title: Alpha-Amanitin 500nM Round-00 (exp5)

description:
Library name: Alpha-Amanitin 500nM_Round-00 (exp5)
sgRNAs PCR-amplified from genomic DNA

value: Alpha-Amanitin 500nM


title: Hep G2 cells, Glutamin deprivation_24hours_Rep_03

status: Public on Mar 13 2026

type: SRA

city: Zhengzhou

first: QIang

last: Ji

state: Henan

address: Jinshui Rd

department: Translational Research Institute

country: China

institute: Henan People's Hospital

description:
Library name: Gln_Dep_24h_3
Column name in FPKM_anno_Gln_deprivation.xls: DE24-3

library_source: transcriptomic

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.  The clean  reads were mapped to the GRCh38 using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCh38
Supplementary files format and content: xlsx files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Liver

growth_protocol: Hep G2 cells were maintained in DMEM high glucose supplemented with 10% fetal bovine serum (FBS) and antiviotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: For the glutamine deprivation experiment, cells were seeded in 60 mm culture dishes. At 24 hours post-seeding, the culture medium was replaced with glutamine-free DMEM (supplemented with GlutaMAX™ as a glutamine substitute), and cells were cultured for an additional 12 or 24 hours.

tag: tissue

value: Liver

tag: cell line

value: Hep G2

tag: cell type

value: tumor cells

tag: treatment

value: Glutamine deprivation


title: LJH685 5uM Round-02 (exp73)

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description:
Library name: LJH685 5uM_Round-02 (exp73)
sgRNAs PCR-amplified from genomic DNA

library_source: genomic

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
For each round (batch of simultaneously-run screens), read counts for all control samples (untreated, DMSO 0.1%-0.3% or ethanol 0.1%-0.3% treated) were summed together. Read counts for samples that were grown together for part of the 8 days of the screen were also summed together so that each sample represented in the processed data files is independent in terms of genetic drift.
Assembly: sgRNAs from the Extended knock-out (EKO) library (Bertomeu et al. 2017).
Supplementary files format and content: sgrna_read_counts_refseq_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted refSeq gene symbols (January 2016) and updated HGNC gene symbols (2020).
Supplementary files format and content: sgrna_read_counts_exons_and_hypothetical_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted exons (hg19 coordinates) and hypothetical genes (AceView or Gencode symbols).
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C. Media was changed every two days and cells diluted to 400,000 cells/ml.

extract_protocol:
genomic DNA extracted using the Gentra Puregene kit according to the manufacturer’s instructions (QIAGEN), and sgRNA sequences were PCR-amplified
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 8 days (see Bertomeu et al., 2017 for details). The pooled EKO library was split in different T-75 flasks, compounds added, and propagated for 8 days. Fresh media and compound was added at each cell passage. The untreated control sample with multiple collected time-points was grown in T-175 spinner flasks.

value: pre-B lymphoid cell line

value: LJH685 5uM

tag: batch


title: Meningeal mast cells, KO, NC, rep 2

city: Beijing

first: Qingqing

last: Li

address: Shuangqing Road, No. 30

department: Institute for Immunology and School of Basic Medical Sciences

institute: Tsinghua University

description: Library name: Sample5

data_processing:
The sequencing data was filtered with SOAPnuke.
The clean reads were mapped to the reference genome using HISAT.
Bowtie2 was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include TPM values for samples

molecule: polyA RNA

organism: Mus musculus

source_name: Meningeal mast cells

extract_protocol:
Isolated cell samples were lysed using the Discover-sc WTA Kit V2.
Libraries were constructed using the Discover-sc WTA Kit V2.

value: Meningeal mast cells

tag: genotype

value: No infection


title: Hep G2 cells, Glutamin deprivation_12hours_Rep_03

description:
Library name: Gln_Dep_12h_3
Column name in FPKM_anno_Gln_deprivation.xls: DE12-3


title: Hep G2 cells, Glutamin deprivation_12hours_Rep_02

description:
Library name: Gln_Dep_12h_2
Column name in FPKM_anno_Gln_deprivation.xls: DE12-2


title: Hep G2 cells, Glutamin deprivation_24hours_Rep_01

description:
Library name: Gln_Dep_24h_1
Column name in FPKM_anno_Gln_deprivation.xls: DE24-1


title: Brain, APP23, 7 months, Male, ZT0, rep2

city: La Jolla

first: Paula

last: Desplats

state: CA

address: 9500 Gilman Dr. MTF346 MC0624

department: Department of Neuroscience and  Department of Pathology

country: USA

institute: University California San Diego

description: Fresh frozen spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to a custom mm10 genome with the human APP transgene gene added.
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: Brain

extract_protocol:
Brain hemispheres collected and placed in OCT and then flash frozen in isopentane in liquid nitrogen. One hemibrain from each mouse was cryosectioned at -18°C sagittally to a thickness of 10 mm.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Brain

tag: age

value: 7 months

tag: Sex

value: Male

tag: zeitgeber time


title: Brain, APP23, 7 months, Male, ZT0, rep1


title: Meningeal mast cells, WT, NC, rep 3

description: Library name: Sample3


title: Golgicide A 2uM Round-03 (exp121)

description:
Library name: Golgicide A 2uM_Round-03 (exp121)
sgRNAs PCR-amplified from genomic DNA

value: Golgicide A 2uM


title: Rotenone 20uM Round-00 (exp34)

description:
Library name: Rotenone 20uM_Round-00 (exp34)
sgRNAs PCR-amplified from genomic DNA

value: Rotenone 20uM


title: Hep G2 cells, Normal medium_Rep_03

description:
Library name: Gln_Normal_3
Column name in FPKM_anno_Gln_deprivation.xls: ADD-3

value: GlutaMAX supplement for supply


title: Brain, APP23, 7 months, Male, ZT12, rep1


title: Brain, APP23, 7 months, Female, ZT6, rep1

value: Female


title: Spinner flask No treatment Day 8 Round-02 (exp568)

description:
Library name: SF No treatment D8_Round-02 (exp568)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Meningeal mast cells, KO, NC, rep 1

description: Library name: Sample4


title: Meningeal mast cells, WT, NC, rep 2

description: Library name: Sample2


title: Hep G2 cells, Normal medium_Rep_02

description:
Library name: Gln_Normal_2
Column name in FPKM_anno_Gln_deprivation.xls: ADD-2


title: Brain, APP23, 7 months, Female, ZT18, rep2


title: Brain, APP23, 7 months, Female, ZT6, rep2


title: Meningeal mast cells, WT, NC, rep 1

description: Library name: Sample1


title: MLN-4924 200nM Round-00 (exp21)

description:
Library name: MLN-4924 200nM_Round-00 (exp21)
sgRNAs PCR-amplified from genomic DNA


title: MLN-4924 2uM Round-00 (exp22)

description:
Library name: MLN-4924 2uM_Round-00 (exp22)
sgRNAs PCR-amplified from genomic DNA


title: Spinner flask No treatment Day 4 Round-00 (exp553)

description:
Library name: SF No treatment D4_Round-00 (exp553)
sgRNAs PCR-amplified from genomic DNA


title: Hep G2 cells, Normal medium_Rep_01

description:
Library name: Gln_Normal_1
Column name in FPKM_anno_Gln_deprivation.xls: ADD-1


title: Brain, APP23, 7 months, Female, ZT18, rep1


title: PCMCs, KO, IL-33 prime, ATP stimulation, rep 3

description: Library name: Sample18

source_name: Peritoneal cells derived mast cells

growth_protocol: The peritoneal lavage fluid was collected after euthanasia and cultured in RPMI 1640 medium (Sigma) supplemented with 10 ng/ml IL-3 (Sino Biological), 30 ng/ml SCF (Sino Biological), 10% FBS, Penicillin-Streptomycin. The medium was changed every 3-4 days, and after 10 days, flow cytometry was employed to determine the maturation rate of peritoneal cell-derived mast cells (>98%).

extract_protocol:
Total RNA from the cells was extracted using Trizol (AidLab) following the chloroform/isoamyl alcohol method.
Libraries were constructed using the Optimal Dual-mode mRNA Library Prep Kit.

treatment_protocol: PCMCs were primed with 200 ng/ml IL-33 (PeproTech) for 24 h, followed by 10 nM clozapine (Macklin) stimulation for 4 h, before undergoing transcriptome sequencing analysis.

value: Peritoneal cells derived mast cells

value: IL-33 prime, ATP stimulation


title: PNU96415E 10uM Round-03 (exp145)

description:
Library name: PNU96415E 10uM_Round-03 (exp145)
sgRNAs PCR-amplified from genomic DNA


title: PCMCs, KO, IL-33 prime, ATP stimulation, rep 2

description: Library name: Sample17


title: MYD01222021

city: Pittsburgh

first: Sharon Ann

last: George

state: PA

address: 200 Lothrop Street W1355

institute: University of Pittsburgh

description:
Library name: MYD01222021
Male, Old, DOX

data_processing:
Possible adaptor sequences and poor quality nucleotides were removed by trimming reads using Trimmomatic v.0.36.
Assembly: Trimmed reads were mapped to Homo sapiens reference genome GRCh38 using STAR aligner v2.5.2b to generate the BAM files.
Supplementary files format and content: BAM files were generated from the raw data files and these contain the reads maps to the GRCh38 genome.

source_name: Heart

extract_protocol:
RNA extraction was performed using RNeasy fibrous tissue Mini kit form Qiagen and RNA purity and yield was confirmed with the Agilent Bioanalyzer by RIN > 6 and amount > 2 ug.
Library preparation and sequencing was performed by Azenta Life Sciences. Sequencign was performed using Illumina HiSeq 2500 to obtain 20-30 million paired end 150bp reads/sample.

treatment_protocol: Human left ventricular slices were generated and cultured for 24 hours in the absence (Control) or presence of DOX (50 uM).

value: Heart

value: DOX

tag: age group

value: Old


title: Hep G2 cells, Glutamin deprivation_12hours_Rep_01

description:
Library name: Gln_Dep_12h_1
Column name in FPKM_anno_Gln_deprivation.xls: DE12-1

value: Liver

value: Hep G2

value: tumor cells

value: Glutamine deprivation


title: Brain, APP23, 7 months, Female, ZT12, rep1

value: Brain


title: MYD07192018

description:
Library name: MYD07192018
Male, Old, DOX


title: DMSO 0.3% Round-03 (exp119)

description:
Library name: Ctl DMSO 0.3_ D8_Round-03 (exp119)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: DMSO 0.3%


title: PCMCs, KO, IL-33 prime, NC stimulation, rep 3

description: Library name: Sample15

value: IL-33 prime, nc stimulation


title: MYD12082018

description:
Library name: MYD12082018
Male, Old, DOX

value: Male


title: PCMCs, KO, IL-33 prime, ATP stimulation, rep 1

description: Library name: Sample16


title: PCMCs, KO, IL-33 prime, NC stimulation, rep 2

description: Library name: Sample14


title: MYD01022019

description:
Library name: MYD01022019
Male, Old, DOX


title: Brain, APP23, 7 months, Female, ZT12, rep2

description: Fresh frozen spatial transcriptomics sequencing

value: 7 months


title: Trametinib 10uM Round-02 (exp83)

description:
Library name: Trametinib 10uM_Round-02 (exp83)
sgRNAs PCR-amplified from genomic DNA

value: Trametinib 10uM


title: Brain, APP23, 7 months, Female, ZT0, rep1

value: Female


title: Bortezomib 5nM Round-00 (exp6)

description:
Library name: Bortezomib 5nM_Round-00 (exp6)
sgRNAs PCR-amplified from genomic DNA

