title: embryos_dsGFP_38hr_R4

city: Boston

first: Flaminia

last: Catteruccia

address: 655 huntington ave

institute: Harvard University

data_processing:
Sequencing reads were aligned to the A. gambiae genome (PEST strain, version 4.14, VectorBase release 62) using HISAT2 (version 2.2.1) with the default parameters. Reads with mapping quality (MAPQ) scores <30 were removed using Samtools (version 1.17). The numbers of reads mapped to genes were counted using htseq-count (version 2.0.2) with the default parameters. Calculation of normalized read counts and analysis of differential gene expression was performed using the DESeq2 package (version 1.40.2) in R (version 4.3.1).
Assembly: Anopheles gambiae genome (PEST strain, version 4.14, VectorBase release 62)
Supplementary files format and content: plain text, raw read counts for each gene

organism: Anopheles gambiae

source_name: embryos

extract_protocol:
Embryos were collected at different time points after oviposition from control and TL2-depleted blood fed An. gambiae females in four biological replicates and stored in -80C until the day of RNA extraction. After homogenization in a bead-beater, RNA was extracted according to manufacturer's instruction, with mnor modifications. RNA pellets were washed three times with 75% ethanol in RNase-Free water and air-dried for 7-8 minutes. Pellets were resuspended in heated water for 10 minutes, DNase-treated using Turbo DNase according to manufacturer’s instructions (Thermo Fisher Scientific), and then purified using PureLink RNA purification mini kit according to manufacturer’s instructions (Invitrogen).
Libraries were prepared using a SciClone G3 NGSx workstation (Perkin Elmer) using the Kapa mRNA HyperPrep kit (Roche Applied Science). Polyadenylated mRNAs were captured using oligo-dT-conjugated magnetic beads (Kapa mRNA HyperPrep kit, Roche Sequencing) from 300 ng of total RNA on a Perkin Elmer SciClone G3 NGSx automated workstation. Poly-adenylated mRNA samples were immediately fragmented to 300-400bp using heat and magnesium. First-strand synthesis was completed using random priming followed by second-strand synthesis and A-tailing. A dUTP was incorporated into the second strand to allow strand-specific sequencing of the library. Libraries were enriched and indexed using 11 cycles of amplification (Kapa mRNA HyperPrep kit, Roche Sequencing) with PCR primers, which included dual 8bp index sequences to allow for multiplexing (IDT for Illumina unique dual 8bp indexes). Excess PCR reagents were removed through magnetic bead-based cleanup using Kapa Pure magnetic beads on a SciClone G3 NGSx workstation (Perkin Elmer). The resulting libraries were assessed using a 4200 TapeStation (Agilent Technologies) and quantified by QPCR (Roche Sequencing). Libraries were pooled and sequenced on one Illumina NovaSeq S4 lane l using paired-end, 100bp reads.

value: embryos

value: dsGFP

tag: replicate


title: day 1

status: Public on Nov 08 2024

type: SRA

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: human primordial germ cell-like cell (PGCLC) induction from human iPSC 585B1-868 cell line, day 1

library_source: transcriptomic single cell

data_processing:
Raw data were demultiplexed with the mkfastq command in Cell Ranger (v XXXX) with default setting to generate fastq files. The fastq files were processed with count command in Cell Ranger v5.0.0 with or without "--include-intron" option to map to the reference genome for human GRCh38.p12 (hard masked PAR of chrY).
Resulting "possorted_genome_bam.bam" files were processed with dropEst (v0.8.6) with "-L eiEBA" option and configuration file for 10X data, 10x.xml with modification at “<umi_length>” from 10 to 12 for Chromium Single Cell Kits v3.1 data.
The output .rds files for each sample, including UMI counts for both exon and intron of genes, were imported into R and used for following analysis.
Assembly: GRCh38.p12 (hard masked PAR of chrY)
Supplementary files format and content: csv file containing dropEst output,read count matrix within exonic regions
Supplementary files format and content: csv file containing dropEst output,read count matrix within intronic regions
Supplementary files format and content: R data in h5ad format countaining all file timepoint data
Supplementary files format and content: cellranger output CSV files including UMI counts per genes

molecule: polyA RNA

organism: Homo sapiens

source_name: PGCLC

extract_protocol:
All protocols are same as in GSE175525.  The suspension of cells were generated as the same manner with passage or the induction of differentiation.
For the aggregates of PGCLC induction at day 0.5, 1, 1.5 and 2, the aggregates were collected, washed once in PBS, and dissociated with 0.25% Trypsin–EDTA for 10–15 min at 37°C with gentle pipetting every 5 min. Trypsin was neutralized with a 5× volume of 10% FBS in DMEM and washed once with 0.1% BSA in PBS.  Prior to proceeding the scRNA-seq analysis, the live single cells were sorted using FACS Aria III system (BD Biosciences) by FSC-SSC and DRAQ7 (ab109202) staining for iMeLC, or FSC-SSC and EGFP-tdTomato gating with DRAQ7 staining for day 0.5, 1, 1.5 and 2 PGCLCs.
Single-cell RNA-seq libraries of 10X data were generated using the 10X Genomics Chromium Controller (10X Genomics) and Chromium Single Cell 39 Reagent Kits v3.1 according to the manufacturer’s instructions.  The final libraries were quantified using a KAPA library quantification kit (KK4824), and the fragment size distribution of the libraries was determined using a LabChip GX DNA high sensitivity kit (Perkin Elmer).  Pooled libraries were then sequenced using a NovaSeq 6000 Illumina Sequencer with a NovaSeq 6000 S1 Reagent Kit (100 Cycles, 20012865).

tag: tissue

value: PGCLC

tag: strain

tag: cell line

tag: transgene

value: PRDM1-tdTomato, TFAP2C-EGFP

tag: time point

value: day 1


title: 202312717_06

type: genomic

city: Miami

first: Lily

last: Wang

address: 1120 NW 14th St

country: USA

institute: University of Miami

description: study sample

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina MethylationEPIC v2.0 BeadChip using standard Illumina protocol.

scan_protocol: Standard recommended Illumina scanner setting.

data_processing:
idat files were read using minfi::read.metharray.exp, converted to beta values with minfi::getBeta
The beta.csv contains beta values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Blood:Buffy Coat

label_protocol: Standard Illumina Protocol.

extract_protocol: Bisulfite conversion of genomic DNA from peripheral blood was performed using the EZ DNA methylation kit according to manufacturer's instructions (Zymo Research).

value: Blood:Buffy Coat


title: Atopic Dermatitis 023

type: RNA

city: Lausanne

first: JEREMY

last: DI DOMIZIO

state: Vaud

address: Av Boveresses 155, 1066 Epalinges

country: Switzerland

institute: CHUV

description:
internal positive and negative controls were used
AD_023

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Data were normalized and log2 transformed using nSolver® 4.0 (Nanostring Technologies). Basically, housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: NanoString indexing

molecule: total RNA

source_name: skin biopsy

label_protocol: NanoString indexing

extract_protocol: mRNA expression of 600 targets was analysed with the nCounter Human Immunology V2 panel including 20 customized probes (Nanostring Technologies, Seattle, WA, USA) on the nCounter® platform (Nanostring Technologies) using 100 ng of RNA per skin sample.

treatment_protocol: samples were snap-frozen without any treatment

tag: disease

value: Atopic Dermatitis


title: RPE1_CTRL_KO_3

city: Haining

first: Mikael

last: Bjorklund

address: International Campus

country: China

institute: Zhejiang University-University of Edinburgh Institute

library_source: transcriptomic

data_processing:
After removal of poor-quality reads, the remaining reads were mapped against human transcriptome (Ensembl v100) using Salmon to obtain transcript abundances. Gene level summaries were generated by tximport. Differential gene expression analysis was done using DESeq2 from vst normalized counts.
Assembly: human transcriptome (Ensembl v100)
Supplementary files format and content: Vst normalized counts from DESeq2 output

growth_protocol: RPE1 control KO and PEBP1 KO cells were seeded at the density of 0.6x105 cells/ml in a 10cm dish. Cells were incubated at 37℃ 5% CO2 for 42h to reach ~90% confluence.

extract_protocol:
Cells were washed twice with PBS and lysed in 1 ml TRIzol on ice. Lysates were frozen in liquid nitrogen and stored at -80℃.
RNA library preparation and sequencing was performed at Novogene (Beijing). Briefly, sequencing libraries were generated from total RNA using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Cat.No. E7530L) following manufacturer’s recommendations. After random fragmentation, 370~420 bp cDNA fragments were selected for paired end sequencing of 150bp.

treatment_protocol: Three dishes of control and PEBP1 KO cells were treated with 1uM Oligomycin A or equal volume of DMSO as control for 6 hours.

tag: genotype

value: WT

tag: treatment

value: DMSO


title: 202312718_06

description: study sample


title: day 0.5

description: human primordial germ cell-like cell (PGCLC) induction from human iPSC 585B1-868 cell line, day 0.5

value: day 0.5


title: Atopic Dermatitis 022

description:
internal positive and negative controls were used
AD_022


title: embryos_dsTL2_24hr_R4

state: MA

tag: time


title: iMeLC (day 0)

description: incipient mesoderm- like cells (iMeLC)  derived from human iPSC 585B1-868 cell line

source_name: iMeLC

value: iMeLC

value: iMeLC (day 0)


title: embryos_dsGFP_24hr_R4


title: 202312716_06

description: study sample


title: embryos_dsTL2_6hr_R4


title: 202312715_06

description: study sample


title: PDX, baseline UCLHN04 biol rep3

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analysed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline.
In this pipeline, reads were mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Homo_sapiens.GRCh38.cdna.all.fa file.
Then, estimated transcript abundances from Salmon were imported into R using the tximeta package
Assembly: Homo_sapiens.GRCh38.cdna.all.fa
Supplementary files format and content: CSV with the matrix of reads counts

source_name: human oral cavity

extract_protocol:
RNA extraction with phenol/chloroform and purification on RNeasy mini columns (Qiagen), according to manufacturer's instructions.
Libraries are prepared with NEBNext UltraII Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations.
Briefly the key stages of this protocol are successively, the purification of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 1μg total RNA (with the Magnetic mRNA Isolation Kit from NEB), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. Sequencing is then carried out on Paired End 100b reads of Illumina NovaSeq.Image analysis and base calling is performed using Illumina Real Time Analysis (3.4.4) with default parameters.

treatment_protocol: We induced acquired resistance to anti-EGFR therapy in a cetuximab-sensitive PDX model of HNSCC (UCLHN04) by treating it chronically with anti-EGFR monoclonal antibody (cetuximab, 30 mg/kg/week) until resistance ensues.

