title: Young HP1gKO replicate 2 BS

city: Berlin

first: Andrew

last: Newman

address: Charitéplatz 1

department: Institute for Cell and Neurobiology

institute: Charité Universitätsmedizin Berlin

data_processing:
Reads were trimmed using Trim Galore with the following parameters:           --paired            -a AGATCGGAAGAGC            -a2 AAATCAAAAAAAC
Read adapters were trimmed using the NuGEN diversity script
6-base UMIs were moved from the index read (R2) to the 5' end of Read 1 using move_fq_seq.py.
6-base UMIs were then moved from the 5' end of Read one and appended to the read name using umi_tools.
Reads were aligned to the mm10 bisulfite converted genome using bismark with the following parameters: bismark -p 2 \               -N 1 \               --genome {params.genome_folder} \               -1 {input.read1} \               -2 {input.read2} \               --gzip \               --multicore 8
methylation was called using the bismark_methylation_extractor with --ignore_r2 3, as per Tecan guidelines
Respective oxBS bismark coverage files were subtracted from BS bismark coverage files using the R script Extract_5hmC.R
Differentially Methylated Regions (DMRs) were tested using methylkit. All Processing scripts can be seen at https://github.com/qoldt/HP1-Deficiency-Neurodegeneration
Assembly: mm10
Supplementary files format and content: Bismark Coverage files, Master dataframe of Methylkit output, dataframe of significant positions & meth.diff by sample

source_name: Hippocamus

extract_protocol:
QIAamp Fast DNA Tissue Kit cat. 51404
Tecan Ovation RRBS methylseq with oxBS
Oxidative Bisulfite Sequencing (oxBS) profiles 5mc, while normal Bisulfite Sequencing (BS) profiles 5mC + 5hmC.  True 5mC is measured and true 5hmC is inferred by subtraction.  R1 = read 1, R2 = index read, R3 = read 2

treatment_protocol: Young animals: 3-4 months, Aged Animals 14-16 months

value: Hippocamus

value: Cbx3fl/fl, EMX1Cre

value: Young


title: Young HP1gKO replicate 2 oxBS

status: Public on Jun 04 2024

type: SRA

country: Germany

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: retinal organoid, BM, day 20, clone 2, rep 1

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

country: United Kingdom

institute: UCL

library_source: transcriptomic

data_processing:
Adapter sequences and low quality scoring bases were removed using TrimGalore (v3.4). Ribosomal RNA and potential contaminating sequences were removed using SortMeRNA. Low quality sequences with PHRED quality scores below 6 were trimmed from reads using trim galore
Reads passing these quality filters were aligned using HISAT2 (v2.2.1). Alignment output BAM files were sorted by coordinate and indexed using SAMtools.
Alignment statistics including exonic mapping, intronic, intergenic and total reads mapped per sample library were reported. Gene count tables were generated for all samples using featurecounts from the subread package (v2.0.0), and differential expression analysis carried out with DESeq2 v1.34 where WALD analysis, with p-values corrected for multiple testing using the Benjamini-Hochberg method were carried out
Samples were normalised for sequencing library size, and exploratory data analysis carried out, allowing characterisation of samples via principle component analysis, distance to distance correlations and DEGs were subjected to gene ontology (GO) analysis using the Bioconductor R package GOseq (v1.32.0)488 and g:Profiler.
Data was analysed using cofactors of time, condition, clone and replicate. Gene regulatory networks were constructed using literature searches and public databases such as Enrichr and STRING
Assembly: GRCh38, annotation version 102
Supplementary files format and content: Tab-delimited text file including the raw counts of each sample
Supplementary files format and content: Tab-delimited text file including the TPM values of each sample

molecule: total RNA

organism: Homo sapiens

source_name: in vitro iPSC-derived optic vesicles

growth_protocol: Embryonic bodies (EBs) were formed from iPSC lines by culture in mTeSR1 and 10 μM Y-27632 overnight. 48hours after EB formation, EBs were cultured in Neural Induction Media (NIM), (DMEM/F12, 20% knock-out serum residue (KOSR), 2% B27, 1x Non-Essential Amino Acids (NEAA), 1% P/S, 1xGlutamax and 5 ng/mL IGF-1. Cells were cultured in NIM with decreasing KOSR concentrations, 20% from day 2-7, 15% from day 7-11 and 10% from day 11-18 with all other media components identical. From day 18, cells were cultured in Retinal Differentiation Media (DMEM/F12, 10% FBS, 2% B27, 1×NEAA, 1×Glutamax, 1% P/S, 5 ng/mL IGF-1, 0.1 mM taurine, 40 ng/mL triiodothyronine and 0.5 μM retinoic acid added immediatelybeforeuse.

extract_protocol:
Clontech SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Clontech SMART-seq v4 Ultra Low Input RNA Kit for Sequencing

tag: cell type

value: in vitro iPSC-derived optic vesicles

value: MAC

value: retinal differentiation


title: retinal organoid, BM, day 20, clone 1, rep 4


title: retinal organoid, BM, day 20, clone 1, rep 3


title: Young WT replicate 2 oxBS

value: Cbx1fl/fl, Cbx3 fl/fl


title: Young HP1gKO replicate 1 oxBS


title: Young WT replicate 2 BS


title: DC, CONTROL, M0008118-3

city: Boston

first: Maria

last: Gutierrez-Arcelus

address: 1 Blackfan Circle

country: USA

institute: Boston Children's Hospital

data_processing:
Read alignment was performed using STAR (v2.4.2) with the following parameters: -- twopassMode Basic, -- alignIntronMax 1000000, --alignMatesGapMax 1000000, --sjdbScore 2, --quantMode TranscriptomeSAM, --sjdbOverhang 24. RSEM (v1.2.21) was then used for gene quantification with paired-end mode. We used the hg38 reference genome and GENCODE annotation version 24 (Ensembl 83).
Assembly: hg38
Supplementary files format and content: counts.txt.gz is a tab-delimeted file with expected gene counts as calculated by RSEM.
Supplementary files format and content: log2tpm.txt.gz is a tab-delimeted file with the TPM values as calculated by RSEM that were then scaled to log2(tpm+1).
Supplementary files format and content: metadata.txt.gz is a tab-delimeted file with metadata for each sample.

source_name: DC

growth_protocol: Peripheral blood mononuclear cell (PBMC) samples from patients who had been infected with Mtb and either progressed to active TB disease (cases) or remained TB-disease free until sampling (controls) were separated using standard Ficoll density gradient centrifugation from 50mL of venous blood and cryopreserved at 5e6 cells/vial. PBMC samples were thawed, and CD14-expressing monocytes were magnetically sorted using the Miltenyi pan monocyte isolation kit, humans (Miltenyi) following the manufacturer’s instructions in magnetic-associated cell sorting (MACS) buffer: 0.5% bovine serum albumin, 2mM ethylene-diamine-tetra-acetic acid (EDTA) in 1X phosphate-buffered saline (PBS). To generate either monocyte-derived dendritic cells (DC) or macrophages (MP), monocytes were washed and resuspended in supplemented complete RPMI (5% fetal calf serum, 1mM 2-mercaptoethanol, penicillin-streptomycin, L-Glutamine, HEPES buffer, both essential and non-essential amino acids, and sodium hydroxide). The media was either supplemented with 300 Units/mL of granulocyte-macrophage colony stimulating factor (GM-CSF) and 200 Units/mL of interleukin (IL)-4 to generate monocyte-derived dendritic cells (DCs), or 20ng/mL of macrophage colony stimulating factor (M-CSF) to generate monocyte-derived macrophages (MPs). For both cell types, monocytes were differentiated in 6-well tissue culture plates for 6 days, then split between analytical flow cytometry to test viability and differentiation, and cell sorting to generate pure populations for RNA extraction.

extract_protocol:
Cells were lysed with TCL buffer (Qiagen).
RNA-seq library preparation was performed at the Broad Technology Labs (Broad Institute) using a modified Smart-seq protocol for low-input RNA-sequencing, which improves detection of full-length transcripts using template switching and pre-amplification. There were 3 plates of 96 samples each including blank samples. Samples from cases and controls and the two cell-types were randomized across all three plates. Sequencing was performed in an Illumina NextSeq500 as paired-end 2 x 25 bp reads with an additional 8 cycles for each index.

value: DC

tag: tb status

value: CONTROL

tag: Sex

value: M

tag: age


title: DC, CASE, M0011249-1

value: CASE

value: F


title: Young WT replicate 1 oxBS


title: Young HP1gKO replicate 1 BS


title: DC, CASE, M0012987-5


title: Young WT replicate 1 BS


title: MP, CASE, M0020202-9

source_name: MP

value: MP


title: retinal organoid, BM, day 20, clone 1, rep 2


title: Young HP1DKO replicate 2 oxBS

value: Cbx1fl/fl, Cbx3 fl/fl, EMX1Cre


title: DC, CASE, M0008346-0


title: Young HP1DKO replicate 2 BS


title: Young HP1DKO replicate 1 oxBS


title: retinal organoid, BM, day 20, clone 1, rep 1


title: Young HP1DKO replicate 1 BS


title: MP, CONTROL, M0015874-2


title: retinal organoid, PX, day 35, clone 2, rep 4

value: PAX


title: Young HP1BKO replicate 2 oxBS

value: Cbx1fl/fl, EMX1Cre


title: Young HP1BKO replicate 2 BS


title: retinal organoid, PX, day 35, clone 2, rep 3


title: Young HP1BKO replicate 1 oxBS


title: Young HP1BKO replicate 1 BS


title: Aged HP1gKO replicate 2 oxBS

value: Aged


title: retinal organoid, PX, day 35, clone 2, rep 1


title: MP, CASE, M0019365-7


title: Aged HP1gKO replicate 2 BS

value: Hippocamus


title: Aged HP1gKO replicate 1 oxBS

value: Cbx3fl/fl, EMX1Cre


title: MP, CONTROL, M0019745-0


title: Aged HP1gKO replicate 1 BS


title: MP, CONTROL, M0013027-9


title: retinal organoid, PX, day 35, clone 1, rep 4


title: retinal organoid, PX, day 35, clone 1, rep 3


title: Aged WT replicate 2 oxBS

value: Cbx1fl/fl, Cbx3fl/fl


title: Aged WT replicate 2 BS


title: Aged WT replicate 1 oxBS


title: DC, CASE, M0022752-1


title: Aged WT replicate 1 BS


title: Aged HP1DKO replicate 2 oxBS


title: DC, CONTROL, M0009548-0


title: retinal organoid, PX, day 35, clone 1, rep 2

value: in vitro iPSC-derived optic vesicles


title: Aged HP1DKO replicate 2 BS

value: Cbx1fl/fl, Cbx3fl/fl, EMX1Cre


title: MP, CONTROL, M0006618-4


title: Aged HP1DKO replicate 1 oxBS


title: retinal organoid, PX, day 35, clone 1, rep 1

value: retinal differentiation


title: retinal organoid, PX, day 35, clone 2, rep 2


title: retinal organoid, PX, day 20, clone 2, rep 4


title: Aged HP1DKO replicate 1 BS


title: MP, CONTROL, M0023354-5


title: retinal organoid, PX, day 20, clone 2, rep 3


title: Aged HP1BKO replicate 2 oxBS


title: Aged HP1BKO replicate 1 oxBS


title: DC, CONTROL, M0017901-1


title: retinal organoid, PX, day 20, clone 2, rep 2


title: Aged HP1BKO replicate 1 BS


title: DC, CASE, M0010368-0


title: DC, CONTROL, M0013027-9


title: MP, CASE, M0008723-0


title: retinal organoid, PX, day 20, clone 2, rep 1


title: retinal organoid, PX, day 20, clone 1, rep 4


title: MP, CONTROL, M0008325-4


title: mESC_DKO_WGBS_rep1

city: Grand Rapids

first: Gerd

middle: P.

last: Pfeifer

state: Michigan

address: 333 Bostwick Ave. NE.

