title: CEMBA190716_8E_3_CEMBA190716_8E_4_D1_ad004


title: CEMBA190716_8E_3_CEMBA190716_8E_4_D1_ad012

status: Public on Sep 19 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male

tag: age

tag: strain


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title: CEMBA190716_8E_1_CEMBA190716_8E_2_C12_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C12_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C12_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C2_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C12_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C4_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C11_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C11_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C12_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C11_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C11_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C11_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C11_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C3_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C12_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C10_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C10_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C10_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C1_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C10_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C10_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C10_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C10_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C1_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C10_ad001


title: VEH11_1

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description:
experiment1_deSeq2_counts.txt
experiment1_deSeq2_NormCounts.txt

library_source: transcriptomic

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRCm38 + Gencode-M22 Annotation, GRChg38 + Gencode-31 Annotation
Supplementary_files_format_and_content: Raw and normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: KGN cells

growth_protocol: KGN cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum and seeded into a 12-well plate to ~50% confluency, then serum starved for 24 hours before treatment with 25 nM DHT or ethanol for 12 hours.

extract_protocol:
mRNA was extracted from pelleted mouse granulosa cells or cultured KGN cells using Rneasy Plus Mini Kit (Qiagen, Valencia, CA).
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome.

treatment_protocol: 18-week-old female mice were injected into the peritoneum with 29 mcg of DHT suspended in a mixture of 90% sesame oil and 10% ethanol in a 100 microliter volume, and sacrificed 18 hours later. Ovaries were dissected in sterile PBS, then transferred into DMEM/F12 medium where granulosa cells were extruded by the poke-and-press method and pelleted.

tag: treatment

value: ethanol

tag: cell type

value: KGN cells


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C1_ad007


title: VEH12_4


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C11_ad006


title: VEH10_23


title: DHT11_5

value: DHT


title: DHT12_4


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C1_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C1_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B9_ad012


title: VEH11_5


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B9_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B9_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_C1_ad001


title: DHT10_23


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B9_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B9_ad002


title: DHT10_28


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B9_ad008


title: VEH10_28


title: DIO-NASH 1

city: Hørsholm

first: Kristoffer

middle: G

last: Rigbolt

address: Hørsholm Kongevej 11B

country: Denmark

institute: Gubra

description:
scRNA-seq
10x polyA RNA

data_processing:
Basecalling software: bcl2fastq v2.20.0.422.
Alignment and preprocessing: CellRanger (v. 1.1.0, 10x Genomics) software.
Cell filtering and normalization: Seurat R package (v. 3.1.1).
Genome_build: GRCm38 v89
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include normalized expression values for each sample.

source_name: Liver biopsy

extract_protocol:
RNA extraction was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
Library preparation was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.

tag: tissue

value: Liver

tag: diagnosis

value: DIO-NASH


title: DIO-NASH 2

description:
scRNA-seq
10x polyA RNA


title: Lean-chow 2

description:
scRNA-seq
10x polyA RNA

value: Healthy


title: Lean-chow 4

description:
scRNA-seq
10x polyA RNA


title: DHT11_1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B8_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B8_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B8_ad006


title: ML-24

city: Fayetteville

first: Michael

last: Lehmann

state: AR

address: SCEN 601

department: Biological Sciences

institute: University of Arkansas

description:
toptable_Female_NLS_Fed.vs.Female_NLS_Starved
toptable_Female_WT_Starved.vs.Female_NLS_Starved
feature_counts

data_processing:
Base Calling: Illumina bcl2fastq
Quality control (QC): Pre-alignment QC (FastQC version 0.11.8); Post-alignment QC (Picard Tools version 2.18.7); MultiQC (version 1.6)
Reference-based alignment and expression quantification (for QC purposes): STAR (version 2.7.2a); Picard Tools (version 2.18.7)
Alignment-free expression quantification Transciptome quantification (Kallisto version 0.46.0); summarize at the gene level (tximport R package)
Differential expression analysis: Limma-voom (limma R package)
Functional analysis: GO term and pathway over-representation analysis (clusterProfiler R package)
Genome_build: Drosophila melanogaster assembly BDGP6.22 (Ensembl release 98)
Supplementary_files_format_and_content: xlxs workbooks containing toptable, differentially expressed genes, and functional enrichment analysis results
Supplementary_files_format_and_content: raw_feature_counts_without_nomalization

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Whole flies

extract_protocol:
RNA was extracted from three biological replicates for each combination of genotype, sex, and condition (fed, starved). Flies were snap-frozen in liquid nitrogen and transferred into Trizol Reagent (Invitrogen Life Sciences) for homogenization and RNA extraction. RNA was further purified using a Qiagen RNeasy Mini Kit and its quality determined using an Agilent TapeStation.
Illumina TruSEQ as protocolled by Illumina

treatment_protocol: Freshly eclosed male and female flies of the genotype LipinDNLS/Df(2R)Exel7095 and control flies of the genotype Lipin/Df(2R)Exel7095, carrying the wild-type Lipin allele of the CRISPR/Cas9 injection stock, were collected and kept on regular food for three days. Male and female flies were then separated and placed in groups of 15 and 10, respectively, in food-containing vials or starvation vials containing only a source of water. After 24 hours under continued feeding or fasting conditions the flies were processed for RNA-seq.