value: Bortezomib 5nM


title: Brain, APP23, 7 months, Female, ZT0, rep2


title: PCMCs, KO, IL-33 prime, NC stimulation, rep 1

description: Library name: Sample13

value: Peritoneal cells derived mast cells


title: PCMCs, WT, IL-33 prime, ATP stimulation, rep 3

description: Library name: Sample12

value: IL-33 prime, ATP stimulation


title: UM0131593 100nM Round-01 (exp58)

description:
Library name: UM0131593 100nM_Round-01 (exp58)
sgRNAs PCR-amplified from genomic DNA


title: Brain, APP23, 14 months, Male, ZT6, rep1

value: 14 months


title: Brain, APP23, 14 months, Male, ZT6, rep2


title: Chloramphenicol 20uM Round-00 (exp13)

description:
Library name: Chloramphenicol 20uM_Round-00 (exp13)
sgRNAs PCR-amplified from genomic DNA

value: Chloramphenicol 20uM


title: MYC01222021

description:
Library name: MYC01222021
Male, Young, Control

value: Heart

value: Control

value: Young


title: PCMCs, WT, IL-33 prime, ATP stimulation, rep 2

description: Library name: Sample11


title: Brain, APP23, 14 months, Male, ZT18, rep2


title: PCMCs, WT, IL-33 prime, ATP stimulation, rep 1

description: Library name: Sample10


title: (S)-(-)-1,1'-Binaphthyl-2,2'-diamine 8uM Round-03 (exp112)

description:
Library name: (S)-(-)-1,1_-Binaphthyl-2,2_-diamine 8uM_Round-03 (exp112)
sgRNAs PCR-amplified from genomic DNA


title: MYC01022019

description:
Library name: MYC01022019
Male, Young, Control


title: Brain, APP23, 14 months, Male, ZT18, rep1


title: MOD10282018

description:
Library name: MOD10282018
Male, Old, DOX

value: DOX

value: Old


title: MYC12082017

description:
Library name: MYC12082017
Male, Young, Control


title: SB202190 10uM Round-03 (exp148)

description:
Library name: SB202190 10uM_Round-03 (exp148)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: MS094 2uM Round-03 (exp136)

description:
Library name: MS094 2uM_Round-03 (exp136)
sgRNAs PCR-amplified from genomic DNA

value: MS094 2uM


title: Nicotinamide 1000uM Round-03 (exp101)

description:
Library name: Nicotinamide 1000uM_Round-03 (exp101)
sgRNAs PCR-amplified from genomic DNA

value: Nicotinamide 1000uM


title: MOD07232018

description:
Library name: MOD07232018
Male, Old, DOX

value: Male


title: MOD01312019

description:
Library name: MOD01312019
Male, Old, DOX


title: PCMCs, WT, No prime, ATP stimulation, rep 1

description: Library name: Sample7

value: No prime, ATP stimulation


title: UNC2400 2uM Round-03 (exp156)

description:
Library name: UNC2400 2uM_Round-03 (exp156)
sgRNAs PCR-amplified from genomic DNA

value: UNC2400 2uM


title: PCMCs, WT, No prime, ATP stimulation, rep 3

description: Library name: Sample9


title: Brain, APP23, 14 months, Male, ZT12, rep2

value: Brain


title: Brain, APP23, 14 months, Male, ZT0, rep1


title: PCMCs, WT, IL-33 prime, NC stimulation, rep 3

description: Library name: Sample6

value: IL-33 prime, nc stimulation


title: Nicotinamide 2000uM Round-01 (exp50)

description:
Library name: Nicotinamide 2000uM_Round-01 (exp50)
sgRNAs PCR-amplified from genomic DNA

value: Nicotinamide 2000uM


title: MOD01232019

description:
Library name: MOD01232019
Male, Old, DOX


title: Brain, APP23, 14 months, Male, ZT0, rep2

description: Fresh frozen spatial transcriptomics sequencing


title: MYC07192018

description:
Library name: MYC07192018
Male, Young, Control


title: MOC10282018

description:
Library name: MOC10282018
Male, Old, Control


title: UMK57 1uM Round-01 (exp59)

description:
Library name: UMK57 1uM_Round-01 (exp59)
sgRNAs PCR-amplified from genomic DNA

value: UMK57 1uM


title: PCMCs, WT, IL-33 prime, NC stimulation, rep 2

description: Library name: Sample5

value: Peritoneal cells derived mast cells


title: MOC07232018

description:
Library name: MOC07232018
Male, Old, Control


title: Brain, APP23, 14 months, Male, ZT12, rep1

value: 14 months


title: Brain, APP23, 14 months, Female, ZT6, rep2

value: Female


title: PCMCs, WT, IL-33 prime, NC stimulation, rep 1

description: Library name: Sample4


title: PCMCs, WT, No prime, NC stimulation, rep 3

description: Library name: Sample3

value: No prime, nc stimulation


title: Brain, APP23, 14 months, Female, ZT18, rep2


title: MOC01312019

description:
Library name: MOC01312019
Male, Old, Control

value: Heart

value: Control


title: Nocodazole 200nM Round-00 (exp24)

description:
Library name: Nocodazole 200nM_Round-00 (exp24)
sgRNAs PCR-amplified from genomic DNA

value: Nocodazole 200nM


title: PCMCs, WT, No prime, ATP stimulation, rep 2

description: Library name: Sample8


title: MOC01232019

description:
Library name: MOC01232019
Male, Old, Control

value: Old


title: Brain, APP23, 14 months, Female, ZT18, rep1


title: PCMCs, WT, No prime, NC stimulation, rep 2

description: Library name: Sample2


title: Brain, APP23, 14 months, Female, ZT6, rep1


title: PCMCs, WT, No prime, NC stimulation, rep 1

description: Library name: Sample1


title: BI-2536 1nM Round-01 (exp41)

description:
Library name: BI-2536 1nM_Round-01 (exp41)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: Oligomycin A 2uM Round-00 (exp25)

description:
Library name: Oligomycin A 2uM_Round-00 (exp25)
sgRNAs PCR-amplified from genomic DNA

value: Oligomycin A 2uM


title: Actinomycin D 1nM Round-00 (exp3)

description:
Library name: Actinomycin D 1nM_Round-00 (exp3)
sgRNAs PCR-amplified from genomic DNA

value: Actinomycin D 1nM


title: PCMCs, IL-33 prime, clozapine stimulation, rep 3

data_processing:
The sequencing data was filtered with SOAPnuke.
The clean reads were mapped to the reference genome using HISAT.
Bowtie2 was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include TPM values for each sample

value: IL-33 prime, clozapine stimulation


title: FYD11062020

description:
Library name: FYD11062020
Female, Young, DOX

value: DOX

value: Young


title: Brain, APP23, 14 months, Female, ZT12, rep1

value: Brain


title: Brefeldin A 20nM Round-00 (exp8)

description:
Library name: Brefeldin A 20nM_Round-00 (exp8)
sgRNAs PCR-amplified from genomic DNA

value: Brefeldin A 20nM


title: PCMCs, IL-33 prime, clozapine stimulation, rep 2


title: FYD10252018

description:
Library name: FYD10252018
Female, Young, DOX


title: NFN1 100nM Round-01 (exp49)

description:
Library name: NFN1 100nM_Round-01 (exp49)
sgRNAs PCR-amplified from genomic DNA

value: NFN1 100nM


title: Brain, APP23, 14 months, Female, ZT0, rep1


title: PCMCs, IL-33 prime, clozapine stimulation, rep 1

value: Peritoneal cells derived mast cells


title: FYD08072018

description:
Library name: FYD08072018
Female, Young, DOX


title: Brain, APP23, 14 months, Female, ZT12, rep2

value: 14 months


title: Mubritinib 200nM Round-01 (exp48)

description:
Library name: Mubritinib 200nM_Round-01 (exp48)
sgRNAs PCR-amplified from genomic DNA

value: Mubritinib 200nM


title: Nocodazole 200nM Round-02 (exp64)

description:
Library name: Nocodazole 200nM_Round-02 (exp64)
sgRNAs PCR-amplified from genomic DNA


title: PCMCs, No prime, clozapine stimulation, rep 3

value: No prime, clozapine stimulation


title: FYD11072020

description:
Library name: FYD11072020
Female, Young, DOX

value: Heart

value: Female


title: FYC11062020

description:
Library name: FYC11062020
Female, Young, Control

value: Control


title: FYC11072020

description:
Library name: FYC11072020
Female, Young, Control


title: GFI1-FOXO1-DKO M2 NK cells, Exp3, Rep2

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

data_processing:
Read quality was assessed and low quality reads trimmed with fastp.
Reads were mapped to the mouse genome (mm10) using STAR v2.7.10
After mapping, reads were quantified with featureCounts v2.0.1
Assembly: mm10
Supplementary files format and content: Read counts following mapping to mm10 using featurecount

source_name: spleen

extract_protocol:
RNA was extracted from NK cells using RNeasy Plus Micro kit (Qiagen)
Libraries were prepared with TruSeq Stranded Total RNA kit (Illumina) or NEBNext Single Cell/low Input Library prep kit (New England Biolabs).

value: spleen

value: NK cells


title: Brain, APP23, 14 months, Female, ZT0, rep2

description: Fresh frozen spatial transcriptomics sequencing


title: Cycloheximide 200nM Round-00 (exp15)

description:
Library name: Cycloheximide 200nM_Round-00 (exp15)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Cycloheximide 200nM


title: NCR-cre Imm NK cells, Exp3, Rep3


title: Vinblastine 2nM Round-01 (exp60)

description:
Library name: Vinblastine 2nM_Round-01 (exp60)
sgRNAs PCR-amplified from genomic DNA

value: Vinblastine 2nM


title: FYC10252018

description:
Library name: FYC10252018
Female, Young, Control


title: GFI1-FOXO1-DKO Imm NK cells, Exp3, Rep2


title: PCMCs, IL-33 prime, NC stimulation, rep 3

value: IL-33 prime, nc stimulation


title: GFI1-FOXO1-DKO M1 NK cells, Exp3, Rep2


title: FOXO1-KO M2 NK cells, Exp3, Rep2


title: FYC08072018

description:
Library name: FYC08072018
Female, Young, Control

value: Young


title: PCMCs, No prime, clozapine stimulation, rep 2


title: Pimelic Diphenylamide 106 5uM Round-00 (exp28)

description:
Library name: Pimelic Diphenylamide 106 5uM_Round-00 (exp28)
sgRNAs PCR-amplified from genomic DNA

value: Pimelic Diphenylamide 106 5uM


title: FOD09252020

description:
Library name: FOD09252020
Female, Old, DOX

value: DOX

value: Old


title: PCMCs, IL-33 prime, NC stimulation, rep 2

value: Peritoneal cells derived mast cells


title: FOXO1-KO Imm NK cells, Exp3, Rep2


title: Nicotinate 1000uM Round-03 (exp140)

description:
Library name: Nicotinate 1000uM_Round-03 (exp140)
sgRNAs PCR-amplified from genomic DNA

value: Nicotinate 1000uM


title: PCMCs, IL-33 prime, NC stimulation, rep 1


title: PCMCs, No prime, clozapine stimulation, rep 1


title: DMSO 1% Round-03 (exp120)

description:
Library name: DMSO 1__Round-03 (exp120)
sgRNAs PCR-amplified from genomic DNA

value: DMSO 1%


title: PCMCs, No prime, NC stimulation, rep 2

value: No prime, nc stimulation


title: PCMCs, No prime, NC stimulation, rep 3


title: FOD09242020

description:
Library name: FOD09242020
Female, Old, DOX

value: Heart


title: FOD07312018

description:
Library name: FOD07312018
Female, Old, DOX

value: Female


title: GF1-KO M2 NK cells, Exp3, Rep2


title: GF1-KO M1 NK cells, Exp3, Rep2


title: Spinner flask No treatment Day 2 Round-02 (exp565)

description:
Library name: SF No treatment D2_Round-02 (exp565)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: L-741,742 5uM Round-03 (exp131)

description:
Library name: L-741,742 5uM_Round-03 (exp131)
sgRNAs PCR-amplified from genomic DNA


title: PCMCs, No prime, NC stimulation, rep 1


title: No treatment Round-02 (exp92)

description:
Library name: Ctl No treatment D8_Round-02 (exp92)
sgRNAs PCR-amplified from genomic DNA


title: GF1-KO Imm NK cells, Exp3, Rep2

value: spleen


title: NCR-cre M2 NK cells, Exp3, Rep2

value: NK cells


title: BMMCs, IL-33 prime, ATP stimulation, rep 3

source_name: Bone marrow derived mast cells

growth_protocol: After euthanizing the mice, the large and small leg bones were collected, and the bone marrow was cultured in IMDM medium (Corning) supplemented with 10 ng/ml IL-3 (Sino Biological), 30 ng/ml SCF (Sino Biological), 10% FBS, and Penicillin-Streptomycin. The medium was refreshed every 3-4 days, and flow cytometry was utilized to assess the maturation rate of bone marrow-derived mast cells (BMMC) after 1 month (>98%).

