title: sorted macrophages, NE + LPS stimulation,rep3

city: Hangzhou

first: Xiangming

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road, Xihu District, Hangzhou, Zhejiang Province, China

institute: Zhejiang University

description:
Library name: NELPS3
column names in raw_counts.tsv : NELPS3

data_processing:
Raw RNA-seq reads were filtered using Cutadapt, and sequence quality was assessed using FastQC.
The filtered reads were then aligned to the Mus musculus (GRCm38) reference genome using HISAT2.
The mapped reads for each sample were assembled into transcriptomes with StringTie, using default parameters. All transcriptomes from the samples were merged to construct a comprehensive transcriptome using the gffcompare software. Following transcriptome reconstruction, StringTie and Ballgown were used to estimate the expression levels of all transcripts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Then, the RNA from the sorted cells was extracted using the RNeasy Plus Micro Kit as per manufacturer instructions.
Poly(A)mRNA was isolated using mRNA Capture Beads2.0 (Yeasen Cat.12629ES,CHN) with two rounds of purification, followed by RNA fragmentation with magnesium ions at 94˚C (Yeasen Cat.12340ES97,CHN) .RNA sequencing library preparation was performed using the TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: Mac2 were FACsorted (BD FACSAria Fusion) from the lung tissues of WT mice. Samples were stained with antibodies to CD45, Ly6G, CD11b, F4/80, CD11c, Ly6C,CD64, CX3CR1,ADRB2 and one population was analyzed as follows: Mac2(CD45+, Ly6G-, CD11b+, F4/80+, CD11c-, Ly6C-,CD64+, CX3CR1+,ADRB2+). The sorted cells were divided into four groups: the control group, which received no treatment; the LPS-only group, which was treated with LPS (10 ng/mL) for 3 hours; the Norepinephrine (NE)-only group, which was treated with Norepinephrine (10 μM) for 3 hours; and the final group, which was pretreated with Norepinephrine (10 μM) for 3 hours and subsequently treated with LPS (10 ng/mL) for 3 hours.

value: Macrophage

value: NE + LPS stimulation


title: Vector rep2

status: Public on May 25 2025

type: SRA

city: Tianjin

first: Hao

last: Wu

state: Tianjin

address: No. 22, Weidai Road, Heping District

department: Department of Immunology

country: China

institute: Tianjin Medical University

library_source: transcriptomic

data_processing:
The image data are transformed into sequence data (reads) by CASAVA v1.6
The raw paired end reads were trimmed and quality controlled using a custom Perl script.
Trimmed sequencing reads were aligned to the reference genome using Hisat2 (v2.0.5).
The FeatureCounts software (version 1.5.0-p3) was employed to extract reads count mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RAW counts for each sample.
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
Total RNA was extracted from the cells using TRIzol® Reagent according the manufacturer’s instructions.
Libraries were generated with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s instructions, and carried out with the Illumina NovaSeq 6000.

tag: tissue

value: Lung

tag: cell line

tag: cell type

value: Lung adenocarcinoma cells

tag: genotype

value: wild type


title: sorted macrophages, NE + LPS stimulation,rep2

description:
Library name: NELPS2
column names in raw_counts.tsv : NELPS2

organism: Mus musculus

value: WT

tag: treatment


title: KO1 rep1

value: BCKDK Knockout


title: Vector rep3


title: sorted macrophages,LPS stimulation,rep3

description:
Library name: LPS3
column names in raw_counts.tsv : LPS3

value: LPS stimulation


title: SH-SY5Y, H1.5 OE_rep2

city: Tel Aviv

first: Gil

last: Ast

state: Israel

address: Haim Levanon 55

country: Israel

institute: Tel Aviv University

description: Library name: H1.5 OE_rep2

data_processing:
Sequenced reads were aligned to the UCSC Genome Sequencing Consortium reference genome (human hg38) using the vast-tools v2.5.1 67 align command with default options.
The quality of sequenced reads was evaluated using the FASTQC tool
Assembly: hg38
Supplementary files format and content: tab-delimited files including cRPKM values for each Sample , no quantile normalization

source_name: Bone; Marrow

extract_protocol:
Total RNA extraction was performed using TRI reagent (Sigma) according to the manufacturer’s instructions.
TruSeq Stranded Total RNA with Ribo-Zero H/M/R

value: Bone; Marrow

value: Neuroblastoma

value: H1.5 OE


title: sorted macrophages, NE + LPS stimulation,rep1

description:
Library name: NELPS1
column names in raw_counts.tsv : NELPS1


title: MDDC cells, day4, B2A-ICP0-FxE_donor5

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

library_source: genomic

data_processing:
Data processing was done following ATAC-seq pipeline version 1.0.0 by Institute Curie Bioinformatic platform (https://github.com/bioinfo-pf-curie/ATAC-seq) using Nextflow version 20.10.0.
Paired-end ATAC-seq reads were processed for adapter trimming and aligned to the hg38 primary assembly (accession: GCF_000001305.14) using BWA-MEM version 0.7.17 with default parameters (with option - M for Picard compatibility). BAM files are then sorted and indexed using samtools v1.10
Duplicate fragments were identified with MarkDuplicates from Picard v2.19.0. Unmapped reads, duplicated, non-properly paired reads (mate reverse strand for the first in pair), not primary alignment reads, mitochondrial reads and reads from blacklisted regions are filtered out.
Only properly-paired reads with a mapping quality R > 20 were retained.
BAMs are shifted by aligmentSieve from deepTools v3.2.1, trimming 4bp to the right on left end, 5bp to the left on right end, to account for Tn5 transposase insertion bias.
BigWig files were generated by bamCoverage from deepTools v3.2.1, normalized to 1 million mapped reads.
Assembly: hg38
Supplementary files format and content: Normalized bigwig files

molecule: genomic DNA

source_name: Blood

growth_protocol: RPMI medium, 10% fetal bovine serum, 1X Penicillin-Streptomycin, Gentamicin (50 µg/ml), HEPES. Cells were cultured at 37C and 5% CO2.

extract_protocol:
100,000 cells were collected and processed according to manufacturer's instructions (Active Motif, 53150).
Lysis, tagmentation reactions, washes, DNA extraction, indexing of libraries were done following the manufacturer's instructions (Active Motif, 53150).

treatment_protocol: Cells were treated as described in the Methods section of the paper.

value: Blood

value: MDDC

tag: individual


title: Vector rep1


title: sorted macrophages,LPS stimulation,rep1

description:
Library name: LPS1
column names in raw_counts.tsv : LPS1


title: MDDC cells, day4, B2A-ICP0_donor5


title: sorted macrophages,LPS stimulation,rep2

description:
Library name: LPS2
column names in raw_counts.tsv : LPS2


title: sorted macrophages,NE stimulation,rep3

description:
Library name: NE3
column names in raw_counts.tsv : NE3

value: NE stimulation


title: MDDC cells, day4, B2A-Control_donor5

value: control


title: SH-SY5Y, H1.2 OE_rep2

description: Library name: H1.2 OE_rep2

value: H1.2 OE


title: MDDC cells, day4, B2A-ICP0-FxE_donor4


title: sorted macrophages,NE stimulation,rep2

description:
Library name: NE2
column names in raw_counts.tsv : NE2


title: KO2 rep2


title: MDDC cells, day4, B2A-ICP0_donor4


title: sorted macrophages,NE stimulation,rep1

description:
Library name: NE1
column names in raw_counts.tsv : NE1


title: sorted macrophages,no stimulation,rep3

description:
Library name: Ctrl3
column names in raw_counts.tsv : Ctrl3

value: no stimulation


title: MDDC cells, day4, B2A-Control_donor4


title: MDDC cells, day4, B2A-ICP0-FxE_donor3


title: sorted macrophages,no stimulation,rep2

description:
Library name: Ctrl2
column names in raw_counts.tsv : Ctrl2

value: Macrophage


title: sorted macrophages,no stimulation,rep1

description:
Library name: Ctrl1
column names in raw_counts.tsv : Ctrl1


title: MDDC cells, day4, B2A-ICP0_donor3


title: MDDC cells, day4, B2A-Control_donor3


title: w. MMF, 817, HFbD

city: Lübeck

first: Kristian

last: Händler

address: Ratzeburger Allee 160

department: Human Genetics

country: Germany

institute: UKSH

description: QuantSeq 3‘

data_processing:
nf-core/rnaseq pipeline v3.12.0
TrimGalore! v0.6.7
SortMeRNA v4.3.4 and BBMap-BBSplit v39.01
STAR 2.7.10a
Salmon v1.10.1
Shiny-Seq
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing the normalized and batch corrected values for each sample

molecule: polyA RNA

source_name: bone marrow

growth_protocol: Mice were anaesthetized with isoflurane and sacrificed by decapitation. The bone marrow was flushed from the tibia and femur. To obtain a single-cell suspension, the bone marrow was passed through a 23-gauge needle and samples were centrifuged for 10 min at 240 x g and 4o C. By using Percoll (Cytiva, Merck) gradient with a density of 52, 69 and 78%, neutrophils were centrifuged using an ultracentrifuge (Boxio et al., 2004). The cells were collected from the layers of 69/78 and 78% and purified from remaining erythrocytes by adding erythrocyte lysis buffer. After 2 min, incubation was stopped by adding HBSS buffer (10 ml). After centrifugation (10 min, 350 x g, room temperature), the cell pellet was resuspended in HEPES buffer (1ml). Neutrophil purity was > 90%, as assessed by CytoSpin followed by Wright-Giemsa staining or FACS analysis.

extract_protocol:
Treated neutrophils (3 - 5 x 106 cells per sample) were then pelleted and resuspended in TRIzol (1 ml, Invitrogen) before total RNA extraction via RNeasy Plus Universal Mini Kit (Qiagen) following manufacturer’s protocol.
Libraries were generated using total RNA (5 µl per sample) and QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen) following manufacturer’s instructions.

treatment_protocol: Neutrophils were isolated in 5 biological replicates from mice fed LA, NC, or HFb diets (5 mice per diet). Isolated neutrophils were incubated with either MMF (100 µM) or PBS as a control for 3 hours.

value: bone marrow

value: neutrophils

value: HFbDiet, MMF


title: wo. MMF, 817, HFbD

description: QuantSeq 3‘

value: HFbDiet, PBS


title: MDDC cells, day4, B2A-ICP0-FxE_donor2


title: AF+Nmnat1-LKO4

city: hangzhou

first: Qinchao

last: Ding

state: zhejiang

address: 548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

description: Library name: Sample 8

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method
Assembly: genome assembly
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: liver

