title: SPNS1 KO liver 3

first: Thi Thuy Hoa

last: Ha

address: 28 Medical Drive

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: all_compare.txt: Tab-delimited text file contains raw counts and FPKM values for each sample.

source_name: Liver

extract_protocol:
RNAs were extracted using the RNeasy Mini Plus kit from Qiagen. About 8ug was used to send to Novogene company for RNA-sequencing service.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Liver

value: SPNS1 KO


title: PC9 Input, treatment,  H3K9me2, rep1

status: Public on Jun 12 2024

type: SRA

city: Shenyang

first: cheng

last: yang

address: wenhua street  number 103

country: China

institute: Shenyang Pharmaceutical University

library_source: genomic

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of GRCh38 using STAR software (version 2.5.3a) with default parameters.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The differentially binding peaks were identified by csaw(version 1.30.1).
The Homer（version 4.10）was used for motifs analysis.
Assembly: GRCh38
Supplementary files format and content: Bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: lung

extract_protocol:
The cell was fixed in 1% formaldehyde for 10 min at room temperature. After quenching cell was treated with cell lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bp were enriched and quantified.

tag: tissue

value: lung

tag: cell line

tag: cell type

value: lung cell line

tag: treatment

value: post-SCLC transformation

tag: chip antibody


title: C2

city: Shanghai

first: xiuxian

last: guo

state: Shanghai

address: 393 Middle Huaxia Road, Pudong

institute: ShanghaiTech University

library_source: transcriptomic

data_processing:
For RNA-seq data analysis, raw reads were filtered using Seqtk (v.1.4) to remove adapters and low-quality regions, and mapped to the GRCm38 genome using Hista258 (v.2.0.4). Reads on each gene were counted by Stringtie59 (v.1.3.0). Differential expressed genes (DEGs) were identified using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts  for each sample

molecule: total RNA

organism: Mus musculus

source_name: Dentate Gyrus

extract_protocol:
The DG was microdissected and dissociated with papain-based enzymatic digestion. 2,000 EYFP+ cells were sorted using the BD FACS Aria III instrument into a 200-μl PCR tube containing lysis buffer and RNase inhibitor. After sorting, the tubes were immediately snap-frozen.
Total RNA was reverse transcribed using the SMART-Seq HT Kit (Clontech, 634437), and cDNAs were used to produce the sequencing library. The libraries were purified and sequenced using the Illumina HiSeq 2500 system.

value: Dentate Gyrus

value: control shRNA


title: SPNS1 KO liver 2

city: Singapore

country: Singapore

institute: National University of Singapore

tag: genotype


title: C1


title: Vpr_27

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

country: USA

institute: National Institutes of Health

library_source: transcriptomic single cell

data_processing:
Illumina RTA v3.4.4 software was used fro base calling, Cellranger 6.1.2 (Bcl2fastq v2.20) was used for sample demultiplexing
The analysis was performed with the Cell Ranger v6.1.2 software using the default parameters with premRNA analysis turned on. The reference was built from mm10 reference genome and HIV-1 virus sequence added.
Assembly: mm10 and HIV-1: NC_001802.1
Supplementary files format and content: tar.gz files contain filtered_features_bc_matrix folder output from CellRanger Count

molecule: polyA RNA

source_name: Mouse Kidney Cortex

extract_protocol:
Nuclei from frozen mouse kidney outer cortex tissue samples were prepared following the published protocol. Briefly, ~ 8 mm3 tissue fragments were cut by razor blade in EZlysis buffer (#NUC101-1KT, Sigma, Darmstadt, Germany) and homogenized 30 times using a loose Dounce homogenizer and 5 times by tight pestle. After 5 mins of incubation, the homogenate was passed through a 40 µm filter (PluriSelect, El Cajon, CA) and centrifuged at 500g at 4°C and for 5 min. The pellet was washed with EZlysis buffer (Sigma Aldrich, St Louis, MO) and again centrifuged at 500g at 4°C for 5 min. The pellet was resuspended with DPBS with 1% FBS and passed through a 5 µm filter (PluriSelect, El Cajon, CA) to make final nuclei prep for loading on to a 10xChromium Chip G (10X Genetics, San Francisco, CA) for formation of gel beads in emulsion (GEM).
10x Genomics Chromium 3’ V3.1 mRNA-seq library protocol

treatment_protocol: Mice were maintained on a diet containing doxycycline (TD 98186, Envigo, Madison, WI) to inhibit the expression of Vpr. Mice were switched from doxycycline diet to 65% protein food (TD 190088, Envigo) for two weeks to induce transgene promoter activity. Then, the mice were fed with freshly prepared semi-solid sodium-deficient food [TD 90228 (3 g), containing casein (33.3%), agar (0.5%), sodium (0.045%), and 2.67 mL of water] for four days.

value: Kidney Cortex

value: Pepck-Vpr

value: Salt Depletion


title: SPNS1 KO liver 1


title: CRC tumor T161 [DREAM]

city: Camden

first: Jean-Pierre

middle: J

last: Issa

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
library strategy: Digital Restriction Enzyme Analysis of Methylation (DREAM)
Illumina HiSeq 2500 or NovaSeq 6000 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to mm10 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Assembly: mm9
Supplementary files format and content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_mm9 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

source_name: colon

extract_protocol:
tissues were lysed in 2% SDS and 25 mM EDTA overnight. Ammonium acetate (10M) was added to make the precipitate of SDS with proteins and was removed by centrifugation at 12,000 rpm. Next, DNA was precipitated using isopropanol, washed with 70% ethanol, and dissolved in dissolved in LTET (Tris 10 mM, EDTA, 0.1 mM + Tween 20,0.1% )
Two micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

value: colon

tag: tissue type

value: CRC tumor


title: wild-type liver 2

value: WT


title: MMT Tumor Hsp72 KO sample 5

city: Boston

first: Benjamin

last: Lang

state: MA

address: 330 Brookline Ave

institute: BIDMC

data_processing:
Raw RNA-seq data was processed in a high-performance computing environment using Trimmomatic 0.36 to remove adapters and filter for high-quality reads (Bolger, Lohse, and Usadel 2014). Read quality was confirmed using FastQC 0.11.5 (Andrews), and aligned to the Mus musculus annotated genome GRCm38 (release 103) (Frankish et al. 2019), using STAR 2.5.4a aligner with the --quantMode GeneCounts option (Dobin et al. 2013). Read alignment and feature counts assigned to the PyMT (coordinates sourced from J02288.1) and human MUC1 (Gene ID 4582) transgenes were included in the workflow by addition of the PyMT and MUC1 coding sequences to the GRCm38 primary assembly genome files created with STAR --runMode genomeGenerate using an edited Gencode vM25 annotation file to include appropriate coordinates for the two transgenes.
Assembly: GRCm38 (release 103)
Supplementary files format and content: tab delimited file includes raw counts for each sample

source_name: Mammary tumor

extract_protocol:
Mammary tumors were excised from euthanized animals, dissected into small 1-3 mm pieces and transferred to a 50 ml tube containing 2 ml serum-free DMEM. A Collagenase I/1 x trypsin solution was added (3 mg/ml Collagenase I) to make a 5 ml solution that was then incubated in a water bath at 37°C for 35-50’ to facilitate cell dissociation. The mammary tumor solution was then mashed through a 100 µm nylon cell strainer into a 50 ml centrifuge tube. The cell dissociate solution was then made to 50 ml with DMEM / 10 % FBS and dissociated cells were pelleted by centrifugation. The supernatant was discarded, and the cell pellet was transferred to a microcentrifuge tube with 1 ml DMEM / 10 % FBS. Cells were pelleted at 4°C and then washed in ice-cold 1 x PBS. The cells were again pelleted, and the supernatant discarded, cell pellets were resuspended in 700 µl of Qiazol lysis buffer and homogenized by passing through a Qiashredder column. RNA was extracted as per the miRNeasy kit protocol (Qiagen). Purified RNA samples were stored at -80°C until the full sample set was collected.
RNA integrity of samples was assessed by Bioanalyzer (Agilent) with samples of RIN ≥ 6.5 used for cDNA library synthesis. cDNA library synthesis was performed on ribosome RNA-depleted total RNA using a KAPA Stranded RNA-Seq with RiboErase (KAPA Biosystems, KK8483) and Illumina adapters. cDNA libraries were pooled and sequenced with an Illumina HiSeq 2500 (50 cycles, paired-end) to give 10-20 million reads per sample. RNA integrity analysis, cDNA library pooling and NGS services were provided by Harvard Biopolymers Facility.

value: Mammary tumor

tag: strain

value: C57BL/6 MUC1.Tg MMTV-PyMT (MMT)

tag: age

value: 120 days

tag: Sex

value: female


title: MMT Tumor Hsp72 KO sample 4

value: 125 days


title: K1

value: Kdm4a shRNA


title: wild-type liver 3

value: Liver


title: CRC tumor T160 [DREAM]


title: MMT Tumor Hsp72 KO sample 3


title: CRC tumor T159 [DREAM]


title: Wild Type female fly, repeat2

first: Zhan

last: Ding

address: 300 Feng Lin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

description: Female_WT rep2

data_processing:
The adapter sequences were removed from raw reads by cutadapt (version 1.15).
Clean reads from RNA-seq were quality filtered, and then mapped to the human genome (hg38) and Drosophila melanogaster genome (dm6) by STAR.
Assembly: dm6, hg38
Supplementary files format and content: tab-delimited text files include TPM values for mRNA samples.

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Total RNAs from the human and Drosophila cells and tissues were isolated by TRIzol (Sigma) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, reverse transcription was performed using PrimeScript RT reagent Kit with gDNA Eraser (TaKaRa) and the obtained cDNA was amplified by 2×Hieff PCR Master Mix (Yeasen). the construction of cDNA libraries and sequencing were performed using Illumina HiseqXten-PE150 by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body


title: wild-type liver 1


title: MMT Tumor Hsp72 KO sample 1

value: 122 days


title: CRC tumor T158R [DREAM]


title: Wild Type female fly, repeat1

description: Female_WT rep1


title: MMT Tumor Hsp72 WT sample 4

value: 124 days


title: MMT Tumor Hsp72 KO sample 2

value: 123 days


title: Posion exon exclusion in female fly, repeat3

description: Female_PE- rep3


title: MMT Tumor Hsp72 WT sample 3


title: PC9 Input, control, H3K9me2, rep1

value: lung

value: lung cell line

value: pre-LUAD


title: CRC tumor T162 [DREAM]

value: colon


title: MMT Tumor Hsp72 WT sample 2

value: 132 days


title: Posion exon exclusion in female fly, repeat2

description: Female_PE- rep2


title: Posion exon exclusion in female fly, repeat1

description: Female_PE- rep1


title: CRC tumor T151R [DREAM]

value: CRC tumor


title: MMT Tumor Hsp72 WT sample 1

value: Mammary tumor


title: CRC tumor T149 [DREAM]


title: SH-SY5Y cells co-treated with 10 µM oleacein and 5 µg/ml LPS_rep1

type: RNA

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

description:
Gene expression data from SH-SY5Y cells incubated for 24 hours in OPTI-MEM followed by co-treated with 10 µM oleacein and 5 µg/ml LPS for 24 hours
SST-RMA

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Human; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space)
signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4)