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Paired-end reads were trimmed using Trim_Galore(version 0.6.7) with the following parameters : --length 50, --clip_R1 10, --clip_R2 18, --three_prime_clip_R1 10, and --three_prime_clip_R2 10.
Trimmed reads were aligned to the mm10 using Bismark version 0.19.0 and Bowtie2 (v2.3.3.1) with the following parameters: -X 1000, --nucleotide_coverage and --bowtie2.
Duplication were removed using the deduplicate_bismark script provided with Bismark.
CpG methylation values were called by the bismark_methylation_extractor script provided with Bismark and the following parameters: --no_overlap, --comprehensive, --merge_non_CpG, and --cytosine_report.
Methylation of CpG tracks for IGV browser were generated with bigwig tools.
Assembly: mm10
Supplementary files format and content: bigwig, methylation coverage

growth_protocol: J1 mouse embryonic stem cells (mESCs) were grown on gelatin-coated plates without feeder cell layers in knockout DMEM supplemented with 15% (v/v) ES-qualified fetal bovine serum (FBS), 1x non-essential amino acids, 2 mM L-glutamine, 100 mM b-mercaptoethanol, and 1,000 U/ml LIF at 37°C in a 5% CO2 standard incubator.

extract_protocol:
Genomic DNA was extracted using a Quick-DNA Miniprep Plus kit (Zymo Research, D4070).
The Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024) was used according to the manufacturer’s instructions to perform bisulfite conversion and library preparation.

tag: cell line

value: mESC

value: CXXC4 and CXXC5 knockout


title: mESC_WT_WGBS_rep2

value: Wildtype


title: mESC_DKO_WGBS_rep2


title: mESC_WT_WGBS_rep1


title: retinal organoid, PX, day 20, clone 1, rep 3


title: DC, CASE, M0009777-5

value: DC


title: Neuron_Day9_DKO_RNA_rep2

data_processing:
Quality and adaptor trimming of Fastq files were performed using Trim_Galore v.0.6.7
The reads were aligned to the mouse reference genome (mm10) and counted with HISAT2 (version 2.2.1) provided on the Galaxy web platform.
Differential gene expression was analyzed using DESeq2 (Galaxy Version 2.11.40.8) provided on the Galaxy web platform.
Assembly: mm10
Supplementary files format and content: bigwig, counts coverage

molecule: polyA RNA

extract_protocol:
Total RNAs were isolated from the cells with PureLink RNA Mini Kit according to the manufacturer's protocol. RNA quality was evaluated with Bioanalyzer 2100.
The RNA-seq libraries were prepared with the KAPA RNA HyperPrep kit according to the manufacturer’s instructions

treatment_protocol: To neuronal differentiation, mESCs were cultured on bacterial dishes in medium lacking LIF and with 10% FBS to induce the formation of embryoid body (EB) for 4 days followed by additional incubation in culture medium with 5 μM retinoic acid (RA) for 4 days. The RA treated cells were trypsinized and plated on PORN/laminin-coated plates. The cells were further cultured for 2 days in N2 medium (DMEM/F12 mixture, 1:1 with 1x N2 supplement) and 7 days in B27 media.

value: Retinoic Acid treatment


title: Neuron_Day9_WT_RNA_rep1


title: Neuron_Day9_DKO_RNA_rep1


title: DC, CONTROL, M0010961-2

value: CONTROL

value: M


title: Neuron_Day9_WT_RNA_rep2


title: retinal organoid, PX, day 20, clone 1, rep 2


title: mESC_DKO_RNA_rep2


title: Aged HP1BKO replicate 2 BS


title: mESC_DKO_RNA_rep1


title: mESC_WT_RNA_rep2


title: MP, CONTROL, M0011972-8

value: MP

value: F


title: retinal organoid, PX, day 20, clone 1, rep 1

value: PAX


title: mESC_WT_RNA_rep1


title: B4GALNT1 KO LPS+CTB #3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA 3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: peritoneal cavity

extract_protocol:
Total RNA was extracted with RNeasy micro kit (QIAGEN).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina) or a combination of SMART-Seq HT Kit (Takara Bio, Japan) and NexteraXT DNA Library Preparation Kit (Illumina).

value: peritoneal cavity

value: resident peritoneal macrophages

value: LPS+CTB culture


title: MP, CASE, M0010648-5

value: CASE


title: B4GALNT1 KO LPS+CTB #2


title: B4GALNT1 KO LPS+CTB #1


title: MP, CASE, M0021316-6


title: MP, CASE, M0018532-3


title: B4GALNT1 KO LPS+CT #2

value: LPS+CT culture


title: retinal organoid, control, day 35, clone 2, rep 1

value: in vitro iPSC-derived optic vesicles

value: WT


title: B4GALNT1 KO LPS #3

value: LPS culture


title: B4GALNT1 KO LPS #2


title: B4GALNT1 KO LPS+CT #1


title: retinal organoid, control, day 35, clone 2, rep 2

value: retinal differentiation


title: B4GALNT1 KO LPS+CT #3


title: B4GALNT1 KO LPS #1


title: DC, CONTROL, M0013569-0


title: DC, CONTROL, M0023045-9


title: Wildtype LPS＋CTB #3

value: Wildtype


title: DC, CASE, M0009274-3

value: DC


title: retinal organoid, control, day 35, clone 1, rep 3


title: retinal organoid, control, day 35, clone 2, rep 4


title: retinal organoid, control, day 35, clone 1, rep 4


title: Wildtype LPS＋CTB #1


title: retinal organoid, control, day 35, clone 2, rep 3


title: Wildtype LPS＋CT #4


title: retinal organoid, control, day 35, clone 1, rep 2


title: DC, CONTROL, M0007170-5


title: Wildtype LPS＋CT #3


title: Wildtype LPS＋CT #2


title: MP, CONTROL, M0007170-5


title: DC, CONTROL, M0012538-6


title: Wildtype LPS＋CT #1


title: retinal organoid, control, day 20, clone 2, rep 4


title: DC, CONTROL, M0007827-0


title: Wildtype LPS #4


title: MP, CASE, M0017483-0


title: retinal organoid, control, day 20, clone 2, rep 3


title: Wildtype LPS #3


title: Wildtype LPS #2


title: Wildtype LPS #1


title: DC, CONTROL, M0011766-4


title: retinal organoid, control, day 20, clone 2, rep 2


title: LPS+CTB_1


title: DC, CONTROL, M0006310-8


title: LPS+CT_2


title: DC, CONTROL, M0017830-2


title: retinal organoid, control, day 20, clone 2, rep 1


title: LPS+CT_1


title: retinal organoid, control, day 20, clone 1, rep 4


title: MP, CONTROL, M0017901-1


title: LPS+CTB_2


title: Wildtype LPS＋CTB #2


title: retinal organoid, control, day 35, clone 1, rep 1


title: LPS_2


title: retinal organoid, control, day 20, clone 1, rep 3


title: MP, CASE, M0009274-3


title: NAIVE,10 ug/ml,ATAC-seq, rep3

city: Beijing

first: Hai

last: Qi

address: Haidian District

country: China

institute: Tsinghua University

data_processing:
ATAC-seq reads were trimmed from 3'end until the final base had a quality score >20, using trim_galore (v0.6.6), discarding reads left with <20 bp
Trimmed reads were firstly aligned to the mouse genome (NCBI build 37, mm9) using the bowtie2 program with default parameters.
Mappable reads were further processed by samtools (v1.3.1). Duplicates were removed using picard-tools-1.114.
Peaks were called using the MACS program with default settings followed by a detailed analysis by bedtools (v2.27.1).
Track files were generated by samtools (v1.3.1). The score represents CPM (number of reads per bin/number of mapped reads (in millions))
Assembly: mm9
Supplementary files format and content: bigWig

source_name: spleen

extract_protocol:
Three unimmunized mice were used for B cell isolation. Splenocyte single cell suspensions were generated by crushing spleens in MACS buffer (PBS supplemented with 1% FBS and 5 mM EDTA). Cells were filtered through 70 uM nylon mesh and washed at 1700 RPM, 4 ⁰C, 5 minutes. Pellets were resuspended in RT ACK lysis buffer and incubated RT for 3 minutes, followed by addition of 5-10 volumes of MACS buffer and washing at 1700 RPM, 4 ⁰C, 5 minutes. B cells were then isolated by CD19 Microbeads (Miltenyi Biotec). CD19+ cells were then cultured in the presence of indicated stimuli for 2 h at 37°C before being harvested for ATAC-seq.
ATAC-seq was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® (TD502, Vazyme Biotech). Briefly, around 5,000-10,000 sorted cells in 5 μl were lysed in 50 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) for 10 min on ice. Lysed nuclei were then incubated with the Tn5 transposase and tagmentation buffer at 37 °C for 30 min. Fragmented DNA was purified using 2× VAHTS DNA Clean Beads (Vazyme Biotech) following manufacturer’s instructions. PCR was performed to amplify the library for 15 cycles using the following PCR conditions: 72 °C for 3 minutes; 98 °C for 30 seconds; thermocycling at 98 °C for 15 seconds, 60 °C for 30 seconds and 72 °C for 30 seconds; then 72 °C for 5 min. After the PCR reaction, libraries were purified with 1.2× beads and sent for high-throughput sequencing.

value: spleen

value: CD19+ B cells

value: 10 ug/ml anti IgM for 2 hrs


title: NAIVE,10 ug/ml,ATAC-seq, rep2


title: retinal organoid, control, day 20, clone 1, rep 2


title: NAIVE,10 ug/ml,ATAC-seq, rep1


title: MP, CASE, M0009421-0

value: MP


title: MP, CONTROL, M0016539-0

value: CONTROL

value: M


title: retinal organoid, control, day 20, clone 1, rep 1


title: NAIVE,0.1 ug/ml,ATAC-seq, rep3

value: 0.1 ug/ml anti IgM for 2 hrs


title: MP, CONTROL, M0025011-9

value: F


title: NAIVE,untreated,ATAC-seq, rep3

value: Untreated


title: NAIVE,0.1 ug/ml,ATAC-seq, rep1


title: MP, CASE, M0014277-9

value: CASE


title: tdTomato-,LZGC, D21,ATAC-seq, rep2

extract_protocol:
10-20 mice were used for cell-sorting in each experiment. Splenocyte single cell suspensions were generated by crushing spleens in MACS buffer (PBS supplemented with 1% FBS and 5 mM EDTA). Cells were filtered through 70 uM nylon mesh and washed at 1700 RPM, 4 ⁰C, 5 minutes. Pellets were resuspended in RT ACK lysis buffer and incubated RT for 3 minutes, followed by addition of 5-10 volumes of MACS buffer and washing at 1700 RPM, 4 ⁰C, 5 minutes. Single-cell suspension of splenocytes was stained in MACS buffer containing Fc blocker (supernatant from 2.4G2 cell culture) for 20 min on ice before surface staining with primary antibodies in appropriate concentrations on ice for 25 min. Cells were washed again with 5-10 volumes of MACS, and resuspended in MACS for analysis on BD Aria II.
ATAC-seq was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® (TD502, Vazyme Biotech). Briefly, around 5,000-10,000 sorted cells in 5 μl were lysed in 50 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) for 10 min on ice. Lysed nuclei were then incubated with the Tn5 transposase and tagmentation buffer at 37 °C for 30 min. Fragmented DNA was purified using 2× VAHTS DNA Clean Beads (Vazyme Biotech) following manufacturer’s instructions. PCR was performed to amplify the library for 15 cycles using the following PCR conditions: 72 °C for 3 minutes; 98 °C for 30 seconds; thermocycling at 98 °C for 15 seconds, 60 °C for 30 seconds and 72 °C for 30 seconds; then 72 °C for 5 min. After the PCR reaction, libraries were purified with 1.2× beads and sent for high-throughput sequencing.

value: S1pr2-creERT2, Rosa26-Ai14, C57BL/6

value: NP-KLH/LPS/Alum 21dpi


title: NAIVE,untreated,ATAC-seq, rep1


title: MP, CONTROL, M0008905-3


title: LPS_1

value: peritoneal cavity

value: resident peritoneal macrophages


title: embryonic liver , DNAJ1B-PKA_Overexpression-S7

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

country: Austria

institute: Medical University of Vienna

description:
OE-S7
embryonicliverprocessed_data.txt

data_processing:
Read were mapped against mm10 with STAR version 2.5.1b. Gene counts were normalized using DEseq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts and FPM

source_name: embryonic liver

extract_protocol:
total RNA
Poly-A enrichment RNA library

value: embryonic liver


title: embryonic liver , DNAJ1B-PKA_Overexpression-S8

description:
OE-S8
embryonicliverprocessed_data.txt


title: embryonic liver , DNAJ1B-PKA_Overexpression-S9

description:
OE-S9
embryonicliverprocessed_data.txt


title: tdTomato-,LZGC, D21,ATAC-seq, rep1


title: embryonic liver , DNAJ1B-PKA_Overexpression-S6

description:
OE-S6
embryonicliverprocessed_data.txt


title: tdTomato-, LZGC, D10,ATAC-seq, rep2

value: NP-KLH/LPS/Alum 10dpi


title: tdTomato-, LZGC, D10,ATAC-seq, rep1


title: RT_3

first: Chuan

last: Ye

address: 38 Xueyuan Road, Haidian District

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling. Trim-galore v0.6.7 was used for adapter trimming and low-quality reads. Clean reads mapping was conducted by Hisat2 v2.2.1, and mm10 was used as mouse reference genome. Gene expression was quantified by featureCounts v2.0.1.
Assembly: mm10
Supplementary files format and content: For RNA-Seq data, an Excel file contain count values for each gene of each sample.