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: liver

value: NMNAT1flox/flox-albumin Cre+/-


title: wo. MMF, 819, LAD

description: QuantSeq 3‘

value: LADiet, PBS


title: AF+Nmnat1-LKO3

description: Library name: Sample 7


title: AF+Nmnat1-LKO2

description: Library name: Sample 6


title: wo. MMF, 820, LAD

description: QuantSeq 3‘


title: w. MMF, 820, LAD

description: QuantSeq 3‘

value: LADiet, MMF


title: w. MMF, 819, LAD

description: QuantSeq 3‘


title: MDDC cells, day4, B2A-ICP0_donor2


title: AF+Nmnat1-LKO1

description: Library name: Sample 5


title: wo. MMF, 803, NCD

description: QuantSeq 3‘

value: NCDiet, PBS


title: w. MMF, 803, NCD

description: QuantSeq 3‘

value: NCDiet, MMF


title: AF+Nmnat1-Ctrl4

description: Library name: Sample 4


title: MDDC cells, day4, B2A-Control_donor2

value: Blood


title: MDDC cells, day4, B2A-ICP0_donor1

value: MDDC


title: AF+Nmnat1-Ctrl2

description: Library name: Sample 2


title: AF+Nmnat1-Ctrl3

description: Library name: Sample 3


title: MDDC cells, day4, B2A-Control_donor1


title: wo. MMF, 805, NCD

description: QuantSeq 3‘


title: wo. MMF, 807, NCD

description: QuantSeq 3‘


title: wo. MMF, 816, HFbD

description: QuantSeq 3‘


title: TBI_WT3_RNA-Seq of TBI in mus musculus

city: Shanghai

first: Fang

last: Yuan

address: Yi Shan Road

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: TBI_WT3

data_processing:
Quality control:Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Mapping:Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
Quantification of gene expression level:FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped toeach gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
3.4 Differential expression analysis:Differential expression analysis was performed using the DESeq2m(http://bioconductor.org/packages/release/bioc/html/DESeq2.html) , DEGs with |log2FC|>1 and,Padj <0.05 were considered to be significantly different expressedmgenes.
Assembly: GRCm39
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text file includes FPKM or TMP value for each sample

source_name: Wild-type mice at 7days after traumatic brain injury

growth_protocol: Adult male C57BL/6J mice (20–25 g) were purchased from Shanghai JieSiJie Laboratory Animal Co.,Ltd. and housed under pathogen-free conditions.

extract_protocol:
Total RNA was extracted from the brain using TRIzol® Reagent according the manufacturer’s instructions (Magen).
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system.

treatment_protocol: A controlled cortical impact (CCI) induced TBI model (PinPoint Precision Cortical Impactor PCI3000; Hatteras Instruments Inc., Cary, NC, United States) was performed as previously described (Wang et al., 2022; Yuan et al., 2016). The injury severity parameters were 3-mm diameter impactor tip, velocity of 1.5 m/s, deformation depth of 1.5 mm, and dwell time of 100 ms. Sham animals underwent exactly the same procedure as the injured mice, but the impact was not performed.Mice in drug treatment group received intraperitoneal injection of Zileuton (CSN17529, CSN pharm, dissolved in corn oil) at 10 mg per kg body weight per day after TBI.

value: TBI

tag: batch


title: TBI_WT2_RNA-Seq of TBI in mus musculus

description: Library name: TBI_WT2


title: w. MMF, 805, NCD

description: QuantSeq 3‘


title: w. MMF, 816, HFbD

description: QuantSeq 3‘


title: HaCaT cells, shATF4

first: Qiqi

last: Yang

address: dongchuan road

department: School of Biomedical Engineering

institute: Shanghai Jiao Tong University

description:
Library name: Sample 2
Column name in all.fpkm.xls: shATF4

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data. Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1). Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data. Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: GRCh38.p13
Supplementary files format and content: Column shControl and column shATF4 in all.fpkm.xls represent raw counts, and column shControl_FPKM and column shATF4_FPKM represent associated FPKM.

source_name: HaCaT

growth_protocol: HaCaT cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S).

extract_protocol:
Total RNA was extracted from HaCaT cells using a TRIzol Reagent (YaMei) according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using Asenta‘s protocols

value: HaCaT

value: keratinocyte

value: ATF4 knockdown


title: wo. MMF, 811, LAD

description: QuantSeq 3‘


title: wo. MMF, 806, NCD

description: QuantSeq 3‘


title: w. MMF, 806, NCD

description: QuantSeq 3‘


title: w. MMF, 811, LAD

description: QuantSeq 3‘


title: w. MMF, 807, NCD

description: QuantSeq 3‘


title: TBI_WT1_RNA-Seq of TBI in mus musculus

description: Library name: TBI_WT1


title: Zi_7d3_RNA-Seq of TBI in mus musculus

description: Library name: Zi_7d3

source_name: Zileuton treated wild-type mice at 9days after traumatic brain injury

value: Zileuton


title: MDDC cells, day4, B2A-ICP0-FxE_donor1


title: w. MMF, 808, NCD

description: QuantSeq 3‘

value: bone marrow


title: Zi_7d2_RNA-Seq of TBI in mus musculus

description: Library name: Zi_7d2

source_name: Zileuton treated wild-type mice at 8days after traumatic brain injury


title: wo. MMF, 810, LAD

description: QuantSeq 3‘

value: neutrophils


title: HaCaT cells, shControl

description:
Library name: Sample 1
Column name in all.fpkm.xls: shControl

value: WT


title: wo. MMF, 808, NCD

description: QuantSeq 3‘


title: SH_WT3_RNA-Seq of TBI in mus musculus

description: Library name: SH_WT3

source_name: Controlled wild-type mice without traumatic brain injury

value: control


title: w. MMF, 810, LAD

description: QuantSeq 3‘


title: shSMYD3#2_3

city: Guangzhou

first: Liping

last: Zhang

address: 54 S. Xianlie Road

institute: Sun Yat-sen University Zhongshan Ophthalmic Center

description: Library name: sample 9

data_processing:
The sequencing was performed by HiSeq2500 sequencer (Illumina), and then paired–end sequencing reads (125 bp/150 bp) were aligned to homo_sapiens_Ensembl_97 by using STAR aligner with ensemble gtf (v75) which provides as junctions file.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each Sample
Supplementary files format and content: tab-delimited text file includes gene FPKM for each Sample

growth_protocol: MOLM-13 cells were cultured in RPMI 1640 containing 10% fetal bovine serum, 2 mmol/L L-glutamine, 100 U/ml penicillin , and 100 μg/mL streptomycin.

extract_protocol:
Total RNA was extracted from MOLM-13 cells stably expressing lentiviral Scramble or shRNA targeting two different fragments of SMYD3 using Trizol reagent and subjected to RNA sequencing  analysis.
Sequencing libraries were generated using the NEB Next Ultra TM RNA Library Prep Kit for Illumina (NEB, USA), following the manufacturer’s recommendations (28).

value: AML cells

value: SMYD3 knowdown


title: TBI_7d2_RNA-Seq of TBI in mus musculus

description: Library name: TBI_7d2


title: TBI_7d3_RNA-Seq of TBI in mus musculus

description: Library name: TBI_7d3


title: wo. MMF, 809, LAD

description: QuantSeq 3‘

value: LADiet, PBS


title: C11_AB_3, Apical Bud tissues of Clone11 replcate 3

city: Fuzhou

first: Yu

last: Chen

state: Fujian

address: NO.15 Shangxiadian Road

institute: Fujian Agriculture and Forestry University

description: Library name: Sample18

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud(www.biocloud.net) online platform.
Assembly: Bioproject PRJNA668674
Supplementary files format and content: tab-delimited text file includes raw counts of each sample

organism: Cunninghamia lanceolata

source_name: Apical Bud

extract_protocol:
The plant total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) according the instructions provided by the manufacturer.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Apical Bud


title: shSMYD3#2_2

description: Library name: sample 8


title: SH_WT1_RNA-Seq of TBI in mus musculus

description: Library name: SH_WT1


title: TBI_7d1_RNA-Seq of TBI in mus musculus

description: Library name: TBI_7d1


title: shSMYD3#1_3

description: Library name: sample 6


title: AF+Nmnat1-Ctrl1

description: Library name: Sample 1

value: liver


title: Zi_7d1_RNA-Seq of TBI in mus musculus

description: Library name: Zi_7d1

source_name: Zileuton treated wild-type mice at 7days after traumatic brain injury


title: shSMYD3#2_1

description: Library name: sample 7


title: C11_AB_2, Apical Bud tissues of Clone11 replcate 2

description: Library name: Sample17


title: C11_AB_1, Apical Bud tissues of Clone11 replcate 1

description: Library name: Sample16


title: w. MMF, 809, LAD

description: QuantSeq 3‘

value: LADiet, MMF


title: SH_WT2_RNA-Seq of TBI in mus musculus

description: Library name: SH_WT2


title: Scramble3

description: Library name: sample 3


title: C1_AB_2, Apical Bud tissues of Clone1 replcate 2

description: Library name: Sample14


title: shSMYD3#1_2

description: Library name: sample 5


title: Scramble2

description: Library name: sample 2


title: P5_Postmitotic_Labelled_Mutant_Neurons_3

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

description:
P5_Lhx2_Postmitotic_RNASeq_CountMatrix.txt
P5_Lhx2_Postmitotic_DESeq2_results.txt

data_processing:
Read alignment software - HISAT2
Read mapping tool - FeatureCounts
Read normalization - DESeq2
Assembly: mm10
Supplementary files format and content: CSV and TXT file format; Raw Counts
Supplementary files format and content: CSV and TXT file format; Normalized Counts

source_name: Cerebral Cortex

growth_protocol: in vivo neurons isolated using microdissection.