value: female

tag: genotype

value: LipinDNLS

value: starved

tag: batch


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B8_ad010


title: ML-23

description:
toptable_Male_NLS_Fed.vs.Male_NLS_Starved
toptable_Male_WT_Starved.vs.Male_NLS_Starved
feature_counts


title: ML-21

description:
toptable_Male_WT_Starved.vs.Male_NLS_Starved
toptable_Male_WT_Fed.vs.Male_WT_Starved
feature_counts

value: wild-type control


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B8_ad004


title: ML-22

description:
toptable_Female_WT_Starved.vs.Female_NLS_Starved
toptable_Female_WT_Fed.vs.Female_WT_Starved
feature_counts


title: ML-20

description:
toptable_Female_NLS_Fed.vs.Female_NLS_Starved
toptable_Female_WT_Fed.vs.Female_NLS_Fed
feature_counts

value: fed


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B7_ad012


title: ML-17

description:
toptable_Male_WT_Fed.vs.Male_NLS_Fed
toptable_Male_WT_Fed.vs.Male_WT_Starved
feature_counts


title: ML-19

description:
toptable_Male_NLS_Fed.vs.Male_NLS_Starved
toptable_Male_WT_Fed.vs.Male_NLS_Fed
feature_counts


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B8_ad008


title: Lean-chow 3

description:
scRNA-seq
10x polyA RNA


title: ML-14


title: ML-18

description:
toptable_Female_WT_Fed.vs.Female_NLS_Fed
toptable_Female_WT_Fed.vs.Female_WT_Starved
feature_counts


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B7_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B7_ad001


title: ML-15


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B7_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B7_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B7_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B7_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B7_ad010


title: Lean-chow 1

description:
scRNA-seq
10x polyA RNA


title: ML-11


title: ML-10


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B8_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B6_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B6_ad001


title: VEH5

description:
experiment2_deSeq2_counts.txt
experiment2_deSeq2_NormCounts.txt

source_name: Granulosa cells

value: vehicle

value: Granulosa cells


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B6_ad010


title: ML-09


title: ML-08


title: VEH4


title: VEH3


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B6_ad004


title: ML-16


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B6_ad006


title: VEH2


title: ML-07


title: VEH1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B5_ad012


title: DHT5


title: ML-06


title: ML-12


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B6_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B6_ad008


title: ML-13


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B5_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B5_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B6_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B5_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B5_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B5_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B5_ad008


title: DHT4


title: ML-03


title: DHT3


title: ML-02


title: DHT2


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B4_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B4_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B4_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B5_ad001


title: ML-01


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B4_ad001


title: ML-04


title: DHT1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B3_ad010


title: ML-05


title: scRNA-seq bone marrow long-lived plasma

first: Kees

last: Murre

state: CALIFORNIA

address: 9500 gilman drive, NSB 5114A

department: Biology

institute: UCSD

data_processing:
CellRanger v 2.1 was used for demultiplexing, alignment, filtering of cells, and generation of read count tables using default parameters.
Filtering steps:
1. cells with > 300 genes UMI > 0, and 0.05% 10% of their UMIs mapping to mitochondria genes were kept.
2. If a sample have more than 2000 cells detected, then only 2000 cells were randomly selected.
3. Only genes that had UMI > 0 in more than 2% of cells of at least one sample were kept.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated value files containing unique molecular identifier sequences and transcript counts for all cells passing quality control

source_name: bone marrow

growth_protocol: Primary ex vivo plasma cells

extract_protocol:
Samples were prepared using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2
10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2

treatment_protocol: untreated

value: Blimp-GFP mice

tag: markers


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B4_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B3_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B3_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B3_ad004


title: scRNA-seq spleen short-lived plasma

source_name: spleen


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B4_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B3_ad006


title: scRNA-seq bone marrow short-lived plasma


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B3_ad001


title: T07_OE18_inoculated

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

country: China

institute: Northeast Forestry University

description:
OE18 inoculated with M. larici-populina for 2 days
stem tip with 2 pieces of leaves

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The RNA-seq reads were aligned to the Populus genome (version 3.0, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa) using TopHat (version 2.1.1) .
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: text file with raw and normalized count

organism: Populus ussuriensis

growth_protocol: The in vitro plants of Populus ussuriensis were kept under16-h-light/8-h-dark cycles at 120 μmol m−2 s−1 irradiation at 25°C.

extract_protocol:
Leaves were removed, flash frozen on dry ice, and RNA was harvested using CTAB method. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plants were inoculated by thoroughly spraying pathogen spore suspension (± 10^5 spores mL-1) onto the abaxial leaf surfaces according to the method in (Ullah et al., 2017). Immediately after spraying, each plant was covered with a polyethylene terephthalate bag to maintain high humidity and kept in the dark to facilitate spore germination. After 24 hours, the bags were taken out until the 2nd day. Control seedlings were sprayed with distilled water instead.

value: leaf

value: 21-day old plants


title: T08_OE18_inoculated

source_name: OE18 inoculated with M. larici-populina for 2 days


title: T05_OE14_inoculated

description:
OE14 inoculated with M. larici-populina for 2 days
stem tip with 2 pieces of leaves


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B3_ad012

value: CA

value: male


title: T06_OE14_inoculated

source_name: OE14 inoculated with M. larici-populina for 2 days


title: scRNA-seq 3d in-vitro activated plasma cell

source_name: in vitro activated, sorted plasma cells

growth_protocol: Splenocytes were incubated with CD23-biotin (eBioscience, clone B3B4, cat. 13-0232-81) and purified using anti-biotin microbeads (Miltenyi Biotec, cat. 130-090-485) on MACs LS columns. Selected cells were cultured at 0.5 million/mL in 24-well plates in RPMI media containing 10% FBS, 2% PSG, and B-me.

treatment_protocol: Cultured CD23+ cells were stimulated with 10ug/mL LPS for 3 days (Sigma).