source_name: Intestinal epithelia

growth_protocol: Mice were pretreated with antibiotics for 3 days, then mice were fed with a high-fat diet and gavaged with PBS or R. torques (108 CFU/mouse) every 3 days for 2 weeks. Finally the intestinal epithelia was collected.

extract_protocol:
The polyA mRNA isolation was performed using Oligo(dT) beads
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestinal epithelia

value: R. torques gavage


title: MP, CASE, M0014546-7


title: NAIVE,0.1 ug/ml,ATAC-seq, rep2

value: spleen

value: CD19+ B cells


title: RT_2


title: RT_1


title: retinal organoid, BM, day 20, clone 2, rep 3

value: in vitro iPSC-derived optic vesicles

value: MAC

value: retinal differentiation


title: NAIVE,untreated,ATAC-seq, rep2


title: Control_2

value: PBS gavage


title: embryonic liver , control-S4

description:
control-S4
embryonicliverprocessed_data.txt

value: control


title: Control_1


title: MP, CONTROL, M0009885-6

value: MP

value: CONTROL

value: F


title: Blm_nit3

first: Yunshu

last: Wu

address: No.22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

data_processing:
CLC Genomics Workbench v.11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction seuqencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: skin

value: tissue

value: WT


title: Control_3


title: embryonic liver , control-S2

description:
control-S2
embryonicliverprocessed_data.txt

value: embryonic liver


title: MP, CASE, M0015230-7

value: CASE

value: M


title: MP, CASE, M0021395-0


title: Blm_nit2


title: embryonic liver , control-S5

description:
control-S5
embryonicliverprocessed_data.txt


title: embryonic liver , control-S1

description:
control-S1
embryonicliverprocessed_data.txt


title: Blm3


title: Blm2


title: MP, CASE, M0012604-6


title: embryonic liver , control-S3

description:
control-S3
embryonicliverprocessed_data.txt


title: AML_NY

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
All samples raw reads were mapped and counted with cell ranger version 3.0.2 to the Human genome GRCh38.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell ranger generated one mtx file and two tsv files for gene ID and cell barcode ID

source_name: Immune cell fraction

extract_protocol:
The mononuclear fractions after Ficoll gradient separation were FACS sorted for CD34-CD45+ fraction and processed using 10x Genomics Single Cell Kit (v2 or v3) according to manufacturer’s recommendations.
Reads were sequenced using 150bp PE reads on the Illumina HiSeq 4000 or NextSeq 500/550.

value: bone marrow

tag: disease state

value: Denovo acute myeloid leukemia

tag: gender

value: male


title: ctrl3


title: Healthy_NY

value: Healthy


title: DC, CASE, M0024566-3

value: DC


title: MP, CONTROL, M0010687-3


title: ctrl1


title: MP, CONTROL, M0011710-2


title: ctrl2


title: Knockout, Ai3+ MBC, D30, rep4

data_processing:
RNA-seq reads were trimmed from 3'end until the final base had a quality score >20, using trim_galore (v0.6.6), discarding reads left with <20 bp
Trimmed reads were mapped to the mouse genome (mm10) through STAR v2.2.0 with default settings.
Read count extraction was performed  using STAR v2.2.0
FeatureCounts software was used to collect reads located in the coding sequence (CDS) of each gene. CDS counts normalized to mappable reads were used for measuring gene expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized CDS counts for each sample

extract_protocol:
5 mice were used for cell-sorting in each experiment. Splenocyte single cell suspensions were generated by crushing spleens in MACS buffer (PBS supplemented with 1% FBS and 5 mM EDTA). Cells were filtered through 70 uM nylon mesh and washed at 1700 RPM, 4 ⁰C, 5 minutes. Pellets were resuspended in RT ACK lysis buffer and incubated RT for 3 minutes, followed by addition of 5-10 volumes of MACS buffer and washing at 1700 RPM, 4 ⁰C, 5 minutes. Single-cell suspension of splenocytes was stained in MACS buffer containing Fc blocker (supernatant from 2.4G2 cell culture) for 20 min on ice before surface staining with primary antibodies in appropriate concentrations on ice for 25 min. Cells were washed again with 5-10 volumes of MACS, and resuspended in MACS for analysis on BD Aria II. Approximately 200 cells of desired type were sorted into 6 μl lysis buffer (0.2% Triton X-100 and 2 U/μl of RNase inhibitor).
Lysates were mixed with 3 μl of anchored oligo-dT primer (10 μM, 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 μl of dNTP mix (10 mM, Fermentas), denatured at 72 °C for 3 min and immediately placed on ice afterwards. The first-strand reaction mix containing 1 μl SuperScript II reverse transcriptase (Invitrogen), 0.5 μl RNAse inhibitor (Clontech), 4 μl Superscript II First-Strand Buffer (Invitrogen), 1 μl DTT (100 mM, Invitrogen), 4 μl betaine (5 M, Sigma), 0.12 μl MgCl2 (1 M, Sigma), 0.2 μl TSO (100 μM) and 0.58 μl nuclease-free water, were added to each sample. Reverse transcription reaction was carried out by incubating at 42 °C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min). Finally, the reverse transcriptase was inactivated by incubation at 70 °C for 15 min. PCR mix containing 25 μl KAPA HiFi HotStart ReadyMix, 0.5 μl IS PCR primers (10 μM) and 1.1 μl nuclease-free water were added to each sample. The reaction was incubated at 98 °C for 3 min, then cycled 17 times (98 °C 20 s, 67 °C 15 s, 72 °C 6 min), with a final extension at 72 °C for 5 min. cDNAs were purified by Vazyme DNA clean beads following manufacturer's instructions. 1 ng of cDNA were used for the tagmentation reaction using Tn5 (Vazyme). The tagmentation reaction (20 μl) was incubated at 55 °C for 10 min and stopped by addition of 2 μl 0.2%SDS and incubated at 70 °C for 20 min. A second amplification was performed using Q5 polymerase (NEB) as follows: 72 °C 3 min, 98 °C 30 s, then 12 cycles of (98 °C 15 s, 60 °C 30 s, 72 °C 3 min), final extension at 72 °C 5 min. Libraries were purified using Vazyme DNA clean beads.

value: spleen

value: B220+CD138-GL7-FAS-CD38+ NIP-binding B cells

value: NP-KLH/LPS/Alum 30dpi


title: Knockout, Ai3+ MBC, D30, rep3


title: DC, CASE, M0022181-3


title: Knockout, Ai3+ MBC, D30, rep2


title: Knockout, Ai3+ MBC, D30, rep1


title: Blm_nit1


title: MP, CONTROL, M0008363-5

value: MP


title: Wildtype, Ai3+ MBC, D30, rep4


title: Col-0, cold (4°C), 12h, Bio Replicate 1

city: Umea

first: Peter

last: Kindgren

state: Vasterbotten

address: KB5C5, KBC building, Linnaeus väg 6

department: Department of Forest Genetics and Plant Physiology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
UPSC pipeline was used to generare salmon files. More information can be found at doi: 10.5281/zenodo.4001773.
Trimmmomatic was used to trim adapter sequences and SortMeRNA was used to remove rRNA contamination.
FastQC was used to monitor the quality of reads at each step. Salmon was used to determine the read counts with AtRTD2 as reference.
Salmon files generated above were used for differential gene expression analysis using Deseq2
Assembly: Araport11
Supplementary files format and content: Salmon files

organism: Arabidopsis thaliana

source_name: 10-day seedling

growth_protocol: Seeds were surface sterilized and stratified at 4°C for 48-72h in the dark. Growth media constituted of 1/2 MS media.

extract_protocol:
RNA was isolated using RNeasy Plant mini kit (Qiagen). Isolated RNA was treated with TURBO DNAse to remove DNA contamination.
Strand specific libraries were prepared by Novogene Europe.

treatment_protocol: 12 day old seedlings were subjected to 4°C cold stress and samples were collected after 12h.

value: 10-day seedling

value: Cold

tag: time


title: MP, CASE, M0017541-5


title: DC, CASE, M0018455-7


title: Blm1

value: skin


title: Col-0, cold (4°C), 3h, Bio Replicate 3


title: Naive, knockout, rep3

extract_protocol:
One mouse was used for cell-sorting in each experiment. Splenocyte single cell suspensions were generated by crushing spleens in MACS buffer (PBS supplemented with 1% FBS and 5 mM EDTA). Cells were filtered through 70 uM nylon mesh and washed at 1700 RPM, 4 ⁰C, 5 minutes. Pellets were resuspended in RT ACK lysis buffer and incubated RT for 3 minutes, followed by addition of 5-10 volumes of MACS buffer and washing at 1700 RPM, 4 ⁰C, 5 minutes. Single-cell suspension of splenocytes was stained in MACS buffer containing Fc blocker (supernatant from 2.4G2 cell culture) for 20 min on ice before surface staining with primary antibodies in appropriate concentrations on ice for 25 min. Cells were washed again with 5-10 volumes of MACS, and resuspended in MACS for analysis on BD Aria II. Approximately 200 cells of desired type were sorted into 6 μl lysis buffer (0.2% Triton X-100 and 2 U/μl of RNase inhibitor).
Lysates were mixed with 3 μl of anchored oligo-dT primer (10 μM, 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 μl of dNTP mix (10 mM, Fermentas), denatured at 72 °C for 3 min and immediately placed on ice afterwards. The first-strand reaction mix containing 1 μl SuperScript II reverse transcriptase (Invitrogen), 0.5 μl RNAse inhibitor (Clontech), 4 μl Superscript II First-Strand Buffer (Invitrogen), 1 μl DTT (100 mM, Invitrogen), 4 μl betaine (5 M, Sigma), 0.12 μl MgCl2 (1 M, Sigma), 0.2 μl TSO (100 μM) and 0.58 μl nuclease-free water, were added to each sample. Reverse transcription reaction was carried out by incubating at 42 °C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min). Finally, the reverse transcriptase was inactivated by incubation at 70 °C for 15 min. PCR mix containing 25 μl KAPA HiFi HotStart ReadyMix, 0.5 μl IS PCR primers (10 μM) and 1.1 μl nuclease-free water were added to each sample. The reaction was incubated at 98 °C for 3 min, then cycled 17 times (98 °C 20 s, 67 °C 15 s, 72 °C 6 min), with a final extension at 72 °C for 5 min. cDNAs were purified by Vazyme DNA clean beads following manufacturer's instructions. 1 ng of cDNA were used for the tagmentation reaction using Tn5 (Vazyme). The tagmentation reaction (20 μl) was incubated at 55 °C for 10 min and stopped by addition of 2 μl 0.2%SDS and incubated at 70 °C for 20 min. A second amplification was performed using Q5 polymerase (NEB) as follows: 72 °C 3 min, 98 °C 30 s, then 12 cycles of (98 °C 15 s, 60 °C 30 s, 72 °C 3 min), final extension at 72 °C 5 min. Libraries were purified using Vazyme DNA clean beads.