extract_protocol:
Trypsin-based tissue dissociation and PCI-based RNA isolation
NEBNext RNA Ultra II directional protocol 2x150bp

treatment_protocol: Layer II/III microdissection from live brain cortical coronal sections

value: Cerebral Cortex

tag: developmental stage

value: Cortical layer II/III Neurons

value: NexCre/+; Lhx2lox/lox

value: EGFP electroporation


title: wo. MMF, 812, HFbD

description: QuantSeq 3‘

value: HFbDiet, PBS


title: C1_AB_3, Apical Bud tissues of Clone1 replcate 3

description: Library name: Sample15


title: shSMYD3#1_1

description: Library name: sample 4


title: wo. MMF, 814, HFbD

description: QuantSeq 3‘


title: wo. MMF, 815, HFbD

description: QuantSeq 3‘


title: w. MMF, 812, HFbD

description: QuantSeq 3‘

value: HFbDiet, MMF


title: C1_AB_1, Apical Bud tissues of Clone1 replcate 1

description: Library name: Sample13


title: P5_Postmitotic_Labelled_Mutant_Neurons_2


title: w. MMF, 815, HFbD

description: QuantSeq 3‘


title: Scramble1

description: Library name: sample 1


title: C11_UP_3, Upper Phloem tissues of Clone11 replcate 3

description: Library name: Sample12

source_name: Upper Phloem

value: Upper Phloem


title: C11_UP_2, Upper Phloem tissues of Clone11 replcate 2

description: Library name: Sample11


title: w. MMF, 814, HFbD

description: QuantSeq 3‘

value: bone marrow


title: P5_Postmitotic_Labelled_Mutant_Neurons_1


title: C11_UP_1, Upper Phloem tissues of Clone11 replcate 1

description: Library name: Sample10


title: severe,scRNAseq

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Tab-separated values file includes cell type annotation for the single-cell RNA-seq data

source_name: lung tissue

extract_protocol:
Single cells were collected into RPMI 1640 containing 5% FBS. Trypan blue exclusion confirmed the cell viability. Sorted cells were counted and concentration adjusted to 700 – 1,200 cells/μl. Then single-cell suspensions were loaded to a 10x Chromium to capture no more than 10,000 single cells by Chromium Single Cell 3’ Reagent kits v.3 (10x Genomics). The cells were partitioned into Gel Beads in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: lung tissue

value: immune cell


title: P5_Postmitotic_Labelled_Control_Neurons_3


title: C1_UP_3, Upper Phloem tissues of Clone1 replcate 3

description: Library name: Sample9


title: mild,scRNAseq


title: P5_Postmitotic_Labelled_Control_Neurons_1


title: MT,skin 2

city: Xuzhou

first: Cen

middle: Ai

state: Jiangsu

address: No.2 Kunpeng

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

description: Library name: MT-S 2

data_processing:
Fastp (v0.21.0) (Chen et al. 2018) (--length_required=50) was used for removing adapter and low-quality reads of the raw sequencing data. The filtered clean reads were then mapped to the Beauregard (v3) reference genome (http://sweetpotato.uga.edu/sweetgains_Beauregard_v3_asm_anno.shtml) using HISAT2 (v2.0.5) with default parameters.
The RNA-seq reads within per gene were counted using the featureCounts (Liao et al. 2014), with the multiple align reads filtered out.
The counts matrix of all samples was used as the input of R package DESeq2 (v1.40.2) (Love et al. 2014) for the identification of DEGs. Genes with padj < 0.05 and |log2(foldchange)| > 1 were confirmed as DEGs.
Assembly: Beauregard（v3）
Supplementary files format and content: txt file of gene counts for each sample

organism: Ipomoea batatas

source_name: storage root skin

extract_protocol:
Total RNA was prepared from flesh and root skin samples using TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA). The concentration and integrity of RNA were measured by an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and RNase-free agarose gel electrophoresis, respectively. Following the removal of rRNA using the Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA), the mRNA was enriched by Oligo (dT) beads.
The completed mRNA was then used for library construction following the manufacturer’s protocol of NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA).  All mRNA-seq libraries were sequenced on Illumina NovaSeq 6000 platform in Gene Denovo Biotechnology Company, Guangzhou, China.

value: storage root skin

value: MT

value: normal


title: MT,skin 1

description: Library name: MT-S 1


title: P5_Postmitotic_Labelled_Control_Neurons_2


title: MT,flesh 3

description: Library name: MT-F 3

source_name: storage root flesh

value: storage root flesh


title: C1_UP_2, Upper Phloem tissues of Clone1 replcate 2

description: Library name: Sample8


title: P5_Progenitor_Labelled_Mutant_Neurons_4

description:
P5_Lhx2_Progenitor_countsMatrix.csv
P5_Lhx2_Progenitor_DESeq2_Results.csv

value: Cre-EGFP electroporation


title: C1_UP_1, Upper Phloem tissues of Clone1 replcate 1

description: Library name: Sample7


title: sham,replicate2,scRNAseq


title: MT,flesh 2

description: Library name: MT-F 2


title: P5_Progenitor_Labelled_Mutant_Neurons_3


title: sham,replicate1,scRNAseq


title: C11_LB_3, Lateral Bud tissues of Clone11 replcate 3

description: Library name: Sample6

source_name: Lateral Bud

value: Lateral Bud


title: P5_Progenitor_Labelled_Mutant_Neurons_2


title: MT,flesh 1

description: Library name: MT-F 1


title: WT,skin 3

description: Library name: S 3

value: WT


title: C11_LB_2, Lateral Bud tissues of Clone11 replcate 2

description: Library name: Sample5


title: MT,skin 3

description: Library name: MT-S 3


title: Control-2

city: Chengdu

first: Tingting

last: Jia

state: None Selected

address: No. 37, Guoxue Street, Chengdu, Sichuan, China

institute: West China Hospital of Sichuan University

description: Library name: Control-2

data_processing:
Raw RNA-seq reads were first quality-checked using FastQC and trimmed to remove adapters and low-quality bases with Trimmomatic. Clean reads were then aligned to the Drosophila melanogaster reference genome using HISAT2. The resulting alignments were processed to quantify gene expression levels with featureCounts. Differential expression analysis between BuGZ-overexpressing and control groups was performed using DESeq2, and significantly altered genes were identified based on adjusted p-value and fold-change thresholds.
Assembly: Drosophila melanogaster genome assembly dm6 (BDGP6)
Supplementary files format and content: Processed data files and detailed protocols are available upon request from the corresponding author.

organism: Drosophila melanogaster

source_name: Abdomen

extract_protocol:
After 24 hours of starvation, the abdomens of adult female flies were dissected on ice and immediately transferred into TRIzol reagent. Tissues were homogenized thoroughly, and total RNA was extracted following the standard TRIzol protocol, including chloroform phase separation, isopropanol precipitation, ethanol washing, and resuspension in RNase-free water. RNA quality and concentration were assessed using a Nanodrop or Qubit before sequencing.
Total RNA was treated with DNase I to remove genomic DNA contamination, and mRNA was enriched using poly(A) selection. The purified mRNA was fragmented and reverse transcribed into cDNA using random primers. After second-strand synthesis, the cDNA was end-repaired, A-tailed, and ligated to sequencing adapters. The ligated products were PCR-amplified to generate the final sequencing libraries, which were quantified, assessed for quality, and then subjected to high-throughput sequencing.

value: Abdomen

value: Control


title: Control-3

description: Library name: Control-3


title: WT,skin 2

description: Library name: S 2


title: C11_LB_1, Lateral Bud tissues of Clone11 replcate 1

description: Library name: Sample4


title: Control-1

description: Library name: Control-1


title: P5_Progenitor_Labelled_Mutant_Neurons_1

value: Cerebral Cortex

value: Cortical layer II/III Neurons


title: P5_Progenitor_Labelled_Control_Neurons_4

value: EGFP electroporation


title: WT,skin 1

description: Library name: S 1


title: C1_LB_3, Lateral Bud tissues of Clone1 replcate 3

description: Library name: Sample3


title: BuGZ-FL-3

description: Library name: BuGZ-FL-3

value: BuGZ-overexpressing


title: P5_Progenitor_Labelled_Control_Neurons_3


title: WT, flesh 3

description: Library name: F 3


title: WT, flesh 2

description: Library name: F 2


title: BuGZ-FL-2

description: Library name: BuGZ-FL-2


title: C1_LB_1, Lateral Bud tissues of Clone1 replcate 1

description: Library name: Sample1


title: P5_Progenitor_Labelled_Control_Neurons_1


title: WT, flesh 1

description: Library name: F 1


title: BuGZ-FL-1

description: Library name: BuGZ-FL-1


title: KD_IP-2

status: Public on May 24 2025

first: Guofeng

last: Feng

address: 94 Weijin Road

institute: Nankai University

data_processing:
The quality control with the software FastQC v0.11.9
Clean reads were aligned to the reference genome (mm10) by using HISAT2 software (v2.2.1)
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via SAMtools (v.1.7) .Finally, the BAM-format reads for each paired IP + input samples were processed by exome-Peak2 software (v1.8.1) to identify significant acetylation peaks in each IP sample.
Assembly: mm10
Supplementary files format and content: raw counts
Library strategy: acRIP-seq

extract_protocol:
The RNA is first extracted from the Nat10 CON and Nat10 KD mESCs by TRIzol, the RNA is quality controlled, and the concentration and purity of the RNA is detected. Total RNA was subjected to immunoprecipitation with the GenSeq® ac4C RIP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to about 200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4 ℃ for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced in a NovaSeq platform (Illumina).
Libraries were prepared for sequencing using standard Illumina protocols

value: mouse embryonic stem cells

value: Nat10 KD

value: with Dox


title: KD_input-2


title: KD_input-1


title: KD_IP-1


title: CON_input-2

value: Nat10 WT

value: without Dox


title: CON_input-1


title: CON_IP-2


title: CON_IP-1


title: wDox_IP-2

data_processing:
The quality control with the software FastQC v0.11.9
Clean ChIP-seq reads were aligned to mouse genome assembly (mm10) by BOWTIE2 with the parameter “--local -k 1”.
excluding reads from repetitive elements, multiple-hit reads are evenly distributed over highly similar repeat elements across the genome. Bam files were obtained using SAMtools (v.1.7).
Assembly: mm10
Supplementary files format and content: raw counts

extract_protocol:
About 2×107 of Nat10 CON and Nat10 KD mESCs were first fixed with 1% paraformaldehyde, and then lysed and sonicated to achieve the majority of DNA fragments at 100–500bp. DNA fragments were then enriched by immunoprecipitation with 5 μg H3K9me3 antibody (ab8898, Abcam) and Dynabeads M280 (Life Technologies), rocked at 4 ℃ overnight. The immunoprecipitated material was eluted from the beads by heating for 30 min at 65 ℃. Then, samples were incubated at 65 ℃ for overnight to reverse crosslinking. The samples were then extracted with phenol: chloroform: isoamyl alcohol (25: 24: 1, pH > 7.8) followed by chloroform, ethanol precipitated in the presence of glycogen, and re-suspended in ddH2O. ChIP enriched DNA was used for library construction by Novogene Corporation. Each library was subsequently sequenced, resulting in ~20 million reads (125 bp).
Libraries were prepared for sequencing using standard Illumina protocols