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: SH-SY5Y cells (2 × 106 cells/5 ml growth medium) were seeded into 60 mm dishes. Twenty-four hours after seeding, the SH-SY5Y cells were incubated for 48 hours in OPTI-MEM.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Oleacein was dissolved in dimethyl sulfoxide (DMSO, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) and further diluted in serum-free Eagle's minimum essential medium (OPTI-MEM, Gibco) to achieve treatment concentration 10 µM. Twenty-four hours after seeding, the SH-SY5Y cells were incubated for 48 hours in OPTI-MEM without or with oleacein. For inflammation model, following seeding of SH-SY5Y cells in 60 mm dishes, the cells were transitioned from growth medium to OPTI-MEM and incubated for 24 hours. Subsequently, 10 µM oleacein and 5 µg/ml LPS (FUJIFILM Wako Pure Chemical Corporation) were co-administered to the cells for an additional 24 hours in OPTI-MEM.


title: CRC tumor T148 [DREAM]


title: RPCRS.2

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

data_processing:
Raw reads were aligned to mm10 genome using STAR
Raw counts in each known gene from the Ensembl database were enumerated using htseq-count from the HTSeq package
Assembly: mm10
Supplementary files format and content: raw count for all samples in csv format

source_name: RNA from melanocytes with mutant RAC1 expressed

growth_protocol: Melanocytes were maintained in OptiMEM supplemented with 7% horse serum, 2% fetal bovine serum, and 1% antibiotic in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was isolated with TRI-reagent and chloroform.
RNA libraries for RNA-seq were constructed following the Illumina Stranded mRNA Prep Ligation guide protocol (Illumina Document #1000000124518 v03)

treatment_protocol: Melanocytes were treated with with DMSO or 1 uM SHLD1 compound for 24 hours. After 24 hours total RNA was exracted

value: melanocytes

value: Pten KO + RAC1P29S inducible vector


title: RPCRS.1


title: RAW264.7-oxldl, E3

city: Xiamen

first: Binbin

last: Liu

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

institute: Xiamen University

data_processing:
The sequencing reads were mapped to the reference mouse genome GRCm39 by HISAT 2.2.1
Read counts per gene locus were obtained with featureCounts
Assembly: mm10
Supplementary files format and content: table-delimited txt file containing raw counts for each sample

source_name: RAW264.7 cells

growth_protocol: C57BL6/J male mice (8-9 weeks old) were housed in specific pathogen free facilities with 12 h light:12 h dark cycles at 22-23°C in Xiamen University.;RAW 264.7 cells, a macrophage cell line, were cultured in Dulbecco's modified eagle medium with 10% fetal bovine serum, 100 U/ml penicillin and 0.1 mg/ml streptomycin at 37°C under 5% CO2.

extract_protocol:
RNAs were purified from the livers  by Trizol Reagent
A cDNA library was prepared by using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: esculetin (0 or 90mg/kg/d) were daily administered to the mice by oral gavage for 7 days. In the first 4 days, the mice were fed with a control diet (CD) containing 10% kcal from fat. Then the mice were fed with a high- fat diet (HFD) containing 60% kcal from fat for additional 3 days to understand lipid-rich meals-induced postprandial lipid circulation. ;RAW264. 7 cells were treated with 25 ug/mL DIL-oxLDL and esculetin (0 or 40 ug/mL) for 24 hr.

value: RAW264.7 cells

value: macrophages

value: WT

value: 40 ug/mL esculetin


title: CRC tumor T155 [DREAM]


title: CRC tumor T152 [DREAM]


title: RAW264.7-oxldl, E2


title: RPCR.2

source_name: RNA from melanocytes with mutant RAC1 not expressed

value: DMSO


title: SH-SY5Y cells treated with 5 µg/ml LPS_rep1

description:
Gene expression data from SH-SY5Y cells incubated for 24 hours in OPTI-MEM followed by treated with 5 µg/ml LPS for 24 hours.
SST-RMA

source_name: SH-SY5Y cells treated with 5 µg/ml LPS


title: RAW264.7-oxldl, E1


title: CRC tumor T145 [DREAM]


title: SH-SY5Y cells treated with 5 µg/ml LPS_rep2

description:
Gene expression data from SH-SY5Y cells incubated for 24 hours in OPTI-MEM followed by treated with 5 µg/ml LPS for 24 hours
SST-RMA


title: CRC tumor T144 [DREAM]


title: RPCR.1


title: RAW264.7-oxldl, C3


title: SH-SY5Y cells incubated for 48 hours in OPTI-MEM_rep1

description:
Gene expression data from SH-SY5Y cells incubated for 48 hours in OPTI-MEM
SST-RMA


title: Mosquito Transmitted P. chabaudi CB Infection Day 60 Rep 4

city: London

first: Jean

last: Langhorne

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Fastq files QC using Multi QC (Babraham Institute)
Transcript were aligned and counted to the Mus musculus reference genome GRCm38 v86 using STAR v2.5.2 and RSEM v1.3.0
Libraries normalised for size through DESeq2 v1.26 in R v3.6.3
Genome_build: GRCm38 v 86

source_name: Spleen

extract_protocol:
Spleen RNA was extracted using the RiboPure™ RNA extraction kit (Invitrogen, ThermoFisher) according to the manufacturer’s instructions. The quantity and quality of the RNA samples was verified using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific) and Bioanalyser
RNA was used for cDNA library preparation using the KAPA RNA Hyperprep with Riboerase kit

treatment_protocol: Serially Blood Passaged: mice were i.p. injected ,with 10e5 infected red blood cell; moquito transmitted: mice were infected with 20 infected mosquitoes

value: Spleen

tag: gender

value: female

tag: infection

value: P. c. chabaudi CB

tag: day


title: SH-SY5Y cells incubated for 48 hours in OPTI-MEM and 10 µM oleacein_rep2

description:
Gene expression data from SH-SY5Y cells incubated for 48 hours in OPTI-MEM and 10 µM oleacein.
SST-RMA


title: CRC tumor T141 [DREAM]


title: SH-SY5Y cells incubated for 48 hours in OPTI-MEM and 10 µM oleacein_rep1


title: Mosquito Transmitted P. chabaudi CB Infection Day 60 Rep 3


title: SH-SY5Y cells co-treated with 10 µM oleacein and 5 µg/ml LPS_rep2


title: RAW264.7-oxldl, C1


title: CRC tumor T147 [DREAM]


title: CRC tumor T139 [DREAM]


title: Mosquito Transmitted P. chabaudi CB Infection Day 60 Rep 2


title: Liver, E3

source_name: livers

value: livers

value: 90mg/kg/d esculetin


title: Mosquito Transmitted P. chabaudi CB Infection Day 60 Rep 1


title: Liver, E2


title: CRC tumor T137 [DREAM]


title: CRC tumor T138 [DREAM]


title: ND93_HCC1937_infected_24h

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with RNeasy  kit (Qiagen) in accordance with the manufacture's protocol.

value: infected

tag: time


title: ND96_HCC1937_infected_24h


title: Mosquito Transmitted P. chabaudi CB Infection Day 30 Rep 2


title: Liver, E1


title: Mosquito Transmitted P. chabaudi CB Infection Day 30 Rep 1


title: CRC tumor T136R [DREAM]

value: colon


title: ND92_HCC1937_none_24h


title: RAW264.7-oxldl, C2


title: Liver, C3


title: ND91_HCC1937_none_24h


title: CRC tumor T140 [DREAM]


title: CRC tumor T133R [DREAM]


title: CRC tumor T133 [DREAM]


title: Liver, C2


title: Mosquito Transmitted P. chabaudi CB Infection Day 12 Rep 3


title: SH-SY5Y cells incubated for 48 hours in OPTI-MEM_rep2


title: ND95_HCC1937_infected_24h


title: Liver, C1


title: ND88_MDAMB231_infected_24h


title: Mosquito Transmitted P. chabaudi CB Infection Day 12 Rep 2


title: ND89_HCC1937_none_24h


title: CRC tumor T132 [DREAM]


title: 7_Pepck_Vpr

value: Kidney Cortex

value: Pepck-Vpr

value: Salt Depletion


title: Mosquito Transmitted P. chabaudi CB Infection Day 12 Rep 1


title: Mosquito Transmitted P. chabaudi CB Infection Day 30 Rep 3


title: ND90_HCC1937_none_24h


title: CRC tumor T129 [DREAM]

value: CRC tumor


title: ND87_MDAMB231_infected_24h


title: Mosquito Transmitted P. chabaudi CB Infection Day 9 Rep 3


title: CRC tumor T126R [DREAM]


title: Mosquito Transmitted P. chabaudi CB Infection Day 9 Rep 2


title: 6_WT_V


title: Hippocampus, F2 of sedentary mice, mouse 6

city: Madrid

first: José Luis

middle: Trejo

last: Pérez

state: Madrid

address: Av. Dr. Arce, 37

department: Neurociencia Traslacional

country: Spain

institute: Instituto Cajal, CSIC

data_processing:
Quality of reads per sample was calculated with MutltiQC and miRTrace
Python package miRge3.0 was used to perform the alignment (with Bowtie v1.3.0), miRNA detection and to produce interactive graphical output
Differential expression analysis was performed using Deseq2 (R software package). P-values < 0.05 were considered as statistically sifnificant and differentially expressed
The miRNA Enrichment Analysis and Annotation Tool (miEAA) was used for the functional analysis of the differentially expressed miRNAs.
An Over-Representation Analysis (ORA) was performed with Gene Ontology (GO) Knowledgebase and KEGG pathways as background databases
Assembly: mm10
Supplementary files format and content: tab-delimited text files

source_name: Hippocampus

extract_protocol:
miRNA was extracted using miRNAeasy kit (Qiagen).
miRNA libraries for miRNA-seq were prepared using NEB Next Multiplex Small RNA Library Prep Set for Illumina (Set 1) following manufacturer's protocols.