value: B220+CD138-GL7-FAS-IgM+ B cells


title: Wildtype, Ai3+ MBC, D30, rep3


title: Wildtype, Ai3+ MBC, D30, rep2


title: Col-0, cold (4°C), 3h, Bio Replicate 2

value: WT


title: Wildtype, Ai3+ MBC, D30, rep1


title: Col-0, cold (4°C), 3h, Bio Replicate 1


title: Naive, knockout, rep1


title: MP, CONTROL, M0010508-1

value: CONTROL


title: Naive, knockout, rep2


title: Col-0, cold (4°C), 12h, Bio Replicate 3


title: Naive, wildtype, rep3


title: Col-0, cold (4°C), 12h, Bio Replicate 2


title: Naive, wildtype, rep1


title: Col-0, control (22°C), 0h, Bio Replicate 3

value: Control


title: Naive, wildtype, rep2


title: Induced, tdTomato+ MBC, D7, rep4

value: B220+CD138-GL7-FAS-CD38+ NP-binding B cells

value: NP-OVA/LPS/Alum 7dpi


title: Col-0, control (22°C), 0h, Bio Replicate 1


title: HCC1143, 72 hour Paclitaxel

city: Portland

first: Laura

last: Heiser

state: Oregon

address: 2730 S. Moody Ave

department: BME

institute: OHSU

description: 10x Genomics Single Cell 3' v2

library_source: transcriptomic single cell

data_processing:
BCL files were converted to fastq using the bamtofastq tool (Illumina). Reads were aligned to GRCh38-2020-A and counted using CellRange (v6.0.2, 10X Genomics) to produce bam file and count matrices.
Assembly: GRCh38-2020-A
Supplementary files format and content: Both filtered (cell containing) and raw (all droplet) feature_bc_matrix.h5 files output from Cellranger 6.0.2

growth_protocol: Cells were cultured in RPMI supplemented with 10% FBS

extract_protocol:
Media was aspirated and cells were washed twice with PBS. Cells were incubated in TrypLE Express for approximately 5 minutes until detached from the well surface, then gently titurated before enzyme neutralization (10% FBS in PBS). Cells were spun at 300xG for 5 minutes and then resuspended in PBS for library preparation (LH2400, LH2401, LH7200, LH7201) or HTO staining (CEL190419LH) following manufacturer protocol (TotalSeq-A, BioLegend).
LH2400, LH2401, LH7200, LH7201: Libraries were prepared following manufacturer protocol (10X Genomics Single Cell 3' v2). CEL190419LH: Libraries were prepared for both single-cell RNA and antibody feature following manufacturer protocol (10X Genomics Single Cell 3' v3).

treatment_protocol: Cells were plated 24 hours prior to treatment in RPMI supplemented with 2% FBS. At the treatment timepoint, perturbation containing media was added such that it doubled the culture volume and maintained 2% FBS.

value: Ductal Carcinoma

value: 1nM Paclitaxel (72 hours)


title: HD BM-MNC

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: 10x Genomics

data_processing:
Preliminary analysis using the 10X Genomics pipeline relying on cellranger (base calling, alignment, feature count) using default parameters
Filtering, Normalization, Scaling using the R package Seurat
Identification of clusters using the Louvain algorithm provided by the R package Seurat
Identification of cell types annotations using SingleR algorithm
Identification of differentially expressed genes using the MAST algorithm provided by the R package Saurat
Assembly: GRCh38
Supplementary files format and content: Sparse Cellranger matrix

source_name: blood

extract_protocol:
Droplet-based digital 3′ end scRNA-Seq was performed on a Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s instructions. Single cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (12-14 cycles, according to the available cDNA quantity).
scRNA-Seq libraries were prepared according to the manufacturer’s instructions

value: blood

value: bone marrow-derived mononuclear cells

value: untreated


title: Induced, tdTomato+ MBC, D7, rep3

value: spleen


title: SAVI BM-MNC

description: 10x Genomics

value: STING1 (c.806T>C)


title: Induced, tdTomato+ MBC, D7, rep2


title: Uninduced, tdTomato+ MBC, D7, rep4


title: DC, CASE, M0021711-8

value: DC

value: CASE

value: M


title: Induced, tdTomato+ MBC, D7, rep1


title: mP4_E+G_Week12_Res45

city: Copenhagen

first: Yifan

last: Dai

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: Copenhagen University

description: Drug Acute

data_processing:
Fastqc (version 0.11.5) and Multiqc (version 1.748) were used to investigate potential RNA-Seq library (paired-end) artifacts.
The 13 bp 5' adapter sequences in all the libraries were removed using Trim Galore (0.4.4) with the options '–paired –clip_R1 13 –clip_R2 13'.
Salmon (1.3.0) with the parameters '-l IU' was used to map the adapter-trimmed reads on the mouse transcriptome (M25 GRCm38.p6 Gencode release50).
Read Counts and TPM values are extracted from Salmon output.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with counts values for each sample
Supplementary files format and content: tab-delimited text files with TPM values for each sample

growth_protocol: mP4 (PanIN) mouse pancreatic cancer organoids were cultured in 24 well plates (BioLite Multidish, Thermo Fisher Scientific, #930186), suspended in a 50 µL dome of Matrigel (Matrigel Growth Factor Reduced, Phenol Red Free, Corning, # 356231). They were fed with 500 µl Mouse Complete Feeding Medium 26 that was changed every 3-4 days. Organoids were split according to the Tuveson lab protocol approximately twice a week.

extract_protocol:
Organoid cultures (3-4 50 µl domes/condition) were harvested with cold Cell Recovery Solution (Corning, 354253) and incubated on ice for 30 minutes to dissolve Matrigel and release the cells. RNA from the organoid pellets was isolated and purified using RNeasy Mini Kit (QIAGEN, 74106) according to the manufacturer's protocol, including DNase digestion step. RNA concentration was measured using NanoDrop 2000 spectrophotometer and samples were stored at –80°C.
RNA-seq libraries were prepared following the standard protocol of DNBSEQ

treatment_protocol: Organoids were treated with the indicated concentrations (nM) of Erlotinib (E), Gemcitabine (G), or both drugs in combination (E+G) for 5 days in Growth Medium.

value: Pancreatic Ductal Cells

value: Kras G12D/-

value: E+G

value: Week 12

tag: ph


title: Uninduced, tdTomato+ MBC, D7, rep3


title: Uninduced, tdTomato+ MBC, D7, rep2


title: HCC1143, 72 hour DMSO

description: 10x Genomics Single Cell 3' v2

value: 0.1percent  DMSO (72 hours)


title: mP4_E+G_Week12_Res44

description: Drug Acute


title: HCC1143, 24 hour Paclitaxel

description: 10x Genomics Single Cell 3' v2

value: 1nM Paclitaxel (24 hours)


title: Col-0, control (22°C), 0h, Bio Replicate 2

value: 10-day seedling

value: WT

value: Control


title: Uninduced, tdTomato+ MBC, D7, rep1

value: B220+CD138-GL7-FAS-CD38+ NP-binding B cells

value: NP-OVA/LPS/Alum 7dpi


title: Knockout, tdTomato+ MBC, D7, rep4


title: HCC1143, 24 hour DMSO

description: 10x Genomics Single Cell 3' v2

value: Ductal Carcinoma

value: 0.1percent  DMSO (24 hours)


title: mP4_G_Week12_Res42

description: Drug Acute

value: G


title: Knockout, tdTomato+ MBC, D7, rep1

value: spleen


title: Knockout, tdTomato+ MBC, D7, rep2


title: Heterozygous, tdTomato+ MBC, D7, rep4


title: mP4_G_Week12_Res41

description: Drug Acute


title: Knockout, tdTomato+ MBC, D7, rep3


title: mP4_G_Week12_Res40

description: Drug Acute


title: Heterozygous, tdTomato+ MBC, D7, rep2


title: Heterozygous, tdTomato+ MBC, D7, rep1


title: mP4_E_Week12_Res39

description: Drug Acute

value: E


title: mP4_E_Week12_Res38

description: Drug Acute


title: 14_DNMT3A-CD4-2_S205_R1

city: Chengdu

first: Hui

last: WANG

state: Sichuan

address: No.14,3Rd Section Of Ren Min Nan Rd

department: periodontics

institute: Sichuan University

data_processing:
quality of the data checked using FastQC
alignment using Biscuit
DMR analysis by metilene
Assembly: mm10
Supplementary files format and content: html file for FastQC
Supplementary files format and content: gzip file for metilene
Supplementary files format and content: flagstat file for Biscuit

extract_protocol:
High-Molecular-Weight (HMW) DNA of cells were isolated using MagAttract HMW DNA Kit according to the manufacturer’s instructions (Qiagen)
WGBS was performed using the Zymo-Seq WGBS Library Kit (Zymo research) according to the manufacturer’s recommendations at the High Throughput Sequencing Core of Children’s Hospital of Philadelphia, PA, USA

value: CD4+ cells


title: 16_DNMT3A-CD4-4_S207_R1


title: mP4_E_Week12_Res37

description: Drug Acute

value: Pancreatic Ductal Cells


title: mP4_E+G_Week12_Res36

description: Drug Adaptation

value: Kras G12D/-


title: 12_WT-CD4-4_S120_R1


title: 11_WT-CD4-3_S119_R1


title: mP4_E+G_Week12_Res43

description: Drug Acute

value: E+G


title: 13_DNMT3A-CD4-1_S204_R1


title: 09_WT-CD4-1_S118_R1


title: 08_DNMT3A-CD11b-4_S117_R1

value: CD11b+ cells


title: 10_WT-CD4-2_S203_R1


title: 08_DNMT3A-CD11b-4_S202_R1


title: 05_DNMT3A-CD11b-1_S114_R1


title: 07_DNMT3A-CD11b-3_S116_R1


title: 04_WT-CD11b-4_S113_R1


title: 06_DNMT3A-CD11b-2_S115_R1


title: 07_DNMT3A-CD11b-3_S201_R1


title: mP4_G_Week12_Res31

description: Drug Adaptation

value: Week 12


title: mP4_E+G_Week12_Res35

description: Drug Adaptation


title: 15_DNMT3A-CD4-3_S206_R1


title: 03_WT-CD11b-3_S112_R1


title: mP4_E+G_Week12_Res34

description: Drug Adaptation


title: mP4_G_Week12_Res33

description: Drug Adaptation


title: Heterozygous, tdTomato+ MBC, D7, rep3


title: mP4_G_Week12_Res32

description: Drug Adaptation


title: 01_WT-CD11b-1_S110_R1


title: monocytes, MI, replicate 3, D7

city: wenzhou

first: Wei

last: Xie

address: ouhai

institute: Wenzhou Medical University

data_processing:
Raw reads of fastq format were firstly processed using fastp (v 0.20.1) and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2 v 2.1.0.
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count v 0.11.2.
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 v 1.22.2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: C57BL/BJ (six-week-old, male) were fed with CDAHFD diet for 4 weeks.The mice were maintained under specific-pathogen-free conditions, with ad libitum access to chow and water, and housed under a 12-hour light-dark cycle.

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

treatment_protocol: Permanent left anterior descending artery (LAD) ligation or sham operation was performed.  Peripheral blood (PB): Peripheral blood cells were obtained from the retroorbital vein and anticoagulated using EDTA. The sample was supplemented with red blood cell lysis buffer and incubated on ice for 10 minutes for the lysis process.The Moflo Astrios EQ flow cytometer (Beckman) was used to collect CD45+CD115+Ly6Chi monocytes for flow cytometry sorting experiments. The collected cells were suspended in PBS buffer supplemented with 20% FBS and centrifuged to obtain cells for subsequent RNA isolation.