treatment_protocol: BMMCs were primed with 200 ng/ml IL-33 (PeproTech) for 24 h, followed by 1 mM ATP (Sigma) stimulation for 4 h, before undergoing transcriptome sequencing analysis.

value: Bone marrow derived mast cells

value: wildtype

value: IL-33 prime, ATP stimulation


title: FOC09252020

description:
Library name: FOC09252020
Female, Old, Control

value: Control


title: FOXO1-KO M1 NK cells, Exp3, Rep2


title: Suberoylanilide-Hydroxamic-Acid 20nM Round-01 (exp53)

description:
Library name: Suberoylanilide-Hydroxamic-Acid 20nM_Round-01 (exp53)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Suberoylanilide-Hydroxamic-Acid 20nM


title: FOD03152020

description:
Library name: FOD03152020
Female, Old, DOX

value: DOX


title: FOC09242020

description:
Library name: FOC09242020
Female, Old, Control

value: Old


title: BMMCs, IL-33 prime, ATP stimulation, rep 1


title: FOC03152020

description:
Library name: FOC03152020
Female, Old, Control


title: CUT&Tag of G4-DNA in HepG2 cellsinfected with TRIB3 sh2 lentivirus_Rep2

description: Library name: HepG2_TRIB3sh2_Rep2

data_processing:
The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools.
Assembly: GRCh38
Supplementary files format and content: bigwig for CUT&Tag
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.

treatment_protocol: For the glutamine deprivation experiment, cells were seeded in 60 mm culture dishes. At 24 hours post-seeding, the culture medium was replaced with glutamine-free DMEM (supplemented with GlutaMAX™ as a glutamine substitute), and cells were cultured for an additional 12 or 24 hours. For the TRIB3 knockdown experiment, Hep G2 cells were infected with lentivirus carrying either Control shRNA, TRIB3 sh1, or TRIB3 sh2. After 48 hours of infection, cells were selected with puromycin for another 48 hours.

value: Liver

value: Hep G2

value: tumor cells

value: lentivirus infected


title: Oligomycin A 20uM Round-00 (exp26)

description:
Library name: Oligomycin A 20uM_Round-00 (exp26)
sgRNAs PCR-amplified from genomic DNA

value: Oligomycin A 20uM


title: BMMCs, No prime, ATP stimulation, rep 2

value: No prime, ATP stimulation


title: BMMCs, IL-33 prime, ATP stimulation, rep 2


title: NCR-cre M1 NK cells, Exp3, Rep2


title: GFI1-FOXO1-DKO M1 NK cells, Exp3, Rep1


title: No treatment Round-03 (exp158)

description:
Library name: Ctl No treatment D8_Round-03 (exp158)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: TRAIL 5ng/mL Round-00 (exp35)

description:
Library name: TRAIL 5ng/mL_Round-00 (exp35)
sgRNAs PCR-amplified from genomic DNA

value: TRAIL 5ng/mL


title: FOC07312018

description:
Library name: FOC07312018
Female, Old, Control

value: Heart

value: Female


title: CUT&Tag of G4-DNA in HepG2 cellsinfected with TRIB3 sh2 lentivirus_Rep1

description: Library name: HepG2_TRIB3sh2_Rep1


title: BMMCs, IL-33 prime, NC stimulation, rep 3

value: Bone marrow derived mast cells

value: wildtype

value: IL-33 prime, nc stimulation


title: Spinner flask No treatment Day 0 Round-02 (exp564)

description:
Library name: SF No treatment D0_Round-02 (exp564)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: WYE-354 6uM Round-02 (exp90)

description:
Library name: WYE-354 6uM_Round-02 (exp90)
sgRNAs PCR-amplified from genomic DNA

value: WYE-354 6uM


title: NCR-cre Imm NK cells, Exp3, Rep2

value: spleen

value: NK cells


title: GFI1-FOXO1-DKO M2 NK cells, Exp3, Rep1


title: FOXO1-KO M1 NK cells, Exp3, Rep1


title: CUT&Tag of G4-DNA in HepG2 cellsinfected with TRIB3 sh1 lentivirus_Rep2

description: Library name: HepG2_TRIB3sh1_Rep2

value: Liver


title: CUT&Tag of G4-DNA in HepG2 cellsinfected with control shRNA lentivirus_Rep1

description: Library name: HepG2_shCtrl_Rep1

value: Hep G2


title: SGC0946 7uM Round-03 (exp151)

description:
Library name: SGC0946 7uM_Round-03 (exp151)
sgRNAs PCR-amplified from genomic DNA

value: SGC0946 7uM


title: CUT&Tag of G4-DNA in HepG2 cellsinfected with control shRNA lentivirus_Rep2

description: Library name: HepG2_shCtrl_Rep2

value: tumor cells

value: lentivirus infected


title: MS023 7uM Round-03 (exp135)

description:
Library name: MS023 7uM_Round-03 (exp135)
sgRNAs PCR-amplified from genomic DNA

value: MS023 7uM


title: CUT&Tag of G4-DNA in HepG2 cellsinfected with TRIB3 sh1 lentivirus_Rep1

description: Library name: HepG2_TRIB3sh1_Rep1


title: BMMCs, No prime, ATP stimulation, rep 1

value: No prime, ATP stimulation


title: BMMCs, No prime, NC stimulation, rep 2

value: No prime, nc stimulation


title: FOXO1-KO M2 NK cells, Exp3, Rep1


title: BMMCs, No prime, ATP stimulation, rep 3


title: GF1-KO M2 NK cells, Exp3, Rep1


title: BMMCs, IL-33 prime, NC stimulation, rep 2


title: BMMCs, No prime, NC stimulation, rep 3


title: Nifurtimox 1uM Round-03 (exp141)

description:
Library name: Nifurtimox 1uM_Round-03 (exp141)
sgRNAs PCR-amplified from genomic DNA

value: Nifurtimox 1uM


title: CUT&Tag of G4-DNA in HepG2 cells with Glutamine deprivation_Rep2

description: Library name: HepG2_GlnDep_BG4_Rep2

value: Glutamine deprivation for 12hours


title: Etoposide 1uM Round-00 (exp19)

description:
Library name: Etoposide 1uM_Round-00 (exp19)
sgRNAs PCR-amplified from genomic DNA

value: Etoposide 1uM


title: Spinner flask No treatment Day 8 Round-00 (exp546)

description:
Library name: SF No treatment D8_Round-00 (exp546)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: GFI1-FOXO1-DKO Imm NK cells, Exp3, Rep1


title: BMMCs, No prime, NC stimulation, rep 1

value: Bone marrow derived mast cells

value: wildtype


title: CUT&Tag of G4-DNA in HepG2 cells with normal condition_Rep2

description: Library name: HepG2_Normal_BG4_Rep2

value: GlutaMAX supplement for supply


title: FOXO1-KO Imm NK cells, Exp3, Rep1

value: spleen


title: BI-6727 1nM Round-01 (exp42)

description:
Library name: BI-6727 1nM_Round-01 (exp42)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: BMMCs, IL-33 prime, NC stimulation, rep 1

value: IL-33 prime, nc stimulation


title: GF1-KO M1 NK cells, Exp3, Rep1

value: NK cells


title: BMDM, IL-4+TLR2,24hrs, rep2

city: Los Angeles

first: Anthony

last: Jones

address: 650 Charles E Young Dr. South, Room 23-305

department: Department of Molecular and Medical Pharmacology

institute: University of California, Los Angeles

description: Library name: Sample 17

data_processing:
The peaks for all the ATAC-seq samples were used to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBamSummary91. EdgeR92 was used to determine the IL-4 significantly induced regions by applying a cutoff FDR <0.01 and LFC > 1 of triplicate data upon IL-4 stimulation on WT BMDMs and to determine the Pam3CSK4 co-treatment significant regions by applying a cutoff FDR <0.05 and LFC > 0.5.
Assembly: mm10
Supplementary files format and content: narrowpeak

source_name: Primary bone marrow-derived macrophages

growth_protocol: BMDMs are isolated and differentiated in  10% (v/v) conditioned medium from CMG-14-12 cells as a source of macrophage colony stimulate factor (M-CSF)

extract_protocol:
50,000  BMDMs per sample were lysed to collect nuclei and treated with Tn5 transposase (Illumina) for 30 min at 37°C with gentle agitation.
The DNA was isolated with DNA Clean & Concentrator Kit (Zymo) 598 and PCR amplified and barcoded with NEBNext High-Fidelity PCR Mix (New England Biolabs) and unique dual indexes (Illumina). The ATAC-seq library amplification was confirmed by real-time PCR, and additional barcoding PCR cycles were added as necessary while avoiding overamplification. Amplified ATAC-seq libraries were purified with DNA Clean & Concentrator Kit (Zymo). The purified libraries were quantified with Kapa Library Quant Kit (KAPA Biosystems) and quality assessed on a 4200 TapeStation System (Agilent). The libraries were pooled based on molar concentrations and 605 sequenced on a HiSeq 4000 platform single end, 75 bp).

treatment_protocol: On the 8th day of differentiation, BMDMs were incubated with the indicated treatment for the listed amount of time.