value: Hippocampus

tag: group

value: F2 of sedentary mice

value: male


title: Hippocampus, F2 of sedentary mice, mouse 5

value: WT


title: Mosquito Transmitted P. chabaudi CB Infection Day 9 Rep 1


title: CRC tumor T125 [DREAM]


title: Hippocampus, F2 of sedentary mice, mouse 4


title: ND83_MDAMB231_none_24h


title: ND84_MDAMB231_none_24h


title: ND85_MDAMB231_infected_24h


title: CRC tumor T130 [DREAM]


title: Mosquito Transmitted P. chabaudi CB Infection Day 6 Rep 3


title: Mosquito Transmitted P. chabaudi CB Infection Day 6 Rep 2


title: ND82_MDAMB231_none_24h


title: CRC tumor T122 [DREAM]


title: Hippocampus, F2 of sedentary mice, mouse 2


title: Hippocampus, F2 of sedentary mice, mouse 3


title: CRC tumor T120 [DREAM]


title: Mosquito Transmitted P. chabaudi CB Infection Day 6 Rep 1


title: Hippocampus, F2 of sedentary mice, mouse 1


title: Mosquito Transmitted P. chabaudi CB Infection Day 3 Rep 3


title: ND94_HCC1937_infected_24h


title: CRC tumor T119 [DREAM]


title: Hippocampus, F2 of exercised mice, mouse 6

value: F2 of exercised mice


title: ND79_MCF7_infected_24h


title: Mosquito Transmitted P. chabaudi CB Infection Day 3 Rep 1


title: CRC tumor T124 [DREAM]


title: Hippocampus, F2 of exercised mice, mouse 5


title: ND80_MCF7_infected_24h


title: CRC tumor T118R [DREAM]


title: ND86_MDAMB231_infected_24h


title: Hippocampus, F2 of exercised mice, mouse 4


title: CRC tumor T117 [DREAM]


title: Serially Blood Passaged P. chabaudi CB Infection Day 60 Rep 3


title: CRC tumor T114R [DREAM]


title: ND77_MCF7_infected_24h


title: Hippocampus, F2 of exercised mice, mouse 3


title: CRC tumor T114 [DREAM]


title: Hippocampus, F2 of exercised mice, mouse 2


title: ND81_MDAMB231_none_24h


title: Serially Blood Passaged P. chabaudi CB Infection Day 60 Rep 2


title: Serially Blood Passaged P. chabaudi CB Infection Day 60 Rep 1


title: ND76_MCF7_none_24h


title: Mosquito Transmitted P. chabaudi CB Infection Day 3 Rep 2


title: CRC tumor T107 [DREAM]


title: Serially Blood Passaged P. chabaudi CB Infection Day 30 Rep 4


title: CRC tumor T106 [DREAM]


title: Hippocampus, F2 of exercised mice, mouse 1


title: ND74_MCF7_none_24h


title: ND75_MCF7_none_24h


title: Serially Blood Passaged P. chabaudi CB Infection Day 30 Rep 3


title: CRC tumor T104R [DREAM]


title: CRC tumor T103 [DREAM]


title: Liver-6,WT-3, scTCR-Seq

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 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.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: mm10 and refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: comma-delimited text files include raw counts for all cells detected
Supplementary files format and content: clonotypes.csv: the comma-delimited text file contains the TCR clonotype and frequency information
Library strategy: TCR-seq

source_name: liver

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

treatment_protocol: Livers were dissociated over 40-µm nylon mesh and  suspended with 40 % Percoll (Cytiva) and centrifuged over a 80% Percoll to isolate the lymphocyte-containing fraction. Thymocyte were isolate by homoginizer.

value: liver

value: liver cells

value: wild type


title: Serially Blood Passaged P. chabaudi CB Infection Day 30 Rep 1

value: Spleen

value: female

value: P. c. chabaudi CB


title: MS63 HCC1937 7 days

value: infected

value: 7 days


title: MS57 HCC1937 7 days


title: Liver-5,KO-2, scTCR-Seq

value: Sult2a delta1-8/delta1-8


title: Serially Blood Passaged P. chabaudi CB Infection Day 30 Rep 2


title: CRC tumor T101 [DREAM]

value: colon


title: Liver-4,KO-1, scTCR-Seq


title: CRC tumor T100R [DREAM]


title: Liver-3,KO-3, scTCR-Seq


title: Serially Blood Passaged P. chabaudi CB Infection Day 12 Rep 2


title: CRC tumor T099 [DREAM]


title: MS51 HCC1937 7 days


title: Liver-2,WT-2, scTCR-Seq


title: Serially Blood Passaged P. chabaudi CB Infection Day 12 Rep 3


title: CRC tumor T097 [DREAM]


title: Serially Blood Passaged P. chabaudi CB Infection Day 12 Rep 1


title: ND73_MCF7_none_24h


title: Thymus, scTCR-Seq

source_name: thymus

value: thymus

value: thymocyte

value: wild type / Sult2a delta1-8/delta1-8


title: Serially Blood Passaged P. chabaudi CB Infection Day 9 Rep 3


title: Liver-1,WT-1, scTCR-Seq


title: MS45 HCC1937 7 days


title: MS60 HCC1937 7 days


title: CRC tumor T096 [DREAM]

value: CRC tumor


title: ND78_MCF7_infected_24h


title: MS54 HCC1937 7 days


title: Thymus, scRNA-Seq_HTO

description:
Hashtag definitions:
C0302,Hash_tag_2,Wild Type
C0303,Hash_tag_3,Wild Type
C0304,Hash_tag_4,Sult2a1-8 KO
C0305,Hash_tag_5,Sult2a1-8 KO
C0306,Hash_tag_6,Sult2a1-8 KO
C0307,Hash_tag_7,Wild Type

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 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.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: mm10 and refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: comma-delimited text files include raw counts for all cells detected
Supplementary files format and content: clonotypes.csv: the comma-delimited text file contains the TCR clonotype and frequency information
Library strategy: CITE-seq


title: Serially Blood Passaged P. chabaudi CB Infection Day 9 Rep 2


title: MS48 HCC1937 7 days


title: CRC tumor T095 [DREAM]


title: Serially Blood Passaged P. chabaudi CB Infection Day 9 Rep 1


title: CRC tumor T094 [DREAM]


title: Thymus, scRNA-Seq

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 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.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: mm10 and refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: comma-delimited text files include raw counts for all cells detected
Supplementary files format and content: clonotypes.csv: the comma-delimited text file contains the TCR clonotype and frequency information


title: Serially Blood Passaged P. chabaudi CB Infection Day 6 Rep 3


title: Liver-5,KO-2, scRNA-Seq


title: MS56 MDAMB231 7 days


title: CRC tumor T089R [DREAM]


title: MS62 MDAMB231 7 days


title: CRC tumor T077 [DREAM]


title: Liver-4,KO-1, scRNA-Seq


title: CRC tumor T071 [DREAM]


title: Liver-3,KO-3, scRNA-Seq


title: Liver-2,WT-2, scRNA-Seq


title: Serially Blood Passaged P. chabaudi CB Infection Day 3 Rep 3


title: Serially Blood Passaged P. chabaudi CB Infection Day 3 Rep 2


title: MS50 MDAMB231 7 days


title: MS42 HCC1937 7 days


title: Serially Blood Passaged P. chabaudi CB Infection Day 3 Rep 1


title: Liver-1,WT-1, scRNA-Seq


title: CRC tumor T067 [DREAM]


title: CRC tumor T063R [DREAM]


title: CRC tumor T069 [DREAM]


title: Serially Blood Passaged P. chabaudi CB Infection Day 6 Rep 1


title: Liver-6,WT-3, scRNA-Seq


title: Mosquito Transmitted P. chabaudi AS Infection Day 60 Rep 3

value: P. c. chabaudi AS


title: MS44 MDAMB231 7 days


title: MS59 MDAMB231 7 days


title: YFP RNA barcodes from CiBER-seq on NMD pre guide induction, replicate-2

city: Berkeley

first: Joseph

middle: Heimlich

last: Lobel

state: CA

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: UC berkeley

library_source: other

data_processing:
Adaptors were removed with cutadapt
trimmed reads were  aligned to a table of barcode:guide pairs by bowtie2
Counts were summed with samtools
Assembly: Custom dual barcoded gRNA library plasmids
Supplementary files format and content: text file containing raw, unnormalized read counts for each sample
Library strategy: Amplicon sequencing of barcodes

molecule: other

organism: Saccharomyces cerevisiae

source_name: strain

growth_protocol: Yeast populations transformed with either plasmid or bxb1 libraries and inoculated in a custom turbidostat (McGeachy et al. 2019) . Cells were maintained in SCD -URA media with appropriate progesterone concentration at OD600 = ~1. Guides were induced after ~6 doublings (9 hours) and samples collected before or after guide induction. for NMD, cycloheximide was added for 1 hour and cells were allowed to continue to grow

extract_protocol:
RNA was extracted by phenol:chloroform, DNAse treated, and reverse transcribed. DNA was isolated by yeast miniprep kit
Libraries were prepared as previously described (Muller, Science, 2020)

treatment_protocol: Guides were induced wadding anyhydrotetracycline to both the growth chamber and the turbidostat media reservoir, in order to achieve a final concentration of 250 ng/ml. For cycloheximide treatment, cycloheximide was added to the growth chambers at 100 µg/mL. In all cases with progesterone, the specified amount of progesterone was included at all stages in the growth chamber and media reservior

value: strain

value: dCas9-Mxi1/TetR, Bxb1 landing pad


title: CRC tumor T059 [DREAM]


title: Mosquito Transmitted P. chabaudi AS Infection Day 60 Rep 2


title: scarlet RNA barcodes from CiBER-seq on NMD pre guide induction, replicate-2


title: MS53 MDAMB231 7 days


title: CRC tumor T057R [DREAM]


title: MS47 MDAMB231 7 days


title: MS41 MDAMB231 7 days


title: MS55 MCF7 7 days


title: scarlet RNA barcodes from CiBER-seq on NMD pre guide induction, replicate-1


title: MS49 MCF7 7 days


title: CRC tumor T051 [DREAM]


title: CRC tumor T055 [DREAM]


title: Mosquito Transmitted P. chabaudi AS Infection Day 30 Rep 4


title: scarlet RNA barcodes from CiBER-seq on NMD post guide induction, replicate-2

value: 250 ng/mL anhydrotetracycline


title: Serially Blood Passaged P. chabaudi CB Infection Day 6 Rep 2


title: Mosquito Transmitted P. chabaudi AS Infection Day 60 Rep 1


title: Mosquito Transmitted P. chabaudi AS Infection Day 30 Rep 3


title: Mosquito Transmitted P. chabaudi AS Infection Day 30 Rep 2


title: YFP RNA barcodes from CiBER-seq on NMD post guide induction, replicate-1


title: CRC tumor T047 [DREAM]


title: YFP RNA barcodes from CiBER-seq on NMD pre guide induction, replicate-1


title: CRC tumor T041R [DREAM]


title: YFP RNA barcodes from CiBER-seq on NMD post guide induction, replicate-2


title: scarlet RNA barcodes from CiBER-seq on NMD post guide induction, replicate-1


title: Mosquito Transmitted P. chabaudi AS Infection Day 30 Rep 1


title: CRC tumor T033 [DREAM]


title: MS61 MCF7 7 days


title: MS52 MCF7 7 days


title: MS43 MCF7 7 days


title: MS58 MCF7 7 days


title: YFP RNA barcodes from CiBER-seq on NMD after cycloheximide treatment, replicate-2

value: 250 ng/mL anhydrotetracycline, 100 µg/mL cycloheximide


title: Mosquito Transmitted P. chabaudi AS Infection Day 12 Rep 3


title: Liver,SWTX2

data_processing:
The sequencing reads were mapped to the reference mouse genome GRCm39 by HISAT 2.2.1
Read counts per gene locus were obtained with featureCounts
Assembly: mm10
Supplementary files format and content: table-delimitted txt files containing raw counts for each smaplws

growth_protocol: ApoE-/- male mice with a C57BL/6J background (Gempharmatech, Guanzhou, China) at 8 weeks of age were used in this study. The mice were housed in specific pathogen-free facilities maintained at a temperature of 22-23°C with a 12-hour light:12-hour dark circadian cycle. They were fed a Paigen atherogenic diet (PAD, Dyets, Wuxi, China) containing 12.5 g/kg cholesterol and 5 g/kg sodium cholic acid for a duration of 8 weeks.

extract_protocol:
RNAs were purified from the livers  by Trizol Reagent
A cDNA library was prepared by using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (NR604, Vazyme, Nanjing, China)

treatment_protocol: The mice were randomly divided into two groups: the model group, which received NS administered by gavage, and the SWTX group, which received a dosage of 3.5 g/kg/d administered by gavage.

