. Then, MISA (v1.0) (Thiel et al., 2003) and Primer3 (v2.2.2) (Untergasser et al., 2012) were used for the detection of unigenes and the designment of primer for SSR detection.
The differential genes within and between group were performed using DESeq and PossionDis. The differential expressed genes were identified with |Fold change| ≥ 1.5 and Q_value ≤ 0.05. The expression heatmap were performed via TBtools-II (v2.007) software (C. Chen et al., 2020).
Assembly: The assembled unigenes were annotated with multiple functional databases Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.genome.jp/kegg/), Gene Ontology (GO, https://www.geneontology.org/), Non-Redundant Protein Sequence Database (NR, ftp://ftp.ncbi.nlm.nih.gov/blast/db), Nucleotide Sequence Database (NT, ftp://ftp.ncbi.nlm.nih.gov/blast/db), Swiss-Prot (https://www.expasy.org/resources/uniprotkb-swiss-prot), Protein family (Pfam, http://pfam.xfam.org/), and Clusters of orthologous groups for eukaryotic complete genomes (KOG, ftp://ftp.ncbi.nih.gov/pub/COG/KOG/kyva).

organism: Skeletonema costatum

source_name: cells

growth_protocol: 12:12 light dark cycle

extract_protocol:
About 10 million cells of alga sample in 100th days were collected and frozen in liquid nitrogen. Each group included three replicates. After that, the frozen alga samples were sent to BGI Genomic Center (Shenzhen, China) for the extraction, purification, and check of RNA.
The RNA samples were isolated via denatured and mRNA was enriched by oligo (dT) -attached magnetic beads. Then, the mRNA was fragmented at the suitable temperature. The cDNA was synthesis via the method of sequencing by synthesis (SBS). Furthermore, the double-stranded cDNA fragments are subjected to end-repair, adding poly A, ligating the adaptor and enrichment(Peredo & Cardon, 2020). After the construction of cDNA libraries, it was tested via Agilent 2100 Bioanalyzer and then sequenced via the Illumina HiSeq™ 4000 platform (Rädecker et al., 2021).

value: cells

value: wild type

value: HC


title: 2nd exp h10.100nM.24h dup2

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: 2nd exp h10.100nM.24h dup2

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.0.11
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes.
Assembly: mm10/GRCm38
Supplementary files format and content: Gene expression in text format, content include gene name, symbol, chromosome, length of transcripts, raw reads, and normalized reads per kilobase per million (RPKM)

source_name: spleen

growth_protocol: Murine CD8+ T cells were isolated from the spleens of 6- to 8-week-old C57BL/6 mice through negative selection and magnetic separation (Stem Cell Technologies Cat# 19853). Purified murine CD8+ T cells were pre-activated with plate-bound anti-mouse CD3 (2 µg/mL; clone 145-2C11, BioXCell Cat# BE0001-1) and soluble anti-mouse CD28 (1 µg/mL; clone 37.51, BioXCell Cat# BE0015-1) and cultured in complete RPMI media for 48 hours at 37°C.

extract_protocol:
Cells were then lysed in TRIzol reagent (Invitrogen Cat# 15596026), RNA was isolated using Direct-zol RNA MiniPrep Kit (Zymo Research Cat# R2052)
RNA-Sequencing libraries were prepared  using KAPA mRNA HyperPrep Kit (Roche Cat# KK8440), after quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina NovaSeq system.

treatment_protocol: Cells were rested overnight and restimulated with mIL-21 or 21h10 at 100 pM, 1 nM, 10 nM, and 100 nM concentrations for 24 hours in complete RPMI media at 37°C.

value: spleen

tag: strain

value: CD8+ T cells

value: wild-type

value: pre-activated


title: Nip_LJ_2

description: Library name: Sample2

value: lamina joint


title: RAT-seq random control in NK-92MI

city: Changchun

first: Xiumin

last: Shi

state: Jilin

address: No.1 Xinmin Street

department: Department of Hematology

institute: The First Hospital of Jilin University

description: Library name: RAT control dataset

data_processing:
ChIP-Seq reads were trimmed from 3' end until the fianl base had a quality score >20. Using fastx (version: 0.0.13), discarding reads left with <20 bp.
ChIP-Seq reads were aligned to the UCSC hg38 genome using Bowtie (version: 0.12.8). Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS(version: 1.4.2) with the significance cut-off q-value<=0.05
Bedgraph files were generated using the genomic Ranges R package DiffBind Software with parameter settings Fold change≥2 or ≤1/2 and p-value＜0.05.
Assembly: hg38
Supplementary files format and content: Bedgraph files

growth_protocol: NK-92MI cells were cultured in α-minimum essential medium containing 2 mM L-glutamine, 1.5 g/L sodium bicarbonate, 0.2 mM inositol, 0.1 mM β-mercaptoethanol, 0.02 mM folic acid, 12.5% horse serum, and 12.5% fetal bovine serum.