title: wDox_input-2


title: wDox_input-1


title: wDox_IP-1


title: woDox_input-2


title: woDox_IP-2


title: woDox_IP-1


title: KD-3

data_processing:
The quality control with the software FastQC v0.11.9
Clean reads were aligned to the mouse mm10 genome with the STAR 2.5.3a software
The counts were calculated with the software featurecounts
Assembly: mm10
Supplementary files format and content: raw counts

extract_protocol:
RNA was harvested using TRIzol. About 2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols


title: KD-1


title: KD-2


title: C1_LB_2, Lateral Bud tissues of Clone1 replcate 2

description: Library name: Sample2


title: CON-3


title: P5_Progenitor_Labelled_Control_Neurons_2


title: CON-2


title: CON-1


title: Fasting_Pre_L7

city: Burlinton

first: Arti

last: Sukla

state: VT

address: 89 Beaumont Avenue

department: Pathology and Laboratory Medicine

country: USA

institute: University of Vermont

description: Library name: L7_1_S11

data_processing:
The Illumina sequences were trimmed of bases with a Phred quality score < 15 and any contaminating adapters used in cDNA and sequencing library preparation. Only single end reads which survived trimming and were ≥ 60 bases in length were mapped to the human (GRCh37, version 17, Ensembl 72) genome using StringTie.
Raw reads were normalized to library DNA input and mapped to the Human reference Genome 38 using StringTie at a depth greater than those prescribed by the 2017 ENCODE guidelines for transcriptome sequencing depth. Raw counts were imported and analyzed using the edgeR package and gene names were extracted using ballgown in R (version 4.0.2).
Counts were adjusted for library size and normalized using the using the TMM (trimmed mean of M values) method. Counts were retained only if a gene counts per million reads (CPM) were ≤ 2 and occurred in at least three samples.
To generate gene expression, gene levels were assessed separately in each of the two sequencing lanes run. P-values were determined based on the comparison of the post to pre groups; high-calorie post:pre and fasting post:pre.
Differential expressed genes were determined to have a p-value < 0.05 and a fold change > 2.0 or a fold change < -2.0.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: Bone marrow adipocytes

extract_protocol:
Samples were de-identified, so the sex of each sample is unknown. Also, the 6 pre-samples and 6 post-samples are from the same participants for each dietary phase (i.e., L6 (post)/L5 (pre) are from one participant).
Bone marrow adipocytes were collected from bone marrow biopsy of the iliac crest, as previously described (Fazeli et al, JCI 2021). A subset of samples from the high calorie diet and fasting cohorts (High calorie diet pre n = 6, post n = 6; Fasting: pre n = 6, post n = 6) were shipped to the Vermont Biomedical Research Network (University of Vermont, Burlington, VT) for total RNA extraction and high-throughput RNA-sequencing analysis. RNA was extracted using a modified MagMAX mirVana RNA extraction protocol with a double clean up step added to remove excess phenol (Applied Biosystems A27828). Final RNA was protected by adding Ribolock RNase inhibitor (ThermoFisher, cat. no. EO0381, Waltham, MA USA) to a final concentration of 0.25 U/µL of RNA. RNA was evaluated for quality based on 28S and 18S rRNA using the RNA Picochip (Agilent cat. no. 5067–1513) on the Agilent Bioanalyzer 2100 (Santa Clara, Ca). The 260/280 ratio was assessed on a Nanodrop ND1000 (ThermoFisher, Waltham, MA) and quantified using the RNA HS kit using the Quantus Fluorometer (Promega Madison, WI).
RNA-sequencing libraries for Illumina sequencing were constructed using 6 ng of total RNA with the Takara SMARTer Stranded Total RNA-Seq Kit v2 (634412) and evaluated using the Agilent Bioanalyzer 2100 and DNA HS chip. Equal amounts of each library were pooled for sequencing and combined with 10% PhiX control prior to sequencing using HiSeq 1500 with a single read V3 rapid flow cell for a total of 80bp (Illumina Corp San Diego, CA).

treatment_protocol: Male and female participants (age range: 22–44 years) were of normal weight or overweight (BMI range: 23.3–27.9). No participant had a history of diabetes mellitus or a history of an eating disorder, and none of the participants were taking chronic medications. All women were premenopausal and had a history of regular menstrual cycles. Participants were initially admitted to the Translational and Clinical Research Center at the Massachusetts General Hospital for a 10-day high-calorie visit. Based on body weight, the Mifflin St Jeor equation was used with an activity factor of 1.3 to calculate their caloric needs for 7% weight gain. After completion of the high-calorie protocol, participants returned to their normal diet for 13 to 18 days (median: 15 days), referred to as the 2-week stabilization period. Subjects were subsequently re-admitted for a second inpatient visit (fasting visit), during which subjects did not consume any calories for 7 to 10 days but were permitted to drink water ad libitum and received a multivitamin containing 400 IU of cholecalciferol daily as well as 20 mEq of potassium chloride.

value: Bone marrow adipocytes


title: Fasting_Pre_M3A

description: Library name: M3A_2_S10


title: Fasting_Pre_N1

description: Library name: N1_3_S5


title: Fasting_Pre_O7

description: Library name: 07_7_S9


title: Pooled monoclonal mouse EBs with CRISPR perturbations

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Library name: monoclonal_screen

data_processing:
Single-cell transcriptome data (10X) were processed using Cell Ranger 7.2.0 with default settings, followed by filtering of low-quality cells based on UMI counts, detected genes, and doublet detection. Additional quality control included filtering cells based on mitochondrial and ribosomal read percentages.
Assembly: GRCm38
Supplementary files format and content: The gene-by-cell matrix (sparse matrix), cell and gene metadata (CSV)

source_name: Embryoid bodies (EBs)

extract_protocol:
To obtain a single-cell suspension for downstream single-cell experiments, EBs at a given time point, typically at day 21 for the mosaic perturbation screens or at day 7, 14, or 21 for the wildtype time series experiment, were collected into 50 mL conical tubes at a density of three plates per tube and allowed to settle by gravity. The old CA medium was carefully removed and replaced with PBS (-/-) for two sequential washes, allowing EBs to settle by gravity after each wash. After removing the final wash, 3 mL of 0.25% trypsin was added to the tube, and the EBs were incubated at 37C for 5 min with gentle agitation. To achieve a uniform single-cell suspension, the trypsinized EBs were carefully pipetted up and down using a P1000 pipette followed by quenching with CA medium. The cell suspension was passed through a 40 um cell strainer, centrifuged at 300g for 5 min, and the cell pellet resuspended to a final concentration of 2 million cells / mL. FAC sorting was performed to enrich for a clean single-cell population, after which the cells were centrifuged at 400g for 5 min and resuspended in cold PBS containing 0.04% BSA at a concentration of approximately 1200 cells/uL. The resulting single-cell suspension was then processed following the 10x Genomics protocol as per the manufacturer’s instructions, loading 16K cells per lane for an estimated recovery of 10K cells.  For dissociating monoclonal EBs into a single-cell suspension, CA media was removed from each 2 mL tube, and 750 µL of 0.25% trypsin was added. Tubes were incubated at 37°C on a thermomixer set to 1100 rpm, with dissociation monitored under an epifluorescence microscope at 5-minute intervals. At the 10-minute mark, gentle trituration with a P1000 pipette was performed to aid dissociation, with additional trypsin added if necessary. Complete dissociation was typically achieved within 20 minutes. Trypsin was inactivated by adding CA media, and the cell suspension was further diluted before being passed through a 45 µm strainer into a 50 mL conical tube containing 10 mL of CA media. Cells were counted using a hemocytometer, transferred to a 15 mL conical tube for ease of handling, and centrifuged at 400g for 5 minutes. The supernatant was removed, and the cell pellet was resuspended in PBS + 0.04% BSA. The initial cell concentration was adjusted to 2400 cells/µL. A second cell count was performed, and the suspension was further diluted to a final concentration of 1200 cells/µL. Single-cell suspensions from each condition were then processed using the 10X Genomics High Throughput (HT) kit, with cells loaded across 16 lanes.
Wild-Type Time Series: Libraries were prepared using the 10x Genomics Single Cell 3' v2 kit. Three time points (days 7, 14, and 21) were sequenced, with one lane per time point, for a total of three lanes. Final libraries were sequenced on a NextSeq 500 using a 75-cycle high-output kit (R1: 26 bp, I1: 8 bp, I2: 0 bp, R2: 57 bp).  Pilot Screen: Libraries were prepared using the 10x Genomics Single Cell 3' v3 kit. Replicate 1: Six lanes were sequenced: two lanes for CRISPRcut sorted, two lanes for CRISPRi sorted, one lane for CRISPRcut unsorted, and one lane for CRISPRi unsorted. Final libraries were sequenced on a NextSeq 500 using two 75-cycle high-output kits (R1: 26 bp, I1: 8 bp, I2: 0 bp, R2: 57 bp). Replicate 2: Six lanes were sequenced: three lanes for CRISPRcut and three lanes for CRISPRi. Final libraries were sequenced on a NextSeq 500 using two 75-cycle high-output kits (R1: 28 bp, I1: 8 bp, I2: 0 bp, R2: 55 bp).  All TF Screen: Libraries were prepared using the 10x Genomics Single Cell 3' v3 kit. A total of 32 lanes were sequenced for CRISPRcut. Final libraries were sequenced by the Northwest Genomics Center on a NovaSeq 6000 using one S2 flow cell and one S4 flow cell (R1: 28 bp, R2: 80 bp, I1: 10 bp).  125TF Screen: Libraries were prepared using the 10x Genomics Single Cell 3' v3 kit. A total of 32 lanes were sequenced for CRISPRcut. Final libraries were sequenced by the Northwest Genomics Center using both a NovaSeq 6000 with one S4 flow cell (R1: 28 bp, I1: 10 bp, I2: 0 bp, R2: 91 bp) and a NextSeq 2000 with a P3 100-cycle kit (R1: 28 bp, I1: 8 bp, I2: 0 bp, R2: 91 bp).  piggyFlex and monoclonal EB validation: Sequencing was performed using four lanes of the 10X Genomics Single Cell 3' v3 kit, with two lanes allocated for replicate 1 and two lanes for replicate 2. Final libraries, capturing both gene expression and directly captured gRNAs, were sequenced on a NextSeq 2000 P2 100-cycle kit (R1: 28 bp, I1: 8 bp, I2: 0 bp, R2: 91 bp). Organoid barcode (BC) transcripts were separately sequenced using a NextSeq High 75-cycle kit (R1: 28 bp, I1: 10 bp, I2: 0 bp, R2: 53 bp).  TF screen in monoclonal EBs: Sequencing for the TF screen in monoclonal EBs was performed using 16 lanes of the 10X Genomics Single Cell 3’ HT Kit v3.1, with 12 lanes dedicated to conditions 1–10 and 4 lanes for condition 11. Final libraries, capturing gene expression, directly captured gRNAs, and organoid BCs, were sequenced on a NextSeq 2000 P3 100-cycle kit (R1: 28 bp, I1: 10 bp, I2: 10 bp, R2: 90 bp).