value: livers

tag: background strain

value: male

value: Apoe-/-

value: 3.5 g/kg/d SWTX


title: CRC tumor T031 [DREAM]


title: Liver,SWTX1


title: MS46 MCF7 7 days


title: Mosquito Transmitted P. chabaudi AS Infection Day 12 Rep 1

value: Spleen

value: female


title: scarlet RNA barcodes from CiBER-seq on NMD after cycloheximide treatment, replicate-2


title: CRC tumor T029 [DREAM]


title: Mosquito Transmitted P. chabaudi AS Infection Day 9 Rep 3


title: CRC tumor T035RR [DREAM]


title: YFP RNA barcodes from CiBER-seq on NMD after cycloheximide treatment, replicate-1


title: Liver,NS1

value: normal saline


title: Liver,NS2


title: Mosquito Transmitted P. chabaudi AS Infection Day 9 Rep 2


title: MS40 MCF7 7 days

value: 7 days


title: CRC tumor T023 [DREAM]

value: colon


title: Pectin_PFOS_5, bio rep 4

city: Lexington

first: Yekaterina

last: Zaytseva

state: KY

address: 760 Press ave

department: Toxicology and Cancer Biology

institute: University of Kentucky

data_processing:
Samples were tested using the DNBSEQ platform, with an average yield of 4.52G data per sample. The average alignment ratio of the sample comparison genome was 97.13%, which was comparative The average alignment of the gene set was 81.84%; a total of 18472 genes were detected
Reads filtering
HISAT was used to align the clean reads to the reference genome; Bowtie2 was used to align the clean reads to the reference genes
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: Tab separated values includes raw counts for each sample
Supplementary files format and content: Tab separated values includes raw TPM values for each sample

source_name: intestinal tissue

growth_protocol: 7-week-old C57BL/6 male mice  were kept on an irradiated diet supplemented with one of three fibers: cellulose (control), inulin, or pectin.  The mice were exposed to PFOS at 3μg/Kg BW per day by drinking water and maintained on the diet for 7 weeks. The composition of the diets was the following: Fiber: 8% wt/wt, Fat: 35% kcal, protein: 20% kcal and carbohydrate: 45% kcal. Mice was euthanized and intestinal tissues were collected and preserved in RNAlater in -80 frezer.

extract_protocol:
RNA was extracted intestinal tissues using RNeasy mini plus kit (Quiagen). Samples were processed by BGI genoimics. Concentrations, 28S/18S, and RINwere determined by Fragment Analyzer
RNA was costructed based on the protocol for BGI Pipeline of DNBSEQ Eukaryotic Stranded Transcriptome library preparation

value: intestinal tissue

value: WT

value: PFOS at 3μg/Kg BW per day by drinking water and different diets for 7 weeks


title: Mosquito Transmitted P. chabaudi AS Infection Day 9 Rep 1

value: P. c. chabaudi AS


title: CRC tumor T027 [DREAM]

value: CRC tumor


title: scarlet RNA barcodes from CiBER-seq on NMD after cycloheximide treatment, replicate-1

value: strain

value: dCas9-Mxi1/TetR, Bxb1 landing pad


title: YFP RNA barcodes from CiBER-seq on Z3PM-CL1 from pre-guide induction, replicate-2

value: Z3PM-CL1, Z4PM, dCas9-Mxi1/TetR, Bxb1 landing pad

value: 135 nM progesterone


title: Pectin_PFOS_3, bio rep 3

value: male


title: CRC tumor T021 [DREAM]


title: Mosquito Transmitted P. chabaudi AS Infection Day 12 Rep 2


title: CFP RNA barcodes from CiBER-seq on Z3PM-CL1 from pre-guide induction, replicate-2


title: YFP RNA barcodes from CiBER-seq on Z3PM-CL1 from pre-guide induction, replicate-1


title: Mosquito Transmitted P. chabaudi AS Infection Day 6 Rep 3


title: CRC tumor T019 [DREAM]


title: Pectin_PFOS_2, bio rep 2


title: Mosquito Transmitted P. chabaudi AS Infection Day 6 Rep 2


title: CFP RNA barcodes from CiBER-seq on Z3PM-CL1 from pre-guide induction, replicate-1


title: CRC tumor T017 [DREAM]


title: Mosquito Transmitted P. chabaudi AS Infection Day 6 Rep 1


title: Pectin_PFOS_1, bio rep 1


title: Pectin_5, bio rep 4

value: Pectin


title: CRC tumor T015 [DREAM]


title: Pectin_3, bio rep 3


title: Mosquito Transmitted P. chabaudi AS Infection Day 3 Rep 3


title: YFP RNA barcodes from CiBER-seq on Z3PM-CL1 from post-guide induction, replicate-2

value: 250 ng/mL anhydrotetracycline, 135 nM progesterone


title: CRC tumor T013R [DREAM]


title: Mosquito Transmitted P. chabaudi AS Infection Day 3 Rep 2

value: Spleen


title: YFP RNA barcodes from CiBER-seq on Z3PM-CL1 from post-guide induction, replicate-1


title: CFP RNA barcodes from CiBER-seq on Z3PM-CL1 from post-guide induction, replicate-1


title: Pectin_1, bio rep 1


title: PBMC_2, HTO-derived cDNA

description:
Hashtag-condition.xlsx
feature_reference.csv

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.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: refdata-gex-GRCh38-2020-A and refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: comma-delimited text files including raw counts for all cells detected
Supplementary files format and content: airr_rearrangement.tsv: tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv: comma-delimited text file including the TCR clonotype information
Supplementary files format and content: feature_reference.csv: comma-delimited text file including barcode sequences associated with each TotalSeq(BioLegend) hashtag ID and name
Supplementary files format and content: Hashtag-condition.xlsx: Excel file including condition/treatment information for each hashtag

molecule: protein

source_name: peripheral blood

extract_protocol:
Single 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 Next GEM Single Cell 5' Reagent Kits v2 User Guide.

treatment_protocol: Human PBMCs were prepared from the blood by density gradient centrifugation using Lymphocyte Separation Solution（d=1.077）(Nacalai tesque). PBMCs were stimulated with 5-OP-RU and CA7S at 30 µM or 3000 µM in RPMI 1640 medium (Sigma) supplemented with 10% fetal bovine serum, penicillin (Sigma), streptomycin (MP Biomedicals), and 2-mercaptoethanol (Nacalai tesque). A day later, anti-CD161+MR1-5-OP-RU tetramer+ cells within a CD3+-gated population were sorted by SH800S Cell Sorter (Sony Biotechnology) and used for single-cell TCR- and RNA-seq analyses.

value: peripheral blood

value: T cell

tag: antibodies

value: Anti CD298 + Anti β2 microglobulin

value: none or stimulation with 5-OP-RU or CA7S

tag: fraction

value: Hashtag oligonucleotide (HTO)


title: Serially Blood Passaged P. chabaudi AS Infection Day 60 Rep 2

tag: tissue

value: female


title: Inulin_PFOS_5, bio rep 3

value: intestinal tissue

value: WT

value: PFOS at 3μg/Kg BW per day by drinking water and different diets for 7 weeks


title: YFP RNA barcodes from CiBER-seq on Z3PM+Z4PM from pre-guide induction, replicate-2

value: strain

tag: cell line

tag: cell type

value: Z3PM, Z4PM, dCas9-Mxi1/TetR

value: 200 nM progesterone


title: Inulin_PFOS_3, bio rep 2

tag: treatment


title: CRC tumor T005R [DREAM]

value: colon

value: CRC tumor


title: YFP RNA barcodes from CiBER-seq on Z3PM+Z4PM from pre-guide induction, replicate-1

tag: genotype


title: Pectin_2, bio rep 2

value: male

value: Pectin


title: Mosquito Transmitted P. chabaudi AS Infection Day 3 Rep 1

value: Spleen

value: P. c. chabaudi AS


title: CRC tumor T001 [DREAM]

tag: tissue type


title: Serially Blood Passaged P. chabaudi AS Infection Day 60 Rep 1

tag: strain


title: PBMC_2, TCR-derived cDNA

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.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: refdata-gex-GRCh38-2020-A and refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: comma-delimited text files including raw counts for all cells detected
Supplementary files format and content: airr_rearrangement.tsv: tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv: comma-delimited text file including the TCR clonotype information
Supplementary files format and content: feature_reference.csv: comma-delimited text file including barcode sequences associated with each TotalSeq(BioLegend) hashtag ID and name
Supplementary files format and content: Hashtag-condition.xlsx: Excel file including condition/treatment information for each hashtag
Library strategy: scTCR-seq

value: peripheral blood

value: T cell

value: TCR V(D)J segments


title: Inulin_PFOS_1, bio rep 1


title: PBMC_1, TCR-derived cDNA

value: Anti CD298 + Anti β2 microglobulin

value: none or stimulation with 5-OP-RU or CA7S


title: Serially Blood Passaged P. chabaudi AS Infection Day 60 Rep 3

value: female


title: PBMC_1, HTO-derived cDNA

value: Hashtag oligonucleotide (HTO)


title: Inulin_5, bio rep 3

value: intestinal tissue

value: WT

value: PFOS at 3μg/Kg BW per day by drinking water and different diets for 7 weeks

value: Inulin


title: Serially Blood Passaged P. chabaudi AS Infection Day 30 Rep 3


title: Serially Blood Passaged P. chabaudi AS Infection Day 12 Rep 2


title: CFP RNA barcodes from CiBER-seq on Z3PM-CL1 from post-guide induction, replicate-2

value: strain

value: Z3PM-CL1, Z4PM, dCas9-Mxi1/TetR, Bxb1 landing pad

value: 250 ng/mL anhydrotetracycline, 135 nM progesterone


title: CFP RNA barcodes from CiBER-seq on Z3PM+Z4PM from post-guide induction, replicate-2

value: Z3PM, Z4PM, dCas9-Mxi1/TetR

value: 250 ng/mL anhydrotetracycline, 200 nM progesterone


title: YFP RNA barcodes from CiBER-seq on Z3PM+Z4PM from post-guide induction, replicate-2


title: HESC-2

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: GRCh37
Supplementary files format and content: Tab delimited file (txt) for featureCounts raw hit counts

source_name: HESC exposed to control media

growth_protocol: hTERT-immortalized human endometrial stromal cells (HESCs, ATCC) were grown in phenol red-free DMEM/F12 media supplemented with 10% charcoal stripped fetal bovine serum, 1% ITS+premix and 500 ng/mL puromycin and maintained in a humidified incubator under standard culture conditions.

extract_protocol:
Total RNA was isolated from HESCs with the Rneasy Plus Mini Kit (Qiagen) after 24h of co-culture with MSCs or control media and RNA integrity number determined.
Illumina polyA+

treatment_protocol: 2x10^5 HESCs per well were plated in 6-well dishes, and BM-MSCs were plated onto 0.4 µm pore size cell culture inserts at 1x10^5 cells per insert.  BM-MSCs and HESCs were cultured independently for 24h, washed with PBS, then exposed to co-culture media (phenol red-free DMEM supplemented with 10% charcoal-stripped FBS and 1%ITS+premix) in the transwell system for 24 hours.  HESCs cultured in the transwell system without MSCs served as controls.