value: Primary bone marrow-derived macrophages

value: WT

value: IL-4+ Pam3CSK4


title: NFN1 400nM Round-03 (exp99)

description:
Library name: NFN1 400nM_Round-03 (exp99)
sgRNAs PCR-amplified from genomic DNA

value: NFN1 400nM


title: BMDM, IL-4+TLR2,24hrs, rep1

description: Library name: Sample 16


title: NCR-cre M1 NK cells, Exp3, Rep1


title: CUT&Tag of DDX5 in HepG2 cells with Glutamine deprivation_Rep2

description: Library name: HepG2_GlnDep_DDX5_Rep2

value: Liver

value: Hep G2

value: tumor cells


title: CUT&Tag of G4-DNA in HepG2 cells with Glutamine deprivation_Rep1

description: Library name: HepG2_GlnDep_BG4_Rep1

value: Glutamine deprivation for 12hours


title: CUT&Tag of DDX5 in HepG2 cells with Glutamine deprivation_Rep1

description: Library name: HepG2_GlnDep_DDX5_Rep1


title: CUT&Tag of G4-DNA in HepG2 cells with normal condition_Rep1

description: Library name: HepG2_Normal_BG4_Rep1


title: BMDM, IL-4,24hrs, rep2

description: Library name: Sample 14


title: NCR-cre M2 NK cells, Exp3, Rep1


title: CUT&Tag of DDX5 in HepG2 cells with normal condition_Rep1

description: Library name: HepG2_Normal_DDX5_Rep1


title: GF1-KO Imm NK cells, Exp3, Rep1


title: Deguelin 50nM Round-02 (exp69)

description:
Library name: Deguelin 50nM_Round-02 (exp69)
sgRNAs PCR-amplified from genomic DNA

value: Deguelin 50nM


title: NCR-cre Imm NK cells, Exp3, Rep1


title: Selumetinib 20uM Round-02 (exp81)

description:
Library name: Selumetinib 20uM_Round-02 (exp81)
sgRNAs PCR-amplified from genomic DNA

value: Selumetinib 20uM


title: CUT&Tag of TRIB3 in HepG2 cells with normal condition_Rep2

description: Library name: HepG2_Normal_TRIB3_Rep2


title: 1,1'-Binaphthyl-2,2'-diamine 20uM Round-00 (exp17)

description:
Library name: 1,1_-Binaphthyl-2,2_-diamine 20uM_Round-00 (exp17)
sgRNAs PCR-amplified from genomic DNA

value: 1,1'-Binaphthyl-2,2'-diamine 20uM


title: BMDM, IL-4,24hrs, rep3

description: Library name: Sample 15


title: GFI1-FOXO1-DKO M1 NK cells, Exp2, Rep2


title: BMDM, IL-4+TLR2,24hrs, rep3

description: Library name: Sample 18


title: Spinner flask No treatment Day 6 Round-02 (exp567)

description:
Library name: SF No treatment D6_Round-02 (exp567)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: SGC2096 2.6uM Round-03 (exp153)

description:
Library name: SGC2096 2.6uM_Round-03 (exp153)
sgRNAs PCR-amplified from genomic DNA


title: CUT&Tag of DDX5 in HepG2 cells with normal condition_Rep2

description: Library name: HepG2_Normal_DDX5_Rep2

value: GlutaMAX supplement for supply


title: GFI1-FOXO1-DKO M1 NK cells, Exp2, Rep3

value: spleen


title: GFI1-FOXO1-DKO Imm NK cells, Exp2, Rep2


title: CUT&Tag of TRIB3 in HepG2 cells with normal condition_Rep1

description: Library name: HepG2_Normal_TRIB3_Rep1


title: BrM_RNA_fpkm_Tumor

first: Yu

last: Wang

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

department: Department of Neurosurgery

institute: Peking Union Medical College Hospital

description:
Library name: BrM115_RNA_fpkm_Tumor
fpkm for tumor samples

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
Assembly: Human GRCh38
Supplementary files format and content: csv files included raw counts information for tumor or peritumor samples
Supplementary files format and content: csv files included Fragments Per Kilobase of transcript per Million mapped reads  information for tumor or peritumor samples

source_name: Brain Metastasis

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). 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. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). 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.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Reference genome and gene model annotation files were downloaded from genome website directly.

value: Brain Metastasis

tag: group

value: Tumor tissue


title: BMDM, NT,24hrs, rep2

description: Library name: Sample 11

value: No Treatment


title: MKC9989 10uM Round-03 (exp133)

description:
Library name: MKC9989 10uM_Round-03 (exp133)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: BMDM, NT,24hrs, rep3

description: Library name: Sample 12

value: Primary bone marrow-derived macrophages

value: WT


title: GFI1-FOXO1-DKO M2 NK cells, Exp2, Rep2

value: NK cells


title: BMDM, IL-4+TLR2,12hrs, rep3

description: Library name: Sample 9

value: IL-4+ Pam3CSK4


title: 5-Fluorouracil 20uM Round-00 (exp2)

description:
Library name: 5-Fluorouracil 20uM_Round-00 (exp2)
sgRNAs PCR-amplified from genomic DNA

value: 5-Fluorouracil 20uM


title: BMDM, IL-4,24hrs, rep1

description: Library name: Sample 13


title: BMDM, IL-4,12hrs, rep3

description: Library name: Sample 6


title: Carbonyl cyanide 3-chlorophenylhydrazone 100nM Round-00 (exp10)

description:
Library name: Carbonyl cyanide 3-chlorophenylhydrazone 100nM_Round-00 (exp10)
sgRNAs PCR-amplified from genomic DNA


title: BrM_RNA_PeriTumor

description:
Library name: BrM115_RNA_count_PeriTumor
raw_counts for peri-tumor samples

value: Peritumor tissue


title: GFI1-FOXO1-DKO M2 NK cells, Exp2, Rep1


title: CUT&Tag of TRIB3 in HepG2 cells with Glutamine deprivation_Rep2

description: Library name: HepG2_GlnDep_TRIB3_Rep2

value: Liver

value: Hep G2

value: tumor cells

value: Glutamine deprivation for 12hours


title: FOXO1-KO Imm NK cells, Exp2, Rep2


title: wild type sample8

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Library name: W8

library_source: transcriptomic single cell

data_processing:
Sequence alignment, cell calling, ambient RNA correction and doublet removal were performed on eight replicates separately and before pooling for batch correction, dimension reductions and clustering.
Sequence alignment and cell calling were performed using CellRanger v7.1.0 (10X genomics) in ‘count’ mode using --force-cells=10000.
DecontX was performed under default setting and used empty drops from each sample as background. After background correction, cells with less than 50 genes or 80 UMIs were removed. Cells with log10GenesPerUMI>1 and UMI larger than 100,000 were also removed. DoubletFinder with 5% doublet formation rate(according to 10X suggestion) were used to remove potential multiplets from downstream analysis. After these quality control steps, ~5000 high quality cells were retained for downstream analysis.
Harmony was performed on the remaining cells and top 30 PC of the harmony corrected PCs were used for UMAP visualization and Leiden clustering. Cells were grouped and annotated under clustering resolution=1 for best separation of rarer cell types by top marker genes.
Assembly: BDGP6.32
Supplementary files format and content: FC_07633_matrix.txt, tab delimited, raw expression matrix
Supplementary files format and content: FC_07633_meta.txt,tab delimited, cell-barcode2cell-type annotation

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: body, 3rd instar larvae

growth_protocol: Larvae were raised at 25ºC on standard lab food and conditions until 5 days after egg deposition.

extract_protocol:
For each sample, 16 wandering third instar larvae (8 male, 8 female) that had not everted their spiracles were collected, washed with PBS, snap-frozen in liquid nitrogen, and stored at −80°C. Frozen larvae were homogenized in a glass dounce. Nuclei were released and lysate containing nuclei was filtered sequentially through cell strainers. The nuclei sample was filtered and washed, labeled with 1µM DRAQ7 Dye, and 500,000 healthy nuclei were isolated by a Sony SH800Z Cell Sorter. FACS sorted nuclei were adjusted to a final concentration of 1,000 nuclei/µL in 1xPBS/1%BSA.
Libraries were generated according to 10X genomics Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1

value: body, 3rd instar larvae


title: BrM_RNA_Tumor

description:
Library name: BrM115_RNA_count_Tumor
raw_counts for tumor samples


title: CUT&Tag of TRIB3 in HepG2 cells with Glutamine deprivation_Rep1

description: Library name: HepG2_GlnDep_TRIB3_Rep1


title: wild type sample4

description: Library name: W4


title: FOXO1-KO M2 NK cells, Exp2, Rep2


title: BMDM, IL-4+TLR2,12hrs, rep2

description: Library name: Sample 8


title: s5d1 and s6d7, control vs 0.175uM latA, hashed

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

description: Library name: s5d1 and s6d7 (hashed)

data_processing:
Data was generated and processed by McDonnell Genome Institute (MGI) at Washington University
Multiomic sequencing files were processed using cellranger-arc-2.0.0
Assembly: GRCh38
Supplementary files format and content: Processed files are in "barcodes" files, "features" files, and "matrix" files.

growth_protocol: Human pluripotent stem cells were cultured, grown, and differentiated into SC-islets as previously described (Hogrebe et al., Nature Protocols 2021).

extract_protocol:
Cells were barcoded with unique BioLegend TotalSeq A antibodies using the 10X single cell 3’ v 3.1 hashing protocol.
Samples were processed according to the 10X chromium protocol (CG000315) to generate single-cell libraries

treatment_protocol: During the first 24 hours of differentiation in stage 1, latA was added to the media. The remainder of the differentiation protocol was carried out normally. For the conditions specifically studying latA treated stem cells, either 0.175uM or 1.5uM latA were added in mTeSR1 rather than the stage 1, day 1 differentiation media, as was done in all other experiments.

value: stem cell-derived pancreatic progenitors and pancreatic endocrine

value: control vs 0.175uM latA added on stage 1 day 1


title: BMDM, IL-4,12hrs, rep1

description: Library name: Sample 4


title: wild type sample6

description: Library name: W6


title: BrM_RNA_fpkm_PeriTumor

description:
Library name: BrM115_RNA_fpkm_PeriTumor
fpkm for peri-tumor samples

value: Brain Metastasis


title: wild type sample3

description: Library name: W3


title: BMDM, IL-4,12hrs, rep2

description: Library name: Sample 5


title: BMDM, NT,24hrs, rep1

description: Library name: Sample 10


title: wild type sample5

description: Library name: W5


title: s3d1 and s4d1, control vs 0.175uM latA, hashed

description: Library name: s3d1 and s4d1 (hashed)

value: stem cell-derived primitive gut tube and pancreatic progenitors


title: BMDM, IL-4+TLR2,12hrs, rep1

description: Library name: Sample 7


title: wild type sample7

description: Library name: W7


title: GFI1-FOXO1-DKO M1 NK cells, Exp2, Rep1

value: spleen


title: FOXO1-KO M2 NK cells, Exp2, Rep1


title: wild type sample2

description: Library name: W2


title: FOXO1-KO Imm NK cells, Exp2, Rep1


title: s1d1 (stem cells), s1d2 (0, 0.1, 0.175uM latA), s1d3 (0uM latA), hashed

description: Library name: s1d1, s1d2, and s1d3 (hashed)

value: stem cells differentiating to definitive endoderm

value: control vs latA added on stage 1 day 1


title: FOXO1-KO M1 NK cells, Exp2, Rep2


title: BMDM, NT,12hrs, rep3

description: Library name: Sample 3

value: Primary bone marrow-derived macrophages

value: WT

value: No Treatment


title: s2d1 (0.1, 0.175uM latA), stem cells (0.175, 1.5uM latA), hashed

description: Library name: s2d1 and latA-treated stem cells (hashed)


title: BMDM, NT,12hrs, rep1

description: Library name: Sample 1


title: wild type sample1

description: Library name: W1


title: s1d3 (0.1, 0.175uM latA), s1d4 (0, 0.1, 0.175uM latA), hashed

description: Library name: s1d3 and s1d4 (hashed)


title: GF1-KO M1 NK cells, Exp2, Rep3

value: NK cells


title: FOXO1-KO M1 NK cells, Exp2, Rep1


title: s6d15, 0.175uM latA, RNA

description: Library name: stage 6, day 15, latA treated_RNA

data_processing:
Data was generated and processed by McDonnell Genome Institute (MGI) at Washington University
Multiomic sequencing files were processed using cellranger-arc-2.0.0
Assembly: GRCh38
Supplementary files format and content: Processed files are in "atac_fragments" files, "atac_peaks" files, "filtered_feature_bc_matrix" files, and "per_barcode_metrics" files.