value: patient-derived xenograft (PDX) model of HNSCC

value: no treatment

tag: phenotype

value: control


title: 202312722_06

description: study sample


title: Atopic Dermatitis 021

description:
internal positive and negative controls were used
AD_021


title: Atopic Dermatitis 020

description:
internal positive and negative controls were used
AD_020


title: embryos_dsGFP_6hr_R4


title: 202312713_06

description: study sample


title: embryos_dsTL2_38hr_R4


title: embryos_dsTL2_38hr_R3


title: Atopic Dermatitis 018

description:
internal positive and negative controls were used
AD_018


title: 202312712_06

description: study sample


title: PDX, resistant to cetuximab UCLHN04 biol rep3

value: Cetuximab

value: Cetuximab-resistant


title: 202312709_06

description: study sample

source_name: Blood:Whole Blood

value: Blood:Whole Blood


title: PDX, resistant to cetuximab UCLHN04 biol rep1


title: Atopic Dermatitis 017

description:
internal positive and negative controls were used
AD_017


title: 202312710_06

description: study sample


title: embryos_dsTL2_24hr_R3

value: embryos


title: PDX, resistant to cetuximab UCLHN04 biol rep2


title: Atopic Dermatitis 015

description:
internal positive and negative controls were used
AD_015


title: Atopic Dermatitis 016

description:
internal positive and negative controls were used
AD_016


title: embryos_dsGFP_24hr_R3

value: dsGFP


title: PDX, baseline UCLHN04 biol rep2


title: embryos_dsGFP_6hr_R3


title: embryos_dsTL2_6hr_R3


title: Atopic Dermatitis 014

description:
internal positive and negative controls were used
AD_014


title: MCF7.Baicalein.2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.5.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCh38
Supplementary files format and content: gene_expected_count.annot.txt
Supplementary files format and content: tab-delimited text files include expected counts values for each sample

growth_protocol:
C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
T47D cells were maintained in RPMI-1640 media, 10% FBS, 1% Pen/Strep; MCF-7 cells were maintained in DMEM, 10 FBS, 1% Pen/Strep, 1mg/ml insulin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA was assessed using the TapeStation (Agilent) and Qubit RNA broad-range assay (Thermofisher).
Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), xGen Broad-range RNA Library Prep (IDT), and xGen Normalase UDI Primer Plate 2 (IDT).
820ng of total RNA was converted to mRNA using polyA purification.
Final libraries were checked for quality and quantity by Qubit hsDNA (Thermofisher) and LabChip (Perkin Elmer).

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
Cells were treated with 100 uM Baicalein for 24h
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: cell type

value: breast cancer cell line

value: Baicalein (100 uM)


title: 202312707_06

description: study sample


title: MCF7.Baicalein.3


title: Atopic Dermatitis 019

description:
internal positive and negative controls were used
AD_019


title: Atopic Dermatitis 013

description:
internal positive and negative controls were used
AD_013


title: MCF7.Baicalein.1


title: PDX, baseline UCLHN04 biol rep1


title: 202312706_06

description: study sample


title: embryos_dsTL2_38hr_R2


title: 202312711_06

description: study sample

value: Blood:Buffy Coat


title: embryos_dsGFP_38hr_R3


title: embryos_dsGFP_38hr_R2


title: Atopic Dermatitis 012

description:
internal positive and negative controls were used
AD_012

value: Atopic Dermatitis


title: MCF7.Control.3

value: Control


title: 202312705_06

description: study sample


title: 202312708_06

description: study sample


title: MCF7.Control.2


title: embryos_dsTL2_24hr_R2


title: Atopic Dermatitis 010

description:
internal positive and negative controls were used
AD_010


title: 202312704_06

description: study sample


title: 202312703_06

description: study sample


title: Atopic Dermatitis 009

description:
internal positive and negative controls were used
AD_009


title: MCF7.Control.1


title: embryos_dsGFP_24hr_R2


title: 202312702_06

description: study sample


title: T47D.Baicalein.3


title: embryos_dsTL2_6hr_R2


title: Atopic Dermatitis 008

description:
internal positive and negative controls were used
AD_008


title: Atopic Dermatitis 007

description:
internal positive and negative controls were used
AD_007


title: 202312701_06

description: study sample


title: T47D.Baicalein.1


title: embryos_dsTL2_38hr_R1


title: T47D.Baicalein.2


title: 202312699_06

description: study sample


title: Atopic Dermatitis 006

description:
internal positive and negative controls were used
AD_006


title: T47D.Control.3


title: embryos_dsTL2_24hr_R1


title: 202312698_06

description: study sample


title: T47D.Control.2


title: Atopic Dermatitis 011

description:
internal positive and negative controls were used
AD_011


title: embryos_dsGFP_38hr_R1


title: 202312697_06

description: study sample


title: T47D.Control.1


title: Atopic Dermatitis 004

description:
internal positive and negative controls were used
AD_004


title: 202312696_06

description: study sample


title: embryos_dsGFP_24hr_R1


title: embryos_dsGFP_6hr_R2


title: embryos_dsTL2_6hr_R1


title: Atopic Dermatitis 003

description:
internal positive and negative controls were used
AD_003


title: C. braunii CMT3 in cmt3-11 Line9

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

library_source: genomic

data_processing:
For all samples in Col-0 background, sequencing raw reads were trimmed using FASTP and aligned to the Arabidopsis thaliana TAIR10 genome using bsmap version 2.9; allowing 4% mismatches, trimmed anything with a quality score of 33 or less, and removed any reads with more than five N's. Methylation at every cytosine was determined by bsmap's methratio.py script, processing only unique reads and removing duplicates. Differentially methylated regions (DMRs) were identified using methylKit with the cutoffs: 40% difference for CG, 20% for CHG and 10% difference for CHH DMRs, and a p-value <0.01.
Assembly: TAIR10
Supplementary files format and content: bigwig format

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seedlings were grown on 1/2 MS medium containing 1% sucrose for 10 days in long-day growth conditions (16 hrs light: 8 hours dark) at 22°C.

extract_protocol:
DNA was extracted using conventional CTAB method.
For bisulfite sequencing, the genomic DNA was fragmented to a mean size of 100-300 bp by sonication using a Covaris S220 focused-ultrasonicator, followed by end-repair, 3'-end adenylation and methylated adaptor ligation using Illumina TruSeq DNA kit. Then, bisulfite conversion was performed using a Zymo EZ DNA Methylation-Lightning kit, and the bisulfite-converted, adaptor-ligated DNA was enriched by PCR for 12 cycles using KAPA HiFi HotStart Uracil+ Kit, purified with Agencourt beads and quantified by Qubit HS dsDNA kit.

value: whole seedling


title: embryos_dsGFP_6hr_R1


title: 202312694_06

description: study sample


title: M. polymorpha CMT3 in cmt3-11 Line5


title: Atopic Dermatitis 002

description:
internal positive and negative controls were used
AD_002


title: 202312695_06

description: study sample


title: M. polymorpha CMT3 in cmt3-11 Line4


title: 202312693_06

description: study sample


title: Treated E. faecalis

city: Taipei

first: KungTa

last: Lee

address: No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: National Taiwan University

data_processing:
Quality Control: Initial read quality is assessed using FastQC, which identifies issues such as low-quality bases and adapter contamination.  Quality Assurance:
AfterQC is then employed to filter out low-quality reads and trim adapters, ensuring high-quality data for downstream analysis."
Alignment: Reads are mapped to the reference genome with Bowtie2 using default parameters.  Alignment Quality Control: Alignment quality metrics, such as coverage uniformity and distribution along coding sequences, are generated and analyzed with RSeQC for both single and paired-end reads.
Gene Expression Quantification: Total reads per gene are calculated using featureCounts, and normalized expression values are provided as TPM and CPM.
Differential Expression Analysis: NOISeq is employed to estimate differential expression.
Reference genome: E. faecalis OG1RF (NC_017316.1)
Supplementary files format and content: The processed data file include TPM values of every gene for each treatment.

organism: Enterococcus faecalis

growth_protocol: E. faecalis was statically cultured at 37 °C in TSB medium.

extract_protocol:
Total RNA was subsequently extracted via an RNeasy Mini Kit (Qiagen Ltd., Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: E. faecalis was cultured with or without surfactin (15.6 ug/mL) from B. subtilis natto at 37 °C for 1 hour.

value: wild type

value: surfactin


title: cmt3-11 mutant in Col-0


title: Atopic Dermatitis 005

description:
internal positive and negative controls were used
AD_005


title: Tomato root 6 dpi macA∆ biological replicate 2

status: Public on Nov 07 2024

city: Córdoba

first: Antonio

last: Di Pietro

state: Córdoba

address: Campus Rabanales, Edificio Gregor Mendel, 1

department: Genetics

country: Spain

institute: Universidad de Cordoba

data_processing:
Illumina Casava software used for basecalling.
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome sequence of Fusarium oxysporum f. sp. lycopersici 4287 (Refeseq GCF_000149955.1_ASM14995v2) using Salmon v1.6.0 to map clean reads to reference transcripts.
Read count and TPMs extraction were performed with txiport R package version 1.28.0
Assembly: Fusarium oxysporum f. sp. lycopersici 4287 (Refeseq GCF_000149955.1_ASM14995v2)
Supplementary files format and content: tab delimited file includes salmon quantified transcript abundances
Supplementary files format and content: tab delimited file includes raw counts and TPMs per gene

source_name: microconidia

growth_protocol: (Axenic culture samples) 5x10^8 microconidia were germinated in 200 ml PDB at 170 rpm and 28 °C for 15 hours. (Infected plant samples) Two-week-old tomato seedlings were inoculated by immersing the roots in a microconidial suspension (2,5x10^8/50 ml H2O) planted in vermiculite and maintained in a growth chamber with determined conditions (temperature of 28 ºC, relative humidity of 40-70% and a photoperiod of 14 hours of 36 W white fluorescent light and 10 hours of darkness).

extract_protocol:
The frozen material was lyophilized using a freeze-drying system and then pulverized using a FastPrep-24™ 5G homogenizer (MP Biomedicals™) and 1-5 mm diameter glass beads. Total RNA was extracted using RNeasy® PLant Mini Kit (Quiagen) and treated with DNAse I using the Turbo DNA-FreeTM Kit (InvitrogenTM) according to the manufacturer's instructions. RNA integrity and quantity were analyzed by electrophoresis on a 1.5% agarose gel and with the Nanodrop® ND1000 spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: (Axenic culture samples)  The obtained germlings were collected by filtration through a nylon filter (Monodur; mesh size 10 μm) membrane and washed three times with sterile Milli-Q water. Germlings were collected with a sterile spatula and divided in two flask containing 100 ml each of 20mM L-glutamine (from 0.3 mM L-glutamine pH 6.5 stock) MM-TE-Cu pH 6.5, one of them supplemented with 100 µM CuSO4 ∙ 5H2O, and were incubated for 6 h at 28 °C and 170 rpm. The mycelium was collected by through a Monodur filter membrane and frozen in liquid nitrogen. (Infected plant samples) Roots of three plants were collected after 2 or 6 days post inculation, and considered as one biological replicate. Tomato roots were carefully washed under running water and frozen at -80 °C.