value: Embryoid bodies (EBs)


title: Fasting_Pre_L1

description: Library name: L1_7_S5


title: Fasting_Post_M4

description: Library name: M4_4_S8


title: Fasting_Post_N2

description: Library name: N2_4_S6


title: 106 pooled monoclonal gastruloids derived from mouse embryonic stem cells, 10X

description: Library name: tree_of_trees

data_processing:
For the sci_RNA_seq3 data, transcriptome data from six plates were processed independently, with alignment, gene count matrix generation, and quality filtering performed using a custom pipeline. The process included demultiplexing, trimming, read alignment, duplicate removal, and creation of gene expression matrices, followed by filtering out low-quality cells. For the other two experiments, single-cell transcriptome data (10X) were processed using Cell Ranger with default settings, followed by filtering of low-quality cells based on UMI counts, detected genes, and doublet detection. Additional quality control included filtering cells based on mitochondrial and ribosomal read percentages.
Assembly: GRCm39 (sci_RNA_seq3) and GRCm38 (eight_gastruloids and tree_of_trees)
Supplementary files format and content: The gene-by-cell matrix (sparse matrix), cell and gene metadata (CSV)

source_name: Mouse gastruloids

extract_protocol:
For the cell extraction contructing the sci_RNA_seq3 library, we used cell fixation protocol published by Martin et al., Nature Protocol 2023 (doi: 10.1038/s41596-022-00752-0, PMCID: PMC9839601). For the cell extraction contructing the eight_gastruloids and tree_of_trees library, we used 10X Genomics' scRNA-seq kit (Chromium Next GEM Single Cell 3' HT v3.1).
For the sci_RNA_seq3 library construction, we used single-cell combinatorial indexing protocol (sci-RNA-seq3) by Martin et al., Nature Protocol 2023 (doi: 10.1038/s41596-022-00752-0, PMCID: PMC9839601). For the eight_gastruloids and tree_of_trees library, we used 10X Genomics' scRNA-seq kit (Chromium Next GEM Single Cell 3' HT v3.1).

value: Mouse gastruloids


title: 8 pooled monoclonal gastruloids derived from mouse embryonic stem cells, 10X

description: Library name: eight_gastruloids


title: 149 pooled monoclonal gastruloids derived from mouse embryonic stem cells (plate 6), sci-RNA-seq3

description: Library name: sci_RNA_seq3_plate_6


title: 148 pooled monoclonal gastruloids derived from mouse embryonic stem cells (plate 5), sci-RNA-seq3

description: Library name: sci_RNA_seq3_plate_5


title: Fasting_Post_L4A

description: Library name: L4A_12_S1


title: woDox_input-1


title: Fasting_Post_O8

description: Library name: 08_8_S10


title: Fasting_Post_L2

description: Library name: L2_8_S4


title: 146 pooled monoclonal gastruloids derived from mouse embryonic stem cells (plate 3), sci-RNA-seq3

description: Library name: sci_RNA_seq3_plate_3


title: High Calorie_Pre_N9

description: Library name: N9_5_S7

value: High Calorie_Pre


title: High Calorie_Pre_N5

description: Library name: N5_D710_S6


title: 147 pooled monoclonal gastruloids derived from mouse embryonic stem cells (plate 4), sci-RNA-seq3

description: Library name: sci_RNA_seq3_plate_4


title: 15 manually selected, pooled monoclonal mouse EBs at day 8

description: Library name: monoclonal_proof


title: Fasting_Pre_L3A

description: Library name: L3A_10_S2


title: 144 pooled monoclonal gastruloids derived from mouse embryonic stem cells (plate 1), sci-RNA-seq3

description: Library name: sci_RNA_seq3_plate_1


title: High Calorie_Pre_M7

description: Library name: M7_D708_S1


title: MRC5 cells, luteolin plus TGF-β1 treatment in MRC5 cell line,  48h  (miRNA)

city: Kaohsiung

first: Yu-Hsin

last: Tseng

address: No.100, Tzyou 1st Rd., Sanmin Dist.

department: Department of Pediatrics

country: Taiwan

institute: Kaohsiung Medical University Hospital

description: Library name: M4TL9_miRNA

data_processing:
Low-quality bases and adapter sequences in the raw data were trimmed using the fastp tool (version 0.20.0). The resulting high-quality reads were aligned to reference genomes with HISAT2 (version 2.1.0). Gene expression levels were quantified using FeatureCounts (version 2.0.1). Differentially expressed genes (DEGs) were identified through EdgeR (version 3.36.0), and functional enrichment analysis was conducted using ShinyGO (version 0.76).
Assembly: hg38
Supplementary files format and content: A excel file include TPM values for each samples.

source_name: cell line

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA). For library construction, 1 μg of total RNA was used for RNA-seq and an additional 1 μg for small RNA-seq.
RNA and small RNA libraries were prepared using the TruSeq Stranded mRNA and TruSeq Small RNA Library Prep Kits, respectively (Illumina, San Diego, CA, USA).

value: cell line

value: luteolin plus TGF-β1


title: High Calorie_Pre_M5

description: Library name: M5_5_S7


title: High Calorie_Post_N10

description: Library name: N10_6_S8

value: High Calorie_Post


title: High Calorie_Pre_M1

description: Library name: M1_D711_S5


title: High Calorie_Pre_L5

description: Library name: L5_D712_S7


title: Pooled mosaic mouse EBs with CRISPR perturbation targeting 125 selected TFs

description: Library name: validated_125TF


title: MRC5 cells,TGF-β1 treatment, 48h  (miRNA)

description: Library name: M4TD2_miRNA

value: WT


title: MRC5 cells, control, 48h  (miRNA)

description: Library name: M0TD1_miRNA

value: DMSO


title: Fasting_Post_L8

description: Library name: L8_2_S4


title: Sample_Waga DMSO H3K27ac HiChIP

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
library strategy: AQuA-HiChIP
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.  DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
HiChIP: Paired end reads were mapped once to the human genome (hg19), and in parallel also mapped to the mouse genome (mm10), using bowtie2 within the HiC-pro pipeline
HiChIP: Mapped read pairs were then filtered first for junction validity (containing two fragments from restriction digestion), then duplicates were removed, using HiC-pro pipeline
HiChIP: AQuA factor incorporation was done by calculating the Contacts Per Million (CPM=Raw contact frequency matrix*1,000,000/total valid contacts), then converting to Reference normalized Contacts Per Million (RCPM=CPM*hg19 valid contacts/mm10 valid contacts).
HiChIP: Contact maps were converted to Juicebox compatible *.hic file format using the hicpro2juicebox.sh tool (https://github.com/nservant/HiC-Pro) provided with HiC-pro, and matrices were extracted using the Juicer33 dump tool (https://github.com/theaidenlab/juicer/wiki/Data-Extraction).
Assembly: Hg19
Supplementary files format and content: peak files are tab delimited text files for each sample.
Supplementary files format and content: HiChIP: processed file is in Juicer and Juicebox compatible .hic format, that is a contact matrix

source_name: Waga

growth_protocol: MCC cell lines were grown in RPMI with 10% FBS, 100U/ml penicillin and 0.1 mg/mL streptomycin.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.  DNase-seq DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: Samples were then harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

value: Waga

value: Merkel Cell carcinoma (MCC) cell line

tag: antibody

value: H3K27ac (Active Motif, 39133)

tag: enrichment target

value: DMSO 6 hours

tag: molecule subtype

value: DNA (ChIP-enriched)


title: High Calorie_Post_M8

description: Library name: M8_D707_S2


title: High Calorie_Post_M2

description: Library name: M2_1_S3


title: High Calorie_Post_M6

description: Library name: M6_6_S6


title: T2-9, Treatment with 1.0 W/cm2 intensity for 4 weeks

city: Hefei

first: Wang

last: Zhou

address: Mozitan Road

institute: Anhui

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads.   Approximately 50M raw reads were obtained per sample.   Raw reads in fastq format were processed using the fastp software to remove low-quality reads, resulting in clean reads for subsequent analysis.   The clean reads were aligned to the reference genome using HISAT2, and gene expression levels were quantified in terms of FPKM (Fragments Per Kilobase of exon per Million mapped reads).   Read counts for each gene were obtained using HTSeq-count.   Principal Component Analysis (PCA) and plotting of gene counts were performed using R (v 3.2.0) to assess the biological replicates of the samples.
Differential expression analysis was performed using the DESeq2 software, with genes meeting the criteria of q-value < 0.05 and fold change > 2 or fold change < 0.5 defined as differentially expressed genes (DEGs). Hierarchical clustering analysis of DEGs was conducted using R (v 3.2.0) to illustrate gene expression patterns across different groups and samples. A radar plot of the top 30 DEGs was generated using the R package ggradar to visualize the changes in expression levels of upregulated or downregulated genes.
Subsequently, GO, KEGG Pathway, Reactome, and WikiPathways enrichment analyses were performed on the differentially expressed genes using the hypergeometric distribution algorithm to identify significantly enriched functional terms. Bar plots, chord plots, or enrichment circles of the significantly enriched functional terms were generated using R (v 3.2.0). Gene set enrichment analysis (GSEA) was conducted using GSEA software. The predefined gene sets were ranked according to the degree of differential expression between the two sample groups, and the analysis tested whether the predefined gene sets were enriched at the top or bottom of this ranked list.
After sequence reassembly using StringTie2, the known annotated genes were compared with the reference genome using Cuffcompare software to extend gene structures and identify novel transcripts. Differentially regulated transcripts or exons were analyzed for alternative splicing using ASprofile. SNPs and InDels were analyzed using SAMtools and BCFtools, with detailed information available at SAMtools (http://samtools.sourceforge.net/mpileup.shtml). Variants were then annotated and their effects on genes (e.g., amino acid changes) predicted using SnpEff.
Assembly: Rat RGSC 6.0/rn6
Supplementary files format and content: The file named "FPKM_anno.txt" contains the following columns:
Supplementary files format and content: Gene ID: Identifier for each gene based on the reference genome annotation.
Supplementary files format and content: Gene Symbol: Standard gene symbols as recognized by official databases.
Supplementary files format and content: FPKM Values: Expression levels quantified as Fragments Per Kilobase of transcript per Million mapped reads, representing normalized gene expression to account for differences in gene length and sequencing depth.
Supplementary files format and content: Sample IDs: Each column after the gene expression metrics corresponds to a different sample, with the column header indicating the unique identifier for each sample.
Supplementary files format and content: Annotations: Additional information about each gene, such as gene function or relevant gene ontology (GO) terms, is included to facilitate the interpretation of gene expression data.