value: CD23+ IgD+ CD19+ Blimp1+


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B2_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B2_ad001


title: scRNA-seq 2hr in-vitro activated plasma cell

source_name: in vitro activated cells

treatment_protocol: Cultured CD23+ cells were stimulated with 10ug/mL LPS for 2 hr (Sigma).

value: CD23+ IgD+ CD19+


title: T03_WT_inoculated

description:
WT  inoculated with M. larici-populina for 2 days
stem tip with 2 pieces of leaves

value: WT


title: T09_OE18_inoculated


title: T02_WT_inoculated

source_name: WT  inoculated with M. larici-populina for 2 days


title: scRNA-seq Naïve B


title: T04_OE14_inoculated


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B2_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B2_ad010


title: T01_WT_inoculated


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B2_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B2_ad002


title: MK_R1_001

city: Kaohsiung City

first: Tsung-Hua

last: Hsieh

address: 6 Yi-Da Rd., Yan-Chau District

country: Taiwan

institute: E-Da Hospital

data_processing:
bcl2fastq v2.20.0.422, default parameters
trimmomatic v0.36, ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
RSEM v1.2.28, rsem-calculate-expression --bowtie2 --paired-end --forward-prob
RSEM v1.2.28, rsem-run-ebseq
Genome_build: hg19

source_name: Human ovarian cancer cell lines

growth_protocol: Human lung cancer cell lines H1299(BCRC, Taiwan) and MCAS (JCRB Cell Bank, Japan) were grown in MEM (Life Technologies) supplemented with 10% fetal bovine serum (FBS, Life Technologies) and 5% Antibiotic-Antimycotic (Life Technologies) and maintained at 378C in a humidified incu- bator with 5% CO2.

extract_protocol:
RNA was isolated from the cell lines using TRIZOL reagent (Invitrogen).
The Human Whole Genome OneArray v7 (Phalanx Biotech Group, Taiwan) containing 29,204 DNA oligonucleotide sense probes of 5060 nucleotides in length was recommended based on previous studies and was used according to the manufacturer’s instructions. Included were 28,264 probes and 940 controls corresponding to the annotated genes from the RefSeq v70 and Ensembl v80 database.

treatment_protocol: 1 × 105 cells were seeded into a 6-well plate and incubated at 37 °C for 24h. The plasmid was transfected with TurboFect transfection reagent (Fermentas, Hanover, MD) following the manufacturer’s protocol. The pBabe-KrasG12D was purchased from addgene (#58902).

tag: cell lines

value: MCAS

tag: transfection


title: MC_R1_001

value: KRASWT


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B2_ad004


title: MQ_R1_001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B12_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B12_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B12_ad004


title: HQ_R1_001

source_name: Human lung cancer cells lines


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B12_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B12_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B2_ad006


title: 15__-_1_R1

city: Adelaide

first: Lachlan

last: Baer

address: North Terrace

country: Australia

institute: The University of Adelaide

description: Wild type 6-month-old zebrafish brain

data_processing:
Raw data was trimmed with AdapterRemoval v2.2.1 with parameters: --minquality 20 –minlength 35.
Trimmed data was aligned to GRCz11 using STAR v2.5.3 with default parameters.
Aligned data was summarised at the gene-level with featureCounts from the Subread package v1.5.2 with default parameters.
Genome_build: GRCz11
Supplementary_files_format_and_content: Estimated raw counts in tab delimited file format.

organism: Danio rerio

source_name: Whole-brain

growth_protocol: A N140fs/+ fish was mated with a T141_L142delinsMISLISV/+ fish. The progeny of a single spawning event were raised together in a single tank until 6 months of age, at which time their brains were removed, their sex was confirmed by dissection, and their genotype was determined by allele-specific PCRs. After sequencing, one sample was identified to be incorrectly genotyped and actually had genotype (N140fs/T141_L142delinsMISLISV).

extract_protocol:
Total RNA was extracted from individual entire brains using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. The resulting total RNA was DNaseI treated using the DNA-free kit (Life Technologies) to remove any contaminating genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: gender

value: Female

tag: psen2 genotype


title: 15__-_1_2_R1

description: Wild type 6-month-old zebrafish brain


title: MA_R1_001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B12_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B11_ad012


title: HA_R1_001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B11_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B11_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B11_ad010


title: HC_R1_001


title: 5X_TREM2_KO

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road, Room 3200

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Alignment with CellRanger v3.02, expected cells=5000
Genome_build: GRCh38/GRCm38
Supplementary_files_format_and_content: Text files containing the gene names (features.tsv), cell barbodes (barcodes.tsv), and UMI counts (matrix.mtx) for each single-cell sample.

source_name: iPSC-derived xenotransplanted microglia

extract_protocol:
Half brains were enzymatically digested using the Miltenyi Tumor Dissociation Kit and the gentleMACS octodissociator with heaters. 5ug/mL actinomycin D, 10uM triptolide, and 27.1 ug/mL anisomycin were added to the enzymatic mixture to limit transcriptional and translational changes induced by the digestion. Isolated cells were then centrifuged in 23% Percoll to remove myelin and debris and human cells were negatively sorted using the Miltenyi Mouse Cell Depletion kit. Cells were then resuspended at a concentration of 1000 cells/uL in preparation for single-cell sequencing.
Libraries were prepared according to standard 10X genomics 3' v3 protocols

treatment_protocol: iHPCs were transplanted into the ventricles and overlying cortex of MITRG or 5X-MITRG mice at postnatal day 1. Mice were subsequently aged for 6 months.