value: microconidia

value: Knockout for macA locus. HygR

tag: substrate

value: tomato root

tag: sampling time

value: 6 days post infection


title: Tomato root 6 dpi wt biological replicate 3

organism: Fusarium oxysporum f. sp. lycopersici 4287


title: Tomato root 2 dpi macA∆ biological replicate 3

value: 2 days post infection


title: Tomato root 2 dpi macA∆ biological replicate 1


title: Tomato root 2 dpi macA∆ biological replicate 2


title: Untread E. faecalis


title: Tomato root 2 dpi wt biological replicate 3


title: Tomato root 6 dpi wt biological replicate 2


title: Tomato root 6 dpi macA∆ biological replicate 3


title: Tomato root 6 dpi wt biological replicate 1


title: Tomato root 2 dpi wt biological replicate 2


title: Tomato root 2 dpi wt biological replicate 1


title: macA∆ +1Cu biological replicate 3

value: MM, 20mM Glut, pH 6.5, TE-Cu + 100µM CuSO4

value: 6 hours


title: macA∆ -Cu biological replicate 2

value: MM, 20mM Glut, pH 6.5, TE-Cu


title: macA∆ +Cu biological replicate 1


title: macA∆ -Cu biological replicate 3


title: macA∆ +Cu biological replicate 2


title: Atopic Dermatitis 001

description:
internal positive and negative controls were used
AD_001


title: wt +Cu biological replicate 3


title: wt -Cu biological replicate 3


title: macA∆ -Cu biological replicate 1


title: wt +Cu biological replicate 2


title: wt -Cu biological replicate 2


title: Tomato root 6 dpi macA∆ biological replicate 1


title: wt +Cu biological replicate 1


title: 15D_hs3

city: Philadelphia

first: Ruofan

last: Yu

state: PA

address: 3400 civic center blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
For RNA-seq, htseq-count
Assembly: hg19
Supplementary files format and content: normalized count for RNAseq.

source_name: HeLa kyoto

growth_protocol: Hela and passage 25-35 IMR90 cells grown in DMEM high glucose with 10% FBS. LCLs in RPMI with 20% FBS; HCT116 HaloTAG-CTCF cells were cultured in McCoy media with 10% FBS and 1%Pen/Strep.

extract_protocol:
For RNAseq, RNA was isolated by Trizol and subjected to poly-A selection..
NEBNext Ultra II DNA Library Prep Kit; NEB ultra2 directional RNA library prep kit

value: HeLa kyoto

value: cervical cancer cells

value: IAA-1hr+RAD21--dSTM  transfection+45c


title: 15D_hs2


title: 15D_hs1


title: wt -Cu biological replicate 1


title: 15D_NT3

value: IAA-1hr+RAD21-dSTM transfection+37c


title: RAD21wt_hs1

value: IAA-1hr+RAD21-WT transfection+45c


title: 15D_NT1


title: RAD21wt_hs3


title: 15D_NT2


title: RAD21wt_NT2

value: IAA-1hr+RAD21-WT transfection+37c


title: RAD21wt_NT3


title: RAD21wt_NT1


title: RAD21wt_hs2


title: PDT38

city: Rotterdam

first: Tokameh

last: Mahmoudi

address: Dr. Molewaterplein 40

department: Department of Urology, Department of Biochemistry, Department of Pathology

country: Netherlands

institute: Erasmus MC Cancer Institute

data_processing:
Base calling was performed using bcl2fastq software.
Fastq files were mapped to the Genome Reference Consortium Human Build 37 (GRCh37), using a two-step alignment process. Firstly, reads were mapped with hisat2, using default parameters. Next, the unmapped reads were mapped with bowtie2 using the --local and --very-sensitive parameters.
Counting the reads on the 3’ UTRs was performed with metaseqR2  and were normalized with DESEQ. For the ARID1A KD comparisons, we employed the PANDORA algorithm within the metaseqR2 package by integrating the DESEQ, DESEQ2, edgeR, limma, NBPSeq, and NOISeq algorithms. Differentially expressed genes were identified based on a meta p-value threshold of < 0.05 and a log2 fold change > 1.
Assembly: hg19
Supplementary files format and content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for Quant-Seq data.

source_name: Bladder

growth_protocol: Tumoroids and organoids were cultured in a culture medium containing Ad+++ supplemented with 1 × B-27 (Gibco), 1.25 mM N-acetylcysteine (Sigma), 10 mM nicotinamide, 20μM TGFβ receptor inhibitor A83-01, 100ng/ml recombinant human FGF10 (Peprotech), 25 ng/ml recombinant human FGF7 (Peprotech), 12.5 ng/ml recombinant human FGF2 (Peprotech), 10μM Y27632 Rho Kinase (ROCK) Inhibitor (Sigma) and conditioned media for recombinant Rspondin (2.5% v/v), and Wnt3A (2.5% v/v)

extract_protocol:
Protocol for Phenol/Chloroform RNA Extraction
QuantSeq-LEXOGEN (3’ mRNA-seq Library Prep Kit for Ion Torrent)

value: Bladder

value: Patient-derived tumoroids

tag: disease state

value: Bladder Cancer


title: PDT37


title: PDT36


title: I-TR5

city: Hefei

first: weibin

last: wu

address: Changjiang Western Road 130

institute: Anhui Agricultural University

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oar_v4.0 whole genome.
Fragment per kilobase of exon model per million mapped reads (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Oar_v4.0
Supplementary files format and content: RPKM values for each Sample

organism: Ovis aries

source_name: ileum

growth_protocol: Ewes at 115 days of gestation.

extract_protocol:
RNA was harvested using  Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Restricted feeding.

value: ileum

tag: breed

value: Hu sheep

tag: age

value: Ewes at 115 days of gestation

value: WT

value: Restricted feeding


title: I-TR3


title: I-TR2


title: I-TR1


title: I-CON5

value: Normal feeding


title: I-CON2


title: I-CON4


title: I-CON3


title: I-CON1


title: J-TR5

source_name: jejunum

value: jejunum


title: J-TR4


title: J-TR2


title: J-TR1


title: J-CON4


title: J-CON5


title: PDT39


title: J-CON1


title: J-CON2


title: J-CON3


title: PDT35


title: DGAT2sa13945 homozygous mutants pooled, clutch 4

city: Baltimore

first: Steven

last: Farber

state: MD

address: 3400 N Charles St

institute: Johns Hopkins University

data_processing:
RNA sequencing data were processed using the nf–core/rnaseq v3.12.0 pipeline (https://doi.org/10.5281/zenodo.1400710).
Adapter sequences were trimmed from the reads and ribosomal RNA reads were filtered.
The remaining reads were mapped to the GRCz11 genome with Ensembl 110 annotation using STAR 2.7.9a and then RNA abundances were quantified using Salmon 1.10.1.
RNA abundance data were imported using tximport 1.30.0  and differentially expressed genes were identified using DESeq2 1.42.
Assembly: GRCz11 genome with Ensembl 110 annotation
Supplementary files format and content: merged.gene_counts.tsv contains gene counts for all genes from each of the 6 samples
Supplementary files format and content: merged.gene_tpm.tsv contains transcripts per million for all genes from each of the 6 samples

organism: Danio rerio

source_name: YSL and dorsal musculature

extract_protocol:
RNA was isolated from a pool of 6 wild-type or 6 dgat2sa13945 mutant sibling mid-bodies from each of three clutches using the Machery-Nagel NucleoSpin® RNA XS kit with no carrier RNA (740902.50, Takara Bio USA Inc.), eluting in 10 µL nuclease-free H2O.
cDNA libraries were constructed from poly(A)-selected RNA using the Illumina TruSeq RNA sample prep kit v2.

value: YSL and dorsal musculature

tag: developmental stage

value: 3 days post fertilization


title: WT pooled, clutch 4

tag: tissue

value: wild-type


title: WT pooled, clutch 3


title: WT pooled, clutch 2


title: DGAT2sa13945 homozygous mutants pooled, clutch 2


title: GM97_4

city: Notre Dame

first: Jessica

middle: A

last: Brown

state: IN

address: 251 Nieuwland Science Hall

department: Chemistry and Biochemistry

institute: University of Notre Dame

data_processing:
Raw reads were obtained (approximately 60-70 × 106 reads by paired-end sequencing for each replicate) and subjected to quality control using FastQC.
The Trimmomatic software was then used to remove adapters from the RNA reads and any poor-quality reads indicated by FastQC
HISAT2 software aligned the reads to the hg38 genome
Stringtie software was used for transcript assembly and quantification
Assembly: hg38
Supplementary files format and content: fastq.gz files for the raw data file from paired-end sequencing for S1 through 8
Supplementary files format and content: .csv files for the DESeq2 processed file for the S1 through 8

source_name: GM06097 cells

growth_protocol: BJ and GM06097 cells were cultured in complete Minimal Eagle Medium (MEM, Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using Rneasy Plus Mini kit (Qiagen). 500 ng of total RNA was used for the library preparation.
NEBNext Ultra II Directional RNA library prep (mRNA workflow) with sample purification beads were used in the RNA-seq library preparation according to the manufacturer's instructions

value: GM06097 cells

value: Human fibroblast cells

tag: group

value: Disease (MDS) cells


title: I-TR4


title: PDT43

tag: cell line


title: DGAT2sa13945 homozygous mutants pooled, clutch 3


title: GM97_1


title: GM97_3


title: BJ_2 control

source_name: BJ cells

value: BJ cells

value: Healthy/ control line


title: GM97_2


title: BJ_3 control


title: BJ_4 control


title: J-TR3


title: BJ_1 control


title: osatxr5c;osatxr6kd-2_rep3

city: Beijing

first: Xiaoyi

last: Li

address: west beichen

department: Chinese Academy of Sciences

institute: Institute of Genetics and Developmental Biology

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were aligned to the rice genome (RGAP, version 7.0) using Hisat2 version 2.1.10
Transcripts per million (TPM) values were generated using R
Differential gene expression analysis was performed using DESeq2 version 1.26.0
Genes were considered as differentially expressed if they exhibited a fold change greater than two and a P adjust value < 0.05
Assembly: RGAP
Supplementary files format and content: *.txt: TPM values for all samples