value: hTERT-immortalized HESC cell culture

tag: bm-msc source


title: CFP RNA barcodes from CiBER-seq on Z3PM+Z4PM from post-guide induction, replicate-1


title: Serially Blood Passaged P. chabaudi AS Infection Day 30 Rep 2

value: Spleen

value: P. c. chabaudi AS


title: PFOS_2, bio rep 2

tag: Sex

value: male

value: PFOS


title: PBMC_2, mRNA-derived cDNA

value: peripheral blood

value: T cell

value: Anti CD298 + Anti β2 microglobulin

value: none or stimulation with 5-OP-RU or CA7S

value: poly A RNA


title: YFP RNA barcodes from CiBER-seq on Z3PM+Z4PM from post-guide induction, replicate-1


title: Inulin_4, bio rep 2

value: intestinal tissue

value: WT

value: PFOS at 3μg/Kg BW per day by drinking water and different diets for 7 weeks


title: Inulin_1, bio rep 1

value: Inulin


title: CFP RNA barcodes from CiBER-seq on Z3PM+Z4PM from pre-guide induction, replicate-2

value: strain

value: 200 nM progesterone


title: HESC+BM-MSC-2-3

source_name: HESC exposed to BM-MSC secretome

value: isolated from healthy female donor


title: Serially Blood Passaged P. chabaudi AS Infection Day 30 Rep 1

tag: gender

value: female


title: HESC-3

value: hTERT-immortalized HESC cell culture


title: Serially Blood Passaged P. chabaudi AS Infection Day 9 Rep 3

value: Spleen

tag: infection

value: P. c. chabaudi AS


title: PFOS_4, bio rep 3

value: male

value: PFOS


title: PBMC_1, mRNA-derived cDNA

value: peripheral blood

value: T cell


title: PFOS_5, bio rep 4


title: Serially Blood Passaged P. chabaudi AS Infection Day 12 Rep 3

tag: day


title: Serially Blood Passaged P. chabaudi AS Infection Day 12 Rep 1


title: DNA barcodes from CiBER-seq on Z3PM+Z4PM from pre-guide induction, replicate-1

value: Z3PM, Z4PM, dCas9-Mxi1/TetR


title: PFOS_1, bio rep 1


title: Serially Blood Passaged P. chabaudi AS Infection Day 9 Rep 2


title: CFP RNA barcodes from CiBER-seq on Z3PM+Z4PM from pre-guide induction, replicate-1


title: HESC+BM-MSC-2-2


title: Control_3, bio rep 3

value: Control


title: DNA barcodes from CiBER-seq on Z3PM+Z4PM from pre-guide induction, replicate-2


title: DNA barcodes from CiBER-seq on Z3PM+Z4PM from post-guide induction, replicate-1

value: 250 ng/mL anhydrotetracycline, 200 nM progesterone


title: Serially Blood Passaged P. chabaudi AS Infection Day 9 Rep 1


title: Serially Blood Passaged P. chabaudi AS Infection Day 6 Rep 2


title: Control_2, bio rep 2

value: intestinal tissue

value: WT


title: HESC-1


title: Serially Blood Passaged P. chabaudi AS Infection Day 6 Rep 3


title: HESC+BM-MSC-1-3

value: purchased from ATCC


title: HESC+BM-MSC-1-2


title: HESC+BM-MSC-1-1


title: Serially Blood Passaged P. chabaudi AS Infection Day 3 Rep 3


title: Control_5, bio rep 4

value: PFOS at 3μg/Kg BW per day by drinking water and different diets for 7 weeks


title: PBMC-scCITE-Seq

description: scCITE-Seq

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 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.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: GRCh38 and refdata-cellranger-vdj-GRCh38-alts-ense  mbl-4.0.0
Supplementary files format and content: hPBMC_5DE_genematrix.csv: comma-delimited text files include raw counts for all cells detected
Supplementary files format and content: surface_protein.csv: the list of tag sequences to identify surface proteins
Supplementary files format and content: clonotypes.csv: the comma-delimited text file contains the TCR-VDJ clonotype and frequency information

source_name: PBMC

treatment_protocol: Human PBMCs were prepared from the blood by density gradient centrifugation using Lymphocyte Separation Solution（d=1.077）(Nacalai tesque). PBMCs were labeled with CellTraceTM Violet (Invitrogen) and stimulated with 5-OP-RU, CA3S and CA7S at 10 µM or 1000 µM in RPMI 1640 medium (Sigma) supplemented with 10% fetal bovine serum, penicillin (Sigma), streptomycin (MP Biomedicals), and 2-mercaptoethanol (Nacalai tesque). Indicated days after stimulation, anti-CD161+MR1:5-OP-RU tetramer+ cells within a CD3+-gated population were sorted by SH800S Cell Sorter (Sony Biotechnology) and used for single-cell TCR- and RNA-seq analyses.

value: PBMC

value: multiplexed sample:5-OR-RU / CA3S / CA7S


title: DNA barcodes from CiBER-seq on Z3PM+Z4PM from post-guide induction, replicate-2

value: strain


title: 23_NASH_Chrebp_alpha-LKO

city: Ann Arbor

first: Sujuan

last: Wang

state: MI

address: 2800 Plymouth Road

department: Molecular & Integrative Physiology

institute: University of Michigan

data_processing:
Sequencing data Filtering: remove the reads mapped to rRNA and get raw data, and then processed and removed the sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads
Genome Mapping: mapped clean reads to reference genome using HISAT2
Gene Expression Analysis
Assembly: HISAT2(http://daehwankimlab.github.io/hisat2/)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Chrebp{alpha}-LKO, NASH

growth_protocol: All mice are housed on a 12 hours:12 hours light/dark cycle at 25℃ with free access to water and regular chow (26.8% kcal from protein, 16.6% kcal from fat, and 56.4% kcal from starch).

extract_protocol:
RNA was harvested using Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit).
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription:Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The  synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol:
Chrebpα-flox/flox mice were injected with AAV-TBG-GFP (Chrebpα-WT) and AAV-TBG-Cre (Chrebpα-LKO) and fed NASH diet (40 kcal% Fat (Either Palm Oil), 20 kcal% Fructose and 2% Cholesterol) for 12 weeks.
2 month old wildtype mice were fed HFLMCD diet (45 kcal% Fat, Without Choline and With 0.1% Added Methionine) for weeks, and injected with Adenovirus overexpressing GFP (Ad-GFP) and Chrebpα (Ad-Chrebpα) and fed for another 1 week befroe dissection.

value: Liver

value: Chrebp{alpha}-LKO

value: NASH diet feed 12 weeks


title: Serially Blood Passaged P. chabaudi AS Infection Day 3 Rep 2

value: Spleen

value: female

value: P. c. chabaudi AS


title: HESC+BM-MSC-2-1

value: hTERT-immortalized HESC cell culture

value: isolated from healthy female donor


title: PBMC-scTCR-Seq

description: scTCR-Seq

value: T cell


title: PBMC-scRNA-Seq

description: scRNA-Seq


title: 21_NASH_Chrebp_alpha-LKO


title: Serially Blood Passaged P. chabaudi AS Infection Day 3 Rep 1


title: Naïve Day 60 Rep 2

value: Naïve


title: reversed cells, biological rep3

city: Shenyang

first: cheng

last: yang

address: wenhua street  number 103

institute: Shenyang Pharmaceutical University

hyb_protocol: Adding the fragmented labeled samples into the corresponding chips, putting them into the GeneChip Hybridization Oven 645 hybridization furnace, and performing chip hybridization at a specific temperature and rotation speed; After reaching the specified time, use GeneChip Fluidics Station 450 to wash and dye according to the corresponding Protocol

scan_protocol: Using GeneChip 3000 7G scanner to scan.

data_processing: The scanner captures the fluorescence signal and converts the signal by GCOS software, thus obtaining the signal value of each probe and generating the CEL file.

source_name: EHMT2 inhibitor treat cells

label_protocol: Total RNA (adding PolyA control), the first and second strands of cDNA were synthesized, and cRNA was synthesized by in vitro transcription and biotin labeling. After purification and quantification, cRNA was diluted to 468.75ng/ul for fragmentation.

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% FBS (Gibco) at 37 °C in a 5% CO2 incubator.

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

treatment_protocol: Erlotinib-resistant cells were identified after induction for one year in gradually increasing doses of the drug

value: non small cell lung cancer cell

tag: agent

value: UNC0638 treatment


title: SHAP

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to GRCh38.p10 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: xls file includes TPM values for each Sample.

source_name: HGC-27 cells

growth_protocol: Cells were incubated with RPMI 1640 medium with 10% FBS in CO2 incubators at 37℃.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent (Cat#15596-018) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Illumina Hiseq 4000 SBS Kit (Cat#FC-410-1003) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treat with control DMSO, disulfiram, thiram or SHAP peptide using RNAIMAX (Thermo) reagent for 72 hours

value: gastric cancer cells

value: SHAP


title: reversed cells, biological rep2


title: Serially Blood Passaged P. chabaudi AS Infection Day 6 Rep 1


title: Naïve Day 60 Rep 1


title: transformed cells, biological rep3

source_name: transformed cells

value: Erlotinib treatment leads to phenotypic transformation


title: 20_NASH_Chrebp_alpha-WT

source_name: Chrebp{alpha}-WT, NASH

value: Chrebp{alpha}-WT


title: thiram

value: thiram


title: Control_1, bio rep 1

value: intestinal tissue

value: male

value: WT

value: PFOS at 3μg/Kg BW per day by drinking water and different diets for 7 weeks

value: Control


title: 24_NASH_Chrebp_alpha-LKO

value: Liver

value: Chrebp{alpha}-LKO

value: NASH diet feed 12 weeks


title: transformed cells, biological rep2


title: 19_NASH_Chrebp_alpha-WT


title: Naïve Day 30 Rep 2

value: Spleen

value: female


title: 22_NASH_Chrebp_alpha-LKO


title: transformed cells, biological rep1

value: non small cell lung cancer cell


title: 18_NASH_Chrebp_alpha-WT


title: 17_NASH_Chrebp_alpha-WT


title: parental cells, biological rep3

source_name: parental cells


title: Naïve Day 12 Rep 2

source_name: Spleen

value: Naïve


title: Naïve Day 30 Rep 1


title: reversed cells, biological rep1

value: UNC0638 treatment


title: Ctrl

value: gastric cancer cells

value: Ctrl


title: parental cells, biological rep2


title: Sham [GC_47220]

city: Liverpool

first: Rebecca

last: Burton

address: Nuffield Red Block, Sherrington Building

department: Pharmacology and Therapeutics

institute: University of Liverpool

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N  sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. The Stringtie was used to assemble the set of transcript  isoforms of each bam file obtained in the mapping step. gffcompare can compare Strintie assemblies to reference annotation files and help sort out new genes from known ones. Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of  the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. The  resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by  DESeq2 were assigned as differentially expressed.
Supplementary files format and content: read counts for all samples

organism: Capra hircus

source_name: Left atria

extract_protocol:
RNA from tissue was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA)
RNA libraries were prepared for sequencing using standard NEB protocols

value: Left atria

value: Sham


title: Sham [GC_41566]


title: disulfiram

value: disulfiram


title: Rhytidome-like 20

city: 17003 Girona

first: Mercè

last: Figueras

state: Girona

address: C/ Mª Aurèlia Campmany, 41 (campus Montilivi)