organism: Rattus norvegicus

source_name: prostate tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA purity and quantification were assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit according to the manufacturer's protocol. Transcriptome sequencing and analysis were performed by OE Biotech Co., Ltd. (Shanghai, China).

value: prostate tissue

tag: strain

value: SD rat

value: low intensity pulsed ultrasound was treated at 1.5 W/cm2 for 4 weeks


title: Sample_MKL1 Pano H3K27ac HiChIP

value: Panobinostat 6 hours


title: High Calorie_Post_L6

description: Library name: L6_D704_S3

value: Bone marrow adipocytes


title: Sample_MKL1 DMSO H3K27ac HiChIP


title: MRC5 cells, luteolin plus TGF-β1 treatment in MRC5 cell line,  48h (mRNA)

description: Library name: M4TL9


title: 145 pooled monoclonal gastruloids derived from mouse embryonic stem cells (plate 2), sci-RNA-seq3

description: Library name: sci_RNA_seq3_plate_2

value: Mouse gastruloids


title: T2-8, Treatment with 1.0 W/cm2 intensity for 4 weeks


title: MRC5 cells, control, 48h (mRNA)

description: Library name: M0TD1


title: T2-7, Treatment with 1.0 W/cm2 intensity for 4 weeks


title: Sample_MKL2 SOX2

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.  DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
HiChIP: Paired end reads were mapped once to the human genome (hg19), and in parallel also mapped to the mouse genome (mm10), using bowtie2 within the HiC-pro pipeline
HiChIP: Mapped read pairs were then filtered first for junction validity (containing two fragments from restriction digestion), then duplicates were removed, using HiC-pro pipeline
HiChIP: AQuA factor incorporation was done by calculating the Contacts Per Million (CPM=Raw contact frequency matrix*1,000,000/total valid contacts), then converting to Reference normalized Contacts Per Million (RCPM=CPM*hg19 valid contacts/mm10 valid contacts).
HiChIP: Contact maps were converted to Juicebox compatible *.hic file format using the hicpro2juicebox.sh tool (https://github.com/nservant/HiC-Pro) provided with HiC-pro, and matrices were extracted using the Juicer33 dump tool (https://github.com/theaidenlab/juicer/wiki/Data-Extraction).
Assembly: Hg19
Supplementary files format and content: peak files are tab delimited text files for each sample.
Supplementary files format and content: HiChIP: processed file is in Juicer and Juicebox compatible .hic format, that is a contact matrix

value: anti-SOX2 (R&D Systems cat#AF2018)

value: untreated


title: RNA-seq of human: shTIA1_3 HMC3 cells after OGD

city: Hangzhou

first: hong

last: yu

address: 2318 Yuhangtang Road

department: School of Pharmacy

institute: Hangzhou Normal University

description: Library name: shTIA1_3

data_processing:
Alignment Analysis: Software is hisat2, version 2.0.5, parameters are default parameters. Protein - Protein Interaction Analysis: Software is diamond, version 0.9.14, parameters are e - value = 1e - 10. Alternative Splicing: Software is rMATS, version 4.1.0, parameters are default parameters. Variation Analysis: Software is GATK, version 4.1.1.0, parameters are MQ < 40.0 and QD < 2.0 and FS > 30.0 and DP < 10 and QUAL < 20. Variation Analysis: Software is snpEff, version 4.3.1q, parameters are default parameters.
Differential Analysis: Software is DESeq2, version 1.20.0, parameters are ∣log2(FoldChange)∣>1 & padj<0.05.
Differential Analysis: Software is edgeR, version 3.22.5, parameters are ∣log2(FoldChange)∣>1 & padj<0.05.
Enrichment Analysis: Software is clusterProfiler, version 3.8.1, parameters are padj<0.05.
GSEA Analysis: Software is gsea, version v4.3.2, parameters are -permute phenotype -metric Signal2Noise -set_min 15 -set_max 5000 -plot_top_x 50.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: txt files include FPKM values for each Sample

source_name: brain

growth_protocol: HMC3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from HMC3 cells that had been subjected to oxygen - glucose deprivation (OGD) for 4 hours using RNAiso Plus reagent (Takara, Japan).
RNA libraries for RNA - seq were prepared by using poly - T oligo - attached magnetic beads to purify mRNA from total RNA, fragmenting it with divalent cations in First Strand Synthesis Reaction Buffer, synthesizing first and second strand cDNA, converting overhangs to blunt ends, adenylating 3' ends and ligating adapters, purifying with AMPure XP system, performing PCR with specific enzymes and primers, and finally purifying PCR products and assessing library quality on the Agilent Bioanalyzer 2100 system.

value: brain

value: Human microglia cells

tag: genetic modification

value: TIA1 knockdown

value: Oxygen - Glucose Deprivation

value: 4 h


title: RNA-seq of human: shTIA1_2 HMC3 cells after OGD

description: Library name: shTIA1_2


title: Sample_MKL1 SOX2

value: Merkel Cell carcinoma (MCC) cell line


title: Sample_Waga Pano H3K27ac HiChIP

value: Waga

value: H3K27ac (Active Motif, 39133)


title: T2-6, Treatment with 1.0 W/cm2 intensity for 4 weeks


title: RNA-seq of human: shTIA1_1 HMC3 cells after OGD

description: Library name: shTIA1_1


title: Sample_MKL2 POU4F3

value: anti-POU4F3 (abcam cat#ab58128)

value: DNA (ChIP-enriched)


title: Sample_MKL1 POU4F3


title: RNA-seq of human: ctrl_2 HMC3 cells after OGD

description: Library name: ctrl_2

value: Ctrl


title: High Calorie_Post_N6

description: Library name: N6_D709_S4

value: High Calorie_Post


title: RNA-seq of human: ctrl_1  HMC3 cells after OGD

description: Library name: ctrl_1


title: T2-10, Treatment with 1.0 W/cm2 intensity for 4 weeks

value: prostate tissue

value: SD rat

value: low intensity pulsed ultrasound was treated at 1.5 W/cm2 for 4 weeks


title: M9, Model

value: No


title: Sample_MKL2 LXH3

value: anti-LHX3 (abcam cat#ab14555)

value: untreated


title: MRC5 cells,TGF-β1 treatment, 48h (mRNA)

description: Library name: M4TD2

value: cell line

value: WT


title: Sample_MKL1 LXH3


title: M6, Model


title: Sample_MKL1 ISL1

value: anti-Islet1 (abcam cat#ab109517)


title: Sample_MKL2 ISL1


title: M7, Model


title: C10, Control


title: C9, Control


title: Sample_MKL1 INSM1

value: anti-INSM1 (Santa Cruz cat# sc-271408)


title: Sample_MKL2 INSM1

value: Merkel Cell carcinoma (MCC) cell line


title: C8, Control


title: Sample_MKL2 ATOH1


title: C7, Control


title: C6, Control


title: RNA-seq of human: ctrl_3 HMC3 cells after OGD

description: Library name: ctrl_3

value: brain

value: Human microglia cells

value: Oxygen - Glucose Deprivation

value: 4 h


title: Sample_UISO input

source_name: UISO

value: UISO

value: input

value: DNA (input control)


title: Sample_MKL1 ATOH1

value: DNA (ChIP-enriched)


title: M10, Model

value: prostate tissue

value: SD rat


title: Sample_Waga input

value: Waga


title: Sample_MKL2 input

value: untreated


title: Sample_MKL1 input


title: Arabidopsis, nrp1-1 nrp2-2, 12DAG, B, Rep1

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

description:
Library name: nrp1_1nrp2_2_RNASEQ_B_R1
Treatment

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).
Assembly: TAIR 10
Supplementary files format and content: Txt files include TPM values for each sample.

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: Plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C.  seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
total RNA was extracted by using RNA extraction  columns (Axygen, UE-MN-MS-RNA-250) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.

value: 12DAG seedling

value: nrp1-1 nrp2-2


title: Arabidopsis, nrp1-1 nrp2-2, 12DAG, B, Rep5

description:
Library name: nrp1_1nrp2_2_RNASEQ_B_R5
Treatment


title: Sample_MS1 input


title: Arabidopsis, nrp1-1 nrp2-2, 12DAG, B, Rep3

description:
Library name: nrp1_1nrp2_2_RNASEQ_B_R3
Treatment


title: Arabidopsis, nrp1-1 nrp2-2, 12DAG, B, Rep2

description:
Library name: nrp1_1nrp2_2_RNASEQ_B_R2
Treatment


title: Arabidopsis, nrp1-1 nrp2-2, 12DAG, B, Rep4

description:
Library name: nrp1_1nrp2_2_RNASEQ_B_R4
Treatment


title: M8, Model

value: No


title: Arabidopsis, gcn5-7 nrp1-1 nrp2-2, 12DAG, B, Rep5

description:
Library name: gcn5_7nrp1_1nrp2_2_RNASEQ_B_R5
Treatment

value: gcn5-7 nrp1-1 nrp2-2


title: hiPSC-CMs (201B7)

city: Shinjuku

first: Tomohiko

last: Umei

state: Tokyo

address: 35 Shinanomachi

department: Department of Cardiology

country: Japan

institute: Keio University School of Medicine

description: Library name: B7-CMs-2

data_processing:
RNA sequencing was performed using the NovaSeq 6000 System (Illumina) with 101 base-pair paired-end reads.
Sequencing adaptors, low-quality reads, and bases were trimmed using the Trimmomatic-0.39 tool.
Sequence reads were aligned to the human reference genome (hg38) using STAR 2.7.10b.
The aligned reads were subjected to downstream analyses using the StrandNGS software (version 4.0; Agilent Technologies).
The read counts allocated for each gene and transcript (Ensembl Database 2016.12.01) were quantified using the transcripts-per-million (TPM) method.
Assembly: human reference genome (hg38)
Supplementary files format and content: An excel file includes raw counts and TPM values for all samples.