organism: Oryza sativa

source_name: leaves of 40-day-old rice plants

growth_protocol: Rice plants were grown in paddy fields in Beijing, China

extract_protocol:
Total RNA was extracted using Minibest plant RNA extraction kit (Takara)
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction

treatment_protocol: Total RNA was extracted from leaves of 40-day-old rice plants

value: leaves of 40-day-old rice plants


title: osatxr5c;osatxr6kd-2_rep2


title: NO14 shARID1A

value: Bladder

value: Patient-derived organoids

value: Macroscopic normal urothelium


title: osatxr5c;osatxr6kd-2_rep1


title: PDT19.2

value: Patient-derived tumoroids

value: Bladder Cancer


title: osatxr5c;osatxr6kd-1_rep2


title: osatxr5c;osatxr6kd-1_rep3


title: NO31


title: NO10.1


title: NO18 shARID1A


title: NO33


title: NP_rep3

value: WT


title: NP_rep1


title: osatxr5c;osatxr6kd-1_rep1


title: NO30


title: NO29


title: NP_rep2


title: HES2 hESC shDDX18#1 [RNA-seq]

city: New York

first: XIANLE

last: SHI

state: NY

address: 168 street

institute: CUMC

data_processing:
Alignment was done by Bowtie2 (v2.3.4.3).
Sorting was done by name using Samtools (v1.9)
Count was done by Htseq (v0.11.2)
Normalization was done by using edgeR (v3.26.8)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with expression levels for every gene and every sample

source_name: HES2 hESC shDDX18#1

growth_protocol: Human ES cells were maintained on irradiated inactivated MEFs in human ES cell medium composed of DMEM/F12 (Cellgro, Mediatech) containing 20% Knockout serum (Invitrogen), penicillin/streptomycin, L-glutamine, non-essential amino acids, β-merceptoethanol (β-ME, sigma), and bFGF (R&D Systems).

extract_protocol:
Cells were lysed in Trizol (Invitrogen). RNA integrity was evaluated using a Eukaryotic RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Up to 1 µg of total RNA from each sample was used for library preparation with the TruSeq RNA Sample Preparation Kit (Illumina)

treatment_protocol: Human ES cells were infected with shLuc and shDDX18 Virus, samples are collected at day 4.

tag: cell types

value: human ESC


title: HES2 hESC shDDX18#3 [RNA-seq]

source_name: HES2 hESC shDDX18#3


title: NO16


title: HES2 hESC shLuc [RNA-seq]

source_name: HES2 hESC shLuc

value: shLuc


title: NO14 Parental

value: NO14 Parental


title: H9 hESC shDDX18#3 [RNA-seq]

source_name: H9 hESC shDDX18#3


title: PDT3


title: SL1344∆CpxA, PolB, rep3

city: Qinhuangdao

first: Xiaoqing

last: Zhang

address: No. 360 West Section of Hebei Street, Qinhuangdao, Hebei, China. 066004

institute: Hebei Normal University of Science and Technology

data_processing:
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels .
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3
Supplementary files format and content: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels .

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: S.typhimurium culture

extract_protocol:
S.typhimurium and its CpxA-delated strain were inoculated into LB broth containing 0.125 μg/ml polymyxin B, and cultured overnight at 37°C, followed by dilution and subculture. After growing to the logarithmic phase, the bacteria were washed twice with PBS, collected, quickly frozen in liquid nitrogen, and then sent to Beijing Novogene Bioinformatics Technology Co., Ltd. for transcriptome sequencing and analysis.
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was purified from total RNA using probes to remove rRNA. 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, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. 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. Then USER Enzyme was used to degrade the second strand of cDNA containing U, 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.

value: S.typhimurium culture

value: CpxA knockout

value: cultured in 0.125 μg/ml polymyxin B


title: SL1344∆CpxA, PolB, rep2


title: H9 hESC shDDX18#1 [RNA-seq]

source_name: H9 hESC shDDX18#1


title: PDT30


title: SL1344, PolB, rep3

value: wild type


title: PDT33


title: H9 hESC shLuc [RNA-seq]

source_name: H9 hESC shLuc


title: SL1344, PolB, rep2


title: 3XFlag-DDX18-R2 [iCLIP-seq]

description: iCLIP_FLAG-DDX18_hESC_H9_1-400_Hs_NNNAATANN_20170607_Mm_19

data_processing:
library strategy: iCLIP-seq
FastQC (v0.10.1) was used to check the sequencing quality.
Alignment are done according to CTK instruction. Here I aligned to hg19 using BWA, reads shorter than 15 bp were removed.
Peak calling were done using tag2Peak.pl script with statistical assessment.
For aligned reads annotation, I annotated them according to GENCODE annotation with some other reference databases such as GtRNAdb, RepeatMasker program, etc.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

source_name: 3XFlag-DDX18 expressing human ESC

extract_protocol:
Cells were irradiated by UV once with 160 mJ/cm2 using Stratalinker 1800 at 254 nm. DDX18 was immunoprecipitated with protein A Dynabeads (10002D,  Invitrogen) conjugated to mouse-anti Flag (Sigma-Aldrich, F1804)
iCLIP libraries were made following Illumina Library preparation kit (New England BioLabs).

treatment_protocol: Under normal culture

tag: genotype/variation

value: 3XFlag-DDX18 expression

value: Under normal culture


title: SL1344, PolB, rep1


title: PDT32


title: mac1st_plusCu_2

data_processing:
Illumina Casava software used for basecalling.
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic 0.36
Mapping was performed using BWA and further processing was done using samtools v1.7 and bedtools v2.27.1 to obtain normalized genome coverage tracks.
Peaks were called using R function locate_peak_height (https://github.com/symbiocyte/MNase).
Assembly: Fusarium oxysporum f. sp. lycopersici 4287 (Refeseq GCF_000149955.1_ASM14995v2)
Supplementary files format and content: wig files tab-limited format to represent continuous values

source_name: microconidia

growth_protocol: 5x10^8 microconidia were germinated in 200 ml PDB at 170 rpm and 28 °C for 15 hours.

extract_protocol: Mycelium was grinded with mortar and pestle in liquid nitrogen and 200 mg of mycelium was transferred to a 2 ml Eppendorf tube. Powdered mycelium was dissolved 1 ml of ChIP Lysis Buffer by vortexing and distributed in 3 aliquots of 330 µl in 1.5 ml Eppendorf tubes. Samples were subjected to sonication using Gracthe Bioruptor™ 200 (Diagenode) for 30 min with cycles of 2 min maximum intensity followed by a 1 min pause. Then the three aliquots were combined in one and centrifuged at 13400 rpm for 1 min at 4 °C. The upper face was recovered and transferred to a new 1.5 ml tube. Then Chromatin Immunoprecipitation was carried out as described in (Boedi and Strauss, 2010, Methods Mol Biol, 944, 221-236). The α-S-tag antibody (SAB2702227, Sigma-Aldrich®) and Protein G DynabeadsTM (10003D, InvitrogenTM) were used for the immunoprecipitation.

treatment_protocol: The obtained germlings were collected by filtration through a nylon filter (Monodur; mesh size 10 μm) and washed three times with sterile Milli-Q water. Germlings were collected with a sterile spatula and divided in two flask containing 100 ml each of 20mM L-glutamine (from 0.3 mM L-glutamine pH 6.5 stock) MM-TE-Cu pH 6.5, one of them supplemented with 100 µM CuSO4 ∙ 5H2O, and were incubated for 6 h at 28 °C and 170 rpm. DNA was crosslinked to proteins by adding 1% formaldehyde (v/v) and incubating for 15 min at 28 ºC and 170 rpm. Crosslinking was then stopped by the addition of 125 mM glycine (final concentration) and the incubation with shaking for 5 minutes. The mycelium was the collected by filtration through a Monodur filter membrane and immediately frozen in liquid nitrogen.The mycelium was collected by through a Monodur filter membrane and frozen in liquid nitrogen.

value: microconidia

value: Wild type, expressing Mac1 tagged with S-tag in the C-terminus

value: MM, 20mM Glut, pH 6.5, TE-Cu + 100µM CuSO5

value: 6 hours


title: mac1st_plusCu_3

value: MM, 20mM Glut, pH 6.5, TE-Cu + 100µM CuSO6


title: mac1st_plusCu_1

value: MM, 20mM Glut, pH 6.5, TE-Cu + 100µM CuSO4


title: 3XFlag-DDX18-R1 [iCLIP-seq]

description: iCLIP_FLAG-DDX18_hESC_H9_1-400_Hs_NNNGGTTNN_20170607_Mm_18


title: NO18 Parental

value: Bladder

value: Patient-derived organoids

value: NO18 Parental

value: Macroscopic normal urothelium


title: PDT28

value: Patient-derived tumoroids

value: Bladder Cancer


title: PDT29


title: mac1st_noCu_2

value: MM, 20mM Glut, pH 6.5, TE-Cu


title: PDT27


title: mac1st_noCu_3


title: mac1st_noCu_1


title: PDT5


title: 3XFlag-DDX18-Input

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality.
Alignment was done by using Bowtie2
Reads that mapped to multiple locations in the genome were discarded
Annotation was done by using the script annotatePeaks.pl of HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: TDF file

extract_protocol:
3XFlag-DDX18 hESCs were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with glycine to a final concentration of 0.125 M for another 10 min.Chromatin was sheared by sonication to about 100-500 base pair fragments, cleared by centrifugation, and incubated and IPed  by using FLAG antibody (Sigma,F1804)
ChIP DNA libraries were made following Illumina ChIP-Seq Library preparation kit (New England BioLabs).

value: human ESC


title: PDT16


title: AF3291LN non adherent (fl)

city: London

first: Leanne

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation.
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Raw estimated expression counts were upper-quartile normalized to a count of 1000.
Independent Component Analysis (ICA), an unsupervised blind source separation technique, was used on this discrete count-based expression dataset to elucidate statistically independent and biologically relevant signatures.
All RNA-seq analyses were conducted in R.
Assembly: UCSC mm9 mouse genome
Supplementary files format and content: Microsoft Excel file includes normalised read counts (from rsem) per gene for each sample

organism: Mus musculus

source_name: Small Cell Lung Cancer

extract_protocol:
Total RNA from mSCLC-NE/non-NE cell lines was isolated using the miRNeasy kit (Qiagen).
RNA libraries were prepared for sequencing with the Illumina TruSeq kit following the manufacturer's instructions.