extract_protocol:
Samples were prepared using the 10X Multiome ATAC and Gene Expression (GEX) protocol (CGOOO338)
Sample libraries were constructed using the 10X Chromium Protocol.

treatment_protocol: During the first 24 hours of differentiation in stage 1, 0.175uM latA was added to the media. The remainder of the differentiation protocol was carried out normally.

value: stem cell-derived islets

value: 0.175uM latA on stage 1 day 1


title: s6d15, 0.175uM latA, ATAC

description: Library name: stage 6, day 15, latA treated_ATAC


title: Sample 65, Veh treated, IP

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: Sample_65

data_processing:
FASTQ files were processed with the NGS-Data-Charmer pipeline (https://github.com/shenlab-sinai/NGS-Data-Charmer). In brief, adapter trimming was performed, forllowed by alignment to the mm10 genome build using HISAT2, and duplicate alignments were removed using the Picard ‘MarkDuplicates’ module.
Assembly: mm10
Supplementary files format and content: Narrowpeak files were annotated with ChIPSeekeR. Each annotated file contains peak locations and the associated genomic annotations of the peaks.
Library strategy: CUT&Run

source_name: Hippocampus

extract_protocol:
CUT&RUN was performed using a primary anti-ΔFOSB antibody.
Libraries were generated using the NEB Next® Ultra™ II DNA Library Prep Kit (New England BioLabs) and sequenced on an Illumina HiSeq 4000 with a 2 × 150 bp paired-end configuration at a minimum depth of 20 million reads per sample.

treatment_protocol: Nuclei were isolated from the dorsal hippocampus tissue of APP mice after infusion of vehicle or JPC0661. Tissue was homogenized in lysis buffer (320 mM sucrose, 5 mM CaCl2, 0.1 mM EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT, 0.1% Triton X-100, 1.5 mM spermidine, and protease inhibitors) using a Dounce homogenizer (30-40 strokes per pestle). Homogenates were filtered through a 40 μm strainer and transferred to ultracentrifuge tubes. A sucrose cushion (1.8 M sucrose, 10 mM Tris-HCl, pH 8.0, 1 mM DTT, 1.5 mM spermidine, and protease inhibitors) was layered beneath, and nuclei were pelleted by ultracentrifugation at 24,000 rpm for 1.25 h at 4 °C.

value: Hippocampus

value: Veh

tag: gender

value: F

tag: chip antibody

value: IP


title: GF1-KO M1 NK cells, Exp2, Rep2


title: MIA_3

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description:
Library name: MIA_3_Pla
10X Genomics

data_processing:
Nuclei from individual replicates underwent strict quality control filtering and were normalized using SCTransform. Cells with ≥ 5% mitochondrial genes, ≤ 200, and ≥ 2,500 unique feature counts were excluded from the datasets. To remove nuclei free mRNA contamination, SoupX was run on each sample. Replicates were integrated using Harmony. Seurat v5 (R v4.2.1) was used to perform data normalization, dimensional reduction using PCA, and graph-based clustering with UMAP
Assembly: mm10
Supplementary files format and content: tab-delimited matrix file and value files for each sample

source_name: Placenta

growth_protocol: 6 mouse placenta (n=3 control, n=3 MIA) were extracted from E13.5 pregnant mice.

extract_protocol:
For single-nucleus sequencing, placentas from saline-exposed and poly(I:C)mod-treated male mice (n = 3) were snap-frozen in liquid nitrogen. Frozen tissues were thawed in 1 ml of high sucrose buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl₂, 20 mM Tricine-KOH, pH 7.8, 0.15 mM spermine tetrahydrochloride, 0.5 mM spermidine trihydrochloride, 1 mM DTT) in presence of RNAse inhibitors. The samples were mechanically dissociated using a dounce homogenizer containing IGEPAL CA-630 (Sigma-Aldrich). Nuclei were collected from interface of 30% and 40% of iodixanol after 18 minutes of density gradient ultracentrifugation at 10,000 g. Purified nuclei were counted using a hemocytometer.
Nuclei were extracted from placenta samples and processed using the 10x Genomics Chromium System. Libraries were sequenced using the Nextseq platform at the Centre for Applied Genomics (TCAG; The Hospital for Sick Children) in Toronto, ON, Canada.

treatment_protocol: Pregnant mice are intraperitoneally administered 20 mg/kg of poly(I:C), a synthetic double stranded RNA that predominantly (but not exclusively) binds Toll-like receptor 3 (TLR3) to induce the same innate immune pathways as a viral infection21,22. Administration of poly(I:C) (or saline as control) occurs at E12.5, and embryos were collected for study 24 hr later.

value: Placenta

tag: developmental age

value: PolyIC


title: Sample 64, Veh treated, IP

description: Library name: Sample_64

value: APP


title: CTL_3

description:
Library name: CTL_3_Pla
10X Genomics

value: PBS


title: s6d15, control, ATAC

description: Library name: stage 6, day 15, control_ATAC

value: control


title: MIA_2

description:
Library name: MIA_2_Pla
10X Genomics


title: GF1-KO Imm NK cells, Exp2, Rep2

value: spleen


title: BMDM, NT,12hrs, rep2

description: Library name: Sample 2


title: Sample 63, JPC0661 treated, IP

description: Library name: Sample_63

value: M


title: Sample 64, Veh treated, IGG

description: Library name: Sample_64-I

value: IGG


title: GF1-KO M2 NK cells, Exp2, Rep1


title: CTL_2

description:
Library name: CTL_2_Pla
10X Genomics


title: s6d15, control, RNA

description: Library name: stage 6, day 15, control_RNA


title: GFI1-FOXO1-DKO Imm NK cells, Exp2, Rep1


title: CTL_1

description:
Library name: CTL_1_Pla
10X Genomics


title: s2d1, 0.175uM latA, ATAC

description: Library name: stage 2, day 1, latA treated_ATAC

value: stem cell-derived definitive endoderm


title: Sample 62, JPC0661 treated, IP

description: Library name: Sample_62

value: WT


title: Cochlear epithelium, E16se_3

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description:
Library name: E16se_3
10X Genomics

data_processing:
Libraries were sequenced on a Nextseq 500 instrument (Illumina, San Diego, CA) and reads were subsequently processed using 10x Genomics CellRanger analytical pipeline using default settings and 10× Genomics downloadable GRCm38 as previously described
Note:  Four samples (E14se_1, E14se_2, E16se_2 and E16se_3) were previously reported by Kolla et al. 2020 and are part of GSE137299. These samples were re-mapped and analyzed together with other samples unique to this GEO data set. The nomenclature from GSE137299 was retained for sake of clarity. The "se" stands for "sensory epithelium".
Assembly: GRCm38
Supplementary files format and content: Tab-separated tables and matrix files

source_name: Cochlear epithelium

extract_protocol:
The cochleae were dissected from embryos of timed pregnant females and treated with thermolysis to remove the mesenchyme, the roof of the cochlea, and the lateral wall. The epithelial floor of the cochlear duct was then isolated. Cells were dissociated using pre-warmed papain.
Single cell captures were performed following manufacturer's recommendations on a 10× Genomics Controller device (Pleasanton, CA).  Library preparation was performed according to the instructions in the 10x Genomics Chromium Single Cell 3′ Chip Kit V2.

value: Cochlear epithelium

tag: strain

value: pooled male and female


title: GF1-KO M1 NK cells, Exp2, Rep1

value: NK cells


title: GF1-KO M2 NK cells, Exp2, Rep2


title: Sample 61, Veh treated, IP

description: Library name: Sample_61

value: Hippocampus


title: NCR-cre M2 NK cells, Exp2, Rep4


title: GF1-KO Imm NK cells, Exp2, Rep1


title: Sample 62, JPC0661 treated, IGG

description: Library name: Sample_62-I


title: Cochlear epithelium, E16_Fgfr3_WT2

description:
Library name: E16_Fgfr3_WT2
10X Genomics


title: NCR-cre M1 NK cells, Exp2, Rep4


title: Cochlear epithelium, E16_Fgfr3_WT1

description:
Library name: E16_Fgfr3_WT1
10X Genomics


title: Cochlear epithelium, E16se_2

description:
Library name: E16se_2
10X Genomics


title: s2d1, control, RNA

description: Library name: stage 2, day 1, control_RNA


title: Kasumi_IgG

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description:
Library name: Sample 6
CUT&Tag DNA

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS3 (v3.0.2)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).


title: s2d1, control, ATAC

description: Library name: stage 2, day 1, control_ATAC


title: NCR-cre M1 NK cells, Exp2, Rep3


title: Sample 63, JPC0661 treated, IGG

description: Library name: Sample_63-I


title: Cochlear epithelium, E16_Fgfr3_WT4

description:
Library name: E16_Fgfr3_WT4
10X Genomics


title: Kasumi_MEF2D

description:
Library name: Sample 4
CUT&Tag DNA


title: NCR-cre M2 NK cells, Exp2, Rep3


title: Kasumi_RUNX2

description:
Library name: Sample 5
CUT&Tag DNA


title: Sample 60, JPC0661 treated, IGG

description: Library name: Sample_60-I


title: Sample 61, Veh treated, IGG

description: Library name: Sample_61-I

value: Veh


title: Cochlear epithelium, E16_Fgfr3_KO4

description:
Library name: E16_Fgfr3_KO4
10X Genomics


title: NCR-cre Imm NK cells, Exp2, Rep2


title: Kasumi_IRF1

description:
Library name: Sample 3
CUT&Tag DNA


title: s2d1, 0.175uM latA, RNA

description: Library name: stage 2, day 1, latA treated_RNA

value: 0.175uM latA on stage 1 day 1


title: Sample 59, Veh treated, IP

description: Library name: Sample_59

value: IP


title: NCR-cre M1 NK cells, Exp2, Rep2


title: Sample 60, JPC0661 treated, IP

description: Library name: Sample_60


title: Kasumi_ETV6

description:
Library name: Sample 2
CUT&Tag DNA


title: Cochlear epithelium, E16_Fgfr3_KO3

description:
Library name: E16_Fgfr3_KO3
10X Genomics


title: Cochlear epithelium, E16_Fgfr3_KO2

description:
Library name: E16_Fgfr3_KO2
10X Genomics


title: NCR-cre M2 NK cells, Exp2, Rep2


title: Sample 58, JPC0661 treated, IP

description: Library name: Sample_58

value: F


title: NCR-cre M1 NK cells, Exp2, Rep1


title: Sample 58, JPC0661 treated, IGG

description: Library name: Sample_58-I


title: Sample 59, Veh treated, IGG

description: Library name: Sample_59-I


title: Cochlear epithelium, E16_Fgfr3_KO1

description:
Library name: E16_Fgfr3_KO1
10X Genomics


title: Sample 56, Veh treated, IP

description: Library name: Sample_56


title: Cochlear epithelium, E14se_2

description:
Library name: E14se_2
10X Genomics


title: NCR-cre M2 NK cells, Exp2, Rep1


title: Kasumi_ELF1

description:
Library name: Sample 1
CUT&Tag DNA


title: NCR-cre Imm NK cells, Exp2, Rep1


title: HCT116,RSRC2si,biol repl 2

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

description: Library name: RSRC2si_e2

data_processing:
RNA-Seq paired-end reads were quality trimmed using trimgalore  v0.6.5 and were mapped to the human genome (hg38, Genome Reference Consortium GRCh38)  using STAR 2.7.0f
Number of reads aligned to the exonic region of each gene were counted using rsem v1.3.1 and gencode.v38
Assembly: hg38
Supplementary files format and content: tab-delimited text files contain rsem counts for each sample

source_name: colon cancer cell line

growth_protocol: HCT116 cells were grown in McCoy’s 5A medium (Gibco, 36600-021) supplemented with 10% FBS (Gibco, A5256801). The cells were cultured in a sterile, humidified incubator at 37 °C with 5% CO2, and were regularly tested for mycoplasma contamination.