tag: mouse genotype

tag: cell genotype

value: TREM2 KO

tag: tissue/cell type

value: iPSC-derived xenotransplanted microglia


title: HK_R1_001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B11_ad008

tag: brain region

tag: Sex


title: 5X_TREM2_WT

value: TREM2 WT


title: 13__-_3_2_R1

description: Wild type 6-month-old zebrafish brain


title: 13__-_3_R1

description: Wild type 6-month-old zebrafish brain


title: 14__-_2_R1

description: Wild type 6-month-old zebrafish brain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B12_ad007

tag: age

tag: strain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B10_ad012


title: 12__-_4_R1

description: Wild type 6-month-old zebrafish brain

value: Male


title: 14__-_2_2_R1

description: Wild type 6-month-old zebrafish brain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B11_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B11_ad001


title: 11__-_5_R1

description: Wild type 6-month-old zebrafish brain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B10_ad010


title: 11__-_5_2_R1

description: Wild type 6-month-old zebrafish brain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B10_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B11_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B10_ad007


title: MITRG_TREM2_WT

value: MITRG


title: TREATED_3

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
The Illumina Hiseq 4000 generates raw images utilizing HCS (HiSeq Control Software v3.3) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v2.7.3). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v2.16.0.10).
Sequenced reads were quality control checked using NGS-QC tool kit v2.3. ).  Sequence reads with 70% of the bases with >20 Phred score were considered as high quality and taken for further analysis.
The reads are then mapped to hg38 human reference genome using Tophat2 version 2.0.12.
The resulting Cufflinks assemblies of the two samples were combined together using cuffmerge v2.2.0
Cuffdiff v2.2.0 was then employed on the combined transcripts to identify differentially expressed genes/transcripts with parameters set at ‘‘-r -frag-bias-correct -multi-read-correct’’.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file containing FPKM values for each sample

source_name: HCT-116 colon cancer cells

growth_protocol: HCT-116 colon cancer cells were cultured in DMEM supplemented with 10% FBS, 100u/ml penicillin/streptomycin

extract_protocol:
RNA was isolated from the cells using Trizol reagent
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to PCR Amplification for Sequencing Library Construction.

treatment_protocol: Lysophosphatidic acid was treated to the serum starved cells at a concentration of 10uM for 24hr

value: colon

tag: cell line


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B1_ad012

source_name: C57BL/6J Male P56 Mouse Brain


title: 12__-_4_2_R1

description: Wild type 6-month-old zebrafish brain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B10_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B10_ad006


title: 10_FS_1_R1

description: Heterozygous mutant (N140fs/+) 6-month-old zebrafish brain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B1_ad010


title: CONTROL_3

tag: tissue


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B1_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B1_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B1_ad007


title: 10_FS_1_2_R1


title: 9_FS_3_2_R1


title: 8_FS_4_R1

description: Heterozygous mutant (N140fs/T141_L142delisnMISLISV) 6-month-old zebrafish brain


title: 8_FS_4_2_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A9_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A9_ad012


title: 9_FS_3_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B1_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B1_ad008


title: MITRG_TREM2_KO


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A9_ad010


title: 7_FS_5_2_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A9_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A9_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A9_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A9_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A8_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_B1_ad006


title: 7_FS_5_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A8_ad010


title: 6_FAD_1_R1

description: Heterozygous mutant (T141_L142delinsMISLISV/+) 6-month-old zebrafish brain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A8_ad006


title: 6_FAD_1_2_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A8_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A8_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A7_ad002


title: 5_FS_2_R1


title: 5_FS_2_2_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A8_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A7_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A7_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A7_ad006


title: 4_FAD_2_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A7_ad001


title: 3_FAD_3_2_R1


title: P25W1_Mid4

city: Beijing

first: Shu

last: Zhang

state: Beijing

address: Peking University, No.5 Yiheyuan Road Haidian District

institute: BIOPIC

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw data sets were processed as previously described (Dong et al., 2018; Li et al., 2017; Zhong et al., 2018). Cells were split by the first 8-bp barcode in Reads2, and then the next 8-bp UMIs in Reads2 were added to the header in Reads1. After trimming the template switch oligo (TSO) and polyA sequences and removing the short reads (length<37 bp) and low-quality reads (N>10%) in Reads1, the clean reads were aligned by Tophat (version 2.0.12) to the hg19 genome downloaded from UCSC. Then, HTSeq was applied to count the uniquely mapped reads (Anders et al., 2015), and the number of different UMIs for each gene in each cell was considered the transcriptional count.
Genome_build: hg19
Supplementary_files_format_and_content: .csv files which include the count values of genes.

source_name: fetal pituitary cells

extract_protocol:
We used a mouth pipette to randomly pick single cells and used a modified STRT-seq protocol to construct an scRNA-seq library as previously described (Dong et al., 2018; Li et al., 2017; Zhong et al., 2018).
The cells were lysed in a lysis buffer with a 8-nt cell barcode and 8-nt UMI. Then, mRNA was reverse transcribed into cDNA with SuperScript™ II Reverse Transcriptase (18064014, Invitrogen). After preamplification, the samples with different cell barcodes were pooled together, and the mixture was labeled with a biotin modification by 4 cycles of PCR. Then, the full-length cDNA was sheared into fragments with approximately 300-bp lengths by Covaris (S2), and the 3’ cDNA was enriched by Dynabeads MyOne Streptavidin C1 (65002, Invitrogen) to construct a library according to the Kapa Hyper Prep Kit protocol (KK8505, Kapa Biosystems). Cleaned libraries were sequenced as paired-end 150-base reads on Illumina platform.