value: blood

value: monocytes

value: Ly6Chi monocytes

value: MI surgery


title: monocytes, MI, replicate 2, D7

value: WT


title: monocytes, MI, replicate 1, D7


title: mP4_E_Week12_Res29

description: Drug Adaptation


title: mP4_E_Week12_Res28

description: Drug Adaptation


title: monocytes, sham, replicate 2, D7

value: sham sugery


title: monocytes, sham, replicate 3, D7


title: mP4_CTRL_Week12_Res27

description: Drug Adaptation

value: CTRL


title: monocytes, sham, replicate 1, D7


title: MPC5 HG/PA3 24h

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

data_processing:
Quality control of data FastQC
genome matching Hisat2
Transcript assembly and quantification StringTie
Analysis of variances DEseq2/edgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: podocyte

value: HG/PA

tag: time point


title: 02_WT-CD11b-2_S111_R1

value: spleen


title: mP4_CTRL_Week12_Res26

description: Drug Adaptation


title: MPC5 HG/PA1 24h


title: MPC5 Ctrl2


title: MPC5 Ctrl1


title: mP4_CTRL_Week12_Res25

description: Drug Adaptation


title: mP4_CTRL_Week1_Res12

description: Drug Adaptation

value: Week 1


title: MPC5 Ctrl3


title: LZGC, D21,ATAC-seq, rep3

value: B220+CD138-GL7+FAS+CD86+CXCR4- B cells

value: S1pr2-creERT2, Rosa26-Ai14, C57BL/6

value: NP-KLH/LPS/Alum 21dpi


title: mP4_CTRL_Week1_Res11

description: Drug Adaptation

value: Pancreatic Ductal Cells

value: Kras G12D/-


title: mP4_E_Week12_Res30

description: Drug Adaptation

value: E

value: Week 12


title: mP4_CTRL_Week1_Res10

description: Drug Adaptation


title: LZGC, D21,ATAC-seq, rep1


title: LZGC, D10,ATAC-seq, rep3

value: NP-KLH/LPS/Alum 10dpi


title: LZGC, D10,ATAC-seq, rep2


title: LZGC, D10,ATAC-seq, rep1


title: BMPC, D14, rep8

data_processing:
RNA-seq reads were trimmed from 3'end until the final base had a quality score >20, using trim_galore (v0.6.6), discarding reads left with <20 bp
Trimmed reads were mapped to the mouse genome (mm10) through STAR v2.2.0 with default settings.
Read count extraction was performed  using STAR v2.2.0
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bone marrow

extract_protocol:
20 mice were used for cell-sorting in each experiment. Splenocyte single cell suspensions were generated by crushing spleens in MACS buffer (PBS supplemented with 1% FBS and 5 mM EDTA). Cells were filtered through 70 uM nylon mesh and washed at 1700 RPM, 4 ⁰C, 5 minutes. Pellets were resuspended in RT ACK lysis buffer and incubated RT for 3 minutes, followed by addition of 5-10 volumes of MACS buffer and washing at 1700 RPM, 4 ⁰C, 5 minutes. Single-cell suspension of splenocytes was stained in MACS buffer containing Fc blocker (supernatant from 2.4G2 cell culture) for 20 min on ice before surface staining with primary antibodies in appropriate concentrations on ice for 25 min. Cells were washed again with 5-10 volumes of MACS, and resuspended in MACS for analysis on BD Aria II. Approximately 200 cells of desired type were sorted into 6 μl lysis buffer (0.2% Triton X-100 and 2 U/μl of RNase inhibitor).
Lysates were mixed with 3 μl of anchored oligo-dT primer (10 μM, 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 μl of dNTP mix (10 mM, Fermentas), denatured at 72 °C for 3 min and immediately placed on ice afterwards. The first-strand reaction mix containing 1 μl SuperScript II reverse transcriptase (Invitrogen), 0.5 μl RNAse inhibitor (Clontech), 4 μl Superscript II First-Strand Buffer (Invitrogen), 1 μl DTT (100 mM, Invitrogen), 4 μl betaine (5 M, Sigma), 0.12 μl MgCl2 (1 M, Sigma), 0.2 μl TSO (100 μM) and 0.58 μl nuclease-free water, were added to each sample. Reverse transcription reaction was carried out by incubating at 42 °C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min). Finally, the reverse transcriptase was inactivated by incubation at 70 °C for 15 min. PCR mix containing 25 μl KAPA HiFi HotStart ReadyMix, 0.5 μl IS PCR primers (10 μM) and 1.1 μl nuclease-free water were added to each sample. The reaction was incubated at 98 °C for 3 min, then cycled 17 times (98 °C 20 s, 67 °C 15 s, 72 °C 6 min), with a final extension at 72 °C for 5 min. cDNAs were purified by Vazyme DNA clean beads following manufacturer's instructions. 1 ng of cDNA were used for the tagmentation reaction using Tn5 (Vazyme). The tagmentation reaction (20 μl) was incubated at 55 °C for 10 min and stopped by addition of 2 μl 0.2%SDS and incubated at 70 °C for 20 min. A second amplification was performed using Q5 polymerase (NEB) as follows: 72 °C 3 min, 98 °C 30 s, then 12 cycles of (98 °C 15 s, 60 °C 30 s, 72 °C 3 min), final extension at 72 °C 5 min. Libraries were purified using Vazyme DNA clean beads.

value: bone marrow

value: NP-KLH/LPS/Alum 14dpi


title: mP4_CTRL_Week1_Res9

description: Drug Adaptation


title: BMPC, D14, rep7


title: BMPC, D14, rep5


title: mP4_CTRL_Week1_Res8

description: Drug Adaptation


title: MPC5 HG/PA2 24h


title: BMPC, D14, rep6


title: mP4_CTRL_Week1_Res7

description: Drug Adaptation


title: BMPC, D14, rep4


title: BMPC, D14, rep3


title: MBC, D14, rep8

value: B220+CD138-GL7-FAS-CD38+IgD- NIP-binding B cells


title: mP4_CTRL_Week1_Res6

description: Drug Adaptation


title: BMPC, D14, rep1


title: BMPC, D14, rep2


title: mP4_CTRL_Week1_Res5

description: Drug Adaptation


title: MBC, D14, rep7


title: MBC, D14, rep5


title: MBC, D14, rep4


title: MBC, D14, rep6


title: LZGC, D21,ATAC-seq, rep2


title: MBC, D14, rep3


title: mP4_CTRL_Week1_Res4

description: Drug Adaptation


title: mP4_CTRL_Week1_Res3

description: Drug Adaptation


title: mP4_CTRL_Week1_Res2

description: Drug Adaptation


title: MP, CONTROL, M0011248-3

data_processing:
Read alignment was performed using STAR (v2.4.2) with the following parameters: -- twopassMode Basic, -- alignIntronMax 1000000, --alignMatesGapMax 1000000, --sjdbScore 2, --quantMode TranscriptomeSAM, --sjdbOverhang 24. RSEM (v1.2.21) was then used for gene quantification with paired-end mode. We used the hg38 reference genome and GENCODE annotation version 24 (Ensembl 83).
Assembly: hg38
Supplementary files format and content: counts.txt.gz is a tab-delimeted file with expected gene counts as calculated by RSEM.
Supplementary files format and content: log2tpm.txt.gz is a tab-delimeted file with the TPM values as calculated by RSEM that were then scaled to log2(tpm+1).
Supplementary files format and content: metadata.txt.gz is a tab-delimeted file with metadata for each sample.

extract_protocol:
Cells were lysed with TCL buffer (Qiagen).
RNA-seq library preparation was performed at the Broad Technology Labs (Broad Institute) using a modified Smart-seq protocol for low-input RNA-sequencing, which improves detection of full-length transcripts using template switching and pre-amplification. There were 3 plates of 96 samples each including blank samples. Samples from cases and controls and the two cell-types were randomized across all three plates. Sequencing was performed in an Illumina NextSeq500 as paired-end 2 x 25 bp reads with an additional 8 cycles for each index.

value: MP

value: CONTROL

value: M


title: MBC, D14, rep2


title: mP4_CTRL_Week1_Res1

description: Drug Adaptation

value: CTRL


title: GC, D14, rep4

value: spleen

value: B220+CD138-GL7+FAS+ B cells


title: MBC, D14, rep1


title: mN10_bb_Week11_186

description: Acid Adaptation

growth_protocol: Mouse pancreatic organoids were cultured in 24 well plates (BioLite Multidish, Thermo Fisher Scientific, #930186), suspended in a 50 µL dome of Matrigel (Matrigel Growth Factor Reduced, Phenol Red Free, Corning, # 356231). They were fed with 500 µl Mouse Complete Feeding Medium 26 that was changed every 3-4 days. Organoids were split approximately twice a week.

extract_protocol:
Confluent organoid cultures (3-4 50 µl domes/condition) were harvested with cold Cell Recovery Solution (Corning, 354253) and incubated on ice for 30 minutes to dissolve Matrigel and release the cells. RNA from the organoid pellets was isolated and purified using RNeasy Mini Kit (QIAGEN, 74106) according to the manufacturer's protocol, including DNase digestion step. RNA concentration was measured using NanoDrop 2000 spectrophotometer and samples were stored at –80°C.
RNA-seq libraries were prepared following the standard protocol of DNBSEQ

treatment_protocol: Culture medium was acidified by titration with 1M hydrochloric acid (HCl), and then filtered through sterile 0.22 µm filters (Millex®-GP, Millipore express PES membrane Filter Unit, #SLGP033RB). Resulting pH was validated using pH determination strips (Sigma Aldrich) inside the CO2 incubator.

value: WT

value: Week 11

tag: batch


title: GC, D14, rep3


title: GC, D14, rep2


title: GC, D14, rep1


title: mN10_bb_Week11_185

description: Acid Adaptation


title: Naive, rep4

value: B220+CD138-GL7-FAS-IgD+ B cells


title: Naive, rep3


title: Naive, rep2


title: Naive, rep1


title: mP4_p53R273H_bb_Week11_183

description: Acid Adaptation

value: Pancreatic Ductal Cells


title: PC, ATAC-seq, rep3

extract_protocol:
10-20 mice were used for cell-sorting in each experiment. Splenocyte single cell suspensions were generated by crushing spleens in MACS buffer (PBS supplemented with 1% FBS and 5 mM EDTA). Cells were filtered through 70 uM nylon mesh and washed at 1700 RPM, 4 ⁰C, 5 minutes. Pellets were resuspended in RT ACK lysis buffer and incubated RT for 3 minutes, followed by addition of 5-10 volumes of MACS buffer and washing at 1700 RPM, 4 ⁰C, 5 minutes. Single-cell suspension of splenocytes was stained in MACS buffer containing Fc blocker (supernatant from 2.4G2 cell culture) for 20 min on ice before surface staining with primary antibodies in appropriate concentrations on ice for 25 min. Cells were washed again with 5-10 volumes of MACS, and resuspended in MACS for analysis on BD Aria II.
ATAC-seq was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® (TD502, Vazyme Biotech). Briefly, around 5,000-10,000 sorted cells in 5 μl were lysed in 50 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) for 10 min on ice. Lysed nuclei were then incubated with the Tn5 transposase and tagmentation buffer at 37 °C for 30 min. Fragmented DNA was purified using 2× VAHTS DNA Clean Beads (Vazyme Biotech) following manufacturer’s instructions. PCR was performed to amplify the library for 15 cycles using the following PCR conditions: 72 °C for 3 minutes; 98 °C for 30 seconds; thermocycling at 98 °C for 15 seconds, 60 °C for 30 seconds and 72 °C for 30 seconds; then 72 °C for 5 min. After the PCR reaction, libraries were purified with 1.2× beads and sent for high-throughput sequencing.

value: Bach2tdRFP/+ Blimp-1-YFR B1-8hi PA-GFP C57BL/6

value: NP-OVA/LPS/Alum 7dpi


title: mP4_p53R273H_bb_Week11_182

description: Acid Adaptation


title: PC, ATAC-seq, rep1


title: RFP, ATAC-seq, rep3

value: B220+CD138-GL7-FAS-CD38+IgD-RFP+ NP-binding B cells


title: mP4_p53R273H_bb_Week11_181

description: Acid Adaptation


title: PC, ATAC-seq, rep2


title: RFP, ATAC-seq, rep2


title: YFP, ATAC-seq, rep2

value: B220+CD138-GL7-FAS-CD38+IgD-YFP+ NP-binding B cells


title: YFP, ATAC-seq, rep3


title: mP4_p53KO_bb_Week11_180

description: Acid Adaptation


title: RFP, ATAC-seq, rep1


title: YFP, ATAC-seq, rep1


title: mP4_bb_Week11_178

description: Acid Adaptation

value: Kras G12D/-


title: mP4_p53KO_bb_Week11_179

description: Acid Adaptation


title: GC, ATAC-seq, rep3


title: mP4_bb_Week11_177

description: Acid Adaptation


title: GC, ATAC-seq, rep1


title: mN10_bb_Week11_184

description: Acid Adaptation


title: Naïve, ATAC-seq, rep2

value: No


title: Sample_10_Neutrophil_APOE3_4_MCI_IR18RI_High

first: Neta

last: Rosenzweig

state: Massachusetts

address: 60 Fenwood Road, 10002K, Brigham and Women’s Hospital

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Technical outliers were removed for further analysis. Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Biological outliers were determined using PCA and heatmap visualization and removed for final analysis.
Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: GRCh38
Supplementary files format and content: zip file of salmon outputs including plain text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters.

source_name: Neutrophil

extract_protocol:
Blood was drowned in CPT tubes (BD Bioscience) and centrifuged at 1700g for 30min, to pellet polymorphonuclear leukocytes (neutrophils) below the gel barrier. Following the removal of plasma and peripheral blood mononuclear cells (PBMCs) from the fraction above the gel barrier, a syringe attached to an 18-gauge needle was used to extract the erythrocyte/neutrophil fraction below the gel as previously described. Cells collected in a 50ml tube were washed in PBS and centrifuged at 600g for 5min at 4°C. Cell pellet was resuspended twice in 10ml of ACK (ammonium chloride potassium) to lyse erythrocytes at RT and washed with PBS. Cells were stained with FITC anti-CD66b (1:100, Biolegend, 305103) in PBS supplemented with 2% fetal bovine serum (FBS) for 20min at 4°C. After staining, cells were washed and sorted using BD FACSAriaTM II (BD Bioscience).
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25 bp reads.