institute: Universitat de Girona

data_processing:
RNA-seq data were first analysed for quality control with FastQC (Andrews, 2010)
First low-quality 12 bp removal was performed with Trimmomatic v. 0.40 (Bolger et al., 2014)
Reads were mapped with GSNAP (Wu et al., 2016) against Q. suber genome (GCF_002906115.1_CorkOak1.0_genomic.fna)
Reads from each library were assembled with Cufflinks 2.2.1 (Trapnell et al., 2010)
The consensus transcriptome for all the samples was generated assembling each library with the Cuffmerge script from Cufflinks
different isoforms were collapsed and total counts were estimated by HTSeq-count 0.11.1 (Anders et al., 2015)
The count matrix generated was used to identify differentially expressed genes (DEGs) using the DESeq2 package v.1.38.3
Read counts per locus were corrected by rlog transformation and DEGs were obtained by pairwise comparisons
Assembly: GCF_002906115.1_CorkOak1.0
Supplementary files format and content: One unique file with a matrix table with regularized and log transformed read counts for each cork oak gene (locus identifier) and sample

organism: Quercus x morisii

source_name: outer bark of tree trunk

extract_protocol:
Total RNA was extracted from outer barks by some modifications of the method described previously (Chang et al., 1993; Chaves et al., 2014).
cDNA libraries were obtained using the MGIEasy RNA Library Prep Kit V3.1 and 3 µg of each sample

value: outer bark of tree trunk


title: Rhytidome-like 14


title: Naïve Day 12 Rep 1

data_processing:
Fastq files QC using Multi QC (Babraham Institute)
Transcript were aligned and counted to the Mus musculus reference genome GRCm38 v86 using STAR v2.5.2 and RSEM v1.3.0
Libraries normalised for size through DESeq2 v1.26 in R v3.6.3
Genome_build: GRCm38 v 86


title: Rhytidome-like 18


title: Sham [GC_38658]


title: Rhytidome-like 21


title: Naïve Day 9 Rep 1


title: parental cells, biological rep1


title: Naïve Day 9 Rep 2


title: 13_HFLMCD_Ad-Chrebp_alpha

source_name: HFLMCD diet, Ad-Chrebp{alpha}

value: Ad-Chrebp{alpha}

value: HFLMCD diet 3 weeks


title: Sham [GC_33246]


title: 15_HFLMCD_Ad-Chrebp_alpha


title: 14_HFLMCD_Ad-Chrebp_alpha


title: Atrial Fibrillation/ Diseased [AF_542016]

value: Atrial Fibrillation/ Diseased


title: Cork-like 4 (west)


title: Atrial Fibrillation/ Diseased [AF_303201]


title: 12_HFLMCD_Ad-GFP

source_name: HFLMCD diet, Ad-GFP

value: Liver

value: WT


title: Naïve Day 6 Rep 1


title: 16_HFLMCD_Ad-Chrebp_alpha


title: Naive Day 3 Rep 2


title: Cork-like 2 (south)


title: 11_HFLMCD_Ad-GFP


title: Atrial Fibrillation/ Diseased [AF_39703]


title: Naive Day 3 Rep 1


title: 10_HFLMCD_Ad-GFP


title: 9_HFLMCD_Ad-GFP


title: Cork-like 1 (north)


title: C. rodentium wild-type, 37°C, replicate D

status: Public on Jun 11 2024

city: Claremont

first: Daniel

last: Stoebel

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

data_processing:
Sequencing reads from each sample in a pool were demultiplexed based on their associated barcode sequence using custom scripts. Up to 1 mismatch in the barcode was allowed provided it did not make assignment of the read to a different barcode possible. Barcode sequences were removed from the first read as were terminal G’s from the second read that may have been added by SMARTScribe during template switching.
Reads were aligned to the reference genomes using BWA v0.7.17 . Reads were counted with htseq-count v2.0.1
Assembly: 6 species are present here, so there are six reference sequences: GCF_000005845.2,GCF_000022165.1,GCF_000027085.1,GCF_000281535.2,GCF_000025565.1,GCF_000513215.1
Supplementary files format and content: Processed files are text files of (unnormalized) counts for each sample.

organism: Citrobacter rodentium

growth_protocol: Bacteria were grown in LB at 37°C

extract_protocol:
1.5 mL of bacterial culture was pelleted and resuspended in 500 μL of Trizol pre-heated to 65°C and then stored at -80°C until use. Samples were purified on a column using the Zymo Direct-Zol RNA Miniprep kit. They were then treated twice with DNase I using Turbo DNA-free (Invitrogen) for 30 minutes each at 37˚C to ensure that all DNA was degraded. The samples were further purified on a column using the Zymo RNA Clean and Concentrator Kit and again stored at -80˚C until sequencing.
Illumina cDNA libraries were generated using a modified version of the RNAtag-seq protocol. Briefly, 500 ng to 1 μg of total RNA was fragmented by heating to 94°C in NEB Alkaline Phosphatase Buffer, depleted of any residual genomic DNA, dephosphorylated, and ligated to DNA adapters carrying 5’-AN8-3’ barcodes of known sequence with a 5’ phosphate and a 3’ blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (Epicentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor with addition of an adapter to the 3’ end of the cDNA by template switching using SMARTScribe (Clontech) as described (23); (ii) PCR amplification using primers whose 5’ ends target the constant regions of the 3’ or 5’ adaptors and whose 3’ ends contain the full Illumina P5 or P7 sequences. cDNA libraries were sequenced on the Illumina [NextSeq 500] platform at the Broad Institute to generate paired end reads.

treatment_protocol: At time 0, samples were taken and cultures shifted to 15°C. Cells grew at 15°C for 3 hours, and then sampleres were taken again

value: wild-type

tag: biological replicate

value: D


title: C. rodentium wild-type, 15°C, replicate E

value: E


title: Naïve Day 6 Rep 2

value: Spleen

value: female


title: C. rodentium wild-type, 15°C, replicate D


title: C. rodentium wild-type, 37°C, replicate E


title: C. rodentium wild-type, 37°C, replicate A

value: A


title: C. rodentium wild-type, 15°C, replicate B

value: B


title: C. rodentium wild-type, 37°C, replicate B


title: Cork-like 3 (east)


title: C. rodentium wild-type, 15°C, replicate A


title: CK_24_3h_3

city: Hangzhou

first: xueting

last: gu

address: yuhangtang road 866

institute: Zhejiang university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. 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: Chrysanthemum x morifolium

source_name: root

growth_protocol: The experiment was conducted in a greenhouse with a 16 h of light (25℃) and 8 h of darkness (20℃)

extract_protocol:
Total RNA was extracted using the Tiangen RNA Extraction Kit with the RNase-Free DNase Set (Tiangen Biotech, Beijing, China), according to the manufacturer’s instructions.
Libraries for mRNA-seq were constructed and sequenced by Novogene (Beijing).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. 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.

treatment_protocol: 8-week-old seedlings of EWT and CK were subjected to waterlogging stress by submerging them in water up to 2 cm above the upper leaves

value: root

value: CK


title: EWT_24_3h_1

value: EWT


title: Atrial Fibrillation/ Diseased [AF_45158]

value: Left atria


title: EWT_24_3h_4


title: EWT_24_3h_3


title: CK_24_3h_4


title: EWT_24h_2


title: EWT_24h_3


title: CK_24_3h_2


title: CK_24_3h_1


title: EWT_24h_4


title: EWT_24h_1


title: CK_24h_3


title: CK_24h_4


title: CK_24h_1


title: EWT_12h_3


title: EWT_12h_4


title: CK_24h_2


title: EWT_24_3h_2


title: EWT_12h_2


title: EWT_12h_1


title: CK_12h_2


title: CK_12h_1


title: EWT_03h_3


title: EWT_03h_2


title: EWT_03h_1


title: CK_12h_3


title: EWT_03h_4


title: CK_03h_3


title: EWT_00h_3


title: EWT_00h_1


title: EWT_00h_4


title: CK_00h_3


title: CK_03h_4


title: CK_03h_2


title: CK_00h_4


title: EWT_00h_2


title: CK_03h_1


title: CK_00h_1


title: CK_00h_2


title: WTZ3DPI,3,S7

first: Scott

last: Handley

state: MO

address: 660 S Euclid Ave

institute: Washington University in St.Louis

description: 10x Genomics

data_processing:
The demultiplexing,barcode processing,gene counting and aggregation were made using Cell Ranger software v2.1.1
https://bioinformatics-core-shared-training.github.io/UnivCambridge_ScRnaSeq_Nov2021/Markdowns/03_CellRanger.html
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: placenta

extract_protocol:
Two placentas from the same genotype and condition were pooled and processed for isolation of nuclei. Nuclear extraction was adapted from a previously described protocol for jejunal segments (Chang et al., 2024). Briefly, tissues were thawed and minced in lysis buffer (25 mM citric acid, 250 mM sucrose, 0.1% NP-40, and 1X protease inhibitor (Roche)). Nuclei were released from cells using a Dounce homogenizer (Wheaton) then washed 3 times with buffer (25 mM citric acid, 0.25 M sucrose, 1X protease inhibitor (Roche)), and then filtered successively through 100 μm, 70 μm, and 40 μm diameter strainers (pluriSelect) to obtain single nuclei in resuspension buffer (25 mM KCl, 3 mM MgCl2, 50 mM Tris, 1 mM DTT, 0.4 U/μL RNase inhibitor (Sigma) and 0.4 U/μL Superase inhibitor (ThermoFisher)).
Approximately 10,000 nuclei per sample were subjected to gel bead-in-emulsion (GEM) generation, reverse transcription, and construction of libraries for sequencing according to the protocol provided in the 3' gene expression v3.1 kit manual (10X Genomics). Briefly, cDNA was prepared after GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before clean-up using SPRI select beads (Beckman Coulter, B23318). Samples were then run on a Bioanalyzer to determine cDNA concentrations. Gene expression libraries (GEX libraries) were prepared as recommended by the 10x Genomics Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

value: placenta

tag: developmental age

value: ZIKV


title: WTN6DPI,2,S6

description: 10x Genomics

value: Mock


title: KOZ3DPI,7,S3

description: 10x Genomics

value: MAVS -/-


title: KON6DPI,6,S2

description: 10x Genomics


title: WTN3DPI,1,S5

description: 10x Genomics


title: WTZ6DPI,4,S8

description: 10x Genomics


title: KON3DPI,5,S1

description: 10x Genomics


title: CK_12h_4


title: CD45.1 MD4 GC B cells, 838840_GX95 and 836436_GX95, HTO

city: Oxford

first: Mukta

last: Deobagkar

address: Centre for Human Genetics, Roosevelt Drive

department: Nuffield Department of Medicine

institute: University of Oxford

description:
Hashtag-derived oligonucleotides (HTOs)
CD45.1_GCB_HTO-TSB

data_processing:
*library strategy: CITE-seq
Single cell sequencing outputs were mapped to transcriptome mm10-2020-A and quantified with 10XGenomics CellRanger v5.0.1. The EmptyDroplets algorithm was used to call cells and the gene expression (RNA) and hashtag information (HTO) libraries were filtered on cell barcodes identified in the RNA assay via CellRanger. Filtered gene matrix was used to construct a Seurat object and analysed in R using the Seurat v4.0 or higher  package. scRNA-Seq data were filtered on gene features >100 or <5500, and mitochondrial % <10. The CD45.1 and CD45.2 datasets were integrated using the SCTransform pipeline before dimensionality reduction and guided clustering.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output

extract_protocol:
Gene libraries from FACS-sorted splenic CD45.1 and CD45.2 GC B cells were constructed with droplet-based single-cell RNA sequencing using the 10XGenomics Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1. Single cells  were load at 1,000 nuclei/ul for a targeted 20,000 nuclei for the CD45.2 sample and 5000 nuclei for the CD45.1 sample.
Samples were sent to the Oxford Genomics Centre for library preparation (HTO and 3' gene expression libraries),  and sequencing on the Illumina NovoSeq6000. SubsequentIllumina runs were demultiplexed and the resulting fastq files were processed through the 10X Genomics Cellranger v5.01 pipeline on the command line.
Both mRNA (GEX) and HTO libraries were prepared using standard protocols as recommended by 10XGenomics.