extract_protocol:
RNA was extracted from HCT116 cells 48hrs after transfection using RNeasy® mini kit (74106, QIAGEN) and treated with DNase I (79254, QIAGEN) according to the manufacturer’s instructions. RNA quality was analysed on the Tapestation (Agilent) before proceeding with the library preparation. 1ug of RNA was used for library preparation.
RNA-seq libraries were prepared from HCT116 cells using the CORALL™ Total RNA-Seq V2 Library Prep Kit with UDIs set B1 (184.96, Lexogen) with Lexogen RiboCop rRNA Depletion Kit for Human/Mouse/Rat V2 following the workflow for generation of long insert sizes.

treatment_protocol: The HCT116 cells were plated and the next day the cells (at 60-70% confluency) were transfected with Lipofectamine RNAiMAX (13778150, Invitrogen) using either siRNAs (a pool of four; Horizon Discovery) or antisense Locked Nucleic Acid (LNA) GapmeRs (QIAGEN) following the manufacturer’s instructions.  We used two negative controls: silencer™ Negative Control No. 1 siRNA (Ambion, 4390843) and nontargeting LNA A (300611-00, QIAGEN). The final concentrations were 5 nM for siRNAs and 10 nM for LNA gapmers.

value: colon cancer cell line


title: HCT116,RSRC2si,biol repl 4

description: Library name: RSRC2si_e4


title: HCT116,RSRC2si,biol repl 3

description: Library name: RSRC2si_e3


title: HCT116,RSRC2si,biol repl 1

description: Library name: RSRC2si_e1


title: Cochlear epithelium, E14_4

description:
Library name: E14_4
10X Genomics


title: meninges, LCMV

data_processing:
The raw sequencing data underwent initial processing using Fastp to trim primer sequences and remove low-quality bases. SeekOne®Tools were employed for sequence data processing and alignment to the mouse GRCm38 reference genome, resulting in the generation of gene expression matrices.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dural meninges

extract_protocol:
After harvesting, the meninges of 10 mice from different groups were washed in ice-cold RPMI1640 and dissociated using Collagenase IV (Sigma), Collagenase II (Sigma), Collagenase I (Sigma), and DNase I (Sigma). Cell count and viability were analyzed using a fluorescence Cell Analyzer (Countstar) with AO/PI reagent after removing erythrocytes (Solarbio). The debris and dead cells were removed (Miltenyi). Finally, fresh cells were prepared for library construction.
Single-cell RNA-Seq libraries were prepared using the SeekOne Digital Droplet Single Cell 5’ library preparation kit (SeekGene).

value: Dural meninges

value: wildtype

tag: infection

value: LCMV


title: Cochlear epithelium, E14se_1

description:
Library name: E14se_1
10X Genomics


title: Sample 55, JPC0661 treated, IP

description: Library name: Sample_55

value: APP


title: HCT116,Ctlsi,biol repl 4

description: Library name: Ctlsi_e4


title: Cochlear epithelium, E13_3

description:
Library name: E13_3
10X Genomics


title: Sample 54, JPC0661 treated, IP

description: Library name: Sample_54


title: HCT116,Ctlsi,biol repl 3

description: Library name: Ctlsi_e3


title: Sample 56, Veh treated, IGG

description: Library name: Sample_56-I


title: E6843

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: WT mice with 28-day Angiotensin-II (500ng/kg/min) and ETH (10mg/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:Check the sample for contamination and, if there is pollution, remove it If the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window; Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed; if the truncated read length is less than 50 bp, the entire read is removed Remove unmatched reads Q30，Q20 explanation： Q30 indicates that the sequencing error rate of the base is 0.1%. Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: cardiac tissue

extract_protocol:
The hearts were dissected and cardiac tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: cardiac tissue

value: Angiotensin-II+Ethoxysanguinarine


title: Meninges, PBS

value: No infection


title: Cochlear epithelium, E13_2

description:
Library name: E13_2
10X Genomics

value: WT


title: E1695


title: Cochlear epithelium, E13_1

description:
Library name: E13_1
10X Genomics

value: Cochlear epithelium


title: Cochlear epithelium, E14_5

description:
Library name: E14_5
10X Genomics

value: pooled male and female


title: HCT116,Ctlsi,biol repl 2

description: Library name: Ctlsi_e2


title: Sample 53, Veh treated, IP

description: Library name: Sample_53


title: Sample 54, JPC0661 treated, IGG

description: Library name: Sample_54-I

value: IGG


title: HCT116,Ctlsi,biol repl 1

description: Library name: Ctlsi_e1


title: E961


title: E960


title: Sample 53, Veh treated, IGG

description: Library name: Sample_53-I

value: Hippocampus


title: Cochlear epithelium, E12_WT_7

description:
Library name: E12_WT_7
10X Genomics


title: Sample 52, Veh treated, IP

description: Library name: Sample_52

value: Veh

value: M


title: Cochlear epithelium, E12_WT_6

description:
Library name: E12_WT_6
10X Genomics


title: E962


title: E959


title: Sample 55, JPC0661 treated, IGG

description: Library name: Sample_55-I


title: HCT116,C1QTNF1-AS1,LNAA,biol repl 4

description: Library name: C1_LNAA_e4


title: HCT116,C1QTNF1-AS1,LNAA,biol repl 3

description: Library name: C1_LNAA_e3


title: Cochlear epithelium, E12_WT_5

description:
Library name: E12_WT_5
10X Genomics


title: Sample 52, Veh treated, IGG

description: Library name: Sample_52-I


title: HCT116,C1QTNF1-AS1,LNAA,biol repl 2

description: Library name: C1_LNAA_e2


title: Cochlear epithelium, E12_WT_4

description:
Library name: E12_WT_4
10X Genomics


title: A926

description: WT mice with 28-day Angiotensin-II (500ng/kg/min) treatment

value: Angiotensin-II


title: Cochlear epithelium, E11_WT_4

description:
Library name: E11_WT_4
10X Genomics


title: Sample 48, JPC0661 treated, IP

description: Library name: Sample_48

value: F

value: IP


title: Sample 51, JPC0661 treated, IP

description: Library name: Sample_51


title: A938


title: HCT116,C1QTNF1-AS1,LNAA,biol repl 1

description: Library name: C1_LNAA_e1

value: colon cancer cell line


title: CONTROL23WK4

city: Madrid

first: Yulia

middle: A

last: Nevzorova

state: Madrid

address: C/Doctor Severo Ochoa, 9, pl. 2, Lab IV

department: Department of Immunology, Ophthalmology & ENT

country: Spain

institute: Complutense University (UCM) School of Medicine

description: Library name: CTRL133

data_processing:
Quality control and preprocessing of RNAseq: Adapter sequences and low-quality reads are removed using TrimGalore version 0.6.0 with Cutadapt version 1.18.
Clean reads are aligned to the reference genome using a splice aware aligner STAR version 020201 over genome version mm39
Aligned reads are then queantified at the gene level using Htseq version 0.11.0
EdgeR version 3.28.1 for R software version 3.6.3 (hereafter referred to as R) requires raw read counts as input and performs normalization using the trimmed mean of M-values (TMM) method
TMM normalization accounts for library size differences and composition biases, ensuring accurate comparisons between samples
Assembly: GRCm39
Supplementary files format and content: TMM normalized read counts

extract_protocol:
Total RNA was isolated through Trizol/Chloroform method. Input RNA was quantified with QuantiFluor RNA System and QC was assessed using a Bioanalyzer 2100.
RNA libraries for RNAseq were prepared using Collibri 3'mRNA library prep kit following manufacturer´s protocol

value: Liver

value: male


title: HCT116,C1QTNF1-AS1,LNA5,biol repl 2

description: Library name: C1_LNA5_e2


title: Cochlear epithelium, E11_WT_2

description:
Library name: E11_WT_2
10X Genomics


title: Sample 46, JPC0661 treated, IP

description: Library name: Sample_46

value: APP


title: HCT116,C1QTNF1-AS1,LNA5,biol repl 4

description: Library name: C1_LNA5_e4


title: Cochlear epithelium, E11_WT_1

description:
Library name: E11_WT_1
10X Genomics


title: C964

description: WT mice with 28-day Saline treatment

value: cardiac tissue

value: Saline


title: A946


title: Cochlear epithelium, E11_WT_3

description:
Library name: E11_WT_3
10X Genomics


title: HCT116,C1QTNF1-AS1,LNA5,biol repl 1

description: Library name: C1_LNA5_e1


title: A942


title: DUAL23WK5

description: Library name: DUAL132


title: HCT116,C1QTNF1-AS1,LNA4,biol repl 3

description: Library name: C1_LNA4_e3


title: A1687


title: Sample 51, JPC0661 treated, IGG

description: Library name: Sample_51-I


title: HCT116,C1QTNF1-AS1,LNA5,biol repl 3

description: Library name: C1_LNA5_e3


title: Sample 46, JPC0661 treated, IGG

description: Library name: Sample_46-I


title: Sample 48, JPC0661 treated, IGG

description: Library name: Sample_48-I


title: Sample 45, Veh treated, IP

description: Library name: Sample_45


title: C951

description: WT mice with 28-day Saline treatment


title: DUAL23WK3

description: Library name: DUAL128


title: A925


title: HCT116,C1QTNF1-AS1,LNA4,biol repl 2

description: Library name: C1_LNA4_e2


title: DUAL23WK4

description: Library name: DUAL131


title: HCT116,C1QTNF1-AS1,LNA4,biol repl 4

description: Library name: C1_LNA4_e4


title: Sample 45, Veh treated, IGG

description: Library name: Sample_45-I


title: C929

description: WT mice with 28-day Saline treatment


title: HCT116,C1QTNF1-AS1,LNA4,biol repl 1

description: Library name: C1_LNA4_e1


title: CONTROL23WK3

description: Library name: CTRL125


title: Sample 43, Veh treated, IGG

description: Library name: Sample_43-I


title: C976

description: WT mice with 28-day Saline treatment


title: Sample 43, Veh treated, IP

description: Library name: Sample_43


title: HCT116,C1QTNF1-AS1,LNA1,biol repl 4

description: Library name: C1_LNA1_e4


title: C928

description: WT mice with 28-day Saline treatment


title: HCT116,C1QTNF1-AS1,LNA1,biol repl 2

description: Library name: C1_LNA1_e2


title: Sample 42, Veh treated, IGG

description: Library name: Sample_42-I


title: CONTROL23WK2

description: Library name: CTRL124


title: Sample 42, Veh treated, IP

description: Library name: Sample_42


title: DUAL23WK2

description: Library name: DUAL121


title: HCT116,C1QTNF1-AS1,LNA1,biol repl 1

description: Library name: C1_LNA1_e1


title: pooled activated T cells [TCR_rerun]

city: Leiden

first: Jannie

last: Borst

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

description: Sample contains pooled activated T cells from 8 experimental conditions: Day-5-Help-dLN, Day-5-Help-ndLN, Day-5-No-Help-dLN, Day 5-No-Help-ndLN, Day-10-Help-dLN, Day-10-Help-ndLN, Day-10-No-Help-dLN, Day 10-No-Help-ndLN. Cells from each experimental condition were labeled with a separate HTO. scRNAseq (Project_202102035) and scTCRseq (Project_202102035a) were performed on the same sample.