value: Small Cell Lung Cancer

value: Neuroendocrine


title: SL1344∆CpxA, PolB, rep1

value: S.typhimurium culture

value: CpxA knockout

value: cultured in 0.125 μg/ml polymyxin B


title: WKM Ctrl replicate 1

first: Paul

last: Zumbo

address: 1300 York Ave

department: Applied Bioinformatics Core

institute: Weill Cornell Medicine

data_processing:
Demultiplexing, alignment, filtering, and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command.
Sample integration (batch correction), expression value normalization, clustering, cell type annotation and so on were done scater and scran. For more details and the cell type annotation information, see https://github.com/abcwcm/CZI_MI_mouseZebrafish
Assembly: GRCz11
Supplementary files format and content: CellRanger produced filtered feature-barcode matrix in H5 format.

source_name: Whole Kidney Marrow

growth_protocol: Standard zebrafish husbandry protocol.

extract_protocol:
Heart ventricles were placed in the ice-cold PBS buffer with 1% BSA. After several washes removing blood cells, ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer (0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum) for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum, and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re-suspended in HBSS with 0.05% BSA. The cell suspension (2 ml) was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. After spinning down at 200 g for 5 min at 4°C, the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly, kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re-suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer (0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum) at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar (Bel-Art Products), and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. After spinning down at 300 g for 5 min, pellets were washed one more time with PBS plus 0.05% BSA. After centrifuging at 300 g for 5 min, the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer.
Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3, and Chromium Single Cell B Chip Kit.

treatment_protocol: Heart cryoinjury or untreated

value: Whole Kidney Marrow

value: wild type

value: Heart cryoinjury


title: WKM Ctrl replicate 2


title: AF3291LN adherent

value: Mesenchymal


title: PDT23

source_name: Bladder

value: Bladder


title: Pancreas Ctrl replicate 2

source_name: Pancreas

value: Pancreas

value: whole organ


title: 3XFlag-DDX18-Flag

value: 3XFlag-DDX18 expression

value: Under normal culture

tag: chip antibody

value: FLAG antibody (Sigma,F1804)


title: PDT25

value: Patient-derived tumoroids

value: Bladder Cancer


title: AF3062C

value: Small Cell Lung Cancer


title: wt_plusCu_1

value: microconidia

tag: genotype

value: Wild type

value: MM, 20mM Glut, pH 6.5, TE-Cu + 100µM CuSO7

value: 6 hours


title: Pancreas Ctrl replicate 1

tag: treatment


title: siliquelhp1_16C_rep2

city: Norwich

first: William

last: Bezodis

address: Norwich Research Park, Colney Lane

department: Crop Genetics

institute: John Innes Centre

data_processing:
Counts matrices generated using CellRanger
Assembly: TAIR10
Supplementary files format and content: Counts matrices generated using CellRanger

molecule: nuclear RNA

source_name: Whole silique

extract_protocol:
Nuclei extraction and FACS sorting by DAPI
10x Genomics Chromium Next GEM Single Cell 3'

value: Whole silique


title: siliquelhp1_16C_rep1


title: AF1281m1

value: Neuroendocrine


title: siliqueCol-0_22C_rep2


title: PDT19.1


title: liver Ctrl replicate 2

source_name: Liver

value: Liver

value: wild type

value: Heart cryoinjury


title: wt_noCu_1

value: MM, 20mM Glut, pH 6.5, TE-Cu


title: PDT10.2

value: Bladder


title: liver Ctrl replicate 1

value: whole organ


title: siliqueCol-0_22C_rep1


title: PDT20


title: PDT1.2


title: heart Ctrl replicate 2

source_name: Heart

value: Heart


title: IC_mac1st_noCu_1 input control

value: Wild type, expressing Mac1 tagged with S-tag in the C-terminus


title: AF1165


title: AD984LN non adherent (fl)


title: heart Ctrl replicate 1


title: siliqueCol-0_16C_rep2


title: AD984LN adherent

value: Mesenchymal


title: siliqueCol-0_16C_rep1


title: PDT24

value: Patient-derived tumoroids

value: Bladder Cancer


title: WKM 7 dpi replicate 2

value: Whole Kidney Marrow


title: HCT116_halo2

data_processing:
*library strategy: CUT&Tag
For CnR and C&T, Bowtie2:--local --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 1000- x hg19. For RNAseq, STAR2.7.1a: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
filtered with samtools view -q 5 and deduplicated with Picard
Bigwig and BedGraph files were generated with deepTools: bamCompare -b1 $SON -b2 $IGG -bs 5000 --smoothLength 15000 --effectiveGenomeSize 2864785220 --exactScaling --normalizeUsing RPKM --scaleFactorsMethod None -bl blacklistPEAK.merge.bed
For RNA-seq, htseq-count
Assembly: hg19
Supplementary files format and content: SON/IGG normalized bigwig file for C&R; rpkm normalized bigwig file for C&T; normalized count for RNAseq.

extract_protocol:
For C&R condition, nuclei from ~600k cells was isolated using nuclear isolation buffer [10mM HEPES-KOH (pH 7.9), 10mM KCl, 0.1% NP40, 0.5mM spermidine, 1x Halt protease inhibitor cocktail] and bound to concanavalin A lectin beads which had been washed in binding buffer [BioMag Plus; binding buffer: 20mM HEPES-KOH (pH 7.9), 10mM KCl, 1mM CaCl2, 1mMnCl2], as described. For Cut& Tag, 1 million cells were used. After bead binding, samples were split into two tubes, one for each antibody, where binding buffer was replaced with 1:100 antibody diluted in blocking buffer [20mM HEPES-KOH (pH 7.5), 150mM NaCl, 0.1% BSA, 0.5mM spermidine, 1x Halt protease inhibitor cocktail, 2mM EDTA](IgG antibody: Millipore 06-371); SON antibody: abcam ab121759) and incubated overnight at 4°C. Samples were washed in washing buffer [20mM HEPES-KOH (pH 7.5), 150mM NaCl, 0.1% BSA, 0.5mM spermidine, 1x Halt protease inhibitor cocktail], and treated with pA-MNase and CaCl2 for 30 minutes on an ice cold pre-chilled metal block on ice. The reaction was stopped by addition of STOP buffer [200mM NaCl, 20mM EDTA, 4mM EGTA, 50µg/mL RNase A, 40µg/mL glycogen] while gently vortexing, and DNA fragments were released by incubation at 37°C for 10 minutes. The DNA fragments were collected from bead supernatants, treated with Proteinase K for 10 minutes at 70°C, then subject to PCI-choroform purification.  For RNAseq, RNA was isolated by Trizol and subjected to poly-A selection..
NEBNext Ultra II DNA Library Prep Kit; NEB ultra2 directional RNA library prep kit

treatment_protocol: as described in sample information

value: Blood cells

value: HaloTAG-CTCF

tag: antibody

value: CUT&Tag with SON antibody


title: PDT10.1


title: HCT116_halo1


title: PDT26


title: WKM 7 dpi replicate 1


title: 1dpa_opa1mitolow_1.fq.gz

city: 杭州市

first: li

last: yucong

state: 浙江省

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
fastaq RNA-seq data adapter trimming by fastap
scRNA-seq and snRNA-seq data quality control
Supplementary files format and content: smed_20140614_60aa_genes-noref.gtf

organism: Schmidtea mediterranea

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: pKmito low cells

value: head trunk tail mix

value: stemcell

value: 1dpa opa1;egfp RNAi worms


title: opa1+drp1mitolow_1.clean.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: 1dpa opa1;drp1 RNAi worms


title: HCT116_DMSO2


title: Pancreas 7 dpi replicate 2

value: Pancreas

value: wild type

value: Heart cryoinjury


title: PDT7

value: Bladder


title: TP2031T2

value: Small Cell Lung Cancer


title: 1dpa_egfpmitolow_1.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

source_name: 1dpa_egfp;egfp_mitolow repeat

value: 1dpa egfp;egfp RNAi worms


title: HCT116_DMSO1


title: Pancreas 7 dpi replicate 1

value: whole organ


title: NO10.1 shARID1A

value: Patient-derived organoids

value: Macroscopic normal urothelium


title: E+Emitolow_1.clean.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: E+drp1mitolow_1.clean.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: 1dpa drp1;egfp RNAi worms


title: liver 7 dpi replicate 2

value: Liver


title: opa1drp1_1dpa_S1_L001_R1_001.fastq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: cell nuclei

value: cell nucleus

value: 1dpa opa1;drp1RNAi worms


title: liver 7 dpi replicate 1


title: NO10.1 shCTRL

value: shCTRL


title: NO8 shARID1A


title: SONRT1

data_processing:
For CnR and C&T, Bowtie2:--local --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 1000- x hg19. For RNAseq, STAR2.7.1a: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
filtered with samtools view -q 5 and deduplicated with Picard
Bigwig and BedGraph files were generated with deepTools: bamCompare -b1 $SON -b2 $IGG -bs 5000 --smoothLength 15000 --effectiveGenomeSize 2864785220 --exactScaling --normalizeUsing RPKM --scaleFactorsMethod None -bl blacklistPEAK.merge.bed
For RNA-seq, htseq-count
Assembly: hg19
Supplementary files format and content: SON/IGG normalized bigwig file for C&R; rpkm normalized bigwig file for C&T; normalized count for RNAseq.