extract_protocol:
For RAT-Seq, NK-92MI cells were first cross-linked to fix the lncRNA-chromatin structure. The regulatory element-interacting RNAs were reverse transcribed in situ in the nucleus using lncRNA-specific complementary primers in a reaction mixture containing biotin-dCTP. The RNA-biotin cDNA chromatin complex was pulled down with streptavidin beads and the target gene DNAs were purified for library sequencing. As the RAT control, RAT control dataset was generated by random oligo primers.
RAT-DNA libraries were prepared using Illumina's Kit (Part# 0801-0303).

tag: cell line


title: WT_B16F10

value: tumor

tag: cell type

value: tumor cells

value: WT


title: HC2

tag: genotype


title: 2nd exp h10.100nM.24h dup1

description: 2nd exp h10.100nM.24h dup1

tag: treatment


title: Nip_LJ_1

description: Library name: Sample1

value: Wild type


title: HC1


title: A549 cells, shTRIM22, 3 days after ionizing radiation3

city: Beijing

first: Li

last: Xinyan

address: No.17, Panjiayuan Nanli, Chaoyang District, Beijing

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
DESeq2 R package (1.20.0)
Assembly: hg38
Supplementary files format and content: xls file includes raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used was used for the construction of sequencing libraries
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magneticbeads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized usingrandom hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.Remaining overhangs were converted into blunt ends via exonuclease/polymerase activitiesAfter adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure wereligated to prepare for hybridization.In order to select cDNA fragments of preferentially370~420 bp in length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-FidelityDNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products werepurified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer2100 system.

value: non-small cell lung cancer cell lines

value: TRIM22 knockdown

value: ionizing radiation


title: NKCLR3 RAT-seq in NK-92MI

description: Library name: NKCLR3 RAT


title: A549 cells, shTRIM22, 3 days after ionizing radiation2


title: 2nd exp h10.10nM.24h dup2

description: 2nd exp h10.10nM.24h dup2


title: 2nd exp h10.10nM.24h dup1

description: 2nd exp h10.10nM.24h dup1


title: A549 cells, shTRIM22, 3 days after ionizing radiation1


title: T13-5_Humanized CJ HCC- ZT18

city: Houston

first: Loning

last: Fu

state: Texas

address: One Baylor Plaza

department: Medicine

institute: Baylor College of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 and mm10 using STAR aligner with parameter ( --outSAMattributes NM).
FeatureCounts implemented in Subread package was used to count the sequencing reads from mapped BAM files.The number of reads falling in the exons of this meta-transcript were counted
Differential gene expression was evaluated using the R package EdgeR and expression was further normalized using the R package RUVr
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text files include raw read count for each annoted gene

organism:
Homo sapiens
Mus musculus

source_name: Humanized CJ HCC

extract_protocol:
Liver or HCC were removed, flash frozen in liquid nitrogen, RNA was processed using PureLinkTM RNA Minikit (Cat#12183018A), and extracted RNAs were used for the construction of RNA libraries using Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)

value: h-HCC


title: GC2

last: Chen

value: cells

value: GC


title: A549 cells, shTRIM22, sham irradiation3

value: sham irradiation


title: 2nd exp WT.100nM.24h dup2

description: 2nd exp WT.100nM.24h dup2

value: spleen


title: T13-4_Humanized CJ HCC- ZT18


title: GC1

value: wild type


title: A549 cells, shTRIM22, sham irradiation2


title: DKD, Control, rep1

description: 10x Genomics

value: Kidney

value: non-infection


title: 2nd exp WT.100nM.24h dup1

description: 2nd exp WT.100nM.24h dup1

value: CD8+ T cells

value: wild-type

value: pre-activated


title: A549 cells, shTRIM22, sham irradiation1


title: LC3

value: LC


title: 2nd exp WT.10nM.24h dup2

description: 2nd exp WT.10nM.24h dup2


title: T18_Humanized CJ HCC- ZT18


title: WT spleen-derivedCD11b+cells control 1

description: Gene expression in spleen-derived CD11b+ cells of  normal diet-fed WT mice

source_name: WT, spleen-derived CD11b+ cells, control

value: male

value: WT

value: control


title: LC2


title: A549 cells, shControl, 3 days after ionizing radiation3

value: non-small cell lung cancer cell lines

value: ionizing radiation


title: T14_Humanized CJ HCC- ZT18

value: (129Sv or hybrid 129Sv-C57BL/ 6j), (B6.129S4- Il2rgtm1Wjl/J), (RagN12)

value: h-HCC


title: 2nd exp WT.10nM.24h dup1

description: 2nd exp WT.10nM.24h dup1


title: LC1

value: cells