tag: cell type

value: fetal pituitary cells

tag: week post fertilization


title: P25W1_Mid1


title: 4_FAD_2_2_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A6_ad001


title: P25W1_Mid2


title: 3_FAD_3_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A6_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A7_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A6_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A6_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A7_ad010


title: 2_FAD_4_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A5_ad012


title: 2_FAD_4_2_R1


title: 1_FAD_5_2_R1


title: P25W1_G9


title: P25W1_G8


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A5_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A5_ad007


title: P25W1_G7


title: P25W1_G6


title: P25W1_Mid3


title: 1_FAD_5_R1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A6_ad004


title: P25W1_G5


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A5_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A5_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A5_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A6_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A5_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A4_ad010


title: CPL4RNAi(+)_rep2

city: College Station

first: Akihito

last: Fukudome

state: Texas

address: Dept. Horticultural Sciences MS2133 Texas A&M Univ.

institute: Texas A&M University

description:
CPL4RNAi(+)2
Processed data file: Gene_differential_exp.txt

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.58 and RTA 1.18.64 software with default parameter settings. Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
Adapter-free raw sequenced reads (.fastq files) were uploaded to Galaxy (https://usegalaxy.org/). All data processing was done using Galaxy.
The uploaded reads were mapped with Tophat (v2.0.14) against reference assembly Ensembl TAIR10 from Illumina iGenome, using default parameters except -i/--min-intron-length 60 -I/--max-intron-length 6000.
Differential expression levels of genes were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) by running Cuffdiff (v2.2.1.3) with default parameters.
Genome_build: Arabidopsis TAIR10 (Ensembl)
Supplementary_files_format_and_content: Gene_differential_exp.txt: Tab-delimited text file including FPKM and fold-change.

organism: Arabidopsis thaliana

source_name: root, CPL4 KO, with cytokinin

growth_protocol: Wild-type (Col-0 gl1) and CPL4RNAi seeds were sown and germinated on ½ MS media containing 1% sucrose and 1.5% agar. Aerial portions of ten-day-old seedlings were removed, and the root segments were subjected to CIM-pre-incubation for 5-days. Then, the root tissues were transferred to modified SIM containing 1/10 of standard CK (0.05 mg/L 2iP) or none (0 mg/L 2iP) and incubated for 72 hours.

extract_protocol:
Explants were flash frozen immediately after harvesting and subjected to total RNA extraction using miRNeasy Plant Mini kit (QIAGEN).
The total RNA was submitted to Texas A&M AgriLife Genomics & Bioinformatics Service for RNA-seq analysis (paired-end, 125-bp). After validating the integrity and purity of total RNA using NanoDrop, sequencing libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Plant kit and sequenced by Illumina HiSeq (125 nt, paired-end).

tag: ecotype/background

value: Columbia

tag: genotype/variation

value: CPL4 KO

value: 18 days

value: root

tag: condition

value: shoot-induction media (SIM) with cytokinin


title: P25W1_G3

value: male


title: P25W1_G2


title: CPL4RNAi(+)_rep1

description:
CPL4RNAi(+)1
Processed data file: Gene_differential_exp.txt


title: CPL4RNAi(+)_rep3

description:
CPL4RNAi(+)3
Processed data file: Gene_differential_exp.txt


title: P25W1_G4


title: WT(+)_rep3

description:
WT(+)3
Processed data file: Gene_differential_exp.txt

source_name: root, WT, with cytokinin

value: WT


title: WT(+)_rep2

description:
WT(+)2
Processed data file: Gene_differential_exp.txt


title: P25W1_G10


title: CPL4RNAi(-)_rep3

description:
CPL4RNAi(-)3
Processed data file: Gene_differential_exp.txt

source_name: root, CPL4 KO, without cytokinin

value: shoot-induction media (SIM) without cytokinin


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A3_ad010

value: CA


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A3_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A4_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A4_ad004


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A3_ad001


title: WT(+)_rep1

description:
WT(+)1
Processed data file: Gene_differential_exp.txt


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A3_ad006


title: P24W1_G3

value: female


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A6_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A4_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A4_ad002


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A3_ad008


title: CPL4RNAi(-)_rep1

description:
CPL4RNAi(-)1
Processed data file: Gene_differential_exp.txt


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A2_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A3_ad002


title: P24W1_G4


title: WT(-)_rep3

description:
WT(-)3
Processed data file: Gene_differential_exp.txt

source_name: root, WT, without cytokinin


title: WT_OCs_PU.1

city: Baltimore

first: Vivek

last: Thumbigere Math

state: MD

address: 650 W Baltimore Street

department: Periodontics

institute: Universityof Maryland

data_processing:
Convert from BCL and demultiplex using Casava 1.8.4 or bcl2fastq 2.17.1
Sorted cells: Map to mm10 using Bowtie2 version 2.2.6
Reads were aligned with default parameters to generate the alignment BAM files and clonal reads were removed from further analysis. A minimum of 10 million uniquely mapped reads were obtained for each of the conditions.
The appropriate input-DNA background was set with the ‘--control' parameter. In all cases, redundant reads were removed, and only one mapped read to each unique regions of the genome was kept and used in peak calling. ChIP-seq data were visualized by preparing custom tracks for the UCSC Genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files

source_name: cultured BMMs

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to New England Biolabs instructions accompanying the NEBNext RNA Library Prep Kit (Cat# E7645).

treatment_protocol: BMMs from Irf8 cWT and Irf8 cKO mice were cultured in the presence of 20 ng/ml MCSF and 40 ng/mL RANKL for 4 days to generate terminally differentiated osteoclasts.