source_name: HeLa kyoto

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID


title: NO8 shCTRL


title: heart 7 dpi replicate 2

value: Heart

value: wild type


title: SONRT2


title: heart 7 dpi replicate 1

value: Heart cryoinjury


title: SONHS3


title: WKM 1 dpi replicate 2

value: Whole Kidney Marrow


title: SONHS2


title: egfpopa1_1dpa_S1_L001_R1_001.fastq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: head trunk tail mix

value: 1dpa opa1;egfp RNAi worms


title: ChIPseq H3K27me3, Th0

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

institute: IDIBAPS

data_processing:
Aligment - Bowtie2, Cellranger v6
PeakCalling - MACS2
Downstream - DiffBind, Seurat, Signac, GenomicRanges, Trackviewer…
Assembly: GRCm38.p6
Supplementary files format and content: Peakset; differential peaks called
Supplementary files format and content: feature count matrices

source_name: Spleen

extract_protocol:
Cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630), washed, and right after resuspended in transposase reaction mix.
Library fragments were amplified using 1x NEB Next PCR master mix (New England BioLabs) and 1.25 μM of custom Nextera PCR primers forward and reverse. Libraries were rendered using the barcoded primers Ad1_noMX as forward and Ad2.1-6 as reverse and purified using a PCR cleanup kit (Qiagen), yielding a final concentration of about 30 nM in 20 μL. Libraries were then analyzed on Bioanalyzer using an Agilent DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA, USA) to estimate the quantity and size distribution. Next, they were quantified by qPCR using the KAPA Library Quantification Kit before amplification with Illumina’s cBot.
Libraries were loaded at 3.33 pM onto the flowcell and sequenced 1 x 50 on Illumina’s HiSeq 2500

value: Spleen

tag: strain

value: NOD mouse

value: KLH immunization

value: H3K27me3 (Cell Signaling)


title: ChIPseq H3K27me3, vaccination-induced TFH

tag: cell type

value: Vaccionation-induced TFH


title: egfpdrp1_1dpa_S1_L001_R1_001.fastq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: cell nuclei

value: cell nucleus

value: 1dpa drp1;egfp RNAi worms


title: WKM 1 dpi replicate 1


title: ChIPseq H3K27me3, Tet+

value: Tet+

value: pMHCII-NP


title: SONHS1

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID


title: SONRT3


title: Pk-Mitolow

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
fastaq RNA-seq data adapter trimming by fastap
scRNA-seq data quality control
Assembly: smed_20140614_60aa_genes-noref.gtf
Supplementary files format and content: high_filtered_feature_bc_matrix
Supplementary files format and content: low_filtered_feature_bc_matrix

source_name: Pk-mitocell

extract_protocol:
RNA was harvested using TRIGene Reagent(Genstar Cat#ZP118-101S). 400 ng of total RNA was used for the construction of sequencing libraries.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: stemcell

value: tails

value: WT

value: no treatment

tag: time

value: Day 0


title: Pancreas 1 dpi replicate 2

value: Pancreas

value: whole organ

value: wild type

value: Heart cryoinjury


title: NegRT3


title: ChIPseq H3K4me3, Th0

value: Spleen

value: NOD mouse

value: KLH immunization

value: H3K4me3 (Sigma)


title: Pk-Mitohigh

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: NegRT2


title: Pancreas 1 dpi replicate 1


title: ChIPseq H3K4me3, vaccination-induced TFH

value: Vaccionation-induced TFH


title: Larvae_Hybrid_OO3

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue

institute: Wesleyan University

data_processing:
FASTQC on each of the 72 raw fastq files
Bowtie2 alignment using the D. simulans or D. sechellia reference genome available at the time of analysis.
Cufflinks for quantification and normalization was followed tiht custom R scripts to perform statiistical analyses.
Hybrids had allele specific expression measured by aligning hybrid sample reads to one secies genome then taking the unaligned reads and aligning to the other species genome in both directions to determine which reads were allele specific for each speices in the F1 hybrids. This results in two data columns in the processed data with the species of allele indicated in the header name as _Sim or _Sec for hybrid sample quantification.
Assembly: Drosophila_simulans_ASM75419v3.39.gff3 and Drosophila_simulans_ASM75419v3.dna.toplevel.fa or Drosophila_sechellia.dsec_caf1.38.gff3 and Drosophila_sechellia.dsec_caf1.dna.toplevel.fa
Supplementary files format and content: Processed data are all in one lager table that is a tab delimited text ffile

organism: Drosophila simulans x Drosophila sechellia

source_name: Larvae

growth_protocol: Fruit  flies were reared on standard food or food supplemented with octanoic acid and mainteind in a 16:8 light:dark cycle at 20 ̊C

extract_protocol:
RNA was extracted from a single tissue homogenate of either 10 whole adult females or 10 whole female L3 larvae using the Promega SV total RNA extraction system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fruit flies were fed standard media or octanoic acid media and these treatments were conducted on both species and hybrids in both larval and adult flies in all different combinations of standard or octanoic acid food provided in the previous generation and the current generation.

value: Larvae

tag: previous media

value: Octanoic Acid Media

tag: current media

tag: biological replicate


title: ChIPseq H3K4me3, Tet+

value: Tet+

value: pMHCII-NP


title: liver 1 dpi replicate 2

value: Liver


title: NegRT1

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID


title: Larvae_Hybrid_OO2


title: NegHS3


title: liver 1 dpi replicate 1


title: egfpegfp_1dpa_S1_L001_R1_001.fastq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: cell nuclei

value: head trunk tail mix

value: cell nucleus

value: 1dpa egfp;egfp RNAi worms


title: Larvae_Hybrid_OO1


title: heart 1 dpi replicate 2

value: Heart

value: whole organ

value: wild type

value: Heart cryoinjury


title: ChIPseq H3K27Ac, vaccination-induced TFH

value: Spleen

value: Vaccionation-induced TFH

value: NOD mouse

value: KLH immunization

value: H3K27Ac (Abcam)


title: Larvae_Hybrid_OS3

value: Larvae

value: Octanoic Acid Media

value: Standard Media


title: NegHS1

value: HeLa kyoto

value: cervical cancer cells

value: CTCF-AID


title: Larvae_Hybrid_OS2


title: ChIPseq H3K27Ac, Tet+

value: Tet+

value: pMHCII-NP


title: heart 1 dpi replicate 1

value: Heart


title: GSK101_3

first: Xiaotong

address: 22# Zhongguancun South Avenue, Haidian District

institute: Peking university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Rattus_norvegicus from Rattus_norvegicus.Rnor_6.0 using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: Rnor_6.0
Supplementary files format and content: All_samples_rpkm.txt

organism: Rattus norvegicus

source_name: TMJ disc cell

extract_protocol:
Total RNAs were extracted from disc cells in control group and GSK101 group using TRIzol Reagent (Invitrogen, cat. NO 15596026). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: TMJ disc cell


title: ATACseq Th0, replicate 3


title: HelaIAA2_SON

data_processing:
*library strategy: CUT&RUN
For CnR and C&T, Bowtie2:--local --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 1000- x hg19. For RNAseq, STAR2.7.1a: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
filtered with samtools view -q 5 and deduplicated with Picard
Bigwig and BedGraph files were generated with deepTools: bamCompare -b1 $SON -b2 $IGG -bs 5000 --smoothLength 15000 --effectiveGenomeSize 2864785220 --exactScaling --normalizeUsing RPKM --scaleFactorsMethod None -bl blacklistPEAK.merge.bed
For RNA-seq, htseq-count
Assembly: hg19
Supplementary files format and content: SON/IGG normalized bigwig file for C&R; rpkm normalized bigwig file for C&T; normalized count for RNAseq.

value: CUT&RUN with IGG/SON antibody


title: Larvae_Hybrid_OS1


title: HelaIAA2_IGG


title: ATACseq Th0, replicate 2


title: Larvae_Hybrid_SO2


title: Ctrl_3

value: Ctrl


title: ATACseq Th0, replicate 1

value: Spleen


title: HelaIAA1_IGG


title: Larvae_Hybrid_SO3


title: HelaIAA1_SON


title: Larvae_Hybrid_SO1


title: Ctrl_2


title: ChIPseq H3K27Ac, Th0


title: HelaDMSO2_SON


title: ATACseq vaccination-induced TFH, replicate 3

value: Vaccionation-induced TFH


title: ATACseq vaccination-induced TFH, replicate 2

value: NOD mouse


title: Ctrl_1


title: Larvae_Hybrid_SS3


title: ATACseq vaccination-induced TFH, replicate 1

value: KLH immunization


title: Larvae_Hybrid_SS2


title: HelaDMSO2_IGG


title: HelaDMSO1_SON


title: atxr5;atxr5;atxr6hyp;atxr6c-1_H3K27me3_rep2

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2
Duplicate reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard)
H3K27me3 peaks in WT Col were called using MACS2 version 2.1.2 with default parameters. Only peaks identified in both biological replicates were retained
For data visualization, data from two biological replicates were merged, and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp
Assembly: TAIR10
Supplementary files format and content: bigwig

source_name: leaves of 3-week-old Arabidopsis plants

growth_protocol: Plants were grown under long day conditions (16h light/8h dark) at 22°C

extract_protocol:
Materials were ground with liquid nitrogen into fine powder and fixed with 1% formaldehyde.To profile H3K27me3, nuclei were extracted and mononucleosomes were generated with micrococcal nuclease (MNase)(Sigma, N5386) digestion. Immunoprecipitation was conducted with anti-H3K27me3 antibody (Merck, 07-449). After antibody incubation, Protein A Dynabeads (Life technologies, 10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification.
Immunoprecipitated DNA were subjected to library preparation with the VAHTS universal DNA library prep kit for Illumina (Vazyme, ND607-02) according to the manufacturer’s instruction

treatment_protocol: ChIP-seq was performed using leaves from 3-week-old Arabidopsis plants

value: leaves of 3-week-old Arabidopsis plants


title: Larvae_Hybrid_SS1

value: Larvae


title: ATACseq Tet+, replicate 4


title: NegHS2


title: Adult_Hybrid_OO3

source_name: Adult

value: Adult

value: Octanoic Acid Media


title: GSK101_2


title: Col_H3K27me3_rep2

value: WT


title: Hippocampus, CLO-3

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

institute: University of Toyama

data_processing:
Raw reads with low quality and adapter sequences were removed using Cutadapt 2.9. The remaining reads were mapped to the human genome (GRCm39.104) by HISAT2 v 2.2.0 (PMID: 25751142) and the gene expression was quantified using featureCounts v 2.6.0 (PMID: 24227677).
Assembly: human genome (GRCm39.104)
Supplementary files format and content: Excel file includes raw counts in each sample.
Supplementary files format and content: Excel file includes TPM values in each sample.

source_name: Hippocampus

extract_protocol:
Total RNA from the hippocampus of offspring mice was extracted using the NucleoSpin® Plus (Macherey-Nagel GmbH & Co., Düren, Germany).
300 ng of total RNA samples, which met the quality guideline, RIN: 8 or higher, were treated with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich poly-A mRNA and to remove rRNA molecules. cDNA synthesis followed by transcriptome library preparation were conducted by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB), where dUTP were incorporated in the process of the 2nd strand cDNA synthesis, instead of dTTP, that block PCR amplification against the 2nd strand templates. This enables to maintain the strandness of RNA transcripts. A 10-cycle PCR amplification was performed to increase library yield and also to incorporate sample barcodes into the library fragments. Resulting transcriptome libraries were quantified by Qubit DNA Assay (Thermofisher) and their fragment size distribution was estimated by TapeStation D1000 ScreenTape (Agilent).