data_processing:
CellRanger (10X Genomics, v6.0.1)
scRNAseq reads were aligned to the mouse reference genome mm10 and barcode counting was performed using ‘cellranger count’.
TCRseq reads were aligned to the mouse reference genome mm10 and consensus TCR sequences were determined using ‘cellranger vdj’
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: lymph node

extract_protocol:
Activated T cells (CD19-CD3+CD44+CD62L-) were sorted from pooled dLN or pooled ndLN of 3 mice per group. T cells from 8 samples were labeled with 8 distinct hashtag oligonucleotides (HTO)-conjugated antibodies to MHC-II/CD45, after which all samples were pooled for 10X sequencing.
scRNAseq libraries were prepared using a 10X Chromium single cell 5’ v2 chemistry kit (10X Genomics), according to the manufacturer’s protocol.
TCRseq libraries were prepared using a 10X Chromium single cell V(D)J enrichment kit for mouse T cells (10X Genomics), according to the manufacturer’s protocol.

treatment_protocol: Mice were vaccinated under Help or No Help conditions at day 0, 3 and 6 and were sacrificed at day 5 or at day 10 after first vaccination.

value: lymph node


title: pooled activated T cells [Pool_T_GEX]

value: WT


title: CONTROL23WK1

description: Library name: CTRL123

source_name: Liver


title: C984

description: WT mice with 28-day Saline treatment


title: Sample 41, JPC0661 treated, IP

description: Library name: Sample_41


title: Sample 41, JPC0661 treated, IGG

description: Library name: Sample_41-I


title: cPDS_rG4-2

status: Public on Mar 12 2026

city: Guangzhou

first: Tiegang

last: Meng

address: Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health

institute: Guangdong Second Provincial General Hospital

data_processing:
High-quality sequencing reads were obtained through preprocessing with fastp (v0.21.0) using stringent filtering parameters: base correction, poly-X trimming, minimum quality score 20, minimum length 36 nt, low complexity filtering, maximum 40% unqualified bases, maximum 4 N bases, paired-end adapter detection, and 8 threads (-g -x -q 20 -l 36 -y -c -u 40 -n 4 --detect_adapter_for_pe -w 8). Filtered reads were aligned to the mouse reference genome (mm9) using Bowtie2 (v2.5.1) with optimized local alignment settings: very-sensitive-local mode, no mixed alignments, no discordant pairs, Phred+33 quality scores, minimum insert size 10 bp, maximum insert size 700 bp, and 10 parallel threads (--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 10). Peak calling was performed on uniquely mapped reads using MACS3 (v3.0.0b3) with disabled lambda and model building (-nolambda -nomodel), applying a q-value threshold of 0.05. Genome-wide enrichment patterns were visualized using deepTools (v3.5.4), with average tag density plots generated via plotHeatmap. Read enrichment across genomic loci was visualized by converting sorted BAM files to BigWig format using bamCoverage. Genomic distribution analysis was conducted using ChIPSeeker, while pausing index calculations followed established protocols (https://github.com/MiMiroot/PIC). For differential binding analysis, a comprehensive approach was implemented. Initially, MACS3 identified peak regions across all samples. These regions were consolidated using BEDTools' mergeBed function to create a unified peak set. Read quantification for each region was performed using featureCounts, followed by differential binding analysis using DESeq2.
Sequencing reads were aligned to the mouse reference genome (mm9) using HISAT2 (v2.1.0). Gene-level quantification was performed using FeatureCount (v2.0.1) with Gencode mm9 annotations as reference. Read count normalization and differential expression analysis were conducted using the DESeq2 package, with size factors estimated prior to differential testing. Alternative splicing events were identified using Rmats (v4.0.2), with splice junction visualization generated through rmats2sashimiplot. For comparative analysis with published RNA-seq datasets, expression quantification followed identical computational procedures to ensure methodological consistency.
Raw sequencing reads were processed by Cutadapt (v1.15) for adapter removal with the following parameters: minimum length 18 nt, 8 threads, maximum N bases 4, N-end trimming, double trimming rounds, and maximum error rate 0.1 (-m 18 -j 8 --max-n 4 --trim-n --times 2 -e 0.1 -O 3). Adapter sequences for parameters -a, -A, and -G are available in the Supplementary Table. Overlapping paired-end reads (>30 nucleotides) were merged into single reads using fastp (v0.21.0). After UMI sequence extraction, clean reads underwent a two-stage alignment process. First, reads were aligned to mouse pre-rRNA using Bowtie2 (v2.5.1). The remaining unmapped reads were then aligned to the mouse reference genome (mm9) using STAR (v2.5.2b) with the following specifications: unique splice junction filtering, 5' read extension, maximum mismatch ratio 0.04, unrestricted total mismatches, and single mapping requirement (--outSJfilterReads Unique --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1). PCR duplicates were removed using UMI information, and the resulting unique reads were subjected to peak identification using PureCLIP (v1.3.1). For motif discovery, LACE-seq peaks were extended by 30 nucleotides upstream, and enriched motifs within these extended sequences were identified using Homer's findMotifsGenome.pl function. Inter-replicate correlation analysis was conducted using Pearson correlation coefficients according to established protocols.
Assembly: mm9
Supplementary files format and content: bw files
Supplementary files format and content: csv files
Supplementary files format and content: txt files
Library strategy: ULI-rG4-seq

source_name: ovary

extract_protocol:
Growing oocytes were collected from control and Dhx36fl/fl;SKO mice
Library construction was performed following Illumina manufacturer suggestions.

value: ovary

value: oocyte


title: rG4-WO-2


title: rG4-WO-1


title: HCT116,C1QTNF1-AS1,LNA1,biol repl 3

description: Library name: C1_LNA1_e3


title: DUAL23WK1

description: Library name: DUAL120


title: cPDS_rG4-1


title: RG4-control-4_combined


title: RG4-Dhx36-cKO-6_combined


title: JZ24100002-GV-polii-180-control-2_combined

data_processing:
High-quality sequencing reads were obtained through preprocessing with fastp (v0.21.0) using stringent filtering parameters: base correction, poly-X trimming, minimum quality score 20, minimum length 36 nt, low complexity filtering, maximum 40% unqualified bases, maximum 4 N bases, paired-end adapter detection, and 8 threads (-g -x -q 20 -l 36 -y -c -u 40 -n 4 --detect_adapter_for_pe -w 8). Filtered reads were aligned to the mouse reference genome (mm9) using Bowtie2 (v2.5.1) with optimized local alignment settings: very-sensitive-local mode, no mixed alignments, no discordant pairs, Phred+33 quality scores, minimum insert size 10 bp, maximum insert size 700 bp, and 10 parallel threads (--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 10). Peak calling was performed on uniquely mapped reads using MACS3 (v3.0.0b3) with disabled lambda and model building (-nolambda -nomodel), applying a q-value threshold of 0.05. Genome-wide enrichment patterns were visualized using deepTools (v3.5.4), with average tag density plots generated via plotHeatmap. Read enrichment across genomic loci was visualized by converting sorted BAM files to BigWig format using bamCoverage. Genomic distribution analysis was conducted using ChIPSeeker, while pausing index calculations followed established protocols (https://github.com/MiMiroot/PIC). For differential binding analysis, a comprehensive approach was implemented. Initially, MACS3 identified peak regions across all samples. These regions were consolidated using BEDTools' mergeBed function to create a unified peak set. Read quantification for each region was performed using featureCounts, followed by differential binding analysis using DESeq2.
Sequencing reads were aligned to the mouse reference genome (mm9) using HISAT2 (v2.1.0). Gene-level quantification was performed using FeatureCount (v2.0.1) with Gencode mm9 annotations as reference. Read count normalization and differential expression analysis were conducted using the DESeq2 package, with size factors estimated prior to differential testing. Alternative splicing events were identified using Rmats (v4.0.2), with splice junction visualization generated through rmats2sashimiplot. For comparative analysis with published RNA-seq datasets, expression quantification followed identical computational procedures to ensure methodological consistency.
Raw sequencing reads were processed by Cutadapt (v1.15) for adapter removal with the following parameters: minimum length 18 nt, 8 threads, maximum N bases 4, N-end trimming, double trimming rounds, and maximum error rate 0.1 (-m 18 -j 8 --max-n 4 --trim-n --times 2 -e 0.1 -O 3). Adapter sequences for parameters -a, -A, and -G are available in the Supplementary Table. Overlapping paired-end reads (>30 nucleotides) were merged into single reads using fastp (v0.21.0). After UMI sequence extraction, clean reads underwent a two-stage alignment process. First, reads were aligned to mouse pre-rRNA using Bowtie2 (v2.5.1). The remaining unmapped reads were then aligned to the mouse reference genome (mm9) using STAR (v2.5.2b) with the following specifications: unique splice junction filtering, 5' read extension, maximum mismatch ratio 0.04, unrestricted total mismatches, and single mapping requirement (--outSJfilterReads Unique --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1). PCR duplicates were removed using UMI information, and the resulting unique reads were subjected to peak identification using PureCLIP (v1.3.1). For motif discovery, LACE-seq peaks were extended by 30 nucleotides upstream, and enriched motifs within these extended sequences were identified using Homer's findMotifsGenome.pl function. Inter-replicate correlation analysis was conducted using Pearson correlation coefficients according to established protocols.
Assembly: mm9
Supplementary files format and content: bw files
Supplementary files format and content: csv files
Supplementary files format and content: txt files
Library strategy: CUT&Tag