value: Bone Marrow Derived Monocytes

tag: genotype

value: OCs

tag: chip antibody

value: Anti-PU.1 antibody, Laboratory of Michael Ostrowski (Carey et al., 2018)


title: CPL4RNAi(-)_rep2

description:
CPL4RNAi(-)2
Processed data file: Gene_differential_exp.txt


title: cKO_OCs_PU.1


title: cKO_BMMs_PU.1

value: BMMs


title: P24W1_G5

tag: gender


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A2_ad001


title: WT(-)_rep1

description:
WT(-)1
Processed data file: Gene_differential_exp.txt


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A2_ad010


title: P24W1_G2


title: P23W2_G8


title: WT(-)_rep2

description:
WT(-)2
Processed data file: Gene_differential_exp.txt


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A2_ad007


title: P23W2_G9


title: THP-1 S80A 3hr n3

city: Glasgow

first: Emma

last: Smith

address: 120 University Place

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description: S80A 3hr n3

data_processing:
Read quality was checked for each sample using FastQC
Reads were aligned to human reference sequence iGenome NCBI GRCh38 using HISAT
Aligned reads were assembled into transcripts using Stringtie for CuffDiff differential gene expression testing
Aligned reads were counted using htseq-count for DESeq2 differential expression testing
Differential gene expression was determined using CuffDiff and DESeq2
Genome_build: iGenome NCBI GRCh38
Supplementary_files_format_and_content: CuffDiff differential gene expression testing ; DESeq2 differential gene expression testing

source_name: THP-1 cells

growth_protocol: THP-1 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 media, supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2mM L-glutamine, and 100 units/ml of streptomycin and penicillin. Cells were maintained at 37ºC in a humidified environment with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using RNeasy kits (Qiagen), according to the manufacturer’s instructions.
1 μg of total RNA was used for library construction. For PolyA selection, the TruSeq stranded mRNA sample prep kit was used. Illumina NextSeq™500 platform was used to sequence single-end 75bp reads to a depth of 20 million.

treatment_protocol: For differentiation, THP-1 cells were treated with 25ng/ml PMA for 72 hours. Following differentiation, PMA-containing media was removed, cells were washed once in THP-1 culture media, and cells were replaced with fresh THP-1 culture media. Following 4 days rest in culture, cells were treated with 10ng/ml LPS for 3 hours prior to RNA extraction.

tag: time point


title: WT_BMMs_PU.1


title: WT_OCs_K27ME3

value: Anti-Histone H3 (tri methyl K27) antibody, Millipore, Cat# 07-449


title: P23W2_G6


title: P24W1_G1


title: THP-1 S80A 3hr n1

description: S80A 3hr n1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A2_ad002


title: cKO_OCs_K27ME3


title: P23W2_G7


title: WT_BMMs_K27ME3


title: cKO_BMMs_K27ME3


title: P23W2_G5


title: THP-1 S80A 0hr n3

description: S80A 0hr n3


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A12_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A12_ad012


title: P23W2_G4


title: cKO_OCs_K27AC

value: Anti-H3K27ac antibody, Abcam, Cat# ab4729


title: P23W2_G3

value: fetal pituitary cells


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A12_ad007


title: P23W2_G1


title: THP-1 S80A 0hr n2

description: S80A 0hr n2


title: P23W2_G2


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A12_ad008


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A2_ad008


title: THP-1 S80A 3hr n2

description: S80A 3hr n2


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A4_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A12_ad004


title: P23W2_G14


title: cKO_BMMs_K27AC


title: cKO_OCs_K4ME3

value: Anti-Histone H3 (tri methyl K4) antibody, Abcam, Cat# ab8580


title: THP-1 WT 3hr n2

description: WT 3hr n2


title: THP-1 WT 3hr n3

description: WT 3hr n3


title: P23W2_G15


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A12_ad006


title: WT_OCs_K4ME3


title: WT_BMMs_K27AC


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A12_ad001


title: THP-1 WT 3hr n1

description: WT 3hr n1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A12_ad002


title: P23W2_G12


title: THP-1 WT 0hr n2

description: WT 0hr n2


title: THP-1 WT 0hr n3

description: WT 0hr n3


title: cKO_BMMs_K4ME3


title: WT_OCs_K27AC


title: THP-1 S80A 0hr n1

description: S80A 0hr n1


title: P23W2_G13


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A11_ad007


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A11_ad010


title: WT_BMMs_K4ME3


title: WT_OCs_K4ME1

value: Anti-Histone H3 (mono methyl K4) antibody, Abcam, Cat# ab8895


title: infected_Mincle-/-_stomach_rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description:
KO_5
mRNA-seq

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values.

source_name: stomachs of H. pylori-infected Mincle–/– mice after 8 weeks

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

tag: strain/background

value: Mincle-/-

value: stomach

tag: treatment

value: H. pylori infection

value: 8 weeks


title: P23W2_G11

value: male


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A11_ad008

tag: brain region


title: cKO_OCs_K4ME1


title: WT_BMMs_K4ME1

value: WT


title: infected_Mincle-/-_stomach_rep2

description:
KO_9
mRNA-seq


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A11_ad006

value: CA

tag: Sex


title: P23W1_G2


title: P23W2_G10


title: THP-1 WT 0hr n1

description: WT 0hr n1


title: P22W1_G6


title: P23W1_G1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A11_ad004

tag: age


title: infected_wt_stomach_rep3

description:
WT_7
mRNA-seq

source_name: stomachs of H. pylori-infected WT mice after 8 weeks

value: wild type


title: infected_wt_stomach_rep1

description:
WT_3
mRNA-seq


title: infected_wt_stomach_rep2

description:
WT_5
mRNA-seq


title: INPUT_OCs_WT

value: Bone Marrow Derived Monocytes


title: INPUT_OCs_cKO

value: OCs


title: cKO_BMMs_K4ME1


title: INPUT_BMMs_cKO


title: P22W1_G4


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A11_ad001

tag: strain


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A10_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A10_ad012