extract_protocol:
RNA was extracted from hPSCs or hPSC-CMs on Day 30, using the ReliaPrep™ RNA Cell Miniprep System.
The total RNA obtained from each sample was used to construct sequencing libraries with the TruSeq® Stranded mRNA Library Prep Kit (20020595, Illumina, San Diego, CA, USA), following the manufacturer’s protocols.


title: 1200 pooled mosaic mouse EBs with CRISPR perturbation targeting 1,644 TFs

description: Library name: big_screen

value: Embryoid bodies (EBs)


title: hESC-CMs (NKX2-5eGFP/w)

description: Library name: NKX2-5-CMs


title: Sample_MCC13 input

value: Merkel Cell carcinoma (MCC) cell line


title: Sample_Waga H3K27ac

value: H3K27ac (Active Motif, 39133)


title: Arabidopsis, gcn5-7 nrp1-1 nrp2-2, 12DAG, B, Rep3

description:
Library name: gcn5_7nrp1_1nrp2_2_RNASEQ_B_R3
Treatment


title: TGFb1

city: Tokyo

first: Takao

last: Seki

state: Ota-ku

address: 5-21-16 Omori-Nishi

department: Department of Biochemistry

institute: Toho University School of Medicine

description: Library name: Bulk RNA-seq HSCs sample3

data_processing:
Sequences were mapped to mouse reference genome GRCm38 using RaNA-seq (https://ranaseq.eu/index.php) was used to normalize sequence count data and conduct differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: RDS

source_name: Liver

extract_protocol:
To isolate HSCs, we used wild-type female C57BL/6 mice over 24 weeks old with the Nycodenz density gradient centrifugation method. Vitamin A-containing granules are increased in HSCs along with aging, enabling sufficient numbers of HSCs for qPCR. Briefly, after perfusing livers with 0.3 mg/mL collagenase for 8 min, the livers were perfused with LPB2 (136 mM NaCl, 5.4 mM KCl, 5 mM CaCl2, 0.5 mM NaH2PO3 2H2O, 0.42 mM Na2HPO3, 10 mM HEPES pH 7.5, 5 mM glucose and 4.2 mM NaHCO3) containing 0.6 mg/mL pronase E (KA-002, KNF) and 0.06 mg/ml DNase I at a flow rate of 3 ml/min for 8 min. The perfused livers were transferred to a glass dish and dispersed with tweezers in LPB2 containing 0.6 mg/ml of pronase and collagenase. The cell suspension was transferred to a beaker and incubated at 37°C for 30 min with occasional stirring. Cells were passed through a 70 mm cell strainer and centrifugated at 600 × g for 10 min. The pellet was resuspended in GBSS/B (136 mM NaCl, 5 mM KCl, 1 mM MgCl2 6H2O, 0.28 mM MgSO4 7H2O, 0.22 mM KH2PO4, 0.42 mM Na2HPO4 12H2O, 5.5 mM glucose, 2.7 mM NaHCO3, 1.5 mM CaCl2 2H2O) containing 0.06 mg/ml DNase I, and centrifuged at 600 × g for 10 min two times. The pellets were resuspended in GBSS/B containing 8.8% Nycodenz (18003, SEW), and GBSS/B was gently added to the cell suspension. After centrifugation at 1500 × g for 22 min without braking, HSCs were identified as a condensed white band at the interphase. The HSC fractions were collected with a Pasteur pipette and centrifuged at 600 × g for 10 min. Typically, 1.0 × 106 cells from two mice. Approximately 80-90% of cells were UV-positive by confocal microscopy.
Total RNA was extracted from HSCs using RNeasy Micro Kit (74004, QIAGEN). RNA libraries were prepared using the SMART-Seq HT PLUS Kit (R400748, Takara Bio) according to the manufacturer's protocol. Briefly, first-strand cDNA was synthesized using SMARTScribe Reverse Transcriptase with template switching activity at the 5' end of the RNA template. After PCR amplification and purification of double-stranded cDNA, the libraries were enzymatically fragmented and ligated with stem-loop adapters. The libraries were then amplified and indexed with unique dual indexes. Library quality and quantity were assessed using an Agilent 2100 Bioanalyzer with High Sensitivity DNA Kit (Agilent Technologies). Paired-end sequencing (2 × 150 bp) was performed on a NovaSeq 6000 system (Illumina) to generate approximately 40M reads (20M pairs) per sample, with a target of 6G bases per sample.

treatment_protocol: HSCs were plated onto 48 well plates (1 × 105 cells) and starved with DMEM containing 0.2% FBS for the indicated days and then left untreated or stimulated with recombinant human FGF18 (100 ng/mL), and TGFb1 (1 ng/mL) for 24 hours.

value: Liver

value: Hepatic stellate cells


title: FGF18

description: Library name: Bulk RNA-seq HSCs sample2


title: hESC-CMs (H9)

description: Library name: H9-CMs


title: hiPSC-CMs (253G4)

description: Library name: G4-CMs


title: untreated

description: Library name: Bulk RNA-seq HSCs sample1


title: Sample_UISO H3K27ac

value: UISO


title: hESCs (NKX2-5eGFP/w)

description: Library name: NKX2-5-hES


title: Sample_MS1 H3K27ac


title: Slc12a1_INTACT_Medulla

city: Los Angeles

first: Jonathan

middle: William

last: Nelson

state: CA

address: 1333 San Pablo St.

department: Medicine

institute: University of Southern California

description:
Library name: Slc12a1_INTACT_Medulla
Pipseq

data_processing:
Fastq files were prepared using bcl2fastq (Illumina) and then aligned to a reference genome using Pipseeker v. 3.3.0 (Fluent Biosciences). Reads were mapped to both exonic and intronic regions to include the pre-mRNA transcriptome.
Ambient RNA contamination was estimated and removed using SoupX v. 1.6.2
Cells with cleaned-up reads were then subjected to doublet removal using DoubletFinder v. 2.0.4
Mitochondrial features were manually removed by excluding all features starting with mt-
The normalized count matrix integration, batch effect correctiong, and cell clustering were performed using Seurat v. 4.4.0
Assembly: pipseeker-gex-reference-GRCm39-2022.04
Supplementary files format and content: Raw and filtered feature-barcode matrices from each sample for the sensativities from the PIP
Supplementary files format and content: Integrated seurat objects containing both samples

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
Kidney was dissected out after PBS washout via aortic perfusion and snap-frozen in liquid nitrogen immediately after dissection. Frozen tissue was stored at -80 °C until subsequent tissue processing. Nuclei were isolated using the 10X Chromium Nuclei extraction kit according to the manufacture protocol. The resulting pellet was resuspended in 10 ml NSB (10mL DPBS + 10µl RNasin Plus). The nuclei suspension was mixed with 5µl Vybrant Ruby stain and incubated on ice for 15 min. The nuclei were sorted in 500 µl final resuspension buffer (FSB, 1ml DPBS with 1% BSA + 5 µl Protector RNase inhibitor) with a low flow rate and pressure to ensure high viability. Two main gates were used. A 561+683 emission for the ruby stain and a 488 530/40 emission for GFP. Low trigger pulse width was used as singlet discriminator. One hundred and fifty thousand nuclei were collected and centrifuged at 500g for 10 min at 4°C in a swinging bucket rotor. The top supernatant was carefully removed, and 6 µl volume was left to resuspend the nuclei pellet.
Single nucleus RNA-seq was performed using a PIPseq™ T10 3ʹ Single Cell RNA Kit v5.0 (Fluent BioSciences). Single nucleus suspensions with a maximal concentration of 3,400 nuclei/uL (for a total of 17,000 nuclei per sample) were added directly into Particle-templated Instant Partition (PIP) tubes. Following the manufacturers protocol, with subsequent vortexing the nuclei were partitioned into PIPs. Following capture and lysis of the RNA and downstream cDNA generation and amplification, the resulting cDNA was run out 2% gel electrophoresis for approximate band size (greater than 500bp). The cDNA was then used as a template for library preparation according to the reagent kit protocol. https://www.fluentbio.com/resource-category/user-guides/. The libraries were profiled on a Bioanalyzer NanoChip (Agilent), and then subsequent sequencing was performed on a NextSeq2000 (Illumina).

tag: Sex

value: male

value: WT

value: Kidney

tag: age


title: Arabidopsis, gcn5-7 nrp1-1 nrp2-2, 12DAG, B, Rep2

description:
Library name: gcn5_7nrp1_1nrp2_2_RNASEQ_B_R2
Treatment


title: Arabidopsis, gcn5-7 nrp1-1 nrp2-2, 12DAG, B, Rep1

description:
Library name: gcn5_7nrp1_1nrp2_2_RNASEQ_B_R1
Treatment


title: Sample_MKL2 H3K27ac

value: DNA (ChIP-enriched)


title: Sample_MCC26 input

value: input

value: DNA (input control)


title: Sample_MCC26 H3K27ac

value: untreated


title: Slc12a1_INTACT_Cortex

description:
Library name: Slc12a1_INTACT_Cortex
Pipseq


title: Arabidopsis, gcn5-7 nrp1-1 nrp2-2, 12DAG, B, Rep4

description:
Library name: gcn5_7nrp1_1nrp2_2_RNASEQ_B_R4
Treatment

value: 12DAG seedling


title: SA3198

city: West Haven

first: S

last: Agabiti

address: 840 West Campus Drive

department: Genetics

institute: Yale University

data_processing:
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA3) software. Base calls are transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis. Primary analysis - sample de-multiplexing and alignment to the mouse genome - is performed using Illumina's CASAVA 1.8.2 software suite bcl2fastq2/2.20.0-GCCcore-10.2.0.
Reads were trimmed using cutadapt, FASTQC, and Trim Galore. Alignment was done using STAR and downstream analysis was done using DESeq2 on R.
Assembly: UCSC mm10
Supplementary files format and content: normalized expression counts and differential expression analysis of adenomas and adenocarcinomas

source_name: Lung

growth_protocol: Autochthonous lung tumors were generated in genetically-engineered mice and isolated at 30-31 weeks post-intratrachael instillation with lentiviral Cre.