title: JZ24100002-GV-polii-180-RHcKO-2_combined


title: JZ24100002-GV-polii-180-cPDS-2_combined


title: GZ24047476-GV-TE-HEXIM1-control-1_combined


title: RG4-Dhx36-cKO-5_combined


title: JZ24100002-GV-polii-180-control-1_combined


title: JZ24100002-GV-polii-180-RHcKO-1_combined


title: GZ24047476-GV-TE-CDK9-control-2_combined


title: GZ24047476-GV-TE-HEXIM1-Dhx36cKO-2_combined


title: JZ24100002-GV-polii-180-cPDS-1_combined


title: GZ24047476-GV-TE-CDK9-Dhx36cKO-2_combined


title: RG4-control-3_combined


title: GZ24037765-Dh36-RNA-mix-240720-Dhx36-3h-control-1_combined

data_processing:
High-quality sequencing reads were obtained through preprocessing with fastp (v0.21.0) using stringent filtering parameters: base correction, poly-X trimming, minimum quality score 20, minimum length 36 nt, low complexity filtering, maximum 40% unqualified bases, maximum 4 N bases, paired-end adapter detection, and 8 threads (-g -x -q 20 -l 36 -y -c -u 40 -n 4 --detect_adapter_for_pe -w 8). Filtered reads were aligned to the mouse reference genome (mm9) using Bowtie2 (v2.5.1) with optimized local alignment settings: very-sensitive-local mode, no mixed alignments, no discordant pairs, Phred+33 quality scores, minimum insert size 10 bp, maximum insert size 700 bp, and 10 parallel threads (--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 10). Peak calling was performed on uniquely mapped reads using MACS3 (v3.0.0b3) with disabled lambda and model building (-nolambda -nomodel), applying a q-value threshold of 0.05. Genome-wide enrichment patterns were visualized using deepTools (v3.5.4), with average tag density plots generated via plotHeatmap. Read enrichment across genomic loci was visualized by converting sorted BAM files to BigWig format using bamCoverage. Genomic distribution analysis was conducted using ChIPSeeker, while pausing index calculations followed established protocols (https://github.com/MiMiroot/PIC). For differential binding analysis, a comprehensive approach was implemented. Initially, MACS3 identified peak regions across all samples. These regions were consolidated using BEDTools' mergeBed function to create a unified peak set. Read quantification for each region was performed using featureCounts, followed by differential binding analysis using DESeq2.
Sequencing reads were aligned to the mouse reference genome (mm9) using HISAT2 (v2.1.0). Gene-level quantification was performed using FeatureCount (v2.0.1) with Gencode mm9 annotations as reference. Read count normalization and differential expression analysis were conducted using the DESeq2 package, with size factors estimated prior to differential testing. Alternative splicing events were identified using Rmats (v4.0.2), with splice junction visualization generated through rmats2sashimiplot. For comparative analysis with published RNA-seq datasets, expression quantification followed identical computational procedures to ensure methodological consistency.
Raw sequencing reads were processed by Cutadapt (v1.15) for adapter removal with the following parameters: minimum length 18 nt, 8 threads, maximum N bases 4, N-end trimming, double trimming rounds, and maximum error rate 0.1 (-m 18 -j 8 --max-n 4 --trim-n --times 2 -e 0.1 -O 3). Adapter sequences for parameters -a, -A, and -G are available in the Supplementary Table. Overlapping paired-end reads (>30 nucleotides) were merged into single reads using fastp (v0.21.0). After UMI sequence extraction, clean reads underwent a two-stage alignment process. First, reads were aligned to mouse pre-rRNA using Bowtie2 (v2.5.1). The remaining unmapped reads were then aligned to the mouse reference genome (mm9) using STAR (v2.5.2b) with the following specifications: unique splice junction filtering, 5' read extension, maximum mismatch ratio 0.04, unrestricted total mismatches, and single mapping requirement (--outSJfilterReads Unique --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1). PCR duplicates were removed using UMI information, and the resulting unique reads were subjected to peak identification using PureCLIP (v1.3.1). For motif discovery, LACE-seq peaks were extended by 30 nucleotides upstream, and enriched motifs within these extended sequences were identified using Homer's findMotifsGenome.pl function. Inter-replicate correlation analysis was conducted using Pearson correlation coefficients according to established protocols.
Assembly: mm9
Supplementary files format and content: bw files
Supplementary files format and content: csv files
Supplementary files format and content: txt files


title: GZ24037765-Dh36-RNA-mix-240720-Dhx36-3h-Trim21-3_combined


title: GZ24047476-GV-TE-HEXIM1-Dhx36cKO-1_combined


title: GZ24037765-Dh36-RNA-mix-240720-Dhx36-3h-Trim21-1_combined


title: GZ24047476-GV-TE-CDK9-control-1_combined


title: GZ24037765-Dh36-RNA-mix-240720-Dhx36-3h-control-2_combined


title: GZ24037765-Dh36-RNA-mix-240720-Dhx36-3h-Trim21-2_combined


title: GZ23093786-M-rhau-sko7-DRB_combined


title: GZ23093786-M-rhau-sko8-DRB_combined


title: GZ24047476-GV-TE-CDK9-Dhx36cKO-1_combined


title: GZ24047476-GV-TE-HEXIM1-control-2_combined


title: GZ23093786-M-c1_combined


title: GZ24037765-Dh36-RNA-mix-240720-Dhx36-3h-control-3_combined


title: GZ23093786-M-GV-C1_combined


title: GZ23093786-M-c2_combined


title: GZ23093786-M-GV-C3_combined


title: GZ23093786-M-GV-C2_combined


title: GZ23093786-M-GV-cPDS-12h-3_combined


title: DHX36-GFP-LACE-4

data_processing:
High-quality sequencing reads were obtained through preprocessing with fastp (v0.21.0) using stringent filtering parameters: base correction, poly-X trimming, minimum quality score 20, minimum length 36 nt, low complexity filtering, maximum 40% unqualified bases, maximum 4 N bases, paired-end adapter detection, and 8 threads (-g -x -q 20 -l 36 -y -c -u 40 -n 4 --detect_adapter_for_pe -w 8). Filtered reads were aligned to the mouse reference genome (mm9) using Bowtie2 (v2.5.1) with optimized local alignment settings: very-sensitive-local mode, no mixed alignments, no discordant pairs, Phred+33 quality scores, minimum insert size 10 bp, maximum insert size 700 bp, and 10 parallel threads (--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 10). Peak calling was performed on uniquely mapped reads using MACS3 (v3.0.0b3) with disabled lambda and model building (-nolambda -nomodel), applying a q-value threshold of 0.05. Genome-wide enrichment patterns were visualized using deepTools (v3.5.4), with average tag density plots generated via plotHeatmap. Read enrichment across genomic loci was visualized by converting sorted BAM files to BigWig format using bamCoverage. Genomic distribution analysis was conducted using ChIPSeeker, while pausing index calculations followed established protocols (https://github.com/MiMiroot/PIC). For differential binding analysis, a comprehensive approach was implemented. Initially, MACS3 identified peak regions across all samples. These regions were consolidated using BEDTools' mergeBed function to create a unified peak set. Read quantification for each region was performed using featureCounts, followed by differential binding analysis using DESeq2.
Sequencing reads were aligned to the mouse reference genome (mm9) using HISAT2 (v2.1.0). Gene-level quantification was performed using FeatureCount (v2.0.1) with Gencode mm9 annotations as reference. Read count normalization and differential expression analysis were conducted using the DESeq2 package, with size factors estimated prior to differential testing. Alternative splicing events were identified using Rmats (v4.0.2), with splice junction visualization generated through rmats2sashimiplot. For comparative analysis with published RNA-seq datasets, expression quantification followed identical computational procedures to ensure methodological consistency.
Raw sequencing reads were processed by Cutadapt (v1.15) for adapter removal with the following parameters: minimum length 18 nt, 8 threads, maximum N bases 4, N-end trimming, double trimming rounds, and maximum error rate 0.1 (-m 18 -j 8 --max-n 4 --trim-n --times 2 -e 0.1 -O 3). Adapter sequences for parameters -a, -A, and -G are available in the Supplementary Table. Overlapping paired-end reads (>30 nucleotides) were merged into single reads using fastp (v0.21.0). After UMI sequence extraction, clean reads underwent a two-stage alignment process. First, reads were aligned to mouse pre-rRNA using Bowtie2 (v2.5.1). The remaining unmapped reads were then aligned to the mouse reference genome (mm9) using STAR (v2.5.2b) with the following specifications: unique splice junction filtering, 5' read extension, maximum mismatch ratio 0.04, unrestricted total mismatches, and single mapping requirement (--outSJfilterReads Unique --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1). PCR duplicates were removed using UMI information, and the resulting unique reads were subjected to peak identification using PureCLIP (v1.3.1). For motif discovery, LACE-seq peaks were extended by 30 nucleotides upstream, and enriched motifs within these extended sequences were identified using Homer's findMotifsGenome.pl function. Inter-replicate correlation analysis was conducted using Pearson correlation coefficients according to established protocols.
Assembly: mm9
Supplementary files format and content: bw files
Supplementary files format and content: csv files
Supplementary files format and content: txt files
Library strategy: LACE-seq


title: GZ23093786-M-GV-cPDS-12h-1_combined


title: GZ23093786-M-rhau-sko5_combined


title: DHX36-HA-4


title: GZ23093786-M-rhau-sko6_combined


title: GZ23093786-M-c4-DRB_combined


title: DHX36-HA-3


title: 04-Dhx36_sko


title: 06-Dhx36_sko


title: DHX36-IgG


title: GZ23093786-M-GV-cPDS-12h-2_combined


title: DHX36-Flag-1


title: DHX36-GFP-LACE-3


title: RPE1, Pacbio

city: Shenzhen

first: Wei

last: Chen

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

department: School of Life Sciences

institute: Southern University of Science and Technology

description: RPE1, Pacbio

data_processing:
The primer of raw PacBio sequencing reads was removed using lima (version 2.0.0, --isoseq --peek-guess). Then, the concatemer and poly(A) were removed by IsoSeq3 refine (version 3.4.0, --require-polya).
Proovread (verision 2.14.1, with default parameters) and LoRDEC (verision 0.9, with -k 17, -k 19 and -k 21, separately) were used to correct the sequencing errors in PacBio sequencing reads by taking advantage of the more accurate NGS reads. PacBio reads were corrected by Proovread and LoRDEC in parralle. After correction, GMAP (version 2021-02-22, Genome GRCh38, --sampling 1 -B 2 -n 0 -k 15 --min-intronlength 20) was used to align the corrected reads and reads with the best alignments (the largest alignment with the minimum number of mismatches) were kept for further analyses.
IsoSeq3 cluster (version 3.4.0) was applied to cluster and get the consensus sequences from the corrected PacBio sequencing reads. Pbmm2 align (version 1.9.0, with --preset ISOSEQ) was used to align the consensus sequences to genome GRCh38 and cDNA_Cupcake (collapse_isoforms_by_sam.py) was applied to collapse any identical isoforms based on the aligned exonic structure.
SQANTI3 (version 3.6.1, with default parameters) was used to annotate the full-length transcripts with known GENCODE transcripts (gencode.v40.comprehensive.annotation.gtf downloaded from GENCODE) as well as discover novel transcripts.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include SQANTI3 annotated isoforms; gtf for annotatetd isoforms.

source_name: hTERT RPE-1

growth_protocol: hTERT RPE-1 cells were purchased from ATCC (CRL-4000) and maintained in DMEM/F-12 (1:1) + GlutaMAXTM medium (GIBCO 31331-093) containing 10% fetal calf serum (FCS) (PAN-Biotech). Cells were grown and propagated at 37˚C with 5% CO2 in humidified atmosphere.

extract_protocol:
Total RNA from RPE-1 cells was extracted using TRIzol reagent (Life Technologies) following the manufacturer's protocol, and then was converted to cDNA using the Clontech SMARTer PCR cDNA Synthesis kit.
Then we proceed to PCR cycle optimization, and use the cycle number to generate a sufficient amount of double stranded cDNA products. After purification of PCR products by using AMPure purification methods, SMRTbellTM template preparation was performed.

value: hTERT RPE-1

value: hTERT-immortalized retinal pigment epithelial cells.


title: GZ23093786-M-c3-DRB_combined


title: 05-Dhx36_sko


title: DHX36-Flag-2


title: 03-control


title: 01-control


title: CS3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

data_processing:
Sequencing was performed on a DNBSEQ-G400 platform in 2 x 100 bp paired-end mode.
The DNBSEQ control software operated base calling analysis software and delivered raw sequencing data.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.0.13, in combination with Bowtie2, version 2.2.3, and SAMtools, version 0.1.19.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA isolation was performed using the PAXgene Blood RNA System (BD Bioscience, San Jose, CA, USA).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: peripheral blood mononuclear cells

tag: disease state

value: healthy donor

tag: time

value: after climbing to the summit


title: CS1


title: 02-control

tag: tissue


title: CM2

tag: cell type

value: while climbing a mountain


title: CP2

value: before climbing a mountain


title: CS2


title: HC4

value: not available


title: HC1_CP1


title: CM1


title: CP3


title: HS7

value: heat stroke

value: on admission


title: HC3


title: HS2


title: HC5


title: HC2


title: HS5


title: HS1