value: Neutrophil

value: MCI

value: F

tag: il18r1 profile

value: High


title: Sample_9_Neutrophil_APOE3_4_CN_IR18RI_High

value: CN


title: mN10_AA_Week11_176

description: Acid Adaptation

value: AA


title: Naïve, ATAC-seq, rep1

value: spleen


title: mN10_AA_Week11_175

description: Acid Adaptation

value: WT


title: mN10_AA_Week11_174

description: Acid Adaptation

value: Week 11


title: 48h_IFNa_rep3

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Trim Galore was used to remove the low quality reads(parametrs- --quality 20 --stringency 3 )
HISAT2 was used to align reads to the mouse genome(parameters- --dta )
StringTie was used for alignments assembly analysis (parameters- -eB)
Assembly: mm10
Supplementary files format and content: tab delimited text files includes FPKM values for each sample

growth_protocol: MC38 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
6h, 24h and 48h after treatment, RNA was isolated from the harvested MC38 cells using TRIzol Reagent.
RNA libraries for RNA-seq was prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: MC38 cells were inoculated with or without 1 µg/mL recombinant IFN-α.

value: murine colorectal cancer cell lines


title: 48h_IFNa_rep1


title: 48h_Medium_rep2


title: 48h_Medium_rep1


title: Sample_6_Neutrophil_APOE3_4_CN_IR18RI_High


title: Sample_7_Neutrophil_APOE3_4_MCI_IR18RI_High


title: 48h_Medium_rep3


title: 24h_IFNa_rep1


title: Sample_5_Neutrophil_APOE3_4_MCI_IR18RI_Low

value: Low


title: Naïve, ATAC-seq, rep3

data_processing:
ATAC-seq reads were trimmed from 3'end until the final base had a quality score >20, using trim_galore (v0.6.6), discarding reads left with <20 bp
Trimmed reads were firstly aligned to the mouse genome (NCBI build 37, mm9) using the bowtie2 program with default parameters.
Mappable reads were further processed by samtools (v1.3.1). Duplicates were removed using picard-tools-1.114.
Peaks were called using the MACS program with default settings followed by a detailed analysis by bedtools (v2.27.1).
Track files were generated by samtools (v1.3.1). The score represents CPM (number of reads per bin/number of mapped reads (in millions))
Assembly: mm9
Supplementary files format and content: bigWig

value: B220+CD138-GL7-FAS-IgD+ B cells

value: Bach2tdRFP/+ Blimp-1-YFR B1-8hi PA-GFP C57BL/6


title: mP4_p53R273H_AA_Week11_173

description: Acid Adaptation

value: Pancreatic Ductal Cells


title: 24h_IFNa_rep3


title: mP4_p53R273H_AA_Week11_171

description: Acid Adaptation


title: 24h_IFNa_rep2


title: mP4_p53R273H_AA_Week11_172

description: Acid Adaptation


title: 24h_Medium_rep3


title: GC, ATAC-seq, rep2

value: B220+CD138-GL7+FAS+ B cells

value: NP-OVA/LPS/Alum 7dpi


title: 24h_Medium_rep2


title: Sample_4_Neutrophil_APOE3_4_CN_IR18RI_Low


title: Sample_3_Neutrophil_APOE3_4_CN_IR18RI_Low


title: 24h_Medium_rep1


title: mP4_p53KO_AA_Week11_170

description: Acid Adaptation


title: 48h_IFNa_rep2


title: mP4_p53KO_AA_Week11_169

description: Acid Adaptation


title: 6h_IFNa_rep2


title: 6h_IFNa_rep3


title: Sample_8_Neutrophil_APOE3_4_CN_IR18RI_High


title: Sample_2_Neutrophil_APOE3_4_MCI_IR18RI_Low


title: 6h_Medium_rep2


title: mP4_AA_Week11_168

description: Acid Adaptation

value: Kras G12D/-


title: 6h_Medium_rep3


title: CV1_rep3

data_processing:
Trim Galore was used to remove the low quality reads(parametrs- --quality 20 --stringency 3 )
HISAT2 was used to align reads to the mouse genome(parameters- --dta )
StringTie was used for alignments assembly analysis (parameters- -eB)
Assembly: mm10
Supplementary files format and content: tab delimited text files includes raw counts for each sample

growth_protocol: C57BL/6 mice were transplanted s.c. with 5×105 MC38 cells.

extract_protocol:
Two days after the third treatment, CD45- cells were sorted. RNA was isolated from the harvested MC38 cells using TRIzol Reagent.
RNA libraries for RNA-seq was prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: MC38 bearing mice were treated i.t. with 50 μg CV-1 or hIgG every three days.


title: Sample_47_Female_Neutrophil_APOE2_3_MCI

extract_protocol:
Blood was drowned in CPT tubes (BD Bioscience) and centrifuged at 1700g for 30min, to pellet polymorphonuclear leukocytes (neutrophils) below the gel barrier. Following the removal of plasma and peripheral blood mononuclear cells (PBMCs) from the fraction above the gel barrier, a syringe attached to an 18-gauge needle was used to extract the erythrocyte/neutrophil fraction below the gel as previously described. Cells collected in a 50ml tube were washed in PBS and centrifuged at 600g for 5min at 4°C. Cell pellet was resuspended twice in 10ml of ACK (ammonium chloride potassium) to lyse erythrocytes at RT and washed with PBS. Cells were stained with FITC anti-CD66b (1:100, Biolegend, 305103) in PBS supplemented with 2% fetal bovine serum (FBS) for 20min at 4°C. After staining, cells were washed and sorted using BD FACSAriaTM II (BD Bioscience).
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25bp reads.

value: Neutrophil


title: mP4_AA_Week11_167

description: Acid Adaptation


title: mN10_bb_Week10_166

description: Acid Adaptation

value: Week 10


title: hIgG_rep3

value: hIgG


title: CV1_rep2


title: mN10_bb_Week10_164

description: Acid Adaptation


title: Sample_46_Female_Neutrophil_APOE2_3_MCI

value: MCI

value: F


title: CV1_rep1


title: E. acervulina t24-C

city: Beltsville

first: Matt

last: Tucker

state: MD

address: 10300 Baltimore Ave, BARC-East Bldg 1040 Rm 104-5

department: Agricultural Research Service

institute: USDA

description:
12-19-19 t24-C
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

data_processing:
Libraries were sequenced on an Illumina NextSeq 500. Each sequencing run resulted in eight separate .fastq files per sample, containing two paired reads per lane. Reads were converted to .fastq format using Bcl2Fastq and demultiplexed. Forward and reverse reads from the four lanes were concatenated per sample to produce single, combined forward and reverse read files.
Sequence reads were analyzed in Geneious Prime 2020.2.4. Reads were paired and trimmed with the package BBDuk (version 38.84) and aligned to the NCBI E. acervulina Houghton reference strain sequence using the Geneious RNA mapper. After mapping, expression metrics werre calculated per sample, including Transcripts Per Million (TPM). Data were screened for genes with >1,000 TPM throughout the time course.
The DESeq2 package, as implemented in Geneious, calculated pairwise differential expression of time points in grouped biological replicates.  We used thresholds of log2 fold change (FC) ±1.5 with adjusted p-value <0.05 to determine significantly differentially expressed genes between immature and mature oocysts. Significantly up-regulated genes >1,000 TPM at initial and final time points were identified for further analysis.
The functional analysis module in OmicsBox 1.4.12 incorporated Blast2GO methodology, identifying similarities to known and predicted proteins, scanning InterPro domains, and assigning Gene Ontology (GO) terms to each of the sequences associated with proteins identified by NCBI BLASTP (through CloudBlast). Additionally, the EggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) mapper inferred orthology relationships, gene evolutionary histories, and functional annotations to improve the Blast2GO sequence characterization. The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway mapper enabled biochemical pathway enrichment analysis.
Genome_build: NCBI assembly EAH001 and ToxoDB v51
Supplementary_files_format_and_content: Excel files included TPM per sample and gene and differential expression log2 FC and adjusted p-value per sample and gene

organism: Eimeria acervulina

source_name: oocysts from chicken feces

growth_protocol: Three male broiler chickens were infected by oral gavage with 150,000 oocysts of E. acervulina (APU-1).

extract_protocol:
Total RNA was extracted from frozen oocyst Trizol pellets using two methods. Oocysts were thawed and ground with a Teflon pestle. Homogenates were vortexed with 0.5 mm beads, mixed with chloroform, and centrifuged at 12,000 g for 15 minutes at 4°C. The organic phase was transferred to new tubes and mixed with 70% ethanol. Total RNA was then isolated using a RNeasy kit  following manufacturer’s instructions. The second method included these modifications: Organic layers from chloroform extraction were mixed with isopropanol and incubated for 10 min at room temperature. Tubes were centrifuged at 12,000 g for 10 min at 4°C. Pellets were resuspended in 1 ml of 75% ethanol, vortexed, and centrifuged at 7,500 g for 5 min at 4°C. Isolated RNA was resuspended in RNase-free water and incubated at 65°C for 15 min. Total RNA was quantified using a Qubit 3.0 fluorometer and quality was assessed using a Bioanalyzer 2100. RNA samples were frozen at -80°C. Prior to RNA-Seq, DNA was removed from total RNA with a Turbo DNA-free kit.
Libraries were produced from 200 ng of total RNA from 2-3 biological replicates using an Illumina TruSeq Stranded mRNA kit. cDNA libraries were selected for fragment sizes of between 120-210 bp.

treatment_protocol: On day six post-inoculation, feces from each bird (A, B, C, representing biological replicates) were harvested. Unsporulated E. acervulina oocysts were isolated from chicken feces by flotation on saturated salt solution and washed with water.  The final preparation of oocysts was resuspended in 2% v/v potassium dichromate and incubated in a 29°C shaking water bath with aeration. At the beginning of the time course (T0) and other time points (every four hours up to 24 hours [T4, T8, T12, T16, T20, T24]), a sample was taken from each replicate flask. Oocysts were washed with deionized water and then incubated with sodium hypochlorite. Oocysts were washed again repeatedly and Trizol was added to the pellets before freezing at -80°C.

tag: strain

value: 24 hr

tag: development stage

value: oocyst

tag: bird id

value: C


title: Sample_1_Neutrophil_APOE3_4_CN_IR18RI_Low

tag: genotype

value: CN


title: E. acervulina t24-B

description:
12-19-19 t24-B
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: B


title: hIgG_rep2

value: murine colorectal cancer cell lines

value: WT

tag: treatment


title: mN10_bb_Week10_165

description: Acid Adaptation

tag: cell type


title: Sample_44_Female_Neutrophil_APOE2_3_CN


title: E. acervulina t24-A

description:
12-19-19 t24-A
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: A


title: E. acervulina t20-C

description:
12-19-19 t20-C
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: 20 hr


title: Sample_43_Female_Neutrophil_APOE2_3_MCI


title: E. acervulina t20-B

description:
12-19-19 t20-B
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx


title: 6h_Medium_rep1


title: mP4_p53R273H_bb_Week10_163

description: Acid Adaptation

value: Pancreatic Ductal Cells


title: E. acervulina t16-C

description:
12-19-19 t16-C
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: 16 hr


title: E. acervulina t12-B

description:
12-19-19 t12-B
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: 12 hr


title: E. acervulina t16-B

description:
12-19-19 t16-B
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx


title: E. acervulina t12-C

description:
12-19-19 t12-C
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx


title: Sample_41_Female_Neutrophil_APOE2_3_CN

value: Neutrophil


title: mP4_p53R273H_bb_Week10_161

description: Acid Adaptation

value: Week 10


title: Sample_40_Female_Neutrophil_APOE2_3_MCI


title: E. acervulina t12-A

description:
12-17-19 t12-A
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx


title: Sample_39_Female_Neutrophil_APOE2_3_CN


title: E. acervulina t8-C

description:
12-17-19 t8-C
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: 8 hr


title: E. acervulina t4-B

description:
12-17-19 t4-B
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: 4 hr


title: mP4_p53KO_bb_Week10_159

description: Acid Adaptation


title: Sample_45_Female_Neutrophil_APOE2_3_CN

value: F


title: Sample_38_Female_Neutrophil_APOE2_3_CN


title: E. acervulina t8-A

description:
12-17-19 t8-A
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx


title: E. acervulina t4-C

description:
12-17-19 t4-C
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx


title: mP4_bb_Week10_158

description: Acid Adaptation

value: Kras G12D/-


title: E. acervulina t8-B

description:
12-17-19 t8-B
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: oocyst


title: E. acervulina t4-A

description:
12-17-19 t4-A
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx


title: mP4_bb_Week10_157

description: Acid Adaptation


title: Sample_37_Female_Neutrophil_APOE2_3_CN


title: mP4_p53R273H_bb_Week10_162

description: Acid Adaptation


title: mN10_AA_Week10_156

description: Acid Adaptation

value: AA


title: E. acervulina t0-C

description:
12-17-19 t0-C
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: 0 hr

value: C


title: A12 high BFI

city: quebec

first: ying

last: zhang

address: 735 Ave.Neree tremblay

country: Canada

institute: UNIVERSITY LAVAL

data_processing:
Adapter-removal and quality trimming of the libraries were performed with TRIMMOMATIC. BISMARK was then used to align the bisulfite-converted libraries to a synthetic converted bovine genome (ARS-UCD1.2,  bosTau9)
The MethylKit package was also used for cytosine methylation analysis and searching of hypermethylated and hypomethylated regions with an adjusted p value.
Assembly: ARS-UCD1.2 and Btau_5.0.1
Supplementary files format and content: tab-delimited text files include corrected p value for DMR identification
Library strategy: EM-seq

organism: Bos taurus

source_name: sperm

extract_protocol:
Genomic DNA was extracted with the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA).
EM-seq (Enzymatic methylation seq) workflow was adopted to perform the whole genome methylation sequencing, which reduced the DNA fragmentation and damage compared to the traditional bisulfite sequencing

value: sperm cell

value: male


title: Sample_42_Female_Neutrophil_APOE2_3_CN

value: CN


title: A10 high BFI


title: E. acervulina t0-A

description:
12-17-19 t0-A
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: A


title: Sample_36_Female_Neutrophil_APOE2_3_CN


title: E. acervulina t0-B

description:
12-17-19 t0-B
E. acervulina TPM all samples.xlsx
E. acervulina T24-T0 differential expression data for GEO.xlsx

value: B


title: mN10_AA_Week10_155

description: Acid Adaptation

value: Pancreatic Ductal Cells

value: WT


title: Sample_35_Female_Neutrophil_APOE2_3_CN

value: Neutrophil


title: mP4_p53KO_bb_Week10_160

description: Acid Adaptation

value: Week 10


title: Sample_34_Female_Neutrophil_APOE2_3_MCI

value: MCI


title: A9 high BFI


title: A11 high BFI


title: mP4_p53R273H_AA_Week10_153

description: Acid Adaptation


title: A6 low BFI


title: mN10_AA_Week10_154

description: Acid Adaptation


title: A7 high BFI


title: A3 low BFI


title: mP4_p53R273H_AA_Week10_152

description: Acid Adaptation


title: A5 low BFI


title: Sample_33_Female_Neutrophil_APOE2_3_MCI


title: mP4_p53R273H_AA_Week10_151

description: Acid Adaptation


title: A1 low BFI


title: Sample_31_Female_Neutrophil_APOE2_3_CN


title: A2 low BFI


title: mP4_p53KO_AA_Week10_150

description: Acid Adaptation


title: mP4_p53KO_AA_Week10_149

description: Acid Adaptation


title: Sample_30_Female_Neutrophil_APOE2_3_CN


title: mP4_AA_Week10_148

description: Acid Adaptation


title: ABI2_OE1

city: Dalian

first: Linlin

last: Lv

address: No.2 Linggong Road

institute: Dalian University of Technology

data_processing:
FastQC,Version0.11.2
Sequence reads were trimmed for adaptor sequence/low-guality sequence using Trimmomatic（Version 0.36）(parameter- Qualty limit. 0 .05)
Trimmed sequence reads were mapped to Human GRCh38/hg38 using HISAT2 (Version 2.1.0)
Read count extraction and normalization were performed using StringTie (Version 1.3.3b)
Assembly: Human GRCh38/hg38
Supplementary files format and content: md5 file includes raw counts for each Sample
Supplementary files format and content: gene_expression file includes RPKM values for each Sample

source_name: MDA-MB-231 cells

extract_protocol:
RNA was harvested using the total RNA Extractor (Trizol)(Sangon). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA ibraries for RNA-seq were prepared using MaxUp Dual-mode mRNA Library Prep Kit for Illumina(YEASEN) folowing manufacturer's protocols.

value: MDA-MB-231 cells

value: ABI2 OE


title: A8 high BFI


title: mP4_AA_Week10_147

description: Acid Adaptation

value: Kras G12D/-


title: Sample_32_Female_Neutrophil_APOE2_3_MCI

value: F


title: Ctrl2

value: Control


title: Sample_29_Female_Neutrophil_APOE2_3_MCI


title: ABI2_OE3


title: Sample_27_Female_Neutrophil_APOE2_3_CN


title: A4 low BFI


title: Ctrl3


title: Sample_28_Female_Neutrophil_APOE2_3_MCI


title: Ctrl1


title: Sample_26_Female_Neutrophil_APOE3_3_MCI


title: C3


title: C2


title: mN10_AA_Week8_145

description: Acid Adaptation

value: AA

value: Week 8


title: mN10_AA_Week8_146

description: Acid Adaptation


title: Sample_25_Female_Neutrophil_APOE3_3_CN


title: C1


title: K3


title: K2


title: mN10_AA_Week8_144

description: Acid Adaptation


title: mP4_p53R273H_AA_Week8_143

description: Acid Adaptation


title: ABI2_OE2


title: Sample_24_Female_Neutrophil_APOE3_3_CN


title: K1


title: Sample_23_Female_Neutrophil_APOE3_3_CN


title: mP4_p53R273H_AA_Week8_142

description: Acid Adaptation


title: Sample_22_Female_Neutrophil_APOE3_3_CN


title: RON+INFECTION9

city: Terre Haute

first: Steven

last: Templeton

state: Indiana

address: 620 Chestnut St HH135 HH135

institute: Indiana University School of Medicine - Terre Haute

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK) for quality control. The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”. To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genome was assessed using bamutils (from ngsutils v.0.4.17). Uniquely mapped reads were used to quantify the gene level expression employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -Q 10”. The data was normalized using TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.4.0.1). False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed with the R package clusterProfiler
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RKPM values for each sample

source_name: Alveolar Macrophage

growth_protocol: 7 to 8 weeks old mice were euthanized. 18-gauge catheter was inserted into the trachea and alveolar macrophages were harvested from mouse lungs with sterile filtered PBS containing 2 mM EDTA (diluted 1:250 from 0.5 M EDTA stock solution) and 0.5% Fetal bovine serum (FBS) in 5ml BAL fluid. Cells were separated from the lavage fluid by centrifugation at 400 ×gfor 6 min at 4°C and the cells were suspended in RPMI 1640 supplemented with penicillin (100 U/ml), streptomycin (100 U/ml), 5% heat-inactivated FBS, 20ng/ml GM-CSF and 143mM beta-mercaptoethanol. The cells were plated in CorningCostar Flat Bottom 12 well Cell Culture Plates at a concentration of 5 × 105cells per well. The cells were allowed to adhere for 24 hours at 37°C under a humidified atmosphere with 5% CO2 and were washed with PBS thrice and cell culture media was added, allowing only the adherent alveolar macrophages to culture in the wells. The cell culture media was changed on day 3, day 6 and day 9 of the cultures. The cells were fully confluent and ready for treatment and infection on day 10.

extract_protocol:
RNA extraction from AMs was done using Qiagen RNeasy Mini kit, following the manufacturer’s protocol.
Total RNA samples were first evaluated for their quantity and quality using Agilent TapeStation. All the samples had good quality with RIN (RNA Integrity Number) of 9.6-10. One hundred nanograms of total RNA was used for library preparation with the Illumina Stranded mRNA Prep, Ligation kit (lllumina), following the manufacturer’s instruction. Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and Agilent TapeStation, and multiple libraries were pooled in equal molarity.

treatment_protocol: AMs were treated with 20 uM AdipoRon or vehicle-treated for 24 hours, followed by infection with AF293 fixed and swollen conidia using RPMI 1640 medium at a concentration of 9 conidia per cell for RT-PCR. After 10 hours of infection, cells were ready for RNA extraction and cDNA synthesis.

value: Alveolar Macrophage

value: APN-/-

value: AdipoRon/infected


title: RON ONLY 12

value: AdipoRon/uninfected


title: RON ONLY 11


title: mP4_p53R273H_AA_Week8_141

description: Acid Adaptation


title: RON ONLY10


title: RON+INFECTION8


title: INFECTION6

value: Vehicle/infected


title: INFECTION5


title: Sample_20_Female_Neutrophil_APOE3_3_CN

city: Boston

value: CN


title: Sample_21_Female_Neutrophil_APOE3_3_MCI


title: mP4_p53KO_AA_Week8_139

description: Acid Adaptation

value: Pancreatic Ductal Cells


title: INFECTION4


title: DMSO3

value: Vehicle/uninfected


title: mP4_AA_Week8_138

description: Acid Adaptation


title: DMSO1


title: DMSO2


title: Trm-like cells, rep 3

city: Philadelphia

first: Hanzhi

last: Wang

address: 422 Curie Blvd

institute: University of Pennsylvania

data_processing:
Raw sequence reads were demultiplexed by Psomagen with commercial protocols. Sequence reads were trimmed with CutAdapt v4.8 using parameter -m = 10
Trimmed reads were mapped to Mus musculus genome GRCm39(M34) using Rsubread v2.14.2 with default parameters
Reads were extracted and normalized using DESeq2 v1.40.2.
Assembly: GRCm39 (M34)
Supplementary files format and content: Tab-delimited tsv file including raw reads for all the samples

source_name: T cell

extract_protocol:
quick-RNA miniprep kit (Zymo research, CA, USA)
RNA libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA) with the commercial protocol.  0.5ug of total RNA per sample was used to generate the libraries.

value: T cell


title: Trm-like cells, rep 1


title: mP4_AA_Week8_137

description: Acid Adaptation


title: mN10_AA_Week5_136

description: Acid Adaptation

value: WT

value: Week 5


title: Sample_16_Female_Neutrophil_APOE3_4_MCI

value: Neutrophil

value: MCI


title: Trm-like cells, rep 2


title: RON+INFECTION7


title: mP4_p53KO_AA_Week8_140

description: Acid Adaptation


title: T effector cells, rep 3


title: T effector cells, rep 2


title: Sample_14_Female_Neutrophil_APOE3_4_MCI

value: F


title: T effector cells, rep 1


title: Sample_15_Female_Neutrophil_APOE3_4_MCI


title: mN10_AA_Week5_135

description: Acid Adaptation


title: Sample_13_Female_Neutrophil_APOE3_4_CN


title: mN10_AA_Week5_134

description: Acid Adaptation


title: mP4_p53R273H_AA_Week5_132

description: Acid Adaptation


title: mP4_p53R273H_AA_Week5_133

description: Acid Adaptation


title: Sample_18_Female_Neutrophil_APOE3_3_CN


title: Sample_19_Female_Neutrophil_APOE3_3_CN


title: Sample_11_Female_Neutrophil_APOE3_4_CN


title: Sample_17_Female_Neutrophil_APOE3_3_CN


title: mP4_p53KO_AA_Week5_130

description: Acid Adaptation


title: mP4_p53R273H_AA_Week5_131

description: Acid Adaptation


title: mP4_p53KO_AA_Week5_129

description: Acid Adaptation


title: Sample_10_Female_Neutrophil_APOE3_4_CN


title: SG-309-Rep2

type: RNA

city: Saskatoom

first: wentao

state: SK

address: 110 Gymnasium Pl

institute: NRC-Canada

description:
SG-85-cy3 vs SG-309-cy5 (1).gpr
Biological replicate 2

hyb_protocol: Purified cRNAs (2 µg) were fragmented and hybridized to the Agilent 4x44K Brassica arrays (Parkin et al., 2010) for 17 h at 65°C with a rotation of 10 rpm according to the manufacturer’s protocol.

scan_protocol: Arrays were washed with the Agilent Gene Expression Washing buffers according to the manufacturer’s protocol and scanned with GenePix 4000B as described by Parkin et al. (2010). Four and two biological replications were performed for the parental lines and the SG lines, respectively, with dye-swaps applied to the biological replicates to minimize dye effects from the two colour systems (Lee et al., 2004).