extract_protocol:
Flash frozen tumor samples were biopulverized in liquid nitrogen and RNA was extracted using the Qiagen All Prep Kit per manufacturer's instructions. RNA quality and purity was assessed using an Agilent Bioanalyzer.
mRNA is purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments. Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP are not amplified. Indexed libraries are quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat#KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.

treatment_protocol: All mice were housed in specific-pathogen free cages and given free access to food and water ad libitum. Lentiviral Cre was administered to all mice via intratracheal instillation.

value: Lung

value: Treated with Lentiviral Cre


title: SA3337


title: SA3174


title: Arabidopsis, gcn5-7, 12DAG, B, Rep1

description:
Library name: gcn5_7_RNASEQ_B_R1
Treatment


title: SA3338


title: Sample_UISO DNase rep2

value: DNase

value: DNA (DNase-enriched)


title: Arabidopsis, Columbia-0, 12DAG,B, Rep4

description:
Library name: Columbia-0_RNASEQ_B_R4
Control


title: Sample_MKL1 H3K27ac

value: Merkel Cell carcinoma (MCC) cell line


title: Day 3 NCT-503

city: Bunkyo-ku

first: Manami

last: Katoh

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

description:
Library name: Sample3
10× Genomics

data_processing:
Raw FASTQ files were processed for each sample using the Cell Ranger software (version 7.1.0, 10× Genomics), against the Cell Ranger GRCh38 human reference genome.
Raw mapped counts were used as the input for data processing with the Seurat R package (version 4.1.2, 5.0.1).
To exclude ambient RNA contamination, the data were processed using CellBender.
We removed cells with detected genes <2000, detected counts <2000 and >30000, and mitochondrial gene content >15%.
Following the filtering step, we normalized the read counts using the ‘NormalizeData’ function (10,000 default scale factor), separately for each dataset.
Assembly: GRCh38 human reference genome
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz

source_name: Human induced pluripotent stem cells (hiPSCs)

extract_protocol:
8000 cells were prepared to a concentration of 1,000 cells/µL and loaded into the Chromium Controller (10× Genomics) and single-cell cDNA libraries were generated using a Chromium 3′ v3 Chemistry Kit (PN-1000075, 10× Genomics).
Libraries were sequenced on a NovaSeq 6000 System, using the NovaSeq S4 Reagent Kit (20027466, Illumina).


title: Day 5 control

description:
Library name: Sample4
10× Genomics

value: DMSO


title: Arabidopsis, gcn5-7, 12DAG, B, Rep5

description:
Library name: gcn5_7_RNASEQ_B_R5
Treatment


title: SA3195


title: Arabidopsis, gcn5-7, 12DAG, B, Rep4

description:
Library name: gcn5_7_RNASEQ_B_R4
Treatment


title: hiPSCs (201B7)

description: Library name: B7-hiPS


title: hiPSCs (253G4)

description: Library name: G4-hiPS


title: Sample_MS1 DNase rep1


title: SA3331


title: Day 9 NCT-503

description:
Library name: Sample7
10× Genomics


title: ip2,IP

city: Shanghai

first: jia

last: zhang

address: Ruijin 2nd Road 197

institute: Shanghai Jiao Tong University School of Medicine Department of Hypertension

description: Library name: ip2,IP

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2 (2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools (3.5.0)

source_name: Primary human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells were cultured in Endothelial Cell Medium containing 5% fetal bovine serum, 50 mg/mL Endothelial Cell Growth Supplement, and 100 U/mL penicillin and streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine. Cells were lysed in lysis buffer and then sonicated using a M220 focused ultrasonicator.


title: Arabidopsis, gcn5-7, 12DAG, B, Rep3

description:
Library name: gcn5_7_RNASEQ_B_R3
Treatment


title: Arabidopsis, Columbia-0, 12DAG,B, Rep1

description:
Library name: Columbia-0_RNASEQ_B_R1
Control


title: Arabidopsis, gcn5-7, 12DAG, B, Rep2

description:
Library name: gcn5_7_RNASEQ_B_R2
Treatment


title: SA3173


title: Day 9 control

description:
Library name: Sample6
10× Genomics


title: Sample_MCC13 H3K27ac

value: H3K27ac (Active Motif, 39133)


title: SA3309


title: Arabidopsis, arp6-1, 12DAG, A, Rep3

description:
Library name: arp6_1_RNASEQ_A_R3
Treatment


title: Arabidopsis, Columbia-0, 12DAG,B, Rep5

description:
Library name: Columbia-0_RNASEQ_B_R5
Control


title: Sample_Waga DNase rep1

value: Waga


title: SA3318


title: Day 5 NCT-503

description:
Library name: Sample5
10× Genomics


title: Sample_Waga DNase rep2


title: hESCs (H9)

description: Library name: H9-hES


title: Sample_UISO DNase rep1

value: UISO


title: SA3326


title: input2,INPUT

description: Library name: input2,INPUT

value: Primary human umbilical vein endothelial cells


title: Sample_MKL2 DNase rep1


title: Arabidopsis, Columbia-0, 12DAG,B, Rep3

description:
Library name: Columbia-0_RNASEQ_B_R3
Control


title: Day 3 control

description:
Library name: Sample2
10× Genomics


title: Sample_MS1 DNase rep2


title: ip1,IP

description: Library name: ip1,IP


title: Arabidopsis, Columbia-0, 12DAG,B, Rep2

description:
Library name: Columbia-0_RNASEQ_B_R2
Control


title: Arabidopsis, arp6-1, 12DAG, A, Rep1

description:
Library name: arp6_1_RNASEQ_A_R1
Treatment


title: AdKLF15

description: Library name: AdKLF15

data_processing:
ATAC-seq reads were aligned to the hg38 reference genome using Bowtie2 (2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools (3.5.0)

extract_protocol:
The ATAC experiments were performed as described (Buenrostro et al., 2013).
Cells were  vehicle treated and then collected and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen). All samples were then amplified by PCR using NEBNextHigh-Fidelity 2× PCR Master Mix (New Englands Labs) with primers containing a barcode to generate libraries. DNA was again purified using AMPure Beads.DNA libraries for ATAC-seq were prepared using NextEra Library Prep Kit following manufacturer's protocols.


title: Arabidopsis, gcn5-7 arp6-1, 12DAG, A, Rep2

description:
Library name: gcn5_7arp6_1_RNASEQ_A_R2
Treatment

value: gcn5-7 arp6-1


title: AdCTL

description: Library name: AdCTL


title: Arabidopsis, gcn5-7 arp6-1, 12DAG, A, Rep1

description:
Library name: gcn5_7arp6_1_RNASEQ_A_R1
Treatment


title: Clec5a_KO_CLP_1

city: Shenyang

first: Chunfeng

last: Liu

state: Liaoning

address: No.36 SanHao Street

institute: Shengjing Hospital of China Medical University

description: 10X Genomics

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software（version2.20）. Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger，version 5.0.1) and scRNA-seq data were aligned to Ensembl genome, a total of 64,581 single cell captured from 3 WT littermates and 3 CLEC5A-/- mice were processed using 10X Genomics Chromium Single Cell 3’Solution. The Cell Ranger output was loaded into Seurat(version 3.1.1) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data. Overall, 55,177 cells passed the quality control threshold: all genes expressed in less than three cells （default parameters：1 cell）were removed, number of genes expressed per cell >500 as low cut-off, the percent of mitochondrial-DNA derived gene-expression <25%. To visualize the data, we further reduced the dimensionality of all cells using Seurat and used t-SNE to project the cells into 2D space. The steps includes: Using the LogNormalize method of the Normalization function of the Seurat software to calculated the expression value of genes; PCA (Principal component analysis) analysis was performed using the normalized expression value, and the top 10 PCs were used to do clustering and t-SNE analysis；Selecting weighted Shared Nearest Neighbor (SNN) graph-based clustering method to find clusters. Marker genes for each cluster were identified with default parameters via the FindAllMarkers function in Seurat. This selects markers genes which are expressed in more than 10% of the cells in a cluster and average log(Fold Change) of greater than 0.26.
Assembly: Ensembl genome GRCm39 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The lung tissue was placed in a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 × PBS on ice and cut it into pieces, and then they were washed with 1 × PBS and remove non-purpose tissues. Tissues were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS，V/V）, and the resulting cell suspension was filtered and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads and remove dead cells. Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability (above 85%) was confirmed by trypan blue exclusion, and single cell suspensions were counted and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’kit (V3).The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150bp) by LC-Bio Technology co.ltd. at a minimum depth of 20,000 reads per cell.

value: CLP


title: Sample_MKL2 DNase rep2


title: MKN45-R cells

first: Peidong

last: Ni

address: 199 Jiefang South Road

department: General Surgery

institute: xuzhou central hospital

description: Library name: sample 2

data_processing:
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to alculate the distance and Complete Linkage method to cluster.
Assembly: GRCh38
Supplementary files format and content: MKN45 v MKN45-R.DESeq.xlsx
Supplementary files format and content: diff_gene_of_all_groups.xlsx
Supplementary files format and content: all_cluster.xlsx

growth_protocol: The cells were cultured in RPMI-1640 medium, and the former medium was supplemented with 10% fetal bovine serum and 1% antibiotics (a mixture of 100mg/ml streptomycin and 100 U/ml penicillin). All cells were incubated in a humidified environment at 37°C with 5% CO₂.

extract_protocol:
RNA as extracted using the Trizol kit of Beyotime Company. 3 micrograms of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.

value: gastric cancer cells

value: radioresistant cells

value: WT


title: Sample_MCC13 DNase

value: untreated


title: Arabidopsis, gcn5-7, 12DAG, A, Rep3

description:
Library name: gcn5_7_RNASEQ_A_R3
Treatment

value: 12DAG seedling


title: WT_CLP_3

description: 10X Genomics

value: Lung


title: Arabidopsis, arp6-1, 12DAG, A, Rep2

description:
Library name: arp6_1_RNASEQ_A_R2
Treatment


title: Day 1

description:
Library name: Sample1
10× Genomics


title: SA3170

value: Treated with Lentiviral Cre


title: WT_CLP_2

description: 10X Genomics