value: Hippocampus

value: Exposure to CLO


title: Adult_Hybrid_OO2


title: ATACseq Tet+, replicate 2

value: Tet+


title: Col_H3K27me3_rep1


title: atxr5;atxr5;atxr6hyp;atxr6c-1_rep3

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10
Transcripts per million (TPM) values were generated using R
Differential gene expression analysis was performed using DESeq2 version 1.26.0
Genes were considered as differentially expressed if they exhibited a fold change greater than two and a P adjust value < 0.05
Assembly: TAIR10
Supplementary files format and content: *.txt: TPM values for all samples

extract_protocol:
Total RNA was extracted using Minibest plant RNA extraction kit (Takara)
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction

treatment_protocol: Total RNA was extracted from leaves of 3-week-old Arabidopsis plants


title: Hippocampus, CLO-1


title: 603-4_TG

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

data_processing:
FASTQ files were aligned to the mouse genome reference GrCm38 using STAR v2.7.5b(Dobin et al. 2013), and counts at the gene level were exported using the featureCounts function from the R-package subread.
Assembly: GrCm38
Supplementary files format and content: count.table.genes.tsv (Unfiltered raw counts)

source_name: PLP-α-synuclein (MGI:3604008)

extract_protocol:
RNA was isolated from hemisphere samples using the RNeasy Kit (Qiagen)
Sequencing libraries were prepared with 250 ng of total RNA using Illumina Stranded Total RNA with Ribo-Zero Plus library preparation (Illumina Inc). PCR-enriched fragments were validated on a 2200 TapeStation (Agilent Technologies) and quantitated via qPCR

value: Brain

value: bulk tissue

value: PLP-{alpha}-synuclein (MGI:3604008)

tag: Sex

value: male


title: Adult_Hybrid_OO1

tag: developmental stage


title: atxr5;atxr5;atxr6hyp;atxr6c-1_rep2

tag: tissue


title: Adult_Hybrid_OS2

value: Standard Media


title: 603-3_TG

description: Illumina Stranded Total RNA with Ribo-Zero Plus


title: atxr5;atxr5;atxr6hyp;atxr6c-1_rep1


title: atxr5;atxr5;atxr6hyp;atxr6c-1_H3K27me3_rep1


title: Hippocampus, Ctrl-3

value: Vehicle control


title: 603-1_TG


title: Hippocampus, Ctrl-1


title: ATACseq Tet+, replicate 3

value: Spleen

value: pMHCII-NP


title: Hippocampus, Ctrl-2


title: Adult_Hybrid_OS1


title: HelaDMSO1_IGG

first: Ruofan

value: HeLa kyoto

value: cervical cancer cells

value: CUT&RUN with IGG/SON antibody


title: atxr5;atxr5;atxr6hyp;atxr6hyp_rep3

value: leaves of 3-week-old Arabidopsis plants


title: 602-4_TG

value: female


title: atxr5;atxr5;atxr6hyp;atxr6hyp_rep2


title: Adult_Hybrid_SO3

value: Adult

value: Octanoic Acid Media


title: 602-3_TG


title: AT3-OVA Tumor CDK4/6i+CDK7i (biol rep 2)

first: Hee Won

last: Yang

institute: Columbia University

data_processing:
Data were processed with 10x Genomics' Cell Ranger software (version 8.0.1) using the prebuilt reference genomes (GRCm39-2024-A for mouse).
Assembly: GRCm39-2024-A
Supplementary files format and content: Zip files of samples folders which includes barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz

extract_protocol:
At the experimental endpoint, mice were perfused through the left ventricle with 1% PFA in PBS for 2 minutes. Extracted tumors were minced using razor blade and dissociated into single-cell suspensions by incubating in digestion medium made of FACS buffer (PBS + 2% FBS, 0.1% collagenase IV (Worthington, #LS004188), and 10 U/ml DNase type I (Sigma, #D4527)) for 30 minutes at 37°C. Digested cells were then filtered with 70 µm nylon mesh. Red blood cells (RBC) were lysed by incubating cells in 1× RBC Lysis buffer (eBioscience, #00-4300-54). Tumor cells were suspended in PBS with 0.4% BSA and submitted for 10x Genomics processing at Columbia Genome Center at Columbia University Medical Center.
Libraries were prepared using the 10x Genomics Single Cell Gene Expression platform. The 3' or 5' Single Cell Gene Expression workflow was used to encapsulate individual cells (or nuclei) in droplets, where lysis and reverse transcription occurred with cell- and molecule-specific barcoding. Following cDNA amplification, libraries were constructed with 10x Genomics reagents. The resulting libraries were sequenced on an Illumina NovaSeq 6000 (or NextSeq 500/550 as appropriate).

value: Epithelial

value: AT3-OVA Tumor CDK4/6i+CDK7i


title: Adult_Hybrid_SO2


title: Hippocampus, CLO-2

value: Hippocampus

value: Exposure to CLO


title: Adult_Hybrid_OS3


title: ATACseq Tet+, replicate 1

value: Tet+

value: NOD mouse


title: 602-2_TG

value: Brain

value: bulk tissue

value: PLP-{alpha}-synuclein (MGI:3604008)


title: AT3-OVA Tumor Control (biol rep 2)

value: AT3-OVA Tumor Control


title: atxr5;atxr5;atxr6hyp;atxr6hyp_rep1


title: Adult_Hybrid_SO1

value: Standard Media


title: AT3-OVA Tumor CDK4/6i+CDK7i (biol rep 1)


title: 602-1_TG


title: Col_rep3

value: WT


title: AT3-OVA Tumor Control (biol rep 1)


title: Col_rep2


title: ZS_S26.gz

first: Sasha

middle: Leilani

last: Fulton

address: 3227 Broadway

data_processing:
fastq files were aligned to ensembl mouse reference genome mm10 using HISAT2 (Version 2.1.0).
BAM files resulting from the alignments were summarized to genes using the featureCounts (Version 2.0.1) algorithm
Expression data was normalized using DESEQ2 (Version 2.11.40.6)
Differentially expressed genes (5% false discovery rate) were identified using DESEQ2 based on a model using the negative binomial distribution
Genome_build: mm9 moue genome
Supplementary_files_format_and_content: tab-delimited text files are normalized counts matrix for each sample from DESEQ2 output

source_name: Virally-infected tissue from Orbitofrontal cortex brain reion

extract_protocol:
RNA was isolated using trizol-chloroform extraction followed by cleanup on the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 , according to the manufacturer’s instructions.

treatment_protocol: Virus was injected (AAV6-GFAP-ZBTB7A OE or AAV6-GFAP-GFP) intra-OFC. 3wks later, Animals went through either Subthreshold Social Defeat Stress or Control condition, followed by 3 behavioral tests (social interaction, sucrose preference, forced swim), followed by tissue collection 7d post-stress.

tag: background strain

value: wild-type

value: male

tag: age

value: Virus treatment (@ d0) + Subthreshold Social Defeat stress (@d21) + behavioral tests (@d22-27) + tissue collection (@d28)

tag: virus treatment

value: Virus Treatment AAV6-GFAP-ZBTB7A Overexpression + GFP

tag: stress condition

value: Subthreshold Sress


title: Adult_Hybrid_SS2

value: Adult


title: 330-1_WT

source_name: WT

value: female


title: Larvae_Sim_OO3

organism: Drosophila simulans

value: Larvae

value: Octanoic Acid Media


title: ZS_S17.gz


title: 326-4_WT


title: Larvae_Sim_OO1


title: Larvae_Sim_OO2


title: 330-2_WT


title: Oct1 deficient mESC HBO1 ChIP_2

city: Salt Lake City

first: Yifan

last: Wu

state: UT

address: 2000 Cir of Hope Dr

department: Pathology

institute: University of Utah

data_processing:
paired-end Illumina sequencing reads were aligned to the mouse Mm10 reference genome using Novocraft novoalign v4.03.01
ChIP-seq reads were analyzed using Macs2 with parameters of q 0.005, max-gap 100
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: mouse ESC

growth_protocol: Undifferentiated ESCs were cultured as described previously with “2iV” supplementation: the MEK inhibitor PD03259010 (1 μM, LC laboratories) and the glycogen synthase kinase-3b (GSK3b) inhibitor CHIR99021 (3 μM, LC Laboratories). Culture medium was also supplemented with 50 mg/mL ascorbic acid (Sigma).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min and quenced with 0.125M glycine. The cells are then lysed with Farnham and RIPA buffer and sonicated with EpiShear probe sonicator.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (cat#E7634L) complemented with NEBi5 DNA index. 2ng of DNA was used as starting material for input, and the libraries were amplified for 10 cycles on thermocycler.  PCR-amplified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583) and the molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Libraries were normalized and pooled in preparation for Illumina sequencing.

tag: cell line

value: mouse ESC

value: ESC

value: Oct1 deficient

tag: chip antibody


title: Oct1 deficient mESC Input

tag: genotype


title: Oct1 deficient mESC HBO1 ChIP_1


title: Col_rep1

value: leaves of 3-week-old Arabidopsis plants


title: CX3CR1cre_Tumor_Spleen, mRNA-derived cDNA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

description: poly A RNA

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.4.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format file including raw counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format file including filtered counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: Hashtag-condition.csv: comma-delimited text file including condition/treatment information for each hashtag name and barcode sequence

source_name: tumor or spleen

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: tumor or spleen


title: Adult_Hybrid_SS3


title: ZS_S25.gz

tag: treatment


title: 330-4_WT

value: Brain

value: bulk tissue


title: 330-3_WT

value: WT


title: Adult_Hybrid_SS1

value: Standard Media


title: ZS_S9.gz

value: wild-type

value: male


title: 326-2_WT


title: HFSCs, 2nd telogen, rep1

city: Hangzhou

first: Bing

state: Zhejiang

address: No. 600 Dunyu Road, Sundun Town, Xihu District

department: School of Life Sciences

institute: Westlake University

data_processing:
Adaptor triming: trimmomatic_0.39
Mapping and quantification: Salmon_1.4.0
Differential Expression Analysis: DESeq2_1.36.0
Assembly: mm10
Supplementary files format and content: .xlsx

source_name: skin

extract_protocol:
RNA were purified using RNeasy Plus Micro Kit (Qiagen 74034).
RNA-seq libraries were generated using Single Cell Full Length mRNA-Amplification Kit (Vazyme N712) and TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD503).