value: murine splenic CD45.1+ CD95+ MD4 GC B cell

value: mixed GC B cell sample:3 x WT from WT group and 3 x WT from DOCK8-deficient group

tag: library type

value: HTO

tag: hto

value: TotalSeq™-B (B0301), TotalSeq™-B (B0302), TotalSeq™-B (B0303), TotalSeq™-B (B0304), TotalSeq™-B (B0305), TotalSeq™-B (B0306)


title: CD45.2 MD4 GC B cells, 838840_GX83 and 836436_GX83, HTO

description:
Hashtag-derived oligonucleotides (HTOs)
CD45.2_GCB_HTO-TSB

tag: tissue

value: murine splenic CD45.2+ CD95+ MD4 GC B cell

value: mixed GC B cell sample:3 x WT and 3 x DOCK8-deficient


title: CD45.1 MD4 GC B cells, 838840_GX47 and 836436_GX47, GEX

description:
polyA RNA
CD45.1_GCB_GEX-v3.1

value: Spleen

value: mRNA


title: CD45.2 MD4 GC B cells, 838840_GX35 and 836436_GX35, GEX

description:
polyA RNA
CD45.2_GCB_GEX-v3.1


title: mFL_Ortho_3rd

city: New York

first: Xiuli

last: An

address: 310 E 67th St

institute: New York Blood Center

data_processing:
Low-quality reads were removed and filtered by fastp. Filtered reads were quantified by Kallisto using the mm10 transcriptome index. Pairwise comparison of two groups was performed by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited test files includes raw counts for each Sample

source_name: fetal liver

extract_protocol:
We used a QIAGEN RNA isolation kit (74104; QIAGEN, Dusseldorf, Germany) to extract RNA.
For erythroid progenitors BFU-E and CFU-E, the library was constructed by low input Clontech SMART-Seq HT with Nxt HT, and then sequenced by an Illumina Nova Seq 6000 using 50 bp paired-end strategy. For erythroblasts, the library was constructed by Illumina VAHTS Universal V6 RNA-seq Library Prepkit NR 604-01/02 (Illumina, San Diego, CA), and then sequenced by an Illumina NovaSeq 6000 using 150 bp paired-end strategy.

value: fetal liver

value: sorted primary orthochromatic erythroblasts cells

value: WT

value: no treatment


title: mFL_Poly_3rd

value: sorted primary polychromatic erythroblasts cells


title: mFL_Poly_2nd


title: mFL_Poly_1st


title: mFL_Baso_3rd

value: sorted primary basophilic erythroblasts cells


title: mFL_Ortho_1st


title: mFL_Ortho_2nd


title: mFL_Baso_2nd


title: mFL_Baso_1st


title: mBM_Ortho_3rd

source_name: bone marrow

value: bone marrow


title: KOZ6DPI,8,S4

description: 10x Genomics

value: placenta

value: ZIKV


title: mBM_Ortho_1st


title: mFL_Pro_3rd

value: sorted primary Proerythroblast cells


title: mBM_Poly_3rd


title: mFL_Pro_1st


title: mFL_Pro_2nd


title: mBM_Poly_2nd


title: mBM_Baso_3rd


title: mBM_Pro_1st


title: mBM_Baso_2nd


title: mBM_Baso_1st


title: mBM_Pro_2nd


title: mBM_Poly_1st


title: mFL_CFUE_low_3rd

value: sorted primary CFU-E cells


title: mBM_Pro_3rd


title: mFL_BFUE_low_3rd

value: sorted primary BFU-E cells


title: mBM_Ortho_2nd


title: mFL_BFUE_low_2nd


title: mFL_BFUE_low_1st


title: mBM_BFUE_low_2nd


title: mBM_CFUE_low_3rd


title: mBM_BFUE_low_1st


title: mBM_CFUE_low_2nd


title: mBM_BFUE_low_3rd


title: Myofiber REST-cKO 3

city: Montreal

first: Vahab

middle: D.

last: Soleimani

state: Quebec

address: 3755 Chem. de la Côte-Sainte-Catherine

department: Lady Davis Institute for Medical Research

country: Canada

institute: Jewish General Hospital

data_processing:
Illumina BaseSpace software was used for basecalling.
Data was analysed using the GenPipes pipeline v.3.1.5 (https://academic.oup.com/gigascience/article/8/6/giz037/5513895)
Assembly: mm10
Supplementary files format and content: The bigWig files are normalized genome-wide signal coverage tracks used for visual inspection of the peaks and comparison between conditions

source_name: skeletal muscle/ EDL myofiber

extract_protocol:
Muscle Stem Cells (ITGA7+/VCAM1+/CD11b-/CD45-/CD31-/Ly6a-) were isolated by Fluorescence Activated Cell Sorting (FACS) into SMART lysis buffer. EDL muscle was dissected and myofibers were isolated as previously described (Blackburn, D.M. et al. Journal of Biological Chemistry, 2019). After isolation and selection of a single myofiber, myofibers were lysed SMART lysis buffer and libraries generated as previously described (Blackburn, D.M. et al. Journal of Biological Chemistry, 2019).
RNA-Seq libraries were made using SMART-Seq for the conversion of cDNA followed by Nextera XT for incorporation of Illumina sequencing.

value: skeletal muscle/ EDL myofiber

value: male

value: REST-cKO


title: Myoblasts REST-cKO 2

source_name: skeletal muscle/ cultured myoblasts

value: skeletal muscle/ cultured myoblasts


title: Myofiber WT 3

value: wildtype


title: Myofiber WT 1


title: Myoblasts REST-cKO 3


title: Myofiber REST-cKO 2


title: Myofiber WT 2


title: Myoblasts WT 3


title: Myofiber REST-cKO 1


title: Myoblasts REST-cKO 1


title: MuSCs REST-cKO 3

source_name: skeletal muscle/muscle stem cells

value: skeletal muscle/muscle stem cells


title: MuSCs REST-cKO 1


title: Myoblasts WT 1


title: mFL_CFUE_low_1st

value: fetal liver


title: MuSCs WT 1


title: MuSCs REST-cKO 2


title: mFL_CFUE_low_2nd

value: WT


title: MuSCs WT 3


title: Myoblasts WT 2


title: MuSCs WT 2


title: REST-cKO1_MuSCs-K27ac

data_processing:
Illumina BaseSpace software was used for basecalling.
Data was analysed using the GenPipes pipeline v.3.1.5 (https://academic.oup.com/gigascience/article/8/6/giz037/5513895)
Peaks were called using MACS2(v2.1.1)
Assembly: mm10
Supplementary files format and content: The bigWig files are normalized genome-wide signal coverage tracks used for visual inspection of the peaks and comparison between conditions
Library strategy: Cut&Tag

source_name: skeletal muscle/ muscle stem cells

extract_protocol:
45 000 Muscle stem cells (ITGA7+/VCAM1+/CD11b-/CD45-/CD31-/Ly6a-) were isolated by Fluorescence Activated Cell Sorting (FACS) into 2%FBS in PBS.
Cut&Tag was performed using the CUT&Tag-IT Assay Kit (Active Motif, 53160). The library preparation was performed by incorporation of Illumina Nextera XT adaptors.

value: skeletal muscle/ muscle stem cells


title: WT1_MuSCs-K27ac


title: mBM_CFUE_low_1st

value: no treatment


title: WT2_MuSCs-K27ac


title: REST-cKO2_MuSCs-K27ac


title: WT1_MuSCs-K4me3


title: WT2_MuSCs-K4me3


title: Myofiber_ATAC_ REST-cKO1

data_processing:
Illumina BaseSpace software was used for basecalling.
Data was analysed using the GenPipes pipeline v.3.1.5 (https://academic.oup.com/gigascience/article/8/6/giz037/5513895)
Peaks were called using MACS2(v2.1.1)
Assembly: mm10
Supplementary files format and content: The bigWig files are normalized genome-wide signal coverage tracks used for visual inspection of the peaks and comparison between conditions

extract_protocol:
Muscle Stem Cells (ITGA7+/VCAM1+/CD11b-/CD45-/CD31-/Ly6a-) were isolated by Fluorescence Activated Cell Sorting (FACS) into ATAC-Seq lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin). EDL muscle was dissected and myofibers were isolated as previously described (Blackburn, D.M. et al. Journal of Biological Chemistry, 2019). After isolation and selection of a single myofiber, myofibers were permeabilized with 0.5% Triton X-100 in PBS  for 15 minutes at room temperature (RT). The permeabilization step was followed by two washes with PBS1X. The ATAC-Seq was then performed as previously described (Sahinyan K. et al. eLife, 2022 , Sahinyan K. et al. bioProtocol, 2022).
ATAC-Seq libraries were prepared as previously described (Sahinyan K. et al. eLife, 2022 , Sahinyan K. et al. bioProtocol, 2022) with incorporation of Illumina Nextera XT adaptors.


title: Myofiber_ATAC_ WT 1


title: Myofiber_ATAC_ WT 2


title: Myofiber_ATAC_ REST-cKO2


title: KO4_MuSCs-ATAC

source_name: skeletal muscle / muscle stem cells

value: skeletal muscle / muscle stem cells


title: WT1_MuSCs-ATAC


title: WT2_MuSCs-ATAC


title: KO2_MuSCs-ATAC


title: KO3_MuSCs-ATAC


title: KO1_MuSCs-ATAC


title: Cup.rep2.Neg.Plate1.A5

city: St. Louis

first: Kia

middle: Marie

last: Barclay

email: kbarclay@wustl.edu, qingyunli@wustl.edu

address: 4370 Duncan Ave

department: Neuroscience

institute: Washington University in St. Louis

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
Assembly: mm10
Supplementary files format and content: Common delimited file (csv) containing all 2634 cells and mapped gene counts

source_name: Corpus Callosum and Striatum

extract_protocol:
Microglia (myeloid cells) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+ (microglia) gate were sorted into 96-well plates for library preparation.
Sorted microglia plates were prepared for scRNA-sequencing following the previously published Smart-seq2 protocol (Zhou et al 2019). Plates were thawed and primer annealing was performed at 72°C for 3 minutes.  Reverse transcription was performed by adding 6uL of reverse transcription mixture (95U SMARTScribe Reverse Transcriptase (100U/uL, Clontech 639538), 10U RNase inhibitor (40U/uL), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Rnase free HPLC purified) to each well (PCR protocol - at 42°C for 90 min, followed by 70°C, 5 min). DNA preamplification was done by adding 15 uL of PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/uL, New England BioLabs M0262S) to each well (PCR protocol - (1) 37°C 30 min; (2)95°C 3 min; (3) 23 cycles of 98°C 20 s, 67°C 15 s, 72°C 4 min; (4) 72°C 5 min). cDNA was cleaned using PCRClean DX beads (0.7:1 ratio, Aline C-1003-50) and resuspended in 20uL EB buffer. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6uL (1.2uL Tagment enzyme mix, 0.4uL cDNA) at 55°C, 10 min. To stop the reaction, neutralization buffer was added 0.4uL per well and incubated at room temperature for 5 min. Then 0.8uL Illumina 10-bp dual indexes (0.4uL each, 5uM) and 1.2uL PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72°C 3 min; (2) 95°C 30 s; (3) 10 cycles of 95°C 10 s, 55°C 30 s, 72°C 1 min; (4) 72°C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nova sequencing. To maximize PCR amplification efficiency for cuprizone demyelination samples, biotinylated-oligo-dT30VN oligo and biotinylated-TSO oligo were used in place of Oligo-dT30VN and TSO respectively, as described in an enhanced Smart-seq2 protocol (Gardeux et al 2022).