title: P22W1_G5


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A11_ad002


title: P22W1_G2


title: P22W1_G3


title: 2.10-plus-BMP-input

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Aligned using bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

growth_protocol: Human CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were used.Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with StemSpan CC100 cytokine mix (Stem Cell Technologies Inc.). For studying differentiated cells after day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 mM dexamethasone, and 1 mM b-estradiol). K562 cells (over expressing PU1) were grown and maintained in  RPMI base media with FBS, Pen/Strep. G418 was used to select positive clones. K562 cells (with PU1 knockdown) were grown and maintained in  RPMI base media with FBS, Pen/Strep. puromycin was used to select positive clones.

extract_protocol: The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol:
25ng/ml hrBMP4 for 2hrs prior to collection
Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with antibody
Human CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were used.Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with StemSpan CC100 cytokine mix (Stem Cell Technologies Inc.). For studying differentiated cells after day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 mM dexamethasone, and 1 mM b-estradiol). K562 cells were grown and maintained in  RPMI base media with FBS, Pen/Strep. G418 was used to select positive clones.A72:A74

value: immortalized erythroleukemia cells (knockdown PU1)

tag: purification target


title: INPUT_BMMs_WT

tag: tissue

value: BMMs


title: Vec6-plus-BMP-input

tag: cell type

value: immortalized erythroleukemia cells (empty control)


title: Vec6-plus-BMP

treatment_protocol:
hrBMP4 25ng/ml 2hrs
25ng/ml hrBMP4 for 2hrs prior to collection
Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with antibody
Human CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were used.Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with StemSpan CC100 cytokine mix (Stem Cell Technologies Inc.). For studying differentiated cells after day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 mM dexamethasone, and 1 mM b-estradiol). K562 cells were grown and maintained in  RPMI base media with FBS, Pen/Strep. G418 was used to select positive clones.A72:A74

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog id


title: XA8001-N_S12

city: Syracuse

first: David

last: Pruyne

address: 766 Irving Avenue

department: Cell and Developmental Biology

institute: SUNY Upstate Medical University

description: XA8001 rep 4

data_processing:
mRNA-Seq reads were aligned to annotation model WBcel235-Ensembl95 using bowtie 2-2.2.5 in Partek Flow Build ver 9.0.20.0913
Data were normalized to transcripts per million reads in Partek Flow Build ver 9.0.20.0913
Genome_build: WBcel235-Ensembl95
Supplementary_files_format_and_content: txt files include normalized abundance measurements for genes

organism: Caenorhabditis elegans

source_name: L3 stage RW364 C. elegans larvae

growth_protocol: Embryos were harvested from adult worms that were grown at 15˚C. Embryos were plated to solid medium with E. coli food source and grown at 15˚C until reaching L3 stage of development.

extract_protocol:
Whole larvae were frozen and then thawed and whole RNA extracted using TRIzol Reagent.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit.

tag: developmental stage

value: larvae


title: P21W1_GL_S

value: fetal pituitary cells

tag: week post fertilization


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A10_ad004

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A10_ad006


title: P21W1_GL_B


title: P22W1_G1


title: 2.10-BMP-plus-PU1-ChIP


title: 2.10-plus-BMP


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A10_ad002


title: XA8001-K_S9

description: XA8001 rep 1

tag: genotype


title: Vec6-BMP-plus-PU1-ChIP-input


title: XA8001-M_S11

description: XA8001 rep 3


title: XA8001-L_S10

description: XA8001 rep 2


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A10_ad001


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A1_ad012


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A10_ad008


title: infected_Mincle-/-_stomach_rep3

description:
KO_10
mRNA-seq

tag: genotype/variation


title: P19W2_G5

tag: gender

value: female


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A1_ad001


title: Vec6-BMP-plus-PU1-ChIP


title: RW364-M_S7

description: RW364 rep 3

source_name: L3 stage XA8001 C. elegans larvae


title: 2.10-BMP-plus-PU1-ChIP-input


title: 2.10-BMP-plus-GATA2-ChIP-input


title: P19W2_G3


title: 2.10-BMP-plus-GATA2-ChIP


title: RW364-L_S6

description: RW364 rep 2


title: P19W2_G6


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A1_ad007


title: N2-N_S4

description: N2 rep 4

source_name: L3 stage N2 C. elegans larvae


title: Vec6-BMP-plus-GATA2-ChIP


title: P25W1_G1


title: RW364-N_S8

description: RW364 rep 4


title: P19W1_M2


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A1_ad006


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A1_ad010


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A1_ad004


title: P19W2_G4


title: N2-M_S3

description: N2 rep 3


title: P19W2_G1


title: P19W2_G2


title: N2-L_S2

description: N2 rep 2


title: RW364-K_S5

description: RW364 rep 1


title: p53 low [PATX 137]

city: Smithville

first: Bin

last: Liu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-137-F5-R11_TCTCGCGC-GTACTGAC_BC9WL7ANXX

data_processing:
mapping with Tophat or Star
HT-seq count to count raw reads
DESeq2 for DE analysis
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: excel file

source_name: pancreatic cancer PDX_p53 low

extract_protocol: RNA purification- qiagen micro kit

tag: strain background

value: heterotopic pancreatic cancer tumors implanted in immunodeficient mice

tag: tissue type

value: pancreatic cancer PDX

value: p53 low


title: p53 low [PATX 144]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-144-F4-R11_TCCGCGAA-TATAGCCT_BC9W4UANXX


title: N2-K_S1

description: N2 rep 1


title: p53 low [PATX 136]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-136-F3-R11_TCTCGCGC-CAGGACGT_BC9WL7ANXX