data_processing: The raw array datasets were extracted with Gene Pix Pro 6.0, and were firstly normalized by the lowess LOWNESS (Yang et al., 2002) method within arrays, followed by the quantile (Bolstad et al., 2003) method between arrays, using the R/Bioconductor software (available at http://www.r-project.org/). R package Limma (Smyth, 2005).

organism: Brassica napus

source_name: Seeds at 21 DAF

label_protocol: cRNAs were amplified from total RNA samples (2 µg) and labeled with either cy3 or cy5 using the Quick Amp labeling kit, Two Color (Agilent, Catalogue: 5190-0444) according to the manufacturer’s instructions, followed by purification with the Qiagen RNeasy Mini Kit (Qiagen, Catalogue 74104) and quantification with a NanoDrop ND-1000.

growth_protocol: The B. napus lines used in this study include the two parental lines DH12075, a Canadian spring-type doubled haploid canola line (generated by Dr. Gerhard Rakow and Dr. Ginette Séguin-Swartz, Agriculture and Agri-Food Canada), and PSA12, a resynthesised B. napus line (generated by Dr. Monica Beschorner and Dr. Derek Lydiate, Agriculture and Agri-Food Canada), and 96 doubled haploid segregating (SG) lines generated from the cross of these two parental lines. PSA12 was developed from an interspecific cross between B. oleracea ssp. alboglabra line A12DH and B. rapa line Parkland Sunshine, and DH12075 was derived from a cross between varieties Cresor and Westar (Mayerhofer et al., 2005).

extract_protocol: Total RNA was extracted from the developing seeds using a method modified from that of Oñate-Sánchez and Vicente-Carbajosa (2008) and described in detail by Parkin et al. (2010). Seeds from field grown plants from two trials (2009 and 2010) were harvested for seed quality analysis.

treatment_protocol: The developing seeds at 21 days post-anthesis were collected from B. napus lines grown under field conditions at the AAFC Saskatoon Research Farm in 2009. This time point was selected because approximately 20 days after flowering ( DAF) had previously been identified as a critical stage for cell proliferation and oil deposition (O’Hara et al., 2002; Dong et al., 2004).

tag: sample type

value: tissue

tag: tissue

value: development seeds


title: SG-24-Rep2

description:
Sg-225-cy3 vs SG-24-cy5(1).gpr
Biological replicate 2


title: mP4_AA_Week5_127

description: Acid Adaptation

value: Kras G12D/-

value: AA


title: Sample_12_Female_Neutrophil_APOE3_4_CN

tag: Sex


title: Sample_8_Female_Neutrophil_APOE3_4_CN


title: SG-233-Rep2

description:
SG-90-cy3 vs Sg-233-cy5(2).gpr
Biological replicate 2


title: mP4_AA_Week5_128

description: Acid Adaptation

tag: cell line


title: SG-333-Rep2

description:
SG-67-cy3 vs SG-333-cy5(1).gpr
Biological replicate 2


title: Sample_9_Female_Neutrophil_APOE3_4_CN

tag: disease state


title: SG-317-Rep2

description:
SG-9-cy3 vs SG-317-cy5(2).gpr
Biological replicate 2


title: SG-33-Rep2

description:
SG-65 cy3 vs SG-33 cy5 (2).gpr
Biological replicate 2


title: SG-137-Rep2

description:
SG-54-cy3 vs SG-137-cy5(1).gpr
Biological replicate 2


title: SG-209-Rep2

description:
SG-80-cy3 vs SG-209 cy5 (1).gpr
Biological replicate 2


title: SG-115-Rep2

description:
SG-75-cy3 vs SG-115-cy5 (2).gpr
Biological replicate 2


title: SG-300-Rep2

description:
SG-64-cy3 vs SG-300-cy5 (2).gpr
Biological replicate 2


title: SG-351-Rep2

description:
SG-5-cy3 vs SG-351-cy5 (1).gpr
Biological replicate 2


title: SG-5-Rep2

description:
SG-351- cy3 vs SG-5-cy5 (2).gpr
Biological replicate 2


title: Sample_6_Female_Neutrophil_APOE3_4_CN


title: SG-231-Rep2

description:
SG-330-cy3 vs SG-231-cy5(1).gpr
Biological replicate 2


title: mN10_CTRL_Week1_125

description: Acid Adaptation

value: CTRL

value: Week 1


title: mN10_CTRL_Week1_126

description: Acid Adaptation


title: SG-67-Rep2

description:
SG-333-cy3 vs SG-67-cy5 (2).gpr
Biological replicate 2


title: SG-65-Rep2

description:
SG-33-cy3 vs SG-65 cy5 (1).gpr
Biological replicate 2


title: Sample_5_Female_Neutrophil_APOE3_4_CN


title: mN10_CTRL_Week1_124

description: Acid Adaptation


title: mN10_CTRL_Week1_123

description: Acid Adaptation


title: Sample_3_Female_Neutrophil_APOE3_4_MCI


title: Sample_2_Female_Neutrophil_APOE3_4_CN


title: mN10_CTRL_Week1_122

description: Acid Adaptation


title: mN10_CTRL_Week1_121

description: Acid Adaptation


title: Sample_7_Female_Neutrophil_APOE3_4_MCI


title: SG-254-Rep2

description:
SG-318-cy3 vs SG-254-cy5 (1).gpr
Biological replicate 2


title: SG-85-Rep2

description:
SG-309-cy3 vs SG-85-cy5 (2).gpr
Biological replicate 2


title: SG-261-Rep2

description:
SG-324-cy3 vs SG-261-cy5(1).gpr
Biological replicate 2


title: Sample_1_Female_Neutrophil_APOE3_4_CN


title: mP4_p53R273H_CTRL_Week1_120

description: Acid Adaptation


title: SG-107-Rep2

description:
SG-306-cy3 vs SG-107-cy5 (2).gpr
Biological replicate 2


title: SG-240-Rep2

description:
SG-30-cy3 vs SG-240-cy5 (2).gpr
Biological replicate 2


title: Sample_94_Neutrophil_APOE3_3_CN

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Technical outliers were removed for further analysis. Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Biological outliers were determined using PCA and heatmap visualization and removed for final analysis.
Comparisons were run using LRT, and the cutoff for significant genes was P < 0.05.
Assembly: GRCh38
Supplementary files format and content: zip file of salmon outputs including plain text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters.

value: M

tag: age

tag: qrds

tag: mmse


title: mP4_p53R273H_CTRL_Week1_119

description: Acid Adaptation

data_processing:
Fastqc (version 0.11.5) and Multiqc (version 1.748) were used to investigate potential RNA-Seq library (paired-end) artifacts.
The 13 bp 5' adapter sequences in all the libraries were removed using Trim Galore (0.4.4) with the options '–paired –clip_R1 13 –clip_R2 13'.
Salmon (1.3.0) with the parameters '-l IU' was used to map the adapter-trimmed reads on the mouse transcriptome (M25 GRCm38.p6 Gencode release50).
Read Counts and TPM values are extracted from Salmon output.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with counts values for each sample
Supplementary files format and content: tab-delimited text files with TPM values for each sample

tag: time

tag: ph


title: Sample_93_Neutrophil_APOE3_4_MCI


title: Sample_4_Female_Neutrophil_APOE3_4_CN


title: SG-64-Rep2

description:
SG-300-cy3 vs SG-64-cy5(1).gpr
Biological replicate 2


title: SG-121-Rep2

description:
SG-303-cy3 vs SG-121-cy5 (1).gpr
Biological replicate 2


title: SG-230-Rep2

description:
SG-295-cy3 vs SG-230-cy5 (3).gpr
Biological replicate 2


title: SG-9-Rep2

description:
SG-317-cy3 vs SG-9-cy5(1).gpr
Biological replicate 2


title: mP4_p53R273H_CTRL_Week1_118

description: Acid Adaptation

tag: batch


title: SG-172-Rep2

description:
SG-29-cy3 vs SG-172-cy5(1).gpr
Biological replicate 2


title: SG-122-Rep2

description:
SG-285-cy3 vs SG-122-cy5(1).gpr
Biological replicate 2


title: SG-249-Rep2

description:
SG-281-cy3 vs SG-249-cy5(2).gpr
Biological replicate 2


title: Sample_91_Neutrophil_APOE3_4_CN


title: Sample_92_Neutrophil_APOE3_4_MCI


title: sg-103-Rep2

description:
SG-276-cy3 vs sg-103-cy5 (2).gpr
Biological replicate 2


title: SG-108-Rep2

description:
SG-278-cy3 vs SG-108-cy5(2).gpr
Biological replicate 2


title: SG-271-Rep2

description:
SG-284-cy3 vs SG-271 cy5(1).gpr
Biological replicate 2


title: SG-267-Rep2

description:
SG-294-cy3 vs SG-267-cy5(1).gpr
Biological replicate 2


title: mP4_p53R273H_CTRL_Week1_115

description: Acid Adaptation


title: SG-247-Rep2

description:
SG-269-cy3 vs SG-247-cy5(1).gpr
Biological replicate 2


title: Sample_88_Neutrophil_APOE3_3_MCI


title: mP4_p53R273H_CTRL_Week1_117

description: Acid Adaptation


title: mP4_p53R273H_CTRL_Week1_116

description: Acid Adaptation


title: Sample_90_Neutrophil_APOE3_3_MCI


title: Sample_89_Neutrophil_APOE3_3_CN


title: Sample_87_Neutrophil_APOE3_4_CN


title: mP4_p53KO_CTRL_Week1_112

description: Acid Adaptation


title: SG-270-Rep2

description:
SG-266-cy3 vs SG-270-cy5 (1).gpr
Biological replicate 2


title: SG-284-Rep2

description:
SG-271-cy3 vs SG-284 cy5 (2).gpr
Biological replicate 2


title: SG-294-Rep2

description:
SG-267-cy3 vs SG-294-cy5 (2).gpr
Biological replicate 2


title: Sample_86_Neutrophil_APOE3_3_MCI


title: SG-166-Rep2

description:
SG-262-cy3 vs SG-166-cy5 (2).gpr
Biological replicate 2


title: SG-321-Rep2

description:
SG-259-cy3 vs SG-321-cy5(1).gpr
Biological replicate 2


title: mP4_p53KO_CTRL_Week1_114

description: Acid Adaptation


title: mP4_CTRL_Week1_111

description: Acid Adaptation


title: SG-253-Rep2

description:
SG-273-cy3 vs SG-253-cy5 (1).gpr
Biological replicate 2


title: SG-246-Rep2

description:
SG-265-cy3 vs SG-246-cy5 (1).gpr
Biological replicate 2


title: SG-241-Rep2

description:
SG-258-cy3 vs SG-241-cy5 (2).gpr
Biological replicate 2


title: mP4_p53KO_CTRL_Week1_113

description: Acid Adaptation


title: SG-324-Rep2

description:
SG-261 cy3 vs SG-324 cy5 (2).gpr
Biological replicate 2


title: mP4_CTRL_Week1_110

description: Acid Adaptation


title: Sample_84_Neutrophil_APOE3_4_MCI


title: SG-318-Rep2

description:
SG-254-cy3 vs SG-318-cy5(2).gpr
Biological replicate 2


title: SG-273-Rep2

description:
SG-253-cy3 vs SG-273-cy5(2).gpr
Biological replicate 2


title: SG-281-Rep2

description:
SG-249-cy3 vs SG-281-cy5 (1).gpr
Biological replicate 2


title: SG-269-Rep2

description:
SG-247-cy3 vs SG-269-cy5(2).gpr
Biological replicate 2


title: Sample_85_Neutrophil_APOE3_4_MCI


title: SG-259-Rep2

description:
SG-321-cy3 vs SG-259-cy5 (2).gpr
Biological replicate 2


title: Sample_83_Neutrophil_APOE3_3_CN


title: mP4_p53KO_bb_Week11_108

description: Acid Adaptation

value: Week 11


title: Sample_82_Neutrophil_APOE3_4_MCI


title: mP4_p53KO_bb_Week11_106

description: Acid Adaptation


title: mP4_p53KO_bb_Week11_107

description: Acid Adaptation


title: SG-265-Rep2

description:
SG-246-cy3 vs SG-265-cy5(2).gpr
Biological replicate 2


title: SG-216-Rep2

description:
SG-243-cy3 vs SG-216-cy5 (2).gpr
Biological replicate 2