value: Corpus Callosum and Striatum

tag: cell line

value: Isolated Microglia

tag: condition

value: Demyelination

tag: age

value: 2 months

tag: tdtom

value: Neg


title: Cup.rep2.Neg.Plate1.D5

tag: cell type


title: WT4_MuSCs-ATAC

tag: genotype


title: Cup.rep2.Neg.Plate2.F5


title: WT3_MuSCs-ATAC


title: Cup.rep2.Neg.Plate2.A5


title: Cup.rep2.Neg.Plate2.C5


title: Cup.rep2.Neg.Plate1.B5


title: Cup.rep2.Neg.Plate2.G5


title: Cup.rep2.Neg.Plate1.C5


title: Cup.rep2.Neg.Plate2.E5


title: Cup.rep2.Neg.Plate1.F5


title: Cup.rep2.Neg.Plate2.H5


title: Cup.rep2.Neg.Plate1.F9


title: Cup.rep2.Neg.Plate1.H5


title: Cup.rep2.Neg.Plate2.A9


title: Cup.rep2.Neg.Plate2.D9


title: Cup.rep2.Neg.Plate1.A9


title: Cup.rep2.Neg.Plate1.H9


title: Cup.rep2.Neg.Plate1.G5


title: Cup.rep2.Neg.Plate2.H9


title: Cup.rep2.Neg.Plate1.E9


title: Cup.rep2.Neg.Plate2.B9


title: Cup.rep2.Neg.Plate1.D9


title: Cup.rep2.Neg.Plate2.B5


title: Cup.rep2.Neg.Plate2.G9


title: Cup.rep2.Neg.Plate2.E9


title: Cup.rep2.Neg.Plate1.B9


title: Cup.rep2.Neg.Plate1.E5


title: Cup.rep2.Neg.Plate2.C9


title: Cup.rep2.Neg.Plate1.G9


title: Cup.rep2.Neg.Plate2.D5


title: Cup.rep1.Neg.Plate1.D11


title: Cup.rep1.Neg.Plate1.A11


title: Cup.rep1.Neg.Plate1.C11


title: Cup.rep1.Neg.Plate1.E5


title: Cup.rep2.Neg.Plate2.H4


title: Cup.rep1.Neg.Plate1.G11


title: Cup.rep2.Neg.Plate1.A4


title: Cup.rep2.Neg.Plate1.C9


title: Cup.rep1.Neg.Plate1.H11


title: Cup.rep1.Neg.Plate1.B5


title: Cup.rep1.Neg.Plate1.F5


title: Cup.rep1.Neg.Plate1.D5


title: Cup.rep1.Neg.Plate1.A5


title: Cup.rep2.Neg.Plate1.B4


title: Cup.rep2.Neg.Plate2.E4


title: Cup.rep1.Neg.Plate1.F11


title: Cup.rep1.Neg.Plate1.E11


title: Cup.rep2.Neg.Plate2.F4


title: Cup.rep2.Neg.Plate2.D4


title: Cup.rep1.Neg.Plate1.H5


title: Cup.rep2.Neg.Plate2.A4


title: Cup.rep1.Neg.Plate1.G5


title: Cup.rep1.Neg.Plate1.B11


title: Cup.rep1.Neg.Plate1.C5


title: Cup.rep2.Neg.Plate2.B4


title: Cup.rep2.Neg.Plate2.C4


title: Cup.rep2.Neg.Plate1.D4


title: Cup.rep2.Neg.Plate2.G4


title: Cup.rep2.Neg.Plate1.F4


title: Cup.rep2.Neg.Plate1.G4


title: Cup.rep2.Neg.Plate1.H4


title: Cup.rep1.Neg.Plate1.A2


title: Cup.rep1.Neg.Plate1.F2


title: Cup.rep1.Neg.Plate1.E8


title: Cup.rep2.Neg.Plate1.C4


title: Cup.rep2.Neg.Plate1.E4


title: Cup.rep1.Neg.Plate1.G8


title: Cup.rep1.Neg.Plate1.H8


title: Cup.rep1.Neg.Plate1.D2


title: Cup.rep1.Neg.Plate1.B2


title: Cup.rep1.Neg.Plate1.C2


title: Cup.rep1.Neg.Plate1.E2


title: Cup.rep1.Neg.Plate1.D8


title: Cup.rep2.Neg.Plate2.H10


title: Cup.rep1.Neg.Plate1.A8


title: Cup.rep2.Neg.Plate1.A10


title: Cup.rep1.Neg.Plate1.B8


title: Cup.rep1.Neg.Plate1.F8


title: Cup.rep1.Neg.Plate1.C8


title: Cup.rep2.Neg.Plate2.E10


title: Cup.rep2.Neg.Plate1.D10


title: Cup.rep2.Neg.Plate1.B10


title: Cup.rep1.Neg.Plate1.G2


title: Cup.rep2.Neg.Plate2.B10


title: Cup.rep2.Neg.Plate1.F10


title: Cup.rep1.Neg.Plate1.H2


title: Cup.rep2.Neg.Plate2.F10


title: Cup.rep2.Neg.Plate2.C10


title: Cup.rep2.Neg.Plate2.D10


title: Cup.rep2.Neg.Plate2.A10


title: Cup.rep2.Neg.Plate1.H10


title: Cup.rep2.Neg.Plate1.E10


title: Cup.rep2.Neg.Plate2.H7


title: Cup.rep2.Neg.Plate2.G7


title: Cup.rep2.Neg.Plate1.D7


title: Cup.rep2.Neg.Plate1.A7


title: Cup.rep2.Neg.Plate1.B7


title: Cup.rep2.Neg.Plate2.G10


title: Cup.rep2.Neg.Plate2.F7


title: Cup.rep2.Neg.Plate2.E7


title: Cup.rep2.Neg.Plate2.B7


title: Cup.rep2.Neg.Plate1.G7


title: Cup.rep2.Neg.Plate2.C7


title: Cup.rep2.Neg.Plate1.E7


title: Cup.rep2.Neg.Plate1.G10


title: Cup.rep2.Neg.Plate1.C7


title: Cup.rep2.Neg.Plate2.H6


title: Cup.rep2.Neg.Plate2.G6


title: Cup.rep2.Neg.Plate1.B6


title: Cup.rep2.Neg.Plate1.D6


title: Cup.rep2.Neg.Plate1.F6


title: Cup.rep2.Neg.Plate2.F6


title: Cup.rep2.Neg.Plate2.D6


title: Cup.rep2.Neg.Plate1.C10


title: Cup.rep2.Neg.Plate2.E6


title: Cup.rep2.Neg.Plate2.F9


title: Cup.rep2.Neg.Plate2.A6


title: Cup.rep2.Neg.Plate2.A7


title: Cup.rep2.Neg.Plate1.H7


title: Cup.rep2.Neg.Plate1.H6


title: Cup.rep2.Neg.Plate1.E6


title: Cup.rep2.Neg.Plate2.B6


title: Cup.rep2.Neg.Plate2.D7


title: Cup.rep2.Neg.Plate1.F7


title: Cup.rep2.Neg.Plate2.C6


title: Cup.rep2.Neg.Plate1.C6


title: Cup.rep1.Neg.Plate1.G12


title: Cup.rep1.Neg.Plate1.H12


title: Cup.rep1.Neg.Plate1.D6


title: Cup.rep1.Neg.Plate1.B6


title: Cup.rep2.Neg.Plate1.A6


title: Cup.rep1.Neg.Plate1.F6


title: Cup.rep1.Neg.Plate1.E12


title: Cup.rep1.Neg.Plate1.F12


title: Cup.rep1.Neg.Plate1.A12


title: Cup.rep2.Neg.Plate1.G6


title: Cup.rep1.Neg.Plate1.G6


title: Cup.rep1.Neg.Plate1.B12


title: Cup.rep1.Neg.Plate1.C12


title: Cup.rep2.Neg.Plate2.H2


title: Cup.rep1.Neg.Plate1.C6


title: Cup.rep1.Neg.Plate1.A6


title: Cup.rep2.Neg.Plate1.A2


title: Cup.rep2.Neg.Plate1.D2


title: Cup.rep2.Neg.Plate1.B2


title: Cup.rep2.Neg.Plate2.G2


title: Cup.rep2.Neg.Plate1.G2


title: Cup.rep2.Neg.Plate2.A2


title: Cup.rep2.Neg.Plate2.F2


title: Cup.rep1.Neg.Plate1.D12


title: Cup.rep2.Neg.Plate2.D2


title: Cup.rep2.Neg.Plate1.E2


title: Cup.rep2.Neg.Plate1.H2


title: Cup.rep1.Neg.Plate1.E6


title: Cup.rep2.Neg.Plate2.E2


title: Cup.rep1.Neg.Plate1.H6


title: Cup.rep2.Neg.Plate1.B1


title: Cup.rep2.Neg.Plate2.H1


title: Cup.rep2.Neg.Plate2.G1


title: Cup.rep2.Neg.Plate1.F1


title: Cup.rep2.Neg.Plate2.C2


title: Cup.rep2.Neg.Plate2.F1


title: Cup.rep2.Neg.Plate1.F2


title: Cup.rep2.Neg.Plate2.D1


title: Cup.rep2.Neg.Plate2.A1


title: Cup.rep2.Neg.Plate1.D1


title: Cup.rep2.Neg.Plate2.B2


title: Cup.rep2.Neg.Plate1.G1


title: Cup.rep2.Neg.Plate1.C2


title: Cup.rep2.Neg.Plate1.H1


title: Cup.rep2.Neg.Plate1.A1


title: Cup.rep2.Neg.Plate2.B1


title: Cup.rep2.Neg.Plate1.E1


title: Cup.rep1.Neg.Plate1.H7


title: Cup.rep2.Neg.Plate2.C1


title: Cup.rep1.Neg.Plate1.G7


title: Cup.rep2.Neg.Plate1.C1


title: Cup.rep1.Neg.Plate1.D1


title: Cup.rep1.Neg.Plate1.A1


title: Cup.rep1.Neg.Plate1.A7


title: Cup.rep1.Neg.Plate1.F1


title: Cup.rep1.Neg.Plate1.F7


title: Cup.rep1.Neg.Plate1.H1


title: Cup.rep1.Neg.Plate1.B1


title: Cup.rep1.Neg.Plate1.B7


title: Cup.rep1.Neg.Plate1.E7


title: Cup.rep1.Neg.Plate1.C1


title: Cup.rep1.Neg.Plate1.D7


title: Cup.rep1.Neg.Plate1.G1


title: Cup.rep2.Neg.Plate2.G11


title: Cup.rep2.Neg.Plate2.H11


title: Cup.rep2.Neg.Plate1.D11


title: Cup.rep2.Neg.Plate1.B11


title: Cup.rep2.Neg.Plate1.F11


title: Cup.rep2.Neg.Plate2.F11