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A4_ad012

city: La Jolla


title: P19W1_M1


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A3_ad004


title: sample016_AH46_R1

city: Madrid

first: Alejandro

last: Higuera-Matas

state: Madrid

address: Calle Juan del Rosal 10

department: Psychobiology

country: Spain

institute: Universidad Nacional de Educación a Distancia (UNED)

data_processing:
We used the Chipster analysis suite (https://chipster.csc.fi/) to perform data processing and analysis. Briefly, data quality analysis of the obtained raw data (singleEnd, stranded) was performed on FASTQC and PRINSEQ; no low-quality bases, or very few, were detected at the end of the reads.  Reads were aligned to reference genome Rattus_norvergicus. Rnor_6.0.87 using TOPHAPT and the alignment of the counts per read was performed using HTSeq.  Differential gene expression analysis was performed using CUFFDIFF with replicates analysis to explore the differences in transcriptomic profiles between factor levels.
Genome_build: Rnor_6.0.87
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Female_THC_nucleus accumbens shell

extract_protocol:
Samples were homogenized, and RNA extracted according to the protocol, tools and reagents provided by RNeasy Mini Kit (Qiagen).
Libraries were prepared according to the instructions of the NEBNext Ultra Directional RNA Library Prep kit for Illumina kit (New England Biolabs), as detailed in “Chapter 1: Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module”. The input yield of total RNA to start the protocol was 1 µg quantified by an Agilent 2100 Bioanalyzer using an RNA 6000 nano LabChip kit. We performed the library amplification included in the cited protocol using a PCR of 14 cycles. The obtained libraries were validated and quantified by an Agilent 2100 Bioanalyzer using a DNA7500 LabChip kit and an equimolecular pool of libraries were titrated by quantitative PCR using the “Kapa-SYBR FAST qPCR kit forLightCycler480” (Kapa BioSystems) and a reference standard for quantification.

treatment_protocol: The adolescent chronic Δ9_THC treatment was administered every other day from PND 28 to PND 44. Rats received an intraperitoneal injection (2 mL/kg) of Δ9_THC at a dose of 3 mg/kg or vehicle (2 mL/kg). At PND 90, animals were deeply anaesthetised with isoflurane and sacrificed by decapitation. Brains were extracted and, with the help of a brain matrix, 1 mm thick coronal slices were obtained between 2.28 mm and 1.08 mm, approximately, anterior from bregma. With the help of two dissecting lancet-shaped needles, the NAcb (shell division)  was dissected according to the Paxinos and Watson atlas. The tissue samples were snap-frozen with dry ice and stored at -70º C.

value: Wistar

value: Female

tag: treatment

value: THC

value: Nucleus accumbens shell (bulk tissue)


title: p53 low [PATX 118]

description:
processed data file: PDX.rawreadcount.xlsx
MDA-PATX118_CTGAAGCT_AC8YYWANXX


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A1_ad002

tag: brain region

value: CA

value: male


title: Vec6-BMP-plus-GATA2-ChIP-input


title: P17W1_G6


title: CEMBA190716_8E_1_CEMBA190716_8E_2_A1_ad008

tag: Sex


title: P17W1_G2


title: P17W1_G5


title: sample015_AH14_R1


title: P17W1_G4


title: p53 low [PATX 106]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-106-F3-R11_TCTCGCGC-ATAGAGGC_BC9WL7ANXX


title: p53 low [PATX 179]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-179-F3-R11_AGCGATAG-AGGCGAAG_BC9WL7ANXX


title: P17W1_G1


title: P17W1_G3


title: sample014_AH50_R1


title: p53 low [PATX 92]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-092-F3-R11_TCCGCGAA-TAATCTTA_BC9WL7ANXX


title: sample013_AH35_R1


title: P16W1_G3


title: p53 low [PATX 60]

description:
processed data file: PDX.rawreadcount.xlsx
MDA-PATX60_GAATTCGT_AC8YYWANXX


title: P16W1_G2


title: sample012_AH44_R1

source_name: Female_Vehicle_nucleus accumbens shell

value: Vehicle


title: sample010_AH23_R1


title: p53 low [PATX 76]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-076-F5-R11_TCCGCGAA-ATAGAGGC_BC9W4UANXX


title: p53 low [PATX 66]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-066-F3-R11_CGGCTATG-TAATCTTA_BC9W4UANXX


title: sample011_AH39_R1


title: p53 low [PATX 34]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-034-F2-R11_CGGCTATG-TATAGCCT_BC9W4UANXX


title: p53 high [PATX 148]

description:
processed data file: PDX.rawreadcount.xlsx
MDA-PATX148_CTGAAGCT_BC906JANXX

source_name: pancreatic cancer PDX_p53 high

value: p53 high


title: sample009_AH6_R1


title: p53 high [PATX 153]

description:
processed data file: PDX.rawreadcount.xlsx
MDA-PATX153_ATTACTCG_AC8W8WANXX


title: p53 high [PATX 147]

description:
processed data file: PDX.rawreadcount.xlsx
PDX-PDAC-147-F4-R11_AGCGATAG-TATAGCCT_BC9WL7ANXX


title: P15W1_G_S


title: P15W1_N


title: P16W1_G1