value: skin

value: hair follicle stem cells (HFSCs)

value: Control


title: 326-1_WT


title: 326-3_WT


title: Larvae_Sim_OS3


title: CX3CR1cre_Tumor_Spleen, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein


title: Larvae_Sim_OS2


title: Larvae_Sim_OS1


title: ZC_S23.gz

value: Virus treatment (@ d0) + Subthreshold Social Defeat stress (@d21) + behavioral tests (@d22-27) + tissue collection (@d28)

value: Virus Treatment AAV6-GFAP-ZBTB7A Overexpression + GFP


title: HFSCs, 2nd telogen, rep2


title: ZC_S24.gz


title: ZS_S7.gz

value: Subthreshold Sress


title: HFSCs, long term AL, rep2

value: Ad libitum


title: 561HS_3

city: Philadelphia

last: Yu

address: 3400 civic center blvd

institute: University of Pennsylvania

data_processing:
STAR2.7.1a: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
htseq-counts
Assembly: hg19
Supplementary files format and content: tab limited RNA-seq raw count

source_name: patient derived Lymphoblastoid cell lines

growth_protocol: Hela and passage 25-35 IMR90 cells grown in DMEM high glucose with 10% FBS. LCLs in RPMI with 20% FBS

extract_protocol:
Trizol
NEB ultra2 directional RNA library prep kit

value: Blood cells

value: HS


title: Larvae_Sim_SO3

value: Larvae

value: Octanoic Acid Media


title: HFSCs, long term AL, rep1


title: 561HS_2

value: patient derived Lymphoblastoid cell lines


title: ZC_S15.gz


title: HFSCs, long term ADF, rep2


title: 561HS_1


title: Larvae_Sim_SO1


title: ZC_S14.gz


title: GS_S22.gz

value: Virus treatment AAV6-GFAP-GFP


title: Larvae_Sim_SO2


title: 561NT_3

value: normal temperature


title: 561NT_2


title: OV, WT, replicate 2, scRNAseq

city: Hong Kong

first: Ka Chi

last: Chu

address: 21 Sassoon Rd, Pok Fu Lam

country: Hong Kong

institute: HKU

data_processing:
Raw reads were processed with Cell Ranger (v6.0)
Assembly: mm39
Supplementary files format and content: Cell Ranger output (barcodes, features, matrix)

source_name: Otic vesicle

extract_protocol:
E10.5 OVs were pooled and digested in TryplE (Invitrogen) with 0.05% collagenase (Worthington Biochemical) and dispase (Worthington Biochemical) at 37°C for 30 min. 5U/ml DNaseI (Invitrogen) was added to the digestion mix after 15 min digestion. DPBS with 10% FBS was added to quench the digestion. Dissociated cells were spined at 300 g x 5 min, washed with DPBS with 0.04% BSA, and filtered with 40 μm strainer. Filtered cells were spined at 300 g x 5 min, washed with DPBS with 0.04% BSA, re-spined, and resuspended in 50 μl DPBS with 0.04% BSA for downstream processing.
Single cell encapsulation and cDNA libraries were prepared with Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit. Sequencing was carried out with Illumina NovaSeq 6000 for Pair-End 151bp sequencing.

value: Otic vesicle

value: wild type


title: Larvae_Sim_SS3

value: Standard Media


title: Larvae_Sim_SS2


title: ZC_S6.gz

value: wild-type

value: male


title: GS_S21.gz


title: Larvae_Sim_SS1


title: S2HS_3

value: Healthy control 2


title: HFSCs, long term ADF, rep1

value: skin

value: hair follicle stem cells (HFSCs)

value: WT


title: Adult_Sim_OO3

value: Adult


title: S2HS_2

value: Blood cells


title: 561NT_1


title: OV, WT, replicate 1, scRNAseq


title: GS_S20.gz

value: Virus treatment (@ d0) + Subthreshold Social Defeat stress (@d21) + behavioral tests (@d22-27) + tissue collection (@d28)

value: Subthreshold Sress


title: Adult_Sim_OO2

value: Octanoic Acid Media


title: GS_S12.gz


title: GS_S13.gz


title: matIM, Ezr-KOm, rep 2, 1 dose of LPS

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

institute: Yale University

data_processing:
After quality control (FastQC), reads generated from each sample were aligned to the mouse genome (GRCm39) with STAR (version 2.7.9a, –quantMode GeneCounts), using the Gencode M29 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR package in Bioconductor (https://bioconductor.org). Differentially expressed genes were identified with the glmQLFTest function using a double threshold on gene expression changes and associated statistical significance (absolute log2 fold change > 0.75, p-value < 0.05). Functional annotation and enrichment analysis were performed with the enrichR package (https://maayanlab.cloud/Enrichr) and MetaCore package (https://portal.genego.com)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes number of reads per gene (GeneCounts) for each sample

source_name: lung

extract_protocol:
Lungs of treated WT and Ez-KO mice were perfused to remove circulating blood cells and single cell suspension from lung tissues were isolated using a lung dissociation kit (Miltenyi). Cells were stained and FACS-sorted, and RNA was extracted using miRNEasy Micro kit (Qiagen, MD). Markers used to sort monocytes/macrophages are: moMs: CD45+CD11b+MHC-II-Ly6C+; trIMs: CD45+CD11b+MHC-II+Ly6C+; matIMs: CD45+CD11b+MHC-II+Ly6C-
The RNA integrity (RIN) and quantity was determined on the Agilent 2100 Bioanalyzer (Agilent, CA) with Agilent RNA 6000 Pico Kit (Agilent, CA). Only samples with RIN ≥8.0 were used for library preparation. Reverse transcription and cDNA preamplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, MI), and sequencing libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina, CA, USA), according to manufacturers’ instructions. Libraries were pooled and sequenced on Illumina NovaSeq 6000 (Illumina, CA, USA) using 150bp paired-end sequencing.

treatment_protocol: WT and Ez-KO mice were nebulized with 12.5 mg of LPS of Pseudomonas aeruginosa (L9413 Millipore Sigma) dissolved in 5 ml PBS for 15 minutes and sacrificed 24 h after the neblization.

value: lung

value: primary cells

value: primary lung tissue resident interstitial macrophage

value: Ezr-KOm

value: 1 dose of LPS for 24h


title: Adult_Sim_OO1


title: S2HS_1

value: patient derived Lymphoblastoid cell lines

value: HS


title: Adult_Sim_OS3

value: Standard Media


title: GS_S5.gz

value: wild-type

value: male

value: Virus treatment AAV6-GFAP-GFP


title: matIM, WT, rep 3, 1 dose of LPS

value: WT


title: Adult_Sim_OS2

value: Adult


title: GS_S4.gz


title: S2NT_3

value: Blood cells

value: Healthy control 2

value: normal temperature


title: matIM, Ezr-KOm, rep 1, 1 dose of LPS


title: GS_S3.gz

value: Virus treatment (@ d0) + Subthreshold Social Defeat stress (@d21) + behavioral tests (@d22-27) + tissue collection (@d28)

value: Subthreshold Sress


title: matIM, WT, rep 2, 1 dose of LPS

value: lung

value: primary cells


title: S2NT_1


title: Adult_Sim_OS1

value: Octanoic Acid Media


title: Adult_Sim_SO3


title: trIM, Ezr-KOm, rep 2, 1 dose of LPS

value: primary lung transitional interstitial macrophage

value: Ezr-KOm

value: 1 dose of LPS for 24h


title: S1HS_3

value: patient derived Lymphoblastoid cell lines

value: Healthy control 1

value: HS


title: trIM, Ezr-KOm, rep 3, 1 dose of LPS


title: GC_S11.gz

value: wild-type

value: male

value: Virus treatment AAV6-GFAP-GFP

value: Control


title: Adult_Sim_SO1

value: Adult

value: Standard Media


title: S1HS_1

value: Blood cells


title: GC_S2.gz

value: Virus treatment (@ d0) + Subthreshold Social Defeat stress (@d21) + behavioral tests (@d22-27) + tissue collection (@d28)


title: Adult_Sim_SS3


title: S1NT_3

value: normal temperature


title: trIM, Ezr-KOm, rep 1, 1 dose of LPS

value: lung

value: primary cells


title: GC_S1.gz


title: S1NT_1


title: matIM, WT, rep 1, 1 dose of LPS

value: primary lung tissue resident interstitial macrophage

value: WT


title: S1NT_2


title: GC_S19.gz


title: trIM, WT, rep 2, 1 dose of LPS

value: primary lung transitional interstitial macrophage

value: 1 dose of LPS for 24h


title: Adult_Sim_SS2


title: Larvae_Sec_OO2

organism: Drosophila sechellia

value: Larvae

value: Octanoic Acid Media


title: S2NT_2

value: patient derived Lymphoblastoid cell lines

value: Healthy control 2


title: Adult_Sim_SS1


title: GC_S10.gz

value: wild-type

value: male

value: Virus treatment AAV6-GFAP-GFP


title: S1HS_2

value: Healthy control 1

value: HS


title: Adult_Sim_SO2

value: Adult

value: Standard Media


title: trIM, WT, rep 1, 1 dose of LPS

value: lung


title: Larvae_Sec_OO1


title: IMR90CTCFNUT_3

value: fetal lung fibroblast

value: wt

value: siCTCF+6hr nutlin-3a


title: IMR90CTCFNUT_2


title: trIM, WT, rep 1 dose of LPS

value: primary cells

value: primary lung transitional interstitial macrophage

value: WT


title: 1dpa-sod2-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

data_processing:
fastaq RNA-seq data adapter trimming by fastap
RNA-seq data quality control
Quantification of feature counts to obtain raw counts by STAR  methods
Assembly: smed_20140614_60aa_genes-noref.gtf
Supplementary files format and content: high_filtered_feature_bc_matrix
Supplementary files format and content: low_filtered_feature_bc_matrix

source_name: whole body

extract_protocol:
RNA was harvested using TRIGene Reagent(Genstar Cat#ZP118-101S). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA SMARTER Library Prep Kit for Illumina following manufacturer's protocols.

value: whole body

value: RNAi


title: moM, Ezr-KOm, rep 2, 1 dose of LPS

value: primary lung monocyte derived macrophages

value: Ezr-KOm

value: 1 dose of LPS for 24h


title: Larvae_Sec_OS3

value: Larvae

value: Octanoic Acid Media


title: Larvae_Sec_OS2


title: 1dpa-sod2-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: matIM, Ezr-KOm, rep 3, 1 dose of LPS

value: primary lung tissue resident interstitial macrophage


title: 1dpa-sod2-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: 1dpa-opa1-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: moM, WT, rep 3, 1 dose of LPS


title: IMR90CTCFNUT_1


title: IMR90CTCFNC_3

value: siCTCF


title: IMR90CTCFNC_2


title: moM, Ezr-KOm, rep 1, 1 dose of LPS


title: Larvae_Sec_SO3

value: Standard Media


title: moM, WT, rep 2, 1 dose of LPS

value: lung


title: 1dpa-opa1-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: IMR90CTCFNC_1

value: fetal lung fibroblast


title: 1dpa-opa1-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Larvae_Sec_SO2


title: moM, WT, rep 1, 1 dose of LPS


title: moM, Ezr-KOm, rep 3, 1 dose of LPS


title: 1dpa-drp1-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Larvae_Sec_SO1